Kementerian Riset dan Teknologi/ Badan Riset dan Inovasi Nasional
Republik Indonesia
No. Name Institution Indonesian Counterpart Institution Counterpart Author Title Year Type Detail
1 Nicolas HUBERT Institut de Recherche pour le Développement Daisy Wowor Indonesian Institut of Sciences (LIPI), Research Centre for Biology (RCB), Division of Zoology Hernawati R, Nurhaman U, Busson F, Suryobroto B, Hanner R, Keith P, Wowor D, Hubert N
Species proliferate through evolutionary mechanisms but coexist through ecological dynamics. As such, it might be expected that mechanisms of speciation and species maintenance jointly influence the settlement of ecological communities, a process called community assembly. Disentangling the rela- tive contribution of evolutionary and ecological dynamics might be a difficult task, particularly so for the tropical biotas due to their extreme diversity and large knowledge gaps. Here, we explore genetic diversity and distribution of 23 freshwater shrimp species of the genera Caridina and Macrobrachium in Sundaland to examine patterns of species co-occur- rence based on 1583 observations across 19 sites in Java and Bali islands. DNA-based species delimitation methods applied to 204 cytochrome oxidase I sequences detected 30 operational taxonomic units and a few cases of deep intraspecific divergence. Species co-occurrence and phylogenetic community structure show no departure from expectations under a random distribution of species in landscapes and support a lottery model of community assembly. Species age estimates expand beyond the geological settlement of Sundaland, suggesting that species proliferation and community assembly are driven by mechanisms acting at distinct spatial and temporal scales.
2020 Journal article
2 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Simon Pouil, Reza Samsudin, Jacques Slembrouck, Ahmad Sihabuddin, Gusnia Sundari, Khazaidan Khazaidan, Anang Hari Kristanto, Brata Pantjara, Domenico Caruso
Water ferns (Azolla spp.) are among the main important floating macrophytes used for feeding farmed animals such as fish, because they have high growth potential and high protein content. Nevertheless, their use as feed requires sustainable mass production, which can be difficult to maintain in field conditions. We performed a first experiment to assess the effects of shading and fertilization levels on the growth of Azolla filiculoides with complementary information regarding the morphology and the chemical composition of the plant cultivated under the different experimental conditions. Plants were cultivated in floating 50-L plastic drums at three fertilization levels (“no”, “low” and “high”) using an inorganic multi-nutrient fertilizer rich in P (NPK?=?1:2:1) and maintained under full natural light or shaded by one of two different types of shading materials, transparent polyethylene sheet and 60% shade net, respectively. A second experiment was carried out to evaluate the effects of grazing by the invasive golden apple snail Pomacea canaliculata on A. filiculoides previously cultivated without addition of fertilizer (treatment “no”) or in high fertilizer concentrations (treatment “high”). Fertilization levels and shading materials significantly affected the growth of Azolla. The highest productivity was reached using the highest fertilization level under direct sunlight. Azolla produced in these culture conditions was preferentially grazed by snails compared to Azolla cultivated without added fertilizer. Based on these findings, we make recommendations regarding the best culture conditions for A. filiculoides in ponds for its use as sustainable fish feed.
2020 Article scientifique
3 Christian Lott HYDRA Marine Sciences Jane Mamuaja UNSRAT Manado Christian Lott, Andreas Eich, Boris Unger, Dorothée Makarow, Glauco Battagliarin, Katharina Schlegel, Markus T. Lasut and Miriam Weber
The pollution of the natural environment, especially the world’s oceans, with conventional plastic is of major concern. Biodegradable plastics are an emerging market bringing along potential chances and risks. The fate of these materials in the environment and their possible effects on organisms and ecosystems has rarely been studied systematically and is not well understood. For the marine environment, reliable field test methods and standards for assessing and certifying biodegradation are lacking. In this work we present newly developed field tests to assess the performance of biodegradable plastics under natural marine conditions. These methods were successfully applied and validated in three coastal habitats (eulittoral, benthic and pelagic) and in two climate zones (Mediterranean Sea and tropical Southeast Asia). Additionally, a stand-alone mesocosm test system which integrated all three habitats in one technical system at 400-L scale independent from running seawater is presented as a methodological bridge. Films of the positive control test material polyhydroxyalkanoate copolymer (PHA) and the negative control low density polyethylene (LD-PE) were used to validate the systems. While LD-PE remained intact, PHA disintegrated with speed depending on the habitat and the climate zone. Together with the existing laboratory standard test methods, the field and mesocosm test systems presented in this work provide a 3-tier testing scheme for the reliable assessment of the biodegradation of (biodegradable) plastic in the marine environment. This toolset of tests can be adapted to other aquatic ecosystems.
2020 pre-print submitted to PLOSone
4 Michael David Pashkevich Jr. University of Cambridge Mohammad Naim, PhD SMART Research Institute Pashkevich, MD; Aryawan, AAK; Luke, SH; Dupérré, N; Waters, HS; Caliman, J-P; Naim, M; Turner, EC
Palm oil is the most traded vegetable oil worldwide. Production is concentrated in Southeast Asia, where established oil palm plantations dominate the landscape in many regions. Although levels of biodiversity are much lower than in forest, mature oil palm plantations can support a wide range of generalist species. However, these species may be threatened, as large areas of plantation have already been, or will soon be, replanted as they near the end of their productive life (20–30 years). Replanting changes vegetation complexity and microclimate, but short? and long?term effects on biodiversity are largely unstudied. We surveyed an oil palm chronosequence (first?generation mature palms, and replanted second?generation palms aged 1, 3 and 8 years) in an industrial plantation in Riau, Indonesia to assess the impacts of replanting over an 8?year period on arthropods in the ground, understorey and canopy microhabitats. Replanting was carried out using current recommended strategies, which included staggering replanting events to promote landscape?level heterogeneity, retaining mature oil palm riparian buffers, planting a cover crop immediately after replanting, and using chopped mature palms as mulch after clearance. We assessed changes in total arthropod abundance and order?level community composition, as well as specific changes in spider communities. We observed no significant declines in total arthropod abundance after replanting, but arthropod order?level community composition varied across the chronosequence in all microhabitats. These findings were replicated, or more pronounced, in spider?specific analyses. Spider abundance and species richness decreased in the understorey in the first year after replanting (although these returned to pre?replanting levels after 3 years), and spider species?level community composition in all microhabitats differed significantly across the chronosequence. Synthesis and applications. Our findings indicate that total arthropod abundance is resilient to replanting of oil palm, but that replanting changes total arthropod and spider community composition and decreases spider abundance and species richness in some microhabitats. While it is somewhat encouraging from a management perspective that recommended replanting strategies maintain overall arthropod abundance, the changes in arthropod composition and spider biodiversity that we observed may impact ecosystem processes, such as pest control, in second?generation oil palm plantations, with potential implications for yield. Additional studies that focus on other taxonomic groups and assess the effects of individual replanting strategies are needed before the long?term ecological impacts of replanting on existing oil palm plantations can be fully determined.
2020 Research article
5 Mark Christopher O Hara Messerli Research Institute; University of Veterinary Medicine, Vienna Dewi Malia Prawiradilaga Indonesian Institute of Science (LIPI) Theresa Rössler, Berenika Mioduszewska, Mark O’Hara, Ludwig Huber, Dewi M. Prawiradilaga & Alice M. I. Auersperg
The ability to innovate, i.e., to exhibit new or modified learned behaviours, can facilitate adaptation to environmental changes or exploiting novel resources. We hereby introduce a comparative approach for studying innovation rate, the ‘Innovation Arena’ (IA), featuring the simultaneous presentation of 20 interchangeable tasks, which subjects encounter repeatedly. The new design allows for the experimental study of innovation per time unit and for uncovering group-specific problem-solving abilities – an important feature for comparing animals with different predispositions and life histories. We applied the IA for the first time to investigate how long-term captivity affects innovative capacities in the Goffin’s cockatoo, an avian model species for animal innovation. We found that fewer temporarily-captive wild birds are inclined to consistently interact with the apparatus in comparison to laboratory-raised birds. However, those that are interested solve a similar number of tasks at a similar rate, indicating no difference in the cognitive ability to solve technical problems. Our findings thus provide a contrast to previous literature, which suggested enhanced cognitive abilities and technical problem-solving skills in long-term captive animals. We discuss the impact and discrepancy between motivation and cognitive ability on innovation rate. Our findings contribute to the debate on how captivity affects innovation in animals.
2020 Original research article
6 Satoshi Tanaka College of Information Science and Engineering, Ritsumeikan University Dr. Fadjar I. Thufail Research Center for Regional Resources, Indonesian Institute of Sciences (P2SDR - LIPI) Tomomasa Uchida, Kyoko Hasegawa, Liang Li, Motoaki Adachi, Hiroshi Yamaguchi, Fadjar I. Thufail, Sugeng Riyanto, Atsushi Okamoto, Satoshi Tanaka
We propose a high-quality transparent visualization method suitable for large-scale laser-scanned point clouds. We call the method “stochastic point-based rendering (SPBR),” which is based on a novel stochastic algorithm. SPBR enables us to clearly observe the deep interior of laser-scanned 3D objects with the correct feeling of depth. The high quality of SPBR originates from the effect of “stochastic noise transparentization,” which is an effect to make the measurement noise transparent and invisible in the created images. We mathematically prove that this effect also makes the created transparent images coincide with the results of the conventional methods based on the alpha blending, which is time-consuming and impractical for large-scale laser-scanned point clouds. We also demonstrate the effectiveness of SPBR by applying it to modern buildings, cultural heritage objects, forests, and a factory. For all of the cases, the method works quite well, realizing clear and correct 3D see-through imaging of the laser-scanned objects.
2020 journal paper
7 Frank Drygala National Museum of Natural History Luxembourg Prof (R). Dr. Gono Semiadi Research Centre for Biology - Indonesian Institute of Science (LIPI) Frank Drygala, Johanna Rode-Margonno, Gono Semiadi, Widateti, Alain Frantz
Due to hybridisation and breakdown of reproduction barriers the Java warty pig an endangered suid endemic to Java, may be assimilated into the gene pools of the more common Indonesian banded pig and become extinct. Here, we aimed to detect introgressive hybridisation between both suids by microsatellite genotyping warty pigs from two captive populations and from the wild, as well as a banded pig population. While all but one captive individual were genetically pure, we showed, in contrast to a previous survey based on skull measurements, that five wild-born warty pigs in West Java were hybrids. Moreover, we detected four F2 hybrids in the wild warty pig population (qrange 0.15–0.99) and one F2 hybrid in the wild banded pig population (q = 0.25), confirming reproductive fertility for F1 hybrids. Our results highlight the potential risk of extinction through hybridization and genetic swamping of the endangered warty pig.
2020 paper
8 Nicolas HUBERT Institut de Recherche pour le Développement Daisy Wowor Indonesian Institut of Sciences (LIPI), Research Centre for Biology (RCB), Division of Zoology Delrieu-Trottin E, Durand J-D, Limmon G, Sukmono T, Kadarusman, Sugeha HY, Chen W-J, Busson F, Borsa P, Dahruddin H, Sauri S, Fitriana Y, Zein MSA, Hocde? R, Pouyaud L, Keith P, Wowor D, Steinke D, Hanner R, Hubert N
DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign un- known individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and deline- ated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic com- plexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA- based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the ben- efits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.
2020 Journal article
9 Nicolas HUBERT Institut de Recherche pour le Développement Daisy Wowor Indonesian Institut of Sciences (LIPI), Research Centre for Biology (RCB), Division of Zoology Sholihah A, Delrieu-Trottin E, Sukmono T, Dahruddin H, Risdawati R, Elvyra R, Wibowo A, Kustiati K, Busson F, Sauri S, Nurhaman U, Dounias E, Zein MSA, Fitriana Y, Utama IV, Muchlisin ZA, Agne?se J-F, Hanner R, Wowor D, Steinke D, Keith P, Ru?ber L, Hubert N
Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DnA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.
2020 Journal article
10 Nicolas HUBERT Institut de Recherche pour le Développement Daisy Wowor Indonesian Institut of Sciences (LIPI), Research Centre for Biology (RCB), Division of Zoology Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic re- gions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identifica- tion are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species bounda- ries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
2020 Journal article
11 Alexis Chappuis UNSEEN I Gede Hendrawan Universitas Udayana Gede Indra Putra Pratama, I Gede Hendrawan, I Wayan Gede Astawa Karang, Alexis Chappuis
Amed and Tulamben waters are marine tourism areas located in the western part of the Lombok Strait, which have enormous biodiversity and conservation potential. The abundant biodiversity in the area is because of the process of transporting water masses vertically carrying biogenic and non-biogenic components. Salinity and TDS have an important role in regulating the process of bio-geo-chemical waters. Thus, it can be a parameter in understanding the vertical characteristics of the waters. The purpose of this research was to determine the vertical characteristics of temporal salinity and TDS in these waters. Data was collected for 14 days (February 20 to March 5, 2019) at two locations, namely Batu Niti and Emerald. The data collection method was carried out by reducing the CTD to a depth of approximately 95 meters with a measurement interval of 10 minutes for 2 to 3 hours per day. The results showed that salinity and TDS had a very strong correlation (r = 0.9995). Salinity concentrations ranged from 31.83 to 34.19 PSS, and TDS concentrations ranged from 31,211.12 to 33,396.71 mg l-1. The halocline layer had a gradient characteristic ? 0.01 PSS m-1 found from a depth of 20 meters, while a homogeneous layer was formed above it to a depth of 6 meters. The halocline layer had a higher level of water mass stability (N) than the homogeneous layer. The maximum rate of change in salinity and TDS was found at a depth of 70 meters. The great variability of salinity and TDS in the water column was indicated by the influence of internal tidal currents. Before the highest tide conditions, salinity and TDS have highest variability that compared to the highest tide condition and after its condition.
2020 Article
12 Eleanor Maureen Wyatt University of Exeter Siti Maimunah Universitas Muhammadiyah Palangkaraya Eleanor Wyatt
During an 8 month research trip to the Bornean rainforest to carry out ecological research for my master’s thesis (Lepidoptera diversity and fruiting patterns in a diverse forest landscape) my fellow researchers and I sustained five injuries that required hospital visits. I was bitten by a Bornean keeled pit viper (Subannulatus Borneo) and had to be evacuated from the rainforest - this was an interesting journey, consisting of five different modes of transport over the course of five hours. When we weren’t dealing with injuries that called for hospitalisation we were battling fully body rashes and wasp stings that caused swelling larger than a handprint, but we still had great fun through it all. It was these medical emergencies that really made us appreciate the value of training and team work whilst working in such a remote camp. Without this training our health and research would have suffered, as my fellow researcher and I were trapping animals that needed to be released each day for the safety of the animals themselves. If we were injured it was vital that a team member could continue our research. The importance of maintaining your health when undertaking vital ethical research such as this cannot be expressed enough as, ultimately, the aim of our research is to assist in the forest’s protection. The Bornean rainforest may be magical, but it can also be dangerous, and the risks should not be downplayed. Those working in it should be appropriately trained and aware of the potential dangers, so that they can help keep the rainforest and its inhabitants safe.
2020 On the ground Article
13 Widjaya Yang Hui Jennifer S. Rajaratnam School of International Studies, Nanyang Technological University Prof. Hokky Situngkir Department of Computational Sociology, Bandung Fe Institute, Research Center for Complexity at Surya University Jennifer Yang Hui
Concerns over online falsehoods (popularly called “hoax”) received outsized attention throughout Indonesia’s 2019 elections. Events such as the 212 Defend Islam Rally, past election experiences of intense political mudslinging and the 2016 U.S. presidential election have informed the nation’s perspective about hoax, seeing it as a term that imply division and could potentially tear apart the young democracy. Social media, especially encrypted platforms like WhatsApp, was used to spread hoaxes during the 2019 elections. The combination of the ability to be anonymous online, the rise of horizontal trust and the inability to critically evaluate online information meant that hoax campaigns gained traction during the election campaigning period. As terms like “buzzers” and “cyber troops/armies” were thrown about, it was clear that a climate of distrust had been established. While assessing the impact of hoaxes during the 2019 elections is challenging, overall level of trust in electoral institutions have been affected, serving as a backdrop to the worst national election-related violence to take place in Indonesia since 1999. Going forward, neither regulation of digital architecture nor cultivation of digital literacy alone is sufficient. Instead, a combination of different measures from diverse stakeholders in the society may offer a more practical solution towards resolving the challenges of hoax.
2020 Book Chapter
14 Keerti Gedela Chelsea & Westminster NHS Foundation Trust Professor Irwanto Atma Jaya Catholic University, Jakarta, Indonesia Hendry Luis, Wayan Dede Fridayantara, Pande Agung Mahariski, Frank Stephen Wignall, Irwanto Irwanto, Keerti Gedela
Evolving ART crisis for people living with HIV in Indonesia
2020 Publication The Lancet HIV
15 Paul Macklin Southern Cross University Dr. I Gusti Ngurah Agung Suryaputra Department of Analytical Chemistry Ganesha University of Education Singaraja, Bali, Indonesia Paul A. Macklin, I Gusti Ngurah Agung Suryaputra, Damien T. Maher, Frida Sidik, Isaac R. Santos
Tropical estuaries may release large amounts of carbon dioxide to the atmosphere, but remain understudied relative to temperate systems. Here, we investigate hydrological drivers of pCO2 along ~22 km of an aquatic continuum from the mountain river to the coastal ocean, including highly modified aquaculture and urban zones (Perancak Estuary, Ijo Gading River, Bali, Indonesia). We report seasonal spatial surveys (n = 8) and stationary time series observations (n = 4 days) during a rain event. Overall, pCO2 ranged from 330 µatm to 12,126 µatm, with the lowest values observed near the estuary mouth and in the river upstream of the urban zone, and the highest values in the upper estuary where radon (222Rn, a natural groundwater tracer) revealed elevated groundwater discharge. Average atmospheric CO2 fluxes in the upper estuary (107.3 mmol m-2 d-1) were ~5-fold greater than in the lower estuary (19.1 mmol m-2 d-1), while the river was a minor atmospheric CO2 sink (-0.2 mmol m-2 d-1). Overall, the estuary was a source of CO2 to the atmosphere with area-weighted emissions of ~67 mmol m-2 d-1. Seasonal spatial surveys revealed strong correlations between antecedent rainfall and pCO2 and 222Rn in the estuary, implying pCO2 responds to delayed groundwater discharge. A detailed 4-day time series covering an episodic flooding event revealed sharp transitions in CO2 drivers, including dilution by rainfall followed by inputs of CO2-enriched groundwater. Groundwater discharge, as traced by radon, explained most of pCO2 variability in dry and wet conditions. Overall, we highlight the importance of seasonal and episodic rainfall and how delayed groundwater seepage may drive CO2 distribution in a highly modified tropical estuary.
2020 RESEARCH ARTICLE
16 Paul Macklin Southern Cross University Dr. I Gusti Ngurah Agung Suryaputra Department of Analytical Chemistry Ganesha University of Education Singaraja, Bali, Indonesia Paul Macklin, Judith Rosentreter, Virni Budi Arifanti, I Gusti Ngurah Agung Suryaputra
In this chapter, we aim to provide a comprehensive overview of groundwater research in mangrove ecosystems by 1) briefly describing “what is submarine groundwater discharge (SGD) ?”; 2) by explaining and highlighting the importance of tidal exchange of groundwater or porewater with surface water in mangrove forests and other adjacent coastal systems; and 3) by discussing the impacts of mangrove deforestation and the land conversion from mangroves to aquaculture ponds and urban settlements on the local coastal hydrogeology (groundwater hydrology). We then summarize currently available methods that have been successfully used to measure groundwater in scientific studies - with a focus on natural groundwater tracers (radon & temperature) and remote sensing technology (e.g. aerial thermal infrared imagery). Furthermore, we provide suggestions for future larger-scale and more rapid monitoring options in the context of changing hydrogeological conditions in mangrove ecosystems, based on the thermal anomalies of SGD and other coastal hydrological processes.
2020 RESEARCH ARTICLE
17 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Russon A, Kuncoro P, Ferisa A, Prayunita D
We present evidence for offspring stacking (OS) in wild orangutans of Kutai National Park (KNP), E Indonesian Borneo, and on interbirth intervals (IBI) and El Niño as contributors, then discuss implications for understanding orangutan reproduction. Documented OS is rare in wild orangutans; KNP is not well represented in assessments, however, so additional evidence for KNP should strengthen understanding of its prevalence and determinants. Our findings derive from standard observational data we collected at two KNP sites (01/2010-08/2019), other credible reports of KNP orangutan reproduction (1985-2010), and published research findings on KNP orangutans (1970-1989) and on El Niño’s effects on wild orangutan habitat. Our 2010-19 data documented OS in two adult females, each 21-24 months in duration. In addition, published findings indicate OS in 9 of the 24 KNP adult females studied since 1970. Combined, this evidence provides 4 credible IBI estimates and a KNP IBI estimate of 6.0 years. Published findings also showed El Niño correlated with reproduction scheduling for 4/6 births whose dates are known within 6 months. These findings confirm OS in wild KNP orangutans and indicate its association with short IBI and El Niño cycles. Since the timing and severity of El Niño effects vary across wild orangutan habitat, N to S and E to W, these findings should contribute to understanding variation in adult female reproduction across wild orangutans’ current range.
2020 Abstract (accepted) - 2020 conference presentation
18 Theresa Rössler Messerli Research Institute, University of Veterinary Medicine Vienna Prof. Dr. Dewi Malia Prawiradilaga M.Sc. Lembaga Ilmu Pengetahuan Indonesia (LIPI) Theresa Rössler, Berenika Mioduszewska,, Mark O’Hara, Ludwig Huber, Dewi M. Prawiradilaga & Alice M. I. Auersperg
The ability to innovate, i.e., to exhibit new or modi ed learned behaviours, can facilitate adaptation to environmental changes or exploiting novel resources. We hereby introduce a comparative approach for studying innovation rate, the ‘Innovation Arena’ (IA), featuring the simultaneous presentation of 20 interchangeable tasks, which subjects encounter repeatedly. The new design allows for the experimental study of innovation per time unit and for uncovering group-speci c problem-solving abilities – an important feature for comparing animals with di erent predispositions and life histories. We applied the IA for the rst time to investigate how long-term captivity a ects innovative capacities in the Go n’s cockatoo, an avian model species for animal innovation. We found that fewer temporarily-captive wild birds are inclined to consistently interact with the apparatus in comparison to laboratory-raised birds. However, those that are interested solve a similar number of tasks at a similar rate, indicating no di erence in the cognitive ability to solve technical problems. Our ndings thus provide a contrast to previous literature, which suggested enhanced cognitive abilities and technical problem-solving skills in long-term captive animals. We discuss the impact and discrepancy between motivation and cognitive ability on innovation rate. Our ndings contribute to the debate on how captivity a ects innovation in animals.
2020 Journal Article
19 Yoko Shimizu Center for Infectious Diseases, Kobe University Graduate School of Medicine Maria Inge Lusida Universitas Airlangga Lumbago Penyakit Tropis Arindita N. Novianti, Krisnoadi Rahardjo, Rima R. Prasetya, Aldise M. Nastri, Jezzy R. Dewantari, Adi P. Rahardjo, Agnes T. S. Estoepangestie, Yohko K. Shimizu, Emmanuel D. Poetranto, Gatot Soegiarto, Yasuko Mori, Kazufumi Shimizub
We isolated an avian influenza A/H9N2 virus from an apparently healthy chicken at a live-poultry market in January 2018. This is the first report of a wholegenome sequence of A/H9N2 virus in Indonesia. Phylogenetic analyses indicated that intrasubtype reassortment of genome segments is involved in the genesis of the A/H9N2 virus.
2019 Scientific paper (Microbiology Resource Announcements)
20 Lena Grinsted Royal Holloway University of London Dr Anom Bowolaksono Universitas Indonesia CASSANDRA SMITH1, ADDIE COTTER1, LENA GRINSTED2, ANOM BOWOLAKSONO3, NI LUH WATINIASIH4 and INGI AGNARSSON
Group-living behaviour is rare in spiders but has evolved repeatedly, yielding several species, some showing cooperation among close kin, and others living in colonies where each female builds its own web and is territorial. The most frequent origins of group living are seen in the cobweb spiders (Theridiidae) that commonly build three-dimensional webs and show extensive maternal care, both putatively pre-adaptive traits to spider sociality. A very unusual behaviour was recently discovered in the theridiid genus Chikunia, where two distinct but related species occur in mixed-species colonies with potentially indiscriminate brood care. These mixed colonies consist of Chikunia nigra and a newly discovered species. Here, we describe the new species, Chikunia bilde sp. nov., and summarize the unique biology of this species pair. We also place the origin of mixed-species group living in a phylogenetic context, firmly confirming the placement of Chikunia within the clade (lost colulus clade) previously characterized as containing a concentration of independent origins of group living. The two Chikunia studied here are sister species, representing a rare case of close genetic and behavioural interspecific relationship. We conclude that the loss of aggression that accompanies group living and social behaviour in cobweb spiders might help to explain the origin of mixed-species colonies.ADDITIONAL KEYWORDS: behaviour, phylogenetics – phylogenetics – phylogenetics, sociality – taxonomy, theridiid phylogeny.
2019 International Journal
21 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Twohig KA, Pfeffer DA, Baird JK, Price RN, Zimmerman PA, Hay SI, Gething PW, Battle KE, Howes RE
Effective malaria control strategies require an accurate understanding of the epidemiology of locally transmitted Plasmodium species. Compared to Plasmodium falciparum infection, Plasmodium vivax has a lower asexual parasitaemia, forms dormant liver-stages (hypnozoites), and is more transmissible. Hence, treatment and diagnostic policies aimed exclusively at P. falciparum are far less efficient against endemic P. vivax. Within sub-Saharan Africa, malaria control programmes justly focus on reducing the morbidity and mortality associated with P. falciparum. However, the recent emphasis on malaria elimination and increased accessibility of more sensitive diagnostic tools have revealed greater intricacies in malaria epidemiology across the continent. Since 2010, the number of studies identifying P. vivax endemic to Africa has expanded considerably, with 88 new scientific reports published since a review of evidence in 2015, approximately doubling the available data. There is evidence of P. vivax in all regions of Africa, apparent from infected vectors, clinical cases, serological indicators, parasite prevalence, exported infections, and P. vivax-infected Duffy-negative individuals. Where the prevalence of microscopic parasitaemia is low, a greater proportion of P. vivax infections were observed relative to P. falciparum. This evidence highlights an underlying widespread presence of P. vivax across all malaria-endemic regions of Africa, further complicating the current practical understanding of malaria epidemiology in this region. Thus, ultimate elimination of malaria in Africa will require national malaria control programmes to adopt policy and practice aimed at all human species of malaria.
2019 Publication
22 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman J. Kevin Baird
One Giant Leap… This specially themed issue of the Journal of Vector Borne Diseases highlights the obstacles and opportunities before us in striving to achieve what would be a historic elimination of endemic malaria transmission. Perhaps most readers of this august Journal would not have been born before the 20th of July 1969 when American astronaut Neil Armstrong became the first human to set foot on another celestial body, the Moon. That technological achievement elicited perhaps the single greatest global outpouring in our time of public faith in and enthusiasm for monumental scientific endeavours. And yet, just 4 days later, the 22nd World Health Assembly quietly but firmly surrendered its 14-year global campaign to eradicate malaria. While the resolution politely refers to “…this revised strategy of malaria eradication.”, it also expressed “…in the regions where eradication does not yet seem feasible, control of malaria with means available should be encouraged and may be regarded as a necessary and valid step…”[1]. The resolution, with less than two seemingly unremarkable pages, was a historic white flag of strategic defeat for humanity. It effectively acknowledged that we lacked the resources, tools, know-how, or will need to annihilate the plasmodia. We had to mitigate the harm done by malaria with practical measures of control rather than chase what seemed the unattainable vision of eradication. The historic and technical context of that surrender and its aftermath merits examination today. Even as late as 1969 the accomplishments of the Global Malaria Eradication Campaign remained largely intact and, in retrospect, formidable. Among the 1.8 billion people who had been living with malaria in 1955, endemic transmission had been eliminated where 0.7 billion lived[2]. Estimated global malaria mortality had been reduced by 80%[3], and in India, specifically an estimated 75 million cases in 1947 had been reduced to just under 50,000 by 1961 and fewer than 350,000 in 1969[4]. India and most other nations beyond sub-Saharan Africa had achieved what today appear to have been astonishing successes putting them on the near verge of elimination success[5],[6]. What stopped them?
2019 Publication
23 Jeffrey Neilson University of Sydney Sukrisno Widyotomo Pusat Penelitian Kopi dan Kakao Indonesia Jeff Neilson, Diany Faila Sophia Hartatri, and Mark Vicol
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2019 Article
24 Matthew Wayne Tocheri Lakehead University Drs I Made Geria, M.Si. Pusat Penelitian Arkeologi Nasional Veatch EG, Tocheri MW, Sutikna T, McGrath K, Wahyu Saptomo E, Jatmiko, Helgen KM
Liang Bua, the type locality of Homo floresiensis, is a limestone cave located in the western part of the Indonesianislandof Flores. The relativelycontinuous stratigraphic sequence of the site spansthepast ~190kyrand contains ~275,000 taxonomically identifiable vertebrate skeletal elements, ~80% of which belong to murine rodent taxa (i.e., rats). Six described genera are present at Liang Bua (Papagomys, Spelaeomys, Hooijeromys, Komodomys, Paulamys, and Rattus), one of which, Hooijeromys, is newly recorded in the site deposits, being previously knownonly fromEarly toMiddle Pleistocene sites incentral Flores.Measurements of the proximal femur (n ¼ 10,212) and distal humerus (n ¼ 1186) indicate five murine body size classes ranging from small (mouse-sized) to giant (common rabbit-sized) are present. The proportions of these five classes across successive stratigraphic units reveal two major changes in murine body size distribution due to significant shifts in the abundances ofmore open habitat-adaptedmedium-sized murines versus more closed habitatadapted smaller-sized ones. One of these changes suggests a modest increase in available open habitats occurred ~3 ka, likely the result of anthropogenic changes to the landscape related to farming by modern human populations. The other and more significant change occurred ~60 ka suggesting a rapid shift from more open habitats to more closed conditions at this time. The abrupt reduction of medium-sized murines, along with the disappearance of H. floresiensis, Stegodon florensis insularis (an extinct proboscidean), Varanus komodoensis (Komodo dragon), Leptoptilos robustus (giant marabou stork), and Trigonoceps sp. (vulture) at LiangBua ~60e50ka, is likely the consequence of these animalspreferringand trackingmore openhabitats to elsewhere on the island. If correct, then the precise timing and nature of the extinction of H. floresiensis and its contemporaries must await new discoveries at Liang Bua or other as yet unexcavated sites on Flores.
2019 Journal Article
25 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Simon Pouil, Reza Samsudin, Jacques Slembrouck, Ahmad Sihabuddin, Gusnia Sundari, Khazaidan Khazaidan, Anang Hari Kristanto, Brata Pantjara, Domenico Caruso
Over the past several years, Indonesian freshwater aquaculture has intensified, with a concomitant increase in the use of commercial pellets. To assess the effects of pond aquaculture intensification on nutrient dynamics, we monitored nutrients and fish production in a small-scale fish farm in West Java province. The studied system consisted of semi-intensive giant gourami (Osphronemus goramy) production in four small earthen ponds (353–482m?2 each and 0.46–0.55m deep). Nitrogen (N) and phosphorus (P) fluxes through the ponds were monitored, and data on fish production and nutrient accumulation in sediments were collected during a 5-month production cycle. Results showed that, on average, 61% total N and 77% P inputs were trapped in the accumulated sediments. Only 15% of total N and <3% P inputs introduced into ponds were recovered in harvested fish. Sediment nutrient accumulation increased linearly with total nutrient input. The consequences of intensification of giant gourami aquaculture using this production model are explored in terms of nutrient use efficiency and environmental impact.
2019 Article scientifique
26 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Jacques Slembrouck, Otong Z. Arifin, Simon Pouil, Jojo Subagja, Akhmad Yani, Anang H. Kristanto, Marc Legendre
The giant gourami Osphronemus goramy Lacepède (1801) is one of the main freshwater commodities of economic importance in Indonesia. This species has been produced in small-scale farms for decades. Although giant gourami aquaculture has grown exponentially during the last 15 years, there are still limitations in the availability of fry, in part due to difficulties in sexing broodfish, which leads to non-optimal sex-ratios for breeding. In this study, morphological and behavioral criteria for sex identification based on the Indonesian National Standard and a field survey were assessed on>400 giant gourami broodfish using a random forest algorithm. The actual sex of the fish was confirmed using a urogenital cannulation technique. This analysis demonstrated that, for the so-called “black” phenotype fish, observations of the hump on the forehead, thickening of the lower jaw, and the pigmentation on the pectoral fin are highly reliable for sexing (about 95% success). However, pectoral fin pigmentation was not useful for sexing the so-called “white” phenotype fish. This study also revealed that the criteria often used by fish farmers do not improve sexing success. Based on these findings, recommendations are made for optimizing the sexing of mature giant gourami fish and for selecting preadults as future broodfish.
2019 Article scientifique
27 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Hubert, N., Lumbantobing, D., Sholihah, A., Dahruddin, H., Delrieu?Trottin, E., Busson, F., Sauri, S., Hadiaty R., Keith P.
Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.
2019 article
28 Kazunori Yamahira Tropical Biosphere Research Center, University of the Ryukyus Kawilarang W.A. Masengi Faculty of Fisheries and Marine Science, Sam Ratulangi Universit Javier Montenegro, Koji Mochida, Kumi Matsui, Daniel F. Mokodongan, Bayu K. A. Sumarto, Sjamsu A. Lawelle, Andy B. Nofrianto, Renny K. Hadiaty, Kawilarang W. A. Masengi, Lengxob Yong, Nobuyuki Inomata, Takahiro Irie, Yasuyuki Hashiguchi, Yohey Terai, Jun Kitano, Kazunori Yamahira
Although there are many examples of color evolution potentially driven by sensory drive, only few studies have examined whether distinct species inhabiting the same environments evolve similar body colors via shared sensory mechanisms. In this study, we tested whether two sympatric freshwater fish taxa, halfbeaks of the genus Nomorhamphus and ricefishes of the genus Oryzias in Sulawesi Island, converge in both body color and visual sensitivity. After reconstructing the phylogeny separately for Nomorhamphus and Oryzias using transcriptome?wide sequences, we demonstrated positive correlations of body redness between these two taxa across environments, even after phylogenetic corrections, which support convergent evolution. However, substantial differences were observed in the expression profiles of opsin genes in the eyes between Nomorhamphus and Oryzias. Particularly, the expression levels of the long wavelength?sensitive genes were negatively correlated between the taxa, indicating that they have different visual sensitivities despite living in similar light environments. Thus, the convergence of body colorations between these two freshwater fish taxa was not accompanied by convergence in opsin sensitivities. This system presents a case in which body color convergence can occur between sympatric species via different mechanisms.
2019 Full paper
29 Kazunori Yamahira Tropical Biosphere Research Center, University of the Ryukyus Kawilarang W.A. Masengi Faculty of Fisheries and Marine Science, Sam Ratulangi Universit Nobu Sutra, Junko Kusumi, Javier Montenegro, Hirozumi Kobayashi, Shingo Fujimoto, Kawilarang W. A. Masengi, Atsushi J. Nagano, Atsushi Toyoda, Masatoshi Matsunami, Ryosuke Kimura, Kazunori Yamahira
Sympatric speciation has been demonstrated in few empirical case studies, despite intense searches, because of difficulties in testing the criteria for this mode of speciation. Here, we report a possible case of sympatric speciation in ricefishes of the genus Oryzias on Sulawesi, an island of Wallacea. Three species of Oryzias are known to be endemic to Lake Poso, an ancient tectonic lake in central Sulawesi. Phylogenetic analyses using RAD-seq-derived single nucleotide polymorphisms (SNPs) revealed that these species are monophyletic. We also found that the three species are morphologically distinguishable and clearly separated by population-structure analyses based on the SNPs, suggesting that they are reproductively isolated from each other. A mitochondrial DNA chronogram suggested that their speciation events occurred after formation of the tectonic lake, and existence of a historical allopatric phase was not supported by coalescent-based demographic inference. Demographic inference also suggested introgressive hybridization from an outgroup population. However, differential admixture among the sympatric species was not supported by any statistical tests. These results all concur with criteria necessary to demonstrate sympatric speciation. Ricefishes in this Wallacean lake provide a promising new model system for the study of sympatric speciation.
2019 Full paper
30 Nicholas Robert McClean University of Technology Sydney Dedi Adhuri Pusat Penelitian Kemasyarakatan dan Kebudayaan, Lembaga Ilmu Pengetahuan Indonesia McClean, N., Barclay, K., Fabinyi, M., Adhuri, D.S., Sulu, R., Indrabudi, T.
The key question addressed in this project is how the governance of fisheries affects the wellbeing of coastal communities. The aim of the project is to contribute to the development of a methodology for structured and evidence-based decision-making for policies and projects intending to benefit coastal communities. In developing methods to support these policies, we include consideration of the potential benefits and risks associated with policy changes and projects, who derives those benefits or is exposed to the risks, and to what extent intended benefits are in fact realised over time. These are not usually assessed or monitored in fisheries in relation to social and economic outcomes at the community level.
2019 Report
31 Harry Marshall Manchester Metropolitan University Dr Pramana Yuda Universitas Atma Jaya Yogyakarta Mr Harry Marshall, Dr Nigel Collar, Dr Alexander C. Lees, Dr Andrew Moss, Dr Pramana Yuda, Professor Stuart Marsden.
Many South-East Asian bird species are in rapid decline due to offtake for the cage-bird trade, a phenomenon driven largely by consumption in Indonesia and labelled the ‘Asian Songbird Crisis’. Interventions aimed at reducing this offtake require an understanding of the spatial and temporal dynamics of the trade. We surveyed the bird-keeping habits of over 3,000 households from 92 urban and rural communities across six provinces on Java, Indonesia, and compared prevalence and patterns of bird keeping with those from surveys undertaken a decade ago. We estimate that one-third of Java’s 36 million households keep 66?84 million cage-birds. Despite over half of all birds owned being non-native species, predominantly lovebirds (Agapornis spp.), the majority of bird-keepers (76%) owned native species. Ownership levels were significantly higher in urban than rural areas, and were particularly high in the eastern provinces of the island. Overall levels of bird ownership have increased over the past decade, and species composition has changed. Notably, lovebirds showed a seven-fold increase in popularity while ownership of genera including groups with globally threatened species such as leafbirds (Chloropsis spp.) and white-eyes (Zosterops spp.) also rose sharply. The volume of some locally threatened birds estimated to be in ownership (e.g., >3 million White-rumped Shama Kittacincla malabarica) cannot have been supplied from Java’s forests and research on supply from other islands and Java’s growing commercial breeding industry is a priority. Determining temporal and spatial patterns of ownership is a crucial first step towards finding solutions to this persistent, pervasive and adaptive threat to the regional avifauna.
2019 Journal Article
32 John Stephen Lansing Nanyang Technological University Prof Herawati Sudoyo Eijkman Institute for Molecular Biology Wall, J.D., E. Stawiski, A. Ratan, H. L. Kim, C. Kim, R. Gupta, K. Suryamohan, E.S. Gusareva, R.W. Purbojati, T. Bhangale, V. Stepanov, V. Kharkov, M.S. Schröder, V. Ramprasad, J. Tom, S. Durinck, Q. Bei, J. Li, S. Phalke, A. Basu, J. Stinson, S. Nair, S. Malaichamy, N.K. Biswas, J.C. Chambers, K.C. Cheng, J.T. George, S.S. Khor, C.-U. Kim, B.J. Kim, R. Menon, T. Sattibabu, A. Verma, V. Gopalan, B.M. Md-Zain, K.G. Chan, J.-Y. Shin, M. Pratapneni, S. Santhosh, K. Tokunaga, M. Parani, P. Natarajan, M. Hauser, R.R. Allingham, C. Santiago-Turla, A. Ghosh, S.G.K. Gadde, H. Sudoyo, J.S. Lansing, J. Friedlaender, M.P. Cox, M. Hammer, T. Karafet, K.C. Ang, S.Q. Mehdi, V. Radha, V. Mohan, P.P. Majumder, S. Seshagiri, J.-S. Seo, S. Schuster and A.S. Peterson
The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.
2019 Research article
33 John Stephen Lansing Nanyang Technological University Prof Herawati Sudoyo Eijkman Institute for Molecular Biology Heini Natri, Katalina S. Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, Georgi Hudjashov, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero
Indonesia is the world’s fourth most populous country, host to striking levels of human diversity, regional 36 patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. 37 However, it has been largely excluded from the human genomics sequencing boom of the last decade. 38 To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide 39 CpG methylation and gene expression measurements in over 100 individuals from three locations that 40 capture the major genomic and geographical axes of diversity across the Indonesian archipelago. 41 Investigating between- and within-island differences, we find up to 10% of tested genes are differentially 42 expressed between the islands of Mentawai (Sumatra) and New Guinea. Variation in gene expression is 43 closely associated with DNA methylation, with expression levels of 9.7% of genes strongly correlating 44 with nearby CpG methylation, and many of these genes being differentially expressed between islands. 45 Genes identified in our differential expression and methylation analyses are enriched in pathways 46 involved in immunity, highlighting Indonesia tropical role as a source of infectious disease diversity and 47 the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within48 island variation in DNA methylation and gene expression, likely driven by very local environmental 49 differences across sampling sites. Together, these results strongly suggest complex relationships between 50 DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the 51 environment. This has implications for the application of genomic medicine, both in critically 52 understudied Indonesia and globally, and will allow a better understanding of the interacting roles of 53 genomic and environmental factors shaping molecular and complex phenotypes.
2019 article
34 John Stephen Lansing Nanyang Technological University Prof Herawati Sudoyo Eijkman Institute for Molecular Biology Chung, N.N., G.S. Jacobs, H. Sudoyo, S.G. Malik, L.Y. Chew, J.S. Lansing and M.P. Cox
Population genetics has been successful at identifying the relationships between human groups and their interconnected histories. However, the link between genetic demography inferred at large scales and the individual human behaviours that ultimately generate that demography is not always clear. While anthropological and historical context are routinely presented as adjuncts in population genetic studies to help describe the past, determining how underlying patterns of human sociocultural behaviour impact genetics still remains challenging. Here, we analyse patterns of genetic variation in village-scale samples from two islands in eastern Indonesia, patrilocal Sumba and a matrilocal region of Timor. Adopting a ‘process modelling’ approach, we iteratively explore combinations of structurally different models as a thinking tool. We find interconnected socio-genetic interactions involving sex-biased migration, lineage-focused founder effects, and on Sumba, heritable social dominance. Strikingly, founder ideology, a cultural model derived from anthropological and archaeological studies at larger regional scales, has both its origins and impact at the scale of villages. Process modelling lets us explore these complex interactions, first by circumventing the complexity of formal inference when studying large datasets with many interacting parts, and then by explicitly testing complex anthropological hypotheses about sociocultural behaviour from a more familiar population genetic standpoint.
2019 article
35 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Twohig KA, Pfeffer DA, Baird JK, Price RN, Zimmerman PA, Hay SI, Gething PW, Battle KE, Howes RE
Effective malaria control strategies require an accurate understanding of the epidemiology of locally transmitted Plasmodium species. Compared to Plasmodium falciparum infection, Plasmodium vivax has a lower asexual parasitaemia, forms dormant liver-stages (hypnozoites), and is more transmissible. Hence, treatment and diagnostic policies aimed exclusively at P. falciparum are far less efficient against endemic P. vivax. Within sub-Saharan Africa, malaria control programmes justly focus on reducing the morbidity and mortality associated with P. falciparum. However, the recent emphasis on malaria elimination and increased accessibility of more sensitive diagnostic tools have revealed greater intricacies in malaria epidemiology across the continent. Since 2010, the number of studies identifying P. vivax endemic to Africa has expanded considerably, with 88 new scientific reports published since a review of evidence in 2015, approximately doubling the available data. There is evidence of P. vivax in all regions of Africa, apparent from infected vectors, clinical cases, serological indicators, parasite prevalence, exported infections, and P. vivax-infected Duffy-negative individuals. Where the prevalence of microscopic parasitaemia is low, a greater proportion of P. vivax infections were observed relative to P. falciparum. This evidence highlights an underlying widespread presence of P. vivax across all malaria-endemic regions of Africa, further complicating the current practical understanding of malaria epidemiology in this region. Thus, ultimate elimination of malaria in Africa will require national malaria control programmes to adopt policy and practice aimed at all human species of malaria.
2019 Publication
36 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman J. Kevin Baird
One Giant Leap… This specially themed issue of the Journal of Vector Borne Diseases highlights the obstacles and opportunities before us in striving to achieve what would be a historic elimination of endemic malaria transmission. Perhaps most readers of this august Journal would not have been born before the 20th of July 1969 when American astronaut Neil Armstrong became the first human to set foot on another celestial body, the Moon. That technological achievement elicited perhaps the single greatest global outpouring in our time of public faith in and enthusiasm for monumental scientific endeavours. And yet, just 4 days later, the 22nd World Health Assembly quietly but firmly surrendered its 14-year global campaign to eradicate malaria. While the resolution politely refers to “…this revised strategy of malaria eradication.”, it also expressed “…in the regions where eradication does not yet seem feasible, control of malaria with means available should be encouraged and may be regarded as a necessary and valid step…”[1]. The resolution, with less than two seemingly unremarkable pages, was a historic white flag of strategic defeat for humanity. It effectively acknowledged that we lacked the resources, tools, know-how, or will need to annihilate the plasmodia. We had to mitigate the harm done by malaria with practical measures of control rather than chase what seemed the unattainable vision of eradication. The historic and technical context of that surrender and its aftermath merits examination today. Even as late as 1969 the accomplishments of the Global Malaria Eradication Campaign remained largely intact and, in retrospect, formidable. Among the 1.8 billion people who had been living with malaria in 1955, endemic transmission had been eliminated where 0.7 billion lived[2]. Estimated global malaria mortality had been reduced by 80%[3], and in India, specifically an estimated 75 million cases in 1947 had been reduced to just under 50,000 by 1961 and fewer than 350,000 in 1969[4]. India and most other nations beyond sub-Saharan Africa had achieved what today appear to have been astonishing successes putting them on the near verge of elimination success[5],[6]. What stopped them?
2019 Publication
37 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Walter R.J. Taylor, Kamala Thriemer, Lorenz von Seidlein, Prayoon Yuentrakul, Ashenafi Assefa, Sarah Auburn, Krisin Chand, Nguyen Hoang Chau, Phaik Yeong Cheah, Le Thanh Dong, Mehul Dhorda, Tamiru Shibru Degaga, Angela Devine, Lenny L Ekawati, Fahmi Fahmi, Asrat Hailu, Mohammad Anwar Hasanzai, Tran Tinh Hien, Htee Khu, Benedikt Ley, Yoel Lubell, Jutta Marfurt, Hussein Mohammad, Kerryn Moore, Mohammad Nader Naddim, Ayodhia Pitaloka Pasaribu, Syahril Pasaribu, Cholrawee Promnarate, Awab Ghulam Rahim, Pasathron Sirithiranont, Hiwot Solomon, Herawati Sudoyo, Inge Sutanto, Ngo Viet Thanh, Nguyen Thi Tuyet-Trinh, Naomi Waithira, Adugna Woyessa, Fazal Yamin Yamin, Arjen Dondorp, Julie A Simpson, J Kevin Baird, Nicholas J White, Nicholas P Day, Ric N Price
BACKGROUND: Primaquine is the only widely used drug that prevents Plasmodium vivax malaria relapses, but adherence to the standard 14-day regimen is poor. We aimed to assess the efficacy of a shorter course (7 days) of primaquine for radical cure of vivax malaria. METHODS: We did a randomised, double-blind, placebo-controlled, non-inferiority trial in eight health-care clinics (two each in Afghanistan, Ethiopia, Indonesia, and Vietnam). Patients (aged ?6 months) with normal glucose-6-phosphate dehydrogenase (G6PD) and presenting with uncomplicated vivax malaria were enrolled. Patients were given standard blood schizontocidal treatment and randomly assigned (2:2:1) to receive 7 days of supervised primaquine (1·0 mg/kg per day), 14 days of supervised primaquine (0·5 mg/kg per day), or placebo. The primary endpoint was the incidence rate of symptomatic P vivax parasitaemia during the 12-month follow-up period, assessed in the intention-to-treat population. A margin of 0·07 recurrences per person-year was used to establish non-inferiority of the 7-day regimen compared with the 14-day regimen. This trial is registered at ClinicalTrials.gov (NCT01814683). FINDINGS: Between July 20, 2014, and Nov 25, 2017, 2336 patients were enrolled. The incidence rate of symptomatic recurrent P vivax malaria was 0·18 (95% CI 0·15 to 0·21) recurrences per person-year for 935 patients in the 7-day primaquine group and 0·16 (0·13 to 0·18) for 937 patients in the 14-day primaquine group, a difference of 0·02 (-0·02 to 0·05, p=0·3405). The incidence rate for 464 patients in the placebo group was 0·96 (95% CI 0·83 to 1·08) recurrences per person-year. Potentially drug-related serious adverse events within 42 days of starting treatment were reported in nine (1·0%) of 935 patients in the 7-day group, one (0·1%) of 937 in the 14-day group and none of 464 in the control arm. Four of the serious adverse events were significant haemolysis (three in the 7-day group and one in the 14-day group). INTERPRETATION: In patients with normal G6PD, 7-day primaquine was well tolerated and non-inferior to 14-day primaquine. The short-course regimen might improve adherence and therefore the effectiveness of primaquine for radical cure of P vivax malaria. FUNDING: UK Department for International Development, UK Medical Research Council, UK National Institute for Health Research, and the Wellcome Trust through the Joint Global Health Trials Scheme (MR/K007424/1) and the Bill & Melinda Gates Foundation (OPP1054404).
2019 Publication
38 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK
The notion of the human malaria caused by infection with Plasmodium vivax as benign roots deeply in the scientific and medical history of the malarias. So-called benign tertian malaria contrasts its malignant cousin Plasmodium falciparum – acute infection being relatively mild, and rarely consequential vs. frequent and rapid death by cerebral, pulmonary, hepatic, and nephrotic syndromes. Near the center of this perspective lies an optical illusion: the parasitemias of P. vivax normally occurring at far lower densities than those of P. falciparum seemingly representing the respective biomasses of these infections, i.e., as typically not threatening vs. threatening, respectively. Whereas parasitemias of P. falciparum often exceed 100,000/?L blood, those of P. vivax rarely exceed even 10,000/?L. These disparate numbers are no illusion, but their representation of the depth and danger of the acute infection now appears to be so.
2019 Publication
39 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK
SUMMARYThe technical genesis and practice of 8-aminoquinoline therapy of latent malaria offer singular scientific, clinical, and public health insights. The 8-aminoquinolines brought revolutionary scientific discoveries, dogmatic practices, benign neglect, and, finally, enduring promise against endemic malaria. The clinical use of plasmochin-the first rationally synthesized blood schizontocide and the first gametocytocide, tissue schizontocide, and hypnozoitocide of any kind-commenced in 1926. Plasmochin became known to sometimes provoke fatal hemolytic crises. World War II delivered a newer 8-aminoquinoline, primaquine, and the discovery of glucose-6-phosphate dehydrogenase (G6PD) deficiency as the basis of its hemolytic toxicity came in 1956. Primaquine nonetheless became the sole therapeutic option against latent malaria. After 40?years of fitful development, in 2018 the U.S. Food and Drug Administration registered the 8-aminoquinoline called tafenoquine for the prevention of all malarias and the treatment of those that relapse. Tafenoquine also cannot be used in G6PD-unknown or -deficient patients. The hemolytic toxicity of the 8-aminoquinolines impedes their great potential, but this problem has not been a research priority. This review explores the complex technical dimensions of the history of 8-aminoquinolines. The therapeutic principles thus examined may be leveraged in improved practice and in understanding the bright prospect of discovery of newer drugs that cannot harm G6PD-deficient patients.
2019 Publication
40 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Robert J Commons; Julie A Simpson; Kamala Thriemer; Cindy S Chu; Nicholas M Douglas; Tesfay Abreha; Sisay G Alemu; Arletta Añez; Nicholas M Anstey; Abraham Aseffa; Ashenafi Assefa; Ghulam R Awab; J Kevin Baird; Bridget E Barber; Isabelle Borghini-Fuhrer; Umberto D'Alessandro; Prabin Dahal; André Daher; Peter J de Vries; Annette Erhart; Margarete SM Gomes; Matthew J Grigg; Jimee Hwang; Piet A Kager; Tsige Ketema; Wasif A Khan; Marcus VG Lacerda; Toby Leslie; Benedikt Ley; Kartini Lidia; Wuelton M Monteiro; Dhelio B Pereira; Giao T Phan; Aung P Phyo; Mark Rowland; Kavitha Saravu; Carol H Sibley; André M Siqueira; Kasia Stepniewska; Walter RJ Taylor; Guy Thwaites; Binh Q Tran; Tran T Hien; José Luiz F Vieira; Sonam Wangchuk; James Watson; Timothy William; Charles J Woodrow; Francois Nosten; Philippe J Guerin; Nicholas J White; Ric N Price
Background Malaria causes a reduction in haemoglobin that is compounded by primaquine, particularly in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency. The aim of this study was to determine the relative contributions to red cell loss of malaria and primaquine in patients with uncomplicated Plasmodium vivax. Methods A systematic review identified P. vivax efficacy studies of chloroquine with or without primaquine published between January 2000 and March 2017. Individual patient data were pooled using standardised methodology, and the haematological response versus time was quantified using a multivariable linear mixed effects model with non-linear terms for time. Mean differences in haemoglobin between treatment groups at day of nadir and day 42 were estimated from this model. Results In total, 3421 patients from 29 studies were included: 1692 (49.5%) with normal G6PD status, 1701 (49.7%) with unknown status and 28 (0.8%) deficient or borderline individuals. Of 1975 patients treated with chloroquine alone, the mean haemoglobin fell from 12.22?g/dL [95% CI 11.93, 12.50] on day 0 to a nadir of 11.64?g/dL [11.36, 11.93] on day 2, before rising to 12.88?g/dL [12.60, 13.17] on day 42. In comparison to chloroquine alone, the mean haemoglobin in 1446 patients treated with chloroquine plus primaquine was ??0.13?g/dL [??0.27, 0.01] lower at day of nadir (p?=?0.072), but 0.49?g/dL [0.28, 0.69] higher by day 42 (p??25% to ?5?g/dL. Conclusions Primaquine has the potential to reduce malaria-related anaemia at day 42 and beyond by preventing recurrent parasitaemia. Its widespread implementation will require accurate diagnosis of G6PD deficiency to reduce the risk of drug-induced haemolysis in vulnerable individuals.
2019 Publication
41 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Xi He, Maohua Pan, Weilin Zeng, Chunyan Zou, Liang Pi, Yucheng Qin, Luyi Zhao, Pien Qin, Yuxin Lu, J. Kevin Baird, Yaming Huang, Liwang Cui, Zhaoqing Yang
BACKGROUND: Plasmodium vivax transmission in West Africa, dominant for the Duffy-negative blood group, has been increasingly recognized from both local residents as well as international travelers who contracted P. vivax malaria there. However, the relapsing pattern and sensitivity to antimalarial treatment of P. vivax strains originated from this region are largely unknown. There is evidence that the efficacy of primaquine for radical cure of relapsing malaria depends on host factors such as the hepatic enzyme cytochrome P450 (CYP) 2D6. CASE PRESENTATION: A 49-year-old Chinese man was admitted to the Shanglin County Hospital in Guangxi Province, China, on December 19, 2016, 39?days after he returned from Ghana, where he stayed for one and a half years. He was diagnosed by microscopy as having uncomplicated P. vivax malaria. Treatment included 3?days of intravenous artesunate (420?mg total), and 3?days of chloroquine (1550?mg total), and 8?days of primaquine (180?mg total). Although parasites and symptoms were cleared rapidly and he was malaria-negative for almost two months, he suffered four relapses with relapse intervals ranging from 58 to 232?days. The last relapse occurred at 491?days from his first vivax attack. For the first three relapses, he was treated similarly with chloroquine and primaquine, sometimes supplemented with additional artemisinin combination therapies (ACTs). For the last relapse, he was treated with intravenous artesunate, 3?days of an ACT, and 7?days of azithromycin, and had remained healthy for 330?days. Molecular studies confirmed P. vivax infections for all the episodes. Although this patient was diagnosed to have normal glucose-6-phosphate dehydrogenase (G6PD) activity, his CYP2D6 genotype corresponded to a *2A/*36 allele variant suggesting of an impaired primaquine metabolizer phenotype. CONCLUSIONS: This clinical case suggests that P. vivax malaria originating from West Africa may produce multiple relapses extending beyond one year. The failures of primaquine as an anti-relapse therapy may be attributed to the patient's impaired metabolizer phenotype of the CYP2D6. This highlights the importance of knowing the host G6PD and CYP2D6 activities for effective radical cure of relapsing malaria by primaquine.
2019 Publication
42 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Walter R. J. Taylor, Sim Kheng, Sinoun Muth, Pety Tor, Saorin Kim, Steven Bjorge, Narann Topps, Khem Kosal, Khon Sothea, Phum Souy, Chuor Meng Char, Chan Vanna, Po Ly, Virak Khieu, Eva Christophel, Alexandra Kerleguer, Antonella Pantaleo, Mavuto Mukaka, Didier Menard, J. Kevin Baird
BACKGROUND: Hemoglobin (Hb) data are limited in Southeast Asian glucose-6-phosphate dehydrogenase (G6PD) deficient (G6PD-) patients treated weekly with the World Health Organization-recommended primaquine regimen (ie, 0.75 mg/kg/week for 8 weeks [PQ 0.75]). METHODS: We treated Cambodians who had acute Plasmodium vivax infection with PQ0.75 and a 3-day course of dihydroartemisinin/piperaquine and determined the Hb level, reticulocyte count, G6PD genotype, and Hb type. RESULTS: Seventy-five patients (male sex, 63) aged 5-63 years (median, 24 years) were enrolled. Eighteen were G6PD deficient (including 17 with G6PD Viangchan) and 57 were not G6PD deficient; 26 had HbE (of whom 25 were heterozygous), and 6 had ?-/?-thalassemia. Mean Hb concentrations at baseline (ie, day 0) were similar between G6PD deficient and G6PD normal patients (12.9 g/dL [range, 9?16.3 g/dL] and 13.26 g/dL [range, 9.6?16 g/dL], respectively; P = .46). G6PD deficiency (P = <.001), higher Hb concentration at baseline (P = <.001), higher parasitemia level at baseline (P = .02), and thalassemia (P = .027) influenced the initial decrease in Hb level, calculated as the nadir level minus the baseline level (range, -5.8-0 g/dL; mean, -1.88 g/dL). By day 14, the mean difference from the day 7 level (calculated as the day 14 level minus the day 7 level) was 0.03 g/dL (range, -0.25?0.32 g/dL). Reticulocyte counts decreased from days 1 to 3, peaking on day 7 (in the G6PD normal group) and day 14 (in the G6PD deficient group); reticulocytemia at baseline (P = .001), G6PD deficiency (P = <.001), and female sex (P = .034) correlated with higher counts. One symptomatic, G6PD-deficient, anemic male patient was transfused on day 4. CONCLUSIONS: The first PQ0.75 exposure was associated with the greatest decrease in Hb level and 1 blood transfusion, followed by clinically insignificant decreases in Hb levels. PQ0.75 requires monitoring during the week after treatment. Safer antirelapse regimens are needed in Southeast Asia.
2019 Publication
43 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Katherine E Battle, Tim C D Lucas, Michele Nguyen, Rosalind E Howes, Aniuta K Nandi, Katherine A Thowig, Daniel A Pfeffer, Ewan Cameron, Puja C Rao, Daniel Casey, Harry S Gibson, Jennifer A Rozier, Ursula Dalrymple, Suzanne H Keddie, Emma L Collins, Joseph R Harris, Carlos A Guerra, Michael P Thorn, Donal Bizansio, Nancy Fullman, Chantak K Huynh, Xie Kulikoff, Michael J Kutz, Alan D Lopez, Ali H Mokdad, Mohsen Naghawi, Grant Nguyen, Katya Anne Shackelford, Theo Vos, Haidong Wang, Stephen S Lim, Christopher J L Murray, Ric N Price, J Kevin Baird, David L Smith, Samir Bhatt, Daniel J Weiss, Simon I Hay, Peter W Gething
Background Plasmodium vivax exacts a significant toll on health worldwide, yet few efforts to date have quantified the extent and temporal trends of its global distribution. Given the challenges associated with the proper diagnosis and treatment of P vivax, national malaria programmes—particularly those pursuing malaria elimination strategies—require up to date assessments of P vivax endemicity and disease impact. This study presents the first global maps of P vivax clinical burden from 2000 to 2017. Methods In this spatial and temporal modelling study, we adjusted routine malariometric surveillance data for known biases and used socioeconomic indicators to generate time series of the clinical burden of P vivax. These data informed Bayesian geospatial models, which produced fine-scale predictions of P vivax clinical incidence and infection prevalence over time. Within sub-Saharan Africa, where routine surveillance for P vivax is not standard practice, we combined predicted surfaces of Plasmodium falciparum with country-specific ratios of P vivax to P falciparum. These results were combined with surveillance-based outputs outside of Africa to generate global maps. Findings We present the first high-resolution maps of P vivax burden. These results are combined with those for P falciparum (published separately) to form the malaria estimates for the Global Burden of Disease 2017 study. The burden of P vivax malaria decreased by 41·6%, from 24·5 million cases (95% uncertainty interval 22·5–27·0) in 2000 to 14·3 million cases (13·7–15·0) in 2017. The Americas had a reduction of 56·8% (47·6–67·0) in total cases since 2000, while South-East Asia recorded declines of 50·5% (50·3–50·6) and the Western Pacific regions recorded declines of 51·3% (48·0–55·4). Europe achieved zero P vivax cases during the study period. Nonetheless, rates of decline have stalled in the past five years for many countries, with particular increases noted in regions affected by political and economic instability. Interpretation Our study highlights important spatial and temporal patterns in the clinical burden and prevalence of P vivax. Amid substantial progress worldwide, plateauing gains and areas of increased burden signal the potential for challenges that are greater than expected on the road to malaria elimination. These results support global monitoring systems and can inform the optimisation of diagnosis and treatment where P vivax has most impact. Funding Bill & Melinda Gates Foundation and the Wellcome Trust.
2019 Publication
44 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Xu S, Zeng W, Ngassa Mbenda HG, Liu H, Chen X, Xiang Z, Li C, Zhang Y, Baird JK, Yang Z, Cui L.
BACKGROUND: Chloroquine (CQ) and primaquine (PQ) remain the frontline drugs for radical cure of uncomplicated P. vivax malaria in the Greater Mekong Sub-region (GMS). Recent reports of decreased susceptibility of P. vivax to CQ in many parts of the GMS raise concerns. METHODS: From April 2014 to September 2016, 281 patients with uncomplicated P. vivax infection attending clinics in border settlements for internally displaced people in northeast Myanmar were recruited into this study. Patients were treated with standard regimen of 3-day CQ and concurrent 14-day PQ (3.5?mg/kg total dose) as directly observed therapy, and followed for recurrent parasitemia within 28 days post-patency. RESULTS: Within the 28-day follow-up period, seven patients developed recurrent parasitemia, resulting in a cumulative rate of parasite recurrence of 2.6%. Five of the seven parasitemias recurred within two weeks, and two of those failed to clear within seven days, indicating high-grade resistance. CONCLUSION: Although failure of CQ/PQ treatment of P. vivax was relatively infrequent in northeast Myanmar, this study nonetheless confirms that CQ/PQ-resistant strains do circulate in this area, some of them of a highly resistant phenotype. It is thus recommended that patients who acquire vivax malaria in Myanmar be treated an artemisinin-combination therapy along with hypnozoitocidal primaquine therapy to achieve radical cure.
2019 Publication
45 Skye Turner-Walker Australian-German Climate Energy College, University of Melbourne Dr Riyante Djalante University of Halu Oleo Turner-Walker, Skye; Anantasari, Esti; Retnowati, Arry
Climate Change Research, Policy and Actions in Indonesia: Science, Adaptation and Mitigation (Springer Climate Series), Eds. Djalante, R. Jupesta, J. & Aldrian, E. 2019. Part II: Climate change adaptation, Chapter 16 – Integration into development sectors. Integration into development: translating international frameworks into village-level adaptation Authors: Turner-Walker, Skye, Australian National University (ANU), skye.turner-walker@anu.edu.au Anantasari, Esti, Universitas Gadjah Mada (UGM), esti.anantasari@ugm.ac.id Retnowati, Arry, Universitas Gadjah Mada (UGM), arry_retnowati@ugm.ac.id International climate change commitments have progressively prioritised addressing adaptation, particularly under the mechanisms of the United Nations Framework Convention on Climate Change (UNFCCC). In response, climate change adaptive capacity and resilience enhancing activities have been increasingly directed at local community or village scales. The aim of this chapter is to understand how conceptual underpinnings of adaptation are articulated into the programming of adaptation activities implemented at the local village levels under national adaptation planning in Indonesia. The local level experiences of adaptation programming in implementation, offer several insights to guide adaptation approaches and conceptions in use for informing national adaptation programming implementation at village levels. This chapter, therefore, situates the national adaptation programmes implemented in two case studies of agricultural areas in the Yogyakarta region of Java, amidst Indonesia’s country commitments and priorities on adaptation to village activity level implementation. The chapter presents the local experiences of farmers in two key adaptation projects implemented at the village level as part of broader nation-wide programming. The results of which detail findings captured post-project implementation and provide examples of the implications of adaptation framing on programmatic outcomes over long-range timeframes. This chapter draws conclusions that significant gaps and disjuncture between the top-down approach of national adaptation programming directives exist in the translation of programming into village activities. In particular, in the ways in which local participants are engaged and have the agency to direct the activities of adaptation programming in a manner that is culturally contextually appropriate and locally specific, and able to be sustained in the uptake of the programme activities. These findings suggest that limited engagement and meaningful inclusion with farmer communities in designing programme adaptation activities in the early design, coupled with minimal incorporation of farmers' social processes, the agency in innovation and local knowledge, has led to little impact or adaptive capacity being fostered in the long-term by national adaptation activities. Keywords: climate change adaptation, UNFCCC, development programming, village climate activities.
2019 Book chapter
46 Jae Hyeon Park University of California, Los Angeles Prof. Ir. Bakti Setiawan, MA, Ph.D. Department of Architecture and Planning, Gadjah Mada University Jaehyeon Park, Irsyad Adhi Waskita Hutama, and Deano Damario
The use of ‘civilian’ drones (i.e., unmanned aerial vehicles or UAVs) has been increasingly popular in human lives since the early 2000s. Not only private corporations such as Amazon but many individuals and public/non-public organizations have made use of this innovative and cutting-edge technology for various purposes: item delivery, traffic monitoring, post-disaster detection, and recreation, to name a few. Urban and regional planning is one of the very fields that might benefit, or have already benefitted from this state-of-the-art technology. Using drones becomes an effective and efficient methodological tool for generating, collecting, and analyzing better-quality materials so that it could improve the quality of research. A body of literature has employed drones and shed light on its potentials as an alternative to the existing methods such as satellite remote sensing and bare-eyed observation. In Indonesia, the country with many remote forests and disaster-prone areas in more than 17,000 islands, drones can be useful particularly for pushing forward the ‘one map policy’ under the current Jokowi administration that aims to integrate and standardize all the mapping materials produced by varying sources and tools, thereby reducing land-based conflicts and preventing disaster impacts. However, despite the increasing popularity of drone-based research, a curriculum at Indonesian planning schools which offers students an opportunity to learn how to use drones is still in the early stage as the same as or more rudimentary than other countries. In this sense, this research argues the current trend of drone-based research in Indonesia and identifies the ways in which drone teaching is integrated into the existing planning curriculum. Based on the authors’ own teaching experience through a pilot drone-based research seminar in early 2019 with the financial support of the National Research Foundation of Korea, and surveys and interviews with the participating students in the seminar as well as planning faculty at other universities across the country, opportunities and challenges for a drone research curriculum are discussed in this paper. Although almost all the students show an enhanced understanding of drone-based research and satisfaction over its future introduction and integration into the current program, some issues at the student and department level need to be addressed.
2019 Conference Paper Abstract
47 Matthew Wayne Tocheri Lakehead University Drs I Made Geria, M.Si. Pusat Penelitian Arkeologi Nasional Luong S, Tocheri MW, Hayes E, Sutikna T, Fullagar R, Wahyu Saptomo E, Jatmiko, Roberts RG
2019 Journal Article
48 Nicolas HUBERT Institut de Recherche pour le Développement Daisy Wowor Indonesian Institut of Sciences (LIPI), Research Centre for Biology (RCB), Division of Zoology Hubert N, Lumbantobing D, Sholihah A, Dahruddin H, Busson F, Sauri S, Hadiaty R, Keith P.
Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.
2019 Journal article
49 Tomoya Shibayama Waseda University Dr. Hendra Achiari Bandung Institute of Technology Mikami, T., Shibayama, T., Esteban, M., Takabatake, T., Nakamura, R., Nishida, Y., Achiari, H., Rusli, Marzuki, A., Marzuki, M., Stolle, J., Krautwald, C., Robertson, I., Aranguiz, R. & Ohira, K.
On September 28, 2018, a large earthquake and its accompanying tsunami waves caused severe damage to the coastal area of Palu Bay, in the central western part of Sulawesi Island, Indonesia. To clarify the distribution of tsunami inundation and run-up heights, and damage to coastal communities due to the tsunami, the authors conducted a field survey 1 month after the event. In the inner part of Palu Bay tsunami inundation and run-up heights of more than 4 m were measured at many locations, and severe damage by the tsunami to coastal low-lying settlements was observed. In the areas to the north of the bay and around its entrance the tsunami inundation and run-up heights were lower than in the inner part of the bay. The tsunami inundation distance depended on the topographical features of coastal areas. The southern shore of the bay experienced a longer inundation distance than other shores, though generally severe damage to houses was limited to within around 200 m from the shoreline. The main lessons that can be learnt from the present event are also discussed.
2019 International Journal Paper
50 Dr Aditya Riadi Gusman Institute of Geological and Nuclear Science (GNS Science) Professor Teuku Faisal Fathani Universitas Gadjah Mada Ryan Paulik, Aditya Gusman, James H. Williams, Gumbert Maylda Pratama, Sheng-lin Lin, Alamsyah Prawirabhakti, Ketut Sulendra, Muhammad Yasser Zachari, Zabin Ellyni Dwi Fortuna, Novita Barrang Pare Layuk, Ni Wayan Ika Suwarni
Seven weeks after the earthquake a field survey was carried out in Palu City to measure tsunami flow depths and record damage levels for buildings, roads and electricity infrastructure. Above ground level tsunami flow depths measured at 371 building sites ranged from 0.1 to 3.65 m, with a mean of 1.05 m and standard deviation of 0.55 m. The survey team also recorded attributes and damage levels for 463 buildings, 7.9 km of road and 455 utility poles. We observed that non-engineered ‘light timber’ and ‘lightly reinforced concrete’ construction frame buildings were highly susceptible to ‘non-structural’ component damage when tsunami flow depths exceeded 0.4 m (‘light timber’) and 1 m (‘lightly reinforced concrete’) above the first finished floor level, while unrepairable or complete building damage was regularly observed when flow depths exceeded 1.2 m. Only non-structural component damage was observed for engineered ‘reinforced concrete’ buildings. While tsunami flow depth traces could not be measured for affected road and utility pole components, hazard intensity parameters can be obtained from tsunami inundation maps to estimate the conditions that contributed to observed damage levels. The information presented herein forms an important evidence base to support future tsunami hazard and risk research in Indonesia.
2019 Report
51 Dr Aditya Riadi Gusman Institute of Geological and Nuclear Science (GNS Science) Professor Teuku Faisal Fathani Universitas Gadjah Mada Ryan Paulik, Aditya Gusman, James H. Williams, Gumbert Maylda Pratama, Sheng-lin Lin, Alamsyah Prawirabhakti, Ketut Sulendra, Muhammad Yasser Zachari, Zabin Ellyni Dwi Fortuna, Novita Barrang Pare Layuk, Ni Wayan Ika Suwarni
Palu City building and infrastructure (roads, utility poles) damage information collected following the September 28 2018 Sulawesi Earthquake and Tsunami.
2019 Survey Data
52 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Otong Zenal Arifin, Vitas Atmadi Prakoso, Jojo Subagja, Anang Hari Kristanto, Simon Pouil, Jacques Slembrouck
In this study, the influences of stocking density on growth, food intake and survival were assessed in larval rearing of giant gourami Osphronemus goramy. Eight days post-hatch larvae were raised for three weeks at six stocking densities (A: 0.6, B: 1.2, C: 2.4, D: 4.8, E: 9.6, F: 19.2 fish L-1) in an indoor closed recirculating system. Larvae were fed twice a day using tubifex worms. Performance indicators including food intake (% and g fish-1), survival rate (%), total length (cm), body weight (g), specific growth rate (g day-1), biomass gain (g L-1), feed conversion ratio (FCR), condition factor (K) and coefficients of variation (%) were determined. Water quality was checked throughout the experiment and maintained below critical thresholds for fish. Results shown no effect of stocking density on survival (> 98%) and size heterogeneity (p > 0.05) while growth significantly decreased at increasing stocking density conditions. At the end of the 21-d experiment, the individual body weights were 563.2 ± 64.3, 461.0 ± 28.6, 288.8 ± 19.3, 170.2 ± 13.8, 113.6 ± 6.9 and 81.9 ± 2.3 g, for conditions A, B, C, D, E and F respectively. The decreasing growth can be related to drastic reduction of food intake by the larvae stocked at the highest densities. The consequences of larval rearing intensification should be further investigated on the nursery and grow-out phases.
2019 Short communication
53 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Vitas Atmadi Prakoso, Simon Pouil, Muhammad Naufal Ibrahim Prabowo, Sri Sundaria, Otong Zenal Arifin, Jojo Subagja, Ridwan Affandi, Anang Hari Kristanto, Jacques Slembrouck
The influence of temperature on zootechnical performances and physiology was assessed in giant gourami (Osphronemus goramy) larvae. Larvae aged ten days post-hatching were reared at five temperature treatments (22.5, 25.0, 27.5, 30.0 and 32.5?°C, three replicated per treatment) in indoor closed recirculating systems until they reached, at least, the commercial size of 2.5?cm in total length (i.e. rearing time of 21 to 42?d depending on the temperature). Samples of larvae were collected every week. Survival, growth, and feed intake were used as main indicators of zootechnical performances. In addition, concentration of glucose and cortisol and proximate composition of the young life-stages giant gourami were compared to assess effects of temperature on their physiology. Results showed that temperature strongly affected growth of giant gourami larvae with significantly increased observed at the increasing tested temperatures (from 57.2?±?9.3?mg to 431.9?±?64.2?mg of body weight after three weeks, p?
2019 Article scientifique
54 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Anang Hari Kristanto, Jacques Slembrouck, Jojo Subagja, Simon Pouil, Otong Zenal Arifin, Vitas Ahmadi Prakoso, Marc Legendre
Giant gourami (Osphronemus goramy) is one of the main freshwater fish of economic importance in Indonesia. Although this species has been reared for decades, particularly in the province of West Java, and naturally spawns in captivity, the availability of fry is still a limiting factor in aquaculture. Research efforts on giant gourami aquaculture are, however, limited and do not always address the difficulties encountered by fish farmers. The objectives of the present study were to provide the first description of giant gourami egg and fry production and highlight the main problems faced by farmers through targeted questionnaires and interviews. Our results show that the production of this species from eggs to juveniles is highly segmented, and there are currently no clear and standardized production methods. Farming practices vary greatly from one fish farmer to another. Climate factors (such as rain and temperature), proximity to urban areas, and the availability and quality of food are identified as the main limiting factors for egg and fry production. Based on a strengths, weaknesses, opportunities, threats analysis, we explore possible approaches to improve giant gourami aquaculture in Indonesia. The present study provides guidance for future research.
2019 Article scientifique
55 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Text by Caruso, D., Arifin, Z.O., Subagja, J., Jacques Slembrouck, J. and New, M.
© FAO 2019. Cultured Aquatic Species Information Programme. Osphronemus goramy. Cultured Aquatic Species Information Programme. Text by Caruso, D., Arifin, Z.O., Subagja, J., Jacques Slembrouck, J. and New, M. In: FAO Fisheries and Aquaculture Department [online]. Rome. Updated 26 September 2019. [Cited 19 November 2019].
2019 FAO-Cultured Aquatic Species Information Programme
56 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Otong Zenal Arifin, Jacques Slembrouck, Jojo Subagja, Simon Pouil, Akhmad Yani, Asependi Asependi, Anang Hari Kristanto, Marc Legendre
Reliable production of giant gourami Osphronemus goramy Lacepède (1801) fry is one of the main impediments hindering the aquaculture development of this species. The main objective of the present study was to experimentally assess the influence of various biotic or abiotic factors on the egg production of giant gourami. Egg production (egg-laying frequency, quantity and quality of the eggs produced) was compared across several strategies including different pond settings (open vs. compartmentalized ponds, number of nest supports, size of compartments), as well as broodfish management (sex ratio, duration of egg production period). A total of 705 spawns and >2.2 million eggs were collected from the 533 broodfish of giant gourami monitored throughout this study. The dissection of fully sexually mature broodfish showed that giant gourami males are oligospermic with a GSI <0.1%. In mature females, the GSI was <5%, and the absolute fecundity (number of post-vitellogenic oocytes present in the ovaries) varied between 7800 and 15,200 eggs (mean relative fecundity of 4011 ± 287 eggs per female kg). The best egg production was found in the production system consisting of a pond divided into compartments of 8 m2 with one nest support provided and in which the broodfish were maintained at a sex ratio of 1:1 during egg production periods of 6–7 months separated by resting/reconditioning periods of 1 month. The results showed that a same male can fertilize eggs at 2–4 day-intervals and, in females, the minimum lapse of time found between two successive spawns is 20 days. At best, the number of eggs found in nests averaged 1410 ± 101 eggs per female kg, which, compared with the potential fecundity of the species, indicates that egg losses at the time of spawning generally remain high. Based on these findings, recommendations are made for optimizing giant gourami egg production in aquaculture conditions.
2019 Article Scientific
57 Kieran Hosty Australian National Maritime Museum Shinatria Adhityatama Pusat Penelitian Arkeologi Nasional Kieran Hosty, Dr James Hunter, Shinatria Adhityatama
In2014,the AustralianNationalMaritimeMuseum (ANMM0 received reports from recreational divers that the shipwreck site of HMAS Perth (I) was being systematically salvaged by commercial divers. After extensive discussions with Indonesian Government departments and agencies the ANMM led the ?rst Australian/Indonesian remote sensing survey of Perth in December 2016.This was followed by an in-water survey in May 2017.These investigations revealed Perth has been devastated by systematic,large-scale unauthorized salvage.Following the survey, ANMM and its Indonesian research partner Pusat Penelitian Arkeologi Nasional (ARKENAS),working in conjunction with the Royal Australian Navy and Australian Department of Foreign Affairs and Trade, successfully lobbied the Indonesian Government to have the site declared Indonesia’s ?rst Marine Protected Area.
2019 Journal article - International Journal of Nautical Archaeology
58 Christian Lott HYDRA Marine Sciences Jane Mamuaja UNSRAT Manado Andreas Eich, Christian Lott, Markus T. Lasut and Miriam Weber
The replacement of conventional plastics with biodegradable plastics is discussed as one possible contribution to mitigate plastic pollution in the environment. Several standard tests exist to assess the degradation under various conditions such as in industrial compost, soil or the marine environment. However, so far, a single parameter to compare test results of different plastic materials, i.e. pure polymers and blends, in different conditions is lacking. Here, we show the mathematical modelling of results from tests under marine conditions in the laboratory, in mesocosms and in the field. We describe the calculations applied and discuss the constraints of our method. As an outcome, we propose to use the disintegration or degradation half-life of a material under specific test conditions as a specific material property. This value can serve to compare the degradation of different materials in the same environment and to compare the performance of the same material exposed to different conditions. The principle of biodegradation half-life will help plastic producers, manufacturers and distributors with material development and choice of application. It will also enable decision makers to easily compare different scenarios and to evaluate whether or not a certain material application will perform in the environment as technically or politically desired, claimed or expected.
2019 Conference Abstract
59 Christian Lott HYDRA Marine Sciences Jane Mamuaja UNSRAT Manado Andreas Eich, Christian Lott, Markus T. Lasut and Miriam Weber
The replacement of conventional plastics with biodegradable plastics is discussed as one possible contribution to mitigate plastic pollution in the environment. Several standard tests exist to assess the degradation under various conditions such as in industrial compost, soil or the marine environment. However, so far, a single parameter to compare test results of different plastic materials, i.e. pure polymers and blends, in different conditions is lacking. Here, we show the mathematical modelling of results from tests under marine conditions in the laboratory, in mesocosms and in the field. We describe the calculations applied and discuss the constraints of our method. As an outcome, we propose to use the disintegration or degradation half-life of a material under specific test conditions as a specific material property. This value can serve to compare the degradation of different materials in the same environment and to compare the performance of the same material exposed to different conditions. The principle of biodegradation half-life will help plastic producers, manufacturers and distributors with material development and choice of application. It will also enable decision makers to easily compare different scenarios and to evaluate whether or not a certain material application will perform in the environment as technically or politically desired, claimed or expected.
2019 Conference Poster
60 David Richard Tappin British Geological Survey Eko Yulianto Indonesian Institute of Sciences Grilli, S.T., Tappin, D.R., Carey, S., Watt, S.F.L., Ward, S.N., Grilli, A.R., Engwell, S.L., Zhang, C., Kirby, J.T., Schambach, L. and Muin, M.,
On Dec. 22, 2018, at approximately 20:55–57 local time, Anak Krakatau volcano, located in the Sunda Straits of Indonesia, experienced a major lateral collapse during a period of eruptive activity that began in June. The collapse discharged volcaniclastic material into the 250 m deep caldera southwest of the volcano, which generated a tsunami with runups of up to 13 m on the adjacent coasts of Sumatra and Java. The tsunami caused at least 437 fatalities, the greatest number from a volcanically-induced tsunami since the catastrophic explosive eruption of Krakatau in 1883 and the sector collapse of Ritter Island in 1888. For the first time in over 100 years, the 2018 Anak Krakatau event provides an opportunity to study a major volcanically-generated tsunami that caused widespread loss of life and significant damage. Here, we present numerical simulations of the tsunami, with state-of the-art numerical models, based on a combined landslide-source and bathymetric dataset. We constrain the geometry and magnitude of the landslide source through analyses of pre- and post-event satellite images and aerial photography, which demonstrate that the primary landslide scar bisected the Anak Krakatau volcano, cutting behind the central vent and removing 50% of its subaerial extent. Estimated submarine collapse geometries result in a primary landslide volume range of 0.22–0.30 km3, which is used to initialize a tsunami generation and propagation model with two different landslide rheologies (granular and fluid). Observations of a single tsunami, with no subsequent waves, are consistent with our interpretation of landslide failure in a rapid, single phase of movement rather than a more piecemeal process, generating a tsunami which reached nearby coastlines within ~30 minutes. Both modelled rheologies successfully reproduce observed tsunami characteristics from post-event field survey results, tide gauge records, and eyewitness reports, suggesting our estimated landslide volume range is appropriate. This event highlights the significant hazard posed by relatively small-scale lateral volcanic collapses, which can occur en-masse, without any precursory signals, and are an efficient and unpredictable tsunami source. Our successful simulations demonstrate that current numerical models can accurately forecast tsunami hazards from these events. In cases such as Anak Krakatau’s, the absence of precursory warning signals together with the short travel time following tsunami initiation present a major challenge for mitigating tsunami coastal impact.
2019 Scientific Paper
61 John Stephen Lansing Nanyang Technological University Prof Herawati Sudoyo Eijkman Institute for Molecular Biology Guy S. Jacobs, Georgi Hudjashov, Lauri Saag, Pradiptajati Kusuma, Herawati Sudoyo, J. Stephen Lansing, Murray P. Cox
Genome sequences from Island Southeast Asia suggest two independent Denisovan lineages, distinct from the Altai Denisovan, that have contributed to modern Papuan genomes, with one group potentially present east of the Wallace Line and thus capable of crossing geographical barriers.
2019 Research Article
62 Satoshi Tanaka College of Information Science and Engineering, Ritsumeikan University Dr. Fadjar I. Thufail Research Center for Regional Resources, Indonesian Institute of Sciences (P2SDR - LIPI) Jiao Pan, Liang Li, Hiroshi Yamaguchi, Kyoko Hasegawa, Fadjar I. Thufail, Bramantara, Satoshi Tanaka
We propose an efficient method to achieve 3D visualization directly from a single monocular 2D image for relief-type cultural heritages. To achieve a proper depth feel of 3D visualization, we first reconstruct the 3D point clouds by estimating the depth from the monocular image using a depth estimation network. We then apply our stochastic point-based rendering mechanism to achieve a 3D transparent visualization of the reconstructed point clouds. Herein, we apply our method to the Buddhist temple heritage of Borobudur Temple in Indonesia, a UNESCO World Heritage Site with the complete collection of Buddhist reliefs. The proposed method achieved 90% accuracy of the reconstructed point cloud on average and a promising visualization result with an intuitive understanding.
2019 conference paper
63 Anne Eleanor Russon York University Tri Wijaya Balai Taman Nasional Kutai Alan Tristram Kenneth Lee, Jamie Anthony Carr, Busran Ahmad, Arbainsyah, Agnes Ferisa, Yophi Handoko, Rudi Harsono, Laura Graham, Lita Kabangnga, Nur Patria Kurniawan, Paul Joseph Antonius Keßler, Purwo Kuncoro, Dinda Prayunita, Aldrianto Priadjati, Edy Purwanto, Anne Russon, Douglas Sheil, Nurul Sylva, Agus Wahyudi, Wendy Foden
In Indonesia, Kutai National Park is home to what is likely to be East Kalimantan’s largest population of the Critically Endangered eastern subspecies of the Bornean Orangutan, Pongo pygmaeus morio. It also hosts an astounding diversity of other species including ~80 mammal, 369 bird and 1287 plant species. The park plays an important role in regulating water supply to neighbouring towns, attracts tourism and its forests serve as a valuable carbon sink. Yet East Kalimantan faces many challenges in maintaining and protecting biodiversity from threats, particularly from population expansion into the protected area with associated hunting and forest clearing for agriculture, fire, and coal mining. More recently, climate change has been identified as an emerging threat, with both observed and projected changes indicating with high confidence that higher temperatures are to be expected. These are likely to exacerbate drought conditions, which enable wildfires and lead to a range of other negative impacts on the species of Kutai National Park. To date, however, few initiatives have attempted to assess the vulnerability of the region’s biodiversity to climate change, nor to develop strategies to minimise negative impacts. Forest restoration, also referred to as reforestation, presents a valuable opportunity to restore biodiversity and function to degraded areas that were once forested. Reforestation initiatives are being carried out in Kutai National Park, ranging from protection to enrichment planting in areas that were previously burnt but are now recovering. While several of these programmes have successfully planted large numbers of seedlings, little attention has been placed on restoring species richness, ecological function or selecting species that are of value for orangutan survival. In addition, most fail to consider climate change and hence that selected species must be able to establish and survive in the warmer and drier climatic conditions of the future. There is a clear and pressing need to update Kutai National Park’s existing restoration practices to ensure forest integrity, provide opportunities for threatened species, and guide consideration of how to build climate change resilience. By doing so, the forests that orangutans need to survive into the future are more likely to persist. To meet the need for guidance on climate change resilient reforestation practices, we collaborated with park authorities and other experts to identify the tree species that are most vulnerable to climate change and those likely to be most climate change resilient. The importance of orangutans in Kutai National Park’s conservation objectives led us to expand our scope to identify those tree species that are valuable resources for them, and this extended further to addressing the need for identification of those that are ecologically and commercially important; those that are iconic (have tourist potential); those that are most representative of primary forest; those resilient to fire; as well as those that are locally threatened. To assess climate change vulnerability and resilience, we examined the biological characteristics or traits of species that are associated with their sensitivity and/or adaptive capacity to the anticipated climate changes and the resulting altered fire regimes. We examine restoration case studies, remind readers of restoration best practice, and present sets of tree species from a set of ~250 considered in the analysis that are likely to be suited to various restoration targets for Kutai National Park, e.g. with a focus on habitat restoration for orangutan; or a focus on conservation of rare and useful species. Given the fire prone nature of the area, two species stand out due to their resilience to fire events: Borassodendron borneense, and Eusideroxylon zwageri: known locally as Bendang and Ulin respectively. The following species emerged as most important food plants for Orangutan: Dracontomelon dao, Merremia mammosa, Kleinhovia hospita, Alangium hirsutum, Dillenia reticulata, Callicarpa pentandra, and Ficus obpyramidata. Species that are most likely to be climate change resilient were dominated by pioneer or invasive species.
2019 Professional/Specialist conservation meetings and assessments
64 Shimizu Kazufumi Center for Infectious Diseases, Kobe University Graduate School of Medicine Maria Inge Lusida Universities Airlangga Lumbago penyakit Troops Novianti AN, Rahardjo K, Prasetya RR, Nastri AM, Dewantari JR, Rahardjo AP, Estoepangestie ATS, Shimizu YK, Poetranto ED, Soegiarto G, Mori Y, Shimizu K.
We isolated an avian influenza A/H9N2 virus from an apparently healthy chicken at a live-poultry market in January 2018. This is the first report of a whole-genome sequence of A/H9N2 virus in Indonesia. Phylogenetic analyses indicated that intrasubtype reassortment of genome segments is involved in the genesis of the A/H9N2 virus.
2019 Article
65 Tomoya Shibayama Waseda University Hendra Achiari Sumatra Institute of Technology Takabatake, T., Shibayama, T., Esteban, M., Achiari, H., Nurisman, N., Gelfi, M., Tarigan, T., Kencana, E., Fauzi, M., Panalaran, S., Harnantyari, A. & Thit Oo Kyaw
On the 22nd of December 2018 the shorelines of Sunda Strait, Indonesia, were hit by tsunami waves generated by the flank collapse of the Anak Krakatau volcano. The authors conducted a field survey of the affected areas in both Sumatra and Java islands to collect information on tsunami inundation and run-up heights, damage patterns at each coastal community, and the evacuation behaviour and tsunami awareness of the affected people. The survey results showed that in Sumatra island inundation heights of more than 4 m were measured along the coastline that was situated to the north-north-east of Anak Krakatau, while less than 4 m were measured along the north-western direction. Inundation heights of over 10 m were measured at Cipenyu Beach (Pandeglang Regency) in Java island (south-south-eastern direction from Anak Krakatau). A questionnaire survey conducted by the authors revealed residents’ perception of danger and evacuation patterns during the event. The results indicate the importance of having an operational tsunami warning system in Sunda Strait and the establishment of an appropriate evacuation plan so that residents can start evacuation immediately and reach a safe place without facing severe congestion along evacuation routes.
2019 International Journal Paper
66 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Guild, Ryan (A. Russon supervisor)
The Northeast Bornean orangutan (Pongo pygmaeus morio) currently remains the only orangutan subspecies for which extinction risks cannot be accurately assessed due to a severe lack of information around the habitat conditions and threats that its different population units experience. Despite decades of acknowledgement as a stronghold for the morio subspecies, the orangutan metapopulation in Kutai National Park (KNP) of East Kalimantan, Indonesia is one unit that remains to be adequately studied. This report presents a preliminary analysis of the threats to the orangutan subpopulation in the northeastern region of KNP using habitat assessments and observational notes of the human activities in and around this area. Current threats identified include industrial mining, agricultural activities and clear-cutting around this protected area, while illegal logging, fire sources and severe climate events threaten the interior forests. Poaching in relation to human-orangutan conflicts and negligent tourism practices were also identified as threats to the greater metapopulation in KNP. The results of this study can contribute to the foundation of information required to adequately assess and develop appropriate conservation efforts for the orangutan population unit of KNP.
2019 Master's thesis
67 Daiki Ayuha University of Tokyo Dr. Fadjar I. Thufail Indonesian Institute of Sciences Research center for Regional Resources Daiki Ayuha
Presentasi ini dilakukan pada seminar proyek joint research di Museum Nasional Etnologi, Osaka, Jepang. Di dalam presentasi ini, diteliti proses pembangunan sistem jaminan sosial Indonesia dan fungsinya teknokrat Indonesia yg kerja di bidang kesejahteraan masyarakat.
2018 Materi Presentasi Oral
68 Daiki Ayuha University of Tokyo Dr. Fadjar I. Thufail Indonesian Institute of Sciences Research center for Regional Resources Daiki Ayuha
Di dalam artikel ini, pertama dianalisis studi-studi tentang risiko dan ketidakpastian dari bidang ekonomi, sosiologi dan antropologi, dijelaskan manfaat dan kekurangan studi-studi tersebut. Kedua, dengan analisis data-data yang saya telah mengoleksi di Indonesia, diteliti bagaimana caranya antropologi bisa mengkontribusi untuk penelitian tentang persoalan risiko dan ketidakpastian.
2018 Article for Institutional Periodicals
69 Daiki Ayuha University of Tokyo Dr. Fadjar I. Thufail Indonesian Institute of Sciences Research center for Regional Resources Daiki Ayuha
Di dalam presentasi ini, penbahas menjelaskan manfaatnya pendekatan antropologi di dalam analisi sejerah jaminan sosial dan proses pembangunan jaminan sosial di Indonesia.
2018 Conference Proceeding
70 Daiki Ayuha University of Tokyo Dr. Fadjar I. Thufail Indonesian Institute of Sciences Research center for Regional Resources Daiki Ayuha
Di dalam poster ini, penulis menjelaskan tantangan dihadapi oleh para peneliti di bidang insurance studies and risk studies dan bagaimana metode kualitatif, yaitu metode antropologi bisa mengkontribusi kepada studi studi tersebut, dengan studi kasus jaminan kesehatan Indonesia.
2018 Poster presentaions
71 Raph Leonardus Hamers Oxford University Budi Wiweko, MD, OG (REI), PhD Faculty of Medicine University of Indonesia Seth C Inzaule, Raph L Hamers, Marc Noguera Julian, Maria Casadella, Mariona Parera, Cissy Kityo, Kim Steegen, Denise Naniche, Bonaventura Clotet, Tobias F Rinke de Wit, Roger Paredes
Implementation of ultrasensitive HIV drug resistance tests for routine clinical use is hampered by uncertainty about the clinical relevance of drug-resistant minority variants. We assessed different detection thresholds for pretreatment drug resistance to predict an increased risk of virological failure.
2018 paper
72 Raph Leonardus Hamers Oxford University Budi Wiweko, MD, OG (REI), PhD Faculty of Medicine University of Indonesia Seth C Inzaule, Raph L Hamers, Marc Noguera Julian, Maria Casadella, Mariona Parera, Cissy Kityo, Kim Steegen, Denise Naniche, Bonaventura Clotet, Tobias F Rinke de Wit, Roger Paredes
Implementation of ultrasensitive HIV drug resistance tests for routine clinical use is hampered by uncertainty about the clinical relevance of drug-resistant minority variants. We assessed different detection thresholds for pretreatment drug resistance to predict an increased risk of virological failure.
2018 paper
73 Raph Leonardus Hamers Oxford University Budi Wiweko, MD, OG (REI), PhD Faculty of Medicine University of Indonesia Raph L Hamers, Tobias F Rinke de Wit, Charles B Holmes
After 15 years of global scale-up of antiretroviral therapy (ART), rising prevalence of HIV drug resistance in many low-income and middle-income countries (LMICs) poses a growing threat to the HIV response, with the potential to drive an increase in mortality, HIV incidence, and costs. To achieve UNAIDS global targets, enhanced strategies are needed to improve quality of ART services and durability of available ART regimens, and to curb resistance. These strategies include roll out of drugs with greater efficacy and higher genetic barriers to resistance than those that are currently widely used, universal access to and improved effectiveness of viral load monitoring, patient-centred care delivery models, and reliable drug supply chains, in conjunction with frameworks for resistance monitoring and prevention. In this Review, we assess contemporary data on HIV drug resistance in LMICs and their implications for the HIV response, highlighting the potential impact and resistance risks of novel ART strategies and knowledge gaps.
2018 paper
74 Raph Leonardus Hamers Oxford University Budi Wiweko, MD, OG (REI), PhD Faculty of Medicine University of Indonesia Erlangga Yusuf, Raph L. Hamers
On 16 May 2018 the World Health Organization (WHO) released the Model List of Essential In Vitro Diagnostics (EDL), 41 years after the first release of the successful Model List of Essential Medicines [1]. The EDL's purpose is to provide evidence-based guidance to countries to create their own national lists of essential diagnostic tests and tools, anticipating that the EDL will complement the WHO List of Essential Medicines [2] and enhance its impact. National essential medicines lists have been successful in facilitating access to treatment and promoting affordable prices, particularly in low-resourced countries, by prioritizing the most important medicines all countries need to make available to their populations.
2018 paper
75 Raph Leonardus Hamers Oxford University Budi Wiweko, MD, OG (REI), PhD Faculty of Medicine University of Indonesia Raph L Hamers, H Rogier van Doorn
Ann Versporten and colleagues (June, 2018)1 report the findings from the 2015 Global Point Prevalence Survey (Global-PPS)—a simple approach to assess antimicrobial prescribing and resistance in patients in hospitals across regions and countries worldwide. However, their grouping of the data by UN regions and subregions is problematic, because some countries were seriously under-represented, especially some low-income and middle-income countries (LMICs). This under-representation potentially masked important shortcomings and differences between countries within (sub)regions. Estimates for the regions dominated by single countries (ie, western Europe by Belgium, northern Europe by UK, and east and south Asia by Japan) or represented by very few data (eastern Europa, Africa, and Oceania) should instead have been reported at the country or even hospital level. Although the authors acknowledged the misrepresentation in western and northern Europe as a study limitation, they did not comment on the biased samples for some of the other regions, especially those including LMIC. The final conclusions are thus biased for LMICs, where the concerns about rising antibiotic resistance, driven by antibiotic consumption, are most substantial.2, 3 Southeast Asia comprises a large geographical area with more than half the world's population and substantial variations in economic development. Prescribing practices in LMICs are reportedly poor, and robust antibiotic stewardship programmes are often non-existent. For example, a study4 of a random sample of hospitals in Vietnam showed that 55% of indications for empirical antibiotic therapy were inappropriate. However, in the Global-PPS, the reported quality indicators for antibiotic prescriptions denoted that those in the region of east and south Asia were in the same range as those reported for western and northern Europe, probably due to the over-representation of high-income countries such as Japan, Singapore, and South Korea. This over-representation is a crucial limitation, because these favourable findings might provide false reassurance to national policy makers, risking complacency. An additional analysis in which high-income countries are contrasted against LMICs would have been useful. Nonetheless, the limited and patchy data from LMICs in the survey make it difficult to draw any firm conclusions about the quantity and quality of antimicrobial prescribing in these settings. Antibiotic consumption and resistance in LMICs are rising substantially because of rapid economic and population growth coupled with the high burden of infectious diseases.2 We call for the further implementation of global initiatives, such as Global-PPS, endorsed by international agencies and governments, to systematically collect granular and representative data to inform policies around optimising antibiotic prescribing and minimising antibiotic resistance.
2018 paper
76 Maxime Aubert Griffith University, Australia Priyatno Hadi Sulistyarto, National Research Centre of Archaeology (ARKENAS) M. Aubert, P. Setiawan, A. A. Oktaviana, A. Brumm, P. H. Sulistyarto, E. W. Saptomo, B. Istiawan, T. A. Ma’rifat, V. N. Wahyuono, F. T. Atmoko, J.-X. Zhao, J. Huntley, P. S. C. Taçon, D. L. Howard & H. E. A. Brand
Figurative cave paintings from the Indonesian island of Sulawesi date to at least 35,000 years ago (ka) and hand-stencil art from the same region has a minimum date of 40 ka1. Here we show that similar rock art was created during essentially the same time period on the adjacent island of Borneo. Uranium-series analysis of calcium carbonate deposits that overlie a large reddish-orange figurative painting of an animal at Lubang Jeriji Saléh—a limestone cave in East Kalimantan, Indonesian Borneo—yielded a minimum date of 40 ka, which to our knowledge is currently the oldest date for figurative artwork from anywhere in the world. In addition, two reddish-orange-coloured hand stencils from the same site each yielded a minimum uranium-series date of 37.2 ka, and a third hand stencil of the same hue has a maximum date of 51.8 ka. We also obtained uranium-series determinations for cave art motifs from Lubang Jeriji Saléh and three other East Kalimantan karst caves, which enable us to constrain the chronology of a distinct younger phase of Pleistocene rock art production in this region. Darkpurple hand stencils, some of which are decorated with intricate motifs, date to about 21–20 ka and a rare Pleistocene depiction of a human figure—also coloured dark purple—has a minimum date of 13.6 ka. Our findings show that cave painting appeared in eastern Borneo between 52 and 40 ka and that a new style of parietal art arose during the Last Glacial Maximum. It is now evident that a major Palaeolithic cave art province existed in the eastern extremity of continental Eurasia and in adjacent Wallacea from at least 40 ka until the Last Glacial Maximum, which has implications for understanding how early rock art traditions emerged, developed and spread in Pleistocene Southeast Asia and further afield.
2018 Journal article
77 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK, Battle KE, Howes RE.
The hypnozoite reservoir of Plasmodium vivax represents both the greatest obstacle and opportunity for ultimately eradicating this species. It is silent and cannot be diagnosed until it awakens and provokes a clinical attack with attendant morbidity, risk of mortality, and opportunities for onward transmission. The only licensed drug that kills hypnozoites is primaquine, which attacks the hypnozoite reservoir but imposes serious obstacles in doing so—at hypnozoitocidal doses, it invariably causes a threatening acute haemolytic anaemia in patients having an inborn deficiency in glucose-6-phosphate dehydrogenase (G6PD), affecting about 8% of people living in malaria endemic nations. That problem excludes a large number of people from safe and effective treatment of the latent stage of vivax malaria: the G6PD deficient, pregnant or lactating women, and young infants. These groups were estimated to comprise 14.3% of populations resident in the 95 countries with endemic vivax malaria. Another important obstacle regarding primaquine in the business of killing hypnozoites is its apparent metabolism to an active metabolite exclusively via cytochrome P-450 isozyme 2D6 (CYP2D6). Natural polymorphisms of this allele create genotypes expressing impaired enzymes that occur in over 20% of people living in Southeast Asia, where more than half of P. vivax infections occur globally. Taken together, the estimated frequencies of these primaquine ineligibles due to G6PD toxicity or impaired CYP2D6 activity composed over 35% of the populations at risk of vivax malaria. Much more detailed work is needed to refine these estimates, derive probabilities of error for them, and improve their ethnographic granularity in order to inform control and elimination strategy and tactics.
2018 Publication
78 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Lover AA, Baird JK, Gosling R, Price R.
Important strides have been made within the past decade toward malaria elimination in many regions, and with this progress, the feasibility of eradication is once again under discussion. If the ambitious goal of eradication is to be achieved by 2040, all species of Plasmodium infecting humans will need to be targeted with evidence-based and concerted interventions. In this perspective, the potential barriers to achieving global malaria elimination are discussed with respect to the related diversities in host, parasite, and vector populations. We argue that control strategies need to be reorientated from a sequential attack on each species, dominated by Plasmodium falciparum to one that targets all species in parallel. A set of research themes is proposed to mitigate the potential setbacks on the pathway to a malaria-free world.
2018 Publication
79 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Sutanto I, Kosasih A, Elyazar I, Simanjuntak DR, Larasati TA, Dahlan S, Wahid I, Mueller I, Koepfli C, Kusriastuti R, Surya A, Laihad FJ, Hawley WA, Collins FH, Baird JK, Lobo NF.
Background Mass screening and treatment (MST) aims to reduce malaria risk in communities by identifying and treating infected persons without regard to illness. Methods A cluster-randomized trial evaluated malaria incidence with and without MST. Clusters were randomized to 3, 2, or no MST interventions: MST3, 6 clusters (156 households/670 individuals); MST2, 5 clusters (89 households/423 individuals); and MST0, 5 clusters (174 households/777 individuals). All clusters completed the study with 14 residents withdrawing. In a cohort of 324 schoolchildren (MST3, n = 124; MST2, n = 57; MST0, n = 143) negative by microscopy at enrollment, we evaluated the incidence density of malaria during 3 months of MST and 3 months following. The MST intervention involved community-wide expert malaria microscopic screening and standard therapy with dihydroartemisinin-piperaquine and primaquine for glucose-6 phosphate dehydrogenase–normal subjects. All blood examinations included polymerase chain reaction assays, which did not guide on-site treatment. Results The risk ratios for incidence density of microscopically patent malaria in MST3 or MST2 relative to that in MST0 clusters were 1.00 (95% confidence interval [CI], .53–1.91) and 1.22 (95% CI, .42–3.55), respectively. Similar results were obtained with molecular analysis and species-specific (P. falciparum and P. vivax) infections. Microscopically subpatent, untreated infections accounted for 72% of those infected. Conclusions Two or 3 rounds of MST within 3 months did not impact the force of anopheline mosquito-borne infection in these communities. The high rate of untreated microscopically subpatent infections likely explains the observed poor impact.
2018 Publication
80 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Robert J Commons, MBBS FRACP; Julie A Simpson; Kamala Thriemer; Georgina S Humphreys; Tesfay Abreha; Sisay G Alemu; Arletta Añez; Nicholas M Anstey; Ghulam R Awab; J. Kevin Baird; et al.
Summary Background Chloroquine remains the mainstay of treatment for Plasmodium vivax malaria despite increasing reports of treatment failure. We did a systematic review and meta-analysis to investigate the effect of chloroquine dose and the addition of primaquine on the risk of recurrent vivax malaria across different settings. Methods A systematic review done in MEDLINE, Web of Science, Embase, and Cochrane Database of Systematic Reviews identified P vivax clinical trials published between Jan 1, 2000, and March 22, 2017. Principal investigators were invited to share individual patient data, which were pooled using standardised methods. Cox regression analyses with random effects for study site were used to investigate the roles of chloroquine dose and primaquine use on rate of recurrence between day 7 and day 42 (primary outcome). The review protocol is registered in PROSPERO, number CRD42016053310. Findings Of 134 identified chloroquine studies, 37 studies (from 17 countries) and 5240 patients were included. 2990 patients were treated with chloroquine alone, of whom 1041 (34·8%) received a dose below the target 25 mg/kg. The risk of recurrence was 32·4% (95% CI 29·8–35·1) by day 42. After controlling for confounders, a 5 mg/kg higher chloroquine dose reduced the rate of recurrence overall (adjusted hazard ratio [AHR] 0·82, 95% CI 0·69–0·97; p=0·021) and in children younger than 5 years (0·59, 0·41–0·86; p=0·0058). Adding primaquine reduced the risk of recurrence to 4·9% (95% CI 3·1–7·7) by day 42, which is lower than with chloroquine alone (AHR 0·10, 0·05–0·17; p<0·0001). Interpretation Chloroquine is commonly under-dosed in the treatment of vivax malaria. Increasing the recommended dose to 30 mg/kg in children younger than 5 years could reduce substantially the risk of early recurrence when primaquine is not given. Radical cure with primaquine was highly effective in preventing early recurrence and may also improve blood schizontocidal efficacy against chloroquine-resistant P vivax.
2018 Publication
81 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Joseph Donovan, Nguyen Hoan Phu, Nguyen Thi Hoang Mai, Le Tien Dung, Darma Imran, Erlina Burhan, Lam Hong Bao Ngoc, Nguyen Duc Bang, Do Chau Giang, Dang Thi Minh Ha, Jeremy Day, Le Thi Phuong Thao, Nguyen TT Thuong, Nguyen Nang Vien, Ronald B. Geskus, Marcel Wolbers, Raph L Hamers, Reinout van Crevel, Mugi Nursaya, Kartika Maharani, Tran Tinh Hien, Kevin Baird, et al.
Background: Tuberculous meningitis (TBM) is the most severe form of tuberculosis. Co-infection with HIV increases the risk of developing TBM, complicates treatment, and substantially worsens outcome. Whether corticosteroids confer a survival benefit in HIV-infected patients with TBM remains uncertain. Hepatitis is the most common drug-induced serious adverse event associated with anti-tuberculosis treatment, occurring in 20% of HIV-infected patients. The suggested concentration thresholds for stopping anti-tuberculosis drugs are not evidence-based. This study aims to determine whether dexamethasone is a safe and effective addition to the first 6-8 weeks of anti-tuberculosis treatment of TBM in patients with HIV, and investigate alternative management strategies in a subset of patients who develop drug induced liver injury (DILI) that will enable the safe continuation of rifampicin and isoniazid therapy. Methods: We will perform a parallel group, randomised (1:1), double blind, placebo-controlled multi-centre Phase III trial, comparing the effect of dexamethasone versus placebo on overall survival in HIV-infected patients with TBM, in addition to standard anti-tuberculosis and antiretroviral treatment. The trial will be set in two hospitals in Ho Chi Minh City, Vietnam, and two hospitals in Jakarta, Indonesia. The trial will enrol 520 HIV-infected adults. An ancillary study will perform a randomised comparison of three DILI management strategies with the aim of demonstrating which strategy results in the least interruption in rifampicin and isoniazid treatment. An identical ancillary study will also be performed in the linked randomised controlled trial of dexamethasone in HIV-uninfected adults with TBM stratified by LTA4H genotype (LAST ACT). Discussion: Whether corticosteroids confer a survival benefit in HIV-infected patients remains uncertain, and the current evidence base for using corticosteroids in this context is limited. Interruptions in anti-tuberculosis chemotherapy is a risk factor for death from TBM. Alternative management strategies in DILI may allow the safe continuation of rifampicin and isoniazid therapy.
2018 Publication
82 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Asih PBS, Syafruddin D, Baird JK.
The human malaria parasite Plasmodium vivax imposes unique challenges to its control and elimination. Primary among those is the hypnozoite reservoir of infection in endemic communities. It is the dominant source of incident malaria and exceedingly difficult to attack due to both inability to diagnose latent carriers and the potentially life-threatening toxicity of primaquine in patients with an inborn deficiency of G6PD, the only therapeutic option against hypnozoites. Large segments of endemic populations are not eligible for primaquine, and alternative strategies for managing the threat of relapse in any group have not been optimized or validated. Association of risk of primaquine failure against latent P. vivax with impaired alleles of P450 2D6 exacerbates the substantial pool of primaquine ineligibles. Resistance to chloroquine against acute P. vivax malaria commonly occurs; alternative therapies like ACTs are effective but seldom evaluated as a partner drug to primaquine in the essential radical cure. Many of the Anopheles mosquito vector of P. vivax in South and Southeast Asia, where >90% of infections occur, thrive in a diversity of habitats and exhibit wide ranges of feeding and breeding behavior. This chapter explores many of these challenges and possible approaches in controlling and eliminating endemic vivax malaria.
2018 Publication
83 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman JK Baird, Melva Louisa, Rintis Noviyanti, Lenny Ekawati, Iqbal Elyazar, Decy Subekti, Krisin Chand, Anggi Gayatri, Instiaty, Saraswati Soebianto, Chelzie Crenna-Darusallam, Dwi Djoko, Bambang Pratomo Sulistyanto, Dubel Mariyenes, David Wesche, Erni Nelwan, Inge Sutanto, Herawati Sudoyo, Rianto Setiabudy.
Importance Latent hepatic Plasmodium vivax hypnozoites provoke repeated clinical attacks called relapses. Only primaquine phosphate kills hypnozoites, and its therapeutic activity may depend on naturally polymorphic cytochrome P450 2D6 isotype (CYP2D6) activity. Objective To examine the association of impaired CYP2D6 genotypes and CYP2D6 metabolic phenotypes with therapeutic failure of directly observed high-dose primaquine treatment for P vivax malaria relapse. Design, Setting, and Participants Nested case-control study of patients who, in July 2014, completed a randomized clinical trial of directly observed primaquine treatment for radical cure of acute P vivax malaria in an area of Indonesia where reinfection during 1 year of posttreatment follow-up was improbable. A total of 177 of 180 patients with P vivax malaria completed the clinical trial of primaquine treatment to prevent relapse; 151 were eligible for recruitment as controls. After screening, 59 potential control individuals (no relapse) and 26 potential case patients (relapse) were considered, and 36 controls and 21 cases were enrolled. Exposures Cases and controls were exposed to P vivax malaria and primaquine therapy but had variable exposure to the enzymatic activity of CYP2D6, classified as impaired by a genotype-determined qualitative phenotype (poor or intermediate), genotype-determined activity score less than 1.5, or a log of the 24-hour pooled urine dextromethorphan-dextrorphan metabolic ratio greater than ?1.0. Main Outcomes and Measures Unadjusted odds ratios (ORs) of relapse with impaired CYP2D6 metabolism determined by genotype or measured by urinary dextromethorphan-dextrorphan metabolic ratio. Results Among the 21 cases (mean [SD] age, 30.5 [6.3] years; all male) and 36 controls (mean [SD] age, 29.0 [3.6] years; all male), 6 CYP2D6 alleles (*1, *2, *4, *5, *10, and *41) occurred as 12 distinct genotypes, with model activity scores ranging from 0.0 to 2.0. Among 32 patients with genotypic activity scores of 1.0 or less, 18 had experienced relapse, whereas among the 25 with scores higher than 1.0, 3 had experienced relapse (OR, 9.4; 95% CI, 2.1-57.0; P?=?.001). When the log of the metabolic ratio of dextromethorphan-dextrorphan was ?1.0 or less, only 1 of 18 patients experienced relapse, whereas above that threshold (consistent with low metabolic activity), 20 of 39 patients experienced relapse (OR, 18; 95% CI, 2.2-148.0; P?=?.007). Conclusions and Relevance Genotype-determined and directly measured impaired levels of CYP2D6 activity were associated with elevated risk of therapeutic failure. These findings suggest a natural variability in CYP2D6-dependent metabolism of primaquine as a key determinant of therapeutic efficacy against latent P vivax malaria.
2018 Publication
84 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Christian P. Nixon, Ari W. Satyagraha, Grayson L, Alida Harahap, Lydia V. Panggalo, Lenny L. Ekawati, Inge Sutanto, Din Syafruddin, JK Baird.
Introduction South-East Asian ovalocytosis (SAO) is a common inherited red blood cell polymorphism in South-East Asian and Melanesian populations, coinciding with areas of malaria endemicity. Validation of light microscopy as a diagnostic alternative to molecular genotyping may allow for its cost?effective use either prospectively or retrospectively by analysis of archived blood smears. Methods We assessed light microscopic diagnosis of SAO compared to standard PCR genotyping. Three trained microscopists each assessed the same 971 Giemsa?stained thin blood films for which SAO genotypic confirmation was available by PCR. Generalized mixed modeling was used to estimate the sensitivity, specificity, positive predictive value, and negative predictive value of light microscopy vs “gold standard” PCR. Results Among red cell morphologic parameters evaluated, knizocytes, rather than ovalocytic morphology, proved the strongest predictor of SAO status (odds ratio [OR] = 19.2; 95% confidence interval [95% CI] = 14.6?25.3; P ? 0.0001). The diagnostic performance of a knizocyte?centric microscopic approach was microscopist dependent: two microscopists applied this approach with a sensitivity of 0.89 and a specificity of 0.93. Inter?rater reliability among the microscopists (? = 0.20) as well as between gold standard and microscopist (? = 0.36) underperformed due to misclassification of stomatocytes as knizocytes by one microscopist, but improved substantially when excluding the error?prone reader (? = 0.65 and 0.74, respectively). Conclusion Light microscopic diagnosis of SAO by knizocyte visual cue performed comparable to time?consuming and costlier molecular methods, but requires specific training that includes successful differentiation of knizocytes from stomatocytes.
2018 Publication
85 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK, Nelwan EJ, Taylor WR
Nearly 3 billion people live at risk of malaria across most of the tropics, subtropics, and even some temperate zones. Millions visit these areas, and each year thousands appear in hospitals with posttravel acute malaria. That diagnosis should be managed as a medical emergency. Illness may deteriorate rapidly without prompt diagnosis and effective treatment. Among five species of Plasmodium responsible for human malaria, Plasmodium falciparum most often deteriorates rapidly, but all species potentially threaten life. Malignant and benign species of malaria parasites is a dangerous fallacy. Clinical malaria mimics other common tropical infections and the diagnosis requires laboratory confirmation, but malaria-like symptoms in a patient exposed to risk should be presumed to be malaria until proven otherwise. Intravenous or intramuscular artesunate is used for severe malaria of any species in any patient, including all trimesters of pregnancy. Primaquine is administered with vivax or ovale malarias after affirming glucose-6-phosphate dehydrogenase (G6PD)–normal status.
2018 Publication
86 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Thriemer K, Bobogare A, Ley B, Gudo CS, Alam MS, Anstey NM, Ashley E, Baird JK, Gryseels C, Jambert E, Lacerda M, Laihad F, Marfurt J, Pasaribu AP, Poespoprodjo JR, Sutanto I, Taylor WR, van den Boogaard C, Battle KE, Dysoley L, Ghimire P, Hawley B, Hwang J, Khan WA, Mudin RNB, Sumiwi ME, Ahmed R, Aktaruzzaman MM, Awasthi KR, Bardaji A, Bell D, Boaz L, Burdam FH, Chandramohan D, Cheng Q, Chindawongsa K, Culpepper J, Das S, Deray R, Desai M, Domingo G, Duoquan W, Duparc S, Floranita R, Gerth-Guyette E, Howes RE, Hugo C, Jagoe G, Sariwati E, Jhora ST, Jinwei W, Karunajeewa H, Kenangalem E, Lal BK, Landuwulang C, Le Perru E, Lee SE, Makita LS, McCarthy J, Mekuria A, Mishra N, Naket E, Nambanya S, Nausien J, Duc TN, Thi TN, Noviyanti R, Pfeffer D, Qi G, Rahmalia A, Rogerson S, Samad I, Sattabongkot J, Satyagraha A, Shanks D, Sharma SN, Sibley CH, Sungkar A, Syafruddin D, Talukdar A, Tarning J, Ter Kuile F, Thapa S, Theodora M, Huy TT, Waramin E, Waramori G, Woyessa A, Wongsrichanalai C, Xa NX, Yeom JS, Hermawan L, Devine A, Nowak S, Jaya I, Supargiyono S, Grietens KP, Price RN.
The goal to eliminate malaria from the Asia-Pacific by 2030 will require the safe and widespread delivery of effective radical cure of malaria. In October 2017, the Asia Pacific Malaria Elimination Network Vivax Working Group met to discuss the impediments to primaquine (PQ) radical cure, how these can be overcome and the methodological difficulties in assessing clinical effectiveness of radical cure. The salient discussions of this meeting which involved 110 representatives from 18 partner countries and 21 institutional partner organizations are reported. Context specific strategies to improve adherence are needed to increase understanding and awareness of PQ within affected communities; these must include education and health promotion programs. Lessons learned from other disease programs highlight that a package of approaches has the greatest potential to change patient and prescriber habits, however optimizing the components of this approach and quantifying their effectiveness is challenging. In a trial setting, the reactivity of participants results in patients altering their behaviour and creates inherent bias. Although bias can be reduced by integrating data collection into the routine health care and surveillance systems, this comes at a cost of decreasing the detection of clinical outcomes. Measuring adherence and the factors that relate to it, also requires an in-depth understanding of the context and the underlying sociocultural logic that supports it. Reaching the elimination goal will require innovative approaches to improve radical cure for vivax malaria, as well as the methods to evaluate its effectiveness.
2018 Publication
87 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman JK Baird
BACKGROUND: Endemic malaria occurring across much of the globe threatens millions of exposed travelers. While unknown numbers of them suffer acute attacks while traveling, each year thousands return from travel and become stricken in the weeks and months following exposure. This represents perhaps the most serious, prevalent and complex problem faced by providers of travel medicine services. Since before World War II, travel medicine practice has relied on synthetic suppressive blood schizontocidal drugs to prevent malaria during exposure, and has applied primaquine for presumptive anti-relapse therapy (post-travel or post-diagnosis of Plasmodium vivax) since 1952. In 2018, the US Food and Drug Administration approved the uses of a new hepatic schizontocidal and hypnozoitocidal 8-aminoquinoline called tafenoquine for the respective prevention of all malarias and for the treatment of those that relapse (P. vivax and Plasmodium ovale). METHODS: The evidence and rationale for tafenoquine for the prevention and treatment of malaria was gathered by means of a standard search of the medical literature along with the package inserts for the tafenoquine products Arakoda™ and Krintafel™ for the prevention of all malarias and the treatment of relapsing malarias, respectively. RESULTS: The development of tafenoquine-an endeavor of 40 years-at last brings two powerful advantages to travel medicine practice against the malaria threat: (i) a weekly regimen of causal prophylaxis; and (ii) a single-dose radical cure for patients infected by vivax or ovale malarias. CONCLUSIONS: Although broad clinical experience remains to be gathered, tafenoquine appears to promise more practical and effective prevention and treatment of malaria. Tafenoquine thus applied includes important biological and clinical complexities explained in this review, with particular regard to the problem of hemolytic toxicity in G6PD-deficient patients.
2018 Publication
88 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran I. Made Joni, M. Vanitha, P. Camellia, N. Balasubramanianc
Processing of graphite from its ore has been studied for more than a decade due to the elevated demand for graphite which has a wide range of applications but restricted to the short availability of resources. In the present study, microwave irradiation was used for the graphitization of carbon using different metal (Ni, Co, Fe, Cr) salts as catalysts. Microwave irradiation excels from the classical thermal treatment since in the former case the reaction time and the temperature used is low. The graphitization using nickel sulfate as a catalyst was most effective when compared to the other catalysts and the % degree of graphitization was about 98% for 5 min of reaction time. The mechanism underlying the formation of graphite by microwave irradiation is also discussed in brief. Hence this study provides a new approach for processing graphite by a simple, fast and effective microwave technique. In addition, the preparation of graphene oxide (GO) from the graphitized carbon was also attempted and compared with GO prepared from commercial graphite.
2018 Journal
89 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran M. Vanitha, I Made Joni, P. Camellia, N. Balasubramanian
Ce doped ZnO/rGO composite materials were prepared by a one-pot hydrothermal process without any surfactant. The size, crystallography and morphology of the composite were investigated in detail by X- ray diffraction (XRD) studies, Raman spectroscopy, scanning electron microscopic (SEM), transmission electron microscopic (TEM) studies, UV-Vis spectroscopic analysis and X-ray photoelectron spectroscopic (XPS) analysis. The XRD pattern substantiates the formation of Ce doped ZnO/rGO composite revealing the wurtzite structure of ZnO. The SEM micrograph illustrates flower-like morphology for ZnO/rGO composite which coalesced further after cerium incorporation. Additionally, TEM image illustrated that ZnO hexagons were disoriented from its flower structure in Ce/ZnO/rGO composite. The XPS spectra further reaffirm the formation of cerium doped ZnO/rGO composite. The photoluminescence (PL) spectra confirms that emission occurs in the UV and visible region and several active sub-levels were observed in visible region on deconvolution, due to the incorporation of cerium. Antibacterial activity towards B. subtills and V. harveyi affirmed that the incorporation of Ce in ZnO/rGO composite leads to an improved antibacterial activity. Keywords: Cerium; Graphene; Oxygen vacancies; Composite; Photoluminescence spectra
2018 Journal
90 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran C Panatarani, M Vanitha, L Nulhakim, Z I Hauna and I M Joni
Design and fabrication of Al-air battery were done in this present work with economically viable raw materials. Optimization of anode material, catalyst concentration, current density and electrolyte concentration were carried out. Al 5083 as an anode material results in longer discharge time than Al 7075 and Al 6061 anode used in this study. Catalyst loading of 5% TiCl3, current density of 5 mA cm-2 and 10% of NaCl electrolyte were optimized. A single battery cell is fabricated using Al 5083 as an anode, air cathode which consists of graphite, paint as a binder with 5% TiCl as a catalyst and 10% NaCl as the electrolyte. The single cell exhibits voltage of about 0.8 V with 20 mA h 3 -1 current capacity. The lifecycle of the fabricated battery is tested for four consecutive cycles which demonstrates almost similar shape in the charging and discharging curves representing better stability of the fabricated battery.
2018 Original Research article
91 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran I M Joni, L Nulhakim, M Vanitha and C Panatarani
The crystalline silica (SiO2) particle is successfully prepared using simple solution method from sodium silicate (Na2SiO3) precursor. The FTIR spectrum of the sample confirms the presence of SiO2. The X-ray diffraction (XRD) shows that the sample is cristobalite type of SiO2 which is comparable with ICSD ref. number of 01-076-0941. The crystallite size is about 28 nm as calculated by Scherrer method and the average particle diameter was about 697 nm as confirmed by Particle Size Analyzer (PSA) measurement. The Scanning Electron Microscope (SEM) image reveals that the sample reveal micro-flake with irregular rod-shaped morphology. The purity of sample is examined by X-ray Fluorescence (XRF) which shows about 93.1 mass % of pure SiO2 whereas, the purity of the raw precursor Na2SiO3 before synthesis is about 60.5 Mass %. The synthesized SiO2 particles can be used for several applications, where SiO2 is used in its crystalline phase.
2018 Original Research article
92 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran M. Vanitha, N Balasubramanian, I Made Joni and P. Camellia,
The detection of contaminants in wastewater is of massive importance in today’s situation as they pose a serious threat to the environment as well as humans. One such vital contaminants is mercury and its compound, the reported mercury detectors grieve from low sensitivity, high cost and slow response. In the present work graphene based electrode material is developed for sensing mercury contaminants in wastewater using electrochemical technique. The synthesized material graphene oxide (GO) modified with L-Cysteine in presence of polyvinylpyrrolidone (PVP) as capping agent was characterized using SEM, TEM and Raman Spectroscopic analysis. It is ascertained from the morphological characterization that the nanocomposite exhibits a spherical morphology. The L-cysteine modified graphene oxide electrode is electrochemically characterized using redox couple [Fe(CN)63-/4-] and electrochemical impedance spectroscopic (EIS) analysis. Electrochemical sensing of Hg (II) ions in solution was done using Square wave anodic stripping voltammetry (SWASV). The incorporation of graphene significantly increases the sensitivity and selectivity towards mercury sensing.
2018 Conference
93 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran I Made Joni, Vanitha Muthukannan, Wawan Hermawan, and Camellia Panatarani
Nanotechnology today is regarded as a revolutionary technology that can help to address the key needs related to energy, environment, health and agriculture in developing countries. This paper is a short review on the development and challenges of nanotechnology in Indonesia. Nanotechnology offers great potential benefits, there is emerging concerns arising from its novel physicochemical properties. The main applications of nanotechnology in the different sectors which is vital and its economic impact in Indonesia is also discussed. The achievment and development of nanotechnology including synthesis and dispersion of nanoparticles (NPs) and its applications in various fields is briefly addressed in Nanotehcnology and Graphene Research Center, Universitas Padjadjaran (Unpad). Despite significant progress in developmental goals, many challenges in the development of nanotechnology proccesing need to be resolved such as support infrastructure and evolution of new form of collaborative arrangements between various sectors and policies which is emerged as an important factor enabling development.
2018 conference paper
94 Vanitha Muthukannan Anna University Prof.Dr.Eng. I Made Joni Universitas Padjadjaran Ujang Subhan, Vanitha Muthukannan, Sundoro Yoga Azhary, Muhammad Fakhri Mulhadi, Emma Rochima, Camellia Panatarani, and I Made Joni
The efficiency and productivity of aquaculture strongly depends on the development of advanced technology for water quality management system. The most important factor for the success of intensive aquaculture system is controlling the water quality of fish rearing media. This paper reports the design of fine bubbles (FBs) generator and performance evaluation of the system to improve water quality in thai catfish media (10?g/ind) with density (16.66 ind./L). The FBs generator was designed to control the size distribution of bubble by controlling its air flow rate entry to the mixing chamber of the generator. The performance of the system was evaluated based on the produced debit, dissolved oxygen rate and ammonia content in the catfish medium. The size distribution was observed by using a high speed camera image followed by processing using ImageJ. freeware application. The results show that air flow rate 0.05?L/min and 0.1?L/min received average bubble size of 29?µm and 31?µm respectively. The generator produced bubbles with capacity of 6?L/min and dissolved oxygen rate 0.2?ppm/min/L. The obtained DO growth was 0.455?ppm/second/L while the average decay rate was 0.20?ppm/second/L. (0.011/0.005 fold). In contrast, the recieved DO growth rate is faster compared to the DO consumption rate of the Thai catfish. This results indicated that the potential application of FBs enhanced the density of thai catfish seed rearing. In addition, ammonia can be reduced at 0.0358?ppm/hour/L and it is also observed that the inhibition of bacterial growth of air FBs is postive to Aeromonas hydrophila bacteria compared to the negative control. It is concluded that as-developed FBs system can be potentially applied for intensive thai catfish culture and expected to improve the feeding efficiency rate.
2018 conference paper
95 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Stuart Hawkins, Sofia C. Samper Carro, Julien Louys, Ken Aplin, Sue O'Connor & Mahirta
We report on tetrapod (Reptilia, Amphibia, Mammalia, Aves) vertebrates recovered during excavations at Tron Bon Lei rockshelter on the south coast of Alor Island, eastern Indonesia. These include both archaeological specimens recovered from a 1 m² test pit dating from ?21 kya cal BP to the late Holocene, and a modern eastern barn owl deposit recovered nearby. To discern between the depositional processes that accumulated the small numbers of micro- and macrovertebrate remains from the archaeological deposits, the taphonomic signature of the natural assemblage was quantified and compared to the archaeological record. The taphonomic data indicates that the tetrapod archaeofaunal remains are a combination of barn owl predation of microfauna and human predation of larger fauna. This approach provides new information on human-tetrapod interactions on Alor in Wallacea during the late Quaternary, including an apparent increase in cave site use and hunting intensity during the Pleistocene-Holocene transition, sea turtle butchery and probable transport, and extinctions of previously unknown giant to large rat species.
2018 Journal Article
96 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Sue O'Connor, Mahirta, Shimona Kealy, Clara Boulanger, Tim Maloney, Stuart Hawkins, Michelle C. Langley, Hendri A. F. Kaharudin, Yuni Suniarti, Muhammad Husni, Marlon Ririmasse, Daud A. Tanudirjo, Lucas Wattimena, Wuri Handoko, Alifah & Julien Louys
The occupation of small islands presents particular challenges for people largely related to limited terrestrial resources and susceptibility to natural disasters. Nevertheless, the challenges and risks inherent in maintaining stable populations on small islands can be offset or overcome through the use of maritime technologies and exchange networks. The archaeology of Here Sorot Entapa rockshelter (HSE) on Kisar Island in the Wallacean Archipelago provides an unparalleled record for examining these issues in Southeast Asia. Kisar is the smallest of the Wallacean islands known to have a Pleistocene occupation record, and one of the smallest permanently inhabited today. Our results indicate that Here Sorot Entapa was first occupied in the terminal Pleistocene by people with advanced maritime technology who made extensive use of local marine resources and engaged in social connections with other islands through an obsidian exchange network. As a result, populations appear to have been maintained on the island for approximately 6,000 years. In the early Holocene occupation at HSE ceased for unknown reasons, and the site was not reoccupied until the mid-Holocene, during which time a major change in the lithic resources can be observed and the exchange network appears to have ceased.
2018 Journal Article
97 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Sue O’Connor, Mahirta, Shimona Kealy, Julien Louys, Hendri A. F. Kaharudin, Antony Lebuan & Stuart Hawkins
We report new finds of two painted rock art sites in Lembata Island in Indonesia, one depicting a 'boat', the other an anthropomorph. The style of the anthropomorph is quite distinct from the small dynamic painted anthropomorphs common elsewhere in eastern Indonesia. Based on similarities with figures on Moko drums we hypothesise that this painting dates to the last millennium CE. This find extends our knowledge of the diversity of anthropomorph figures in Indonesian rock art, and indicates continuity in the expression of relationships and obligations to the ancestors through different mediums in the Sunda Islands.
2018 Journal Article
98 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Sue O'Connor, Mahirta, Julien Louys, Shimona Kealy, Sally Brockwell
Engraving sites are rare in mainland and Island Southeast Asia and few examples have been identified in the Indonesian islands. Here we report three new engraving locales in Alor Island, Indonesia. The engravings are executed on boulders and in shelters and include figurative and geometric motifs, some combining cupules. Motifs incorporating cupules occur widely in Papua New Guinea (PNG) and Near Oceania but have not previously been reported to the west in Indonesia. The Alor engraving sites thus extend the known distribution of cupule-based motifs to the west. These recent finds also indicate that the paucity of engravings found in the islands of eastern Indonesia is likely due to the comparatively few archaeological surveys conducted in this region.
2018 Journal Article
99 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Tim Ryan Maloney, Mahirta, Sue O'Connor, Christian Reepmeyer
Excavation in Tron Bon Lei shelter on the Indonesian Island of Alor has uncovered a rich Pleistocene lithic assemblage, which includes obsidian artefacts representing a specialised industry previously undetected in any early stone tool assemblage of Island South East Asia (ISEA). Portable X-ray florescence of the obsidian assemblage has revealed three discrete sources, and that at least one of the sources is likely off-island. This indicates that inter-island exchange networks were active from the terminal Pleistocene onwards. Obsidian from all sources was reduced exclusively using bipolar anvil-resting techniques, resulting in the production of exceptionally small bipolar cores and flakes. The assemblage reveals extraordinary effort to reduce the obsidian, with cores being typically smaller than ten millimetres, and many around six millimetres at discard. Using reduction sequence analyses and technological observations, we document this specialised industry and discuss the role these artefacts may have played in the lifeways of the people of Alor Island.
2018 Journal Article
100 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Julien Louys, Sue O’Connor, Mahirta, Pennilyn Higgins, Stuart Hawkins, Tim Maloney
Gigantism is a common phenomenon observed in murids from islands, particularly the Indonesian islands belonging to the Lesser Sunda chain. Rats in this island group are often considerably larger than their continental sister taxa and have been reported from the islands of Timor, Sumba, and Flores. Here, we describe the first record of a giant rat from the island of Alor, at the northeastern end of the Lesser Sundas. Alormys aplini gen. et sp. nov. is described from isolated molars and a partial lower jaw from excavations in the twilight zone of Makpan Cave, a lava tube cave situated on the southwestern margin of the island. Speleological and taphonomic information suggests that these remains were deposited as a result of owl activities. Alormys aplini is characterized by its large size relative to members of Rattus and a relatively unspecialized, moderately hypsodont dentition. Among the larger rodents of the Lesser Sunda chain, Alormys most closely resembles Milimonggamys and Papagomys. Carbon and oxygen isotope analysis indicates that it consumed C3 plants almost exclusively. Its extinction in the late Holocene appears coeval with the disappearance of Timor’s and Sumba’s giant rats and may be related to increased aridity and deforestation on these islands.
2018 Journal Article
101 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Shimona Kealy, Lucas Wattimena, Sue O'Connor
Survei arkeologi sangat penting untuk penemuan dan interpretasi sisa-sisa yang ditinggalkan oleh aktivitas manusia prasejarah. Saat ini penginderaan jarak jauh dan model prediktif telah meningkatkan jangkauan dan keberhasilan survei arkeologi, namun survei pejalan kaki untuk mengembangkan parameter model dan prediksi kebenaran dasar masih penting untuk keberhasilan suatu penemuan. Penelitian ini merupakan hasil survei arkeologi tahun 2017 di Pulau Babar Besar dan Pulau Wetang yang termasuk dalam bagian dari kelompok Kepulauan Babar, Maluku Barat Daya, Indonesia. Tercatat sebanyak 62 situs arkeologi ditemukan di kedua pulau tersebut, tujuh diantaranya merupakan situs lukisan cadas baru yang ditemukan di Pulau Wetang. Hasil survei ini menunjukkan keberhasilan penggunaan peta geologi dan topografi di samping citra satelit dalam mendeteksi daerah prospektif untuk survei. Hasil penelitian ini juga menunjukkan bahwa pemahaman karakteristik geologi daerah yang lebih rinci dan komparatif diperlukan sebelum dilakukan survei jarak jauh yang lebih lanjut di wilayah Maluku Barat Daya, Indonesia. Archaeological surveys are essential to the discovery and interpretation of remains left by past human activities. While remote sensing and predictive models have greatly improved the reach and success of archaeological survey, pedestrian surveys to develop model parameters and ground-truth predictions is still imperative for successful discoveries. Here we present the results of the 2017 archaeological survey of islands Babar Besar and Wetang in the Babar Island Group, Maluku Barat Daya, Indonesia. A total of 62 archaeological sites were recorded between the two islands; seven of which represent new rock art sites on Wetang island. Our survey results indicate the successful use of geological and topographic maps alongside satellite images in detecting prospective regions for survey. Results also indicate however that a more detailed and comparative understanding of the regions geology is required before more advanced forms of remote survey are conducted in the Maluku Barat Daya region.
2018 Journal Article
102 Wendy Marie Erb Rutgers University Siti Maimunah, MSc Universitas Muhammadiyah Palangkaraya W.M. Erb, E.J. Barrow, A.N. Hofner, S.S. Utami-Atmoko, E.R. Vogel
Indonesia’s peatlands experience frequent and intense wildfires, producing hazardous smoke with consequences for human health, yet there is a lack of research into adverse effects on wildlife. We evaluated the effects of smoke on the activity and energy balance of Bornean orangutans (Pongo pygmaeus wurmbii) in a peat swamp forest at the Tuanan Research Station, Central Kalimantan. We collected behavioural data and urine samples from four adult flanged males before, during, and after wildfires between March 2015 and January 2016. During fires, particulate matter (PM10) concentrations were hazardous. Orangutans increased rest time during and after the smoke period, and decreased travel time and distance and increased fat catabolism post-smoke. The increase in post-smoke ketones was not related to changes in caloric intake and was likely due to an increase in energy expenditure, possibly related to immune response. Results show that wildfire smoke negatively affects orangutan condition, and sustained research is needed to assess the magnitude of the threat to the long-term viability of this Critically Endangered species.
2018 Research article
103 Jeffrey Neilson University of Sydney Sukrisno Widyotomo Pusat Penelitian Kopi dan Kakao Indonesia Mark Vicol, Jeffrey Neilson, Diany Faila Sophia Hartatri and Peter Cooper
Value chain upgrading interventions have emerged in recent years as a dominant approach to rural development. In coffee value chains, upgrading opportunities are presented by the growth in consumption of specialty coffees, which are associated with direct engagement with producer communities by roasting firms, along with an apparent increased commitment to social responsibility. Known in the industry as “relationship coffee”, such interventions align with a value chain approach to development and are promoted as offering upgrading opportunities for otherwise marginalized rural communities. In this article, we critique the dominant development discourse of relationship coffee in Indonesia via three case studies of livelihoods and local agrarian dynamics across three coffee-growing communities on the islands of Sulawesi, Bali and Java. We find that the relationship coffee model does present opportunities for producer upgrading. However, these benefits have been subsequently captured by key individuals within the producer community who are able to accumulate wealth and consolidate their social position. As it is currently implemented in Indonesia, the relationship coffee model has reproduced local patterns of inequality rather than contributing to poverty alleviation efforts. These insights suggest the urgent need to develop a critical political economy of upgrading in the global value chain and rural development literature.
2018 Journal Article
104 Jeffrey Neilson University of Sydney Sukrisno Widyotomo Pusat Penelitian Kopi dan Kakao Indonesia Jeff Neilson, Bill Pritchard, Niels Fold & Angga Dwiartama
Recent models of Global Production Network Theory (known as GPN 2.0) have attempted to theoretically explain the underlying determinants, or causal drivers, of particular industry network configurations, which in turn shape the territorial outcomes for regional development. To date, the ability of this ambitious conceptual model to thereby explain economic geography has remained largely untested beyond the select industry networks examined by its proponents, most notably the electronics, retail and automotive sectors of East Asia. In this paper, we stress-test the causative model for the case of lead firms in the global cocoa-chocolate sector, and assess its ability to subsequently explain industry configurations and territorial outcomes in a particular country, Indonesia. Our application suggests that GPN 2.0 has considerable utility for directing empirical research, but challenges beset its fuller theoretical promise. We identify a problematic relationship between the deductive causality implied by GPN 2.0 and the inherent relationality of GPN 1.0 that remains, in our view, unresolved. As a result, we remain skeptical of the broader theoretical claims that GPN 2.0 possesses explanatory powers capable of deducing industry network configurations from a discrete set of supposedly independent variables.
2018 Journal Article
105 Jeffrey Neilson University of Sydney Sukrisno Widyotomo Pusat Penelitian Kopi dan Kakao Indonesia Jeff Neilson, Russell Toth, Niken Sari, Joshua Bray, Manann Donoghue, Bustanul Arifin, Hanung Ismono
In the Sumatran context, where coffee production is generally considered to contribute to livelihood resilience rather than poverty alleviation, we found little evidence that sustainability programs were providing pathways out of poverty through enhanced coffee-related income. This suggests a need to reconsider the realistic benefits of sustainability standards in the context of local livelihood strategies, and to consider a more adaptive approach where sustainability-related knowledge transfer is oriented towards the needs of prevailing livelihoods. The study does not find significant additional benefits for farmers upgrading from the 4C program to RA certification. This is unsurprising given the case study context, whereby the RA-certified farmers were unable to sell their coffee as such.
2018 Report
106 Francois Xavier Beauducel Institut de recherche pour le developpement Devy Kamil Syahbana Pusat Vulkanologi dan Mitigasi Bencana Geologi Franc?ois Beauducel, Devy Kamil Syahbana, Made Agung Nandaka, Gede Suantika
After the VEI 4+ deadly eruption in 1963 and 54 years of dormancy, Mt. Agung reawakened in September 2017 with a brutal and high energy seismic swarm which lasted about 40 days then progressively decreased. On November 21, 2017, a small explosive phreatomagmatic eruption began and subsequent explosive eruptions on 25-28 November had increased intensity with lava effusion began on November 26. Small deformations were recorded by a tiltmeter and 5 permanent GPS stations, with a maximum of 5 cm of displacements. In this paper we present a robust method to perform automatic source modeling from displacement trends, resulting in continuous time series of volume variations and source depths, as an efficient tool for real-time monitoring. An inflation period was detected from mid-August to mid-September, with a 12±2 km deep source and a maximum of +40±5 Mm3 volume variation. From mid-September to end of November, models show no significant large scale deformation. Sudden deflation began on November 28, 2 days after the magma reached the surface and started to fill in the crater. The subsidence lasted 14 days with a maximum of ?36±4 Mm3 associated to 11±1 km deep source. Models and phenomenology suggest that a limited magma volume has supplied the shallow reservoir, followed by a fracturing episode towards the surface, then the filling of the crater associated with reservoir deflation of a similar volume amount. These results have been obtained during the crisis management, in December 2017, and have been used as phenomenological evidence in order to reduce the evacuation zone around Mt. Agung on January 4th, 2018.
2018 oral session at COV10 Naples
107 Matthew Wayne Tocheri Lakehead University Drs I Made Geria, M.Si. Pusat Penelitian Arkeologi Nasional Thomas Sutikna, Matthew W. Tocheri, J. Tyler Faith, Jatmiko, Rokus Due Awe, Hanneke J.M. Meijer, E. Wahyu Saptomo, Richard G. Roberts
Liang Bua, the type site of Homo floresiensis, is a limestone cave on the Indonesian island of Flores with sedimentary deposits currently known to range in age from about 190 thousand years (ka) ago to the present. Recent revision of the stratigraphy and chronology of this depositional sequence suggests that skeletal remains of H. floresiensis are between ~100 and 60 ka old, while cultural evidence of this taxon occurs until ~50 ka ago. Here we examine the compositions of the faunal communities and stone artifacts, by broad taxonomic groups and raw materials, throughout the ~190 ka time interval preserved in the sequence. Major shifts are observed in both the faunal and stone artifact assemblages that reflect marked changes in paleoecology and hominin behavior, respectively. Our results suggest that H. floresiensis and Stegodon florensis insularis, along with giant marabou stork (Leptoptilos robustus) and vulture (Trigonoceps sp.), were likely extinct by ~50 ka ago. Moreover, an abrupt and statistically significant shift in raw material preference due to an increased use of chert occurs ~46 thousand calibrated radiocarbon (14C) years before present (ka cal. BP), a pattern that continues through the subsequent stratigraphic sequence. If an increased preference for chert does, in fact, characterize Homo sapiens assemblages at Liang Bua, as previous studies have suggested (e.g., Moore et al., 2009), then the shift observed here suggests that modern humans arrived on Flores by ~46 ka cal. BP, which would be the earliest cultural evidence of modern humans in Indonesia.
2018 Journal Article
108 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Jacques Slembrouck, Reza Samsudin, Brata Pantjara, Ahmad Sihabuddin, Marc Legendre and Domenico Caruso.
Several ecological services and functions are attributed to macrophytes, which may represent valuable resource for the ecological intensification of tropical fish farming. However, considering the multiple potential eco-services provided by macrophytes, the choice of the most appropriate species requires multiple criteria to assess these eco-services. Five floating macrophytes (Eichhornia crassipes, Lemna minor, Azolla filiculoides, Salvinia molesta and Salvinia spp.) were selected for this study. The six ecoservices parameters compared among these macrophytes were: productivity (in % of seeded macrophytes), risk of non-productive cycles, nutritional value, impact on water quality, palatability (expressed as the percentage of plant ingested in 4 h) and ease of use. Experiments to determine these indicators were carried out in simple devices (net cages and plastic tanks) partially immerged in earthen ponds. The palatability of fresh macrophytes (whole or chopped) was studied in ponds using Osphronemus goramy juveniles. All indicators were scored from 1 to 5, and the highest score was assigned to the highest performer. These scores corresponded either to the evaluation of a single parameter (e.g. productivity) or to the average from scores of several parameters (e.g. nutritional score). Multiplier coefficients were applied for nutritional value and palatability. Azolla filiculoides showed the best scores for productivity; L. minor for nutritional value and palatability, and E. crassipes for the lowest risk of non-productive cycles and a positive impact on water quality. After integrating the scores in a multi-parameter matrix, A. filiculoides had the best overall score. The results of this approach to select macrophytes are discussed in light of the eco-services provided by macrophytes which may, in turn, promote the ecological intensification of tropical small-scale aquaculture.
2018 scientific article
109 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Keith, P., Dahruddin, H., Limmon, G., Hubert, N.
A new species of Schismatogobius, a freshwater goby, is described from Halmahera (Indonesia). It differs from other species belonging to the genus by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters, including the number of pectoral fin rays, the pattern of the ventral surface of the head, the pectoral fin colour pattern and the jaw length/head length ratio of male and female.
2018 article
110 Mark Christopher O Hara Messerli Research Institute; University of Veterinary Medicine, Vienna Dewi Malia Prawiradilaga Indonesian Institute of Science (LIPI) O'Hara, M; Mioduszewska, B; Haryoko, T; Prawiradilaga, D M; Huber, L; Auersperg, A
When tested under laboratory conditions, Goffin’s cockatoos (Cacatua goffiniana) demonstrate numerous sophisticated cognitive skills. Most importantly, this species has shown the ability to manufacture and use tools. However, little is known about the ecology of these cockatoos, endemic to the Tanimbar Islands in Indonesia. Here we provide first insights into the feeding- and socio-ecology of the wild Goffin’s cockatoos and propose potential links between their behaviour in natural settings and their advanced problem-solving capacities shown in captivity. Observational data suggests that Goffin’s cockatoos rely on a large variety of partially seasonal resources. Furthermore, several food types require different extraction techniques. These ecological and behavioural characteristics fall in line with current hypotheses regarding the evolution of complex cognition and innovativeness. We discuss how the efficiency of (extractive) foraging may preclude tool use in wild Goffin’s cockatoos, even though the corresponding cognitive and ecological prerequisites seem to be present.
2018 International publication
111 Mark Christopher O Hara Messerli Research Institute; University of Veterinary Medicine, Vienna Dewi Malia Prawiradilaga Indonesian Institute of Science (LIPI) Berenika Monika Mioduszewska, Mark Christopher O’Hara, Tri Haryoko, Alice Marie Isabel Auersperg, Ludwig Huber, Dewi Malia Prawiradilaga
Experimental work on captive Goffin’s cockatoos (Cacatua goffiniana) has highlighted the remarkable cognitive abilities of this species. However, little is known about its behavior in the natural habitat on the Tanimbar Archipelago in Indonesia. In order to fully understand the evolutionary roots leading to cognitively advanced skills, such as multi-step problem solving or flexible tool use and manufacture, it is crucial to study the ecological challenges faced by the respective species in the wild. The three-month expedition presented here aimed at gaining first insights into the cockatoos’ feeding ecology and breeding behavior. We could confirm previous predictions that Goffin’s cockatoos are opportunistic foragers and consume a variety of resources (seeds, fruit, inflorescence, roots). Their breeding season may be estimated to start between June and early July and they face potential predation from ground and aerial predators. Additionally, the observational data provide indications that Goffin’s cockatoos are extractive foragers, which together with relying on multiple food sources might be considered a prerequisite of tool use.
2018 Publication
112 Matthew Wayne Tocheri Lakehead University Drs I Made Geria, M.Si. Pusat Penelitian Arkeologi Nasional Luong S, Tocheri MW, Sutikna T, Wahyu Saptomo E, Jatmiko, Roberts RG
2018 Journal Article
113 Nicolas HUBERT Institut de Recherche pour le Développement Daisy Wowor Indonesian Institut of Sciences (LIPI), Research Centre for Biology (RCB), Division of Zoology Keith P, Dahruddin H, Limmon G, Hubert N
a new species of Schismatogobius, a freshwater goby, is described from halmahera (indonesia). it differs from other species belonging to the genus by a high percentage of genetic divergence in partial Coi gene (652 bp) and by several characters, including the number of pectoral fin rays, the pattern of the ventral surface of the head, the pectoral fin colour pattern and the jaw length/head length ratio of male and female.
2018 Journal article
114 Dr Aditya Riadi Gusman Institute of Geological and Nuclear Science (GNS Science) Professor Teuku Faisal Fathani Universitas Gadjah Mada Ryan Paulik, Aditya Gusman, James H. Williams, Gumbert Maylda Pratama, Sheng-lin Lin, Alamsyah Prawirabhakti, Ketut Sulendra, Muhammad Yasser Zachari, Zabin Ellyni Dwi Fortuna, Novita Barrang Pare Layuk, Ni Wayan Ika Suwarni
Presentation on Post-event damage survey of the MW7.4 Sulawesi Earthquake and Tsunami (28/09/2018) delivered at the Meteorological, Climatological, and Geophysical Agency. Ministry for Research and Higher Education, Jakarta, Indonesia.
2018 Presentation
115 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Etienne Baras, Otong Zenal Arifin, Jacques Slembrouck, Jojo Subagja, Anang Hari Kristanto, Marc Legendre.
Here, on the basis of published information upon over 800 species from 39 orders and 202 families, we analyse how the size of oil globules in fish eggs varies between reproductive guilds and environments with contrasting salinities. About 80% of marine fishes produce eggs with oil globules, the volume of which (VO) never exceeds 9% of the egg reserves and averages 2%. These proportions vary very little between marine fish species producing pelagic or demersal eggs. Fewer freshwater fishes (about 40%) produce eggs with oil globules, but their globules are much larger (mean VO of 10%) and their volumes vary considerably between reproductive guilds: VO is on average 3–10 times lower in freshwater species with demersal eggs than among freshwater pelagophils and aphrophils (i.e., bubble nesters), where it averages about 40% (range of 23%–69%) of the egg reserves. These results support the idea that oil globules serve to hydrostatic lift in fresh waters, but not or very little in marine waters, where egg buoyancy can be achieved at a lower energy cost through egg hydration. Advantages and constraints of oil globules in fish eggs are discussed in the light of species producing eggs with very large oil globules (VO > 20%): access to oxygen-rich water layers that are indispensable for egg development vs. smaller size of larvae at first feeding, since the saturated lipids contained in oil globules essentially serve very little to tissue construction
2018 scientific article
116 Kieran Hosty Australian National Maritime Museum Shinatria Adhityatama Pusat Penelitian Arkeologi Nasional Kieran Hosty, Dr James Hunter, Shinatria Adhityatama
The shipwreck of HMAS Perth lies in waters between Java and Sumatra, a victim of the Battle of Sunda Strait in 1942. A joint survey between the Museum and Pusat Penelitian Arkeologi Nasional (Indonesia) has recorded the devastation caused by extensive illegal salvage.
2018 Journal article - Signals
117 Christian Lott HYDRA Marine Sciences Jane Mamuaja UNSRAT Manado Christian Lott, Andreas Eich, Boris Unger, Dorothée Makarow, Markus T. Lasut and Miriam Weber
Replacing conventional plastic with biodegradable plastic is discussed as a possible mitigation strategy for marine plastic pollution. However, there have been hardly any systematic field tests under marine conditions. There is little information and a lot of bias. Some laboratory tests have been performed with natural marine matrices, few tests have been conducted under natural conditions in the field. Thus, there is not a lot of specific information about the performance of biodegradable plastic under marine conditions. Biodegradability is usually tested in a laboratory test in closed systems by following the CO2 production and/or the O2 consumption over time. Various standard laboratory tests exist for compost, soil and also marine conditions. Once proven in the laboratory, it is important to verify whether the material is also biodegrading under natural marine conditions. We have been developing in-situ tests for several marine scenarios, and tested about 20 different polymers and blends of plastic film with 12 - 100 ?g mL-1, DC: 50 ng mL-1). Post-exposurem thickness in natural coastal habitats in the Mediterranean Sea and Southeast Asia. All tested materials that have been proven biodegradable in lab tests showed disintegration in field tests. The half-life of materials range from some weeks to some years. The disintegration of all biodegradable plastic tested is much faster than estimated for conventional plastic. The disintegration depends on climate zone and habitat conditions, such as matrix (water, sand, mud), temperature and nutrients. Some habitats in the same region are more active in the biodegradation of a specific material. Different materials are degraded differently under different conditions, especially with regard to oxygen availability, i.e. apparently some materials degrade faster without, others faster with oxygen. Results of concluded and ongoing field experiments as a baseline for a catalogue of the specific half-life as a material property for the most common biodegradable polymers and blends are given.
2018 Conference Poster
118 Christian Lott HYDRA Marine Sciences Jane Mamuaja UNSRAT Manado Markus T. Lasut, Miriam Weber, Fransisco Pangalila, Natalie D. C. Rumampuk, Joice R. T. S. L. Rimper, Veibe Warouw, Stella T. Kaunang and Christian Lott
Southeast Asia harbours the highest marine diversity of our planet. At the same time the countries in the so-called Coral Triangle have the highest potential/risk of plastic pollution to the marine environment. Biodiversity research is still struggling with the sheer inventory of biota, as many marine organisms already are under risk of becoming extinct by human influence. Manado (North Sulawesi, Indonesia) is a case study in the very heart of the Coral Triangle. It is a booming city with a growing population >500.000, right next to Bunaken, one of the iconic world-class destinations of diving tourism, and a national park. Manado is origin to a stream of mismanaged waste entering the ocean every day with an estimated volume of 330 m3 d-1 in 2016, with drastic effects to the nearby coastal environment, especially coral reefs and mangroves. Waste management strategies are rudimentary, baseline data on sources, quantity and quality of plastic waste are lacking, micro-plastic in special is hardly addressed, thus urgently needed risk assessment and mitigation concepts lack fundamental knowledge. Here we provide observational data as beach clean-up reports, ROV seafloor surveys, and gut content analyses of commercially caught fish, and accidental findings as the plastic gut content of the “living fossil” Latimeria menadoensis, the iconic coelacanth, as the first collection of available information for this region. To overcome this paucity of knowledge we propose an interdisciplinary action plan for the Manado area, that can be extended and adapted to the wider region of the Coral Triangle. The Mediterranean Sea also has a high biodiversity, parts of which are already lost or highly threatened. Plastic pollution has a long history although the problem has been addressed by large only recently. The Coral Triangle could profit from expertise and concepts developed in the Med and give back a region where due to the relative short history of plastic waste, and still spatially restricted heavy urbanization, the impact on near-pristine marine ecosystems can be studied in order to find global solutions.
2018 Conference Paper
119 Christian Lott HYDRA Marine Sciences Jane Mamuaja UNSRAT Manado Christian LOTT, Andreas EICH, Nora-Charlotte PAULI, Tobias MILDENBERGER, Christian LAFORSCH, Jana S. PETERMANN, Markus T. LASUT, Miriam WEBER
Biodegradable plastic is gaining attention, also through market regulation by a growing number of countries. The substitution of conventional plastic by these new materials is discussed as one mitigation measure to the ever-growing global problem of marine plastic litter. Based on available market data of plastic production, littering risk estimations and meta-analyses of the marine litter in the global oceans we present mathematical and conceptual models to assess the substitution potential of biodegradable plastics for conventional polymers, and evaluate the possible role as a mitigation strategy against marine plastic litter accumulation. We estimate substitution potentials from 0.3 to 80 % for different scenarios, which highlights the importance to better understand the ecological impact of biodegradable materials when entered the marine environment. Currently, our knowledge on the fate of conventional plastic and these new materials in the ocean is based on laboratory tests, analysis of materials collected in the field, observational field data, and only a few in-situ studies so far. Functional aspects as the interaction of biofilm and fouling communities with the polymer surface and the metabolism of these biota are largely unknown. Since five years we have been investigating the formation of the microhabitat of marine plastic in consecutive field experiments addressing the shortterm (weeks) biofilm formation and the mid-term (up to one year) fouling succession in two environmental coastal settings, a sublittoral sandy seafloor and the water column in the warm-temperate climate of the Mediterranean Sea. We also report the preliminary results of comparative in-situ experiments currently in progress in the tropical ocean of NE Sulawesi, Indonesia. Data of biofilm and fouling development and composition, metabolic rates and degradation rates of common biodegradable polymers and blends serve as a baseline for further studies towards a comprehensive understanding of the ecological impact of plastic in the marine environment.
2018 Conference Paper
120 Paul Macklin Southern Cross University Dr. I Gusti Ngurah Agung Suryaputra Department of Analytical Chemistry Ganesha University of Education Singaraja, Bali, Indonesia Paul A. Macklin, Gusti Ngurah Agung Suryaputra
Water-to-air carbon dioxide fluxes from tropical lakes and reservoirs (artificial lakes) may be an important but understudied component of global carbon fluxes. Here, we investigate the seasonal dissolved carbon dioxide (CO2) dynamics in a lake and a reservoir on a tropical volcanic island (Bali, Indonesia). Observations were performed over four seasonal surveys in Bali's largest natural lake (Lake Batur) and largest reservoir (Palasari Reservoir). Average CO2 partial pressures in the natural lake and reservoir were 263.7±12.2 ?atm and 785.0 ±283.6 ?atm respectively, with the highest area-weighted partial pressures in the wet season for both systems. The strong correlations between seasonal mean values of dissolved oxygen (DO) and pCO2 in the natural lake (r2 = 0.92) suggest that surface water metabolism was an important driver of CO2 dynamics in this deep system. Radon (222Rn, a natural groundwater discharge tracer) explained up to 77% of the variability in pCO2 in the shallow reservoir, suggesting that groundwater seepage was the major CO2 driver in the reservoir. Overall, the natural lake was a sink of atmospheric CO2 (average fluxes of -2.8 mmol m-2 d-1) while the reservoir was a source of CO2 to the atmosphere (average fluxes of 7.3 mmol m-2 d-1). Reservoirs are replacing river valleys and terrestrial ecosystems, particularly throughout developing tropical regions. While the net effect of this conversion on atmospheric CO2 fluxes remains to be resolved, we speculate that reservoir construction will partially offset the CO2 sink provided by deep, volcanic, natural lakes and terrestrial environments.
2018 RESEARCH ARTICLE
121 Paul Macklin Southern Cross University Dr. I Gusti Ngurah Agung Suryaputra Department of Analytical Chemistry Ganesha University of Education Singaraja, Bali, Indonesia Paul A. Macklin, Gusti Ngurah Agung Suryaputra, Daniel Murdiyarso, Damien Maher, Isaac Santos
Water-to-air carbon dioxide fluxes from tropical coastal waters are an important but understudied component of the marine carbon budget. Here, we investigate drivers of carbon dioxide partial pressure (pCO2) in a relatively pristine mangrove-seagrass embayment on a tropical island (Bali, Indonesia). Observations were performed over eight underway seasonal surveys and a fixed location time series for 55 h. There was a large spatial variability of pCO2 across the continuum of mangrove forests, seagrass meadows and the coastal ocean. Overall, the embayment waters surrounded by mangroves released CO2 to the atmosphere with a net flux rate of 18.1 ± 5.8 mmol m?2 d?1 . Seagrass beds produced an overall CO2 net flux rate of 2.5 ± 3.4 mmol m?2 d?1 , although 2 out of 8 surveys revealed a sink of CO2 in the seagrass area. The mouth of the bay where coral calcification occurs was a minor source of CO2 (0.3 ± 0.4 mmol m?2 d?1 ). The overall average CO2 flux to the atmosphere along the transect was 9.8 ± 6.0 mmol m?2 d?1 , or 3.6 × 103 mol d?1 CO2 when upscaled to the entire embayment area. There were no clear seasonal patterns in contrast to better studied temperate systems. pCO2 significantly correlated with antecedent rainfall and the natural groundwater tracer radon (222Rn) during each survey. We suggest that the CO2 source in the mangrove dominated upper bay was associated with delayed groundwater inputs, and a shifting CO2 source-sink in the lower bay was driven by the uptake of CO2 by seagrass and mixing with oceanic waters. This differs from modified landscapes where potential uptake of CO2 is weakened due to the degradation of seagrass beds, or emissions are increased due to drainage of coastal wetlands.
2018 RESEARCH ARTICLE
122 Shimizu Kazufumi Center for Infectious Diseases, Kobe University Graduate School of Medicine Maria Inge Lusida Universities Airlangga Lumbago penyakit Troops Amin M, Bakhtiar A, Subarjo M, Aksono EB, Widiyanti P, Shimizu K, Mori Y.
There were 211,000 Indonesian Hajj pilgrims going to Mecca through 11 main airports in 2015 who were at risk of contracting the Middle East respiratory syndrome coronavirus (MERS-CoV). We aimed to find out whether there was any occurrence of MERS-CoV by performing screening on 28,197 returning pilgrims. Those with a body temperature of > 38 °C and respiratory symptoms were sent to the airport clinic to have an oropharyngeal swab and a bacterial culture. Fifteen pilgrims had fever (> 38 °C) accompanied by respiratory symptoms; of these, 12 patients were diagnosed with upper and lower respiratory tract infections and three patients with pneumonia. However, none of them were found to be infected with MERS-CoV. The bacterial cultures showed evidence of normal flora growth.
2018 Article
123 Jack Pumpuni Frimpong-Manso University of Bremen Ocha Nurliah Buhari University of Mataram Agyemang, T.K., Pumpuni, J.F., & Owusu-Boateng, G.
The physico-chemical and bacteriological quality of water and sediments and the growth performance of fish following administration of Oreochromis niloticus feeds of two different dietary protein levels were studied in Hapas set in four 200 m2 ponds. Results indicate that water quality parameters monitored were within environmental tolerable limits and for the growth of Oreochromis niloticus. For all the feeds, water temperature was in the range of 27.83°C - 28.67°C, dissolved oxygen 5.01mg/L - 6.11 mg/L and pH 5.4 - 7.01. The levels of biochemical oxygen demand, nitrogen, phosphorus and dissolved organic carbon as well as Salmonella sp, Staphylococcus aureus and Pseudomonas sp were generally beyond acceptable limits with projections of the levels of the physico-chemical parameters indicating further increase. There were no statistical significant differences (P>0.05) in the levels of total nitrogen, phosphorus, biological oxygen demand, dissolved organic carbon and bacteria load before the administration of treatments and at the end of the study.
2018 Journal
124 Dr Guangcheng Chen Third Institute of Oceanography, Ministry of Natural Resources, CHINA Yaya Ihya Ulumuddin, M.Si Research Center for Oceanography ZHENG Xinqing, WANG Chenying, HADI Tri Aryono, YE Youyin, PAN Ke
Due to the elevated atmospheric carbon dioxide, ocean acidification (OA) has recently emerged as a research theme in marine biology due to an expected deleterious effect of altered seawater chemistry on calcification. A system simulating future OA scenario is crucial for OA-related studies. Here, we designed an OA-simulated system (OASys) with three solenoid-controlled CO2 gas channels. The OASys can adjust the pH of the seawater by bubbling CO2 gas into seawaters via feedback systems. The OASys is very simple in structure with an integrated design and is new-user friendly with the instruction. Moreover, the OASys can monitor and record real-time pH values and can maintain pH levels within 0.02 pH unit. In a 15-d experiment, the OASys was applied to simulate OA in which the expected target pH values were 8.00, 7.80 and 7.60 to study the calcifying response of Galaxea fascicularis. The results showed daily mean seawater pH values held at pH 8.00±0.01, 7.80±0.01 and 7.61±0.01 over 15 d. Correspondingly, the coral calcification of G. fascicularis gradually decreased with reduced pH.
2018 pdf
125 Dr Guangcheng Chen Third Institute of Oceanography, Ministry of Natural Resources, CHINA Yaya Ihya Ulumuddin, M.Si Research Center for Oceanography RIANTA Pratiwi, ERNAWATI Widyastuti, CHEN Guangcheng, CHEN Shunyang
Mangrove ecosystems are sites with high biodiversity of benthic fauna, and fiddler crabs (genus Uca) are common benthic fauna in mangroves. The North Sulawesi in Indonesia has a good condition of mangrove while the information of the fiddler crabs is still limited. Manual samplings were conducted in wet, dry and transient seasons at a mangrove in Kema, North Sulawesi to investigate the species composition, density and distribution pattern of fiddler crabs. A total of 168 individuals, subjected to eight species of genus Uca crabs were collected at the mangrove, with U. triangularis having the highest abundance and U. annulipes having the lowest abundance. The densities of fiddle crabs were 27.56 ind./m2 , 32.89 ind./m2 and 14.22 ind./m2 at the seaward, middle and landward zones, respectively, and the density was higher in dry and wet seasons than in transient season.
2018 pdf
126 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Bebko, Adam O (PhD student under my supervision)
Many primates depend on resources that are dispersed non-uniformly. Primates able to encode the locations of such resources and navigate efficiently between them would gain a selective advantage. However, little is currently known about the cognitive mechanisms that help primates achieve this efficiency in the wild. The presence habitual route networks in some primate species suggests they may navigate using route-based “cognitive maps” for encoding spatial information. However, little is known about factors that influence where such route networks are established. Recent evidence of habitual route networks in wild orangutans makes them ideal candidates for examining factors that affect the establishment and use of such networks. I completed three studies using new methodology to examine ecological and cognitive factors that may affect habitual route networks in wild orangutans living in Kutai National Park, East Kalimantan, Indonesia. Results suggest that orangutan habitual route networks are likely the product of both local ecological considerations and how they cognitively encode and use spatial information. Results imply that the spatial configuration of habitual route networks may primarily be a product of local ecology, whereas how orangutans use them day-to-day may be a product of both local ecology and sophisticated cognitive strategies that may include cognitive maps. These studies demonstrate the utility of using modern mapping software and machine learning technology for applications in primate behavior and ecology.
2018 PhD dissertation (3 individual studies on KNP orangutans)
127 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Maria Voigt, Serge A Wich, Marc Ancrenaz, Erik Meijaard, Nicola Abram, Graham L. Banes, Gail Campbell-Smith, Laru J. d'Arcy, Roberto A. Delgado, Andi Erman, David Gaveau, Benoit Goossens, Stefanit Neinicke, Max Houghton, Simon J. Husson, Ashley Leiman, Karmele Llano Sanchez, Niel Makinuddin, Andrew J. Marshall, Ari Meididit, Jukka Mettinen, Roger Mundry, Musnanda, Nardiyono, Anton Nurcahyo, Kisar Odom, Adventus Panda, Didik Prasteyo, Aldrianto Priatdjati, Purnomo, Andjar Rafiastanto, Anne E Russon, Truly Santika, Jamartin Sihite, Stephanie Spehar, Matthew Struebig, Enrique Sulbaran-Romero, Albertus Tiju, Jessie Wells, Kerrie A. Wilson, Hjalmar S. Kuhl
Unsustainable exploitation of natural resources is increasingly affecting the highly biodiverse tropics [1, 2]. Although rapid developments in remote sensing technology have permitted more precise estimates of land-cover change over large spatial scales [3–5], our knowledge about the effects of these changes on wildlife is much more sparse [6, 7]. Here we use field survey data, predictive density distribution modeling, and remote sensing to investigate the impact of resource use and land-use changes on the density distribution of Bornean orangutans (Pongo pygmaeus). Our models indicate that between 1999 and 2015, half of the orangutan population was affected by logging, deforestation, or industrialized plantations. Although land clearance caused the most dramatic rates of decline, it accounted for only a small proportion of the total loss. A much larger number of orangutans were lost in selectively logged and primary forests, where rates of decline were less precipitous, but where far more orangutans are found. This suggests that further drivers, independent of land-use change, contribute to orangutan loss. This finding is consistent with studies reporting hunting as a major cause in orangutan decline [8–10]. Our predictions of orangutan abundance loss across Borneo suggest that the population decreased by more than 100,000 individuals, corroborating recent estimates of decline [11]. Practical solutions to prevent future orangutan decline can only be realized by addressing its complex causes in a holistic manner across political and societal sectors, such as in land-use planning, resource exploitation, infrastructure development, and education, and by increasing long-term sustainability [12].
2018 referreed journal article
128 Thomas Kopp Göttingen University Prof. Dr. Zulkifli Alamsyah Universitas Jambi Thomas Kopp, Bernhard Brümmer, Zulkifli Alamsyah, Raja Sharah Fatricia
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2017 Journal
129 Mareike Huhn Ruhr-University Bochum Dr. Hawis Madduppa Institut Pertanian Bogor Lukehurst, S.S., Joana Dias, P., Huhn, M., Madduppa, H.H., Lee, S.S.C., Teo, S., Gardner, M.G., McDonald, J.I.
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2017 Journal
130 John Stephen Lansing Nanyang Technological University Prof Herawati Sudoyo Eijkman Institute for Molecular Biology Georgi Hudashev et al
Complex Patterns of Admixture across the Indonesian Archipelago
2017 article
131 John Stephen Lansing Nanyang Technological University Prof Herawati Sudoyo Eijkman Institute for Molecular Biology J Stephen Lansing et al
Languages are transmitted through channels created by kinship systems.
2017 article
132 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK.
Malaria in Asia is a pervasive and diverse problem with about 2 billion people at risk. 1 Although Plasmodium falciparum and Plasmodium vivax account for most clinical attacks of malaria in Asia, all four human plasmodia occur, as do zoonoses involving plasmodia of southeast Asian macaques 2 and several dozen species of anopheline mosquito carry malaria in a wide variety of ecological habitats. 3 Despite the broad scope and complexity of malaria in Asia, it represents a fairly small fraction of research endeavour and public funding in global malaria control efforts. 4 , 5 This partly derives from quantitative WHO morbidity and mortality estimates that put less than 10% of the global burden in this region. 6 But do the large denominators of risk conceal more substantial burdens?
2017 Publication
133 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman J. Kevin Baird.
Malaria poses an exceptionally complex problem for providers of travel medicine services. Perceived high risk of exposure during travel typically prompts prescribing protective antimalarial drugs. Suppressive chemoprophylactic agents have dominated strategy for that practice for over 70 years. This broad class of therapeutic agents kills parasites after they emerge from the liver and attempt development in red blood cells. The dominance of suppressive chemoprophylaxis in travel medicine stems largely from the view of Plasmodium falciparum as the utmost threat to the patient – these drugs are poorly suited to preventing Plasmodium vivax and Plasmodium ovale due to inactivity against the latent liver stages of these species not produced by P. falciparum. Those hypnozoites awaken to cause multiple clinical attacks called relapses in the months following infection. Causal prophylactic agents kill parasites as they attempt development in hepatic cells. The only drug proven effective for causal prophylaxis against P. vivax is primaquine. That drug is not widely recommended for primary prophylaxis for travelers despite preventing both primary attacks of all the plasmodia and relapses of P. vivax. The long-held perception of P. vivax as causing a benign malaria in part explains the dominance of suppressive chemoprophylaxis strategies poorly suited to its prevention. Recent evidence from both travelers and patients hospitalized in endemic areas reveals P. vivax as a pernicious clinical threat capable of progression to severe disease syndromes associated with fatal outcomes. Effective prevention of clinical attacks of vivax malaria following exposure during travel requires primary causal prophylaxis or post-travel presumptive anti-relapse therapy following suppressive prophylaxis.
2017 Publication
134 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Xavier C. Ding , Maria Paz Ade, J. Kevin Baird, Qin Cheng, Jane Cunningham, Mehul Dhorda, Chris Drakeley, Ingrid Felger, Dionicia Gamboa, Matthias Harbers, Socrates Herrera, Naomi Lucchi, Alfredo Mayor, Ivo Mueller, Jetsumon Sattabongkot, Arsène Ratsimbason, Jack Richards, Marcel Tanner, Iveth J. González.
The global prevalence of malaria has decreased over the past fifteen years, but similar gains have not been realized against Plasmodium vivax because this species is less responsive to conventional malaria control interventions aimed principally at P. falciparum. Approximately half of all malaria cases outside of Africa are caused by P. vivax. This species places dormant forms in human liver that cause repeated clinical attacks without involving another mosquito bite. The diagnosis of acute patent P. vivax malaria relies primarily on light microscopy. Specific rapid diagnostic tests exist but typically perform relatively poorly compared to those for P. falciparum. Better diagnostic tests are needed for P. vivax. To guide their development, FIND, in collaboration with P. vivax experts, identified the specific diagnostic needs associated with this species and defined a series of three distinct target product profiles, each aimed at a particular diagnostic application: (i) point-of-care of acutely ill patients for clinical care purposes; (ii) point-of-care asymptomatic and otherwise sub-patent residents for public health purposes, e.g., mass screen and treat campaigns; and (iii) ultra-sensitive not point-of-care diagnosis for epidemiological research/surveillance purposes. This report presents and discusses the rationale for these P. vivax-specific diagnostic target product profiles. These contribute to the rational development of fit-for-purpose diagnostic tests suitable for the clinical management, control and elimination of P. vivax malaria.
2017 Publication
135 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Kamala Thriemer, Benedikt Ley, Albino Bobogare, Lek Dysoley, Mohammad Shafiul Alam, Ayodhia P. Pasaribu, Jetsumon Sattabongkot, Elodie Jambert, Gonzalo J. Domingo, Robert Commons, Sarah Auburn, Jutta Marfurt, Angela Devine, Mohammad M. Aktaruzzaman, Nayeem Sohel, Rinzin Namgay, Tobgyel Drukpa, Surender Nath Sharma, Elvieda Sarawati, Iriani Samad, Minerva Theodora, Simone Nambanya, Sonesay Ounekham, Rose Nanti Binti Mudin, Garib Da Thakur, Leo Sora Makita, Raffy Deray, Sang?Eun Lee, onard Boaz, Manjula N. Danansuriya, Santha D. Mudiyanselage, Nipon Chinanonwait, Suravadee Kitchakarn, Johnny Nausien, Esau Naket, Thang Ngo Duc, Ha Do Manh, Young S. Hong, Qin Cheng, Jack S. Richards, Rita Kusriastuti, Ari Satyagraha, Rintis Noviyanti, Xavier C. Ding, Wasif Ali Khan, Ching Swe Phru, Zhu Guoding, Gao Qi, Akira Kaneko, Olivo Miotto, Wang Nguitragool, Wanlapa Roobsoong, Katherine Battle, Rosalind E. Howes, Arantxa Roca?Feltrer, Stephan Duparc, Ipsita Pal Bhowmick, Enny Kenangalem, Jo?Anne Bibit, Alyssa Barry, David Sintasath, Rabindra Abeyasinghe, Carol H. Sibley, James McCarthy, Lorenz von Seidlein, J. Kevin Baird and Ric N. Price.
The delivery of safe and effective radical cure for Plasmodium vivax is one of the greatest challenges for achieving malaria elimination from the Asia–Pacific by 2030. During the annual meeting of the Asia Pacific Malaria Elimination Network Vivax Working Group in October 2016, a round table discussion was held to discuss the programmatic issues hindering the widespread use of primaquine (PQ) radical cure. Participants included 73 representatives from 16 partner countries and 33 institutional partners and other research institutes. In this meeting report, the key discussion points are presented and grouped into five themes: (i) current barriers for glucose-6-phosphate deficiency (G6PD) testing prior to PQ radical cure, (ii) necessary properties of G6PD tests for wide scale deployment, (iii) the promotion of G6PD testing, (iv) improving adherence to PQ regimens and (v) the challenges for future tafenoquine (TQ) roll out. Robust point of care (PoC) G6PD tests are needed, which are suitable and cost-effective for clinical settings with limited infrastructure. An affordable and competitive test price is needed, accompanied by sustainable funding for the product with appropriate training of healthcare staff, and robust quality control and assurance processes. In the absence of quantitative PoC G6PD tests, G6PD status can be gauged with qualitative diagnostics, however none of the available tests is currently sensitive enough to guide TQ treatment. TQ introduction will require overcoming additional challenges including the management of severely and intermediately G6PD deficient individuals. Robust strategies are needed to ensure that effective treatment practices can be deployed widely, and these should ensure that the caveats are outweighed by the benefits of radical cure for both the patients and the community. Widespread access to quality controlled G6PD testing will be critical.
2017 Publication
136 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK.
“The scientific spirit is of more value than its products, and irrationally held truths may be more harmful than reasoned errors.” Thomas Henry Huxley Rational thought or actions accord with reason and logic, and, certainly in the realm of science, verifiable evidence underpins those attributes. This issue of Travel Medicine and Infectious Diseases offers a meta-analysis of a series of clinical trials of primaquine chemoprophylaxis reported 15–24 years ago [1]. Re-examining this evidence today serves the important purpose of considering the primacy of suppressive chemoprophylaxis strategies in the context of profoundly evolved views on the character of infection by the human malaria parasite Plasmodium vivax. The communities of science, medicine, and public health long regarded this species as intrinsically benign and relatively inconsequential. Strategies for chemoprophylaxis against malaria reflected this view – suppressive drugs dominated practice despite poor suitability for preventing attacks of vivax malaria following travel. Work over the past decade reveals P. vivax as often pernicious and threatening and prompts broad reconsideration of what have been ineffective strategies for the diagnosis, treatment, control, and chemoprophylaxis of this infection of many millions [2].
2017 Publication
137 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman J. Kevin Baird
Malaria remains a serious clinical and public health problem, the object of an ongoing technological and humanitarian struggle to abate the very substantial harm done. The manner by which humanity approached malaria control changed abruptly and profoundly after 1945 with the advent of the insecticide DDT. Malariologists in the first half of the twentieth century conceived precise modifications to natural or man-made environments aimed at making those less hospitable to specific anopheline mosquito vector species. This practical malariology achieved very significant reductions in burdens of morbidity and mortality, but the revolutionary insecticide eliminated the need for its specialized knowledge and diverse practices. By 1970 mosquito resistance to DDT and perceived environmental concerns precipitated the collapse of what had been a vigorous global campaign to eradicate malaria. Humanity did not then revitalize practical malariology but turned to another commodity as the foundation of control strategy, the war-spurred suite of synthetic antimalarial drugs developed in the 1940s and 1950s. When those drugs became lost to parasite resistance in the latter twentieth century, malaria resurged globally. Since 2005, tens of billions of dollars mobilized new commodities to control malaria: point-of-care diagnostics, effective artemisinin-based treatments, and longer-lasting insecticide treated bed nets. The know-how of practical malariology is not part of that ongoing commodities-based strategy. This article examines contemporary malaria control in the broad strokes of a strategy mitigating the consequences of infection contrasted to that of the abandoned practical malariology strategy of prevention. The inherent risks and limitations of over-reliance upon commodities in striving to control malaria may prompt consideration of a strategic posture inclusive of the proven methods of practical malariology.
2017 Publication
138 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Sue O’Connor, Mahirta, Daud Tanudirjo, Marlon Ririmasse, Muhammad Husni, Shimona Kealy, Stuart Hawkins & Alifah
Painted rock art occurs throughout the islands of the Western Pacific and has previously been argued to have motif and design elements in common, indicating that it was created within the context of a shared symbolic system. Here we report five new painted rock-art sites from Kisar Island in eastern Indonesia and investigate the commonalities between this art and the painted art corpus in Timor-Leste, the independent nation that forms the eastern part of the neighbouring island of Timor.We examine the motifs in the Kisar art and suggest that, rather than being Neolithic in age, some of the figurative motifs more likely have a Metal Age origin, which in this region places them within the last 2500 years.
2017 Journal Article
139 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Sue O’Connor, Mahirta, Sofía C. Samper Carro, Stuart Hawkins, Shimona Kealy, Julien Louys & Rachel Wood
Fish-hooks discovered among grave goods associated with an adult female burial at the Tron Bon Lei rockshelter on the island of Alor in Indonesia are the first of their kind from a Pleistocene mortuary context in Southeast Asia. Many of the hooks are of a circular rotating design. Parallels found in various other prehistoric contexts around the globe indicate widespread cultural convergence. The association of the fish-hooks with a human burial, combined with the lack of alternative protein sources on the island, suggest that fishing was an important part of the cosmology of this community. The Tron Bon Lei burial represents the earliest-known example of a culture for whom fishing was clearly an important activity among both the living and the dead.
2017 Journal Article
140 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Julien Louys, Shimona Kealy, Sue O’Connor, Gilbert J. Price, Stuart Hawkins, Ken Aplin, Yan Rizal, Jahdi Zaim, Mahirta, Daud A. Tanudirjo, Wahyu Dwijo Santoso, Ati Rati Hidayah, Agus Trihascaryo, Rachel Wood, Joseph Bevitt, &Tara Clark
Caves have been an important source of vertebrate fossils for much of Southeast Asia, particularly for the Quaternary. Despite this importance, the mechanisms by which vertebrate remains accumulate and preserve in Southeast Asian caves has never been systematically reviewed or examined. Here, we present the results of three years of cave surveys in Indonesia and Timor-Leste, describing cave systems and their attendant vertebrate accumulations in diverse geological, biogeographical, and environmental settings. While each cave system is unique, we find that the accumulation and preservation of vertebrate remains are highly dependent on local geology and environment. These factors notwithstanding, we find the dominant factor responsible for faunal deposition is the presence or absence of biological accumulating agents, a factor directly dictated by biogeographical history. In small, isolated, volcanic islands, the only significant accumulation occurs in archaeological settings, thereby limiting our understanding of the palaeontology of those islands prior to human arrival. In karstic landscapes on both oceanic and continental islands, our understanding of the long-term preservation of vertebrates is still in its infancy. The formation processes of vertebrate-bearing breccias, their taphonomic histories, and the criteria used to determine whether these represent syngenetic or multiple deposits remain critically understudied. The latter in particular has important implications for arguments on how breccia deposits from the region should be analysed and interpreted when reconstructing palaeoenvironments.
2017 Journal Article
141 Matthew Wayne Tocheri Lakehead University Drs I Made Geria, M.Si. Pusat Penelitian Arkeologi Nasional Luong S, Hayes E, Flannery E, Sutikna T, Tocheri MW, Wahyu Saptomo E, Jatmiko, Roberts RG
Source determination of use-related residues on prehistoric stone tools is especially challenging, due to issues related to preservation, contamination and the contribution of residues from multiple sources. To increase confidence in this process, an analytical workflow was developed to include: (1) a sampling strategy that retains spatial information of the recovered residues and enables monitoring of environmental contamination; and (2) a sensitive and selective gas chromatography-tandem mass spectrometry (GC-MS/ MS) procedure to quantify non-volatile low molecular weight lipids on stone artefacts. This workflow was applied to 14 stone artefacts excavated from deposits at Liang Bua, a limestone cave on the Indonesian island of Flores. These artefacts range in age between 14 000 and 1000 years old, and were preliminarily classified as either potentially showing traces of use (n ¼ 7) or not (n ¼ 7) using low magnification microscopy. Residues were sampled by direct solvent extraction off the surface of the artefacts. The aliquots were spiked with internal standards and derivatised. The trimethylsilyl derivatives of 40 saturated fatty acids, sterols, di- and tri-terpenoids and their analogues were quantified using optimised multiple reaction monitoring (MRM) transitions. Six of the potentially used artefacts contained sterols, phytosterols and terpenoids, either individually or in combination, whereas none of these compounds was commonly found on the seven artefacts preliminarily classified as unused. This suggests that these six artefacts may have been used as implements to process resources, and provides scope for further investigation. This workflow can also be adapted for the analysis of other archaeological objects.
2017 Journal Article
142 Matthew Wayne Tocheri Lakehead University Drs I Made Geria, M.Si. Pusat Penelitian Arkeologi Nasional Bordes L, Prinsloo LC, Fullagar R, Sutikna T, Hayes E, Jatmiko, Wahyu Saptomo E, Tocheri MW, Roberts RG
Analyses of ancient micro-residues and usewear preserved on stone artefacts can potentially provide detailed information about how prehistoric humans used the artefacts to processmaterials such as food, pigments and/or adhesives. However, ancientmicroresidues are likely degraded, and there are multiple potential sources of contamination, such as contact with sediments, groundwater, recent handling, storage materials or laboratory conditions, any of which can inhibit reliable identification of micro-residues and other traces of prehistoric use. In this pilot study, five stone tools from the archaeological site of Liang Bua (Flores, Indonesia) were used to evaluate the viability of Raman spectroscopy to identity ancient micro-residues preserved on stone artefact surfaces that are due specifically to prehistoric use as opposed to some form of ancient or modern source of contamination. Inorganic and organic deposits that occur commonly in the cave environment, including iron oxide, manganese oxide and biofilms,were identified in both the sediment and on the artefacts. Protein and saturated fatty acidmicro-residueswere identified on edges of all artefacts and may partially originate from modern handling. Proteins, plant fibres and other micro-residues associated with calciumnitrate are possibly archaeologically significant. Detection of plant fibres and starch grainsmay indicate either modern contamination or prehistoric contact with plant material that was transferred incidentally or during tool manufacture and/or tool use. These results demonstrate the viability of Raman microscopy to screen, at an early stage of archaeological residue analysis, for modern contaminants andmicro-residues related to tool manufacture and/or tool use. This approach serves as a base for planning strategies and analytical protocols for future work that targets larger samples of artefacts, integrates Raman microscopy with GC–MS/LC–MS and includes more comprehensive studies of usewear.
2017 Journal Article
143 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Hutama A., Dahruddin H., Busson F., Sauri S., Keith P., Hadiaty R., Hanner, R., Suryobroto, B., Hubert, N.
Delineating Evolutionary Significant Units for conservation purposes is a crucial step in conservation. Across a distribution range, species frequently display population structure that drives the distribution of genetic diversity. These patterns of genetic structure and diversity result from intricate interactions between biogeographic history and demographic dynamics. Prior biogeographic knowledge, however, is scarcely available, a trend particularly pronounced in the tropics where the taxonomic impediment is hampering biogeographic studies and conservation efforts. DNA barcoding has been initially proposed to foster taxonomic studies through the development of an automated molecular system of species identification. While its utility for species identification is increasingly acknowledged, its usefulness for fast and large-scale delineation of ESU remains to be explored. If proved to be useful for that purpose, DNA barcoding may also open new perspectives in conservation by quickly providing preliminary information about population conservation status. The present study aims at assessing the utility of DNA barcoding for the delineation of ESUs among the most common freshwater fish species of Java and Bali through the comparison of population genetic structures and diversification patterns across multiple species. Substantial levels of cryptic diversity are discovered among the three widely distributed freshwater fish species analyzed with a total of 21 evolutionary independent mitochondrial lineages (BINs) observed in Barbodes binotatus, Channa gachua and Glyptothorax platypogon. The maximum genetic distance for each coalescent tree ranges from 6.78 to 7.76 K2P genetic distances for C. gachua and G. platypogon, respectively. Diversification and population genetic analyses support a scenario of allopatric differentiation. The analysis of the BINs spatial distribution indicates concordant distribution patterns among the three species that allow identifying 18 ESUs. Implications for the conservation genetics of these species are discussed at the light of the history of the region.
2017 article
144 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Keith, P., Lord, C., DarHuddin, H., Limmon, G., Sukmono, T., Hadiaty, R., Hubert, N.
The species of Schismatogobius from Indonesia are reviewed and compared to the known species described from the area. Eight species are recognized including four new species. These are described using genetic and morphomeristic approaches. The species differ by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters including the number of pectoral fin rays, the pattern of the ventral surface of the head in males and/or females, the pectoral fin colour pattern, the jaw length/head length ratio or the jaw length of male and/or female.
2017 article
145 SLEMBROUCK Jacques, Louis, Daniel Insitut de Recherche pour le développement (IRD) Jojo Subagja Research Institute for Freshwater Aquaculture and Fisheries Extension Joel Aubin, Myriam Callier, Helene Rey-Valette, Syndhia Mathe, Aurelie Wilfart, Marc Legendre, Jacques Slembrouck, Domenico Caruso, Eduardo Chia, Gerard Masson, Jean Paul Blancheton, Ediwarman, Joni Haryadi, Tri Heru Prihadi, Jorge de Matos Casaca, Sergio T.J. Tamassia, Aurelien Tocqueville and Pascal Fontaine.
Ecological intensification is a new concept in agriculture that addresses the double challenge of maintaining a level of production sufficient to support needs of human populations and respecting the environment in order to conserve the natural world and human quality of life. This article adapts this concept to fish farming using agroecological principles and the ecosystem services framework. The method was developed from the study of published literature and applications at four study sites chosen for their differences in production intensity: polyculture ponds in France, integrated pig and pond polyculture in Brazil, the culture of striped catfish in Indonesia and a recirculating salmon aquaculture system in France. The study of stakeholders’ perceptions of ecosystem services combined with environmental assessment through Life Cycle Assessment and Emergy accounting allowed development of an assessment tool that was used as a basis for co-building evolution scenarios. From this experience, ecological intensification of aquaculture was defined as the use of ecological processes and functions to increase productivity, strengthen ecosystem services and decrease disservices. It is based on aquaecosystem and biodiversity management and the use of local and traditional knowledge. Expected consequences for farming systems consist of greater autonomy, efficiency and better integration into their surrounding territories. Ecological intensification requires territorial governance and helps improve it from a sustainable development perspective
2017 scientific article
146 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Iannicello, Sarah (Master's student under my supervision)
This study examined the positional behaviour of female Pongo pygmaeus morio individuals in Kutai National Park, East Kalimantan, Indonesia during the 2015-2016 El Niño cycle. Several positional behaviour studies have been conducted on the Sumatran orangutan (P. abelii), yet only one had been conducted on P. p morio; this study was conducted by Cant in 1982, during a similarly strong El Niño cycle, and also only sampled female individuals (1987a). As such, this study provided an opportunity to verify the behavioural profile of P. p. morio as found by Cant during a similar environmental year, as well as verify the interspecific comparisons drawn from his sole study 35 years ago. This study verified some of the previous interspecific findings – mainly that P. p. morio employs an elevated use of ‘ipsilateral suspend’. However, some divergences from previous findings were found – mainly that ‘brachiation and forelimb swing’ and ‘sway’ occurred at higher frequencies than previously found in P. p. morio. Lower levels of ‘vertical climb’ and ‘descent’ were also found in P. p. morio here than found in the previous P. p. morio study.
2017 Master's thesis (field data collection) with my research team in KNP
147 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Truly Santika, Marc Ancrenaz, Kerrie A. Wilson, Stephanie Spehar, Nicola Abram, Graham L. Banes, Gail Campbell-Smith, Lisa Curran, Laura d’Arcy, Roberto A. Delgado, Andi Erman, Benoit Goossens, Herlina Hartanto, Max Houghton, Simon J. Husson, Hjalmar S. Kühl, Isabelle Lackman, Ashley Leiman, Karmele Llano Sanchez, Niel Makinuddin, Andrew J. Marshall, Ari Meididit, Kerrie Mengersen, Musnanda, Nardiyono, Anton Nurcahyo, Kisar Odom, Adventus Panda, Didik Prasetyo, Purnomo, Andjar Rafiastanto, Slamet Raharjo, Dessy Ratnasari, Anne E. Russon, Adi H. Santana, Eddy Santoso, Iman Sapari, Jamartin Sihite, Ahmat Suyoko, Albertus Tjiu, Sri Suci Utami-Atmoko, Carel P. van Schaik, Maria Voigt, Jessie Wells, Serge A. Wich, Erik P. Willems, Erik Meijaard
For many threatened species the rate and drivers of population decline are difficult to assess accurately: species’ surveys are typically restricted to small geographic areas, are conducted over short time periods, and employ a wide range of survey protocols. We addressed methodological challenges for assessing change in the abundance of an endangered species. We applied novel methods for integrating field and interview survey data for the critically endangered Bornean orangutan (Pongo pygmaeus), allowing a deeper understanding of the species’ persistence through time. Our analysis revealed that Bornean orangutan populations have declined at a rate of 25% over the last 10 years. Survival rates of the species are lowest in areas with intermediate rainfall, where complex interrelations between soil fertility, agricultural productivity, and human settlement patterns influence persistence. These areas also have highest threats from human-wildlife conflict. Survival rates are further positively associated with forest extent, but are lower in areas where surrounding forest has been recently converted to industrial agriculture. Our study highlights the urgency of determining specific management interventions needed in different locations to counter the trend of decline and its associated drivers.
2017 peer-reviewed journal article
148 Adam Robert BRUMM Griffith University Priyatno Hadi Sulistyarto Pusat Penelitian Arkeologi Nasional (ARKENAS) Thomas Sutikna, Matthew W. Tocheri, Michael J. Morwood‡, E. Wahyu Saptomo, Jatmiko, Rokus Due Awe, Sri Wasisto, Kira E. Westaway, Maxime Aubert, Bo Li, Jian-xin Zhao, Michael Storey, Brent V. Alloway, Mike W. Morley, Hanneke J. M. Meijer, Gerrit D. van den Bergh, Rainer Grün, Anthony Dosseto, Adam Brumm, William L. Jungers & Richard G. Roberts
Homo floresiensis, a primitive hominin species discovered in Late Pleistocene sediments at Liang Bua (Flores, Indonesia)1,2,3, has generated wide interest and scientific debate. A major reason this taxon is controversial is because the H. floresiensis-bearing deposits, which include associated stone artefacts2,3,4 and remains of other extinct endemic fauna5,6, were dated to between about 95 and 12 thousand calendar years (kyr) ago2,3,7. These ages suggested that H. floresiensis survived until long after modern humans reached Australia by ~50?kyr ago8,9,10. Here we report new stratigraphic and chronological evidence from Liang Bua that does not support the ages inferred previously for the H. floresiensis holotype (LB1), ~18 thousand calibrated radiocarbon years before present (kyr cal. BP), or the time of last appearance of this species (about 17 or 13–11?kyr?cal. BP)1,2,3,7,11. Instead, the skeletal remains of H. floresiensis and the deposits containing them are dated to between about 100 and 60?kyr ago, whereas stone artefacts attributable to this species range from about 190 to 50 kyr in age. Whether H. floresiensis survived after 50 kyr ago—potentially encountering modern humans on Flores or other hominins dispersing through southeast Asia, such as Denisovans12,13—is an open question.
2016 Journal Nature
149 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Satyagraha AW, Sadhewa A, Elvira R, Feiandika D, Antonjaya U, Oyong D, Elyazar I, Subekti D, Domingo G, Harahap AR, Baird JK.
Background Patients infected by Plasmodium vivax or Plasmodium ovale suffer repeated clinical attacks without primaquine therapy against latent stages in liver. Primaquine causes seriously threatening acute hemolytic anemia in patients having inherited glucose-6-phosphate dehydrogenase (G6PD) deficiency. Access to safe primaquine therapy hinges upon the ability to confirm G6PD normal status. CareStart G6PD, a qualitative G6PD rapid diagnostic test (G6PD RDT) intended for use at point-of-care in impoverished rural settings where most malaria patients live, was evaluated. Methodology/Principal Findings This device and the standard qualitative fluorescent spot test (FST) were each compared against the quantitative spectrophotometric assay for G6PD activity as the diagnostic gold standard. The assessment occurred at meso-endemic Panenggo Ede in western Sumba Island in eastern Indonesia, where 610 residents provided venous blood. The G6PD RDT and FST qualitative assessments were performed in the field, whereas the quantitative assay was performed in a research laboratory at Jakarta. The median G6PD activity ?5 U/gHb was 9.7 U/gHb and was considered 100% of normal activity. The prevalence of G6PD deficiency by quantitative assessment (<5 U/gHb) was 7.2%. Applying 30% of normal G6PD activity as the cut-off for qualitative testing, the sensitivity, specificity, positive predictive value, and negative predictive value for G6PD RDT versus FST among males were as follows: 100%, 98.7%, 89%, and 100% versus 91.7%, 92%, 55%, and 99%; P = 0.49, 0.001, 0.004, and 0.24, respectively. These values among females were: 83%, 92.7%, 17%, and 99.7% versus 100%, 92%, 18%, and 100%; P = 1.0, 0.89, 1.0 and 1.0, respectively. Conclusions/Significance The overall performance of G6PD RDT, especially 100% negative predictive value, demonstrates suitable safety for G6PD screening prior to administering hemolytic drugs like primaquine and many others. Relatively poor diagnostic performance among females due to mosaic G6PD phenotype is an inherent limitation of any current practical screening methodology.
2016 Publication
150 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Boni F, White NJ, Baird JK.
Summary Points Combination therapy is an effective way to delay or prevent drug-resistance evolution in malaria, but we do not take full advantage of its potential. Deploying multiple first-line combination therapies allows us to challenge parasite populations with many different types of drugs, and thus delay and slow down drug-resistance evolution more than with a single combination therapy. We must take a preemptive, not reactive, policy approach to drug-resistance management in malaria.
2016 Publication
151 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK, Price RN.
Non-falciparum malaria refers to malaria infection due to Plasmodium species other than P. falciparum; these include P. vivax, P. ovale, P. malariae, and P. knowlesi Worldwide, the greatest mortality due to malaria is associated with P. falciparum infection. Infections caused by P. knowlesi and P. vivax are also associated with significant risk of morbidity and mortality [2-4]; patients with uncomplicated malaria due to these species are vulnerable to deterioration even after initiation of treatment, and P. vivax infection may be complicated by recurrent infection and associated anemia [5]. Rarely, severe illness and death occur in the setting of infection with P. malariae or P. ovale The epidemiology, clinical manifestations, diagnosis, and treatment of nonfalciparum malaria in nonpregnant adults and children will be reviewed here. Issues related to non-falciparum malaria in pregnant women are discussed separately, as are issues related to P. falciparum malaria. (See "Prevention and treatment of malaria in pregnant women", section on 'Non-falciparum malaria' and "Treatment of uncomplicated falciparum malaria in nonpregnant adults and children" and "Treatment of severe malaria".)
2016 Publication
152 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK.
Malaria in the Asia-Pacific region has been targeted for elimination by the year 2030. This article asks the question, “by what means?” in the context of proven technical strategies and tools against key challenges imposed by the distinct character of the Asia-Pacific malaria problem. The misperception of malaria in the Asia-Pacific region as a less serious but otherwise essentially similar problem to African malaria lulls us into rote application of the same tools and strategies. Those now mitigating the harm done by malaria in Africa will not suffice to eliminate malaria in the Asia-Pacific region – these tasks and the problems are fundamentally distinct. This article describes the singular characteristics of Asia-Pacific malaria and the bearing of those upon the technical strategy of malaria elimination. Most of the tools needed for that endeavour do not yet exist and spirited calls for elimination within the next 14 years may discourage the patience and investments needed to conceive, optimise and validate them.
2016 Publication
153 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Surjadjaja C, Asik S, Baird JK.
Endemic malaria occurs across much of the vast Indonesian archipelago. All five species of Plasmodium known to naturally infect humans occur here, along with 20 species of Anopheles mosquitoes confirmed as carriers of malaria. Two species of plasmodia cause the overwhelming majority and virtually equal shares of malaria infections in Indonesia: Plasmodium falciparum and Plasmodium vivax. The challenge posed by P. vivax is especially steep in Indonesia because chloroquine-resistant strains predominate, along with Chesson-like strains that relapse quickly and multiple times at short intervals in almost all patients. Indonesia's hugely diverse human population carries many variants of glucose-6-phosphate dehydrogenase (G6PD) deficiency, most of them exhibiting severely impaired enzyme activity. Therefore, the patients most likely to benefit from primaquine therapy by preventing aggressive relapse, may also be most likely to suffer harm without G6PD deficiency screening. Indonesia faces the challenge of controlling and eventually eliminating malaria across > 13,500 islands stretching > 5,000 km and an enormous diversity of ecological, ethnographic, and socioeconomic settings, and extensive human migrations. This article describes the occurrence of P. vivax in Indonesia and the obstacles faced in eliminating its transmission.
2016 Publication
154 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK, Valecha N, Duparc S, White NJ, Price RN.
The diagnosis and treatment of Plasmodium vivax malaria differs from that of Plasmodium falciparum malaria in fundamentally important ways. This article reviews the guiding principles, practices, and evidence underpinning the diagnosis and treatment of P. vivax malaria.
2016 Publication
155 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Howes RE, Battle KE, Mendis KM, Smith DL, Cibulskis RE, Baird JK, Hay SI.
Plasmodium vivax is the most widespread human malaria, putting 2.5 billion people at risk of infection. Its unique biological and epidemiological characteristics pose challenges to control strategies that have been principally targeted against Plasmodium falciparum. Unlike P. falciparum, P. vivax infections have typically low blood-stage parasitemia with gametocytes emerging before illness manifests, and dormant liver stages causing relapses. These traits affect both its geographic distribution and transmission patterns. Asymptomatic infections, high-risk groups, and resulting case burdens are described in this review. Despite relatively low prevalence measurements and parasitemia levels, along with high proportions of asymptomatic cases, this parasite is not benign. Plasmodium vivax can be associated with severe and even fatal illness. Spreading resistance to chloroquine against the acute attack, and the operational inadequacy of primaquine against the multiple attacks of relapse, exacerbates the risk of poor outcomes among the tens of millions suffering from infection each year. Without strategies accounting for these P. vivax-specific characteristics, progress toward elimination of endemic malaria transmission will be substantially impeded.
2016 Publication
156 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Bassat Q, Velarde M, Mueller I, Lin J, Leslie T, Wongsrichanalai C, Baird JK.
There is inadequate understanding of the biology, pathology, transmission, and control of Plasmodium vivax, the geographically most widespread cause of human malaria. During the last decades, study of this species was neglected, in part due to the erroneous belief that it is intrinsically benign. In addition, many technical challenges in culturing the parasite also hampered understanding its fundamental biology and molecular and cellular responses to chemotherapeutics. Research on vivax malaria needs to be substantially expanded over the next decade to accelerate its elimination and eradication. This article summarizes key knowledge gaps identified by researchers, national malaria control programs, and other stakeholders assembled by the World Health Organization to develop strategies for controlling and eliminating vivax malaria. The priorities presented in this article emerged in these technical discussions, and were adopted by expert consensus of the authors. All involved understood the priority placed upon pragmatism in this research agenda, that is, focus upon tools delivering better prevention, diagnosis, treatment, and surveillance of P. vivax.
2016 Publication
157 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK.
Discussions beginning in 2012 ultimately led to a landmark document from the World Health Organization (WHO) titled, Control and Elimination of Plasmodium vivax: A Technical Brief, published in July 2015. That body of work represents multiple expert consultations coordinated by the WHO Global Malaria Program, along with technical consensus gathering from national malaria control programs via the WHO regional offices around the globe. That document thus represents thoroughly vetted state-of-the-art recommendations for dealing specifically with P. vivax, the first assembly of such by the WHO. This supplement to the journal was commissioned by the WHO and compiles the very substantial body of evidence and analysis informing those recommendations. This introductory narrative to the supplement provides the historical and technological context of global strategy for combatting P. vivax and reducing the burdens of morbidity and mortality it imposes.
2016 Publication
158 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Sofía C. Samper Carro, Sue O'Connor, Julien Louys, Stuart Hawkins, Mahirta
The islands of Wallacea are remarkable on a world scale as settlement occurred by at least 43,000 cal BP and must have involved the use of watercraft. The majority of the islands are depauperate in terrestrial fauna and human subsistence must have focused on the marine environment. Although few islands have been archaeologically explored, some such as Timor have yielded abundant remains of pelagic and reef fishes, as well as the earliest evidence of fishhook manufacture, demonstrating that modern humans in this region were well equipped to undertake complex exploitation of the marine environment. However, a holistic understanding of human subsistence strategies on these islands from initial colonisation in the late Pleistocene through to the Recent remains elusive. Here, we present survey and excavation data from the site of Tron Bon Lei on the small island of Alor in Nusa Tenggara Timur, Indonesia. This study focuses on the terminal Pleistocene – early Holocene human fishing behaviour in the region, and specifically the zooarchaeological sequence from Tron Bon Lei dated to this period. The Holocene preference for reef fish relative to pelagic fish, observed in mid-to late Holocene occupation levels in East Timor, occurred earlier in Tron Bon Lei, suggesting a shift from the larger abundance of carnivore taxa observed in the late Pleistocene deposits. Comparisons with other archaeological deposits in Wallacea indicates that fishing was an important subsistence activity in Nusa Tenggara Timur, unlike more northern Wallacean islands where shellfish make up almost all zooarchaeological records. Tron Bon Lei confirms that the faunally limited nature of Alor spans the Holocene, and we find no evidence that terrestrial fauna made up a significant component of the subsistence activities undertaken at this site.
2016 Journal Article
159 Susan Lillian O'Connor Australian National University Mahirta Universitas Gadjah Mada Christian Reepmeyer, Sue O'Connor, Mahirta, Tim Maloney, Shimona Kealy
This study analysed over 1000 obsidian stone artefacts excavated from two adjoining shelters at Tron Bon Lei on Alor Island Indonesia using portable XRF. The study showed an unambiguous separation of three different source locations (Groups 1, 2 and 3). Two sources (Group 2 and 3a, b, c) dominate the assemblage numerically. Group 1 and 2 indicate use of a single volcanic formation with a strong match between Group 1 artefacts and artefacts from sites in Timor Leste. Obsidian occurs in the earliest occupation layer in the Alor sites but does not include Group 1 artefacts which occur only after approx. 12,000 cal BP. Currently the geographical location of the Group 1 outcrop is unknown, however, based on the late appearance of the Group 1 artefacts in the Alor sequence it is likely that the location is not on Alor, but rather on another island of the Sunda chain. The dating of Group 1 artefacts in widely spaced sites on the never geographically connected islands of Timor and Alor indicates that maritime interaction between islands began by at least the terminal Pleistocene. The distribution of the obsidian in Tron Bon Lei shelter Pit B shows that there were periods of more intense interaction punctuated by periods when interaction declined or ceased.
2016 Journal Article
160 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Dahruddin, H., Hutama, A., Busson, F., Sauri, Hanner, R., Keith, P., Hadiaty, R., Hubert, N.
Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies.
2016 article
161 Anne Eleanor Russon York University Tri Wijaya Balai Taman Nasional Kutai Utami-Atmoko, S. Traylor-Holzer, K. Rifqi, M.A., Siregar, P.G., Achmad, B., Priadjati, A., Husson, S., Wich, S., Hadisiswoyo, P., Saputra, F., Campbell-Smith, G., Kuncoro, P., Russon, A., Voigt, M., Santika, T., Nowak, M., Singleton, I., Sapari, I., Meididit, A., Chandradewi, D.S., Ripoll Capilla, B., Ermayanti, Lees, C.M.
In 2016, after more than 10 years since the last PHVA, the Directorate General of Natural Resources and Ecosystem Conservation, in partnership with Forum Orangutan Indonesia (FORINA), the IUCN SSC Primate Specialist Working groups were formed around each of the four taxa. Orangutans are currently distributed across a large geographic area. Within this area there is considerable variation in orangutan numbers, densities, degree of population fragmentation, and nature and severity of human-mediated risks. To explore species viability across this varied landscape it was first necessary to divide it into smaller population units, using the maps and information available. Each working group began by breaking down the geographic range of their taxon into a number of discrete, area-based population units, using a predefined hierarchy of population units (regional, meta-population, habitat blocks, sub-blocks). Once units were agreed upon, population size estimates and trends for each unit were discussed and estimated. For many sites, groups were able to use Geographic Information System (GIS) models to estimate current population sizes, site carrying capacity, and future rates of habitat loss. For other populations these estimates were based on survey data and the results of within-group discussion. Details of these estimations are provided in this report.
2016 Specialist (IUCN) species conservation assessment
162 Shimizu Kazufumi Center for Infectious Diseases, Kobe University Graduate School of Medicine Maria Inge Lusida Universities Airlangga Lumbago penyakit Troops Shimizu K, Wulandari L, Poetranto ED, Setyoningrum RA, Yudhawati R, Sholikhah A, Nastri AM, Poetranto AL, Candra AY, Puruhito EF, Takahara Y, Yamagishi Y, Yamaoka M, Hotta H, Ustumi T, Lusida MI, Soetjipto, Shimizu YK, Soegiarto G, Mori Y.
BACKGROUND: In Indonesia, highly pathogenic avian influenza A(H5N1) virus has become endemic in poultry and has caused sporadic deadly infections in human. Since 2012, we have conducted fixed-point surveillance of avian influenza viruses at a live-poultry market in East Java, Indonesia. In this study, we examined the seroprevalence of avian influenza A(H5N1) virus infection among market workers. METHODS: ?Sera were collected from 101 workers in early 2014 and examined for antibody activity against avian A(H5N1) Eurasian lineage virus by a hemagglutination-inhibition (HI) assay. RESULTS: ?By the HI assay, 84% of the sera tested positive for antibody activity against the avian virus. Further analysis revealed that the average HI titer in 2014 was 2.9-fold higher than in 2012 and that seroconversion occurred in 44% of paired sera (11 of 25) between 2012 and 2014. A medical history survey was performed in 2016; responses to questionnaires indicated that none of workers had had severe acute respiratory illness during 2013. CONCLUSIONS: ?This study provides evidence of a high prevalence of avian A(H5N1) virus infection in 2013 among workers at a live-poultry market. However, because no instances of hospitalizations were reported, we can conclude the virus did not manifest any clinical symptoms in workers.
2016 Article
163 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Utami-Atmoko, S. Traylor-Holzer, K. Rifqi, M.A., Siregar, P.G., Achmad, B., Priadjati, A., Husson, S., Wich, S., Hadisiswoyo, P., Saputra, F., Campbell-Smith, G., Kuncoro, P., Russon, A., Voigt, M., Santika, T., Nowak, M., Singleton, I., Sapari, I., Meididit, A., Chandradewi, D.S., Ripoll Capilla, B., Ermayanti, Lees, C.M.
In 2016, after more than 10 years since the last orangutan PHVA, the Directorate General of Natural Resources and Ecosystem Conservation, in partnership with Forum Orangutan Indonesia (FORINA), the IUCN SSC Primate Specialist Group and the Orangutan Foundation-United Kingdom (OF-UK), conducted the third PHVA for orangutans. The IUCN SSC Conservation Breeding Specialist Group provided neutral facilitation and population viability analyses, and the workshop was made possible by a grant from Arcus Foundation. The resulting assessment, which is documented in this report, will provide important input for the revision of the national conservation strategy and action plan, the planning period for which ends in 2017.
2016 Professional conference report
164 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Hubert, N., Kadarusman, Wibowo, A., Busson, F., Caruso, D., Sulandari, S., Nafiqoh, N., Pouyaud, L., Rüber, L., Avarre, J.-C., Herder, F., Hanner, R., Keith, P., Hadiaty, R.
With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
2015 article
165 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Keith,, P., Busson, F., Sauri, S., Hubert, N., Hadiaty, R.
A new species of Stiphodon, an amphidromous goby, is described from streams of three islands in Indonesia, Java, Bali and Lombok. It differs from other species of the genus by a combination of characters including 14-15 pectoral rays, a second dorsal fin with nine segmented rays, fewer scales in predorsal, transverse forward and transverse back series, and a diagnostic golden and black pattern in male.
2015 article
166 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Keith, P., Lord, C., Busson, F., Sauri, S., Hubert, N., Hadiaty, R.
A new species of Sicyopterus, freshwater goby, is described from Sumatra and Java, Indonesia. It differs from other species belonging to the genus by a combination of characters including two lateral clefts on the crenulated upper lip, a second dorsal fin with one spine and 10 segmented rays, second and third rays of the first dorsal fin filamentous, more lateral, predorsal and transverse back scales, and a reddish caudal fin in male with a slight blue line on the upper and lower parts.
2015 article
167 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Hutama, A., Darhuddin, H., Frederic Busson, F., Sauri, S., Hanner, R.,Keith, P., Hadiaty, R., Hubert, N.
Background: Java and Bali islands belong to the Sundaland biodiversity hotspot, the most speciose hotspot of the Indonesian archipelago. The eastern part of Java and Bali islands are located at the margin of Sundaland, next to the Wallace line that marks the range distribution boundaries of most of the primary freshwater fishes from a continental origin (e.g., Cypriniformes, Siluriformes). Widespread species of primary freshwater fishes are few in Java and Bali but potentially informative on the timing and geography of the colonization of this peripheral area of Sundaland. The biogeogra-phy of the Sundaland ichthyodiversity is still poorly understood, and the spatio-temporal dynamic of colonization of the peripheral islands of Sundaland is still unknown. Results: Three species with widespread distribution have been sampled across nearly 30 sites throughout Java and Bali islands. A total of 100 specimens of Channa gachua (Perciformes, Channidae), 123 specimens of Glyptothorax platypogon (Siluriformes, Sisoridae), and 121 specimens of Puntius binotatus (Cypriniformes, Cyprinidae) were sequenced and analyzed. For each species, mean intra-specific distances were high ranging from 1.31% in P. binotatus to 3.18% in C. gachua, and seven to eight allopatric lineages were observed with maximum pairwise distance ranging from 5.3% to 6.1% among lineages. Patterns of distribution of this cryptic diversity are congruent among species, suggesting that a common history is at the origin of the distribution of the genetic diversity for the three species analyzed. Molecular calibrations suggest that the initial diversification of those mitochondrial lineages happened during the early Pleistocene. Significance: The present study highlights that the evolutionary history of the Javanese and Balinese freshwater fishes has been influenced by the fragmentation of the landscapes during the Pleis-tocene, likely as a result of the volcanic activity in the area during the Pleistocene that promoted the rise of volcanic arches. Background: The nucleotide sequences of the mitochondrial cyto-chrome oxidase subunit 1 (COI) gene were analyzed for the identification of six skate species and one sub species. Probe-based fluorescence melting curve analysis (PNA FMCA) is a powerful tool for mutation detection based on the melting temperature generated by thermal denaturation of a probe-target hybrid. The PNA probes have several advantageous features such as easy probe design and modification, without the risk of false negatives. In this study we have developed a molecular method based on real-time polymerase chain reaction (real-time PCR) technology for the rapid identification of six Skate species. Results: Six PNA probes were designed to identify Raja pulchra sub2, Okamejei kenojei, Zearaja chilensis, Dipturus argentinensis, Raja binoculata, and Zearaja maugeana. Six PNA probes in two reactions were designed to cover the COI gene region. PNA FMCA with color multiplexing was used to identify the skate species. The PNA FMCA system can distinguish target species from others in an efficient and high-throughput manner and can be applied to species identification of skates. The dual-labeled PNA probes offered the advantage of improved flexibility in probe design, which would provide various applications for geno-typing a wide range of spectra. Subterranean pool party: determining the trophic links between subterranean invertebrates in a groundwater system in Western Australia Background: The Yilgarn Region of Western Australia comprises hundreds of physically isolated calcretes, which resembles a subterranean archipelago, and contains a rich diversity of subterranean invertebrates. Each calcrete has a unique combination of subterranean aquatic species (stygofauna), including diving beetles (Dytiscidae), crustaceans (Isopoda, Amphipoda, Copepoda, Ostracoda, and Bathynellacea) and worms (Oli-gochaeta). This project focuses on one calcrete (Sturt Meadows) within the Yilgarn Region and aims to use metabarcoding analyses to identify the food web of its subterranean ecosystem. The project also aims to determine the primary source of energy for the ecosystem and discover if the energy comes from external sources of carbon or whether it is produced directly via chemoautotrophic bacteria. Results: A reference database of the stygofauna, surface flora, and microbes has been developed using multiple genes including COI, 16S, and 12S (for stygofauna), and rbcLa (for flora). Using laser dissection microscopy, the stomach contents from individuals are being removed and analysed using metabarcoding to determine prey items of species within the calcrete. Using this information for multiple individuals and combining the data with stable isotope analysis, insight can be provided into trophic interactions within the ecosystem. Significance: This project will provide critical information for the diversity of species present in a calcrete aquifer ecosystem, and identify the structure of the food web and the source of energy that is driving the system. Many of the calcretes are utilised for mineral processing or provide groundwater for mines, pastoral (agricultural), and domestic use. There is therefore an urgent need to develop a scientific base to improve environmental assessment and monitoring of the impacts of groundwater/ calcrete extraction on the fauna over the long term.
2015 article
168 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Darhuddin, H., Hutama, A., Busson, F., Sauri,S., Keith, P., Hanner, R., Hadiaty, R., Hubert, N.
To date, 224 fish species have been reported from the Javanese and Balinese rivers, among which 38 are endemic to these islands. While some emblematic islands of the Indonesian archipelago have garnered considerable attention in the past due to the occurrence of charismatic species (e.g., Borneo, Sumatra, Sulawesi), the Javanese and Balinese biodiversity has been poorly explored so far, and freshwater fishes are no exception to this. Java Island, with a human population that has grown to more than 180 000 000 people sharing 128 297 km2, is the most densely populated island of the Indonesian archipelago, and its biodiversity is currently the most endangered of the country. The present survey conducted between 2012 and 2014 aims to re-assess the Javanese and Balinese ichthyodiversity based on systematic and standardized molecular screening. Results: Fishes were mainly collected using electrofishing, cast nets, and seine nets between November 2012 and December 2014 at nearly 70 sites distributed across rivers, lakes, ponds, estuaries, and fish markets. More than 1000 specimens belonging to more than 160 nominal species have been sequenced and, together with collection data, submitted to BOLD. Based on DNA barcode data, the number of mitochondrial lineages diverging by more than 2% is higher than the number of nominal species, highlighting cryptic or undescribed diversity. In addition, three new species of amphidromous gobies (e.g., Sicyopus, Lentipes, Stiphodon) are described and each is characterized by private drial lineages. Significance: The present study provides the first DNA barcode reference library for the Javanese and Balinese ichthyofauna and also represents the first large-scale DNA barcoding survey in Indonesia. Given the accuracy of the identification based on DNA barcodes, this preliminary library is expected to benefit a large community of users from academic to managing authorities in Indonesia
2015 article
169 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Yuan L, Wang Y, Parker DM, Gupta B, Yang Z, Liu H, Fan Q, Cao Y, Xiao Y, Lee MC, Zhou G, Yan G, Baird JK, Cui L
Chloroquine-primaquine (CQ-PQ) continues to be the frontline therapy for radical cure of Plasmodium vivax malaria. Emergence of CQ-resistant (CQR) P. vivax parasites requires a shift to artemisinin combination therapies (ACTs), which imposes a significant financial, logistical, and safety burden. Monitoring the therapeutic efficacy of CQ is thus important. Here, we evaluated the therapeutic efficacy of CQ-PQ for P. vivax malaria in northeast Myanmar. We recruited 587 patients with P. vivax monoinfection attending local malaria clinics during 2012 to 2013. These patients received three daily doses of CQ at a total dose of 24 mg of base/kg of body weight and an 8-day PQ treatment (0.375 mg/kg/day) commencing at the same time as the first CQ dose. Of the 401 patients who finished the 28-day follow-up, the cumulative incidence of recurrent parasitemia was 5.20% (95% confidence interval [CI], 3.04% to 7.36%). Among 361 (61%) patients finishing a 42-day follow-up, the cumulative incidence of recurrent blood-stage infection reached 7.98% (95% CI, 5.20% to 10.76%). The cumulative risk of gametocyte carriage at days 28 and 42 was 2.21% (95% CI, 0.78% to 3.64%) and 3.93% (95% CI, 1.94% to 5.92%), respectively. Interestingly, for all 15 patients with recurrent gametocytemia, this was associated with concurrent asexual stages. Genotyping of recurrent parasites at the merozoite surface protein 3? gene locus from 12 patients with recurrent parasitemia within 28 days revealed that 10 of these were the same genotype as at day 0, suggesting recrudescence or relapse. Similar studies in 70 patients in the same area in 2007 showed no recurrent parasitemias within 28 days. The sensitivity to chloroquine of P. vivax in northeastern Myanmar may be deteriorating.
2015 Publication
170 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Baird JK, Dewi M, Subekti D, Elyazar I, Satyagraha AW
Tens of millions of patients diagnosed with vivax malaria cannot safely receive primaquine therapy against repeated attacks caused by activation of dormant liver stages called hypnozoites. Most of these patients lack access to screening for glucose-6-phosphate dehydrogenase (G6PD) deficiency, a highly prevalent disorder causing serious acute hemolytic anemia with primaquine therapy. We optimized CuCl inhibition of G6PD in normal red blood cells (RBCs) to assess G6PD diagnostic technologies suited to point of care in the impoverished rural tropics. The most widely applied technology for G6PD screening-the fluorescent spot test (FST)-is impractical in that setting. We evaluated a new point-of-care G6PD screening kit (CareStart G6PD, CSG) against FST using graded CuCl treatments to simulate variable hemizygous states, and varying proportions of CuCl-treated RBC suspensions to simulate variable heterozygous states of G6PD deficiency. In experiments double-blinded to CuCl treatment, technicians reading FST and CSG test (n = 269) classified results as positive or negative for deficiency. At G6PD activity ?40% of normal (n = 112), CSG test was not inferior to FST in detecting G6PD deficiency (P = 0.003), with 96% vs 90% (P = 0.19) sensitivity and 75% and 87% (P = 0.01) specificity, respectively. The CSG test costs less, requires no specialized equipment, laboratory skills, or cold chain for successful application, and performs as well as the FST standard of care for G6PD screening. Such a device may vastly expand access to primaquine therapy and aid in mitigating the very substantial burden of morbidity and mortality imposed by the hypnozoite reservoir of vivax malaria.
2015 Publication
171 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Satyagraha AW, Sadhewa A, Baramuli V, Elvira R, Ridenour C, Elyazar I, Coutrier FN, Harahap AR, Baird JK
Safe treatment of Plasmodium vivax requires diagnosis of both the infection and status of erythrocytic glucose-6-phosphate dehydrogenase (G6PD) activity because hypnozoitocidal therapy against relapse requires primaquine, which causes a mild to severe acute hemolytic anemia in G6PD deficient patients. Many national malaria control programs recommend primaquine therapy without G6PD screening but with monitoring due to a broad lack of G6PD deficiency screening capacity. The degree of risk in doing so hinges upon the level of residual G6PD activity among the variants present in any given area. We conducted studies on Sumba Island in eastern Indonesia in order to assess the potential threat posed by primaquine therapy without G6PD screening. We sampled 2,033 residents of three separate districts in western Sumba for quantitative G6PD activity and 104 (5.1%) were phenotypically deficient (<4.6U/gHb; median normal 10U/gHb). The villages were in two distinct ecosystems, coastal and inland. A positive correlation occurred between the prevalence of malaria and G6PD deficiency: 5.9% coastal versus inland 0.2% for malaria (P<0.001), and 6.7% and 3.1% for G6PD deficiency (P<0.001) at coastal and inland sites, respectively. The dominant genotypes of G6PD deficiency were Vanua Lava, Viangchan, and Chatham, accounting for 98.5% of the 70 samples genotyped. Subjects expressing the dominant genotypes all had less than 10% of normal enzyme activities and were thus considered severe variants. Blind administration of anti-relapse primaquine therapy at Sumba would likely impose risk of serious harm.
2015 Publication
172 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Battle KE, Cameron E, Guerra CA, Golding N, Duda KA, Howes RE, Elyazar IR, Price RN, Baird JK, Reiner RC Jr, Smith DL, Gething PW, Hay SI
Background Though essential to the development and evaluation of national malaria control programmes, precise enumeration of the clinical illness burden of malaria in endemic countries remains challenging where local surveillance systems are incomplete. Strategies to infer annual incidence rates from parasite prevalence survey compilations have proven effective in the specific case of Plasmodium falciparum, but have yet to be developed for Plasmodium vivax. Moreover, defining the relationship between P. vivax prevalence and clinical incidence may also allow levels of endemicity to be inferred for areas where the information balance is reversed, that is, incident case numbers are more widely gathered than parasite surveys; both applications ultimately facilitating cartographic estimates of P. vivax transmission intensity and its ensuring disease burden. Methods A search for active case detection surveys was conducted and the recorded incidence values were matched to local, contemporary parasite rate measures and classified to geographic zones of differing relapse phenotypes. A hierarchical Bayesian model was fitted to these data to quantify the relationship between prevalence and incidence while accounting for variation among relapse zones. Results The model, fitted with 176 concurrently measured P. vivax incidence and prevalence records, was a linear regression of the logarithm of incidence against the logarithm of age-standardized prevalence. Specific relationships for the six relapse zones where data were available were drawn, as well as a pooled overall relationship. The slope of the curves varied among relapse zones; zones with short predicted time to relapse had steeper slopes than those observed to contain long-latency relapse phenotypes. Conclusions The fitted relationships, along with appropriate uncertainty metrics, allow for estimates of clinical incidence of known confidence to be made from wherever P. vivax prevalence data are available. This is a prerequisite for cartographic-based inferences about the global burden of morbidity due to P. vivax, which will be used to inform control efforts.
2015 Publication
173 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Ley B, Luter N, Espino FE, Devine A, Kalonky M, Lobell Y, Thriemer K, Baird JK, Poirot E, Conan N, Kheong CC, Dysoley L, Khan WA, Diaon Berboso AG, Bancone G, Hwang J, Kumar R, Price RN, von Seidlein L, Domingo GJ.
The only currently available drug that effectively removes malaria hypnozoites from the human host is primaquine. The use of 8-aminoquinolines is hampered by haemolytic side effects in glucose-6-phosphate dehydrogenase (G6PD) deficient individuals. Recently a number of qualitative and a quantitative rapid diagnostic test (RDT) format have been developed that provide an alternative to the current standard G6PD activity assays. The WHO has recently recommended routine testing of G6PD status prior to primaquine radical cure whenever possible. A workshop was held in the Philippines in early 2015 to discuss key challenges and knowledge gaps that hinder the introduction of routine G6PD testing. Two point-of-care (PoC) test formats for the measurement of G6PD activity are currently available: qualitative tests comparable to malaria RDT as well as biosensors that provide a quantitative reading. Qualitative G6PD PoC tests provide a binomial test result, are easy to use and some products are comparable in price to the widely used fluorescent spot test. Qualitative test results can accurately classify hemizygous males, heterozygous females, but may misclassify females with intermediate G6PD activity. Biosensors provide a more complex quantitative readout and are better suited to identify heterozygous females. While associated with higher costs per sample tested biosensors have the potential for broader use in other scenarios where knowledge of G6PD activity is relevant as well. The introduction of routine G6PD testing is associated with additional costs on top of routine treatment that will vary by setting and will need to be assessed prior to test introduction. Reliable G6PD PoC tests have the potential to play an essential role in future malaria elimination programmes, however require an improved understanding on how to best integrate routine G6PD testing into different health settings.
2015 Publication
174 John Kevin Baird Oxford University Professor Amin Soebandrio Lembaga Biologi Molekuler Eijkman Battle KE, Guerra CA, Golding N, Duda KA, Cameron E, Howes RE, Elyazar IR, Baird JK, Reiner RC Jr, Gething PW, Smith DL, Hay SI.
Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique incidence records were collected for the database: 1,187 for P. falciparum and 493 for P. vivax. These data were gathered to model the relationship between clinical incidence and prevalence of infection and can be used for a variety of modelling exercises including the assessment of change in disease burden in relation to age and control interventions. The subset of data that have been used for such modelling exercises are described and identified.
2015 Publication
175 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Russon A, Kuncoro P, Ferisa A
This study aimed to develop a long-term picture of orangutan (Pongo pygmaeus morio) behavioral adjustments to damaged masting forest around Mentoko, Kutai National Park, Indonesia. Mentoko is regenerating from two severe burnings and is one of few areas where orangutans were well-studied before and early after damage. We studied orangutans’ feeding ecology, diet, and activity budgets 12–15 years after the second burning then compared our findings with earlier pre- and post-damage ones to assess the changes and factors involved. By our study, we predicted (1) improved feeding ecology compared to early in regeneration, (2) behavior diverging from the normal foraging strategy and (3) behavior shifting toward pre-damage patterns with improving feeding ecology. Data were behavioral observations on 42 orangutans (422 full day follows, 3,522 hr) and tree plot measures of feeding ecology. Findings were consistent with the first and third predictions but not the second: (1) feeding ecology had improved (plant food abundance was near per-damage levels, but species composition had changed); (2) foraging strategies showed no divergence from normal (fallback-preferred food switches in diet and activity budget adjustments were both normal, notably travel did not reduce), (3) diet and activity budgets had reverted to near pre-damage values by our study. Differently than post-damage studies on other orangutans but consistent with those on other primates, our comparisons showed behavioral adjustments were flexible, multiple vs. single, and influenced by multiple factors. Factors likely involved at Mentoko include type and spatial configuration of damage, duration of regeneration, and P. p. morio’s recognized resilience. Findings have value for orangutan and nature conservation in showing that recovery to near-normal levels from severe habitat damage is possible within ca 15 years and in adding to understanding of the factors and processes that contribute to recovery.
2015 Scientific peer-reviwed journal article
176 Adam Robert BRUMM Griffith University Priyatno Hadi Sulistyarto Pusat Penelitian Arkeologi Nasional (ARKENAS) Aubert*, M., A. Brumm*, M. Ramli, T. Sutikna, E.W. Saptomo, B. Hakim, M.J. Morwood, G.D. van den Bergh, L. Kinsley & A. Dosseto
Archaeologists have long been puzzled by the appearance in Europe ?40–35 thousand years (kyr) ago of a rich corpus of sophisticated artworks, including parietal art (that is, paintings, drawings and engravings on immobile rock surfaces)1,2 and portable art (for example, carved figurines)3,4, and the absence or scarcity of equivalent, well-dated evidence elsewhere, especially along early human migration routes in South Asia and the Far East, including Wallacea and Australia5,6,7,8, where modern humans (Homo sapiens) were established by 50 kyr ago9,10. Here, using uranium-series dating of coralloid speleothems directly associated with 12 human hand stencils and two figurative animal depictions from seven cave sites in the Maros karsts of Sulawesi, we show that rock art traditions on this Indonesian island are at least compatible in age with the oldest European art11. The earliest dated image from Maros, with a minimum age of 39.9 kyr, is now the oldest known hand stencil in the world. In addition, a painting of a babirusa (‘pig-deer’) made at least 35.4 kyr ago is among the earliest dated figurative depictions worldwide, if not the earliest one. Among the implications, it can now be demonstrated that humans were producing rock art by ?40 kyr ago at opposite ends of the Pleistocene Eurasian world.
2014 Journal Nature
177 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Keith, P., Hadiaty, R., Hubert, N., Busson, F., Lord, C.
Three new species of Lentipes (L. argenteus, L. ikeae and L. mekonggaensis), freshwater gobies, are described from streams of Sumatra, Java and Sulawesi (Indonesia). They differ from other species of the genus by a combination of characters including an urogenital papilla lacking lateral lobes and retractable into a sheathlike groove, the number of pectoral fin rays, the number of scales, tricuspid teeth in the upper jaw, and a specific body colour in males.
2014 article
178 Frédéric Olivier BUSSON Institut pour la Recherche et le Développement Daisy WOWOR RCB/LIPI Keith, P., Hadiaty, R., Busson, F., Hubert, N.
Sicyopus rubicundus n. sp., a sicydiine goby, is described from specimens collected in streams of Java and Bali (Indonesia). It differs from other species of this amphidromous genus by a combination of characters includinga first dorsal fin with five spines in both sexes, a second dorsal fin with one spine and nine segmented rays, an anal fin with one spine and nine segmented rays, and a distinctive body colour in male.
2014 article
179 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai Balai TN Kutai & Indianapolis Zoo
Latar Belakang. Taman Nasional Kutai merupakan salah satu kawasan konservasi yang terletak di dataran rendah. Karena posisinya tersebut Taman Nasional ini kaya akan berbagai jenis kehati yang telah diakui sejak tahun 1930-an.Selama 30 tahun terakhir, taman nasional ini telah berulang kali mengalami kerusakan hebat akibat dari kebakaran hutan besar (1982-83,97-98), pembangunan di kawasan sekitarnya, dan perburuan liar, serta perambahan hutan. Namun demikian, kawasan ini tetap merupakan satu-satunya kawasan lindung dengan hutan Dipterokarp campuran terluas terakhir yang ada di Kalimantan Timur. Kawasan lindung ini juga menjadi kawasan perlindungan berbagai spesies yang terancam punah, salah satu populasi terancam punah yang menjadi prioritas diantaranya adalah orangutan Borneo Timur (Pongo pygmaeus morio) yang hanya dapat di temukan di KalimantanTimur (estimasi tahun 2004: 600 individu). Survei terbaru menemukan populasi orangutan (perkiraan 1.000-2.000: Sulaiman, 2010) dan satwa langka lain yang terus berkembang, yang diperkirakan telah punah (misalnya, lutung Hose, Presbytis hosei). Penelitian mengenai pemulihan hutan dari kerusakan yang dilakukan di kawasan hutan lain di Borneo bagian Timur lainnya menunjukkan besarnya kapasitas keanekaragaman hayati dan kapasitas penyimpanan, serta penyerapan karbon (misalnya, Berry et al 2010; Edwards et al 2010). Hasil penelitian????penelitian tersebut menunjukkan bahwa kawasan TNK memiliki nilai konservasi tinggi dan harus diselamatkan. Disisi lain, dibutuhkan lebih banyak masukan ilmiah tentang keanekaragaman hayati dan kondisi hutan untuk meningkatkan pengelolaan habitat dan kegiatan reforestasi kawasan hutan, mengingat nilai konservasi kawasan TNK sebagai hutan yang sedang pulih masih belum dipelajari. Hal ini pada gilirannya dapat memberikan kontribusi untuk konservasi orangutan. Dimana, saat ini masukan ilmiah tersebut sangat dibutuhkan untuk memperbaiki pendekatan yang dilakukan terhadap permasalahan pengelolaan dan konservasi orangutan yang kompleks dan multidisiplin, termasuk untuk mendorong upaya dan langkah pencegahan, serta evaluasi berbasis bukti ilmiah. Tujuan. Tujuan utama dari workshop ini adalah berbagi pengalaman antara pengetahuan lokal dan ilmiah dalam menghadapi permasalahan konservasi yang terjadi di dalam dan sekitar TN Kutai dan pendekatan????pendekatan untuk mengurangi permasalahan tersebut. Lokakarya ini akan difokuskan pada dua isu penting yaitu pemulihan habitat/restorasi serta konflik manusia dan satwa liar, khususnya orangutan. Waktu dan Tempat. Lokakarya ini rencananya akan dilaksanakan pada tanggal 10 – 13 Juni 2013 bertempat di Hotel Royal Victoria, Sangatta, Kabupaten Kutai Timur, Indonesia.
2013 Prosiding Lokakarya
180 Kosuke Mizuno (1). Center for Southeast Asian Studies, Kyoto University; (2). Research Institute for Humanity and Nature (RIHN) (1). Dr. Haris Gunawan (2) Prof. Dr. Almasdi Syahza SE. MP., (1) Badan Restrasi Gambut (BRG), (2) Lembaga Penelitian dan Pengabdian kepada Masyarakat (LPPM) Universitas Riau Shuichi Kasai, Mizuno Kosuke, Fujita Motoko, ed.
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2012 Edited Book
181 Kosuke Mizuno (1). Center for Southeast Asian Studies, Kyoto University; (2). Research Institute for Humanity and Nature (RIHN) (1). Dr. Haris Gunawan (2) Prof. Dr. Almasdi Syahza SE. MP., (1) Badan Restrasi Gambut (BRG), (2) Lembaga Penelitian dan Pengabdian kepada Masyarakat (LPPM) Universitas Riau Mizuno, Kosuke, Haris Gunawan
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2010 Book Chapter
182 Anne Eleanor Russon York University, Toronto, Canada Tri Wijaya S.Hut Balai Taman Nasional Kutai A Russon, P Kuncoro, A Ferisa, D Prayunita, E Purwanto
This document includes all articles our research team submitted to the Balai TN Kutai office for publication in their quarterly journal, Pasak Bumi. BTNK solicited all of these articles, although the topics addressed were chosen by our field research team based on the findings or other information we had available
2010 Author's text of articles submitted
183 Daiki Ayuha University of Tokyo Dr. Fadjar I. Thufail Indonesian Institute of Sciences Research center for Regional Resources Daiki Ayuha
Jakarta. Isu kebijakan kesehatan di Indonesia menarik untuk dikaji terlebih dengan adanya program pelayanan kesehatan seperti BPJS Kesehatan. Program BPJS Kesehatan ditawarkan oleh pemerintah untuk masyarakat Indonesia untuk memastikan bahwa kesehatan masyarakat terjamin. Paparan mengenai kebijakan kesehatan di Indonesia ini disampaikan oleh Daiki Ayuha, M.A. kandidat PhD dari University of Tokyo, Jepang dalam Forum Kajian Wilayah (FKW), P2SDR-LIPI pada 15 Mei 2019 dengan mengusung tema “Governing Health Risk in Current Indonesia: Pendekatan Antropologi ke Aspek Sosial dan Budaya dari Kebijakan Kesehatan”. Diskusi ini mengundang tamu eksternal seperti perwakilan dari Badan Penelitian dan Pengembangan Kementerian Kesehatan. Penelitian menggunakan pendekatan kualitatif dan deskriptif. Salah satu metode pengumpulan data yang digunakan oleh penyaji adalah dengan mengumpulkan informasi dari berbagai pihak baik penyedia dan pengguna pelayanan kesehatan BPJS Kesehatan. Sebelum melihat lebih dalam terkait kebijakan kesehatan di Indonesia menggunakan pendekatan antropologi ke aspek sosial dan budaya, penyaji juga menjelaskan kebijakan kesehatan di Jepang, negara asalnya. Dalam paparan ini, isu trust menjadi topik yang dominan dalam melihat kebijakan kesehatan di Indonesia terutama ketika membahas efektivitas dan efisiensi dari BPJS Kesehatan. Trust pasien atau masyarakat pemilik BPJS Kesehatan menjadi bahan diskusi yang paling banyak diperbincangkan dalam forum. Kegiatan ini merupakan bagian dari sharing knowledge antara peneliti dari negara lain yang telah menyelesaikan penelitian di Indonesia dengan para peneliti di Indonesia. Daiki Ayuha telah melakukan penelitian di Indonesia selama tiga tahun dengan menggandeng Dr. Fadjar I. Thufail (P2SDR) sebagai Indonesian Counterpart (Mitra Kerja Indonesia).
0000 Oral Presentation
184 Daiki Ayuha University of Tokyo Dr. Fadjar I. Thufail Indonesian Institute of Sciences Research center for Regional Resources Daiki Ayuha
Sejak Reformasi pada tahun sekitar 2000, Indonesia berjuang untuk membangunkan Sistem Jaminan Sosial Nasional supaya dapat mengolah risiko kesehatan dan komisikan di antara masyarakat, supaya melindungi kehidupan masyarakat dari ketidakpastian. Sedangkan, di dunia akademisi, sering disebutkan dikotomi risiko vs. ketidakpastian (uncertainty), baik di bidang ekonomi seperti diperlihatkan oleh F. Knight, maupun di bidang Antropologi. Presentasi ini mencoba mengatasi dikotomi tersebut dengan memperlihatkan analisa proses pembuatan SJSN Indonesia, supaya bisa memperlihatkan bahwa dalam manajemen risio tetap dihadapi ketidakpastian oleh stakeholder-stakeholder dalam jalan pembentukan SJSN. Dengan case-study Indonesia yang tersebut, presentasi ini mencoba menggambarkan risiko sebagai salah satu ketidakpastian, untuk mengatasi dikotomi risiko vs. ketidakpastian (Presentasi ini dilakukan dalam bahasa jepang karena konferensi domestik Jepang).
0000 Oral Presentation