Introducing the vectorial Kappa: An index to quantify congruence between vectorial mosaics

This paper introduces the vectorial Kappa (κ_v) that one can utilize to assess congruence between two vectorial mosaics. The vectorial Kappa extends for vectorial mosaics the approach of the so-called Cohen's Kappa index, commonly used to compare raster mosaics. By comparing both approaches, we aim to demonstrate how efficient and convenient a vector-based congruence may be when working on vectorial mosaics.     

The recolonization of the Krakatau islands by termites (Isoptera), and their biogeographical origins

The termite assemblages of the Krakatau islands and five sites in Sumatra and Java were investigated, using a standardized transect sampling method. Five species were found on the Krakatau islands that have not been collected there before. The total number of termites recorded on the islands since the 1883 volcanic eruption is now twelve species, all of which are wood feeders. No termites nesting in or feeding on the soil were found on the Krakataus, suggesting that rafting in wood is the primary method by which the termites recolonized the islands.     

Étude taphonomique d’assemblages fauniques de sites à Homo erectus du dôme de Sangiran (Pléistocène moyen,Java central,Indonésie)

Since the sixties, the National Indonesian Center for Archaeological Research, in collaboration with the Gajah Mada University, organizes field excavations on open-air sites in the Sangiran dome, one of the most famous places of palaeoanthropological discoveries in Southeast Asia. That project led to the discovery of Homo erectus more or less fragmentary fossils, and to the collection of numerous mammal fossils in open-air localities such as Tanjung, Sendang Busik, Ngrejeng Plupuh, Grogol Plupuh and Bukuran. Most of the bone assemblages from these sites come from the volcanic-sedimentary Kabuh layers (Early Middle Pleistocene) deposited in a fluvial context. The herbivores dominate the assemblages. The best-represented species are large bovids like Bubalus palaeokerabau or Bibos palaesondaicus and smaller cervids like Axis lydekkeri. The carnivore are very rare, only a Pachycrocuta brevirostris in Bukuran. The taphonomical study of the collections, involving several common and also modern methods, is among the first carried out on Javanese sites. The high degree of fragmentation is attested by the dominance of splinters among the fossils. In most sites, teeth and member extremities (autopodial) prevail. Conservation and fragmentation of fossil bones is not the same at all sites. Water action, either chemical or mechanical, is predominant, regarding the origin and the modification of the assemblages. The climato-edaphic traces like oxides and concretions are well represented on the bone surface. Different methods were applied to study transportation and to document the sites contexts in the frame of the ancient riverine paleogeography. Carnivores are almost absent in the material and traces of their action are rare, only in Bukuran and Ngrejeng. The tools are rare, only a bola in Tanjung 82 and chalcedony flakes in Tanjung 63–64. Anthropic influence is only obvious at Ngebung 2, a site in the west part of the dome, supported by fossil observation and correlated to the occurrence of lithic artefacts. This site was excavated during the 1990’s by a French-Indonesian team and it is a site of comparison for our study. Several analytical methods could be applied for the first time on Pleistocene faunal assemblages from Java, for example, the study of the fragmentation, that of fissuration and the characterization of the fluviatile transport undergone by the fossils.     

Feeling your way in Java: An essay on society and emotion

This article reconsiders the place of emotion in society. With the example of Java, I argue for an expanded understanding of social sentiments that would recognize a structuring role for emotion beyond the family and the shaping, through emotional practices, of a fluid but crucial level of ‘community’. Using Balinese ethnology as a foil, I contrast the uses of emotion in Java and Bali, drawing, toward the end, upon Bateson's concept of schismogenesis.     

Craniometric Variation within the Pleistocene of Java: The Ngawi 1 Cranium

The recently described cranium from Ngawi, East Java, is an important addition to the human fossil record. Several workers have placed Ngawi 1 into a grouping with the Ngandong and Sambungmacan specimens due to an overall metric and nonmetric similarity to those fossils. Multivariate comparisons of cranial shape have not been performed utilizing Ngawi, however, so it is unknown whether this specimen will fall within the current range of variation in those samples or if it will extend that range. Likewise, the inclusion of the Ngawi skull will allow a new test of the hypothesis that the African and Indonesian specimens currently allocated to Homo erectus exhibit a craniometric pattern that is significantly different from that seen in the Zhoukoudian crania. Mahalanobis distances will be used to examine the levels of variation present in a large sample representing the most complete African, Indonesian, and Chinese specimens of H. erectus. Statistical significance of the distances generated will be calculated using random expectation statistics. The results indicate that Ngawi shares strong shape similarities with the African and Indonesian specimens studied, and exhibits significant differences with the Zhoukoudian fossils. This supports earlier work by a number of scholars that found evidence of a unique craniometric pattern at that Chinese site. In addition, these tests indicate that cranial shape remained relatively invariant on Java for much of the Pleistocene. These findings, in conjunction with evidence for the appearance of unique nonmetric traits in the late-surviving Ngandong crania, suggest that the hominid populations of Java were relatively isolated for extended periods of time.     

Uncertainty and sensitivity analysis of West Java Water Sustainability Index – A case study on Citarum catchment in Indonesia

Water sustainability indices have been recently used to measure the sustainability of water resources within a catchment. Developing a sustainability index involves various steps, some of which have uncertainties associated with them. For the recently developed West Java Water Sustainability Index (WJWSI), three sources of uncertainties were identified, namely uncertainties in the thresholds of non-categorical indicators and sub-indicators, in the weighting schemes, and in the aggregation methods. This paper presents the uncertainty and sensitivity analysis of WJWSI, based on the application of WJWSI to Citarum catchment in West Java, Indonesia. The results of the uncertainty analysis, measured by the coefficient of variation of the thresholds and the sub-indices, indicates that minimum thresholds of Land Use Changes, Coverage, Education, Poverty, Health Impact and Sanitation, and the maximum threshold of Water Quality have higher variation when compared to variation of the other thresholds. The results of the sensitivity analysis, measured by the correlation coefficients between the final index and the thresholds, indicate that changes in the thresholds of WJWSI indicators have not significantly affected the sub-index values of most indicators and sub-indicators. The sensitivity analysis also concluded that either the equal or non-equal weighting scheme can be used for future use of the aggregation of WJWSI indicators and sub-indicators, as changes from equal to non-equal weighting scheme did not significantly affect the final index. However, it was found that the final index values were most sensitive to the aggregation method used (i.e. arithmetic and geometric methods), shown by the significant changes in the final index value when the aggregation method was changed from arithmetic to geometric. The uncertainty and sensitivity analysis presented in this study will not just assist in the efficient use of the WJWSI, but will also help undertake similar analysis for other indices.     

Quaternary rainforest refugia in south-east Asia: using termites (Isoptera) as indicators

In south-east Asia, during Quaternary glaciations, increased seasonality and sea level decreases of ~120 m caused considerable fragmentation of the rainforest. It is believed that most of the region's core was covered with savannah vegetation, and rainforest was confined to a few refugia. We investigated the geographical extent of the savannah vegetation and the positions of the refugia, using a combination of palynonlogical, geological, fossil and termite data. Our results show that during the Last Glacial Maximum, most of Thailand, Peninsula Malaysia, western and southern Borneo, eastern and southern Sumatra, and Java were probably covered by savannah. Rainforest refugia were probably present in northern and eastern Borneo, northern and western Sumatra and the Mentawai islands. We also discuss a possible complete history of the region. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 453–466.     

Oceanography and reefs of recent and Paleozoic tropical epeiric seas

Summary The Java Sea, one of the few modern tropical epeiric seas, is used as an analogue to examine oceanography, stratigraphy, and reefs of Devonian strata in the Appalachian and Michigan Basins. Nearshore patch reefs and offshore “pinnacle” reefs occur in both the Java Sea and the Emsian-Eifelian Onondaga Formation in the Appalachian Basin. Nearshore patch reefs also occur in the Eifelian Formosa Reef Limestone in the Michigan Basin. The Java Sea is characterized by quasi-estuarine circulation, in which runoff and rainfall exceed evaporation. Nutrient and organic matter influx from land and from estuarine upwelling contribute to organic rich facies during transgressions and sea level highstands. Similarly, we propose that high runoff from the Appalachian Mountains and from the Laurentian craton contributed to slightly reduced salinity in the Appalachian basin, including possible density stratification during Middle Devonian highstands. By contrast, the Michigan Basin was characterized by antiestuarine circulation, in which evaporation exceeded combined runoff and rainfall. Contemporaneous Emsian-Eifelian strata in the Michigan Basin are dolomite and dolomitic limestone, rather than cherty and muddy limestone typical of the Appalachian basin. Reef composition generally reflects oceanographic circulation regime within the epicontinental seas we examine. Nearshore reefs of the modern Java Sea and the Onondaga Formation (Appalachian Basin) are dominated by multilobate submassive, dendroid, and phaceloid corals, and virtually no platy corals or tabular stromatoporoids. Multilobate and phaceloid corals are better able to accommodate muddy sedimentation. By contrast, offshore pinnacle reefs of the Java Sea and nearshore reefs of the Formosa Reef Limestone are dominated by platyAcropora (modern) or tabular and laminar stromatoporoids (Devonian). The scarcity of tabular stromatoporoids, and the dominance of phaceloid corals and dendritic branching corals, in the Onondaga Formation (Appalachian Basin) are herein explained by localized high productivity conditions driven by quasi-estuarine circulation, rather than cool water. Quasi-estuarine circulation or localized topographic upwelling leading to highly productive coastal environments may be responsible for other Paleozoic examples of apparent cool-water carbonate deposition within the tropics, including the Ordovician of Eastern Canada.     

The jmzQuantML programming interface and validator for the mzQuantML data standard

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools ( http://code.google.com/p/jmzquantml/ ). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool ( http://code.google.com/p/mzquantml‐validator/ ) for validating mzQuantML files, which is a formal part of the data standard.     

Schistosoma incognitum from Cikurai,West Java,Indonesia

Schistosoma incognitum is reported for the first time from West Java, Indonesia where 84% of ricefield rats, Rattus argentiventer, were infected. Radix auricularia rubiginosa snails were intermediate hosts. The adult stage of the Javanese strain of S. incognitum and lesions in naturally-infected rodents are described. Rattus exulans, Rattus norvegicus and Mus musculus were experimentally infected. Epizootiology is similar to that described in other countries.