jmzTab: A Java interface to the mzTab data standard

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab‐delimited file that can capture identification and quantification results coming from MS‐based proteomics and metabolomics approaches. We here present an open‐source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table‐based sections in the mzTab files. In this article, as two example implementations, we also describe two stand‐alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com .     

Mammals of Borneo – small size on a large island

Aim Island mammals have featured prominently in models of the evolution of body size. Most of these models examine size evolution across a wide range of islands in order to test which island characteristics influence evolutionary pathways. Here, we examine the mammalian fauna of a single island, Borneo, where previous work has detected that some mammal species have evolved a relatively small size. We test whether Borneo is characterized by smaller mammals than adjacent areas, and examine possible causes for the different trajectories of size evolution between different Bornean species. Location Sundaland: Borneo, Sumatra, Java and the Malay/Thai Peninsula. Methods We compared the mammalian body size frequency distributions in the four areas to examine whether the large mammal fauna of Borneo is more depauperate than elsewhere. We measured specimens belonging to 54 mammal species that are shared between Borneo and any of the other areas in order to determine whether there is an intraspecific tendency for Bornean mammals to evolve small body size. Using data on diet, body size and geographical ranges we examine factors that are thought to influence body size. Results Borneo has fewer large mammals than the other areas, but this is not statistically significant. Large Bornean mammals are significantly smaller than their conspecifics in the other regions, while there are no differences between the body sizes of mammals on Sumatra, Java and the Malay/Thai Peninsula. The finding that large mammals show the greatest size difference between Borneo and elsewhere contrasts with some models of size evolution on islands of different areas. Diet does not correlate with the degree of size reduction. Sunda region endemics show a weaker tendency to be small on Borneo than do widespread species. Main conclusions We suggest that soil quality may drive size evolution by affecting primary productivity. On Borneo, where soils are generally poor in nutrients, this may both limit biomass and cause mammals to be reduced in body size. We hypothesize that widespread species respond to low resource abundance by reducing in size, while endemic elements of the fauna have had longer to adjust to local conditions by altering their behaviour, physiology and/or ecology, and are thus similar in size across the region.     

Three new species of fleas belonging to the genus Macrostylophora from the three‐striped ground squirrel,Lariscus insignis,in Java

Three new species of fleas belonging to the genus Macrostylophora (Siphonaptera, Ceratophyllidae) are described from the three‐striped ground squirrel, Lariscus insignis, from Tjibodas, West Java (Jawa Barat), Indonesia at an elevation of 1500 m. Macrostylophora larisci sp. n. is described from three male specimens, Macrostylophora debilitata sp. n. is described from one male and Macrostylophora wilsoni sp. n. is described from one female. Non‐genital morphological characters of the female specimen, including ctenidial spine shapes and lengths, show that it is not the corresponding female for either M. larisci sp. n. or M. debilitata sp. n. It is unusual for three different species of congeneric fleas to parasitize the same host species in the same geographical location. These three new species represent the first known records of Macrostylophora from Java and they could be enzootic vectors between rodents of flea‐borne zoonotic pathogens such as Rickettsia typhi and Yersinia pestis, both of which are established on Java. A list is provided of the 43 known species and 12 subspecies of Macrostylophora together with their known geographical distributions and hosts. A map depicting the distributions of known Indonesian (and Bornean) species of Macrostylophora is also included.     

Missing links: Eugène Dubois and the origins of paleoanthropology

Examining the origins of various scientific fields may help to identify particular individuals whose thought, work, and discoveries have had a disproportionately large influence. Such individuals seem to serve as catalysts for a wider set of intellectual reactions, which then give rise to an entire field of study. In this paper, we propose explicit criteria for recognizing the founders of new fields. We contend that Eugène Dubois, best known as the man who found the “missing link” between apes and humans, should be recognized as one of the founding fathers of paleoanthropology.     

A bitter epidemic: The impact of the 1918 influenza on sugar production in Java

Research about the economic consequences of past epidemics has mostly focused on the experience of industrialized countries, thus providing little knowledge about the effects of health shocks on developing economies. We fill this gap by studying the impact of the 1918 influenza in Java, with a new dataset on aggregate food production and district-level figures on (i) sugar production, the major export commodity and the predominant source of labour demand; (ii) agricultural and plantation wages, and (iii) annual crude death rates. The mortality impact of the influenza on Java was high, as crude mortality rates doubled in 1918 relative to the preceding years, but its economic impact was mixed. Aggregate food production did not decline, but sugar output did fall in 1919. Indeed, our regional panel data analysis does not establish a direct relationship between regional epidemic mortality variation and sugar output decline. Instead, we hypothesize that economic activity was rediverted towards food production in order to avoid famine that could have resulted from the combined effects of disrupted shipping at the end of the First World War, climatic conditions and the public health crisis. This is supported by both qualitative observations and quantitative evidence suggesting that those regions that were highly suitable for rice production saw a larger reduction in sugar production, and that in regions that had more flexibility in land tenure arrangements experienced substantially greater reductions in sugar output.