Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

An overview of explosive volcanism on Mars

International audienceDecades of space exploration reveal that Mars has been reshaped by volcanism throughout its history. The range of observed volcanic landforms shows that effusive and explosive eruptions have occurred, albeit unevenly in time and space. Evidence for explosive volcanism—characterized as eruptions in which magma is disrupted by the expansion of gases dissolved in magma or by an interaction of magma with external volatiles—is less common than evidence for effusive activity. Nonetheless, some indications of explosive volcanism have been identified at various sites. For instance, old, rimless depressions, termed paterae, on the summits of broad topographic rises with very gentle flanks located mainly around the Hellas impact basin. Also various fields of kilometre-sized cones interpreted as scoria cones, tuff rings and tuff cones, and extensive clusters of sub-kilometre-sized pitted cones in the northern lowlands proposed to be rootless cones, are thought to be constructional features caused by accumulation of volcanic fragments. Finally layered deposits widely spread in equatorial areas (e.g., the Medusae Fossae Formation), and layered stacks of ash and a putative volcanic bomb observed by rover, point to a protracted history of explosive volcanism on Mars. Yet some of these interpretations remain the matter of scientific debate. The discovery of explosive volcanism on Mars has triggered an interest in theoretical aspects of such volcanism under gravitational and atmospheric conditions different from those on Earth. These studies indicate that explosive eruptions on Mars would behave differently from those on Earth. This is because a lower atmospheric pressure and gravity can affect all stages of the eruption including the ascent of magma, the process of degassing and magma fragmentation, the transport and deposition of the pyroclasts, and also in some cases the formation of explosive volcanoes themselves. On Earth, explosive eruptions are responsible for the formation of most volcanoes on land, and so a relatively sparse occurrence of explosive volcanism on Mars is surprising, especially considering the martian environmental conditions as well as wide occurrence of external volatiles on Mars. This is because the lower atmospheric pressure than on Earth ought to favour magma fragmentation and hence the formation of pyroclasts and associated explosive volcanic edifices, even if lower volumes of dissolved gases were present in martian magma than is usual on Earth. The relative dearth of explosive activity on Mars therefore represents a gap in our understanding of martian volcanism, suggesting that there may be considerable compositional differences between Mars and Earth or that evidence of explosive volcanism on Mars manifests differently to on Earth. Understanding these differences is important, as explosive volcanism provides insight about the planet’s composition and plays a crucial role in the evolution of a planet’s atmosphere by the release of magmatic gases, which have the ability to affect geological and even biological processes operating on the surface of the planet. In this paper, we present an overview of explosive volcanism on Mars—from both observational and theoretical perspectives—and discuss the implications of explosive eruptions for the evolution of the Red Planet

High salt diet‐induced proximal tubular phenotypic changes and sodium‐glucose cotransporter‐2 expression are coordinated by cold shock Y‐box binding protein‐1

International audienceHigh salt diet (HSD) is a hallmark of blood pressure elevations, weight gain and diabetes onset in the metabolic syndrome. In kidney, compensatory mechanisms are activated to balance salt turnover and maintain homeostasis. Data on the long-term effects of HSD with respect to tubular cell functions and kidney architecture that exclude confounding indirect blood pressure effects are scarce. Additionally we focus on cold shock Y-box binding protein-1 as a tubular cell protective factor. A HSD model (4% NaCl in chow; 1% NaCl in water) was compared to normal salt diet (NSD, standard chow) over 16 months using wild type mice and an inducible conditional whole body knockout for cold shock Y-box binding protein-1 (BL6J/N, Ybx1). HSD induced no difference in blood pressure over 16 months, comparing NSD/HSD and Ybx1 wild type/knockout. Nevertheless, marked phenotypic changes were detected. Glucosuria and subnephrotic albuminuria ensued in wild type animals under HSD, which subsided in Ybx1-deficient animals. At the same time megalin receptors were upregulated. The sodium-glucose cotransporter-2 (SGLT2) was completely downregulated in wild type HSD animals that developed glucosuria. In Ybx1 knockouts, expression of AQP1 and SGLT2 was maintained under HSD; proximal tubular widening and glomerular tubularization developed. Concurrently, amino aciduria of neutral and hydrophobic amino acids was seen. In vitro translation confirmed that YB-1 translationally represses Sglt2 transcripts. Our data reveal profound effects of HSD primarily within glomeruli and proximal tubular segments. YB-1 is regulated by HSD and orchestrates HSD-dependent changes; notably, sets reabsorption thresholds for amino acids, proteins and glucose

A multicenter study benchmarks software tools for label-free proteome quantification

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics