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Data from: A new Magneto-Inductive tracking technique to uncover subterranean activity: what do animals do underground?
1. Despite the importance of the subterranean ecotope, knowledge of underground movement and behaviour has been extremely limited. Previous technologies have relied upon techniques with very low spatial or temporal resolution, such as VHF telemetry. Rather incongruously therefore, relatively simple underground activity regimes have often been assumed, with insufficient attention to the ecological importance of burrow use. 2. We test the capability of Magneto-Inductive (MI) tracking, recording underground movement within a European badger sett over a two week period in February. These data allowed us to: quantify subterranean movement; extrapolate the three-dimensional burrow architecture; simultaneously track multiple individuals; and establish the function of specific movement patterns; demonstrating the technique's utility. Contrasting data generated using MI tracking, against the resolution achievable with VHF tracking, we establish how sampling frequency can influence the percecption of movement. 3. Taking 20 locational fixes per minute, MI collars operated for one year before on-board batteries failed, resulting in an average five billion data points per collar deployment. Socio-ecologically we found that rather than foraging continuously throughout the night, badgers returned to the sett an average of 2.2 times, approximately every 3-4 hours. From burrow mapping, badgers tended to use peripheral chambers for ca. 45 minutes on these return visits,These outlying chambers were used less by day, when badgers selected deeper chambers, suggesting each chamber type fulfils a different function. This technology also exposed that badgers exhibited a far greater extent of underground movement than revealed by former technologies, which by comparison captured less than 0.5% of subterranean activity. Importantly, these high-resolution data showed that individuals left, returned to, and moved about the sett independently, with no tendency for synchronous subterranean activity. 4. In overview, magneto-inductive tracking proved relatively simple and cost effective to deploy, it provided very detailed and accurate subterranean fixes, and was robust enough for long-term field deployment. Furthermore, the capabilities of MI are highly transferable, enabling a better understanding of underground activity and the ecological importance of subterranean burrows for the conservation and management of a wide range of species.
Data from: Negative association between parental care and sibling cooperation in earwigs: a new perspective on the early evolution of family life?
The evolution of family life requires net fitness benefits for offspring, which are commonly assumed to mainly derive from parental care. However, an additional source of benefits for offspring is often overlooked: cooperative interactions among juvenile siblings. In this study, we examined how sibling cooperation and parental care could jointly contribute to the early evolution of family life. Specifically, we tested whether the level of food transferred among siblings (sibling cooperation) in the European earwig Forficula auricularia (1) depends on the level of maternal food provisioning (parental care), and (2) is translated into offspring survival, as well as female investment into future reproduction. We show that higher levels of sibling food transfer were associated with lower levels of maternal food provisioning, possibly reflecting a compensatory relationship between sibling cooperation and maternal care. Furthermore, the level of sibling food transfer did not influence offspring survival, but was associated with negative effects on the production of the second and terminal clutch by the tending mothers. These findings indicate that sibling cooperation could mitigate the detrimental effects on offspring survival that result from being tended by low quality mothers. More generally, they are in line with the hypothesis that sibling cooperation is an ancestral behavior that can be retained to compensate for insufficient levels of parental investment.
Data from: A new phylogeny of Stegosauria (Dinosauria, Ornithischia)
The stegosaurs are some of the most easily recognizable dinosaurs, but are surprisingly rare as fossils. Consequently much remains unknown about their palaeobiology, and every new stegosaurian find contributes to our understanding of the evolution of the clade. Since the last attempt to examine the evolutionary relationships of Stegosauria, new specimens have come to light, including the most complete individual of Stegosaurus ever found, new taxa have been described and, perhaps most importantly, new methods for analysis of cladistic datasets have been produced. In the light of these new data and technological advances, the phylogenetic relationships of the stegosaurs and basal armoured dinosaurs are investigated. The inclusion of continuous data results in much better resolution than was previously obtained, and the resulting single most parsimonious tree supports re-erection of the genera Miragaia and Hesperosaurus, which had previously been synonymized with Dacentrurus and Stegosaurus respectively. The recently described genus Alcovasaurus is resolved as a basal thyreophoran, but this is most likely a consequence of a very high degree of missing data and the questionable ontogenetic stage of the specimen. Examination of the effects of continuous data on the analysis suggest that while it contains a phylogenetic signal congruent with that of discrete data and provides better resolution than discrete data alone, it can affect topologies in unpredictable ways, particularly in areas of the tree where there are large amounts of missing data. The phylogeny presented here will form the basis for future work on the palaeobiology of the plated dinosaurs.
Data from: New insights for Drosophila GAGA factor in larvae
GAGA factor plays important roles during Drosophila embryogenesis and its maternal contribution is essential for early development. Here, the role of GAGA factor was studied in 3rd instar larvae using depletion and overexpression conditions in wing disc and transcriptome analysis. We found that genes changing expression were different to those previously described using GAGA mutants in embryos. No apparent phenotypes on GAGA depletion could usually be observed at larval stages in imaginal discs but a strong effect on salivary gland polytene chromosomes was observed. In the adult, GAGA depletion produced many defects like abnormal cell proliferation in the wing, impaired dorsal closure and resulted in homeotic transformation of abdominal segment A5. Unexpectedly, no effects on Ultrabithorax expression were observed. Short overexpression of GAGA factor in 3rd instar larvae also resulted in activation of a set of genes not previously described to be under GAGA regulation, and in lethality at pupa. Our results suggest a little contribution of GAGA factor on gene transcription in wing discs and a change of the genes regulated in comparison with embryo. GAGA factor activity thus correlates with the global changes in gene expression that take place at the embryo-to-larva and, later, at the larva-to-pupa transitions.
Data from: A first phylogenetic analysis reveals a new arboreal tarantula genus from South America with description of a new species and two new species of Tapinauchenius Ausserer, 1871 (Araneae, Mygalomorphae, Theraphosidae)
Based on molecular and morphological phylogenetic analyses a new genus of Theraphosidae is described, Pseudoclamoris gen. n. Tapinauchenius gigas and Tapinauchenius elenae are transferred to Pseudoclamoris and a new species of Pseudoclamoris from the Amazon Region is described: P. burgessi sp. n. Two new species of Tapinauchenius from the Caribbean are described: T. rasti sp. n. and T. polybotes sp. n. Tapinauchenius subcaeruleus is considered a nomen dubium. Psalmopoeinae subfamily is diagnosed based on molecular and morphological phylogenies, and Pseudoclamoris gen. n. and Ephebopus Simon, 1892 are included. A taxonomic key for Psalmopoeinae genera Tapinauchenius, Pseudoclamoris, Psalmopoeus, and Ephebopus is provided.
Data from: Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara)
Background: Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively derived in their morphology (e.g. Brachyrhinodon), an earlier unknown history of Lepidosauria is implied. However, molecular age estimates for Lepidosauria have been problematic; dates for the most recent common ancestor of all lepidosaurs range between approximately 226 and 289 Mya whereas estimates for crown-group Squamata (lizards and snakes) vary more dramatically: 179 to 294 Mya. This uncertainty restricts inferences regarding the patterns of diversification and evolution of Lepidosauria as a whole. Results: Here we report on a rhynchocephalian fossil from the Middle Triassic of Germany (Vellberg) that represents the oldest known record of a lepidosaur from anywhere in the world. Reliably dated to 238--240 Mya, this material is at least 11 million years older than previously known lepidosaur records and is older than some but not all molecular clock estimates for the origin of lepidosaurs. Using RAG1 sequence data from 77 extant taxa and the new fossil specimens two of several calibrations, we estimate that the most recent common ancestor of Lepidosauria lived at least 242 Mya (238--249.5), and crown-group Squamata originated around 193 Mya (176--213). Conclusion: A Early/Middle Triassic date for the origin of Lepidosauria disagrees with previous estimates deep within the Permian and suggests the group evolved as part of the faunal recovery after the end-Permain mass extinction as the climate became more humid. Our origin time for crown-group Squamata coincides with shifts towards warmer climates and dramatic changes in fauna and flora. Most major subclades within Squamata originated in the Cretaceous postdating major continental fragmentation. The Vellberg fossil locality is expected to become an important resource for providing a more balanced picture of the Triassic and for bridging gaps in the fossil record of several other major vertebrate groups.
Data from: The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies
The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate change. The red coral (Corallium rubrum) lives in the Mediterranean Sea, where at depths ranging from 5 to 600 m, it meets very contrasted thermal conditions. The shallowest populations of this species suffered from mortality events linked with thermal anomalies that have highlighted thermotolerance differences between individuals. We provide here a new transcriptomic resource, as well as candidate markers for the study of local adaptation. We sequenced the transcriptome of six individuals from 5 m and six individuals from 40 m depth at the same site of the Marseilles bay, after a period of common garden acclimatization. We found differential expression maintained between the two depths even after common garden acclimatization, and we analysed the polymorphism pattern of these samples. We highlighted contigs potentially implicated in the response to thermal stress, which could be good candidates for the study of thermal adaptation for the red coral. Some of these genes are also involved in the response to thermal stress in other corals. Our method enables the identification of candidate loci of local adaptation useful for other nonmodel organisms.
Data from: Phylogenetic placement of the unusual jumping spider Depreissia Lessert, and a new synapomorphy uniting Hisponinae and Salticinae (Araneae, Salticidae)
The relationships of the unusual salticid spider Depreissia from central Africa and Borneo have been difficult to resolve, obscured by its highly modified ant-like body. Phylogenetic analysis of the gene 28S strongly supports its placement outside the major clade Salticinae and within the clade of cocalodines, spartaeines and lapsiines, with weaker support for a relationship with the cocalodines in particular. Excluding the genus from the Salticinae is supported also by the presence of a median apophysis on the male palp, and by the lack of a cymbial apical groove cradling the tip of embolus, which is newly presented here as a synapomorphy of Hisponinae plus Salticinae.
Data from: Resolving coiled shapes reveals new reorientation behaviors in C. elegans
We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of 2D worm behavior. We apply our algorithm to show that visually complex, coiled sequences are a superposition of two simpler patterns: the body wave dynamics and a head-curvature pulse. We demonstrate the precise ΩΩ-turn dynamics of an escape response and uncover a surprising new dichotomy in spontaneous, large-amplitude coils; deep reorientations occur not only through classical ΩΩ-shaped postures but also through larger postural excitations which we label here as δδ-turns. We find that omega and delta turns occur independently, suggesting a distinct triggering mechanism, and are the serpentine analog of a random left-right step. Finally, we show that omega and delta turns occur with approximately equal rates and adapt to food-free conditions on a similar timescale, a simple strategy to avoid navigational bias.
Data from: Evidence that metallic proxies are unsuitable for assessing the mechanics of microwear formation and a new theory of the meaning of microwear
Mammalian tooth wear research reveals contrasting patterns seemingly linked to diet: irregularly-pitted enamel surfaces, possibly from consuming hard seeds, vs. roughly-aligned linearly-grooved surfaces, associated with eating tough leaves. These patterns are important for assigning diet to fossils, including hominins. However, experiments establishing conditions necessary for such damage challenge this paradigm. Lucas et al. (2013) slid natural objects against enamel, concluding anything less hard than enamel would rub, not abrade, its surface (producing no immediate wear). This category includes all organic plant matter. Particles harder than enamel, with sufficiently angular surfaces, could abrade it immediately, prerequisites that silica/silicate particles alone possess. Xia et al. (2015) countered with experiments using brass and aluminium balls. Their bulk hardness was lower than enamel, but the latter was abraded. We examined the ball exteriors to address this discrepancy. The aluminium was surfaced by a thin rough oxide layer harder than enamel. Brass surfaces were smoother, but work-hardening during manufacture gave them comparable or higher hardness than enamel. We conclude that Xia et al.'s results are actually predicted by the mechanical model of Lucas et al. To explain wear patterns, we present a new model of textural formation, based on particle properties and presence/absence of silica(tes).
Data from: The role of plasma and urine metabolomics in identifying new biomarkers in severe newborn asphyxia: a study of asphyxiated newborn pigs following cardiopulmonary resuscitation
Background: Optimizing resuscitation is important to prevent morbidity and mortality from perinatal asphyxia. The metabolism of cells and tissues is severely disturbed during asphyxia and resuscitation, and metabolomic analyses provide a snapshot of many small molecular weight metabolites in body fluids or tissues. In this study metabolomics profiles were studied in newborn pigs that were asphyxiated and resuscitated using different protocols to identify biomarkers for subject characterization, intervention effects and possibly prognosis. Methods: A total of 125 newborn Noroc pigs were anesthetized, mechanically ventilated and inflicted progressive asphyxia until asystole. Pigs were randomized to resuscitation with a FiO2 0.21 or 1.0, different duration of ventilation before initiation of chest compressions (CC), and different CC to ventilation ratios. Plasma and urine samples were obtained at baseline, and 2 h and 4 h after return of spontaneous circulation (ROSC, heart rate > = 100 bpm). Metabolomics profiles of the samples were analyzed by nuclear magnetic resonance spectroscopy. Results: Plasma and urine showed severe metabolic alterations consistent with hypoxia and acidosis 2 h and 4 h after ROSC. Baseline plasma hypoxanthine and lipoprotein concentrations were inversely correlated to the duration of hypoxia sustained before asystole occurred, but there was no evidence for a differential metabolic response to the different resuscitation protocols or in terms of survival. Conclusions: Metabolic profiles of asphyxiated newborn pigs showed severe metabolic alterations. Consistent with previously published reports, we found no evidence of differences between established and alternative resuscitation protocols. Lactate and pyruvate may have a prognostic value, but have to be independently confirmed.
Data from: Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes
The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multi-gene dataset, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex, while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically-relevant geological time (10^7-10^8 years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explain global patterns of microbial eukaryote distribution, and that processes of dispersal remain poorly understood.
Data from: Adsorption and corrosion inhibition behavior of new theophylline-triazole based derivatives for steel in acidic medium
The design and synthesis of a series of theophylline derivatives containing 1,2,3-triazole moieties is presented. The corrosion inhibition activities of these new triazole-theophylline compounds were evaluated by studying the corrosion of API 5L X52 steel in 1 M HCl media. The results showed that an increase in the concentration of the theophylline-triazole derivatives also increases the charge transference resistance (Rct) value, enhancing inhibition efficiency and decreasing the corrosion process. The electrochemical impedance spectroscopy under static conditions studies revealed that the best inhibition efficiencies (~90%) at 50 ppm are presented by the all- substituted compounds. According to the Langmuir isotherm, the compounds 4 and 5 analyzed exhibit physisorption-chemisorption process, with exception of the hydrogen 3, bromo 6 and iodo 7 substituted compound, which exhibit chemisorption process. The corrosion when submerging a steel bar in 1 M HCl was studied using SEM-EDS. This experiment showed that the corrosion process decreases considerably in the presence of 50 ppm of the organic inhibitors. Finally, theoretical study showed a correlation between EHOMO, hardness (η), electrophilicity (W), atomic charge and the inhibition efficiency in which the iodo 7 substituted compound presents the best inhibitor behavior.
Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.
Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.
Data from: The influence sampling design on species tree inference: a new relationship for the New World chickadees (Aves: Poecile)
In this study, we explore the long-standing issue of how many loci are needed to infer accurate phylogenetic relationships, and whether loci with particular attributes (i.e., parsimony informativeness, variability, gene tree resolution) outperform others. To do so, we use an empirical dataset consisting of the seven species of chickadees (Aves: Paridae), an analytically tractable, recently diverged group, and well studied ecologically but lacking a nuclear phylogeny. We estimate relationships using 40 nuclear loci and mitochondrial DNA using four coalescent-based species tree inference methods (BEST, *BEAST, STEM, STELLS). Collectively, our analyses contrast with previous studies and support a sister relationship between the Black-capped and Carolina Chickadee, two superficially similar species that hybridize along a long zone of contact. Gene flow is a potential source of conflict between nuclear and mitochondrial gene trees, yet, we find a significant, albeit low, signal of gene flow. Our results suggest that relatively few loci with high information content may be sufficient for estimating an accurate species tree, but that substantially more loci are necessary for accurate parameter estimation. We provide an empirical reference point for researchers designing sampling protocols with the purpose of inferring phylogenies and population parameters of closely related taxa.
Data from: A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group
Evolutionary transitions to marine habitats occurred frequently among Mesozoic reptiles. Only one such clade survives to the present: sea turtles (Chelonioidea). Other marine turtles originated during the Mesozoic, but uncertain affinities of key fossils have obscured the number of transitions to marine life, and the timing of the origin of marine adaptation in chelonioids. Phylogenetic studies support either a highly‐inclusive chelonioid total‐group including fossil marine clades from the Jurassic and Cretaceous (e.g. protostegids, thalassochelydians, sandownids) or a less inclusive chelonioid total‐group excluding those clades. Under this paradigm, these clades belong outside Cryptodira, and represent at least one additional evolutionary transition to marine life in turtles. We present a new phylogenetic hypothesis informed by high resolution computed tomographic data of living and fossil taxa. Besides a well‐supported Chelonioidea, which includes protostegids, we recover a previously unknown clade of stem‐group turtles, Angolachelonia, which includes the Late Jurassic thalassochelydians, and the Cretaceous–Palaeogene sandownids. Accounting for the Triassic Odontochelys, our results indicate three independent evolutionary transitions to marine life in non‐pleurodiran turtles (plus an additional two‐three in pleurodires). Among all independent origins of marine habits, a pelagic ecology only evolved once, among chelonioids. All turtle groups that independently invaded marine habitats in the Jurassic–Cretaceous (chelonioids, angolachelonians, bothremydid pleurodires) survived the Cretaceous–Palaeogene mass extinction event. This highlights extensive survival of marine turtles compared to other marine reptiles. Furthermore, deeply‐nested clades such as chelonioids are found by the middle Early Cretaceous, suggesting a rapid diversification of crown‐group turtles during the Early Cretaceous.
Data from: A new global palaeobiogeographical model for the late Mesozoic and early Tertiary
Late Mesozoic palaeobiogeography has been characterized by a distinction between the northern territories of Laurasia and the southern landmasses of Gondwana. The repeated discovery of Gondwanan lineages in Laurasia has led to the proposal of alternative scenarios to explain these anomalous occurrences. A new biogeographical model for late Mesozoic terrestrial ecosystems is here proposed, in which Europe and 'Gondwanan' territories possessed a common Eurogondwanan fauna during the earliest Cretaceous. Subsequently, following the Hauterivian, Europe severed from Africa and connected to Asiamerica resulting in a faunal interchange. This model explains the presence of 'Gondwanan' taxa in Laurasia and the absence of Laurasian forms in the southern territories during the Cretaceous. In order to test this new palaeobiogeographical model, tree reconciliation analyses (TRAs) were performed based on biogeographical signals provided by a supertree of late Mesozoic archosaurs. The TRAs found significant evidence for the presence of an earliest Cretaceous Eurogondwanan fauna, followed by a relatively short-term Gondwana-Laurasia dichotomy. The analysis recovered evidence for a biogeographical re-connection of the European territories with Africa and South America-Antarctica during the Campanian to Maastrichtian time-slice. This biogeographical scenario appears to continue through the early Tertiary and sheds light on the trans-Atlantic disjunct distributions of several extant plant and animal groups.
Data from: Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae)
Phylogenomic approaches have proven able to resolve difficult branches in the tree of life. New World direct-developing frogs (Terraranae) represent a large evolutionary radiation in which interrelationships at key points in the phylogeny have not been adequately determined, affecting evolutionary, biogeographic, and taxonomic interpretations. We employed anchored hybrid enrichment to generate a data set containing 389 loci and >600,000 nucleotide positions for 30 terraranan and several outgroup frog species encompassing all major lineages in the clade. Concatenated maximum likelihood and coalescent species-tree approaches recover nearly identical topologies with strong support for nearly all relationships in the tree. These results are similar to previous phylogenetic results but provide additional resolution at short internodes. Among taxa whose placement varied in previous analyses, Ceuthomantis is shown to be the sister taxon to all other terraranans, rather than deeply embedded within the radiation, and Strabomantidae is monophyletic rather than paraphyletic with respect to Craugastoridae. We present an updated taxonomy to reflect these results, and describe a new subfamily for the genus Hypodactylus.
Data from: Species richness and the temporal stability of biomass production: a new analysis of recent biodiversity experiments
The relationship between biological diversity and ecological stability has fascinated ecologists for decades. Determining the generality of this relationship, and discovering the mechanisms that underlie it, are vitally important for ecosystem management. Here, we investigate how species richness affects the temporal stability of biomass production by re-analyzing 27 recent biodiversity experiments conducted with primary producers. We find that, in grasslands, increasing species richness stabilizes whole-community biomass but destabilizes the dynamics of constituent populations. Community biomass is stabilized because species richness impacts mean biomass more strongly than its variance. In algal communities, species richness has a minimal effect on community stability because richness affects the mean and variance of biomass nearly equally. Using a new measure of synchrony among species, we find that for both grasslands and algae, temporal correlations in species biomass are lower when species are grown together in polyculture than when grown alone in monoculture. These results suggest that interspecific interactions tend to stabilize community biomass in diverse communities. Contrary to prevailing theory, we found no evidence that species' responses to environmental variation in monoculture predicted the strength of diversity's stabilizing effect. Together, these results deepen our understanding of when and why increasing species richness stabilizes community biomass.
Data from: New criteria for sepsis-induced coagulopathy (SIC) following the revised sepsis definition: a retrospective analysis of a nationwide survey
OBJECTIVE: Recent clinical studies have shown that anticoagulant therapy might be effective only in specific at-risk subgroups of patients with sepsis and coagulation dysfunction. The definition of sepsis was recently modified and old scoring systems may no longer be proper for the diagnosis of sepsis-associated coagulopathy. The aim of this study was to evaluate prognostic factors in patients diagnosed as sepsis and coagulopathy according to the new sepsis definition and assess their accuracy in comparison to existing models. DESIGN, SETTING AND SUBJECTS: The data set was obtained from a post-marketing survey examining recombinant human soluble thrombomodulin and offered by Japanese Society on Thrombosis and Hemostasis. A total of 1498 patients with sepsis and coagulopathy complications who were treated with recombinant thrombomodulin were analyzed in this study. MAIN OUTCOME MEASURES: The platelet count, prothrombin time (PT) ratio, fibrinogen and fibrin degradation products (FDP), systemic inflammatory response syndrome (SIRS) score, and sequential organ failure assessment (SOFA) score obtained just before the start of treatment were examined in relation to the 28-day mortality rate. RESULTS: The platelet count, PT ratio, and total SOFA were independent predictors of a fatal outcome in a logistic regression model. A sepsis-induced coagulation (SIC) score was defined using the 3 above-mentioned variables with a positivity threshold of 4 points or more. The SIC score predicted higher 28-day mortality rate compared to the Japanese Association for Acute Medicine (JAAM)-DIC score (38.4% vs. 34.7%). CONCLUSIONS: The SIC scoring is based on readily available parameters, is easy to calculate and owns a high predictive value for 28-day mortality. Future studies are warranted to evaluate whether the SIC score may guide the decision to initiate anticoagulant therapy.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.