Prey availability and temporal partitioning modulate felid coexistence in Neotropical forests

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids

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

PANC Study (Pancreatitis: A National Cohort Study): national cohort study examining the first 30 days from presentation of acute pancreatitis in the UK

Abstract Background Acute pancreatitis is a common, yet complex, emergency surgical presentation. Multiple guidelines exist and management can vary significantly. The aim of this first UK, multicentre, prospective cohort study was to assess the variation in management of acute pancreatitis to guide resource planning and optimize treatment. Methods All patients aged greater than or equal to 18 years presenting with acute pancreatitis, as per the Atlanta criteria, from March to April 2021 were eligible for inclusion and followed up for 30 days. Anonymized data were uploaded to a secure electronic database in line with local governance approvals. Results A total of 113 hospitals contributed data on 2580 patients, with an equal sex distribution and a mean age of 57 years. The aetiology was gallstones in 50.6 per cent, with idiopathic the next most common (22.4 per cent). In addition to the 7.6 per cent with a diagnosis of chronic pancreatitis, 20.1 per cent of patients had a previous episode of acute pancreatitis. One in 20 patients were classed as having severe pancreatitis, as per the Atlanta criteria. The overall mortality rate was 2.3 per cent at 30 days, but rose to one in three in the severe group. Predictors of death included male sex, increased age, and frailty; previous acute pancreatitis and gallstones as aetiologies were protective. Smoking status and body mass index did not affect death. Conclusion Most patients presenting with acute pancreatitis have a mild, self-limiting disease. Rates of patients with idiopathic pancreatitis are high. Recurrent attacks of pancreatitis are common, but are likely to have reduced risk of death on subsequent admissions. </jats:sec

Mise en œuvre d’un suivi de « cohorte » en Science Sociale : Retours d’expérience sur le dispositif de collecte de données dans l’étude longitudinale et interventionnelle InterMob, Grenoble

InterMob est une recherche « interventionnelle », contrôlée et randomisée, pour analyser les freins et les leviers au changement de comportement de mobilité de personnes habitant la région grenobloise. Elle est soutenue par l'UGA, l'INSERM, le CNRS, l'ADEME, la Région Auvergne-Rhône-Alpes, l'IDEX et Grenoble-Alpes Métropole et le Syndicat Mixte des Mobilités de l'Aire Grenobloise. Cette étude cible notamment la question des obstacles et leviers d’une mobilité plus active et plus durable en lien avec la qualité de l’air. Cette étude longitudinale sur cohorte s’effectue auprès d’un panel de volontaires (> 100) sur une période de 24 mois. Plus exactement des mesures sont effectuées avant une intervention pour avoir un état de départ, de type « base ligne ». Ensuite un dispositif interventionnel est appliqué et suivi pendant une durée de 6 mois et enfin des mesures sont effectuées après l’intervention pour en mesurer les effets dans le temps, pendant 18 mois. Les participants sont intégrés progressivement à l’étude en raison d’un nombre limité d’enquêteurs et de matériels. Ils sont suivis chacun sur 8 sessions de mesures d’une semaine échelonnées sur 24 mois au moyen de dispositifs variés (questionnaires, capteurs de mobilité-GPS et d’activité physique-accélérométrie tri-dimensionnelle, capteurs de pollution-PM2.5, carnet de mobilité). Le suivi d’une telle cohorte « glissante » nécessite l’élaboration d’un plan de gestion des données complexe pour organiser la collecte et gérer les données massives collectées. Des outils et infrastructures informatiques dédiés ont été développées et/ou déployés à cet effet. Cette étude nécessite donc un appui technique important tant sur le terrain pour maintenir la cohorte et collecter les données qu’en laboratoire pour gérer, organiser et ensuite traiter les données collectées (données spatio-temporelles complexes). Ce dispositif d’observation inédit en SHS s’est construit progressivement et a nécessité un long travail préparatoire mais aussi des adaptations et améliorations successives. La présente communication se propose de revenir sur les étapes importantes nécessaires pour construire ce dispositif de collecte de données hétérogènes, notamment le développement d’un outil de gestion de cohorte adapté au protocole (gestion des rendez-vous participants, gestion des enquêteurs, des capteurs, des tâches de l’intervention à réaliser) mais aussi les choix faits dans la mobilisation d’outils existants, comme par exemple Sphinx, utilisé ici comme outil pour les questionnaires en ligne mais aussi pour suivre une partie du « terrain », capitaliser les métadonnées et vérifier les données collectée et comme outil de saisi de données après terrain (carnet de mobilité, initialement papier). Cette présentation se focalisera dès lors sur les deux premières étapes du cycle de vie des données du projet (planification et collecte), étapes importantes voire cruciales pour obtenir in fine des données de recherche les plus FAIR possibles. Ce retour d’expérience vise à montrer aussi l’intérêt d’élaborer un plan de gestion des données et que celui-ci est avant tout un outil de planification et d’anticipation plus qu’une contrainte

Mise en œuvre d’un suivi de « cohorte » en Science Sociale : Retours d’expérience sur le dispositif de collecte de données dans l’étude longitudinale et interventionnelle InterMob, Grenoble

International audienceInterMob est une recherche « interventionnelle », contrôlée et randomisée, pour analyser les freins et les leviers au changement de comportement de mobilité de personnes habitant la région grenobloise. Elle est soutenue par l'UGA, l'INSERM, le CNRS, l'ADEME, la Région Auvergne-Rhône-Alpes, l'IDEX et Grenoble-Alpes Métropole et le Syndicat Mixte des Mobilités de l'Aire Grenobloise. Cette étude cible notamment la question des obstacles et leviers d’une mobilité plus active et plus durable en lien avec la qualité de l’air. Cette étude longitudinale sur cohorte s’effectue auprès d’un panel de volontaires (> 100) sur une période de 24 mois. Plus exactement des mesures sont effectuées avant une intervention pour avoir un état de départ, de type « base ligne ». Ensuite un dispositif interventionnel est appliqué et suivi pendant une durée de 6 mois et enfin des mesures sont effectuées après l’intervention pour en mesurer les effets dans le temps, pendant 18 mois. Les participants sont intégrés progressivement à l’étude en raison d’un nombre limité d’enquêteurs et de matériels. Ils sont suivis chacun sur 8 sessions de mesures d’une semaine échelonnées sur 24 mois au moyen de dispositifs variés (questionnaires, capteurs de mobilité-GPS et d’activité physique-accélérométrie tri-dimensionnelle, capteurs de pollution-PM2.5, carnet de mobilité). Le suivi d’une telle cohorte « glissante » nécessite l’élaboration d’un plan de gestion des données complexe pour organiser la collecte et gérer les données massives collectées. Des outils et infrastructures informatiques dédiés ont été développées et/ou déployés à cet effet. Cette étude nécessite donc un appui technique important tant sur le terrain pour maintenir la cohorte et collecter les données qu’en laboratoire pour gérer, organiser et ensuite traiter les données collectées (données spatio-temporelles complexes). Ce dispositif d’observation inédit en SHS s’est construit progressivement et a nécessité un long travail préparatoire mais aussi des adaptations et améliorations successives. La présente communication se propose de revenir sur les étapes importantes nécessaires pour construire ce dispositif de collecte de données hétérogènes, notamment le développement d’un outil de gestion de cohorte adapté au protocole (gestion des rendez-vous participants, gestion des enquêteurs, des capteurs, des tâches de l’intervention à réaliser) mais aussi les choix faits dans la mobilisation d’outils existants, comme par exemple Sphinx, utilisé ici comme outil pour les questionnaires en ligne mais aussi pour suivre une partie du « terrain », capitaliser les métadonnées et vérifier les données collectée et comme outil de saisi de données après terrain (carnet de mobilité, initialement papier). Cette présentation se focalisera dès lors sur les deux premières étapes du cycle de vie des données du projet (planification et collecte), étapes importantes voire cruciales pour obtenir in fine des données de recherche les plus FAIR possibles. Ce retour d’expérience vise à montrer aussi l’intérêt d’élaborer un plan de gestion des données et que celui-ci est avant tout un outil de planification et d’anticipation plus qu’une contrainte

OLES Online Laboratory for Environmental Sciences

International audienceThe integrated cyber-infrastructure, OLES, provides an access to observation data and to tools and models built to enhance our understanding on the evolution of the Earth's water resources and climate. OLES aims at i) extracting the required data from database portals using OGC webservice (CSW, SOS), ii) building a specific process chain based on modules that use NetCDF format for exchanging data, iii) running the process in chosen computing facilities, OLES can connect outside on a private LAN and iv) visualizing the result of the process. Based on J2EE, the MMI of OLES is a web interface and interacts with EJB objects. OLES uses web services to communicate with a sequencer developed in C++

Measured and modelled sublimation on the tropical Glaciar Artesonraju, Peru

Sublimation plays a decisive role in the surface energy and mass balance of tropical glaciers. During the dry season (May-September) low specific humidity and high surface roughness favour the direct transition from ice to vapour and drastically reduce the energy available for melting. However, field measurements are scarce and little is known about the performance of sublimation parameterisations in glacier mass balance and runoff models. During 15 days in August 2005 sublimation was measured on the tongue of Glaciar Artesonraju (8 degrees 58' S, 77 degrees 38'W) in the Cordillera Blanca, Peru, using simple lysimeters. Indicating a strong dependence on surface roughness, daily totals of sublimation range from 1-3 kg m(-2) for smooth to 25 kg m(-2) for rough conditions. (The 15-day means at that time of wind speed and specific humidity were 4.3m s(-1) and 3.8 g kg(-1), respectively.) Measured sublimation was related to characteristic surface roughness lengths for momentum (z(m)) and for the scalar quantities of temperature and water vapour (z(s)), using a process-based mass balance model. Input data were provided by automatic weather stations, situated on the glacier tongue at 4750 m a.s.l. and 4810m a.s.l., respectively. Under smooth conditions the combination z(m)=2.0 mm and z(s)=1.0 mm appeared to be most appropriate, for rough conditions z(m)=20.0 mm and z(s)=10.0mm fitted best. Extending the sublimation record from April 2004 to December 2005 with the process-based model confirms, that sublimation shows a clear seasonality. 60-90% of the energy available for ablation is consumed by sublimation in the dry season, but only 10-15% in the wet season (October-April). The findings are finally used to evaluate the parameterisation of sublimation in the lower-complexity mass balance model ITGG, which has the advantage of requiring precipitation and air temperature as only input data. It turns out that the implementation of mean wind speed is a possible improvement for the representation of sublimation in the ITGG model

Alpha-1 antitrypsin is markedly decreased following pulmonary F. tularensis challenge

Alpha-1 antitrypsin, a small glycoprotein clade A serpine serine protease inhibitor of neutrophil elastase has been shown to increase in humans following bacterial and viral infection. However, we report here significant reduction of this major inhibitor of elastase in plasma of F. tularensis LVS and SCHU S4 (Type A strain) following pulmonary challenge. Consistent with an imbalance of protease-antiprotease function at the alveolar level in lungs of infected animals, increased elastase activity was observed in lung lavage fluids accompanied by decrease lung function, i.e., loss of lung elastance with concomitant increase of pulmonary hysteresistivity. These data are suggestive of targeted tissue destruction via unchecked neutrophhil elastase activity in infected animals

Climate change and tropical Andean glaciers : past, present and future

Observations on glacier extent from Ecuador, Peru and Bolivia give a detailed and unequivocal account of rapid shrinkage of tropical Andean glaciers since the Little Ice Age (LIA). This retreat however, was not continuous but interrupted by several periods of stagnant or even advancing glaciers, most recently around the end of the 20th century. New data from mass balance networks established on over a dozen glaciers allows comparison of the glacier behavior in the inner and outer tropics. It appears that glacier variations are quite coherent throughout the region, despite different sensitivities to climatic forcing such as temperature, precipitation, humidity, etc. In parallel with the glacier retreat, climate in the tropical Andes has changed significantly over the past 50-60 years. Temperature in the Andes has increased by approximately 0.1 degrees C/decade, with only two of the last 20 years being below the 1961-90 average. Precipitation has slightly increased in the second half of the 20th century in the inner tropics and decreased in the outer tropics. The general pattern of moistening in the inner tropics and drying in the subtropical Andes is dynamically consistent with observed changes in the large-scale circulation, suggesting a strengthening of the tropical atmospheric circulation. Model projections of future climate change in the tropical Andes indicate a continued warming of the tropical troposphere throughout the 21st century, with a temperature increase that is enhanced at higher elevations. By the end of the 21st century, following the SIZES A2 emission scenario. the tropical Andes may experience a massive warming on the order of 4.5-5 degrees C. Predicted changes in precipitation include an increase in precipitation during the wet season and a decrease during the dry season, which would effectively enhance the seasonal hydrological cycle in the tropical Andes. These observed and predicted changes in climate affect the tropical glacier energy balance through its sensitivity to changes in atmospheric humidity (which governs sublimation), precipitation (whose variability induces a positive feedback on albedo) and cloudiness (which controls the incoming long-wave radiation). In the inner tropics air temperature also significantly influences the energy balance, albeit not through the sensible heat flux, but indirectly through fluctuations in the rain-snow line and hence changes in albedo and net radiation receipts. Given the projected changes in climate, based on different IPCC scenarios for 2050 and 2080, simulations with a tropical glacier-climate model indicate that glaciers will continue to retreat. Many smaller, low-lying glaciers are already completely out of equilibrium with current climate and will disappear within a few decades. But even in catchments where glaciers do not completely disappear, the change in streamflow seasonality, due to the reduction of the glacial buffer during the dry season, will significantly affect the water availability downstream. In the short-term, as glaciers retreat and lose mass, they add to a temporary increase in runoff to which downstream users will quickly adapt, thereby raising serious sustainability concerns

Acinetobacter baumannii Gastrointestinal Colonization Is Facilitated by Secretory IgA Which Is Reductively Dissociated by Bacterial Thioredoxin A

Multidrug-resistant Acinetobacter baumannii is among the most common causes of infectious complications associated with combat-related trauma in military personnel serving overseas. However, little is currently known about its pathogenesis. While the gastrointestinal (GI) tract has been found to be a major reservoir for A. baumannii, as well as to potentially contribute to development of multidrug resistance, no studies have addressed the mechanisms involved in gut colonization. In this study, we address this critical gap in knowledge by first assessing the interaction between secretory IgA (SIgA), the principal humoral immune defense on mucosal surfaces, and the A. baumannii clinical isolate Ci79. Surprisingly, SIgA appeared to enhance A. baumannii GI tract colonization, in a process mediated by bacterial thioredoxin A (TrxA), as evidenced by reduction of bacterial attachment in the presence of TrxA inhibitors. Additionally, a trxA targeted deletion mutant (ΔtrxA) showed reduced bacterial burdens within the GI tract 24 h after oral challenge by in vivo live imaging, along with loss of thiol-reductase activity. Surprisingly, not only was GI tract colonization greatly reduced but the associated 50% lethal dose (LD50) of the ΔtrxA mutant was increased nearly 100-fold in an intraperitoneal sepsis model. These data suggest that TrxA not only mediates A. baumannii GI tract colonization but also may contribute to pathogenesis in A. baumannii sepsis following escape from the GI tract under conditions when the intestinal barrier is compromised, as occurs with cases of severe shock and trauma.Acinetobacter baumannii is an emerging bacterial pathogen recently classified as a serious threat to U.S. and global health by both the Centers for Disease Control and Prevention and the World Health Organization. It also is one of the leading causes of combat-related infections associated with injured military personnel serving overseas. Little is known regarding mechanisms of gastrointestinal tract colonization despite this site being shown to serve as a reservoir for multidrug-resistant (MDR) A. baumannii isolates. Here, we establish that secretory IgA, the major immunoglobulin of mucosal surfaces, promotes A. baumannii GI tract colonization via bacterial thioredoxin A as evidenced through significant reduction in colonization in IgA-deficient animals. Additionally, bacterial colonization and mortality were significantly reduced in animals challenged with a thioredoxin A-deficient A. baumannii mutant. Combined, these data suggest that thioredoxin A is a novel virulence factor, for which antithioredoxin therapies could be developed, for this important multidrug-resistant pathogen