Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

The rapid accumulation of biological networks poses new challenges and calls for powerful integrative analysis tools. Most existing methods capable of simultaneously analyzing a large number of networks were primarily designed for unweighted networks, and cannot easily be extended to weighted networks. However, it is known that transforming weighted into unweighted networks by dichotomizing the edges of weighted networks with a threshold generally leads to information loss. We have developed a novel, tensor-based computational framework for mining recurrent heavy subgraphs in a large set of massive weighted networks. Specifically, we formulate the recurrent heavy subgraph identification problem as a heavy 3D subtensor discovery problem with sparse constraints. We describe an effective approach to solving this problem by designing a multi-stage, convex relaxation protocol, and a non-uniform edge sampling technique. We applied our method to 130 co-expression networks, and identified 11,394 recurrent heavy subgraphs, grouped into 2,810 families. We demonstrated that the identified subgraphs represent meaningful biological modules by validating against a large set of compiled biological knowledge bases. We also showed that the likelihood for a heavy subgraph to be meaningful increases significantly with its recurrence in multiple networks, highlighting the importance of the integrative approach to biological network analysis. Moreover, our approach based on weighted graphs detects many patterns that would be overlooked using unweighted graphs. In addition, we identified a large number of modules that occur predominately under specific phenotypes. This analysis resulted in a genome-wide mapping of gene network modules onto the phenome. Finally, by comparing module activities across many datasets, we discovered high-order dynamic cooperativeness in protein complex networks and transcriptional regulatory networks

Regulation of Apoptotic Mediators Reveals Dynamic Responses to Thermal Stress in the Reef Building Coral Acropora millepora

Background: Mass coral bleaching is increasing in scale and frequency across the world's coral reefs and is being driven primarily by increased levels of thermal stress arising from global warming. In order to understand the impacts of projected climate change upon corals reefs, it is important to elucidate the underlying cellular mechanisms that operate during coral bleaching and subsequent mortality. In this respect, increased apoptotic cell death activity is an important cellular process that is associated with the breakdown of the mutualistic symbiosis between the cnidarian host and their dinoflagellate symbionts

Assessment of the accuracy of physiological blood indicators for the evaluation of stress, health status and welfare in Siberian sturgeon (Acipenser baerii) subject to chronic heat stress and dietary supplementation

Abstract There is growing interest in the evaluation of stress, health and welfare of farm-raised fish. However, there is no scientific consensus about the methodology that is used to assess them. Sturgeon aquaculture is a recent industry with increasing interest in the production of caviar, which is characterized by high turnover and costs. To improve aquaculture efficiency, this study was conducted on routine blood samples, taken from Siberian sturgeon (Acipenser baerii), to test the robustness of using only physiological indicators to assess heat stress, health, and welfare. Sampling was performed after 1 month of prebiotic dietary supplementation followed by 4 weeks of sublethal heat stress. Data interpretation was achieved with a multivariate statistical tool. The expression of heat shock proteins (HSP) was assessed for the first time in sturgeon erythrocytes. Hsp70 and hsp90 expression was triggered by both stress and dietary supplementation. Indicators of non-specific immunity were modified mainly by stress. Complement activity increases with stress while lysozyme activity decreases, but to a lesser extent in supplemented fish. The antioxidant capacity increases with stress while oxidant metabolites decrease and overall oxidative stress was lower for fish that received dietary supplementation. The positive impact of dietary supplementation on health status was observable after a stress challenge. A principal component analysis was used to combine all the measured parameters and to observe patterns in physiological fish status. The four experimental groups of fish were clearly discriminated with this statistical tool. Physiological indicators from blood samples may enable heat stress, health, and welfare to be assessed in Siberian sturgeon

The effect of oxygen partial pressure on dislocation creep in polycrystalline uranium dioxide

International audienc

Cumulative Exposure to Infliximab, But Not Trough Concentrations, Correlate With Rate of Infection

International audienceBackground & aims: Infliximab increases the risk of infection in patients with inflammatory bowel diseases (IBD), but there is controversy over the relationship between drug concentration and infections. We aimed to assess factors associated with infection in infliximab-treated patients, including pharmacokinetic features.Methods: We collected data from 209 patients with IBD (102 men; mean age, 39 y; 159 with Crohn's disease; 54 received combination therapy) who received a infliximab maintenance regimen from November 2016 through April 2017 in France. Data were collected from each infusion visit (total of 640 infusions). Infliximab exposure was estimated based on the area under the curve (AUC) of drug concentration in pharmacokinetic models; individual exposures over the 6-month period were estimated based on the sum of the AUC (ΣAUC).Results: The mean infliximab trough level was 5.46 mg/L, and the mean ΣAUC was 3938±1427 mg d/L. A total of 215 infections were collected from the 640 infusion visits; 123 patients (59%) had at least 1 infection. Factors independently associated with infection after multivariate analysis were smoking (odds ratio [OR], 2.05; P=.046), IBD flare (OR, 2.71; P=.006), and a high ΣAUC of infliximab (above 3234 mg x d/L) (OR, 2.02; P=.02). The ΣAUC was higher in patients with an occurrence of infection (P=.04) and correlated with the number of infections (P=.04). Trough concentration of infliximab alone was not associated with infection.Conclusions: Almost two-thirds of patients treated with infliximab developed an infection; risk was individually correlated with cumulative increase in drug exposure, but not infliximab trough level

Differential Acclimation of Juvenile Sea Urchins Transplanted Across a Metallic Trace Element Gradient within the Bay of Toulon (France)

International audienceUrbanized harbors and embayments scattered along marine shorelines act as important sources of a wide range of chemical contaminants, which include metallic trace elements (MTE). Within the semi-enclosed Mediterranean Sea, the high number of such areas might locally challenge the persistence of coastal marine species. In recent decades, biomonitoring studies, using sentinel species such as mussels, have increased knowledge of coastal contamination and provided a number of contentious potential environmental surveillance biomarkers, which contributed to a better comprehension toward the acclimation abilities of marine organisms, to actual anthropogenically derived environments. The aim of this study was to characterize the influence of the chemically, multi-contaminated, Bay of Toulon (France) on the young fauna, using juvenile sea urchins Paracentrotus lividus as a proxy. Hatchery-produced individuals were immersed, for 1 mo, within the bay, at four contrasted sites for MTE concentrations. At the end of the experiment, growth and transcript abundances of key genes, involved in the acclimation process, were assessed. Contrasted phenotypic and molecular responses were observed evidencing a significant environmental influence. Specifically, under the high metallic stress, a dwarfing response was observed, associated with a high level of metallothionein and a low level of hsp response. In addition, the level of DNA methyltransferase transcript abundance was inversely correlated with the level of MTE concentrations, highlighting that the chronic exposure to metallic contaminants would probably increase the risk of genetic mutations, such as those consecutive to transpositions. Overall, this study indicates that further in-depth research into the mechanisms driving plasticity and adaptive changes at the population level is required

Living coral tissue slows skeletal dissolution related to ocean acidification

Climate change is causing major changes to marine ecosystems globally, with ocean acidification of particular concern for coral reefs. Using a 200 d in situ carbon dioxide enrichment study on Heron Island, Australia, we simulated future ocean acidification conditions, and found reduced pH led to a drastic decline in net calcification of living corals to no net growth, and accelerated disintegration of dead corals. Net calcification declined more severely than in previous studies due to exposure to the natural community of bioeroding organisms in this in situ study and to a longer experimental duration. Our data suggest that reef flat corals reach net dissolution at an aragonite saturation state (ΩAR) of 2.3 (95% confidence interval: 1.8-2.8) with 100% living coral cover and at ΩAR > 3.5 with 30% living coral cover. This model suggests that areas of the reef with relatively low coral mortality, where living coral cover is high, are likely to be resistant to carbon dioxide-induced reef dissolution

Six month in situ high-resolution carbonate chemistry and temperature study on a coral reef flat reveals asynchronous pH and temperature anomalies

Understanding the temporal dynamics of present thermal and pH exposure on coral reefs is crucial for elucidating reef response to future global change. Diel ranges in temperature and carbonate chemistry parameters coupled with seasonal changes in the mean conditions define periods during the year when a reef habitat is exposed to anomalous thermal and/or pH exposure. Anomalous conditions are defined as values that exceed an empirically estimated threshold for each variable. We present a 200-day time series from June through December 2010 of carbonate chemistry and environmental parameters measured on the Heron Island reef flat. These data reveal that aragonite saturation state, pH, and pCO2 were primarily modulated by biologically-driven changes in dissolved organic carbon (DIC) and total alkalinity (TA), rather than salinity and temperature. The largest diel temperature ranges occurred in austral spring, in October (1.5 - 6.6°C) and lowest diel ranges (0.9 -3.2°C) were observed in July, at the peak of winter. We observed large diel total pH variability, with a maximum range of 7.7 - 8.5 total pH units, with minimum diel average pH values occurring during spring and maximum during fall. As with many other reefs, the nighttime pH minima on the reef flat were far lower than pH values predicted for the open ocean by 2100. DIC and TA both increased from June (end of Fall) to December (end of Spring). Using this high-resolution dataset, we developed exposure metrics of pH and temperature individually for intensity, duration, and severity of low pH and high temperature events, as well as a combined metric. Periods of anomalous temperature and pH exposure were asynchronous on the Heron Island reef flat, which underlines the importance of understanding the dynamics of co-occurrence of multiple stressors on coastal ecosystems

France-Allemagne-Europe

Ce cycle thématique de l’Institut d’études avancées (IEA) de l’université de Cergy-Pontoise, a été organisé par le CIRAC en coopération avec le centre de recherche Civilisations et identités culturelles comparées (CICC), avec le concours du Centre interdisciplinaire d’études et de recherches sur l’Allemagne (CIERA) et du Deutsch-Französisches Institut (DFI). Composé de trois tables rondes, il a réuni des spécialistes français et allemands de haut niveau qui ont dressé un état des lieux des positions et des approches françaises et allemandes sur les principaux chantiers de l’Union européenne

Espaces de pouvoir, espaces d’autonomie en Allemagne

Alors qu’il s’agit d’un terme clé pour les géographes, « l’espace » a connu dans les sciences historiques et politiques une longue période de quarantaine en Allemagne depuis 1945. Tabou depuis le nazisme, le terme a gardé des relents de revendication nationaliste, en particulier dans l’intérêt récent pour la géopolitique. Or, les sciences historiques et sociales sont affectées depuis une dizaine d’années par un net regain d’intérêt pour l’espace et pour la dimension spatiale des processus et phénomènes qu’elles étudient. C’est là l’une des conséquences de la remise en cause de la pertinence de l’échelle de l’État-nation comme cadre d’analyse. Parce que l’Allemagne présente des particularités dans l’emboîtement et l’interdépendance des différentes échelles spatiales d’exercice du pouvoir, notamment des échelles nationale et régionale qui sont elles-mêmes le produit de l’histoire allemande, elle offre un terrain privilégié pour l’étude de l’articulation de l’espace territorial et des espaces d’exercice du pouvoir. Croisant des approches micro et macro, cet ouvrage rend compte du dialogue de plusieurs disciplines (histoire, science politique, sociologie, études germaniques, géographie) sur les mutations qu’ont connues et que connaissent les espaces d’exercice du pouvoir en Allemagne. Il propose un regard pluridisciplinaire et une réflexion fondée sur les derniers développements de la recherche