Monte Carlo Particle Lists: MCPL

A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular simulation packages

A C. elegans Screening Platform for the Rapid Assessment of Chemical Disruption of Germline Function

Background: Despite the developmental impact of chromosome segregation errors, we lack the tools to assess environmental effects on the integrity of the germline in animals. Objectives: We developed an assay in Caenorhabditis elegans that fluorescently marks aneuploid embryos after chemical exposure. Methods: We qualified the predictive value of the assay against chemotherapeutic agents as well as environmental compounds from the ToxCast Phase I library by comparing results from the C. elegans assay with the comprehensive mammalian in vivo end point data from the ToxRef database. Results: The assay was highly predictive of mammalian reproductive toxicities, with a 69% maximum balanced accuracy. We confirmed the effect of select compounds on germline integrity by monitoring germline apoptosis and meiotic progression. Conclusions: This C. elegans assay provides a comprehensive strategy for assessing environmental effects on germline function

Disruption of VEGFR signaling leading to developmental defects

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Pluripotent stem cell assays: Modalities and applications for predictive developmental toxicity

This manuscript provides a review focused on embryonic stem cell-based models and their place within the landscape of alternative developmental toxicity assays. Against the background of the principles of developmental toxicology, the wide diversity of alternative methods using pluripotent stem cells developed in this area over the past half century is reviewed. In order to provide an overview of available models, a systematic scoping review was conducted following a published protocol with inclusion criteria, which were applied to select the assays. Critical aspects including biological domain, readout endpoint, availability of standardized protocols, chemical domain, reproducibility and predictive power of each assay are described in detail, in order to review the applicability and limitations of the platform in general and progress moving forward to implementation. The horizon of innovative routes of promoting regulatory implementation of alternative methods is scanned, and recommendations for further work are given

From clear lakes to murky waters - tracing the functional response of high-latitude lake communities to concurrent 'greening' and 'browning'

Climate change and the intensification of land use practices are causing widespread eutrophication of subarctic lakes. The implications of this rapid change for lake ecosystem function remain poorly understood. To assess how freshwater communities respond to such profound changes in their habitat and resource availability, we conducted a space-for-time analysis of food-web structure in 30 lakes situated across a temperature-productivity gradient equivalent to the predicted future climate of subarctic Europe (temperature +3 degrees C, precipitation +30% and nutrient +45 mu g L-1 total phosphorus). Along this gradient, we observed an increase in the assimilation of pelagic-derived carbon from 25 to 75% throughout primary, secondary and tertiary consumers. This shift was overwhelmingly driven by the consumption of pelagic detritus by benthic primary consumers and was not accompanied by increased pelagic foraging by higher trophic level consumers. Our data also revealed a convergence of the carbon isotope ratios of pelagic and benthic food web endmembers in the warmest, most productive lakes indicating that the incorporation of terrestrial derived carbon into aquatic food webs increases as land use intensifies. These results, reflecting changes along a gradient characteristic of the predicted future environment throughout the subarctic, indicate that climate and land use driven eutrophication and browning are radically altering the function and fuelling of aquatic food webs in this biome.Peer reviewe

Reduced somatostatin signalling leads to hypersecretion of glucagon in mice fed a high-fat diet

Objectives:&nbsp;Elevated plasma glucagon is an early symptom of diabetes, occurring in subjects with impaired glucose regulation. Here, we explored alpha-cell function in female mice fed a high-fat diet (HFD)&mdash;a widely used mouse model of prediabetes. Methods:&nbsp;We fed female mice expressing the Ca2+&nbsp;indicator GCaMP3 specifically in alpha-cells an HFD or control (CTL) diet. We then conducted&nbsp;in&nbsp;vivo&nbsp;phenotyping of these mice, as well as experiments on isolated (ex&nbsp;vivo) islets and in the&nbsp;in situ&nbsp;perfused pancreas. Results:&nbsp;In&nbsp;vivo,&nbsp;HFD-fed mice exhibited increased fed plasma glucagon levels and a reduced response to elevations in plasma glucose. Glucagon secretion from isolated islets and in the perfused mouse pancreas was elevated under both hypo- and hyperglycaemic conditions. In mice fed a CTL diet, increasing glucose reduced intracellular Ca2+&nbsp;([Ca2+]i) (oscillation frequency and amplitude). This effect was also observed in HFD mice; however, both the frequency and amplitude of the [Ca2+]i&nbsp;oscillations were higher than those in CTL alpha-cells. Given that alpha-cells are under strong paracrine control from neighbouring somatostatin-secreting delta-cells, we hypothesised that this elevation of alpha-cell output was due to a lack of somatostatin (SST) secretion. Indeed, SST secretion in isolated islets from HFD mice was reduced but exogenous SST also failed to suppress glucagon secretion and [Ca2+]i&nbsp;activity from HFD alpha-cells, in contrast to observations in CTL mice. Conclusions:&nbsp;These findings suggest that reduced delta-cell function, combined with intrinsic changes in alpha-cell sensitivity to somatostatin, accounts for the hyperglucagonaemia in mice fed an HFD.</p