35 research outputs found

    SLCO5A1 and synaptic assembly genes contribute to impulsivity in juvenile myoclonic epilepsy

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    Elevated impulsivity is a key component of attention-deficit hyperactivity disorder (ADHD), bipolar disorder and juvenile myoclonic epilepsy (JME). We performed a genome-wide association, colocalization, polygenic risk score, and pathway analysis of impulsivity in JME (n = 381). Results were followed up with functional characterisation using a drosophila model. We identified genome-wide associated SNPs at 8q13.3 (P = 7.5 × 10−9) and 10p11.21 (P = 3.6 × 10−8). The 8q13.3 locus colocalizes with SLCO5A1 expression quantitative trait loci in cerebral cortex (P = 9.5 × 10−3). SLCO5A1 codes for an organic anion transporter and upregulates synapse assembly/organisation genes. Pathway analysis demonstrates 12.7-fold enrichment for presynaptic membrane assembly genes (P = 0.0005) and 14.3-fold enrichment for presynaptic organisation genes (P = 0.0005) including NLGN1 and PTPRD. RNAi knockdown of Oatp30B, the Drosophila polypeptide with the highest homology to SLCO5A1, causes over-reactive startling behaviour (P = 8.7 × 10−3) and increased seizure-like events (P = 6.8 × 10−7). Polygenic risk score for ADHD genetically correlates with impulsivity scores in JME (P = 1.60 × 10−3). SLCO5A1 loss-of-function represents an impulsivity and seizure mechanism. Synaptic assembly genes may inform the aetiology of impulsivity in health and disease

    The European Neuromuscular Centre Consensus Statement on Anaesthesia in Patients with Neuromuscular Disorders.

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    BACKGROUND Patients with neuromuscular conditions are at increased risk of suffering peri-operative complications related to anaesthesia. There is currently little specific anaesthetic guidance concerning these patients. Here we present the European Neuromuscular Centre (ENMC) consensus statement on anaesthesia in patients with neuromuscular disorders as formulated during the 259th ENMC workshop on Anaesthesia in neuromuscular disorders. METHODS International experts in the field of (paediatric) anaesthesia, neurology and genetics were invited to participate in the ENMC workshop. A literature search was conducted in PubMed and EMBASE whose main findings were disseminated to the participants and presented during the workshop. Depending on specific expertise, participants presented the existing evidence and their expert opinion concerning anaesthetic management in six specific groups of myopathies and neuromuscular junction disorders. The consensus statement was prepared according to the Appraisal of Guidelines for REsearch & Evaluation (AGREE II) reporting checklist. The level of evidence has been adapted according to the Scottish Intercollegiate Guidelines Network (SIGN) grading system. The final consensus statement was subjected to a modified Delphi process. RESULTS A set of general recommendations valid for the anaesthetic management of patients with neuromuscular disorders in general have been formulated. Specific recommendations were formulated for 1) neuromuscular junction disorders; 2) muscle channelopathies (non-dystrophic myotonia and periodic paralysis); 3) myotonic dystrophy (type 1 and 2); 4) muscular dystrophies; 5) congenital myopathies and congenital dystrophies and 6) mitochondrial and metabolic myopathies. CONCLUSION This ENMC consensus statement summarizes the most important considerations for planning and performing anaesthesia in patients with neuromuscular disorders

    A genomic catalog of Earth’s microbiomes

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    The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.</p

    Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

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    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

    IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.

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    The Integrated Microbial Genomes &amp; Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) allows registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has grown by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning

    Single-Frame Super-Resolution of Solar Magnetograms: Investigating Physics-Based Metrics \& Losses

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    Breakthroughs in our understanding of physical phenomena have traditionally followed improvements in instrumentation. Studies of the magnetic field of the Sun, and its influence on the solar dynamo and space weather events, have benefited from improvements in resolution and measurement frequency of new instruments. However, in order to fully understand the solar cycle, high-quality data across time-scales longer than the typical lifespan of a solar instrument are required. At the moment, discrepancies between measurement surveys prevent the combined use of all available data. In this work, we show that machine learning can help bridge the gap between measurement surveys by learning to \textbf{super-resolve} low-resolution magnetic field images and \textbf{translate} between characteristics of contemporary instruments in orbit. We also introduce the notion of physics-based metrics and losses for super-resolution to preserve underlying physics and constrain the solution space of possible super-resolution outputs

    Probabilistic Super-Resolution of Solar Magnetograms: Generating Many Explanations and Measuring Uncertainties

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    Machine learning techniques have been successfully applied to super-resolution tasks on natural images where visually pleasing results are sufficient. However in many scientific domains this is not adequate and estimations of errors and uncertainties are crucial. To address this issue we propose a Bayesian framework that decomposes uncertainties into epistemic and aleatoric uncertainties. We test the validity of our approach by super-resolving images of the Sun's magnetic field and by generating maps measuring the range of possible high resolution explanations compatible with a given low resolution magnetogram

    Super-Resolution Maps of the Solar Magnetic Field Covering 40 Years of Space Weather Events

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    As modern society becomes increasingly dependent on technology, space weather events will have a farther-reaching impact than ever before. For nearly 10 years, NASA's Solar Dynamics Observatory (SDO) has continuously monitored the Sun, however, the SDO-era coincides with the weakest solar cycle of the last century: over the last 40 years, there have been nearly 500 X-class solar flares—around 10 times the number of events observed by SDO alone. It is also clear that there is no single observational survey with sufficient time coverage to enable an effective deep learning space weather forecasting application. Crucially, over the past 40 years, numerous observatories have monitored the Sun's magnetic field. However, cross calibrating magnetograms is a complex and non-trivial endeavour as the relationship between observed pixels is strongly affected by a wide range of systematics. Here we present a deep learning application that can convert magnetograms to a target survey while preserving the features and systematics of the target survey. We will first present our approach for upscaling and cross-calibrating images obtained by the Michelson Doppler Imager (MDI; on-board the Solar and Heliospheric Observatory, SOHO), to the resolution of the Helioseismic and Magnetic Imager (SDO/HMI). We will discuss the physics-based metrics, deep learning architectures, and the lessons learned along the way. This work was performed at NASA’s Frontier Development Laboratory (FDL), a public-private partnership to apply AI techniques to accelerate space science discovery and exploration
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