70 research outputs found

    Impact of Aeolian Dry Deposition of Reactive Iron Minerals on Sulfur Cycling in Sediments of the Gulf of Aqaba

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    The Gulf of Aqaba is an oligotrophic marine system with oxygen-rich water column and organic carbon-poor sediments (≤0.6% at sites that are not influenced by anthropogenic impact). Aeolian dust deposition from the Arabian, Sinai, and Sahara Deserts is an important source of sediment, especially at the deep-water sites of the Gulf, which are less affected by sediment transport from the Arava Desert during seasonal flash floods. Microbial sulfate reduction in sediments is inferred from the presence of pyrite (although at relatively low concentrations), the presence of sulfide oxidation intermediates, and by the sulfur isotopic composition of sulfate and solid-phase sulfides. Saharan dust is characterized by high amounts of iron minerals such as hematite and goethite. We demonstrated, that the resulting high sedimentary content of reactive iron(III) (hydr)oxides, originating from this aeolian dry deposition of desert dust, leads to fast re-oxidation of hydrogen sulfide produced during microbial sulfate reduction and limits preservation of reduced sulfur in the form of pyrite. We conclude that at these sites the sedimentary sulfur cycle may be defined as cryptic

    Intercomparison of Gridded Precipitation Datasets over a Sub-Region of the Central Himalaya and the Southwestern Tibetan Plateau

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    Precipitation is a central quantity of hydrometeorological research and applications. Especially in complex terrain, such as in High Mountain Asia (HMA), surface precipitation observations are scarce. Gridded precipitation products are one way to overcome the limitations of ground truth observations. They can provide datasets continuous in both space and time. However, there are many products available, which use various methods for data generation and lead to different precipitation values. In our study we compare nine different gridded precipitation products from different origins (ERA5, ERA5-Land, ERA-interim, HAR v2 10 km, HAR v2 2 km, JRA-55, MERRA-2, GPCC and PRETIP) over a subregion of the Central Himalaya and the Southwest Tibetan Plateau, from May to September 2017. Total spatially averaged precipitation over the study period ranged from 411 mm (GPCC) to 781 mm (ERA-Interim) with a mean value of 623 mm and a standard deviation of 132 mm. We found that the gridded products and the few observations, with few exceptions, are consistent among each other regarding precipitation variability and rough amount within the study area. It became obvious that higher grid resolution can resolve extreme precipitation much better, leading to overall lower mean precipitation spatially, but higher extreme precipitation events. We also found that generally high terrain complexity leads to larger differences in the amount of precipitation between products. Due to the considerable differences between products in space and time, we suggest carefully selecting the product used as input for any research application based on the type of application and specific research question. While coarse products such as ERA-Interim or ERA5 that cover long periods but have coarse grid resolution have previously shown to be able to capture long-term trends and help with identifying climate change features, this study suggests that more regional applications, such as glacier mass-balance modeling, require higher spatial resolution, as is reproduced, for example, in HAR v2 10 km.Peer Reviewe

    Patterns of Cis Regulatory Variation in Diverse Human Populations

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    The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations

    Deciphering the origin and therapeutic targets of cancer of unknown primary: a case report that illustrates the power of integrative whole-exome and transcriptome sequencing analysis

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    Cancer of unknown primary (CUP) represents a significant diagnostic and therapeutic challenge, being the third to fourth leading cause of cancer death, despite advances in diagnostic tools. This article presents a successful approach using a novel genomic analysis in the evaluation and treatment of a CUP patient, leveraging whole-exome sequencing (WES) and RNA sequencing (RNA-seq). The patient, with a history of multiple primary tumors including urothelial cancer, exhibited a history of rapid progression on empirical chemotherapy. The application of our approach identified a molecular target, characterized the tumor expression profile and the tumor microenvironment, and analyzed the origin of the tumor, leading to a tailored treatment. This resulted in a substantial radiological response across all metastatic sites and the predicted primary site of the tumor. We argue that a comprehensive genomic and molecular profiling approach, like the BostonGene© Tumor Portrait, can provide a more definitive, personalized treatment strategy, overcoming the limitations of current predictive assays. This approach offers a potential solution to an unmet clinical need for a standardized approach in identifying the tumor origin for the effective management of CUP

    Variation of BMP3 Contributes to Dog Breed Skull Diversity

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    Since the beginnings of domestication, the craniofacial architecture of the domestic dog has morphed and radiated to human whims. By beginning to define the genetic underpinnings of breed skull shapes, we can elucidate mechanisms of morphological diversification while presenting a framework for understanding human cephalic disorders. Using intrabreed association mapping with museum specimen measurements, we show that skull shape is regulated by at least five quantitative trait loci (QTLs). Our detailed analysis using whole-genome sequencing uncovers a missense mutation in BMP3. Validation studies in zebrafish show that Bmp3 function in cranial development is ancient. Our study reveals the causal variant for a canine QTL contributing to a major morphologic trait

    Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

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    A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

    Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

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    Background Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. Methods We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. Results Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. Conclusions Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.Peer reviewe

    Measurements of top-quark pair differential cross-sections in the eμe\mu channel in pppp collisions at s=13\sqrt{s} = 13 TeV using the ATLAS detector

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