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Dark Matter benchmark models for early LHC Run-2 Searches: Report of the ATLAS/CMS Dark Matter Forum
(2020)Physics of the Dark UniverseThis document is the final report of the ATLAS-CMS Dark Matter Forum, a forum organized by the ATLAS and CMS collaborations with the participation of experts on theories of Dark Matter, to select a minimal basis set of dark matter simplified models that should support the design of the early LHC Run-2 searches. A prioritized, compact set of benchmark models is proposed, accompanied by studies of the parameter space of these models and a ...Journal Article -
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set
(2019)Nature CommunicationsThe current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects ...Journal Article -
DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
(2016)Research Ideas and OutcomesThe protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. ...Journal Article -
International Society of Cardiovascular Infectious Diseases Guidelines for the Diagnosis, Treatment and Prevention of Disseminated Mycobacterium chimaera Infection Following Cardiac Surgery with Cardiopulmonary Bypass
(2020)Journal of Hospital InfectionJournal Article -
High-accuracy determination of the U-238/U-235 fission cross section ratio up to approximate to 1 GeV at n_TOF at CERN
(2015)Physical Review CThe 238U to 235U fission cross section ratio has been determined at n_TOF up to ≈1 GeV, with two different detection systems, in different geometrical configurations. A total of four datasets has been collected and compared. They are all consistent to each other within the relative systematic uncertainty of 3–4%. The data collected at n_TOF have been suitably combined to yield a unique fission cross section ratio as a function of neutron ...Journal Article -
Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico
(2018)Cell Host & MicrobeThe Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, ...Journal Article -
Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
(2019)Proceedings of the National Academy of Sciences of the United States of AmericaArchaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could ...Journal Article -
Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018
(2020)PLoS PathogensSão Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby ...Journal Article -
Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer
(2018)The Journal of Clinical InvestigationBACKGROUND. Understanding the integrated immunogenomic landscape of advanced prostate cancer (APC) could impact stratified treatment selection. METHODS. Defective mismatch repair (dMMR) status was determined by either loss of mismatch repair protein expression on IHC or microsatellite instability (MSI) by PCR in 127 APC biopsies from 124 patients (Royal Marsden [RMH] cohort); MSI by targeted panel next-generation sequencing (MSINGS) ...Journal Article