Showing papers by "University of North Carolina at Chapel Hill published in 2019"
TL;DR: GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models.
Abstract: The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the ‘GO ribbon’ widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.
2,138 citations
TL;DR: The NLRP3 inflammasome mediates pro-inflammatory responses and pyroptotic cell death and how it is being targeted to treat inflammatory diseases is described.
Abstract: NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) is an intracellular sensor that detects a broad range of microbial motifs, endogenous danger signals and environmental irritants, resulting in the formation and activation of the NLRP3 inflammasome. Assembly of the NLRP3 inflammasome leads to caspase 1-dependent release of the pro-inflammatory cytokines IL-1β and IL-18, as well as to gasdermin D-mediated pyroptotic cell death. Recent studies have revealed new regulators of the NLRP3 inflammasome, including new interacting or regulatory proteins, metabolic pathways and a regulatory mitochondrial hub. In this Review, we present the molecular, cell biological and biochemical bases of NLRP3 activation and regulation and describe how this mechanistic understanding is leading to potential therapeutics that target the NLRP3 inflammasome.
2,097 citations
20 Aug 2019
TL;DR: The LXMERT (Learning Cross-Modality Encoder Representations from Transformers) framework, a large-scale Transformer model that consists of three encoders, achieves the state-of-the-art results on two visual question answering datasets and shows the generalizability of the pre-trained cross-modality model.
Abstract: Vision-and-language reasoning requires an understanding of visual concepts, language semantics, and, most importantly, the alignment and relationships between these two modalities. We thus propose the LXMERT (Learning Cross-Modality Encoder Representations from Transformers) framework to learn these vision-and-language connections. In LXMERT, we build a large-scale Transformer model that consists of three encoders: an object relationship encoder, a language encoder, and a cross-modality encoder. Next, to endow our model with the capability of connecting vision and language semantics, we pre-train the model with large amounts of image-and-sentence pairs, via five diverse representative pre-training tasks: masked language modeling, masked object prediction (feature regression and label classification), cross-modality matching, and image question answering. These tasks help in learning both intra-modality and cross-modality relationships. After fine-tuning from our pre-trained parameters, our model achieves the state-of-the-art results on two visual question answering datasets (i.e., VQA and GQA). We also show the generalizability of our pre-trained cross-modality model by adapting it to a challenging visual-reasoning task, NLVR2, and improve the previous best result by 22% absolute (54% to 76%). Lastly, we demonstrate detailed ablation studies to prove that both our novel model components and pre-training strategies significantly contribute to our strong results. Code and pre-trained models publicly available at: https://github.com/airsplay/lxmert
1,729 citations
University of Oklahoma1, University of Vermont2, University of Missouri–Kansas City3, Children's Mercy Hospital4, Boston Children's Hospital5, Harvard University6, University of North Carolina at Chapel Hill7, Ohio University8, American Academy of Pediatrics9, University of Cincinnati10, Cincinnati Children's Hospital Medical Center11, American Academy of Family Physicians12, Centers for Disease Control and Prevention13, Vanderbilt University14, Northwestern University15, American Academy of Child and Adolescent Psychiatry16
TL;DR: Attention-deficit/hyperactivity disorder (ADHD) is the most common neurobehavioral disorder of childhood and can profoundly affect the academic achievement, well-being, and social interactions of children.
Abstract: Attention-deficit/hyperactivity disorder (ADHD) is the most common neurobehavioral disorder of childhood and can profoundly affect the academic achievement, well-being, and social interactions of children; the American Academy of Pediatrics first published clinical recommendations for the diagnosis and evaluation of ADHD in children in 2000; recommendations for treatment followed in 2001.
1,657 citations
TL;DR: In this article, the authors propose guidelines for rigorous experimental characterization of liquid-liquid phase separation processes in vitro and in cells, discuss the caveats of common experimental approaches, and point out experimental and theoretical gaps in the field.
1,482 citations
VU University Amsterdam1, Karolinska Institutet2, deCODE genetics3, Vanderbilt University4, Jönköping University5, University of Oslo6, Oslo University Hospital7, King's College London8, Stavanger University Hospital9, Akershus University Hospital10, University of Tromsø11, Innlandet Hospital Trust12, Norwegian University of Science and Technology13, University of California, San Francisco14, Vanderbilt University Medical Center15, University of Iceland16, University of Cambridge17, University of Bergen18, University College London19, Namsos Hospital20, University of North Carolina at Chapel Hill21, Charité22, Broad Institute23, Harvard University24, VU University Medical Center25
TL;DR: A large genome-wide association study of clinically diagnosed AD and AD-by-proxy identifies new loci and functional pathways that contribute to AD risk and adds novel insights into the neurobiology of AD.
Abstract: Alzheimer's disease (AD) is highly heritable and recent studies have identified over 20 disease-associated genomic loci. Yet these only explain a small proportion of the genetic variance, indicating that undiscovered loci remain. Here, we performed a large genome-wide association study of clinically diagnosed AD and AD-by-proxy (71,880 cases, 383,378 controls). AD-by-proxy, based on parental diagnoses, showed strong genetic correlation with AD (rg = 0.81). Meta-analysis identified 29 risk loci, implicating 215 potential causative genes. Associated genes are strongly expressed in immune-related tissues and cell types (spleen, liver, and microglia). Gene-set analyses indicate biological mechanisms involved in lipid-related processes and degradation of amyloid precursor proteins. We show strong genetic correlations with multiple health-related outcomes, and Mendelian randomization results suggest a protective effect of cognitive ability on AD risk. These results are a step forward in identifying the genetic factors that contribute to AD risk and add novel insights into the neurobiology of AD.
1,460 citations
Lundbeck1, Aarhus University2, Harvard University3, Broad Institute4, Karolinska Institutet5, Cardiff University6, Statens Serum Institut7, QIMR Berghofer Medical Research Institute8, University of Iceland9, deCODE genetics10, Mental Health Services11, Charité12, Semel Institute for Neuroscience and Human Behavior13, University of California, Los Angeles14, University of Queensland15, Oslo University Hospital16, King's College London17, University of Toronto18, VU University Amsterdam19, Radboud University Nijmegen20, Veterans Health Administration21, Yale University22, Children's Hospital of Philadelphia23, Haukeland University Hospital24, University of Bergen25, University of Pennsylvania26, I.M. Sechenov First Moscow State Medical University27, University of Würzburg28, Maastricht University29, Goethe University Frankfurt30, Universidade Federal do Rio Grande do Sul31, Icahn School of Medicine at Mount Sinai32, University of North Carolina at Chapel Hill33, Emory University34, University of Copenhagen35, Aarhus University Hospital36, State University of New York Upstate Medical University37
TL;DR: A genome-wide association meta-analysis of 20,183 individuals diagnosed with ADHD and 35,191 controls identifies variants surpassing genome- wide significance in 12 independent loci and implicates neurodevelopmental pathways and conserved regions of the genome as being involved in underlying ADHD biology.
Abstract: Attention deficit/hyperactivity disorder (ADHD) is a highly heritable childhood behavioral disorder affecting 5% of children and 2.5% of adults. Common genetic variants contribute substantially to ADHD susceptibility, but no variants have been robustly associated with ADHD. We report a genome-wide association meta-analysis of 20,183 individuals diagnosed with ADHD and 35,191 controls that identifies variants surpassing genome-wide significance in 12 independent loci, finding important new information about the underlying biology of ADHD. Associations are enriched in evolutionarily constrained genomic regions and loss-of-function intolerant genes and around brain-expressed regulatory marks. Analyses of three replication studies: a cohort of individuals diagnosed with ADHD, a self-reported ADHD sample and a meta-analysis of quantitative measures of ADHD symptoms in the population, support these findings while highlighting study-specific differences on genetic overlap with educational attainment. Strong concordance with GWAS of quantitative population measures of ADHD symptoms supports that clinical diagnosis of ADHD is an extreme expression of continuous heritable traits.
1,436 citations
Royal Edinburgh Hospital1, Centre for Mental Health2, King's College London3, University of Glasgow4, University of Edinburgh5, Medical Research Council6, University of Münster7, University of Melbourne8, University of Freiburg9, University of Queensland10, Charité11, Harvard University12, Broad Institute13, Karolinska Institutet14, University of North Carolina at Chapel Hill15
TL;DR: A genetic meta-analysis of depression found 269 associated genes that highlight several potential drug repositioning opportunities, and relationships with depression were found for neuroticism and smoking.
Abstract: Major depression is a debilitating psychiatric illness that is typically associated with low mood and anhedonia. Depression has a heritable component that has remained difficult to elucidate with current sample sizes due to the polygenic nature of the disorder. To maximize sample size, we meta-analyzed data on 807,553 individuals (246,363 cases and 561,190 controls) from the three largest genome-wide association studies of depression. We identified 102 independent variants, 269 genes, and 15 genesets associated with depression, including both genes and gene pathways associated with synaptic structure and neurotransmission. An enrichment analysis provided further evidence of the importance of prefrontal brain regions. In an independent replication sample of 1,306,354 individuals (414,055 cases and 892,299 controls), 87 of the 102 associated variants were significant after multiple testing correction. These findings advance our understanding of the complex genetic architecture of depression and provide several future avenues for understanding etiology and developing new treatment approaches.
1,312 citations
TL;DR: Genome-wide analysis identifies 30 loci associated with bipolar disorder, allowing for comparisons of shared genes and pathways with other psychiatric disorders, including schizophrenia and depression.
Abstract: Bipolar disorder is a highly heritable psychiatric disorder. We performed a genome-wide association study (GWAS) including 20,352 cases and 31,358 controls of European descent, with follow-up analysis of 822 variants with P < 1 × 10-4 in an additional 9,412 cases and 137,760 controls. Eight of the 19 variants that were genome-wide significant (P < 5 × 10-8) in the discovery GWAS were not genome-wide significant in the combined analysis, consistent with small effect sizes and limited power but also with genetic heterogeneity. In the combined analysis, 30 loci were genome-wide significant, including 20 newly identified loci. The significant loci contain genes encoding ion channels, neurotransmitter transporters and synaptic components. Pathway analysis revealed nine significantly enriched gene sets, including regulation of insulin secretion and endocannabinoid signaling. Bipolar I disorder is strongly genetically correlated with schizophrenia, driven by psychosis, whereas bipolar II disorder is more strongly correlated with major depressive disorder. These findings address key clinical questions and provide potential biological mechanisms for bipolar disorder.
1,090 citations
TL;DR: The recent advances in passivation of imperfections and suppressing ion migration to achieve improved efficiency and highly stable perovskite solar cells are reviewed.
Abstract: All highly-efficient organic–inorganic halide perovskite (OIHP) solar cells to date are made of polycrystalline perovskite films which contain a high density of defects, including point and extended imperfections. The imperfections in OIHP materials play an important role in the process of charge recombination and ion migration in perovskite solar cells (PSC), which heavily influences the resulting device energy conversion efficiency and stability. Here we review the recent advances in passivation of imperfections and suppressing ion migration to achieve improved efficiency and highly stable perovskite solar cells. Due to the ionic nature of OIHP materials, the defects in the photoactive films are inevitably electrically charged. The deep level traps induced by particular charged defects in OIHP films are major non-radiative recombination centers; passivation by coordinate bonding, ionic bonding, or chemical conversion have proven effective in mitigating the negative impacts of these deep traps. Shallow level charge traps themselves may contribute little to non-radiative recombination, but the migration of charged shallow level traps in OIHP films results in unfavorable band bending, interfacial reactions, and phase segregation, influencing the carrier extraction efficiency. Finally, the impact of defects and ion migration on the stability of perovskite solar cells is described.
1,040 citations
TL;DR: GI diseases contribute substantially to health care use in the United States and total expenditures for GI diseases are $135.9 billion annually-greater than for other common diseases.
University of California, Los Angeles1, University of Mississippi Medical Center2, Fred Hutchinson Cancer Research Center3, Rutgers University4, Public Health England5, Northwestern University6, Columbia University7, University of North Carolina at Chapel Hill8, Stanford University9, National Institutes of Health10
TL;DR: Using large scale validation data from thousands of individuals, it is demonstrated that DNAm GrimAge stands out among existing epigenetic clocks in terms of its predictive ability for time-to-death, and a novel measure of epigenetic age acceleration, AgeAccelGrim.
Abstract: It was unknown whether plasma protein levels can be estimated based on DNA methylation (DNAm) levels, and if so, how the resulting surrogates can be consolidated into a powerful predictor of lifespan. We present here, seven DNAm-based estimators of plasma proteins including those of plasminogen activator inhibitor 1 (PAI-1) and growth differentiation factor 15. The resulting predictor of lifespan, DNAm GrimAge (in units of years), is a composite biomarker based on the seven DNAm surrogates and a DNAm-based estimator of smoking pack-years. Adjusting DNAm GrimAge for chronological age generated novel measure of epigenetic age acceleration, AgeAccelGrim.Using large scale validation data from thousands of individuals, we demonstrate that DNAm GrimAge stands out among existing epigenetic clocks in terms of its predictive ability for time-to-death (Cox regression P=2.0E-75), time-to-coronary heart disease (Cox P=6.2E-24), time-to-cancer (P= 1.3E-12), its strong relationship with computed tomography data for fatty liver/excess visceral fat, and age-at-menopause (P=1.6E-12). AgeAccelGrim is strongly associated with a host of age-related conditions including comorbidity count (P=3.45E-17). Similarly, age-adjusted DNAm PAI-1 levels are associated with lifespan (P=5.4E-28), comorbidity count (P= 7.3E-56) and type 2 diabetes (P=2.0E-26). These DNAm-based biomarkers show the expected relationship with lifestyle factors including healthy diet and educational attainment.Overall, these epigenetic biomarkers are expected to find many applications including human anti-aging studies.
01 Sep 2019
TL;DR: A 3 year update on the current clinical landscape of nanoparticle drug delivery systems and highlight newly approved nanomedicines, provide a status update on previous clinical trials, and highlight new technologies that have recently entered the clinic are provided.
Abstract: Nanoparticle drug delivery systems have been used in the clinic since the early 1990's. Since that time, the field of nanomedicine has evolved alongside growing technological needs to improve the delivery of various therapeutics. Over these past decades, newer generations of nanoparticles have emerged that are capable of performing additional delivery functions that can enable treatment via new therapeutic modalities. In the current clinical landscape, many of these new generation nanoparticles have reached clinical trials and have been approved for various indications. In the first issue of Bioengineering & Translational Medicine in 2016, we reviewed the history, current clinical landscape, and clinical challenges of nanoparticle delivery systems. Here, we provide a 3 year update on the current clinical landscape of nanoparticle drug delivery systems and highlight newly approved nanomedicines, provide a status update on previous clinical trials, and highlight new technologies that have recently entered the clinic.
TL;DR: The proposed method, Approximate Posterior Estimation for generalized linear model, apeglm, has lower bias than previously proposed shrinkage estimators, while still reducing variance for those genes with little information for statistical inference.
Abstract: MOTIVATION In RNA-seq differential expression analysis, investigators aim to detect those genes with changes in expression level across conditions, despite technical and biological variability in the observations. A common task is to accurately estimate the effect size, often in terms of a logarithmic fold change (LFC). RESULTS When the read counts are low or highly variable, the maximum likelihood estimates for the LFCs has high variance, leading to large estimates not representative of true differences, and poor ranking of genes by effect size. One approach is to introduce filtering thresholds and pseudocounts to exclude or moderate estimated LFCs. Filtering may result in a loss of genes from the analysis with true differences in expression, while pseudocounts provide a limited solution that must be adapted per dataset. Here, we propose the use of a heavy-tailed Cauchy prior distribution for effect sizes, which avoids the use of filter thresholds or pseudocounts. The proposed method, Approximate Posterior Estimation for generalized linear model, apeglm, has lower bias than previously proposed shrinkage estimators, while still reducing variance for those genes with little information for statistical inference. AVAILABILITY AND IMPLEMENTATION The apeglm package is available as an R/Bioconductor package at https://bioconductor.org/packages/apeglm, and the methods can be called from within the DESeq2 software. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
TL;DR: Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes.
TL;DR: In this paper, the authors identify three key themes related to digitization (Openness, affordances, and generativity) and outline broad research issues relating to each, and suggest that such themes that are innate to digital technologies could serve as a common conceptual platform that allows for connections between issues at different levels as well as the integration of ideas from different disciplines/areas.
TL;DR: These guidelines indicate the preferred approach to the management of adults with UC and represent the official practice recommendations of the American College of Gastroenterology.
Harvard University1, University of Chicago2, Columbia University3, University of Colorado Boulder4, Duke University5, Baptist Health6, Washington University in St. Louis7, University of Minnesota8, Houston Methodist Hospital9, University of Nebraska Medical Center10, Yale University11, MedStar Washington Hospital Center12, University of Michigan13, Advocate Lutheran General Hospital14, St Thomas' Hospital15, University of North Carolina at Chapel Hill16, Piedmont Hospital17, Abbott Laboratories18
TL;DR: Among patients with advanced heart failure, a fully magnetically levitated centrifugal‐flow left ventricular assist device was associated with less frequent need for pump replacement than an axial‐flow device and was superior with respect to survival free of disabling stroke or reoperation to replace or remove a malfunctioning device.
Abstract: Background In two interim analyses of this trial, patients with advanced heart failure who were treated with a fully magnetically levitated centrifugal-flow left ventricular assist device ...
Daniel Taliun1, Daniel N. Harris2, Michael D. Kessler2, Jedidiah Carlson1 +191 more•Institutions (61)
TL;DR: The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation as well as resources and early insights from the sequence data.
Abstract: Summary paragraph The Trans-Omics for Precision Medicine (TOPMed) program seeks to elucidate the genetic architecture and disease biology of heart, lung, blood, and sleep disorders, with the ultimate goal of improving diagnosis, treatment, and prevention. The initial phases of the program focus on whole genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here, we describe TOPMed goals and design as well as resources and early insights from the sequence data. The resources include a variant browser, a genotype imputation panel, and sharing of genomic and phenotypic data via dbGaP. In 53,581 TOPMed samples, >400 million single-nucleotide and insertion/deletion variants were detected by alignment with the reference genome. Additional novel variants are detectable through assembly of unmapped reads and customized analysis in highly variable loci. Among the >400 million variants detected, 97% have frequency
16 Jul 2019
TL;DR: HotStuff is the first partially synchronous BFT replication protocol exhibiting these combined properties, and its simplicity enables it to be further pipelined and simplified into a practical, concise protocol for building large-scale replication services.
Abstract: We present HotStuff, a leader-based Byzantine fault-tolerant replication protocol for the partially synchronous model. Once network communication becomes synchronous, HotStuff enables a correct leader to drive the protocol to consensus at the pace of actual (vs. maximum) network delay--a property called responsiveness---and with communication complexity that is linear in the number of replicas. To our knowledge, HotStuff is the first partially synchronous BFT replication protocol exhibiting these combined properties. Its simplicity enables it to be further pipelined and simplified into a practical, concise protocol for building large-scale replication services.
TL;DR: The findings indicate that the immunotherapeutic fibrin gel ‘awakens’ the host innate and adaptive immune systems to inhibit both local tumour recurrence post surgery and potential metastatic spread.
Abstract: Cancer recurrence after surgical resection remains a significant cause of treatment failure. Here, we have developed an in situ formed immunotherapeutic bioresponsive gel that controls both local tumour recurrence after surgery and development of distant tumours. Briefly, calcium carbonate nanoparticles pre-loaded with the anti-CD47 antibody are encapsulated in the fibrin gel and scavenge H+ in the surgical wound, allowing polarization of tumour-associated macrophages to the M1-like phenotype. The released anti-CD47 antibody blocks the ‘don’t eat me’ signal in cancer cells, thereby increasing phagocytosis of cancer cells by macrophages. Macrophages can promote effective antigen presentation and initiate T cell mediated immune responses that control tumour growth. Our findings indicate that the immunotherapeutic fibrin gel ‘awakens’ the host innate and adaptive immune systems to inhibit both local tumour recurrence post surgery and potential metastatic spread. A gel with therapeutic nanoformulation that can be sprayed at the tumour resection site after surgery activates immune response in the tissue microenviroment, inhibiting tumour recurrence and potential metastasis.
TL;DR: A model wherein type III IFNs serve as a front-line defense that controls infection at epithelial barriers while minimizing damaging inflammatory responses, reserving the more potent type I IFN response for when local responses are insufficient is discussed.
Stanford University1, University of North Carolina at Chapel Hill2, Fred Hutchinson Cancer Research Center3, Vanderbilt University4, Anschutz Medical Campus5, University of Southern California6, Icahn School of Medicine at Mount Sinai7, University of California, San Francisco8, University of Hawaii9, University of Washington10, University of Texas Health Science Center at Houston11, University of Potsdam12, Johns Hopkins University13, Pennsylvania State University14, National Institutes of Health15, University of California, Davis16, Ohio State University17, Cancer Prevention Institute of California18, University of Vermont19, Rutgers University20
TL;DR: The value of diverse, multi-ethnic participants in large-scale genomic studies is demonstrated and evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications are shown.
Abstract: Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.
Vanderbilt University Medical Center1, The Ohio State University Wexner Medical Center2, Ohio State University3, Sutter Health4, University of California, San Francisco5, Stanford University6, VA Palo Alto Healthcare System7, Innovative Solutions & Support8, University of North Carolina at Chapel Hill9, Tufts Medical Center10, University of Chicago11, Houston Methodist Hospital12, Society of Critical Care Medicine13, Novant Health14, Saint Joseph Mercy Health System15, University of Pennsylvania16, Johns Hopkins University17
TL;DR: ABCDEF bundle performance showed significant and clinically meaningful improvements in outcomes including survival, mechanical ventilation use, coma, delirium, restraint-free care, ICU readmissions, and post-ICU discharge disposition.
Abstract: Objective:Decades-old, common ICU practices including deep sedation, immobilization, and limited family access are being challenged. We endeavoured to evaluate the relationship between ABCDEF bundle performance and patient-centered outcomes in critical care.Design:Prospective, multicenter, cohort st
TL;DR: Th Thin lead oxysalt layers passivate hybrid perovskite surfaces under an ambient atmosphere and enhance solar cell efficiency and formation of the lead oxYSalt layer increases the carrier recombination lifetime and boosts the efficiency of the solar cells to 21.1%.
Abstract: We show that converting the surfaces of lead halide perovskite to water-insoluble lead (II) oxysalt through reaction with sulfate or phosphate ions can effectively stabilize the perovskite surface and bulk material. These capping lead oxysalt thin layers enhance the water resistance of the perovskite films by forming strong chemical bonds. The wide-bandgap lead oxysalt layers also reduce the defect density on the perovskite surfaces by passivating undercoordinated surface lead centers, which are defect-nucleating sites. Formation of the lead oxysalt layer increases the carrier recombination lifetime and boosts the efficiency of the solar cells to 21.1%. Encapsulated devices stabilized by the lead oxysalt layers maintain 96.8% of their initial efficiency after operation at maximum power point under simulated air mass (AM) 1.5 G irradiation for 1200 hours at 65°C.
Humboldt University of Berlin1, Oregon Health & Science University2, Queen Mary University of London3, Lawrence Berkeley National Laboratory4, European Bioinformatics Institute5, Oregon State University6, University of North Carolina at Chapel Hill7, Curtin University8, Government of Western Australia9, Chestnut Hill College10, Vrije Universiteit Brussel11, Garvan Institute of Medical Research12, University of Toronto13, National Institutes of Health14, Medical College of Wisconsin15, Pompeu Fabra University16, Manchester Royal Eye Hospital17, French Institute of Health and Medical Research18, Sanford Health19, Stanford University20, Utrecht University21, Newcastle University22, Icahn School of Medicine at Mount Sinai23, University College London24, University of Strasbourg25, Children's Hospital of Philadelphia26, University of Connecticut27
TL;DR: The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data and plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data.
Abstract: The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
TL;DR: This study shows that clinical response to anti-PD-1 immunotherapy in GBM is associated with specific molecular alterations, immune expression signatures, and immune infiltration that reflect the tumor’s clonal evolution during treatment.
Abstract: Immune checkpoint inhibitors have been successful across several tumor types; however, their efficacy has been uncommon and unpredictable in glioblastomas (GBM), where <10% of patients show long-term responses. To understand the molecular determinants of immunotherapeutic response in GBM, we longitudinally profiled 66 patients, including 17 long-term responders, during standard therapy and after treatment with PD-1 inhibitors (nivolumab or pembrolizumab). Genomic and transcriptomic analysis revealed a significant enrichment of PTEN mutations associated with immunosuppressive expression signatures in non-responders, and an enrichment of MAPK pathway alterations (PTPN11, BRAF) in responders. Responsive tumors were also associated with branched patterns of evolution from the elimination of neoepitopes as well as with differences in T cell clonal diversity and tumor microenvironment profiles. Our study shows that clinical response to anti-PD-1 immunotherapy in GBM is associated with specific molecular alterations, immune expression signatures, and immune infiltration that reflect the tumor’s clonal evolution during treatment. Genomic, transcriptomic, and microenvironmental analyses of samples from patients with glioblastoma treated with nivolumab or pembrolizumab identifies features associated with treatment response that may help in refining patient stratification.
TL;DR: The genetic architecture of anorexia nervosa mirrors its clinical presentation, showing significant genetic correlations with psychiatric disorders, physical activity, and metabolic (including glycemic), lipid and anthropometric traits, independent of the effects of common variants associated with body-mass index.
Abstract: Characterized primarily by a low body-mass index, anorexia nervosa is a complex and serious illness1, affecting 0.9-4% of women and 0.3% of men2-4, with twin-based heritability estimates of 50-60%5. Mortality rates are higher than those in other psychiatric disorders6, and outcomes are unacceptably poor7. Here we combine data from the Anorexia Nervosa Genetics Initiative (ANGI)8,9 and the Eating Disorders Working Group of the Psychiatric Genomics Consortium (PGC-ED) and conduct a genome-wide association study of 16,992 cases of anorexia nervosa and 55,525 controls, identifying eight significant loci. The genetic architecture of anorexia nervosa mirrors its clinical presentation, showing significant genetic correlations with psychiatric disorders, physical activity, and metabolic (including glycemic), lipid and anthropometric traits, independent of the effects of common variants associated with body-mass index. These results further encourage a reconceptualization of anorexia nervosa as a metabo-psychiatric disorder. Elucidating the metabolic component is a critical direction for future research, and paying attention to both psychiatric and metabolic components may be key to improving outcomes.
TL;DR: Using a make-on-demand library that contains hundreds-of-millions of molecules, structure-based docking was used to identify compounds that, after synthesis and testing, are shown to interact with AmpC β-lactamase and the D4 dopamine receptor with high affinity.
Abstract: Despite intense interest in expanding chemical space, libraries containing hundreds-of-millions to billions of diverse molecules have remained inaccessible. Here we investigate structure-based docking of 170 million make-on-demand compounds from 130 well-characterized reactions. The resulting library is diverse, representing over 10.7 million scaffolds that are otherwise unavailable. For each compound in the library, docking against AmpC β-lactamase (AmpC) and the D4 dopamine receptor were simulated. From the top-ranking molecules, 44 and 549 compounds were synthesized and tested for interactions with AmpC and the D4 dopamine receptor, respectively. We found a phenolate inhibitor of AmpC, which revealed a group of inhibitors without known precedent. This molecule was optimized to 77 nM, which places it among the most potent non-covalent AmpC inhibitors known. Crystal structures of this and other AmpC inhibitors confirmed the docking predictions. Against the D4 dopamine receptor, hit rates fell almost monotonically with docking score, and a hit-rate versus score curve predicted that the library contained 453,000 ligands for the D4 dopamine receptor. Of 81 new chemotypes discovered, 30 showed submicromolar activity, including a 180-pM subtype-selective agonist of the D4 dopamine receptor. Using a make-on-demand library that contains hundreds-of-millions of molecules, structure-based docking was used to identify compounds that, after synthesis and testing, are shown to interact with AmpC β-lactamase and the D4 dopamine receptor with high affinity.
TL;DR: This work systematically engineer the structures of passivation molecular functional groups, including carboxyl, amine, isopropyl, phenethyl, and tert-butylphenethyl groups, and study their passivation capability to perovskites to provide guidance for future design of new passivation molecules to realize multiple facets applications in perovkite electronics.
Abstract: Passivation of electronic defects at the surface and grain boundaries of perovskite materials has become one of the most important strategies to suppress charge recombination in both polycrystalline and single-crystalline perovskite solar cells. Although many passivation molecules have been reported, it remains very unclear regarding the passivation mechanisms of various functional groups. Here, we systematically engineer the structures of passivation molecular functional groups, including carboxyl, amine, isopropyl, phenethyl, and tert-butylphenethyl groups, and study their passivation capability to perovskites. It reveals the carboxyl and amine groups would heal charged defects via electrostatic interactions, and the neutral iodine related defects can be reduced by the aromatic structures. The judicious control of the interaction between perovskite and molecules can further realize grain boundary passivation, including those that are deep toward substrates. Understanding of the underlining mechanisms allows us to design a new passivation molecule, D-4- tert-butylphenylalanine, yielding high-performance p-i-structure solar cells with a stabilized efficiency of 21.4%. The open-circuit voltage ( VOC) of a device with an optical bandgap of 1.57 eV for the perovskite layer reaches 1.23 V, corresponding to a record small VOC deficit of 0.34 V. Our findings provide a guidance for future design of new passivation molecules to realize multiple facets applications in perovskite electronics.