Evaluation of WRF-Sfire Performance with Field Observations from the FireFlux experiment

This study uses in-situ measurements collected during the FireFlux field experiment to evaluate and improve the performance of coupled atmosphere-fire model WRF-Sfire. The simulation by WRF-Sfire of the experimental burn shows that WRF-Sfire is capable of providing realistic head fire rate-of-spread and the vertical temperature structure of the fire plume, and, up to 10 m above ground level, fire-induced surface flow and vertical velocities within the plume. The model captured the changes in wind speed and direction before, during, and after fire front passage, along with arrival times of wind speed, temperature, and updraft maximae, at the two instrumented flux towers used in FireFlux. The model overestimated vertical velocities and underestimated horizontal wind speeds measured at tower heights above the 10 m, and it is hypothesized that the limited model resolution over estimated the fire front depth, leading to too high a heat release and, subsequently, too strong an updraft. However, on the whole, WRF-Sfire fire plume behavior is consistent with the interpretation of FireFlux observations. The study suggests optimal experimental pre-planning, design, and execution of future field campaigns that are needed for further coupled atmosphere-fire model development and evaluation

Towards Data-Driven Operational Wildfire Spread Modeling: A Report of the NSF-Funded WIFIRE Workshop

This report presents a record of the discussions that took place during the workshop entitled “Towards Data-Driven Operational Wildfire Spread Modeling” held on January 12-13, 2015, at the University of California, San Diego. The workshop was organized as part of WIFIRE, a collaborative project sponsored by the National Science Foundation (NSF) between San Diego Supercomputer Center, Calit2's Qualcomm Institute and Jacobs School of Engineering at the University of California at San Diego (UCSD) and the Department of Fire Protection Engineering at the University of Maryland (UMD). The objective of WIFIRE is to build a cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior (see http://wifire.ucsd.edu). WIFIRE is funded by NSF Award #1331615 as part of the Interdisciplinary Research in Hazards and Disasters (Hazards SEES) program. The objectives of the WIFIRE workshop were: (1) to identify technical barriers and milestones that need to be overcome in order to develop validated data-driven wildfire spread models and make them operational; and (2) to bring together leading representatives of the wildfire research community, the geosciences community and the fire science community. The wildfire research community has relevant expertise on wildfire operations; the geosciences community has relevant expertise on large-scale effects in wildfires (e.g., the coupling with atmospheric phenomena); the fire science community has relevant expertise on flame-scale effects in wildfires (e.g., the response of the fire to changing local conditions). The workshop was organized around four main topical areas and corresponding breakout groups, including operational rate-of-spread models for wildfire spread, CFD models, wildfire data, and data assimilation (see Appendix A for a description of the WIFIRE workshop program). Our goal in this report is to document and share the substance and scope of the workshop discussions and to thereby invite the wider research community to support, engage in, and contribute to the general effort to develop operational data-driven tools for wildfire spread predictions.The National Science Foundation via Award #1331615 as part of the Interdisciplinary Research in Hazards and Disasters (Hazards SEES) program

Differences in COVID-19 Outcomes Among Patients With Type 1 Diabetes: First vs Later Surges

Background Outcomes of the novel coronavirus SARS-CoV-2 (COVID-19) have improved throughout the pandemic. However, whether outcomes of COVID-19 in the type 1 diabetes (T1D) population improved over time is unknown. Therefore, we aim to investigate differences in COVID-19 outcomes for patients with T1D in the US. Method We analyzed data collected via a registry of patients with T1D and COVID-19 from 56 sites between April 2020 and January 2021. First, we grouped cases into First Surge (04/09/2020 - 07/31/2020, n=188) and Late Surge (08/01/2020 - 01/31/2021, n=410). Then, we compared outcomes between both groups using descriptive statistics and logistic regression models. Results Adverse outcomes were more frequent during the first surge including Diabetic Ketoacidosis (32% versus 15%, p<0.001), severe hypoglycemia (4% versus 1%, p=0.04) and hospitalization (52% versus 22%, p<0.001). The First surge cases were older (28 +/- 18.8 years versus 18.8 +/- 11.1 years, p<0.001), had higher hemoglobin A1c (HbA1c) levels (Median (IQR): 9.3 (4.0) versus 8.4(2.8), <0.001) and use public insurance (n(%): 107 (57) versus 154 (38), p <0.001). There were five times increased odds of hospitalization for adults (OR 5.01 (2.11,12.63) in the first surge compared to the late surge. Conclusion COVID-19 cases among patients with T1D reported during the first surge had a higher proportion of adverse outcomes than those presented in a later surge

Shared heritability and functional enrichment across six solid cancers

Correction: Nature Communications 10 (2019): art. 4386 DOI: 10.1038/s41467-019-12095-8Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, here we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (r(g) = 0.57, p = 4.6 x 10(-8)), breast and ovarian cancer (r(g) = 0.24, p = 7 x 10(-5)), breast and lung cancer (r(g) = 0.18, p = 1.5 x 10(-6)) and breast and colorectal cancer (r(g) = 0.15, p = 1.1 x 10(-4)). We also found that multiple cancers are genetically correlated with non-cancer traits including smoking, psychiatric diseases and metabolic characteristics. Functional enrichment analysis revealed a significant excess contribution of conserved and regulatory regions to cancer heritability. Our comprehensive analysis of cross-cancer heritability suggests that solid tumors arising across tissues share in part a common germline genetic basis.Peer reviewe

Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants

Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling. © 2018 The Author(s).Peer reviewe

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Genomic analysis of male puberty timing highlights shared genetic basis with hair colour and lifespan

Abstract: The timing of puberty is highly variable and is associated with long-term health outcomes. To date, understanding of the genetic control of puberty timing is based largely on studies in women. Here, we report a multi-trait genome-wide association study for male puberty timing with an effective sample size of 205,354 men. We find moderately strong genomic correlation in puberty timing between sexes (rg = 0.68) and identify 76 independent signals for male puberty timing. Implicated mechanisms include an unexpected link between puberty timing and natural hair colour, possibly reflecting common effects of pituitary hormones on puberty and pigmentation. Earlier male puberty timing is genetically correlated with several adverse health outcomes and Mendelian randomization analyses show a genetic association between male puberty timing and shorter lifespan. These findings highlight the relationships between puberty timing and health outcomes, and demonstrate the value of genetic studies of puberty timing in both sexes