ABSTRACT
The purpose of the dbNSFP is to provide a one‐stop resource for functional predictions and annotations for human nonsynonymous single‐nucleotide variants (nsSNVs) and splice‐site variants ...(ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome‐sequencing study. A list of all potential nsSNVs and ssSNVs based on the human reference sequence were created and functional predictions and annotations were curated and compiled for each SNV. Here, we report a recent major update of the database to version 3.0. The SNV list has been rebuilt based on GENCODE 22 and currently the database includes 82,832,027 nsSNVs and ssSNVs. An attached database dbscSNV, which compiled all potential human SNVs within splicing consensus regions and their deleteriousness predictions, add another 15,030,459 potentially functional SNVs. Eleven prediction scores (MetaSVM, MetaLR, CADD, VEST3, PROVEAN, 4× fitCons, fathmm‐MKL, and DANN) and allele frequencies from the UK10K cohorts and the Exome Aggregation Consortium (ExAC), among others, have been added. The original seven prediction scores in v2.0 (SIFT, 2× Polyphen2, LRT, MutationTaster, MutationAssessor, and FATHMM) as well as many SNV and gene functional annotations have been updated. dbNSFP v3.0 is freely available at http://sites.google.com/site/jpopgen/dbNSFP.
The purpose of the dbNSFP is to provide a one‐stop resource for functional predictions and annotations for human non‐synonymous single‐nucleotide variants (nsSNVs) and splice site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome‐sequencing study. Here we report a recent major update of the database to version 3.0 and some preliminary analyses comparing the 24 functional prediction scores and conservation scores in dbNSFP v3.0.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
BioGPS (http://biogps.org) is a centralized gene-annotation portal that enables researchers to access distributed gene annotation resources. This article focuses on the updates to BioGPS since our ...last paper (2013 database issue). The unique features of BioGPS, compared to those of other gene portals, are its community extensibility and user customizability. Users contribute the gene-specific resources accessible from BioGPS ('plugins'), which helps ensure that the resource collection is always up-to-date and that it will continue expanding over time (since the 2013 paper, 162 resources have been added, for a 34% increase in the number of resources available). BioGPS users can create their own collections of relevant plugins and save them as customized gene-report pages or 'layouts' (since the 2013 paper, 488 user-created layouts have been added, for a 22% increase in the number of layouts). In addition, we recently updated the most popular plugin, the 'Gene expression/activity chart', to include ∼ 6000 datasets (from ∼ 2000 datasets) and we enhanced user interactivity. We also added a new 'gene list' feature that allows users to save query results for future reference.
Fast-evolving technologies have enabled researchers to easily generate data at genome scale, and using these technologies to compare biological states typically results in a list of candidate genes. ...Researchers are then faced with the daunting task of prioritizing these candidate genes for follow-up studies. There are hundreds, possibly even thousands, of web-based gene annotation resources available, but it quickly becomes impractical to manually access and review all of these sites for each gene in a candidate gene list. BioGPS (http://biogps.org) was created as a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. BioGPS serves as a convenient tool for users to access known gene-centric resources, as well as a mechanism to discover new resources that were previously unknown to the user. This article describes updates to BioGPS made after its initial release in 2008. We summarize recent additions of features and data, as well as the robust user activity that underlies this community intelligence application. Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS.
Herein, the effect of Fushun oil shale minerals on its kerogen has been investigated. The samples were obtained under non-isothermal conditions at different final temperatures. Scanning electron ...microscope (SEM) analysis revealed that the silicates were layered and the carbonates were tightly bound to each other. The combination of silicates and carbonates led to close combination of minerals and organic matter and the organic matter was contained in the minerals. The Brunner–Emmet–Teller (BET) experiments conclude that during the non-isothermal pyrolysis process, the specific surface area increased, and then, decreased, which proves the adsorption effect of silicates on oil shale pyrolysis products and the adsorption effect of carbonates was weak. The activation energy of four samples was calculated via Flynn–Wall–Ozawa (FWO) and Friedman kinetic analysis under different heating rates in a non-isothermal process, wherein the average activation energy of the sample containing silicate was 177.60 kJ mol −1 at minimum while that of carbonate was 250.45 kJ mol −1 at maximum, which proves that the catalytic promotion effect of silicate was greater than the inhibition effect of carbonate. The pyrolysis products obtained by Flash pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) under isothermal pyrolysis conditions were primarily composed of aliphatic hydrocarbon structures, which had different degrees of impact on the production of heteroatoms. This work provides a reliable theoretical basis for future studies on the influence of minerals on pyrolysis of organic matter in oil shale.
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IJS, KILJ, NUK, UL, UM, UPUK
Material interface-related uncertainties induced by inter-diffusion or reactions between two different materials may deteriorate the actual performance of a structural design achieved by topology ...optimization. Thus a rational methodology is needed to address this issue in the design of hybrid-material engineering products implemented by some novel fabrication techniques such as additive manufacturing. This paper presents a robust shape and topology optimization method accounting for uncertain graded interface properties of multi-material structures. A level set function is used to track the evolving material interfaces during the optimization process, and the material interface uncertainties is modeled by introducing an intermediate zone with graded properties represented by a random field. On the basis of discretizing the input random field by means of the Expansion Optimal Linear Estimation (EOLE) method, the uncertain propagation analysis is implemented with the Polynomial Chaos expansion (PCE) to predict the stochastic response. Then the robust shape and topology optimization problem is stated as a multi-criteria optimization problem, in which the expected value and the standard deviation of the performance function of interest are to be minimized under a given material volume constraint. The shape derivative of the stochastic response is derived in the context of Eulerian description, and then used to advance the evolution of the level set function through the Hamilton-Jacobi equation. In the numerical examples, the proposed robust design method is exemplified by the mean compliance minimization problems.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Lung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. We downloaded the gene expression profile and immune-related gene set from the TCGA and ImmPort database, ...respectively, to establish immune-related gene pairs (IRGPs). Then, IRGPs were subjected to univariate Cox regression analysis, LASSO regression analysis, and multivariable Cox regression analysis to screen and develop an IRGPs signature. The receiver operating characteristic curve (ROC) was applied for evaluating the predicting accuracy of this signature by calculating the area under ROC (AUC) and data from the GEO set was used to validate this signature. The relationship of 22 tumor-infiltrating immune cells (TIICs) to the immune risk score was also investigated. An IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in the TCGA set was 0.867 and 0.870, respectively. Similar results were observed in the AUCs of GEO set 1, 2 and 3 (GEO set 1 1-year: 0.819; 3-year: 0.803; GEO set 2 1-year: 0.834; 3-year: 0.870; GEO set 3 1-year: 0.955; 3-year: 0.827). Survival analysis demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that the risk score was an independent prognostic factor. The immune risk score was highly associated with several TIICs (Plasma cells, memory B cells, resting memory CD4 T cells, and activated NK cells). We developed a novel IRGPs signature for predicting 1- and 3- year overall survival in LUAD, which would be helpful for prognosis assessment of LUAD.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of ...May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.
In this paper, a novel heterostacked tunnel FET (HS-TFET) is proposed for steeper average subthreshold swing (SS). Different from conventional TFETs, HS-TFETs owns a stacked source configuration ...consisting of an upper source layer with a relatively larger bandgap material and an underlying source layer with smaller bandgap materials. Since smaller bandgap materials exhibit much higher band-to-band tunneling efficiency, the underlying layer of HS-TFET could provide extra drain current increment with increasing gate voltage, and thus effectively improve the subthreshold characteristics for steeper average SS. The simulation results show that the proposed Si-Ge-based HS-TFET can achieve much steeper average SS (25 mV/decade) than conventional Si TFET (42 mV/decade), exhibiting more than one decade higher I60 without leakage current degradation.
Different content of Cu has been loaded onto CoFe
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support, and their gas-phase CO oxidation performance has been tested to explore the best Cu loading content and the mechanism of catalyst ...oxidation. The fundamental characteristics of Cu doped CoFe
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are revealed by XRD and TEM. The catalytic mechanism is elucidated by XPS, H
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-TPR, CO-TPD and in-situ DRIFTS. The CO oxidation performance is greatly improved upon Cu doping on the surface of CoFe
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catalysts. It is found that 5 wt% Cu/CoFe
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catalysts showed higher CO oxidation performance.
Graphical Abstract
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Azobenzene functionalized peptides are of great importance in photoresponsive biosystems and photopharmacology. Herein, we report an efficient approach to prepare azobenzene functionalized peptides ...through late-stage modification of tyrosine-containing peptides using a dearomatization–rearomatization strategy. This approach shows good chemoselectivity and site selectivity as well as sensitive group tolerance to various peptides. This method enriches the postsynthetic modification toolbox of peptides and has great potential to be applied in medicinal chemistry and chemical biology.
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IJS, KILJ, NUK, PNG, UL, UM
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