Asterias: a parallelized web-based suite for the analysis of expression and aCGH data

Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the user to obtain additional information for user-selected genes by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data; converting between different types of gene/clone and protein identifiers; filtering and imputation; finding differentially expressed genes related to patient class and survival data; searching for models of class prediction; using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity; searching for molecular signatures and predictive genes with survival data; detecting regions of genomic DNA gain or loss. The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications.Comment: web based application; 3 figure

A survey of dental professionals’ opinions around the use of antibiotics in molar 3 extractions and dental implant placement

© 2023 The authors. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://medpharmareports.com/index.php/mpr/article/view/2634Aim. This survey was conducted to determine the type and frequency of antibiotics (AB) use for the prevention of infections in dental third molar (M3) extraction and implantation procedures (DIP) among UK dentists and the opinions underpinning their practice. Methods and design. Systematic reviews of the evidence were undertaken alongside this survey of practicing dentists in the United Kingdom to identify the opinions and practices of those undertaking the procedures. With ethical approval, a survey was designed for online delivery and was sent to every dental practitioner in the UK with a publicly available email address or social media contact. The opening page provided the project information sheet and proceeding to complete and submit the questionnaire was considered consent to participate. The online survey was circulated to 900 identified addresses and a total of 145 responses were received. Responses were collated in Microsoft® Excel™ and analyzed using IBM® SPSS™ plus thematic analysis of free text responses. Results. There were 42% of participants (n=61) who discouraged AB prophylactic use in M3 extractions in people with no systemic conditions and who also preferred postoperative AB use when required. Where, 57.9% of respondents (n=84) supported the short-term use of ABs (5-7 days) for M3 extraction and 53% (n=77) in DIP placement in patients with no relevant medical history. As an ad hoc finding, dentists reported on the negative impact of heavy smoking and oral parafunctional behavior on DIP success. Conclusion. The use of antibiotics and broad spectrum antibiotics remains higher than current guidelines would recommend. Further research is required to clarify the specific risks arising from underlying medical conditions to further clarify where prophylaxis is required

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite

Asterias (http://www.asterias.info) is an open-source, web-based, suite for the analysis of gene expression and aCGH data. Asterias implements validated statistical methods, and most of the applications use parallel computing, which permits taking advantage of multicore CPUs and computing clusters. Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. These applications cover from array normalization to imputation and preprocessing, differential gene expression analysis, class and survival prediction and aCGH analysis. The source code is available, allowing for extention and reuse of the software. The links and analysis of additional functional information, parallelization of computation and open-source availability of the code make Asterias a unique suite that can exploit features specific to web-based environments

Coagulation factor VIIa binds to herpes simplex virus 1‐encoded glycoprotein C forming a factor X‐enhanced tenase complex oriented on membranes

BackgroundThe cell membrane‐derived initiators of coagulation, tissue factor (TF) and anionic phospholipid (aPL), are constitutive on the herpes simplex virus type 1 (HSV1) surface, bypassing physiological regulation. TF and aPL accelerate proteolytic activation of factor (F) X to FXa by FVIIa to induce clot formation and cell signaling. Thus, infection in vivo is enhanced by virus surface TF. HSV1‐encoded glycoprotein C (gC) is implicated in this tenase activity by providing viral FX binding sites and increasing FVIIa function in solution.ObjectiveTo examine the biochemical influences of gC on FVIIa‐dependent FX activation.MethodsImmunogold electron microscopy (IEM), kinetic chromogenic assays and microscale thermophoresis were used to dissect tenase biochemistry. Recombinant TF and gC were solubilized (s) by substituting the transmembrane domain with poly‐histidine, which could be orientated on synthetic unilamellar vesicles containing Ni‐chelating lipid (Ni‐aPL). These constructs were compared to purified HSV1 TF±/gC ± variants.ResultsIEM confirmed that gC, TF, and aPL are simultaneously expressed on a single HSV1 particle where the contribution of gC to tenase activity required the availability of viral TF. Unlike viral tenase activity, the cofactor effects of sTF and sgC on FVIIa was additive when bound to Ni‐aPL. FVIIa was found to bind to sgC and this was enhanced by FX. Orientation of sgC on a lipid membrane was critical for FVIIa‐dependent FX activation.ConclusionsThe assembly of gC with FVIIa/FX parallels that of TF and may involve other constituents on the HSV1 envelope with implications in virus infection and pathology.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155933/1/jth14790-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155933/2/jth14790.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155933/3/jth14790_am.pd

Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data

The analysis of expression and CGH arrays plays a central role in the study of complex diseases, especially cancer, including finding markers for early diagnosis and prognosis, choosing an optimal therapy, or increasing our understanding of cancer development and metastasis. Asterias (http://www.asterias.info) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI) and run on a server with 60 CPUs for computation; compared to a desktop or server-based but not parallelized application, parallelization provides speed ups of factors up to 50. Most of our applications allow the user to obtain additional information for user-selected genes (chromosomal location, PubMed ids, Gene Ontology terms, etc.) by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data (DNMAD); converting between different types of gene/clone and protein identifiers (IDconverter/IDClight); filtering and imputation (preP); finding differentially expressed genes related to patient class and survival data (Pomelo II); searching for models of class prediction (Tnasas); using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity (GeneSrF); searching for molecular signatures and predictive genes with survival data (SignS); detecting regions of genomic DNA gain or loss (ADaCGH). The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications