513 research outputs found
Strategies for sustaining fidelity: a multi-state qualitative analysis in Housing First programs
No full textBackground: Sustained fidelity of evidence-based interventions (EBI) can improve public health. This study examines Housing First (HF) providers’ strategies to sustain EBI fit within dynamic systems.
Methods: Six focus groups at exemplar HF sites elicited participants’ service approaches, challenges,and strategies. Thematic analysis and strategies for rigor employed.
Results: Building external relationships secured the buy-in necessary to compete for resources and disrupt services as usual. Internally, leadership and rule-bending negotiated frictions in EBI fit and counteracted practice drift.
Conclusions: Novel here is a story of committed providers’ strategies and can inform the prospective planning for EBI sustainability spanning across systems.Peer reviewe
EBI Metagenomics in 2017: Enriching the analysis of microbial communities, from sequence reads to assemblies
No full text\ua9 2017 The Author(s). EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons
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The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.
No full textThe NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data
The role of author identities in peer review
No full textThere is widespread debate on whether to anonymize author identities in peer review. The key argument for anonymization is to mitigate bias, whereas arguments against anonymization posit various uses of author identities in the review process. The Innovations in Theoretical Computer Science (ITCS) 2023 conference adopted a middle ground by initially anonymizing the author identities from reviewers, revealing them after the reviewer had submitted their initial reviews, and allowing the reviewer to change their review subsequently. We present an analysis of the reviews pertaining to the identification and use of author identities. Our key findings are: (I) A majority of reviewers self-report not knowing and being unable to guess the authors’ identities for the papers they were reviewing. (II) After the initial submission of reviews, 7.1% of reviews changed their overall merit score and 3.8% changed their self-reported reviewer expertise. (III) There is a very weak and statistically insignificant correlation of the rank of authors’ affiliations with the change in overall merit; there is a weak but statistically significant correlation with respect to change in reviewer expertise. We also conducted an anonymous survey to obtain opinions from reviewers and authors. The main findings from the 200 survey responses are: (i) A vast majority of participants favor anonymizing author identities in some form. (ii) The “middle-ground” initiative of ITCS 2023 was appreciated. (iii) Detecting conflicts of interest is a challenge that needs to be addressed if author identities are anonymized. Overall, these findings support anonymization of author identities in some form (e.g., as was done in ITCS 2023), as long as there is a robust and efficient way to check conflicts of interest
Mining housekeeping genes with a Naive Bayes classifier
No full textThe first author was supported by the Student Awards Agency for Scotland. The second author is supported by BBSRC grant BBS RC BB/D006473/1, and under the Advanced Knowledge Technologies (AKT) Interdisciplinary Research Collaboration (IRC), which is sponsored by the UK Engineering and Physical Sciences Research Council under grant number GR/N15764/01.Background: Traditionally, housekeeping and tissue specific genes have been classified using direct assay of mRNA presence across different tissues, but these experiments are costly and the results not easy to compare and reproduce. Results: In this work, a Naive Bayes classifier based only on physical and functional characteristics of genes already available in databases, like exon length and measures of chromatin compactness, has achieved a 97% success rate in classification of human housekeeping genes ( 93% for mouse and 90% for fruit fly). Conclusion: The newly obtained lists of housekeeping and tissue specific genes adhere to the expected functions and tissue expression patterns for the two classes. Overall, the classifier shows promise, and in the future additional attributes might be included to improve its discriminating power.Peer reviewe
Shear strength measurement in soft mud deposits: application of GraviProbe and RheoTune
No full textSoft mud deposits are increasingly encountered around the world, from natural offshore deposits and mud layers in estuaries, ports, and waterways to progressively growing leftover from treatment and extraction facilities, mines, and oil refineries. Reliable monitoring of the temporal and spatial strength buildup in such deposits is crucial to optimize their sediment management plan. In this study, two well-established shear strength profilers i.e. GraviProbe 2.0 (dotOcean) and RheoTune (Stema Systems) are investigated. Their working principles are described, and their performance is compared against direct strength measurement. Finally, capabilities, limitations, and points of improvement of both instruments are discussed.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Rivers, Ports, Waterways and Dredging EngineeringOffshore and Dredging Engineerin
Conserved Omp85 lid-lock structure and substrate recognition in FhaC
No full textOmp85 proteins mediate translocation of polypeptide substrates across and into cellular membranes. They share a common architecture comprising substrate-interacting POTRA domains, a C-terminal 16-stranded β-barrel pore and two signature motifs located on the inner barrel wall and at the tip of the extended L6 loop. The observation of two distinct conformations of the L6 loop in the available Omp85 structures previously suggested a functional role of conformational changes in L6 in the Omp85 mechanism. Here we present a 2.5 Å resolution structure of a variant of the Omp85 secretion protein FhaC, in which the two signature motifs interact tightly and form the conserved 'lid lock'. Reanalysis of previous structural data shows that L6 adopts the same, conserved resting state position in all available Omp85 structures. The FhaC variant structure further reveals a competitive mechanism for the regulation of substrate binding mediated by the linker to the N-terminal plug helix H1
Update on Strategies to Reduce Early Brain Injury after Subarachnoid Hemorrhage
No full textPurpose of Review: Early brain injury (EBI) after aneurysmal subarachnoid hemorrhage (SAH) is the most influential clinical determinant of outcomes. Despite significant advances in understanding of the pathophysiology of EBI, currently no treatments to target EBI have been developed. This review summarizes recent advances in EBI research over the past five years with a focus on potential therapeutic targets. Recent Findings: Mechanism-specific translational studies are converging on several pathophysiologic pathways: improved antioxidant delivery and the Sirt1/Nrf2 pathway for reactive oxygen species; NLRP3 inflammasome and microglial polarization for inflammation; and the PI3K/Akt pathway for apoptosis. Recently identified mechanistic components, such as microcirculatory failure and ferroptosis, need particular attention. Clinical studies developing radiographic markers and mechanism-specific, biofluid markers are attempting to bridge the translational therapeutic gap. Summary: There has been an exponential growth in EBI research. Further clinical studies which address specific pathophysiology mechanisms need to be performed to identify novel therapeutic approaches. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.FALSEsciescopu
Author Correction: iLoF: An intelligent Lab on Fiber Approach for Human Cancer Single-Cell Type Identification
No full textAn amendment to this paper has been published and can be accessed via a link at the top of the paper.This work was partially funded by the projects NanoSTIMA and NORTE-01-0145-FEDER-000029, both supported by the North Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, and through the European Regional Development Fund (ERDF); and by the Portuguese Foundation for Science and Technology, within the scope of the PhD grant PD/BD/135023/2017 and the projects: PTDC/BBB-EBI/0567/2014 (to CAR) and UID/BIM/04293/2013. It was also funded by FEDER funds through the Operational Programme for Competitiveness Factors-COMPETE (POCI-01-0145-FEDER-016585; POCI-01-0145-FEDER-007274; PPBI-POCI-01-0145-FEDER-022122). MB acknowledges the Marie Sklodowska-Curie grant agreement No. 748880
Evaluation of bioactive properties and phenolic compounds in different extracts prepared from Salvia officinalis L.
No full textThe therapeutic benefits of medicinal plants are well known. Nevertheless, essential oils have been the main focus of antioxidant and antimicrobial studies, remaining scarce the reports with hydrophilic extracts. Thus, the antioxidant and antifungal activities of aqueous (prepared by infusion and decoction) and methanol/water (80:20, v/v) extracts of sage (Salvia officinalis L.) were evaluated and characterized in terms of phenolic compounds. Decoction and methanol/water extract gave the most pronounced antioxidant and antifungal properties, being positively related with their phenolic composition. The highest concentration of phenolic compounds was observed in the decoction, followed by methanol/water extract and infusion. Fungicidal and/or fungi static effects proved to be dependent on the extracts concentration. Overall, the incorporation of sage decoction in the daily diet or its use as a complement for antifungal therapies, could provide considerable benefits, also being an alternative to sage essential oils that can display some toxic effects.The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for the N. Martins Grant (SFRH/BD/87658/2012), L. Barros researcher contract under "Programa Compromisso corn Ciencia - 2008" and financial support to the research center CIMO (Strategic Project PEst-OE/AGR/UI0690/2011). This work was also supported by the Programa Operacional, Fatores de competitividade - COMPETE and by national funds through FCT - Fundacao para a Ciencia e a Tecnologia on the scope of the Projects FCT PTDC/EBB-EBI/120495/2010, RECl/EBB-EBI/0179/2012 and PEst-OE/EQB/LA0023/2013. The authors thank the Project "BioHealth - Biotechnology and Bioengineering approaches to improve health quality", Ref. NORTE-07-0124-FEDER-000027, co-founded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER. Author CSB is thankful to the Spanish MINECO for financial support through the Project BFU2012-35228
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