Introducing the LATITUDES network: a library of assessment tools and training to improve transparency, utility and dissemination in evidence synthesis.

An assessment of the validity of studies is an essential component of most evidence syntheses (systematic reviews) to understand the risk of bias (ROB) and applicability of the evidence. A formal validity assessment requires a structured and comprehensive approach, which can be implemented using an assessment tool, specifically developed for this purpose. Many different tools are available, marking it difficult for researchers to choose the best tool for their evidence synthesis. We have established the LATITUDES Network to assist researchers in identifying the most appropriate tool to use in their evidence synthesis and to support researchers using these tools. The LATITUDES website (www.latitudes-network.org) includes a searchable library of validity assessment tools designed for use in evidence syntheses, bringing tools together in one place and providing researchers with clear information on suitable tools, categorized by study design. The website also provides links to training on the process of validity assessment and a list of tools currently under development. To be included in the LATITUDES library, tools must meet the following criteria: be designed for use in evidence syntheses; assess multidimensional aspects of validity of individual studies or reviews; and be developed for use by the wider research community rather than for a single research group. We highlight 'key' tools, those that are considered to be the most robust and reliable tools based on prespecified criteria agreed in conjunction with our advisory board, an international group of experts in the area of evidence synthesis and ROB tools.

CrustyBase v.2.0: new features and enhanced utilities to support open science.

BACKGROUND: Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology is frequently employed for describing the genetic response to experimental conditions and has created vast libraries of datasets which shed light on gene function across different tissues, diseases, diets and developmental stages in many species. However, public accessibility of these data is impeded by a lack of suitable software interfaces and databases with which to locate and analyse them. BODY: Here we present an update on the status of CrustyBase.org, an online resource for analysing and sharing crustacean transcriptome datasets. Since its release in October 2020, the resource has provided many thousands of transcriptome sequences and expression profiles to its users and received 19 new dataset imports from researchers across the globe. In this article we discuss user analytics which point towards the utilization of this resource. The architecture of the application has proven robust with over 99.5% uptime and effective reporting of bugs through both user engagement and the error logging mechanism. We also introduce several new features that have been developed as part of a new release of CrustyBase.org. Two significant features are described in detail, which allow users to navigate through transcripts directly by submission of transcript identifiers, and then more broadly by searching for encoded protein domains by keyword. The latter is a novel and experimental feature, and grants users the ability to curate gene families from any dataset hosted on CrustyBase in a matter of minutes. We present case studies to demonstrate the utility of these features. CONCLUSION: Community engagement with this resource has been very positive, and we hope that improvements to the service will further enable the research of users of the platform. Web-based platforms such as CrustyBase have many potential applications across life science domains, including the health sector, which are yet to be realised. This leads to a wider discussion around the role of web-based resources in facilitating an open and collaborative research community.

Quality of Web-Based Sickle Cell Disease Resources for Health Care Transition: Website Content Analysis.

Background: Adolescents and young adults with sickle cell disease (SCD) transitioning from pediatric to adult health care face a high-risk period associated with increased use of acute health care services and mortality. Although 59% of American citizens report using the internet for health care information, the quality of web-based, patient-facing resources regarding transition in SCD care has not been evaluated. Objective: This study aimed to evaluate the quality and readability of web-based health information on SCD, especially as it pertains to the transition to adulthood for inidividuals with SCD. The study also compared the readability and content scores of websites identified in 2018 to those from 2021 to assess any change in quality over time. Methods: Keywords representing phrases adolescents may use while searching for information on the internet regarding transition in SCD care, including "hydroxyurea" and "SCD transition," were identified. A web-based search using the keywords was conducted in July 2021 using Google, Yahoo, and Bing. The top 20 links from each search were collected. Duplicate websites, academic journals, and websites not related to SCD health care transition were excluded. Websites were categorized based on the source: health department, hospital or private clinician, professional society, and other websites. Websites were assessed using Health On the Net Foundation code of conduct (HONcode), Flesch Reading Ease (FRE), Flesch-Kincaid Grade Level (FGL), Ensuring Quality Information for Patients (EQIP), and a novel SCD content checklist (SCDCC). EQIP and SCDCC scores range from 0- to 100. Each website was reviewed by 2 research assistants and assessed for interrater reliability. Descriptive statistics were calculated. Results: Of the 900 websites collected, 67 (7.4%) met the inclusion criteria: 13 health department, 7 hospital or private clinician, 33 professional society, and 14 other websites. A total of 15 (22%) out of 67 websites had HONcode certification. Websites with HONcode certification had higher FRE and EQIP scores and lower FGL scores than those without HONcode certification, reflecting greater readability. Websites without HONcode certification had higher SCDCC scores, reflecting greater clinical content. Only 7 (10%) websites met the National Institutes of Health recommendation of a seventh-grade or lower reading level. Based on EQIP scores, 6 (9%) websites were of high quality. The mean SCDCC score was 20.60 (SD 22.14) out of 100. The interrater reliability for EQIP and SCDCC ratings was good (intraclass correlation: 0.718 and 0.897, respectively). No source of website scored significantly higher mean EQIP, FRE, FGL, or SCDCC scores than the others (all P<.05). Conclusions: Although seeking health care information on the web is very common, the overall quality of information about transition in SCD care on the internet is poor. Changes to current web-based health care information regarding SCD care transitions would benefit transitioning youth by providing expectations, knowledge, skills, and tools to increase self-efficacy.

Development and validation of an online emotional intelligence training program.

Introduction: Emotional intelligence (EI) is associated with a range of positive health, wellbeing, and behavioral outcomes. The present article describes the development and validation of an online training program for increasing EI abilities in adults. The training program was based on theoretical models of emotional functioning and empirical literature on successful approaches for training socioemotional skills and resilience. Methods: After an initial design, programming, and refinement process, the completed online program was tested for efficacy in a sample of 326 participants (72% female) from the general population. Participants were randomly assigned to complete either the EI training program (n = 168) or a matched placebo control training program (n = 158). Each program involved 10-12 hours of engaging online content and was completed during either a 1-week (n = 175) or 3-week (n = 151) period. Results: Participants who completed the EI training program showed increased scores from pre- to post-training on standard self-report (i.e., trait) measures of EI (relative to placebo), indicating self-perceived improvements in recognizing emotions, understanding emotions, and managing the emotions of others. Moreover, those in the EI training also showed increased scores in standard performance-based (i.e., ability) EI measures, demonstrating an increased ability to strategically use and manage emotions relative to placebo. Improvements to performance measures also remained significantly higher than baseline when measured six months after completing the training. The training was also well-received and described as helpful and engaging. Discussion: Following a rigorous iterative development process, we created a comprehensive and empirically based online training program that is well-received and engaging. The program reliably improves both trait and ability EI outcomes and gains are sustained up to six months post-training. This program could provide an easy and scalable method for building emotional intelligence in a variety of settings.

Online resources for information on shoulder arthroplasty: an assessment of quality and readability.

BACKGROUND: Many patients use online resources to educate themselves on surgical procedures and make well-informed healthcare decisions. The aim of our study was to evaluate the quality and readability of online resources exploring shoulder arthroplasty. METHODS: An internet search pertaining to shoulder arthroplasty (partial, anatomic, and reverse) was conducted using the three most popular online search engines. The top 25 results generated from each term in each search engine were included. Webpages were excluded if they were duplicates, advertised by search engines, subpages of other pages, required payments or subscription, or were irrelevant to our scope. Webpages were classified into different source categories. Quality of information was assessed by HONcode certification, Journal of the American Medical Association (JAMA) criteria, and DISCERN benchmark criteria. Webpage readability was assessed using the Flesch reading ease score (FRES). RESULTS: Our final dataset included 125 web pages. Academic sources were the most common with 45 web pages (36.0%) followed by physician/private practice with 39 web pages (31.2%). The mean JAMA and DISCERN scores for all web pages were 1.96±1.31 and 51.4±10.7, respectively. The total mean FRES score was 44.0±11.0. Only nine web pages (7.2%) were HONcode certified. Websites specified for healthcare professionals had the highest JAMA and DISCERN scores with means of 2.92±0.90 and 57.96±8.91, respectively (P<0.001). HONcode-certified webpages had higher quality and readability scores than other web pages. CONCLUSIONS: Web-based patient resources for shoulder arthroplasty information did not show high-quality scores and easy readability. When presenting medical information, sources should maintain a balance between readability and quality and should seek HONcode certification as it helps establish the reliability and accessibility of the presented information. Level of evidence: IV.

LIRcentral: a manually curated online database of experimentally validated functional LIR motifs.

Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.eu), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource. Information incorporated in LIRcentral is useful for accomplishing a variety of research tasks, including: (i) guiding wet biology researchers for the characterization of novel instances of LIR motifs, (ii) giving bioinformaticians/computational biologists access to high-quality LIR motifs for building novel prediction methods for LIR motifs and LIR containing proteins (LIRCPs) and (iii) performing analyses to better understand the biological importance/features of functional LIR motifs. We welcome feedback on the LIRcentral content and functionality by all interested researchers and anticipate this work to spearhead a community effort for sustaining this resource which will further promote progress in studying LIR motifs/LIRCPs.Abbreviations: AIM, Atg8-family interacting motif; Atg8, autophagy related 8; GABARAP, GABA type A receptor-associated protein; LIR, LC3-interacting region; LIRCP, LIR-containing protein; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PMID, PubMed identifier; PPI, protein-protein interaction; SLiM, short linear motif.

An educational visual resource to support understanding of liquid-liquid phase separation.

In collaboration with educators and researchers, we created an online resource called Phase Separation 101 to help undergraduate students understand the basics of liquid-liquid phase separation, an emerging and complex concept in cell biology for which visual resources are still scarce. This work presents the workflow and visual communication strategies that we followed to build scientifically accurate visualizations of dynamic processes.

Quality improvement dissemination in pediatric surgery: The APSA quality and safety toolkit.

Shared experiential learning is critical in the field of pediatric surgery to support the translation of evidence into practice. Surgeons who develop QI interventions in their own institutions based on the best available evidence create work products that can accelerate similar projects in other institutions, rather than continuously reinventing the wheel. The American Pediatric Surgical Association (APSA) Quality and Safety Committee (QSC) toolkit was created to facilitate knowledge-sharing and thereby hasten the development and implementation of QI. The toolkit is an expanding open-access web-based repository of curated QI projects that includes evidence-based pathways and protocols, stakeholder presentations, parent/patient educational materials, clinical decision support (CDS) tools, and other components of successful QI interventions in addition to contact information for the surgeons who developed and implemented them. This resource catalyzes local QI endeavors by showcasing a range of projects that can be adapted to fit the needs of a given institution, and it also serves as a network to connect interested surgeons with successful implementers. As healthcare shifts towards value-based care models, quality improvement becomes increasingly important, and the APSA QSC toolkit will continue to adapt to the evolving needs of the pediatric surgery community.

An online immunohematology educational resource for post-graduate hematology trainees: LearnSerology.ca.

BACKGROUND: Canadian hematology residents are required to demonstrate competencies in transfusion medicine by the end of their 2-year training. Prior evaluation of final year trainees revealed significant variation in knowledge. To address the lack of standardization in serology teaching, an online educational immunohematology resource was created and evaluated. STUDY DESIGN AND METHODS: All Canadian post-graduate trainees completing a residency program in adult hematology during the 2018/2019 academic year were invited to participate. Only trainees from one university were exposed to the program curriculum. A validated exam was administered to trainees at both exposed and unexposed sites at the start of the academic year as a pre-test and in the following year as a post-test. The effectiveness of the program was assessed by both comparing the degree of improvement from pre- to post-test, and by comparing performance on the post-test. RESULTS: 57 trainees from 13 universities completed the pre-test, and 45 trainees from 14 universities completed the post-test. A strong trend towards better performance in the exposed vs non-exposed trainees on the post-test was observed, and the difference was more pronounced, and statistically significant, when analysis was limited to two questions relating to interpretation of an antibody investigation panel. DISCUSSION: LearnSerology.ca is effective and may be potentially superior to traditional immunohematology teaching. The interactive capability of the platform can improve skills related to the resolution of red cell antibody panels.

Phytophthora : taxonomic and phylogenetic revision of the genus.

Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, ß-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.

The Needs, Use and Expectations of People Bereaved by Suicide Regarding Online Resources: An Online Survey.

BACKGROUND: Online resources constitute a new and effective way to obtain support or information during bereavement processes. However, little is known about the needs, use and expectations of people bereaved by suicide regarding online resources. METHOD: The objective of our national cross-sectional online survey was to collect the use, needs and expectations of people bereaved by suicide regarding online resources. The data were collected from July to October 2021 through a 26-item online questionnaire hosted on the website LimeSurvey. RESULTS: A total of 401 respondents fully completed the questionnaire. Their mean age was 45.7. The majority of participants were women bereaved by the suicide of their child or partner. Half of the participants were bereaved for less than 3 years and benefited from counselling during their bereavement process. Three-quarters of the participants used the Internet for their bereavement process, mainly to obtain information on suicide bereavement and suicide prevention and to access testimonies of other people bereaved by suicide. Three-quarters of the participants found that available online resources for people bereaved by suicide are insufficient and expected a dedicated web platform to be developed. Finding information on suicide bereavement and on suicide prevention, discussing with a mental health professional and accessing testimonies of other people bereaved by suicide were expected by a majority of the participants regarding the future platform. Receiving counselling and being bereaved by the death of a child were the most important factors in explaining patterns of use and expectations regarding online resources. DISCUSSION: Our results offer precise insights into the needs, use and expectations of people bereaved by suicide regarding online resources. The development of web platforms offering access to reliable information on suicide bereavement and on suicide prevention to peers bereaved by suicide and help to seek counselling are urgently needed.

FPocketWeb: protein pocket hunting in a web browser.

Detecting macromolecular (e.g., protein) cavities where small molecules bind is an early step in computer-aided drug discovery. Multiple pocket-detection algorithms have been developed over the past several decades. Among them, fpocket, created by Schmidtke and Le Guilloux, is particularly popular. Like many programs used in computational-biology research, fpocket requires users to download and install an executable file. That file must also be run via a command-line interface, further complicating use. An existing fpocket server application effectively addresses these challenges, but it requires users to upload their possibly proprietary structures to a third-party server. The FPocketWeb web app builds on this prior work. It runs the fpocket3 executable entirely in a web browser without requiring installation. The pocket-finding calculations occur on the user's computer rather than on a remote server. A working version of the open-source FPocketWeb app can be accessed free of charge from http://durrantlab.com/fpocketweb .

The Explorer's Guide to Biology: A Free Multimedia Educational Resource to Promote Deep Learning and Understanding of the Scientific Process.

Here, we describe a new open-access digital resource for teaching and learning life science, The Explorer's Guide to Biology (available at explorebiology.org). Biology can often feel like a daunting subject where learners must comprehend a sea of facts before they can participate in meaningful discussions regarding core biology concepts or biological research. In truth, developing an intellectual framework by learning how scientists solve complex biological questions may be more valuable than memorizing a sea of facts. Yet, there is a lack of free educational resources that address this issue or attempt to provide learners with context for the knowledge they are gaining. Our goal is to offer learners a more exciting and accurate window into the life sciences. Our content is designed to help learners educate themselves by engaging with stories of discovery that highlight the process of science. This strategy not only provides an intellectual framework for the content presented but also provides the learner with an accurate view of the process of science. We leverage multiple modes of content delivery (such as videos, images, text, interactive activities, and just-in-time assessments) to create an engaging learning experience and an easily adaptable teaching resource. The resource is targeted for undergraduate or AP high school-level life science educators and learners, however, it is designed so anyone who is interested in learning about life science can engage with the content with little to no prior knowledge.

A Delphi-based approach to developing the contents of an online resource, Care Assist, for male caregivers of women with breast cancer.

OBJECTIVE: Informal male caregivers of women with breast cancer (BC) have significant psychological, emotional, and social burdens that are inadequately addressed by current face-to-face interventions. Online interventions overcome barriers that limit engagement with face-to-face interventions. This study aimed to develop the contents of Care Assist, an online supportive care resource for male caregivers of BC patients, through expert consensus. METHODS: A Delphi study comprising two survey rounds and an expert consultation was conducted. In Round 1, experts in BC care rated the importance of 25 content items. In Round 2, they re-rated content items that failed to reach consensus (i.e. 80% agreement) in Round 1 or were newly developed. Free-text responses were also collected. During expert consultation, the resource was reviewed and revised for clarity. Iterative refinement followed all rounds. Quantitative data was analysed descriptively, and qualitative data was analysed using content analysis. RESULTS: Twenty-two experts participated and reached consensus on 96% of items, with 217 comments provided on: (a) the perceived benefits of Care Assist to caregivers and care recipients, (b) recommendations of newly suggested content items, wording, and use of external links, and (c) concerns regarding information overload and need for tailoring. The expert consultation comments focused on clarifying scope, wording, and information tailoring. CONCLUSION: The rigorous Delphi process resulted in the content for a comprehensive online supportive care intervention for male caregivers. Information overload can be minimised through self-identification of needs and utilisation of eHealth to personalise the resource for the heterogeneous male caregiver population.

Development of a Website for a Living Network Meta-analysis of Atopic Dermatitis Treatments Using a User-Centered Design: Multimethod Study.

BACKGROUND: A rapid expansion of systemic immunological treatment options for atopic dermatitis (AD) has created a need for clinically relevant and understandable comparative efficacy and safety information for patients and clinicians. Given the scarcity of head-to-head trials, network meta-analysis (NMA) is an alternative way to enable robust comparisons among treatment options; however, NMA results are often complex and difficult to directly implement in shared decision-making. OBJECTIVE: The aim of this study is to develop a website that effectively presents the results of a living systematic review and NMA on AD treatments to patient and clinician users. METHODS: We conducted a multimethod study using iterative feedback from adults with AD, adult caregivers of children with AD, dermatologists, and allergists within a user-centered design framework. We used questionnaires followed by workshops among patients and clinicians to develop and improve the website interface. Usability testing was done with a caregiver of a patient with eczema. RESULTS: Questionnaires were completed by 31 adults with AD or caregivers and 94 clinicians. Patients and caregivers felt it was very important to know about new treatments (20/31, 65%). Clinicians felt the lack of evidence-based comparisons between treatments was a barrier to care (55/93, 59%). "Avoiding dangerous side effects" was ranked as the most important priority for patients (weighted ranking 5.2/7, with higher ranking being more important), and "improving patients' overall symptoms" was the most important priority for clinicians (weighted ranking 5.0/6). A total of 4 patients and 7 clinicians participated in workshops; they appreciated visualizations of the NMA results and found the website valuable for comparing different treatments. The patients suggested changes to simplify the interface and clarify terminology related to comparative efficacy. The user in the usability testing found the website intuitive to navigate. CONCLUSIONS: We developed a website, "eczematherapies.com," with a user-centered design approach. Visualizations of NMA results enable users to compare treatments as part of their shared decision-making process.

BGvar: A comprehensive resource for blood group immunogenetics.

BACKGROUND: Blood groups form the basis of effective and safe blood transfusion. There are about 43 well-recognised human blood group systems presently known. Blood groups are molecularly determined by the presence of specific antigens on the red blood cells and are genetically determined and inherited following Mendelian principles. The lack of a comprehensive, relevant, manually compiled and genome-ready dataset of red cell antigens limited the widespread application of genomic technologies to characterise and interpret the blood group complement of an individual from genomic datasets. MATERIALS AND METHODS: A range of public datasets was used to systematically annotate the variation compendium for its functionality and allele frequencies across global populations. Details on phenotype or relevant clinical importance were collated from reported literature evidence. RESULTS: We have compiled the Blood Group Associated Genomic Variant Resource (BGvar), a manually curated online resource comprising all known human blood group related allelic variants including a total of 1700 International Society of Blood Transfusion approved alleles and 1706 alleles predicted and curated from literature reports. This repository includes 1682 single nucleotide variations (SNVs), 310 Insertions, Deletions (InDels) and Duplications (Copy Number Variations) and about 1360 combination mutations corresponding to 43 human blood group systems and 2 transcription factors. This compendium also encompasses gene fusion and rearrangement events occurring in human blood group genes. CONCLUSION: To the best of our knowledge, BGvar is a comprehensive and a user-friendly resource with most relevant collation of blood group alleles in humans. BGvar is accessible online at URL: http://clingen.igib.res.in/bgvar/.

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE).

BACKGROUND: Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. RESULTS: We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. CONCLUSIONS: qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.

Human disease genes website series: An international, open and dynamic library for up-to-date clinical information.

Since the introduction of next-generation sequencing, an increasing number of disorders have been discovered to have genetic etiology. To address diverse clinical questions and coordinate research activities that arise with the identification of these rare disorders, we developed the Human Disease Genes website series (HDG website series): an international digital library that records detailed information on the clinical phenotype of novel genetic variants in the human genome (https://humandiseasegenes.info/). Each gene website is moderated by a dedicated team of clinicians and researchers, focused on specific genes, and provides up-to-date-including unpublished-clinical information. The HDG website series is expanding rapidly with 424 genes currently adopted by 325 moderators from across the globe. On average, a gene website has detailed phenotypic information of 14.4 patients. There are multiple examples of added value, one being the ARID1B gene website, which was recently utilized in research to collect clinical information of 81 new patients. Additionally, several gene websites have more data available than currently published in the literature. In conclusion, the HDG website series provides an easily accessible, open and up-to-date clinical data resource for patients with pathogenic variants of individual genes. This is a valuable resource not only for clinicians dealing with rare genetic disorders such as developmental delay and autism, but other professionals working in diagnostics and basic research. Since the HDG website series is a dynamic platform, its data also include the phenotype of yet unpublished patients curated by professionals providing higher quality clinical detail to improve management of these rare disorders.

Tool to improve qualitative assessment of left ventricular systolic function.

Interactive online learning tools have revolutionized graduate medical education and can impart echocardiographic image interpretive skills. We created self-paced, interactive online training modules using a repository of echocardiography videos of normal and various degrees of abnormal left ventricles. In this study, we tested the feasibility of this learning tool. Thirteen anesthesia interns took a pre-test and then had 3 weeks to complete the training modules on their own time before taking a post-test. The average score on the post-test (74.6% ± 11.08%) was higher than the average score on the pre-test (57.7% ± 9.27%) (P < 0.001). Scores did not differ between extreme function (severe dysfunction or hyperdynamic function) and non-extreme function (normal function or mild or moderate dysfunction) questions on both the pre-test (P = 0.278) and post-test (P = 0.093). The interns scored higher on the post-test than the pre-test on both extreme (P = 0.0062) and non-extreme (P = 0.0083) questions. After using an online educational tool that allowed learning on their own time and pace, trainees improved their ability to correctly categorize left ventricular systolic function. Left ventricular systolic function is often a key echocardiographic question that can be difficult to master. The promising performance of this educational resource may lead to more time- and cost-effective methods for improving diagnostic accuracy among learners.