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1.
BMC Med Educ ; 24(1): 382, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38589833

ABSTRACT

BACKGROUND: Racism contributes to health disparities and is a serious threat to public health. Teaching physicians about racism, how to address it in medical practice, and developing high quality and sustainable curricula are essential to combating racism. OBJECTIVE: This study aimed to (1) describe the experience of racism and anti-racism teaching in residency programs, and elicit recommendations from key informants, and (2) use these data and formative research to develop recommendations for other residencies creating, implementing, and evaluating anti-racism curricula in their own programs. METHODS: From May to July 2023, 20 faculty and residents were recruited via convenience sampling for key informant interviews conducted via Microsoft Teams. Interviews were audio recorded, transcribed, and coded. An initial list of themes was developed using theoretical frameworks, and then refined using a grounded-theory approach. A brief online optional anonymous demographic survey was sent to participants in August of 2023.  RESULTS: Eighty percent (20/25) of participants approached were interviewed. Seventy-five percent (15/20) answered a brief optional demographic survey. Seven themes emerged: (1) Racism in medicine is ubiquitous; (2) Anti-racism teaching in medicine varies widely; (3) Sustainability strategies should be multifaceted and include recruitment, resource allocation, and outcome measures; (4) Resources are widely available and accessible if one knows where to look; (5) Outcomes and metrics of success should include resident- faculty-, patient- community-, and system-focused outcomes; (6) Curricular strategies should be multilayered, longitudinal, and woven into the curriculum; and (7) Self-reflection and discomfort are necessary parts of the process.  CONCLUSIONS: This study is one of the first to qualitatively examine perspectives of key stakeholders invested in anti-racism teaching for residents. The Support - Pipeline - Outcomes - Community (SPOC) Model, that was developed using information collected during this study, can be used in the future as a guide for others working to design and implement sustainable and high quality anti-racism curricula for residents.


Subject(s)
Internship and Residency , United States , Humans , Antiracism , Curriculum , Faculty , Public Health
2.
Ann Am Thorac Soc ; 21(4): 612-619, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38241011

ABSTRACT

Rationale: Over 20,000 children are hospitalized in the United States for asthma every year. Although initial treatment guidelines are well established, there is a lack of high-quality evidence regarding the optimal respiratory support devices for these patients.Objectives: The objective of this study was to evaluate institutional and temporal variability in the use of respiratory support modalities for pediatric critical asthma.Methods: We conducted a retrospective cohort study using data from the Virtual Pediatrics Systems database. Our study population included children older than 2 years old admitted to a VPS contributing pediatric intensive care unit from January 2012 to December 2021 with a primary diagnosis of asthma or status asthmaticus. We evaluated the percentage of encounters using a high-flow nasal cannula (HFNC), continuous positive airway pressure (CPAP), noninvasive bilevel positive pressure ventilation (NIV), and invasive mechanical ventilation (IMV) for all institutions, then divided institutions into quintiles based on the volume of patients. We created logistic regression models to determine the influence of institutional volume and year of admission on respiratory support modality use. We also conducted time-series analyses using Kendall's tau.Results: Our population included 77,115 patient encounters from 163 separate institutions. Institutional use of respiratory modalities had significant variation in HFNC (28.3%, interquartile range [IQR], 11.0-49.0%; P < 0.01), CPAP (1.4%; IQR, 0.3-4.3%; P < 0.01), NIV (8.6%; IQR, 3.5-16.1%; P < 0.01), and IMV (5.1%; IQR, 3.1-8.2%; P < 0.01). Increased institutional patient volume was associated with significantly increased use of NIV (odds ratio [OR], 1.33; 1.29-1.36; P < 0.01) and CPAP (OR, 1.20; 1.15-1.25; P < 0.01), and significantly decreased use of HFNC (OR, 0.80; 0.79-0.81; P < 0.01) and IMV (OR, 0.82; 0.79-0.86; P < 0.01). Time was also associated with a significant increase in the use of HFNC (11.0-52.3%; P < 0.01), CPAP (1.6-5.4%; P < 0.01), and NIV (3.7-21.2%; P < 0.01), whereas there was no significant change in IMV use (6.1-4.0%; P = 0.11).Conclusions: Higher-volume centers are using noninvasive positive pressure ventilation more frequently for pediatric critical asthma and lower frequencies of HFNC and IMV. Treatment with HFNC, CPAP, and NIV for this population is increasing in the last decade.


Subject(s)
Asthma , Noninvasive Ventilation , Respiratory Insufficiency , Humans , Child , Child, Preschool , Retrospective Studies , Asthma/therapy , Respiration, Artificial , Hospitalization , Oxygen Inhalation Therapy , Respiratory Insufficiency/therapy
3.
J Am Soc Cytopathol ; 13(1): 4-9, 2024.
Article in English | MEDLINE | ID: mdl-38184364

ABSTRACT

This report highlights information and outcomes from the November 2022 ASC/IAC joint Cytology Education Symposium, an annual conference organized by the Cytology Programs Review Committee. The manuscript provides information on shared educational opportunities and practices for cytology students and other learners in anatomic pathology, discusses recruitment strategies for schools of cytology, conveys teaching resources, introduces perspectives on virtual microscopy and online learning, and transmits information about wellness of students in schools of cytology.


Subject(s)
Cytological Techniques , Schools , Symbiosis , Humans , Educational Status , North America
4.
Nucleic Acids Res ; 52(D1): D1668-D1676, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37994696

ABSTRACT

Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts and over 9 million full text articles accessible via the website, APIs and bulk download. This publication outlines new developments to the Europe PMC platform since the last database update in 2020 (1) and focuses on five main areas. (i) Improving discoverability, reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints. (ii) Enhancing support for text and data mining by expanding the types of annotations provided and developing the Europe PMC Annotations Corpus, which can be used to train machine learning models to increase their accuracy and precision. (iii) Developing the Article Status Monitor tool and email alerts, to notify users about new articles and updates to existing records. (iv) Positioning Europe PMC as an open scholarly infrastructure through increasing the portion of open source core software, improving sustainability and accessibility of the service.


Subject(s)
Biological Science Disciplines , Databases, Bibliographic , Data Mining , Europe , Software , Databases, Bibliographic/standards , Internet
5.
Cytopathology ; 35(1): 2-6, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37877689

ABSTRACT

This report highlights information and outcomes from the November 2022 ASC/IAC joint Cytology Education Symposium, an annual conference organized by the Cytology Programs Review Committee. The manuscript provides information on shared educational opportunities and practices for cytology students and other learners in anatomic pathology, discusses recruitment strategies for schools of cytology, conveys teaching resources, introduces perspectives on virtual microscopy and online learning, and transmits information about wellness of students in schools of cytology.


Subject(s)
Curriculum , Symbiosis , Humans , Cytological Techniques , Schools , North America
6.
OTA Int ; 6(2): e270, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37719314

ABSTRACT

Objectives: The objective of this study was to describe the relationship between positive toxicology screens and measures of preinjury mental health and physical function in an orthopaedic trauma population. Design: This was a cross-sectional study. Setting: Urban Level 1 trauma center. Patients: A total of 125 trauma patients gave written consent for this study. Main Outcome Measurements: Questionnaires such as, Patient Health Questionnaire-9, General Anxiety Disorder-7, PCL-5, and Short Musculoskeletal Function Assessment, were used to survey patients after surgical intervention. Results: Patient Health Questionnaire-9 (P = 0.05) and PCL-5 (P = 0.04) were not found to have significant differences between positive and negative toxicology screens. Both General Anxiety Disorder-7 (P = 0.004) and Short Musculoskeletal Function Assessment function (P = 0.006) were significantly higher in patients with positive toxicology screens. Conclusions: Positive toxicology seems to be associated with preinjury anxiety. Patient reported preinjury function was not adversely affected by the presence of illicit substances or alcohol, nor were levels of post-traumatic stress disorder and depression found to be higher in patients with positive toxicology screens. Level of Evidence: Level IV Cross-Sectional Study.

7.
J Psychopathol Clin Sci ; 132(4): 461-474, 2023 May.
Article in English | MEDLINE | ID: mdl-37036695

ABSTRACT

Although frequently hypothesized, the evidence for associations between affect and marijuana use in everyday life remains ambiguous. Inconsistent findings across existing work may be due, in part, to differences in study design and analytic decisions, such as study inclusion criteria, the operationalization of affect, or the timing of affect assessment. We used specification curves to assess the robustness of the evidence for affect predicting same-day marijuana use and marijuana use predicting next-day affect across several hundred models that varied in terms of decisions that reflect those typical in this literature (e.g., whether to average affect prior to marijuana use or select the affect report closest in time to marijuana use). We fitted these curves to data from two ecological momentary assessment studies of regular marijuana and/or alcohol using college students (N = 287). Results provided robust evidence that marijuana use was slightly less likely following experiences of negative affect and slightly more likely following positive affect. Specification curves suggested that differences in previous findings are most likely a function of the specific emotion items used to represent affect rather than differences in inclusion criteria, the temporal assessment and modeling of affect, or the covariates added to the model. There was little evidence for an association between marijuana use and next-day affect. Overall, our findings provide evidence against the predictions made by affect reinforcement models in college students and suggest that future research should model the associations of marijuana use with discrete emotional states rather than general negative and positive affect. (PsycInfo Database Record (c) 2023 APA, all rights reserved).


Subject(s)
Marijuana Smoking , Marijuana Use , Substance-Related Disorders , Humans , Marijuana Use/epidemiology , Marijuana Use/psychology , Alcohol Drinking/psychology , Marijuana Smoking/epidemiology , Marijuana Smoking/psychology , Emotions
8.
Curr Protoc ; 3(3): e694, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36946755

ABSTRACT

In the field of life sciences there is a growing need for literature analysis tools that help scientists tackle information overload. Europe PubMed Central (Europe PMC), a partner of PubMed Central (PMC; National Library of Medicine, 2022), is an open access database of over 41 million life science publications and preprints, enriched with supporting data, reviews, protocols, and other relevant resources. Europe PMC is a trusted repository of choice for many life science funders (Europe PMC, 2022a), offering a suite of innovative search tools that allow users to search and evaluate the literature, including finding highly cited articles, preprints with community peer reviews, or papers referencing a proteomics dataset in the figure legend. In addition, Europe PMC utilizes text-mining to help researchers identify key terms and find data and evidence in the literature. First-time users often do not utilize the wealth of tools Europe PMC offers and can feel overwhelmed about how to perform the most effective search. This protocol, describing how to search and evaluate publications and preprints using Europe PMC, demonstrates how to carry out more efficient and effective literature searches using the tools provided by Europe PMC. This includes discovering the latest findings on a research topic, following research from a specific author, journal, or preprint server, exploring literature on a new method, expanding your reading list with relevant articles, as well as accessing and evaluating publications and preprints of interest. © 2023 EMBL-EBI. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Finding articles and preprints on a topic of interest Basic Protocol 2: Accessing an article Basic Protocol 3: Browsing the article Basic Protocol 4: Evaluating the article Basic Protocol 5: Refining search results Basic Protocol 6: Finding research by author Basic Protocol 7: Finding a specific article Basic Protocol 8: Finding information about a methodology Basic Protocol 9: Finding evidence of biological interactions, relations, and modifications Basic Protocol 10: Finding data behind a publication Basic Protocol 11: Expanding a reading list and building a bibliography Basic Protocol 12: Staying on top of the current literature.


Subject(s)
Biological Science Disciplines , Data Mining , PubMed , Europe , Search Engine
9.
J Community Psychol ; 51(5): 2098-2116, 2023 07.
Article in English | MEDLINE | ID: mdl-36776019

ABSTRACT

Study examined predictors and mental health consequences of appraisal (threat, support satisfaction) and coping (active, avoidant) in a sample of low-income women during coronavirus disease 2019 (COVID-19). Pre-COVID-19 contextual risk and individual resources and COVID-19-specific risk factors were examined as predictors of COVID-19 appraisal and coping, which, in turn, were tested as predictors of changes in depression and anxiety across the pandemic. Pre-COVID-19 resilience predicted more active coping, whereas pre-COVID-19 anxiety and depression predicted more avoidant coping and lower support satisfaction, respectively. Increases in anxiety were predicted by lower pre-COVID-19 self-compassion and higher concurrent threat appraisal and avoidant coping. Increases in depression were related to lower pre-COVID-19 self-compassion, active coping and support satisfaction, and higher COVID-19 hardships and health risk. Findings highlight contextual and individual factors and processes that contribute to mental health problems in a vulnerable population during community-level stressors, with implications for prevention and intervention.


Subject(s)
COVID-19 , Humans , Female , COVID-19/psychology , Mental Health , Pandemics , Surveys and Questionnaires , Adaptation, Psychological
10.
J Clin Psychol ; 79(4): 1082-1098, 2023 04.
Article in English | MEDLINE | ID: mdl-36490357

ABSTRACT

OBJECTIVE: How individuals differentially implement specific emotion regulation (ER) strategies is a critical indicator of the progression of depressive and anxiety disorders. Symptoms of anxiety and depression may be associated with differences in ER, but little evidence to date had examined whether anxiety and depression were associated with individual differences in the real-time use of ER strategies. METHODS: This study used ecological momentary assessment (EMA) in two samples (n = 276) of undergraduate students from a single university who were assessed for 8-10 days. Baseline surveys captured participant self-reported anxiety symptoms and depressive symptoms using the PROMIS-Anxiety scale and the PROMIS-Depression scale, respectively. We measured ER through EMA-adapted prompts from the Cognitive Emotion Regulation Questionnaire (CERQ), which participants received on their internet-enabled cell phones. In pre-registered analyses, we tested the associations between anxiety symptoms with the use of discrete ER strategies in EMA using generalized estimating equations with a log-link function to account for nesting of EMA observations within participants, and further tested whether the findings generalized to depression (not pre-registered). RESULTS: Symptoms of anxiety and depression were associated with greater odds of using both maladaptive and adaptive ER strategy use during the EMA period, and with lower odds of reporting no strategy use. Moreover, associations were generally stronger for maladaptive than adaptive ER strategies. CONCLUSION: Anxiety and depressive symptoms are related to increased regulatory efforts overall, and results suggest that individuals with anxiety and depressive symptoms may be especially prone to use maladaptive ER strategies. Tracking ER strategies in a natural environment can further inform our understanding of how anxious and depressed individuals attempt to regulate emotions.


Subject(s)
Depression , Emotional Regulation , Humans , Depression/psychology , Anxiety/psychology , Emotions/physiology , Anxiety Disorders
11.
Emotion ; 23(4): 1011-1027, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36006696

ABSTRACT

Emotion regulation (ER) is an important factor in resilience and overall well-being throughout development, and youth report increased variation in emotion and capacity for regulation across adolescence and early adulthood. Specific emotions may be associated with the use of different ER strategies, but much evidence exclusively collapses across negative and positive affect or may not reflect the daily experience of emotion and emotion regulation. The present study examined associations between the experience of unique positive and negative emotions and the use of common ER strategies in adolescence and early adulthood during daily life using ecological momentary assessment (EMA). The sample included 184 high school and college students (55% female, Mage = 17.88, SD = 1.25) who completed EMA surveys three times daily for 10 days (89% compliance). Participants reported on their recent emotional states and which of eight ER strategies they had used. Multilevel logistic regressions tested emotions as predictors of ER strategies, separately for each emotion-ER strategy combination across 96 total models, using the Benjamini-Hochberg procedure to control the false discovery rate. Individuals had higher odds of engaging in maladaptive ER strategies, particularly suppression or rumination, when reporting most types of negative emotions-with the largest associations among unhappiness and anger. Conversely, positive emotions were generally linked to reported use of no ER strategies, though happiness and engagement were related to higher odds of problem-solving, while calm was related to less use of nearly all strategies. Specific emotion-strategy combinations may have implications for clinical targets. (PsycInfo Database Record (c) 2023 APA, all rights reserved).


Subject(s)
Emotional Regulation , Adolescent , Humans , Female , Adult , Male , Emotional Regulation/physiology , Emotions/physiology , Happiness , Surveys and Questionnaires , Anger , Ecological Momentary Assessment
12.
Front Psychol ; 13: 1011095, 2022.
Article in English | MEDLINE | ID: mdl-36438327

ABSTRACT

While appraisal and coping are known to impact adolescent psychopathology, more vulnerable or resilient responses to stress may depend on individual temperament. This study examined early life temperament as a moderator of the prospective relations of pre-adolescent appraisal and coping with adolescent psychopathology. The sample included 226 (62% female, 14-15 years) adolescents with assessments starting at 3 years of age. Adolescents were predominately White (12% Black 9% Asian, 11% Latinx, 4% Multiracial, and 65% White). Observed early-childhood temperament (fear, frustration, executive control, and delay ability) were tested as moderators of pre-adolescent coping (active and avoidant) and appraisal (threat, positive) on internalizing and externalizing symptoms during the pandemic. Interaction effects were tested using regression in R. Sex and family context of stress were covariates. Early-childhood temperament was correlated with pre-adolescent symptoms, however, pre-adolescent appraisal and coping but not temperament predicted adolescent psychopathology. Frustration moderated the relations of active and avoidant coping and positive appraisal to symptoms such that coping and appraisal related to lower symptoms only for those low in frustration. Executive control moderated the associations of avoidant coping with symptoms such that avoidance reduced the likelihood of symptoms for youth low in executive control. Findings underscore the role of emotionality and self-regulation in youth adjustment, with the impact of coping differing with temperament. These findings suggest that equipping youth with a flexible assortment of coping skills may serve to reduce negative mental health outcomes.

13.
Infant Child Dev ; 31(4)2022.
Article in English | MEDLINE | ID: mdl-36060792

ABSTRACT

This study examined bidirectional relations between television exposure and effortful control accounting for the effects of family contextual risk factors. Methods: Data were from a sample (N=306) of parents and their preschool-age children (T1 M = 36 mos. in 2008-2010) assessed four times, once every 9 mos. Results: At T1, adolescent parent status predicted lower child delay ability (DA), and maternal depression predicted higher TV time. Above these effects, higher T1 and T2 child executive control (EC) prospectively predicted lower T2 and T3 TV time, while higher T1 TV time predicted lower T2 EC. Higher EC at T4 predicted fewer total problems, greater social competence, and greater academic readiness at T4, and higher TV time at T4 predicted lower academic readiness. DA was unrelated to TV time or adjustment. Conclusion: Findings suggest executive control and TV time predict changes in each other in early childhood, and in turn, executive control predicts better child adjustment while TV time might be more relevant for academic readiness. Moreover, family risk factors appear to play a role in both TV viewing time and effortful control.

14.
BMC Public Health ; 22(1): 1620, 2022 08 26.
Article in English | MEDLINE | ID: mdl-36028827

ABSTRACT

BACKGROUND: Over the last decade, the provision of online gambling has intensified with increased access, enhanced betting markets, a broader product range, and prolific marketing. However, little research has explored how this intensification is influencing contemporary gambling experiences. This study focused on two research questions: 1) What changes in online gambling have online gamblers observed over the past decade? 2) How have these changes influenced the online gambling experiences and behaviours reported by treatment-seeking and non-treatment-seeking gamblers? METHODS: Two samples of Australian adults were interviewed: 1) 19 people who had been gambling online for at least a decade and with no history of treatment-seeking for online gambling, and 2) 10 people who had recently sought professional help for an online gambling problem. Telephone interviews were semi-structured, with questions that encouraged participants to consider how their online gambling, including any harmful gambling, had been influenced by changes in operator practices and online gambling environments. Data were analysed using thematic analysis. RESULTS: Both treatment- and non-treatment-seekers noted the increased speed and ease of online gambling, which now enables instant access from anywhere at any time and increased their gambling opportunities. Both groups highlighted the continued proliferation of advertising and inducements for online gambling, particularly during televised sports and racing events, in social media, and through targeted push marketing. Many treatment- and non-treatment-seekers were aware of the vast range of recently introduced bet types, particularly multi-bets. Treatment-seekers disproportionately reported negative effects from these changes, and described how and why they fostered their increased gambling, impulsive gambling, persistence and loss-chasing. They reported limited uptake and effectiveness of current harm minimisation tools. CONCLUSIONS: Counter to stated policy and practice objectives to minimise gambling harm, industry changes that have made online gambling easier, faster, and more heavily incentivised, and increased the array of complex bets with poorer odds, unduly affect addicted and harmed individuals - who are also the most profitable customers. Further consideration is needed to ensure gambling policy, industry practices and public health measures more effectively reduce gambling harm in contemporary settings. Inducements and the poor pricing of complex bets such as multi-bets, and their outsized attraction to players with problems, should be a key focus.


Subject(s)
Gambling , Adult , Advertising , Australia , Humans , Impulsive Behavior , Qualitative Research
15.
Nat Hum Behav ; 6(7): 964-974, 2022 07.
Article in English | MEDLINE | ID: mdl-35484208

ABSTRACT

Prominent theories suggest that self-injurious thoughts and behaviours are negatively reinforced by decreased negative affect. The present meta-analysis quantifies effects from intensive longitudinal studies measuring negative affect and self-injurious thoughts and behaviours. We obtained data from 38 of the 79 studies (48%, 22 unique datasets) involving N = 1,644 participants (80% female, 75% white). Individual-participant data meta-analyses revealed changes in affect pre/post self-injurious thoughts and behaviours. In antecedent models, results supported increased negative affect before nonsuicidal self-injurious behaviour (k = 14, 95% CI 0.09 to 0.31) and suicidal thoughts (k = 14, 95% CI 0.03 to 0.19). For consequence models, negative affect was reduced following nonsuicidal self-injurious thoughts (k = 6, 95% CI -0.79 to -0.44), nonsuicidal self-injurious behaviours (k = 14, 95% CI -0.73 to -0.19) and suicidal thoughts (k = 13, 95% CI -0.79 to -0.23). Findings, which were not moderated by sampling strategies or sample composition, support the affect regulation function of self-injurious thoughts and behaviours.


Subject(s)
Self-Injurious Behavior , Female , Humans , Longitudinal Studies , Male , Suicidal Ideation
16.
Res Child Adolesc Psychopathol ; 50(6): 695-708, 2022 06.
Article in English | MEDLINE | ID: mdl-35039970

ABSTRACT

Parents living in low-income contexts shouldered disproportionate hardships during the COVID-19 pandemic with consequences to maternal mental health and child adjustment. The current study uses a sample of first-time mothers (N = 147) of young toddlers, all living in low-income contexts, to examine the roles of pre-pandemic and COVID-19-specific risk and individual resilience factors in the prediction of changes to maternal mental health coinciding with the onset of the pandemic. Maternal mental health symptoms, in turn, were examined as predictors of child adjustment problems across 6 months of the pandemic and as a potential mechanism conferring pandemic risks to children. While pre-pandemic cumulative contextual risk (i.e., low income, single parent status, adolescent parent status, financial instability) did not predict changes in maternal mental health from prior to during the pandemic, COVID-19-specific health risks predicted changes in maternal mental health from before the pandemic, as well as across 6 months of the pandemic. Regarding individual resilience factors to changes in maternal mental health, pre-pandemic self-compassion predicted better maternal mental health during the pandemic, as did COVID-19-specific appraisal and coping strategies. In turn, maternal mental health predicted children's early pandemic levels of adjustment problems and changes in adjustment problems across 6 months of the pandemic, with maternal mental health serving an indirect pathway of COVID-19-specific health risks to children's adjustment. The findings highlight pathways of risk and resilience during a global health crisis and point to targets for interventions in community level crises to promote maternal and child mental health.


Subject(s)
COVID-19 , Adolescent , COVID-19/epidemiology , Female , Humans , Maternal Health , Mental Health , Mothers/psychology , Pandemics
17.
Nucleic Acids Res ; 50(D1): D11-D19, 2022 01 07.
Article in English | MEDLINE | ID: mdl-34850134

ABSTRACT

The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major data type in the life sciences. This year's service update for EMBL-EBI includes new resources, PGS Catalog and AlphaFold DB, and updates on existing resources, including the COVID-19 Data Platform, trRosetta and RoseTTAfold models introduced in Pfam and InterPro, and the launch of Genome Integrations with Function and Sequence by UniProt and Ensembl. Furthermore, we highlight projects through which EMBL-EBI has contributed to the development of community-driven data standards and guidelines, including the Recommended Metadata for Biological Images (REMBI), and the BioModels Reproducibility Scorecard. Training is one of EMBL-EBI's core missions and a key component of the provision of bioinformatics services to users: this year's update includes many of the improvements that have been developed to EMBL-EBI's online training offering.


Subject(s)
Computational Biology/education , Computational Biology/methods , Databases, Factual , Academies and Institutes , Artificial Intelligence , COVID-19 , Databases, Factual/economics , Databases, Factual/statistics & numerical data , Databases, Pharmaceutical , Databases, Protein , Europe , Genome, Human , Humans , Information Storage and Retrieval , RNA, Untranslated/genetics , SARS-CoV-2/genetics
18.
Nucleic Acids Res ; 49(D1): D1507-D1514, 2021 01 08.
Article in English | MEDLINE | ID: mdl-33180112

ABSTRACT

Europe PMC (https://europepmc.org) is a database of research articles, including peer reviewed full text articles and abstracts, and preprints - all freely available for use via website, APIs and bulk download. This article outlines new developments since 2017 where work has focussed on three key areas: (i) Europe PMC has added to its core content to include life science preprint abstracts and a special collection of full text of COVID-19-related preprints. Europe PMC is unique as an aggregator of biomedical preprints alongside peer-reviewed articles, with over 180 000 preprints available to search. (ii) Europe PMC has significantly expanded its links to content related to the publications, such as links to Unpaywall, providing wider access to full text, preprint peer-review platforms, all major curated data resources in the life sciences, and experimental protocols. The redesigned Europe PMC website features the PubMed abstract and corresponding PMC full text merged into one article page; there is more evident and user-friendly navigation within articles and to related content, plus a figure browse feature. (iii) The expanded annotations platform offers ∼1.3 billion text mined biological terms and concepts sourced from 10 providers and over 40 global data resources.


Subject(s)
Biological Science Disciplines/statistics & numerical data , COVID-19/prevention & control , Data Curation/statistics & numerical data , Data Mining/statistics & numerical data , Databases, Factual/statistics & numerical data , PubMed , SARS-CoV-2/isolation & purification , Biological Science Disciplines/methods , Biomedical Research/methods , Biomedical Research/statistics & numerical data , COVID-19/epidemiology , COVID-19/virology , Data Curation/methods , Data Mining/methods , Epidemics , Europe , Humans , Internet , SARS-CoV-2/physiology
19.
Front Immunol ; 11: 581475, 2020.
Article in English | MEDLINE | ID: mdl-33362767

ABSTRACT

Chronic granulomatous disease (CGD) is a primary immune deficiency due to defects in phagocyte respiratory burst leading to severe and life-threatening infections. Patients with CGD also suffer from disorders of inflammation and immune dysregulation including colitis and granulomatous lung disease, among others. Additionally, patients with CGD may be at increased risk of systemic inflammatory disorders such as hemophagocytic lymphohistiocytosis (HLH). The presentation of HLH often overlaps with symptoms of systemic inflammatory response syndrome (SIRS) or sepsis and therefore can be difficult to identify, especially in patients with a primary immune deficiency in which incidence of infection is increased. Thorough evaluation and empiric treatment for bacterial and fungal infections is necessary as HLH in CGD is almost always secondary to infection. Simultaneous treatment of infection with anti-microbials and inflammation with immunosuppression may be needed to blunt the hyperinflammatory response in secondary HLH. Herein, we present a series of X-linked CGD patients who developed HLH secondary to or with concurrent disseminated CGD-related infection. In two patients, CGD was a known diagnosis prior to development of HLH and in the other two CGD was diagnosed as part of the evaluation for HLH. Concurrent infection and HLH were fatal in three; one case was successfully treated, ultimately receiving hematopoietic stem cell transplantation. The current literature on presentation, diagnosis, and treatment of HLH in CGD is reviewed.


Subject(s)
Granulomatous Disease, Chronic/complications , Granulomatous Disease, Chronic/mortality , Lymphohistiocytosis, Hemophagocytic/etiology , Lymphohistiocytosis, Hemophagocytic/mortality , Adolescent , Hematopoietic Stem Cell Transplantation/methods , Humans , Immunosuppression Therapy/methods , Infant , Male , Sepsis/etiology , Sepsis/mortality
20.
Prev Med ; 138: 106157, 2020 09.
Article in English | MEDLINE | ID: mdl-32473267

ABSTRACT

Adolescents' engage in new behaviours such as substance use and change others, such as reducing physical activity. Risks to health from these tend to be considered separately. We examined the association between multiple risk behaviours at age 16 years and outcomes in early adulthood. 5591 young people enrolled in the Avon Longitudinal Study of Parents and Children provided data on at least one of seven adverse outcomes at age ~18 years. We used logistic regression to examine associations between total number of risk behaviours and rates of depression, anxiety, problem gambling, getting into trouble with the police, harmful drinking, obesity and not in education, employment or training (NEET) at age 18 years. We found strong associations between multiple risk behaviours and all seven adverse outcomes. For each additional risk behaviour engaged in the odds of harmful drinking increased by OR = 1.58[95%CI:1.48,1.69], getting into trouble with the police OR = 1.49[95%CI:1.42,1.57], having depression OR = 1.24[95%CI:1.17,1.31], problem gambling OR = 1.20[95%CI:1.13,1.27], NEET OR = 1.19[95%CI:1.11,1.29], anxiety OR = 1.18[95%CI:1.12,1.24] and obesity OR = 1.09[95%CI:1.03,1.15]. Neither adjustment for sex, parental socio-economic position and maternal risk behaviours, nor confining analyses to adolescents with no previous presentation of these adverse outcomes, resulted in any notable reductions in the odds ratios. Investment in interventions and environments that effectively prevent multiple risk behaviour is likely to improve a range of health outcomes in young adults.


Subject(s)
Risk-Taking , Substance-Related Disorders , Adolescent , Adult , Child , Cohort Studies , Humans , Longitudinal Studies , Prospective Studies , Substance-Related Disorders/epidemiology , Young Adult
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