bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors associated with therapeutic inertia in individuals with type 2 diabetes mellitus started on basal insulin
Authors: Shabnam Sharmin , Gillies Clare L , Davies Melanie J , Dex Terry , Melson Eka , Khunti Kamlesh , Webb David R , Zaccardi Francesco , Seidu Samuel 
Published: July 2023

AbstractAimIn this study we aim to identify the risk factors for treatment inertia in patients with type 2 diabetes mellitus (T2DM) who have been recently started on basal insulin (BI).MethodsUsing UK CPRD GOLD, we identified adults with T2DM with suboptimal glycaemia (HbA1c within 12 months of BI ≥7% (≥53 mmol/mol)). We used multivariable Cox regression model to describe the association between patient characteristics and the time to treatment intensification.ResultsA total of 12,556 patients were analysed. Compared to individuals aged <65 years, those aged ≥65 years had lower risk of treatment intensification (HR: 0.69; 95% CI: 0.64-0.73). Other risk factors included being female (0.93, 0.89-0.99), longer T2DM duration (0.99, 0.98-0.99), living in the most deprived areas (0.90, 0.83-0.98), being a current smoker (0.91, 0.84-0.98), having one (0.91, 0.85- 0.97) or more than one comorbidity (0.88, 0.82-0.94), and patients who were on metformin (0.71, 0.63-0.80), or 2nd generation sulphonylureas (0.85; 0.79-0.92) or DPP4 inhibitors (0.87, 0.82-0.93) compared to those who were not.ConclusionTherapeutic inertia still remains a major barrier, with multiple factors associated with delay in intensification. Interventions to overcome therapeutic inertia need to be implemented at both patient and health care professional level.
Assessment of compliance of baby friendly hospital initiative in tertiary care hospital, South India
Authors: ruban A.charles pon , S Nair Lekshmy , Maria David Linta , V Mahalakshmi , Jerin Grace Manorita , Prithvi K Manoj , K S Jyodhish 
Published: July 2023

AbstractObjectivesTo assess the compliance of a tertiary care hospital, South India with the ten steps of the Baby Friendly Hospital Initiative following the UNICEF/WHO global criteria.DesignCross-sectional studySettingTertiary care hospital, South IndiaParticipantsStaff nurses who are posted in in the obstetrics and gynaecology department and the mothers admitted antenatal, postnatal, and labour wards.ResultsOnly 35% of the staff nurses interviewed received formal training in breastfeeding techniques. Written information about breastfeeding was given to all prenatal mothers (100%) yet, only 75% knew the importance of breastfeeding soon after delivery. Only 62.5% of babies were exclusively breastfed and 51.3% of the babies were breastfed within one hour of birth. Compliance with the Ten Steps of baby friendly initiative was 66.63%, signifying a moderate compliance overall.ConclusionThe compliance to Ten steps of BFHI in low resource setting shows an overall moderate compliance. The Ten Steps of BFHI may be implemented more effectively in all medical facilities through the mother’s absolute affection Programme (MAA). More focused approaches are needed to improve the breastfeeding practices even in tertiary care settings in India.KeypointWhat is already known on this topicGood breast-feeding practices are essential for reducing infant mortality. The effect of interventions by the Government on breast feeding practices especially in a tertiary care hospital setting, South India is poorly studied.What this study addsPractice of exclusive breast feeding is low. Compliance with the Ten Steps of baby friendly initiative was low even in a tertiary care setup in south India.How this study might affect research, practice and/or policyGood breast-feeding practices should be promoted in all health facilities. More focused interventions are needed to fill this gap.
The genetic diversity of Nipah virus across spatial scales
Authors: Azuero Oscar Cortés , Lefrancq Noémie , Nikolay Birgit , McKee Clifton , Cappelle Julien , Hul Vibol , Ou Tey Putita , Hoem Thavry , Lemey Philippe , Rahman Mohammed Ziaur , Islam Ausraful , Gurley Emily S. , Duong Veasna , Salje Henrik 
Published: July 2023

AbstractNipah virus (NiV), a highly lethal virus in humans, circulates silently inPteropusbats throughout South and Southeast Asia. Difficulty in obtaining genomes from bats means we have a poor understanding of NiV diversity, including how many lineages circulate within a roost and the spread of NiV over increasing spatial scales. Here we develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999–2020). In Bangladesh, where most human infections occur, we find evidence of increased spillover risk from one of the two co-circulating sublineages. We divide the four major NiV sublineages into 15 genetic clusters (emerged 20-44 years ago). Within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1,500-2,000 km2. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate that each genetic cluster occupies an average area of 1.3 million km2(95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000 km2(95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most of the genetic clusters have been identified, but only ∼15% of overall NiV diversity has been uncovered. Our findings are consistent with entrenched co-circulation of distinct lineages, even within individual roosts, coupled with slow migration over larger spatial scales.
Leveraging Large Language Models for Generating Responses to Patient Messages
Authors: Liu Siru , McCoy Allison B. , Wright Aileen P. , Carew Babatunde , Genkins Julian Z. , Huang Sean S. , Peterson Josh F. , Steitz Bryan , Wright Adam 
Published: July 2023

ABSTRACTObjectiveThis study aimed to develop and assess the performance of fine-tuned large language models for generating responses to patient messages sent via an electronic health record patient portal.MethodsUtilizing a dataset of messages and responses extracted from the patient portal at a large academic medical center, we developed a model (CLAIR-Short) based on a pre-trained large language model (LLaMA-65B). In addition, we used the OpenAI API to update physician responses from an open-source dataset into a format with informative paragraphs that offered patient education while emphasizing empathy and professionalism. By combining with this dataset, we further fine-tuned our model (CLAIR-Long). To evaluate the fine-tuned models, we used ten representative patient portal questions in primary care to generate responses. We asked primary care physicians to review generated responses from our models and ChatGPT and rated them for empathy, responsiveness, accuracy, and usefulness.ResultsThe dataset consisted of a total of 499,794 pairs of patient messages and corresponding responses from the patient portal, with 5,000 patient messages and ChatGPT-updated responses from an online platform. Four primary care physicians participated in the survey. CLAIR-Short exhibited the ability to generate concise responses similar to provider’s responses. CLAIR-Long responses provided increased patient educational content compared to CLAIR-Short and were rated similarly to ChatGPT’s responses, receiving positive evaluations for responsiveness, empathy, and accuracy, while receiving a neutral rating for usefulness.ConclusionLeveraging large language models to generate responses to patient messages demonstrates significant potential in facilitating communication between patients and primary care providers.
Contextual and psychological factors of mask-wearing among secondary school students: A cross-sectional survey from Toronto
Authors: Liang Thomas , Kraguljac Alan , Science Michelle 
Published: July 2023

AbstractIntroductionAfter the Ontario government withdrew masking regulations, mask-wearing became a personal choice. Many studies have investigated the factors associated with public mask-wearing, but few have explored the knowledge, attitudes, and psychological factors of masking in high school students. Our study aims to fill this gap.MethodsIn February 2023, a cross-sectional survey was distributed online to Grade 9-12 students in a school located in Toronto. Descriptive statistics, correlation analysis, and logistic regression were performed on the quantitative data, while thematic analysis was used to evaluate the qualitative responses.ResultsMost of the 62 participants were male with the median age of 16. Approximately half of the respondents reported some frequency of mask-wearing over the past month. Almost all participants claimed to be knowledgeable about COVID-19’s modes of transmission and preventative measures. More participants supported voluntary masking in schools rather than mandated masking. Demographic variables, existing COVID-19 knowledge, and perceived medical benefits were not significantly correlated with masking behaviour. Students who supported voluntary masking were ∼22 times more likely to wear a mask compared to those who held negative attitudes. Participants who felt a high level of perceived barriers were ∼30 times less likely to wear a mask. Mask-wearing individuals cited protection and aesthetic reasons, while the opposition raised arguments about the reduced concern of COVID-19 and downsides of masks.ConclusionAdolescent mask-wearing is significantly impacted by pre-existing attitudes towards masks, while perceived barriers strongly discourage students from wearing masks. Future research should investigate how to best promote positive beliefs regarding mask-wearing to youth.
Comparison of approaches to control for intracranial volume in research on the association of brain volumes with cognitive outcomes
Authors: Wang Jingxuan , Hill-Jarrett Tanisha , Buto Peter , Pederson Annie , Sims Kendra D. , Zimmerman Scott C. , DeVost Michelle A , Ferguson Erin , Lacar Benjamin , Yang Yulin , Choi Minhyuk , Caunca Michelle R. , La Joie Renaud , Chen Ruijia , Glymour M. Maria , Ackley Sarah F. 
Published: July 2023

AbstractBackgroundConsistent methods for evaluating the link between brain structure and cognition are essential for understanding determinants of neurologic outcomes. Studies examining associations between brain volumetric measures and cognition use various statistical approaches to account for variation in intracranial volume (ICV). It is unclear if commonly used approaches yield consistent results.MethodsUsing a brain-wide association approach in the MRI substudy of UK Biobank (N=41,964; mean age=64.5 years), we used regression models to estimate the associations of 58 regional brain volumetric measures with eight cognitive outcomes, comparing no correction and five ICV correction approaches. Approaches evaluated included: no correction; dividing regional volumes by ICV, with and without further adjustment for ICV (proportional approach); including ICV as a covariate in the regression (adjustment approach); and regressing the regional volumes against ICV in different normative samples and using calculated residuals to determine associations (residual approach). We used Spearman-rank correlations and two consistency measures to quantify the extent to which associations were inconsistent across ICV correction approaches for each possible brain region and cognitive outcome pair across 2,784 regression models.FindingsThe adjustment and residual approaches typically produced similar estimates, which were inconsistent with results from the crude and proportional approaches. Inconsistencies across approaches were largest when estimates from the adjustment and residual approaches were further from the null. That is, the approach used was least important when the association between brain volume and cognitive performance was close to null; in this case, all approaches tend to estimate a null association.InterpretationCommonly used methods to correct for ICV yield inconsistent results and the proportional method diverges from other methods. Adjustment methods are the simplest to implement while producing biologically plausible associations.
Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests
Authors: Chan Lauren E , Casiraghi Elena , Putman Tim , Reese Justin , Harmon Quaker E. , Schaper Kevin , Hedge Harshad , Valentini Giorgio , Schmitt Charles , Motsinger-Reif Alison , Hall Janet E , Mungall Christopher J , Robinson Peter N , Haendel Melissa A 
Published: July 2023

AbstractObjectiveFemale reproductive disorders (FRDs) are common health conditions that may present with significant symptoms. Diet and environment are potential areas for FRD interventions. We utilized a knowledge graph (KG) method to predict factors associated with common FRDs (e.g., endometriosis, ovarian cyst, and uterine fibroids).Materials and MethodsWe harmonized survey data from the Personalized Environment and Genes Study on internal and external environmental exposures and health conditions with biomedical ontology content. We merged the harmonized data and ontologies with supplemental nutrient and agricultural chemical data to create a KG. We analyzed the KG by embedding edges and applying a random forest for edge prediction to identify variables potentially associated with FRDs. We also conducted logistic regression analysis for comparison.ResultsAcross 9765 PEGS respondents, the KG analysis resulted in 8535 significant predicted links between FRDs and chemicals, phenotypes, and diseases. Amongst these links, 32 were exact matches when compared with the logistic regression results, including comorbidities, medications, foods, and occupational exposures.DiscussionMechanistic underpinnings of predicted links documented in the literature may support some of our findings. Our KG methods are useful for predicting possible associations in large, survey-based datasets with added information on directionality and magnitude of effect from logistic regression. These results should not be construed as causal, but can support hypothesis generation.ConclusionThis investigation enabled the generation of hypotheses on a variety of potential links between FRDs and exposures. Future investigations should prospectively evaluate the variables hypothesized to impact FRDs.
Predicting the impact of COVID-19 non-pharmaceutical intervention on short- and medium-term dynamics of enterovirus D68 in the US
Authors: Park Sang Woo , Messacar Kevin , Douek Daniel C. , Spaulding Alicen B. , E. Metcalf C. Jessica , Grenfell Bryan T. 
Published: July 2023

AbstractRecent outbreaks of enterovirus D68 (EV-D68) infections, and their causal linkage with acute flaccid myelitis (AFM), continue to pose a serious public health concern. During 2020 and 2021, the dynamics of EV-D68 and other pathogens have been significantly perturbed by non-pharmaceutical interventions against COVID-19; this perturbation presents a powerful natural experiment for exploring the dynamics of these endemic infections. In this study, we analyzed publicly available data on EV-D68 infections, originally collected through the New Vaccine Surveillance Network, to predict their short- and long-term dynamics following the COVID-19 interventions. Although there are large uncertainties in our predictions, the likelihood of a large outbreak in 2023 appears to be low. Comprehensive surveillance data are needed to narrow uncertainties in future dynamics of EV-D68. The limited incidence of AFM cases in 2022, despite large EV-D68 outbreaks, poses further questions for the timing of the next AFM outbreaks.
Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis
Authors: O’Connor Karen , Weissenbacher Davy , Elyaderani Amir , Lautenbach Ebbing , Scotch Matthew , Gonzalez-Hernandez Graciela 
Published: July 2023

AbstractBackgroundThere has been an unprecedented effort to sequence the SARS-CoV-2 virus and examine its molecular evolution. This has been facilitated by the availability of publicly accessible databases, the Global Initiative on Sharing All Influenza Data (GISAID) and GenBank, which collectively hold millions of SARS-CoV-2 sequence records. Genomic epidemiology, however, seeks to go beyond phylogenetic analysis by linking genetic information to patient characteristics and disease outcomes, enabling a comprehensive understanding of transmission dynamics and disease impact.While these repositories include fields reflecting patient-related metadata for a given sequence, inclusion of these demographic and clinical details is scarce. The extent to which patient-related metadata is reported in published sequencing studies and its quality remains largely unexplored.MethodsThe NIH’s LitCovid collection will be used for automated classification of articles reporting having deposited SARS-CoV-2 sequences in public repositories, while an independent search will be conducted in PubMed for validation. Data extraction will be conducted using Covidence. The extracted data will be synthesized and summarized to quantify the availability of patient metadata in the published literature of SARS-CoV-2 sequencing studies. For the bibliometric analysis, relevant data points, such as author affiliations and citation metrics will be extracted.DiscussionThis scoping review will report on the extent and types of patient-related metadata reported in genomic viral sequencing studies of SARS-CoV-2, identify gaps in this reporting, and make recommendations for improving the quality and consistency of reporting in this area. The bibliometric analysis will uncover trends and patterns in the reporting of patient-related metadata, including differences in reporting based on study types or geographic regions. Co-occurrence networks of author keywords will also be presented. The insights gained from this study may help improve the quality and consistency of reporting patient metadata, enhancing the utility of sequence metadata and facilitating future research on infectious diseases.Strengths and LimitationsClassification of papers using machine learning will help pinpoint more relevant papers reducing time to sift through articles for inclusion.Study will provide an overview of the availability of information required to facilitate genomic epidemiology studies of SARS-CoV-2The bibliometric analysis will analyze publication trends, author affiliations, citation metrics, and other bibliographic information to provide several insights into the broader landscape of research that includes patient metadata reporting in genomic viral sequencing studies of SARS-CoV-2As with any search method for relevant studies, some may be missed by both the automated methods proposed and manually developed queries.
The Contribution of Commonly Diagnosed Genetic Disorders to Small for Gestational Age Birth and Subsequent Morbidity and Mortality in Preterm Infants
Authors: Bomback Miles , Everett Selin , Lyford Alex , Sahni Rakesh , Kim Faith , Baptiste Caitlin , Motelow Joshua E. , Tolia Veeral , Clark Reese , Hays Thomas 
Published: July 2023

AbstractObjectivePreterm infants born small, vs. appropriate for gestational age (SGA, AGA) are at greater risk for morbidity and mortality. The contribution of genetic disorders to preterm SGA birth, morbidity, and mortality is unknown. We sought to determine the association between genetic disorders and preterm SGA birth, and the association between genetic disorders and morbidity or mortality within preterm SGA infants. We hypothesized that genetic disorders were significantly associated with both.Study DesignThis was a retrospective multicenter cohort study of 409 339 infants, born 23–33 weeks’ gestation between 2000 and 2020. The odds of preterm SGA (vs AGA) birth, and the odds of severe morbidity or mortality within SGA preterm infants were determined for infants with genetic disorders, after adjusting for known risk factors.ResultsGenetic disorders were present in 3.0 and 1.3% of SGA and AGA preterm infants respectively; genetic disorders conferred an aOR (95% CI) of 2.06 (1.92, 2.21) of SGA birth. Genetic disorders were present in 4.3 of preterm SGA infants with morbidity or mortality and 2.1% of preterm SGA infants that did not experience morbidity or mortality. Genetic disorders conferred an aOR (95% CI) of 2.12 (2.66, 3.08) of morbidity or mortality.ConclusionsGenetic disorders are strongly associated with preterm SGA birth, morbidity, and mortality. Clinicians should consider genetic testing of preterm SGA infants, particularly in the setting of other comorbidities or anomalies. Prospective, genomic research is needed to clarify the contribution of genetic disorders to disease in this population.
Experiences and attitudes towards Menstrual Suppression among Women with Bacterial vaginosis Randomised to Continuous Use of NuvaRing in Kenya
Authors: Casmir Edinah , Wairimu Njeri , Kiptinness Catherine , Oluoch Lynda , Maina Stephen Gakuo , Walker Kristina Wilbekin , Mugo Nelly , Marrazzo Jeanne , Ngure Kenneth 
Published: July 2023

AbstractBackgroundThe contraceptive vaginal ring (NuvaRing), one of the Multipurpose Prevention Technologies (MPT) products, is effective in preventing unintended pregnancies and may contribute to reducing the frequency of Bacterial Vaginosis (BV), which is a risk factor for HIV acquisition, transmission, and shedding among women. NuvaRing may cause irregular menstruation, including menstrual suppression, which may influence women’s decision on product choice, use, and acceptability. In this prospective cohort study, we assessed women’s experiences with menstruation suppression following continued NuvaRing use.MethodsA total of 18 in-depth interviews were conducted using a semi-structured interview guide among purposively selected women with BV in Thika, Kenya, aged 18-40 years, who used NuvaRing continuously. All women received counseling on possibility of menstrual suppression following continuous NuvaRing use. Audio recordings were transcribed verbatim and thematically analyzed.ResultsParticipants who expected and were aware that menstrual suppression was a possible side effect of Nuvaring accepted its benefits, and expressed acceptance and desire to continue using NuvaRing. Participants who had not anticipated menstrual suppression expressed anxiety and fear, with some expressing desire to continue using NuvaRing but worried about unintended negative consequences. The ability to perform daily activities uninterrupted, reduced expenses on sanitary supplies, enhanced sexual pleasure and relationships, and absence of menstrual pain were benefits of menstrual suppression. Although all participants received counseling on menstrual suppression, some expressed anxiety over the possibility of unintended pregnancy. As a result, they frequented medical facilities for health check-ups and pregnancy tests, and some used combined oral contraceptives to induce menses.ConclusionUnderstanding perceptions regarding menstrual suppression is crucial in offering targeted and comprehensive counseling to improve women’s understanding of menstruation suppression to influence acceptance and use of NuvaRing. Additionally, improved male involvement in reproductive health concerns and women’s autonomy in discussing reproductive health issues with partners is essential.