bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overview and evaluation of a nationwide hospital-based surveillance system for Influenza and COVID-19 in Switzerland (CH-SUR): 2018-2023
Authors: Sobel Jonathan Aryeh , Zanella Marie-Céline , Grant Rebecca , Valera Camille Beatrice , Suveges Mária , Urbini Laura , Mostaguir Khaled , Botero Sara , Roder Ursina , Bosetti Davide , Sommerstein Rami , Heininger Ulrich , Zimmermann Petra , Schreiber Peter W , Flury Domenica , Niederer-Loher Anita , Jent Philipp , Cusini Alexia , Pittet Didier , Harbarth Stephan , Iten Anne , Keiser Olivia ,   the CH-SUR Collaborative Network
Published: September 2024

AbstractBackgroundIn 2018, a hospital-based surveillance system for influenza (CH-SUR) was established in six tertiary care hospitals in Switzerland. From March 2020 onwards, this surveillance system was expanded to include more institutions, as well as COVID-19.AimTo evaluate quantitatively and qualitatively the surveillance system CH-SUR.MethodsAll patients admitted to one of the participating centres for more than 24 hours and who had a laboratory-confirmed influenza virus or SARS-CoV-2 infection were included in CH-SUR. For all cases, we evaluated the quality of the CH-SUR data, including timeliness and completeness of reporting. A qualitative survey among CH-SUR stakeholders assessed perceived importance, understanding, reliability and adaptability of CH-SUR.ResultsUp to 20 centres participated in CH-SUR. Between December 2018 and October 2023, 7,375 cases of influenza were reported and between March 2020 and October 2023, 49,235 cases of COVID-19 were reported to CH-SUR. During the COVID-19 pandemic, time to data entry and completeness improved over time; the median delay of data entry in CH-SUR was 5 days (IQR=2-23) for COVID-19 and 4 days (IQR=2-15) for influenza during the period 2018-2023. The completeness of variables was high (99.4%), with the exception of COVID-19 or annual influenza vaccination status (respectively 15% and 72% of “Unknown” responses). Stakeholders perceived the system as important, relevant, understandable and adaptable.ConclusionCH-SUR has provided critical epidemiological and clinical information on hospitalised influenza and COVID-19 cases across Switzerland during the pandemic. Our evaluation highlighted the importance and relevance of this system among CH-SUR stakeholders, as well as its importance for preparedness and response to future infectious disease outbreaks.
Childhood conduct problems, potential snares in adolescence and problematic substance use in Brazil
Authors: Stocker Fauve , Heron Jon , Hickman Matthew , Wehrmeister Fernando C. , Gonçalves Helen , Menezes Ana Maria B. , Murray Joseph , Hammerton Gemma 
Published: September 2024

AbstractObjectiveExamine whether the relationship between childhood conduct problems and substance use in adulthood is explained through potential snares (police arrest, gang membership, school non-completion) in a Brazilian population-based birth cohort.MethodData were analyzed from 4,599 young people from the 1993 Pelotas Birth Cohort in Brazil. The exposure was conduct problems at age 11 years. Outcomes included hazardous alcohol consumption and illicit drug use (age 22 years). Mediators included police arrest (by age 18 years), gang membership (ages 18 and 22 years), and school non-completion (by age 22 years). We performed counterfactual mediation using the parametric g-computation formula to estimate the indirect effect via all three mediators simultaneously.ResultsAfter adjusting for confounders (including comorbidity), conduct problems were weakly associated with police arrest [OR (95% CI)=1.45 (0.97, 2.16)] and school non-completion [OR (95% CI)=1.46 (1.22, 1.74)], but not with gang membership. Police arrest and gang membership were associated with illicit drug use [OR (95% CI)=3.84 (2.46, 5.99); OR (95% CI)=7.78 (4.30, 14.10), respectively] and with hazardous alcohol use [OR (95% CI)=1.60 (1.08, 2.38); OR (95% CI)=1.88 (1.07, 3.30)]. However, there was no association between school non-completion and either outcome after confounder adjustment. There was little evidence for an indirect effect of conduct problems on hazardous alcohol use and illicit drug use via all three mediators after confounder adjustment.ConclusionThe indirect effects of childhood conduct problems on substance use in early adulthood via police arrest, gang membership, and school non-completion were very small, after accounting for confounders and comorbidity.
Causal relationship between school-entry age and adolescent health: quasi-experimental evidence from 1.6 million participants in Vietnam
Authors: Busireddy Ishaan , Liao Janny , Nguyen Hoa T. , Dat Vu , Minh Tam Tran Ngo , Thuc Duc Le , De Neve Jan-Walter 
Published: September 2024

AbstractBackgroundSchool-entry age has been suggested to affect human capital development. Little is known, however, about the impacts of school-entry age on adolescent health in low- and middle-income countries where most children and adolescents worldwide reside.MethodsData on children’s outcomes were extracted from the longitudinal Young Lives Study in Vietnam, conducted between 2001 and 2016 (N=1,532), and the Vietnam Population and Housing Censuses of 1989, 1999, and 2009 (N=1,595,365). In Vietnam, children need to turn six years old by December 31stto enter Grade 1 in September that school year. As a result of the school-entry age policy, children born on or before December 31ststart school one year earlier compared to children who are born just after December 31st. Using exposure to the policy as an exogenous instrument for school-entry age, we used two-stage least squares regressions to determine the causal effect of school-entry age on education and health outcomes by age 23 years. We considered pre-primary education, school attendance, time spent in school, childbearing, marriage or cohabitation, as well as anthropometric measurements.ResultsChildren born after the school-entry age cut-off were more likely to have participated in pre-primary education and were more likely to be in school when compared to children born before the cut-off. A one-year increase in age at the beginning of Grade 1 because of the policy was associated with an increase in the probability of pre-primary education of 13 percentage points (95% CI: 7.8-18.5), daily time spent in school of 0.9 hours (95% CI: 0.5-1.4) and a reduced probability of having an own child of 25.3 percentage points (95% CI: 4.4-46.2). We observed a qualitatively smaller and statistically non-significant relationship between school-entry age and measured body mass index. These results were generally consistent when using alternative specifications of our model, sample, survey rounds, and data sources.DiscussionChildren who are older when entering primary school stayed in school longer and postponed family formation compared to children who entered school earlier because of the school-entry age policy in Vietnam. Relative age for grade should be considered when designing sexual and reproductive health interventions and programs targeted to adolescents.
Social impact of the JACO wheelchair-mounted robotic arm on users and their caregivers
Authors: Gbètoho Atigossou Orthelo Léonel , Faieta Julie , Corcuff Maëlle , Campeau-Lecours Alexandre , Flamand Véronique H. , Routhier François , Bouffard Jason 
Published: September 2024

AbstractThe efficacious implementation of robotic assistive technologies must be built on a thorough understanding of stakeholders’ experiences and perceptions. This study provides an in-depth insight into the experiences and perceptions of users of the JACO wheelchair-mounted robotic arm and those of their caregivers. A sample of JACO users (n = 21; Female : 6; Male : 15) and caregivers (n = 11; Female: 2; Male: 9) participated in individual interviews used to gain qualitative insight into the impact of JACO on their day-to-day lives. Interview transcripts were analyzed using a hybrid deductive-inductive coding process. Thematic analysis was conducted in accordance with theConsortium on Assistive Technology Outcomes Research(CATOR) taxonomy. This article exclusively reports data on the social impact of the JACO wheelchair-mounted robotic arm. In addition, participants completed three questionnaires to gather more objective data for quantitative assessment, these included theCaregiver Assistive Technology Outcome Measure(CATOM), a sociodemographic questionnaire, and a home-based questionnaire to assess the social impact of using JACO. Findings pointed to highly varied experiences among participants, including instances of positive, negative, and absence of effects from the use of JACO. Participants’ feedback fell within two broad categories,Human Assistance,andCost and Use of Resources. This study provides nuanced and varied insight into the spectrum of the social impact of using JACO as perceived by users and their caregivers, highlighting the importance of considering each user as an individual with unique experiences and needs. Continued research is needed to assess the generalizability of these findings.
Latent class growth mixture modelling of HbA1C trajectories identifies individuals at high risk of developing complications of type 2 diabetes mellitus in the UK Biobank
Authors: Handley Dale , Gillett Alexandra C , Bala Renu , Tyrrell Jess , Lewis Cathryn M 
Published: September 2024

AbstractAimsGlycated Hemoglobin A1c(HbA1c) is widely used for the diagnosis and management of type 2 diabetes mellitus (T2D), with regular testing in primary care recommended every three to six months. We aimed to identify distinct, long-term HbA1c trajectories following a T2D diagnosis and investigate how these glycaemic control trajectories were associated with health-related traits and T2D complications.MethodsA cohort of 12,435 unrelated individuals of European ancestry with T2D was extracted from the UK Biobank data linked to primary care records. Latent class growth mixture modelling was applied to identify classes with similar HbA1c trajectories over the 10-years following T2D diagnosis. We tested for associations of HbA1c class membership with sociodemographic factors, biomarkers, polygenic scores, and T2D-related outcomes, using logistic regression and Cox proportional hazards models.ResultsSix HbA1c trajectory classes were identified. The largest class (76.8%) maintained low and stable HbA1c levels over time. The other five classes demonstrated higher and more variable trajectories and included: two with parabolic shapes (starting low and distinguished by the height of their peaks), two with high initial HbA1c levels that declined over time (one rapidly, one slowly), and one class with a rapid increase in HbA1c five years after diagnosis. Younger age at T2D diagnosis, higher fasting glucose levels, higher random glucose levels, and higher body mass index polygenic score were associated with membership of these five classes. These classes were also more likely to be prescribed glucose-lowering medication at diagnosis and had fewer primary care visits in the month and year prior to diagnosis. Relative to the low and stable class, these five showed increased risks of T2D complications, including stroke (HR=1.55 [1.31-1.84]), kidney disease (HR=1.39 [1.27-1.53]), all-cause mortality (HR=1.36 [1.23-1.51]), and progression to combination therapy (HR=3.22 [3.04-3.41]) or insulin (HR=3.21 [2.89-3.55]).ConclusionIndividuals with T2D who show higher and more variable HbA1c trajectories are at increased risk of developing T2D-related complications. Early identification of patients at risk, based on factors such as age at diagnosis and previous healthcare utilisation could improve patient outcomes.
Automating ACMG Variant Classifications Using BIAS-2015: An Algorithm Overview and Benchmark Against the FDA-Approved eRepo Dataset
Authors: Eisenhart Chris , Mewton Joel , Brickey Rachel , Bayat Vafa 
Published: September 2024

AbstractIn 2015, the American College of Medical Genetics and Genomics (ACMG) in collaboration with the Association of Molecular Pathologists (AMP) published guidelines for the interpretation and classification of germline genomic variants. The ACMG terminology guidelines outlined criteria for assigning one of five categories: benign, likely benign, uncertain significance, likely pathogenic and pathogenic. While the paper laid out 28 different classifiers and the justification for them, it did not provide specific algorithms for implementing these classifiers in an automated manner. Here we present the Bitscopic Interpreting ACMG Standards 2015 (BIAS-2015) software as a complete, open-source algorithm which categorizes variants according to the ACMG classification system. BIAS-2015 evaluates 18 of the 28 ACMG criteria to classify variants in an automated and consistent way while recording the rationale for each classifier to enable in-depth review. We used the genomic data from the ClinGen Evidence Repository (eRepo v1.0.29), one of two FDA-recognized human genetic variant databases, to evaluate the performance of the BIAS-2015 algorithm. All code for BIAS-2015 has been made available on GitHub.
Achievement of diabetes treatment goals in Mexico from 2016–2022: A retrospective analysis of nationally representative surveys
Authors: Ramírez-García Daniel , Méndez-Labra Padme Nailea , Fermín-Martínez Carlos A. , Perezalonso-Espinosa Jerónimo , Díaz-Sánchez Juan Pablo , Paz-Cabrera César Daniel , Vargas-Vázquez Arsenio , Antonio-Villa Neftali Eduardo , Danaei Goodarz , Seiglie Jacqueline A. , Bello-Chavolla Omar Yaxmehen 
Published: September 2024

ABSTRACTBACKGROUNDCardiovascular (CVD) risk factor reduction is a cornerstone of diabetes management. Here, we aimed to estimate the prevalence and determinants of individual and combined CVD risk factor control goals amongst individuals living with diagnosed diabetes in Mexico.METHODSWe analyzed Mexican National Health and Nutrition Surveys from 2016-2022 including individuals aged ≥20 years with diagnosed diabetes. We estimated the prevalence of glycemic, blood pressure, cholesterol, and smoking control, as well as combined control achievement according to current guidelines, as well as the prevalence of antihypertensive, statin and diabetes medication use. We also explored determinants of control achievement amongst individuals with diabetes using weighted logistic regression.RESULTSWe analyzed data from 2,331 adults with diagnosed diabetes. Glycemic control increased over time reaching 41% (95%CI 30%–52%) by 2022. Blood pressure control remained similar over time reaching 45% (95%CI 35%–55%) in 2022, LDL-C control remained low regardless of the definition (<70 vs. <100 mg/dL), whilst smoking control was high and increased over time to 92% (95%CI 88%–96%) in 2022. Combined risk factor control achievement was low, primarily due to suboptimal LDL-C control, despite a high proportion of medication use. Control achievement was more likely in Northern Mexico, in younger individuals, those with college education or living in states with lower social lag.CONCLUSIONSOur results suggest a need to improve comprehensive glycemic and CVD risk factor management for individuals living with diabetes in Mexico to improve diabetes care and reduce risk of adverse outcomes.
The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output
Authors: Trevisan Alexandra J. , Han Katie , Chapman Phillip , Kulkarni Anand S. , Hinton Jennifer M. , Ramirez Cody , Klein Ines , Gatto Graziana , Gabitto Mariano I. , Menon Vilas , Bikoff Jay B. 
Published: September 2024

SUMMARYNeural circuits in the spinal cord are composed of diverse sets of interneurons that play crucial roles in shaping motor output. Despite progress in revealing the cellular architecture of the spinal cord, the extent of cell type heterogeneity within interneuron populations remains unclear. Here, we present a single-nucleus transcriptomic atlas of spinal V1 interneurons across postnatal development. We find that the core molecular taxonomy distinguishing neonatal V1 interneurons perdures into adulthood, suggesting conservation of function across development. Moreover, we identify a key role for En1, a transcription factor that marks the V1 population, in specifying one unique subset of V1Pou6f2interneurons. Loss of En1 selectively disrupts the frequency of rhythmic locomotor output but does not disrupt flexion/extension limb movement. Beyond serving as a molecular resource for this neuronal population, our study highlights how deep neuronal profiling provides an entry point for functional studies of specialized cell types in motor output.
The mechanism and consequences of amyloid-β modulating thiamine pyrophosphokinase-1 expression in microglia
Authors: Cheng Xiaoqin , Zhao Ruoqi , Qiu Hongyan , Song Peiwen , Kou Lanwen , Sang Shaoming , Xia Yingfeng , Cai Wenwen , Jin Boru , Huang Qiang , Yuan Peng , Zhong Chunjiu 
Published: September 2024

AbstractAmple studies attribute cognitive decline in Alzheimer’s disease to amyloid-β deposition1–6. However, brain amyloid-β accumulation that saturates years before the manifestation of clinical symptoms is dissociated with cognitive decline of the disease7. It is unknown how these two processes are mechanistically linked. In this and our accompanied study, we report that thiamine pyrophosphokinase-1 (TPK) deficiency plays essential roles in both processes via distinct mechanisms. Here we describe that diminished microglia Tpk controls the propagation of amyloid-β plaques. In APP/PS1 transgenic mice, microglia showed elevatedTpkexpression at 2-month-old, but reduction in a plaque-centric manner at 8-month-old. Interestingly, lipopolysaccharide, but not amyloid-β, induceedTpkreduction in cultured microglia.Tpkreduction led to microglia dysfunction, showing volatile motility but reduced phagocytosis and weak response to focal tissue injury, with accumulation of intracellular lipid droplets and abnormal mitochrondria. In Alzheimer’s disease mice, microglia-specific knockout ofTpkcaused diminished plaque coverage, exacerbated plaque burden and synaptic loss. However, increased plaques were not accompanied by the development of neurofibrillary tangles or brain atrophy, in contrast to the phenotype described in our accompanied paper with neuronalTpkdeletion. In conclusion, plaque-induced inflammation reducesTpkin microglia, selectively exacerbating the spread of amyloid pathology.
Antagonist actions of CMK-1/CaMKI and TAX-6/Calcineurin along theC. elegansthermal avoidance circuit orchestrate adaptation of nociceptive response to repeated stimuli
Authors: Rudgalvyte Martina , Hu Zehan , Kressler Dieter , Dengjel Joern , Glauser Dominique A. 
Published: September 2024

ABSTRACTResponse decrease following repeated exposure to innocuous or noxious stimuli is a conserved adaptation phenomenon often referred to as habituation. Impaired nociceptive habituation is associated with several pain conditions in human, but the underpinning molecular mechanisms are only partially understood. In the nematodeCaenorhabditis elegans, thermo-nociceptive adaptation to repeated stimuli was previously shown to be regulated by the Ca2+/Calmodulin-dependent protein kinase 1 (named CMK-1), but its downstream effectors were unknown. Here, usingin vitrokinase assays coupled with mass-spectrometry-based phosphoproteomics, we empirically identified hundreds of CMK-1 phospho-substrates. Among them, we found that CMK-1 can phosphorylate the calcineurin A (CnA) protein TAX-6in vitroin a highly conserved regulatory domain, which led us to hypothesize that TAX-6/CnA might be a downstream mediator of CMK-1 signaling in the control of thermo-nociceptive adaptation. Combined genetic and pharmacological manipulations revealed a network of antagonistic actions between CMK-1 and calcineurin pathways in the regulation of the responsiveness of naïve worms and the response adaptation to repeated noxious heat stimuli. However, the results of cell-specific rescue and gain-of-function experiments suggested that CMK-1 acts in AFD and ASER thermosensory neurons and that TAX-6/CnA acts in FLP thermosensory neuron and a set of downstream interneurons to regulate noxious heat avoidance behaviors. Because CMK-1 and TAX-6/CnA act in non-overlapping cell types, the phosphorylation event identifiedin vitromight not be relevant for this phenotype and the complex interaction between the two pathways might rather originate from their action in separate parts of the nervous system. As a whole, our study has identified (i) CMK-1 substrate candidates, which will fuel further research on the intracellular actuation of CMK-1-dependent signaling on various processes, and (ii) a complex set of antagonistic interactions between CMK-1 and calcineurin signaling operating at distributed loci within a sensory-behavior circuit, acting to adjust baseline thermo-nociception and regulate thermo-nociceptive adaptation.
Genomic Analyses Suggest No Risk of Vancomycin Resistance Transfer by Strain VE202-06
Authors: Watson Andrea R. , Chen Wei-An , van Schaik Willem , Norman Jason M. 
Published: September 2024

ABSTRACTIn 2016, the US Food and Drug Administration published guidance for the early development of live biotherapeutic products (LBPs)1. Of particular importance is the characterization of LBP strains and the potential transfer of antimicrobial resistance (AMR) genes to relevant microbial organisms in the recipient’s microbiota. Van der Lelie et al2, make unsupported claims that the LBP strain VE202-06 encodes a transferable vancomycin resistance element. Here we provide our analysis of the potential transfer of AMR by strain VE202-06. These data indicate that strain VE202-06 has no risk of transferring AMR to relevant microbial organisms.
The pericardium forms as a distinct structure during heart formation
Authors: Moran Hannah R. , Nyarko Obed O. , O’Rourke Rebecca , Ching Ryenne-Christine K. , Riemslagh Frederike W. , Peña Brisa , Burger Alexa , Sucharov Carmen C. , Mosimann Christian 
Published: September 2024

ABSTRACTThe heart integrates diverse cell lineages into a functional unit, including the pericardium, a mesothelial sac that supports heart movement, homeostasis, and immune responses. However, despite its critical roles, the developmental origins of the pericardium remain uncertain due to disparate models. Here, using live imaging, lineage tracking, and single-cell transcriptomics in zebrafish, we find the pericardium forms within the lateral plate mesoderm from dedicated anterior mesothelial progenitors and distinct from the classic heart field. Imaging of transgenic reporters in zebrafish documents lateral plate mesoderm cells that emerge lateral of the classic heart field and among a continuous mesothelial progenitor field. Single-cell transcriptomics and trajectories ofhand2-expressing lateral plate mesoderm reveal distinct populations of mesothelial and cardiac precursors, including pericardial precursors that are distinct from the cardiomyocyte lineage. The mesothelial gene expression signature is conserved in mammals and carries over to postnatal development. Light sheet-based live-imaging and machine learning-supported cell tracking documents that during heart tube formation, pericardial precursors that reside at the anterior edge of the heart field migrate anteriorly and medially before fusing, enclosing the embryonic heart to form a single pericardial cavity. Pericardium formation proceeds even upon genetic disruption of heart tube formation, uncoupling the two structures. Canonical Wnt/β-catenin signaling modulates pericardial cell number, resulting in a stretched pericardial epithelium with reduced cell number upon canonical Wnt inhibition. We connect the pathological expression of secreted Wnt antagonists of the SFRP family found in pediatric dilated cardiomyopathy to increased pericardial stiffness: sFRP1 in the presence of increased catecholamines causes cardiomyocyte stiffness in neonatal rats as measured by atomic force microscopy. Altogether, our data integrate pericardium formation as an independent process into heart morphogenesis and connect disrupted pericardial tissue properties such as pericardial stiffness to pediatric cardiomyopathies.