bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scoping review of AI, speech and natural language processing methods for assessment of clinician-patient communication
Authors: Albert Pierre , McKinstry Brian , Luz Saturnino 
Published: December 2024

AbstractIntroductionThere is growing research interest in applying Artificial Intelligence (AI) methods to medicine and healthcare. Analysis of communication in healthcare has become a target for AI research, particularly in the field of analysis of medical consultations, an area that so far has been dominated by manual rating using measures. This opens new perspectives for automation and large scale appraisal of clinicians’ communication skills. In this scoping review we summarised existing methods and systems for the assessment of patient doctor communication in consultations.MethodsWe searched EMBASE, MEDLINE/PubMed, the Cochrane Central Register of Controlled Trials, and the ACM digital library for papers describing methods or systems that employ artificial intelligence or speech and natural language processing (NLP) techniques with a view to automating the assessment of patient-clinician communication, in full or in part. The search covered three main concepts: dyadic communication, clinician-patient interaction, and systematic assessment.ResultsWe found that while much work has been done which employs AI and machine learning methods in the analysis of patient-clinician communication in medical encounters, this evolving research field is uneven and presents significant challenges to researchers, developers and prospective users. Most of the studies reviewed focused on linguistic analysis of transcribed consultations. Research on non-verbal aspects of these encounters are fewer, and often hindered by lack of methodological standardisation. This is true especially of studies that investigate the effects of acoustic (paralinguistic) features of speech in communication but also affects studies of visual aspects of interaction (gestures, facial expressions, gaze, etc). We also found that most studies employed small data sets, often consisting of interactions with simulated patients (actors).ConclusionsWhile our results point to promising opportunities for the use of AI, more work is needed for collecting larger, standardised, and more easily available data sets, as well as on better documentation and sharing of methods, protocols and code to improve reproducibility of research in this area.
Tay-Sachs and Sandhoff Diseases: Diffusion tensor imaging and correlational fiber tractography findings differentiate late-onset GM2 Gangliosidosis
Authors: Lewis Connor J. , Chipman Selby I. , Johnston Jean M. , Acosta Maria T. , Toro Camilo , Tifft Cynthia J. 
Published: December 2024

AbstractGM2 gangliosidosis is lysosomal storage disorder caused by deficiency of the heterodimeric enzyme β-hexosaminidase A. Tay-Sachs disease is caused by variants inHEXAencoding the α-subunit and Sandhoff disease is caused by variants inHEXBencoding the β-subunit. Due to shared clinical and biochemical findings, the two have been considered indistinguishable. We applied diffusion tensor imaging (DTI) and correlational fiber tractography to assess phenotypic differences in these two diseases. 40 DTI scans from 16 Late-Onset GM2 patients (NCT00029965) with either Sandhoff (n = 4), or Tay-Sachs (n = 12) disease. DTI metrics including fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD), and quantitative anisotropy (QA) were calculated in fiber tracts throughout the whole brain, arcuate fasciculus, corpus callosum, and cerebellum. Correlational tractography was also performed to identify fiber tracts with group wide differences in DTI metrics between Tay-Sachs and Sandhoff patients. A linear mixed effects model was used to analyze the differences between Tay-Sachs and Sandhoff patients. Tay-Sachs patients had higher MD in the left cerebellum (p= 0.003703), right cerebellum (p= 0.003435), superior cerebellar peduncle (SCP,p= 0.007332), and vermis (p= 0.01007). Sandhoff patients had higher FA in the left cerebellum (p= 0.005537), right cerebellum (p= 0.01905), SCP (p= 0.02844), and vermis (p= 0.02469). Correlational fiber tractography identified fiber tracts almost exclusively in cerebellar pathways with higher FA and QA, and lower MD, AD, and RD in Sandhoff patients compared to Tay-Sachs patients. Our study shows neurobiological differences between these two related disorders. To our knowledge, this is the first study using correlational tractography in a lysosomal storage disorder demonstrating these differences. This result indicates a greater burden of cerebellar pathology in Tay-Sachs patients compared with Sandoff patients.
Epidemiology of early- and late-onset serious bacterial infections in Australian neonates and infants: A retrospective multicentre study
Authors: Williams Phoebe CM , Mostaghim Mona , Harrison Jackson , Lahra Monica , Greenhalgh Mark , O’Sullivan Matthew , Maley Michael , Oei Ju-Lee , Koirala Archana , Popat Himanshu , Lui Kei , McMullan Brendan , Palasanthiran Pamela , Kesson Alison , Isaacs David , Bartlett Adam W 
Published: December 2024

ABSTRACTBackgroundThere has been little decline in neonatal mortality rates over recent decades, and this is now further challenged by the rising prevalence of antimicrobial resistance (AMR). In Australia, the incidence of neonatal sepsis is low on a global scale, yet there are increasingly frequent outbreaks of multidrug-resistant (MDR) infections in neonatal intensive care units, alongside rising rates of colonisation with MDR bacteria.MethodsWe analysed positive blood and cerebrospinal fluid (CSF) cultures collected from infants (aged 0 to ≤180 days) across five clinical sites in Australia between 2010 and 2019, to determine evolving antimicrobial susceptibility profiles.ResultsAfter excluding presumed contaminants, we analysed 743 pathogenic bacterial isolates cultured from 624 neonates and infants with early- (≤72 hours), late- (>72 hours to ≤28 days), and very late-onset (>28 days to ≤180 days) infections.Escherichia coli(37%) andStreptococcus agalactiae(31%) were the primary pathogens responsible for early-onset bloodstream infections, whilst coagulase-negative staphylococci,E. coliandStaphylococcus aureuswere responsible for most infections in older neonates and infants. Antimicrobial susceptibility to currently-recommended empiric regimens remains high; however, gram-negative bacteria – including MDR bacteria – were responsible for an increasing proportion of very late-onset infections over the study period (22% in 2010-2014 versus 34% in 2015-2019; p=0.07).ConclusionsAlthough empiric antimicrobial regimens remain adequate for most pathogens causing infections in neonates and infants in Australia, there is an increasing burden of invasive infections caused by gram-negative bacteria. Ongoing surveillance is necessary to ensure empiric antimicrobial guidelines remain efficacious and appropriate.
Survival Analysis of Time to First Antenatal Care Visit among Pregnant Women in Ethiopia: Application of Parametric and Non-Parametric Model
Authors: Ayele Yitagesu Eshetu , Gada Zelalem Tolosa , Addisu Tigist Getachew 
Published: December 2024

AbstractObjectiveAntenatal care (ANC) involves monitoring pregnant women to ensure the health of both mother and fetus. This study aimed to assess the timing of the initial ANC visit and its determining factors among Ethiopian pregnant women.Material and MethodsThe analysis used data from the 2016 Ethiopian Demographic and Health Survey (EDHS), focusing on women aged 15-49 who had a live birth within five years prior to the survey across nine regional states and two city administrations. Descriptive statistics and parametric shared frailty models were applied to identify factors influencing the timing of the first ANC visit.ResultsAmong 7,559 women, only 20.4% attended their first ANC visit within the recommended 12 weeks. The median time to the first ANC visit in Ethiopia was 18 weeks (4.5 months). Factors that delayed the first ANC visit included rural residence (□= 1.29), higher birth order (□= 1.06-1.21), and long distance to a health facility (□= 1.08). Conversely, factors that shortened the time to the first ANC visit included higher levels of maternal education (□= 0.87-0.91), higher wealth index (□= 0.86-0.87), media access (□= 0.92), and involvement in healthcare decisions (□< 1).ConclusionRural residence, higher birth order, and long travel distances delay the first ANC visit, while higher education, urban residence, media access, and greater wealth accelerate it. The study recommends enhanced community education on the importance of early ANC visits through health extension workers and stakeholders.
COVID-19 mRNA-vaccination and all-cause mortality in the adult population in Norway during 2021-2023: a population-based cohort study
Authors: Dahl Jesper , Tapia German , Bøås Håkon , Landsjøåsen Bakken Inger Johanne , Løvdal Gulseth Hanne 
Published: December 2024

AbstractIntroductionMost countries worldwide have experienced excess mortality that coincides temporally with the COVID-19 mass vaccination campaigns. This has led to speculation on the potential long-term effects of the vaccines on mortality risk.MethodsThe study was designed as a retrospective cohort study, and included all individuals aged ≥18 years living in Norway during January 1, 2021, through December 31, 2023. Individuals were categorized as either unvaccinated (received no doses), partially vaccinated (received one or two doses) or fully vaccinated (received three or more doses) from the date of vaccination and onwards. Age-stratified Poisson models were used to estimate incidence rate ratios of death (all causes) between vaccination groups, adjusting for sex, calendar time, county of residence and risk group status (nursing home resident or preexisting condition with increased risk of severe COVID-19).ResultsThe study included 4 645 910 individuals (49.8% women) with 132 963 deaths during follow-up. There was a higher proportion of individuals that were part of a risk group among fully vaccinated individuals compared to unvaccinated individuals in all age groups, and a lower unadjusted rate of death: 51.5 vs 73.6 per 100 000 person years (py) among individuals aged 18-44 years, 295.1 vs 405.3 per 100 000 py among 45-64 years, and 3620.2 vs 4783.8 per 100 000 py among 65 years or older. The adjusted IRR of death for the same age groups were 0.42 (95% CI 0.38-0.47), 0.39 (95% CI 0.37-0.41) and 0.42 (95% CI 0.41-0.43), respectively. The differences in rate of death between vaccination groups were larger among men and peaked during 2022.ConclusionVaccinated individuals had a lower rate of all-cause death during 2021-2023 in Norway.Key messagesIn Norway, as in many Western countries, there has been an excess mortality during 2021-2023, surpassing the numerical count of COVID-19-associated deaths. The excess mortality coincides temporally with the COVID-19 mass vaccination campaigns, but longitudinal data regarding mortality post-vaccination remain sparse. Using real-time national health registry data, we estimate the risk of all-cause mortality by vaccination status in the total adult population in Norway during 2021-2023 and demonstrate a lower rate of all-cause death among vaccinated individuals.
Change in aperiodic activity over first year of life is associated with later autism diagnosis and 18-month language development in infants with family history of autism
Authors: Wilkinson Carol L. , Chung Haerin , Dave Amy , Tager-Flusberg Helen , Nelson Charles A. 
Published: December 2024

AbstractDelays in language often co-occur among toddlers diagnosed with autism. Despite the high prevalence of language delays, the neurobiology underlying such language challenges remains unclear. Prior research has shown reduced EEG power across multiple frequency bands in 3-to-6-month-old infants with an autistic sibling, followed by accelerated increases in power with age. Here we apply new methods to decompose the power spectra into aperiodic (broad band neural firing) and periodic (oscillations) activity to explore possible links between aperiodic changes in the first year of life and later language outcomes. Combining EEG data across two longitudinal studies of infants with and without autistic siblings, we assessed whether infants with an elevated familial likelihood (EFL) exhibit altered changes in both periodic and aperiodic EEG activity at 3 and 12 months of age, compared to those with a low likelihood (LL), and whether developmental change in activity is associated with language development. At 3-months of age, we observed that EFL infants have significantly lower aperiodic activity from 6.7-55Hz (p<0.05). However, change in aperiodic activity from 3 to 12 months was significantly increased in infants with a later diagnosis of autism, compared to EFL infants without an autism diagnosis. In addition, greater increases in aperiodic offset and slope from 3-to12-months were associated with worse language development measured at 18 months. Findings suggest that early age-dependent changes in EEG aperiodic power may serve as potential indicators of autism and language development in infants with family history of autism.
Direct expression of CPT1a enables a high throughput platform for the discovery of CPT1a modulators
Authors: Chen Jason , Tran Tuyen , Wong Anthony , Wang Luofei , Annaluru Pranavi , Sreekanth Vibha , Murthy Samika , Munjeti Laasya , Park Tanya , Bhat Utkarsh , Leong Glynnis , Li Yumeng , Chen Simeng , Kong Natalie , Raval Rushika , Xie Yining , Somani Shreya , Bhambhani Aditi , Zhu Zoey , Chu Landen , Dosch Kimai , Njoo Edward , Chen Zhan 
Published: December 2024

AbstractCarnitine palmitoyltransferase 1 (CPT1), which catalyzes the rate-limiting step of fatty acid oxidation, has been implicated in therapeutic approaches to several human diseases characterized by aberrant lipid metabolism. Isoform-specific quantification of CPT1 activity is essential in the characterization of small molecule inhibitors of CPT1, but several existing means to quantify enzymatic activity, including the use of radioisotope labeled carnitine, are not amenable to scalable, high throughput screening. Here, we demonstrate that mitochondrial extracts from Expi293 cells transfected with a CPT1a plasmid are a reliable and robust source of catalytically active human CPT1. Moreover, with a source of catalytically active enzyme in hand, we modified a previously reported colorimetric method of coenzyme A (CoA) easily scalable to a 96-well format for the screening of CPT1a inhibitors. This assay platform was validated by two previously reported inhibitors of CPT1a:R-etomoxir and perhexiline. To further demonstrate the applicability of this method in small molecule screening, we prepared and screened a library of 87 known small molecule APIs, validating the inhibitory effect of chlorpromazine on CPT1.Abstract Figure
Tunicate metatranscriptomes reveal ancient virus-host co-divergence and inter-order recombination in the evolutionary history of disease-causing viruses
Authors: Petrone Mary E. , Grove Joe , Parry Rhys H. , Brussel Kate Van , Mifsud Jonathon C.O. , Dindar Zuhairah , Mei Shi-qiang , Shi Mang , Turnbull Olivia M. H. , Marzinelli Ezequiel M. , Holmes Edward C. 
Published: December 2024

SUMMARYTunicates are a key transitional taxon in animal evolution as the closest extant invertebrate relatives of the vertebrates. Their viruses may also reflect this transitional state. Yet, it is not known whether tunicate viruses are more closely related to vertebrate- or invertebrate-infecting viral lineages. We analysed primary and publicly available RNA libraries to extend the known diversity of tunicate-associated viruses and determine their relationship to viruses of other animals. We present evidence that influenza viruses, alphaviruses, and some mononegaviruses emerged prior to the evolution of vertebrates. We also show that the recombination of glycoproteins between different orders of RNA viruses, including between positive- and negative-sense viruses, may have shaped the evolution of multiple lineages. Our study reveals that some disease-causing RNA virus lineages were present in early chordates and highlights that the evolution of structural genes may be incongruent with that of the highly conserved RNA-dependent RNA polymerase.
The blood metabolome of cognitive function and brain health in middle-aged adults – influences of genes, gut microbiome, and exposome
Authors: Ahmad Shahzad , Wu Tong , Arnold Matthias , Hankemeier Thomas , Ghanbari Mohsen , Roshchupkin Gennady , Uitterlinden André G. , Neitzel Julia , Kraaij Robert , Van Duijn Cornelia M. , Ikram M. Arfan , Kaddurah-Daouk Rima , Kastenmüller Gabi ,   the Alzheimer’s Disease Metabolomics Consortium
Published: December 2024

ABSTRACTIncreasing evidence suggests the involvement of metabolic alterations in neurological disorders, including Alzheimer’s disease (AD), and highlights the significance of the peripheral metabolome, influenced by genetic factors and modifiable environmental exposures, for brain health. In this study, we examined 1,387 metabolites in plasma samples from 1,082 dementia-free middle-aged participants of the population-based Rotterdam Study. We assessed the relation of metabolites with general cognition (G-factor) and magnetic resonance imaging (MRI) markers using linear regression and estimated the variance of these metabolites explained by genes, gut microbiome, lifestyle factors, common clinical comorbidities, and medication using gradient boosting decision tree analysis. Twenty-one metabolites and one metabolite were significantly associated with total brain volume and total white matter lesions, respectively. Fourteen metabolites showed significant associations with G-factor, with ergothioneine exhibiting the largest effect (adjusted mean difference = 0.122,P= 4.65x10-7). Associations for nine of the 14 metabolites were replicated in an independent, older cohort. The metabolite signature of incident AD in the replication cohort resembled that of cognition in the discovery cohort, emphasizing the potential relevance of the identified metabolites to disease pathogenesis. Lifestyle, clinical variables, and medication were most important in determining these metabolites’ blood levels, with lifestyle, explaining up to 28.6% of the variance. Smoking was associated with ten metabolites linked to G-factor, while diabetes and antidiabetic medication were associated with 13 metabolites linked to MRI markers, including N-lactoyltyrosine. Antacid medication strongly affected ergothioneine levels. Mediation analysis revealed that lower ergothioneine levels may partially mediate negative effects of antacids on cognition (31.5%). Gut microbial factors were more important for the blood levels of metabolites that were more strongly associated with cognition and incident AD in the older replication cohort (beta-cryptoxanthin, imidazole propionate), suggesting they may be involved later in the disease process. The detailed results on how multiple modifiable factors affect blood levels of cognition- and brain imaging-related metabolites in dementia-free participants may help identify new AD prevention strategies.
Data Anonymization for Open Science: A Case Study
Authors: Francis Paul , Jurak Gregor , Leskošek Bojan , Otte Karen , Prasser Fabian 
Published: December 2024

ABSTRACTOne of many challenges to open science is anonymization of personal data so that it may be shared. This paper presents a case study of the anonymization of a dataset containing cardio-respiratory fitness and commuting patterns for Slovenian school children. It evaluates three different anonymization tools, ARX, SDV, and SynDiffix. The fitness study was selected because its small size (N=713) and generally low statistical significance make it particularly challenging for data anonymization. Unlike most prior anonymization tool evaluations, this paper examines whether the scientific conclusions of the original study would have been supported by the anonymized datasets. It also considers the burden imposed on researchers using the tools both for data generation and data analysis.
DunedinPACE Predicts Incident Metabolic Syndrome: Cross-sectional and Longitudinal Data from the Berlin Aging Study II (BASE-II)
Authors: Demuth Ilja , Vetter Valentin Max , Homann Jan , Regitz-Zagrosek Vera , Gerstorf Denis , Lill Christina M. , Bertram Lars 
Published: December 2024

AbstractImportanceData on the capacity of more recently developed epigenetic age measures to predict a future onset of Metabolic Syndrome (MetS) are lacking.ObjectiveThe aim of the study was a comparative analysis of different DNA methylation (DNAm)-based epigenetic clocks with regard to their ability to predict a future onset of MetS. In addition, cross-sectional relationships between epigenetic age measures, MetS and its components were investigated.Design, Setting and ParticipantsMetS was diagnosed in participants of the Berlin Aging Study II at baseline (n=1,671, mean age 68.8 ±3.7 years, 51.6% women) and at follow-up (n=1,083; 7.4 ±1.5 years later). DNAm age (DNAmA) and its deviation from chronological age, i.e., DNAmA acceleration (DNAmAA), were calculated for a total of five epigenetic clocks at baseline. In addition, DunedinPACE, a DNAm-based measure of the pace of aging, was calculated. The relationship of MetS with DNAmAA and DunedinPACE was investigated by fitting regression models. Furthermore, receiver operating characteristic statistics were calculated to investigate the capacity of DNAm clocks assessed at baseline to predict incident MetS at follow-up.ExposuresSix different epigenetic age measures including DunedinPACE assessed at baseline to predict MetS in the future.Main Outcomes and MeasuresDiagnosis of incident MetS on average 7.4 ±1.5 years after baseline.ResultsDunedinPACE was associated with incident MetS at follow-up on average 7.4 years later (OR: 9.84, p=0.028). Interestingly, we observed no significant differences (p>0.05) in the area under the curve in predicting MetS between a model that only included clinical parameters and a model that only used GrimAge DNAmAA. Cross-sectional differences between participants with and without MetS remained statistically significant for DunedinPACE only after covariate adjustment (baseline: β=0.042, follow-up: β=0.031, p<0.0001 in both cases).Conclusions and RelevanceSystematic comparison of epigenetic clocks within a single dataset in relation to MetS and its diagnostic components showed strong and consistent associations with DunedinPACE, but not with other epigenetic clocks. Our results highlight the potential of using certain DNAm-based measures of biological ageing in predicting the onset of clinical outcomes, such as MetS.Key PointsQuestionAre epigenetic age measures able to predict the future onset of Metabolic Syndrome?FindingsThis longitudinal observational study revealed that individuals with a one-year faster pace of aging (DunedinPACE) had 2.3-fold increased odds for incident Metabolic Syndrome ∼7.5-years later.MeaningThe data reported here will potentially help to implement epigenetic measures in clinical risk assessment.