bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Review of the Quantitative markers of speech and language of the Frontotemporal Degeneration Spectrum and their potential for cross-linguistic implementation
Authors: Coppieters Rosie , Bouzigues Arabella , Jiskoot Lize , Montembeault Maxime , Tee Boon Lead ,   Genetic Frontotemporal dementia Initiative (GENFI), Rohrer Jonathan D. , Bruffaerts Rose 
Published: January 2024

ABSTRACTFrontotemporal dementia (FTD) is a neurodegenerative disease spectrum with an urgent need for reliable biomarkers for early diagnosis and monitoring. Speech and language changes occur in the early stages of FTD and offer a potential non-invasive, early, and accessible diagnostic tool. The use of speech and language markers in this disease spectrum is limited by the fact that most studies investigate English-speaking patients. This systematic review examines the literature on psychoacoustic and linguistic features of speech that occur across the FTD spectrum across as many different languages as possible. 76 papers were identified that investigate psychoacoustic and linguistic markers in discursive speech. 75% of these papers studied English-speaking patients. The most generalisable features found across different languages, are speech rate, articulation rate, pause frequency, total pause duration, noun: verb ratio, and total number of nouns. While there are clear interlinguistic differences across patient groups, the results show promise for implementation of cross-linguistic markers of speech and language across the FTD spectrum, particularly for psychoacoustic features.
Machine learning enabled prediction of digital biomarkers from whole slide histopathology images
Authors: McCaw Zachary R , Shcherbina Anna , Shah Yajas , Huang Davey , Elliott Serra , Szabo Peter M , Dulken Benjamin , Holland Sacha , Tagari Philip , Light David , Koller Daphne , Probert Christopher 
Published: January 2024

AbstractCurrent predictive biomarkers generally leverage technologies such as immunohis-tochemistry or genetic analysis, which may require specialized equipment, be time-intensive to deploy, or incur human error. In this paper, we present an alternative approach for the development and deployment of a class of predictive biomarkers, leveraging deep learning on digital images of hematoxylin and eosin (H&E)-stained biopsy samples to simultaneously predict a range of molecular factors that are relevant to treatment selection and response. Our framework begins with the training of a pan-solid tumor H&E foundation model, which can generate a universal featurization of H&E-stained tissue images. This featurization becomes the input to machine learning models that perform multi-target, pan-cancer imputation. For a set of 352 drug targets, we show the ability to predict with high accuracy: copy number amplifications, target RNA expression, and an RNA-derived “amplification signature” that captures the transcriptional consequences of an amplification event. We facilitate exploratory analyses by making broad predictions initially. Having identified the subset of biomarkers relevant to a patient population of interest, we develop specialized machine learning models, built on the same foundational featurization, which achieve even higher performance for key biomarkers in tumor types of interest. Moreover, our models are robust, generalizing with minimal loss of performance across different patient populations. By generating imputations from tile-level featurizations, we enable spatial overlays of molecular annotations on top of whole-slide images. These annotation maps provide a clear means of interpreting the histological correlates of our model’s predictions, and align with features identified by expert pathologist review. Overall, our work demonstrates a flexible and scalable framework for imputing molecular measurements from H&E, providing a generalizable approach to the development and deployment of predictive biomarkers for targeted therapeutics in cancer.
Design and development of a flipped classroom-based online software course including online examination for medical statistics
Authors: Muche Rainer , Allgöwer Andreas , Braisch Ulrike , Meule Marianne , Mayer Benjamin 
Published: January 2024

AbstractTeaching medical statistics for students of human medicine should include both theoretical content as well as its implementation in practice using statistical software. The training period with a software may be time-consuming individually, so there is a risk that imparting methodological skills comes up short in such courses. The flipped classroom concept aims at students to familiarize themselves with both the statistical software and the theoretical content in an individual learning phase prior to the course. Then, within an attendance course deepening both aspects under the lecturer’s supervision is possible. Availability of the software as well as a variety of material to prepare the course are essential presumptions for the flipped classroom to be successful. We present the concept and implementation of an online flipped classroom course using the software SAS Studio. Students used their own devices (laptops or tablets) during the self-learning and examination phases, respectively. The pure online implementation in the flipped classroom setting enabled to contribute to an equalisation of the study plan. Moreover, even more students had the opportunity to participate in this practically oriented course in medical statistics. Initial evaluation results demonstrated that the course is well-accepted among students, while the students’ performance level was similar when compared to a non-flipped teaching approach.
Widely accessible prognostication using medical history for fetal growth restriction and small for gestational age in nationwide insured women
Authors: Sufriyana Herdiantri , Amani Fariska Zata , Al Hajiri Aufar Zimamuz Zaman , Wu Yu-Wei , Su Emily Chia-Yu 
Published: January 2024

AbstractObjectivesPrevention of fetal growth restriction/small for gestational age is adequate if screening is accurate. Ultrasound and biomarkers can achieve this goal; however, both are often inaccessible. This study aimed to develop, validate, and deploy a prognostic prediction model for screening fetal growth restriction/small for gestational age using only medical history.MethodsFrom a nationwide health insurance database (n=1,697,452), we retrospectively selected visits of 12-to-55-year-old females to 22,024 healthcare providers of primary, secondary, and tertiary care. This study used machine learning (including deep learning) to develop prediction models using 54 medical-history predictors. After evaluating model calibration, clinical utility, and explainability, we selected the best by discrimination ability. We also externally validated and compared the models with those from previous studies, which were rigorously selected by a systematic review of Pubmed, Scopus, and Web of Science.ResultsWe selected 169,746 subjects with 507,319 visits for predictive modeling. The best prediction model was a deep-insight visible neural network. It had an area under the receiver operating characteristics curve of 0.742 (95% confidence interval 0.734 to 0.750) and a sensitivity of 49.09% (95% confidence interval 47.60% to 50.58% using a threshold with 95% specificity). The model was competitive against the previous models in a systematic review of 30 eligible studies of 381 records, including those using either ultrasound or biomarker measurements. We deployed a web application to apply the model.ConclusionsOur model used only medical history to improve accessibility for fetal growth restriction/small for gestational age screening. However, future studies are warranted to evaluate if this model’s usage impacts patient outcomes.
Occupational hazards and risks among the women in fisher communities in Cox’s Bazar and Chattogram
Authors: Halder Charls Erik , Das Partha Pratim , Rahman S.M. Tareq , Bhoumick Liton Chandra , Tassdik Hamim , Hasan Md Abeed , Mithun Sourav Nath 
Published: January 2024

AbstractBackgroundWomen in the fisher communities in coastal regions of Bangladesh are engaged in a wide range of fishery activities including fish sorting, grading, cutting, dry fish processing, transporting and selling. However, there is limited evidence available on the occupational hazards and risks experienced by them.MethodThe study was conducted among fishing colonies in Cox’s Bazar and Chattogram districts in Bangladesh. This was a cross-sectional study comprised of both qualitative and quantitative approaches. Data were primarily collected through eight focus group discussions (FGD) and a quantitative survey of a sample of 207 women working in fisheries sector.FindingsThe study found a high occurrence of occupational hazards, health risks and disease conditions and limited availability of preventive measures among the women in the fisher communities in the coastal Bangladesh. Occupational hazards include physical safety hazards, like slippery surface, fish cutting instruments, fish sting or bite and contact with fishes; physical hazards, like prolonged sun exposure and noise; chemical hazards like pesticides, salt and salt water; ergonomic hazards, like prolonged sitting or standing in uncomfortable posture and heavy weight lifting; and biological hazards, like inadequate provision of sanitary latrine or hand washing soap at workplace. The study also found occupational risks resulting from the hazards including injuries (87.44%), musculoskeletal conditions (69.08%), skin diseases/conditions (56.52%), eye complaints (33.82%), severe respiratory distress (24.15%) and high incidence of self-reported communicable diseases. Majority of the women did not use personal protection equipment at their workplace (78.26%) and have a first aid kit at their workplace (93.72%).ConclusionThis study highlights the critical occupational health and safety challenges faced by the women in the fisheries sector. A comprehensive multisectoral strategy needs to be undertaken to mitigate the occupational hazards and prevent associated diseases among the women in fisher communities promoting their health and wellbeing.
Immersive Virtual Reality Games in Neuromotor Rehabilitation with Brain-Computer Interfaces: A Scoping Review
Authors: Gaafer Mohamed N. , Ahmed Zeyad M. , El-Husseiny Abdullah S. , Youssef Aliaa Rehan , Al-Kabbany Ahmed 
Published: January 2024

AbstractThe use of immersive virtual reality (VR) is gaining traction among the scientific community as it opens great opportunities in the field of rehabilitation. By making use of video game mechanics and Brain computer interface (BCI) that is based on electroencephalography (EEG) signals, patients undergoing neurorehabilitation can be more engaged in rehabilitation training. This paper reviews the available literature which uses BCI and VR in game rehabilitation and analyses the gaming elements and brain machine interfaces (BMI) used in each study. Four databases (IEEE Xplore, PubMed, Web of Science, Scopus) from inception until October 2023 were queried using a comprehensive searching strategy and then screened by two independent reviewers. A total of 18 articles were found eligible for qualitative synthesis. These are the main findings: (1) A diverse participant demographic spanned age and health conditions; (2) Oculus Rift has gained prominence as a VR device, replacing older CAVE systems; (3) All surveyed studies unanimously relied on the Motor Imagery (MI) paradigm, reflecting its importance in neuro motor rehabilitation and neuroplasticity; (4) Rehabilitation games displayed varied characteristics, emphasizing scoring, embodiment, and customization. Notably, the lack of gamification elements in some games suggests an area for potential enhancement and future research.
Angiographic Tool to Detect Pulmonary Arteriovenous Malformations in Single Ventricle Physiology
Authors: Spurgin Stephen B , Arar Yousef M , Zellers Thomas M , Wang Jijia , Madsen Nicolas L , Veeram Reddy Surendranath R , Cleaver Ondine , Divekar Abhay A 
Published: January 2024

ABSTRACTBackgroundIndividuals with single ventricle physiology who are palliated with superior cavopulmonary anastomosis (Glenn surgery) may develop pulmonary arteriovenous malformations (PAVMs). The traditional tools for PAVM diagnosis are often of limited diagnostic utility in this patient population. We sought to measure the pulmonary capillary transit time (PCTT) to determine its value as a tool to identify PAVMs in patients with single ventricle physiology.MethodsWe defined the angiographic PCTT as the number of cardiac cycles required for transit of contrast from the distal pulmonary arteries to the pulmonary veins. Patients were retrospectively recruited from a single quaternary North American pediatric center, and angiographic and clinical data was reviewed. PCTT was calculated in 20 control patients and compared to 20 single ventricle patients at the pre-Glenn, Glenn, and Fontan surgical stages (which were compared with a linear-mixed model). Correlation (Pearson) between PCTT and hemodynamic and injection parameters was assessed using 84 Glenn angiograms. Five independent observers calculated PCTT to measure reproducibility (intra-class correlation coefficient).ResultsMean PCTT was 3.3 cardiac cycles in the control population, and 3.5, 2.4, and 3.5 in the pre-Glenn, Glenn, and Fontan stages, respectively. PCTT in the Glenn population did not correlate with injection conditions. Intraclass correlation coefficient was 0.87.ConclusionsPulmonary angiography can be used to calculate the pulmonary capillary transit time, which is reproducible between observers. PCTT accelerates in the Glenn stage, correlating with absence of direct hepatopulmonary venous flow.
Immunological imprinting shapes the specificity of human antibody responses against SARS-CoV-2 variants
Authors: Johnston Timothy S. , Li Shuk Hang , Painter Mark M. , Atkinson Reilly K. , Douek Naomi R. , Reeg David B. , Douek Daniel C. , Wherry E. John , Hensley Scott E. 
Published: January 2024

SummaryThe spike glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to accumulate substitutions, leading to breakthrough infections of vaccinated individuals and prompting the development of updated booster vaccines. Here, we determined the specificity and functionality of antibody and B cell responses following exposure to BA.5 and XBB variants in individuals who received ancestral SARS-CoV-2 mRNA vaccines. BA.5 exposures elicited antibody responses that primarily targeted epitopes conserved between the BA.5 and ancestral spike, with poor reactivity to the XBB.1.5 variant. XBB exposures also elicited antibody responses that targeted epitopes conserved between the XBB.1.5 and ancestral spike. However, unlike BA.5, a single XBB exposure elicited low levels of XBB.1.5-specific antibodies and B cells in some individuals. Pre-existing cross-reactive B cells and antibodies were correlated with stronger overall responses to XBB but weaker XBB-specific responses, suggesting that baseline immunity influences the activation of variant-specific SARS-CoV-2 responses.HighlightsVariant breakthrough infections boost ancestral cross-reactive antibodies and B cellsFirst and second BA.5 exposures fail to elicit variant-specific antibodies and B cellsXBB infections and monovalent vaccinations elicit XBB.1.5-specific responses in some individualsXBB.1.5-specific responses correlate with low levels of pre-existing humoral immunity
Climate warming is expanding dengue burden in the Americas and Asia
Authors: Childs Marissa L. , Lyberger Kelsey , Harris Mallory , Burke Marshall , Mordecai Erin A. 
Published: January 2024

AbstractClimate change is expected to pose significant threats to public health, particularly including vector-borne diseases. Despite dramatic recent increases in the burden of dengue that many anecdotally connect with climate change, the effect of past and future anthropogenic climate change on dengue remains poorly quantified. To assess the link between climate warming and dengue we assembled a dataset covering 21 countries in Asia and the Americas, and found a nonlinear relationship between temperature and dengue incidence with the largest impact of warming at lower temperatures (below about 20°C), peak incidence at 27.8°C, and subsequent declines at higher temperatures. Using this inferred temperature response, we estimate that historical climate change has increased dengue incidence by 18% (11 - 27%) on average across our study countries, and that future warming could further increase it by 49% (16 - 136%) to 76% (27 - 239%) by mid-century for low or high emissions scenarios, respectively, with some cooler regions projected to see dengue doubling due to warming and other currently hot regions seeing no impact or even small declines. Under the highest emissions scenario, we estimate that 262 million people are currently living in places in these 21 countries where dengue incidence is expected to more than double due to climate change by mid-century. These insights highlight the major impacts of anthropogenic warming on dengue burden across most of its endemic range, providing a foundation for public health planning and the development of strategies to mitigate future risks due to climate change.
The effect of post-acute rehabilitation setting on 90-day mobility after stroke: A difference-in-difference analysis
Authors: French Margaret A. , Hayes Heather , Johnson Joshua K. , Young Daniel L. , Roemmich Ryan T. , Raghavan Preeti 
Published: January 2024

AbstractBackgroundAfter discharged from the hospital for acute stroke, individuals typically receive rehabilitation in one of three settings: inpatient rehabilitation facilities (IRFs), skilled nursing facilities (SNFs), or home with community services (i.e., home health or outpatient clinics). The initial setting of post-acute care (i.e., discharge location) is related to mortality and hospital readmission; however, the impact of this setting on the change in functional mobility at 90-days after discharge is still poorly understood. The purpose of this work was to examine the impact of discharge location on the change in functional mobility between hospital discharge and 90-days post-discharge.MethodsIn this retrospective cohort study, we used the electronic health record to identify individuals admitted to Johns Hopkins Medicine with an acute stroke and who had measurements of mobility [Activity Measure for Post Acute Care Basic Mobility (AM-PAC BM)] at discharge from the acute hospital and 90-days post-discharge. Individuals were grouped by discharge location (IRF=190 [40%], SNF=103 [22%], Home with community services=182 [(38%]). We compared the change in mobility from time of discharge to 90-days post-discharge in each group using a difference-in-differences analysis and controlling for demographics, clinical characteristics, and social determinants of health.ResultsWe included 475 individuals (age 64.4 [14.8] years; female: 248 [52.2%]). After adjusting for covariates, individuals who were discharged to an IRF had a significantly greater improvement in AM-PAC BM from time of discharge to 90-days post-discharge compared to individuals discharged to a SNF or home with community services (β=-3.5 (1.4), p=0.01 and β=-8.2 (1.3), p=<0.001, respectively).ConclusionsThese findings suggest that the initial post-acute rehabilitation setting impacts the magnitude of functional recovery at 90-days after discharge from the acute hospital. These findings support the need for high-intensity rehabilitation and for policies that facilitate the delivery of high-intensity rehabilitation after stroke.
RFX6 at locus 6q22 confers metastasis and drug resistance in prostate cancer
Authors: Zhong Mengjie , Xu Wenjie , Tian Pan , Zhang Qin , Wang Zixian , Liang Limiao , Zhang Qixiang , Yang Yuehong , Lu Ying , Wei Gong-Hong 
Published: January 2024

AbstractGenetic and nonmutational epigenetic alterations are cancer hallmark characteristics. However, the role of inherited cancer predisposition alleles in co-opting lineage factor epigenetic reprogramming and contributing to tumor progression remains elusive. Here the FinnGen cohort phenome-wide analysis, along with recent multiple genome-wide association studies, has consistently identified the rs339331-RFX6/6q22 locus associated with prostate cancer (PCa) risk across diverse populations. We uncover that rs339331 resides at a reprogrammed androgen receptor (AR) binding site in PCa tumors, with the T risk allele enhancing AR chromatin occupancy under androgen signaling. We establish that RFX6 is an AR-regulated gene, intricately linked with rs339331, exhibiting synergistic prognostic value for PCa recurrence and metastasis. Through comprehensivein vitroandin vivostudies, we establish the oncogenic functions of RFX6 in promoting PCa cell proliferation and metastasis. Mechanistically, RFX6 upregulates transcription factor HOXA10 that profoundly correlates with adverse PCa outcomes and is pivotal in RFX6-mediated PCa progression, facilitating the epithelial-mesenchymal transition (EMT) process and modulating the TGFβ/SMAD signaling axis. Clinically, HOXA10 elevation is associated with increased EMT scores, tumor advancement and PCa recurrence. Remarkably, reducing RFX6 expression restores responsiveness of enzalutamide-resistant PCa cells and tumors to treatment. Our study highlights an interplay of disrupted genetic and epigenetic mechanisms converging on prostate lineage AR signaling, resulting in abnormal expression of RFX6 conferring PCa pathogenesis and enzalutamide resistance.