bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and clinical presentations of post-COVID-19 conditions in Nepal
Authors: Basnet Lila Bahadur , Thapa Pomawati , Bastola Anup , Khanal Narendra , Panta Niranjan , Thapaliya Sabin , Kleine Bingham Melissa Beth , Shrestha Saugat , Adhikari Shital , Khadka Sudesha , Shrestha Priyanka , Paudel Sadhana , Devapitchai Kamaraj Arulmozhi 
Published: April 2024

AbstractIntroductionThe COVID-19 pandemic affected millions worldwide. While the major focus was on diagnosis and treatment of the acute phase of the disease, many individuals experienced long-term health even after recovery. These post-COVID-19 conditions encompass a broad range of physical, psychological, and cognitive symptoms that persist beyond the acute phase of the illness. The aim of this study was to find the prevalence and reported presentations of post-COVID-19 conditions in Nepal.MethodThis is a retrospective cross-sectional study using structured questionnaire to collect hospital-based data available in the record of Curative Service Division, Department of Health Services of Nepal from October 2021 to September 2022. A total of 6151 cases were recorded in the study. Descriptive analysis was done for demographic and symptoms variable. Association of variables to post-COVID-19 condition are shown using univariate and multivariate logistic regression.ResultsAmong 6151 respondents (62.25% males), more than half (59.03%) had at least one symptom after recovery from acute COVID-19. The most common symptoms were anxiety (28.5%), loss of appetite (25.3%), shortness of breath (24.13%), fatigue (23.24%), depressed mood (18.79%), muscle ache (17.59%), chest pain (16.81%), headache (14.78%), and palpitation (13%). Multivariate analysis showed increased odds of post-COVID-19 conditions in smokers (adjusted OR [aOR] 1.53), those with chronic lung disease (aOR 1.71), neurological disorder (aOR 2.43) and those with use of supplementary oxygen during acute illness of COVID-19 (aOR 3.37).ConclusionThe prevalence of post-COVID-19 symptoms among the study population is found to be high. The main symptoms from our study and similar studies are anxiety, fatigue, loss of appetite, shortness of breath, muscle pain, headaches. Patients with smoking, hypoxia during acute illness and presence of chronic lung disease and neurological disorder had higher odds of getting post-COVID-19 conditions. Citing the findings, health system should focus upon the management and recording of such conditions for further evidence.
Prediction of Complicated Ovarian Hyperstimulation Syndrome in Assisted Reproductive Treatment Through Artificial Intelligence
Authors: Ziaee Arash , Khosravi Hamed , Sadeghi Tahereh , Ahmed Imtiaz , Mahmoudinia Maliheh 
Published: April 2024

ABSTRACTBackgroundThis study explores the utility of machine learning (ML) models in predicting complicated Ovarian Hyperstimulation Syndrome (OHSS) in patients undergoing infertility treatments, addressing the challenge posed by highly imbalanced datasets.ObjectiveThis research fills the existing void by introducing a detailed structure for crafting diverse machine learning models and enhancing data augmentation methods to predict complicated OHSS effectively. Importantly, the research also concentrates on pinpointing critical elements that affect OHSS.MethodThis retrospective study employed a ML framework to predict complicated OHSS in patients undergoing infertility treatment. The dataset included various patient characteristics, treatment details, ovarian response variables, oocyte quality indicators, embryonic development metrics, sperm quality assessments, and treatment specifics. The target variable was OHSS, categorized as painless, mild, moderate, or severe. The ML framework incorporated Ray Tune for hyperparameter tuning and SMOTE-variants for addressing data imbalance. Multiple ML models were applied, including Decision Trees, Logistic Regression, SVM, XGBoost, LightGBM, Ridge Regression, KNN, and SGD. The models were integrated into a voting classifier, and the optimization process was conducted. The SHAP package was used to interpret model outcomes and feature contributions.ResultsThe best model incorporated IPADE-ID augmentation along with an ensemble of classifiers (SGDClassifier, SVC, RidgeClassifier), reaching a recall of 0.9 for predicting OHSS occurrence and an accuracy of 0.76. SHAP analysis identified key factors: GnRH antagonist use, longer stimulation, female infertility factors, irregular menses, higher weight, hCG triggers, and, notably, higher number of embryos.ConclusionThis novel study demonstrates ML’s potential for predicting complicated OHSS. The optimized model provides insights into contributory factors, challenging certain conventional assumptions. The findings highlight the importance of considering patient-specific factors and treatment details in OHSS risk assessment.
A preventive school-based paradigm using virtual reality technologies for improving emotional regulation, depressive and anxiety symptoms in children and adolescents (e-Emotio project): a randomized controlled pilot trial
Authors: Carballo-Marquez Anna , Garcia-Casanovas Anna , Ampatzoglou Aikaterini , Rojas-Rincon Juliana , Fernández-Capo María , Gámiz-Sanfeliu María , Freixa Maite Garolera- , Porras-Garcia Bruno 
Published: April 2024

AbstractIntroductionPreventive transdiagnostic interventions for depression and anxiety symptoms in children and adolescents are important in reducing the development of disorders later in life, and emotion regulation (ER) is one potentially relevant factor to consider. Impairments in executive functions play a critical role in emotion development and regulation in these ages. Immersive Virtual Reality (IVR) technology has exhibited potential to augment traditional cognitive training interventions. In this project, we propose to use Enhance IVR, a gamified cognitive training that can be tailored to specific ER strategies that individuals may face, such as difficulty with attention control, inhibition, or cognitive flexibility.Methods and analysisThis is a longitudinal, parallel, single-blind, randomized, controlled pilot trial with an estimated sample of 160 participants. The first group (experimental group) will receive the gamified IVR program (Enhance IVR), while the second group (active control group) will receive a comparable IVR relaxation experience. Both Enhance IVR and the control IVR interventions will last five weeks, two times a week, 30 minutes (10 sessions per participant). Participants will undergo a baseline assessment that includes several measures related to mental health, ER, executive functioning, and cognitive performance, and another post intervention assessment with the same measures. Finally, variables related to system usability and cybersickness with the IVR tool will be evaluated for both groups.Ethics and disseminationThis study was approved by the Ethical Committee of the International University of Catalonia (PSI-2023-04). The findings will be disseminated through peer-reviewed journals, reports, conferences, and other scientific events.Strengths and limitations of this studyThis is a controlled, randomized, and single-blind design, which provides rigorous evidence for a virtual reality (VR) intervention effect.The intervention has a strong ecological validity as it is done in the participants’ natural context (i.e. school) and the assessment involves students, family, and school.The gamified VR design is innovative and engaging, and there is an equivalent active-based VR control condition.One limitation is there is no follow-up assessment and no double-blind experimental design due to the nature of the study.A second limitation is the potential drop-out rates due the preventive nature of the interventions.
Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City
Authors: Zhang Renquan , Tai Jilei , Yao Qing , Yang Wan , Ruggeri Kai , Shaman Jeffrey , Pei Sen 
Published: April 2024

AbstractThe COVID-19 pandemic in New York City (NYC) was characterized by marked disparities in disease burdens across neighborhoods. Accurate neighborhood-level forecasts are critical for planning more equitable resource allocation; however, such spatially high-resolution forecasts remain scarce in operational use. Here, we analyze aggregated foot traffic data derived from mobile devices to measure the connectivity among 42 NYC neighborhoods driven by various human activities such as dining, shopping, and entertainment. Using real-world time-varying contact patterns in different place categories, we develop a parsimonious behavior-driven epidemic model that incorporates population mixing, indoor crowdedness, dwell time, and seasonality of virus transmissibility. This process-based model supports accurate modeling of neighborhood-level SARS-CoV-2 transmission throughout 2020. In the best-fitting model, we estimate that the force of infection in indoor settings increases sublinearly with crowdedness and dwell time. Retrospective forecasting demonstrates that this behavior-driven model generates improved short-term forecasts in NYC neighborhoods. This model may be adapted for use with other respiratory pathogens sharing similar transmission routes.
Cost Savings Associated with Extended Battery Longevity in Cardiac Resynchronization Therapy Defibrillators (CRT-D)
Authors: Williams Jeffrey L. , Sato Ryoko , Jacobsen Caroline M. 
Published: April 2024

AbstractBackgroundCardiac resynchronization therapy-defibrillators (CRT-D) are devices established as treatment for symptomatic heart failure patients with an indication for CRT and at risk of sudden cardiac death. However, battery depletion poses a significant clinical and economic burden; extended service life may reduce costs due to generator changes and associated complications. The purpose of this study was to estimate the potential cost-savings associated with extended battery longevity in a Medicare patient population receiving CRT-D implantation.MethodsA decision tree was used to explore three battery capacities, which represent the leading device manufacturers available in the US: 1.0 ampere-hours (Ah), 1.6Ah, and 2.1Ah. Yearly risk of all-cause mortality, device-related complications, and end of battery life were estimated. Over a time horizon of 6 years, estimated costs included device implantation, replacement, follow-up appointments, and complications. Costs were discounted at 3%. Univariate deterministic sensitivity analysis was completed for patient survival, battery survival, complication incidence and costs, procedure costs, and time horizon.ResultsIn the base-case, the average total costs to Medicare over 6 years were $41,527, $48,515, and $56,647 per person (USD 2023) for the 2.1Ah, 1.6Ah, and 1.0Ah devices, respectively. The total per-person replacement cost for the 1.0Ah devices was more than 4 times that of the 2.1Ah devices ($20,126 versus $5,006). When extrapolated to the total number of CRT-D implants each year over a 6-year period, the difference in costs between the extended (2.1Ah) and lowest (1.0Ah) battery capacity exceeded $500 million.ConclusionsExtended longevity CRT-D batteries demonstrate significant cost savings to Medicare over 6 years compared to those with lower battery capacity. These data indicate long-term economic considerations should be included in device selection.
Bubbles help in troubles: contrast-enhanced ultrasound (CEUS) as predictor of recurrence for TIA/stroke in low-grade internal carotid artery stenosis
Authors: D’Auria Francesca , Santo Danilo Flavio 
Published: April 2024

AbstractIntroductionContrast-enhanced ultrasound (CEUS) allows to visualize atherosclerotic plaque neo-vessels which are the hallmark of carotid plaque instability.AimAim of our prospective study was to check the correlation between carotid CEUS analysis and the recurrence of TIA/stroke in patients with a previous recent TIA/stroke and neurological impairment congruent with the vascular stenosis.Materials and MethodsFrom November 2021 to May 2023, 62 consecutive patients (mean age 73.8 +/- 12.2, female 51) with a TIA/stroke in the previous 30 days, underwent carotid ultrasound and carotid CEUS in outpatients setting after 10 days from the acute event. Inclusion criteria was one atherosclerotic plaque inside the internal carotid artery, congruent with symptoms, which was causing a stenosis less than 50% (low-grade stenosis). Carotid plaque neovascularization scoring method was: score 0: no visible microbubbles within the plaque (A); score 1: minimal microbubbles confined to periadventitial (B); and score 2: microbubbles present throughout the plaque core (C). During the six-month follow-up, we checked TIA/stroke recurrences. A multivariable logistic regression analysis was performed.ResultsIn our series, 22% of patients have CEUS score 0, 35% CEUS score 1, and 43% CEUS score 2. At six-month follow-up we found 21% TIA/stroke recurrences in CEUS score 2, despite of the ongoing best medical therapy as per guidelines. In Cox regression analysis, CEUS-detected neovascularization was independently associated with TIA/stroke recurrence (hazard ratio, 5.37; 95% confidence interval, 1.36–2.31).ConclusionsPlaque neovascularization, detected by CEUS, is an independent predictor of TIA/stroke recurrence at six-month follow-up in patients with carotid atherosclerosis despite of low-grade stenosis.
From raw microalgae to bioplastics: conversion ofChlorella vulgarisstarch granules into thermoplastic starch
Authors: Six A. , Dauvillée D. , Lancelon-Pin C. , Dimitriades-Lemaire A. , Compadre A. , Dubreuil C. , Alvarez P. , Sassi J.-F. , Li-Beisson Y. , Putaux J.-L. , Le Moigne N. , Fleury G. 
Published: April 2024

AbstractMicroalgae are emerging as a promising feedstock for bioplastics, withChlorella vulgarisyielding significant amounts of starch. This polysaccharide is convertible into thermoplastic starch (TPS), a biodegradable plastic of industrial relevance. In this study, we developed a pilot-scale protocol for extracting and purifying starch from starch-enrichedChlorella vulgarisbiomass. From 430.3 ± 0.5 g (dry weight - DW) of microalgae biomass containing 42.2 ± 3.4 % of starch, we successfully extracted 205.8 ± 1.2 gDWof purified starch extract containing 86.9 ± 3.0 % of starch, resulting in a final recovery yield of 98.5%. We have characterized this extracted starch and processed it into TPS using twin-screw extrusion and injection molding. Microalgal starch showed similar properties to those of native plant starch, but with smaller granules. We compared the mechanical properties of microalgal TPS with two controls, namely a commercial TPS and a TPS prepared from commercial potato starch granules. TPS prepared from microalgal starch showed a softer and more ductile behavior compared to the reference materials. This study demonstrates the feasibility of recovering high-purity microalgal starch on a pilot scale with high yields, and highlights the potential of microalgal starch for the production of TPS using industrially relevant processes.Graphical abstract
A Futile Cycle? Tissue Homeostatic Trans-Membrane Water Co-Transport: Kinetics, Thermodynamics, Metabolic Consequences
Authors: Springer Charles S. , Pike Martin M. , Barbara Thomas M. 
Published: April 2024

ABSTRACTThe phenomenon of active trans-membrane water cycling (AWC) has emerged in little over a decade. Here, we consider H2O transport across cell membranes from the origins of its study. Historically, trans-membrane water transport processes were classified into: A) compensating bidirectional fluxes (“exchange”), and B) unidirectional flux (“net flow”) categories. Recent literature molecular structure determinations and molecular dynamic (MD) simulations indicate probably all the many different hydrophilic substrate membrane co-transporters have membrane-spanning hydrophilic pathways and co-transport water along with their substrates, and that they individually catalyze category A and/or B water flux processes, although usually not simultaneously. The AWC name signifies that, integrated over the all the cell’s co-transporters, the rate ofhomeostatic, bidirectional trans-cytolemmal water exchange (category A) is synchronized with the metabolic rate of the crucial Na+,K+-ATPase (NKA) enzyme. A literature survey indicates the stoichiometric (category B) water/substrate ratios of individual co-transporters are often very large. The MD simulations also suggest how different co-transporter reactions can bekineticallycoupled molecularly.Is this (Na+,K+-ATPase rate-synchronized) cycling futile, or is it consequential? Conservatively representative literature metabolomic and proteinomic results enable comprehensive free energy analyses of the many transport reactions with known water stoichiometries. Free energy calculations, using literature intracellular pressure (Pi) values reveals there is anoutwardtrans-membrane H2O barochemical gradient of magnitude comparable to that of the well-knowninwardNa+electrochemical gradient. For most co-influxers, these gradients are finely balanced to maintain intracellular metabolite concentration values near their consuming enzyme Michaelis constants. The thermodynamic analyses include glucose, glutamate-, gamma-aminobutyric acid (GABA), and lactate-transporters. 2%-4% Pialterations can lead to disastrous concentration levels. For the neurotransmitters glutamate-and GABA, very small astrocytic Pichanges can allow/disallow synaptic transmission. Unlike the Na+and K+electrochemical steady-states, the H2O barochemicalsteady-stateis in (or near) chemicalequilibrium. The analyses show why the presence of aquaporins (AQPs) does not dissipate the trans-membrane pressure gradient. A feedback loop inherent in the opposing Na+electrochemical and H2O barochemical gradients regulates AQP-catalyzed water flux as an integral AWC aspect. These results also require a re-consideration of the underlying nature of Pi. Active trans-membrane water cycling is not futile, but is inherent to the cell’s “NKA system” - a new, fundamental aspect of biology.SYNOPSISViaintracellular pressure, membrane co-transported water influences thermodynamic control of cell metabolite maintenance.
Human natural killer cells can activate NLRP1 and NLRP3 inflammasomes and drives pyroptosis
Authors: Astorga-Gamaza Antonio , Muela-Zarzuela Inés , Suárez-Rivero Juan Miguel , López-Pérez Juan , de la Varga-Martínez Raquel , Mazuecos Auxiliadora , Cordero Mario D. 
Published: April 2024

SummaryInnate immunity relies on inflammasomes as key components, defending the host against diverse harmful stimuli by orchestrating the release of pro-inflammatory cytokines and initiating pyroptotic cell death. While extensively studied in myeloid cells, the involvement of natural killer (NK) cells in inflammatory responses through inflammasome signaling remains underexplored. In this study, we elucidate the activation of the inflammasome sensors NLRP1 and NLRP3 in human primary NK cells upon treatment with nigericin and blockade of dipeptidyl peptidases (DPP) using Talabostat (Val-boroPro). Our findings demonstrate the induction of pyroptotic cell death in a subset of NK cells following these stimuli, characterized by the cleavage and activation of gasdermin D, a lytic pore-forming protein. Moreover, we observe the release of lactate dehydrogenase (LDH) and small amounts of interleukin-18 (IL-18). Notably, differential responses are noted between CD56dimand CD56brightNK cell subsets following pro-inflammatory stimulation. Furthermore, analysis of samples from patients with renal dysfunction reveals sustained inflammasome activation in NK cells, particularly NLRP1 and NLRP3, with a tendency towards a more pro-inflammatory phenotype shortly post-kidney transplantation. These findings underscore the significance of considering NK cells in the context of inflammation studies.
Accurate evaluation of live-virus microneutralization for SARS-CoV-2 variant JN.1
Authors: Dowgier Giulia , Hobbs Agnieszka , Greenwood David , Shawe-Taylor Marianne , Stevenson-Leggett Phoebe , Bazire James , Penn Rebecca , Harvey Ruth ,   Crick COVID serology pipeline, Legacy Investigators, Libri Vincenzo , Kassiotis George , Gamblin Steve , Lewis Nicola S , Williams Bryan , Swanton Charles , Gandhi Sonia , Bauer David LV , Carr Edward J , Wall Emma C , Wu Mary Y 
Published: April 2024

AbstractEmerging SARS-CoV-2 variants require rapid assessments of pathogenicity and evasion of existing immunity to inform policy. A crucial component of these assessments is accurate estimation of serum neutralising antibody titres using cultured live virus isolates. Here, we report our updated culture methods for Omicron sub-variant JN.1 using Caco-2 cells and the subsequent evaluation of neutralising antibody titres (nAbTs) in recipients of BNT162b2-XBB.1.5 monovalent and the Ancestral/BA.5 containing bivalent vaccines. We compared culture of JN.1 in either Vero V1 cells or Caco-2 cells, finding culture in Vero V1 either resulted in low-titre stocks or induced crucial mutations at the Spike furin cleavage site. Using the sequence-clean culture stocks generated in Caco-2 cells, we assessed serum samples from 71 healthy adults eligible for a COVID-19 vaccination given as a 5thdose booster: all participants had detectable nAbs against JN.1 prior to vaccination, with baseline/pre-existing nAbTs between both vaccine groups comparable (p = 0.240). However, nAbTs against JN.1 post-vaccination were 2.6-fold higher for recipients of the monovalent XBB1.5 vaccine than the BA.4/5 bivalent vaccine (p<0.001). Regular re-appraisal of methods involved in the evaluation of new variants is required to ensure robust data are used to underpin crucial severity assessments as variants arise and vaccine strain selection decisions.
DANTE and DANTE_LTR: Lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes
Authors: Novák Petr , Hoštáková Nina , Neumann Pavel , Macas Jiří 
Published: April 2024

AbstractLong terminal repeat (LTR) retrotransposons constitute a predominant class of repetitive DNA elements in most plant genomes. With the increasing number of sequenced plant genomes, there is an ongoing demand for computational tools facilitating efficient annotation and classification of LTR retrotransposons in plant genome assemblies. Herein, we introduce DANTE, a computational pipeline for Domain-based ANnotation of Transposable Elements, designed for sensitive detection of these elements via their conserved protein domain sequences. The identified protein domains are subsequently inputted into the DANTE_LTR pipeline to annotate complete element sequences by detecting their structural features, such as LTRs, in adjacent genomic regions. Leveraging domain sequences allows for precise classification of elements into phylogenetic lineages, offering a more granular annotation compared with coarser conventional superfamily-based classification methods. The efficiency and accuracy of this approach were evidenced via annotation of LTR retrotransposons in 93 plant genomes. Results were benchmarked against several established pipelines, showing that DANTE_LTR is capable of identifying significantly more intact LTR retrotransposons. DANTE and DANTE_LTR are provided as user-friendly Galaxy tools accessible via a public server (https://repeatexplorer-elixir.cerit-sc.cz), installable on local Galaxy instances from the Galaxy tool shed or executable from the command line.