bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of anti-SARS-CoV-2 seroconversion in individual patients and at the population level
Authors: Szewczyk-Dąbrowska Alina , Budziar Wiktoria , Baniecki Krzysztof , Pikies Aleksandra , Harhala Marek , Jędruchniewicz Natalia , Kaźmierczak Zuzanna , Gembara Katarzyna , Klimek Tomasz , Witkiewicz Wojciech , Nahorecki Artur , Barczyk Kamil , Grata-Borkowska Urszula , Dąbrowska Krystyna 
Published: March 2022

AbstractThe immune response and specific antibody production in COVID-19 are among the key factors that determine both prognostics for individual patients and the global perspective for controlling the pandemics. So called “dark figure”, that is, a part of population that has been infected but not registered by the health care system, make it difficult to estimate herd immunity and to predict pandemic trajectories.Here we present a follow up study of population screening for hidden herd immunity to SARS-CoV-2 in individuals who had never been positively diagnosed against SARS-CoV-2; the first screening was in May 2021, and the follow up in December 2021. We found that specific antibodies targeting SARS-CoV-2 detected in May as the “dark figure” cannot be considered important 7 months later due to their significant drop. On the other hand, among participants who at the first screening were negative for anti-SARS-CoV-2 IgG, and who have never been diagnosed for SARS-CoV-2 infection nor vaccinated, 26% were found positive for anti-SARS-CoV-2 IgG. This can be attributed to of the “dark figure” of the recent, fourth wave of the pandemic that occurred in Poland shortly before the study in December. Participants who were vaccinated between May and December demonstrated however higher levels of antibodies, than those who undergone mild or asymptomatic (thus unregistered) infection. Only 7% of these vaccinated participants demonstrated antibodies that resulted from infection (anti-NCP). The highest levels of protection were observed in the group that had been infected with SARS-CoV-2 before May 2021 and also fully vaccinated between May and December.These observations demonstrate that the hidden fraction of herd immunity is considerable, however its potential to suppress the pandemics is limited, highlighting the key role of vaccinations.
Home Care Follow up determine the point of inversion of IL-6 levels in relation to C-Reactive Protein as the cytokine storm marker in COVID-19
Authors: de Mello Mendes Filho Sérgio Paulo , Martins Fernanda Simão , Giroldi Paulo Jose , Melo Raul Honorato e , de Oliveira Edcleia Lopes , dos Santos Anibal Borin , Medeiros Dayse Cristina Oliveira , de Almeida Basano Sergio , Lopes Jéssica Amaral , Chaves Yury Oliveira , Pinheiro Rebeca Sousa , Camargo Luís Marcelo Aranha , Zuliani Juliana Pavan , Nogueira Paulo Afonso 
Published: March 2022

AbstractThe IL-6 has been used for the characterization of the cytokine storm induced by SARS-CoV-2, but so far, no one has found out when and in whom the cytokine storm develops. Our study demonstrates how early and longitudinal clinical-based monitoring and dosing of five markers (C-reactive protein, IL-6, fibrinogen, ferritin and D-dimer) helped to identify who’d developed the cytokine storm. The peak of IL-6 in pg/mL proportionally higher than the peak of CRP in mg/L was sufficient to define the timing of the evolution of cytokine storm syndrome. The administration of antibiotic therapy, anticoagulant therapy and pulse therapy resolved the infection and prevented the progressive deterioration of the lung function of the patients with potential for development of severe COVID-19.
Pre-exposure prophylaxis with Evusheld™ elicits limited neutralizing activity against the omicron variant in kidney transplant patients
Authors: Benotmane Ilies , Velay Aurélie , Thaunat Olivier , Vargas Gabriela Gautier , Olagne Jérôme , Fafi-Kremer Samira , Caillard Sophie 
Published: March 2022

AbstractThe combination of cilgavimab-tixagevimab (Evusheld™, Astra Zeneca) became the mainstay for protecting transplant recipients with poor response to vaccination against the omicron variant. Serum neutralizing capacity against SARS-CoV-2 is positively associated with protection against severe forms of Covid-19.Both anti-RBD IgG titers and neutralizing antibody titers against the omicron BA.1 variant were measured in serum samples collected from 63 adult kidney transplant recipients who received prophylactic injections of Evusheld™. Patients who received prophylactic Ronapreve™ (casirivimab-imdevimab, n = 39) and those who were infected with SARS-CoV-2 during the fifth wave of the pandemic (n = 14) served as negative and positive controls, respectively.After a median interval from injection of 29 days (interquartile range 29-33 days), only 9.5% of patients who received Evusheld™ were able to neutralize the omicron variant compared to 71% of patients who were infected with SARS-CoV-2 and 2.6% of those who received Ronapreve™. Interestingly, convalescent patients displayed higher levels of neutralizing antibodies than those who received EvusheldTM (median: 2.3 log IC50, IQR: 1.5-2.7 versus 0.00 log IC50, IQR: 0&[ndash] 0.05; p<0.001). A high interindividual variability in anti-RBD IgG titers was observed after Evusheld™ (range: 262-7032 BAU/mL). This variability was largely explained by the patients’body mass index, which showed an inverse correlation with anti-RBD IgG titers.These findings suggest that Evusheld™ given at a dose of 300 mg is not sufficient to elicit an anti-RDB titer that confers in vivo neutralizing activity and support recent FDA recommendations, derived from in vitro models, regarding the need to increase the dose of Evusheld™
Dynamic coastal pelagic habitat drives rapid changes in growth and condition of juvenile sockeye salmon (Oncorhynchus nerka) during early marine migration
Authors: Garzke Jessica , Forster Ian , Godwin Sean , Johnson Brett T. , Krkosek Martin , Mahara Natalie , Pakhomov Evgeny A. , Rogers Luke A. , Hunt Brian P.V. 
Published: March 2022

AbstractMigrating marine taxa encounter diverse habitats that differ environmentally and in foraging conditions over a range of spatial scales. We examined body (RNA/DNA, length-weight residuals) and nutritional (fatty acid composition) condition of juvenile sockeye salmon (Oncorhynchus nerka) in British Columbia, while migrating through varied oceanographically waters. Fish were sampled in the stratified northern Strait of Georgia (NSoG); the highly mixed Johnstone Strait (JS); and the transitional zone of Queen Charlotte Strait (QCS). In 2015, body and nutritional condition were high in the NSoG and responded rapidly to reach lowest levels in JS with its low prey availability, and showing signs of compensatory growth in QCS. In 2016, juvenile salmon had significantly lower condition in the NSoG than in 2015, although zooplankton biomass was similar, condition remained low in JS, and no compensatory growth was observed in QCS. We provide evidence that differences in juvenile salmon condition between the two years being due to changes in the food quality available to juvenile fish. Further, we propose that the TGH needs to be extended to incorporate food quality as a parameter to understand changes in fish condition and survival between years.
Croatian Genetic Heritage: Renewed Y Chromosome Story Two Decades Later
Authors: Primorac Dragan , Škaro Vedrana , Projić Petar , Missoni Saša , Zanki Ivana Horjan , Merkaš Sinisa , Šarac Jelena , Novokmet Natalija , Ledić Andrea , Makar Adela , Lauc Gordan , Anđelinović Šimun , Bašić Željana , Kružić Ivana , Neuberg Marijana , Smolić Martina , Smolić Robert , Hrstić Irena , Trivanović Dragan , Konjhodžić Rijad , Salihefendić Lana , Jordamović Naida Babić , Marjanović Damir 
Published: March 2022

AbstractAimTo analyze an additional set of Y-Chromosome genetic markers to acquire a more detailed insight into the diversity of the Croatian population.MethodsThe total number of 518 Yfiler™ Plus profiles were genotyped. Allele, haplotype frequencies, and haplotype diversity were calculated using the STRAF software package v2.0.4. Genetic distances were quantified byRst using AMOVA online tool from the YHRD. The evolutionary history was inferred using the neighbor-joining method of phylogenetic tree construction in MEGAX software. Whit Athey’s Haplogroup Predictor v5 was used for additional comparison with available regional and other European populations.ResultsThe total of 507 haplotypes were used for genetic STR analysis. The interpopulation study on 17 Y-STR markers shows the lowest genetic diversity between the Croatian and Bosnian-Herzegovinian populations and the highest between the Croatian and Irish populations. Additional interpopulation comparison with the original 27 Y-STR markers (for the population with available data) was also performed. A total of 518 haplotypes were used in the determination of haplogroup diversity. Haplogroup I with its sublineage I2a expressed the highest prevalence. Haplogroup R, with its major sublineage R1a, is the second most abundant in the studied Croatian population, except for the subpopulation of Hvar, where E1b1b is the second most abundant haplogroup. Rare haplogroups also confirmed in this study are L, T, and Q. G1 is detected for the very first time in the Croatian population.ConclusionNew insight into differences between examined subpopulations of Croatia and their possible (dis)similarities with neighboring abroad populations was notified.
Whole-brain modeling explains the context-dependent effects of cholinergic neuromodulation
Authors: Coronel-Oliveros Carlos , Gießing Carsten , Medel Vicente , Cofré Rodrigo , Orio Patricio 
Published: March 2022

ABSTRACTIntegration and segregation are two fundamental principles of brain organization. The brain manages the transitions and balance between different functional segregated or integrated states through neuromodulatory systems. Recently, computational and experimental studies suggest a pro-segregation effect of cholinergic neuromodulation. Here, we studied the effects of the cholinergic system on brain functional connectivity using both empirical fMRI data and computational modeling. First, we analyzed the effects of nicotine on functional connectivity and network topology in healthy subjects during resting-state conditions and during an attentional task. Then, we employed a whole-brain neural mass model interconnected using a human connectome to simulate the effects of nicotine and investigate causal mechanisms for these changes. The drug effect was modeled decreasing both the global coupling and local feedback inhibition parameters, consistent with the known cellular effects of acetylcholine. We found that nicotine incremented functional segregation in both empirical and simulated data, and the effects are context-dependent: observed during the task, but not in the resting state. In-task performance correlates with functional segregation, establishing a link between functional network topology and behavior. Furthermore, we found in the empirical data that the regional density of the nicotinic acetylcholineα4β2correlates with the decrease in functional nodal strength by nicotine during the task. Our results confirm that cholinergic neuromodulation promotes functional segregation in a context-dependent fashion, and suggest that this segregation is suited for simple visual-attentional tasks.
Decoding trans-saccadic prediction error
Authors: Barne Louise Catheryne , Giordano Jonathan , Collins Thérèse , Desantis Andrea 
Published: March 2022

AbstractWe are constantly sampling our environment by moving our eyes, but our subjective experience of the world is stable and constant. Stimulus displacement during or shortly after a saccade often goes unnoticed, a phenomenon called the saccadic suppression of displacement. Although we fail to notice such displacements, our oculomotor system computes the prediction errors and adequately adjusts the gaze and future saccadic execution, a phenomenon known as saccadic adaptation. In the present study, we aimed to find a brain signature of the trans-saccadic prediction error that informs the motor system but not explicit perception. We asked participants (either sex) to report whether a visual target was displaced during a saccade while recording electroencephalography (EEG). Using multivariate pattern analysis, we were able to differentiate displacements from no displacements, even when participants failed to report the displacement. In other words, we found that trans-saccadic prediction error is represented in the EEG signal 100 ms after the displacement presentation, mainly in occipital and parieto-occipital channels, even in the absence of explicit perception of the displacement.Significance StatementStability in vision occurs even while performing saccades. One suggested mechanism for this counterintuitive visual phenomenon is that external displacement is suppressed during the retinal remapping caused by a saccade. Here, we shed light on the mechanisms of trans-saccadic stability by showing that displacement information is not entirely suppressed and specifically present in the early stages of visual processing. Such a signal is relevant and computed for oculomotor adjustment despite being neglected for perception.
Using data science to identify unusual treatment choices in England: illustrative findings of uncommon antipsychotics Pericyazine and Promazine
Authors: MacKenna Brian , Curtis Helen J , Walker Alex J , Croker Richard , Macdonald Orla , Evans Stephen JW , Inglesby Peter , Evans Dave , Morley Jessica , Bacon Seb CJ , Goldacre Ben 
Published: March 2022

AbstractBackgroundData analysis can be used to identify signals suggestive of variation in treatment choice or clinical outcome. Analyses to date have generally focused on an hypothesis-driven approach.MethodsHere we report an innovative hypothesis-blind approach (calculating chemical-class proportions for every chemical substance prescribed in each Clinical Commissioning Group and ranking chemicals by (a) their kurtosis and (b) a ratio between inter-centile differences) applied to England’s national prescribing data, and demonstrate how this identified unusual prescribing of two antipsychotics.OutcomesWe identified that, while promazine and pericyazine are barely used by most clinicians, they make up a substantial proportion of all antipsychotic prescribing in two small geographic regions in England.InterpretationData-driven approaches can be effective at identifying unusual clinical choices. More widespread adoption of such approaches, combined with clinician and decision-maker engagement could lead to better optimised patient care.FundingNIHR Biomedical Research Centre, Oxford; Health Foundation; National Institute for Health Research (NIHR) School of Primary Care Research and Research for Patient BenefitResearch in contextEvidence before this studyIdentifying variation in clinical activity typically employs a traditional approach whereby measures are prospectively defined, and adherence then assessed in data. We are aware of no prior work using data science techniques hypothesis-blind to systematically identify outliers for any given treatment choice or clinical outcome (numerators) as a proportion of automatically generated denominators.Added value of this studyHere we report an innovative hypothesis-blind approach applied to England’s national prescribing data, to identify chemical substances with substantial prescribing patterns between organisations. As illustrative examples we show that promazine and pericyazine, while rarely used by most clinicians, made up a substantial proportion of all antipsychotic prescribing in two small geographic regions in England.Implications of all the available evidenceThe choice of antipsychotics between English regions could be further investigated using qualitative methods to explore the implications for patient care. More broadly, data-driven approaches can be effective at identifying unusual clinical choices. More widespread adoption of such approaches, combined with clinician and decision-maker engagement could lead to better optimised patient care.
Psychometric properties of upper limb kinematics during functional tasks in children and adolescents with dyskinetic cerebral palsy
Authors: Vanmechelen Inti , Bekteshi Saranda , Konings Marco , Feys Hilde , Desloovere Kaat , Aerts Jean-Marie , Monbaliu Elegast 
Published: March 2022

AbstractAimDyskinetic cerebral palsy (DCP) is characterised by involuntary movements, and the movement patterns of children with DCP have not been extensively studied during upper limb tasks. The aim of this study is to evaluate psychometric properties of upper limb kinematics in participants with DCP and typically developing (TD) participants.MethodsTwenty TD participants and 20 participants with DCP performed three functional tasks: reaching forward, reach and grasp vertical and reach sideways during three-dimensional motion analysis. Joint angles at point of task achievement (PTA) and spatio-temporal parameters were evaluated within-and between sessions using intra-class correlation coefficients (ICC) and standard error of measurement (SEM). Independent t-tests/Mann-Whitney U tests were used to compare all parameters between groups.ResultsWithin-session ICC values ranged from 0.55 to 0.99 for joint angles at PTA and spatio-temporal parameters for both groups during all tasks. Within-session SEM values ranged from 1.1° to 11.7° for TD participants and from 1.9° to 13.0° for participants with DCP. Eight within-session repetitions resulted in the smallest change in ICC and SEM values for both groups. Within-session variability was higher for participants with DCP in comparison with the TD group for the majority of the joint angles and spatio-temporal parameters. Intrinsic variability over time was small for all angles and spatio-temporal parameters, whereas extrinsic variability was higher for elbow pro/supination and scapula angles. Between-group differences revealed lower shoulder adduction and higher elbow flexion, pronation and wrist flexion, as well as higher trajectory deviation and a lower maximal velocity for participants with DCP.ConclusionThis is the first study to assess the psychometric properties of upper limb kinematics in children and adolescents with DCP, showing that children with DCP show higher variability during task execution. However, their variable movement pattern can be reliably captured within- and between-sessions, if sufficient repetitions are taken into account within one session.
Risk of SARS-CoV-2 transmission by fomites: a clinical observational study in highly infectious COVID-19 patients
Authors: Meister Toni Luise , Dreismeier Marielen , Blanco Elena Vidal , Brüggemann Yannick , Heinen Natalie , Kampf Günter , Todt Daniel , Nguyen Huu Phuc , Steinmann Jörg , Schmidt Wolfgang Ekkehard , Steinmann Eike , Quast Daniel Robert , Pfaender Stephanie 
Published: March 2022

AbstractBackgroundThe contribution of droplet-contaminated surfaces for virus transmission has been discussed controversially in the context of the current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic. Importantly, the risk of fomite-based transmission has not been systematically addressed.MethodsWe initiated this single-center observational study to evaluate whether hospitalized COVID-19 patients can contaminate stainless steel carriers by coughing or intensive moistening with saliva and to assess the risk of SARS-CoV-2 transmission upon detection of viral loads and infectious virus in cell culture. Fifteen hospitalized patients with a high baseline viral load (CT value ≤ 25) shortly after admission were included. We documented clinical and laboratory parameters and used patient samples to perform virus culture, quantitative PCR and virus sequencing.ResultsNasopharyngeal and oropharyngeal swabs of all patients were positive for viral RNA on the day of the study. Infectious SARS-CoV-2 could be isolated from 6 patient swabs (46.2 %). While after coughing, no infectious virus could be recovered, intensive moistening with saliva resulted in successful viral recovery from steel carriers of 5 patients (38.5 %).ConclusionsTransmission of infectious SARS-CoV-2 via fomites is possible upon extensive moistening, but unlikely to occur in real-life scenarios and from droplet-contaminated fomites.
Environmental chemical-wide associations with immune biomarkers in the US: A cross-sectional analysis
Authors: Middleton Lauren Y. M. , Nguyen Vy K. , Dou John , Park Sung Kyun , Colacino Justin A. , Bakulski Kelly M. 
Published: March 2022

AbstractExposure to environmental chemicals influence immune system functions, and humans are exposed to a wide range of chemicals, termed the chemical exposome. Thus, a comprehensive analysis of the effects across multiple chemical families with immune biomarkers is needed. In this study, we tested the associations between environmental chemicals and immune biomarkers. We analyzed the United States cross-sectional National Health and Nutrition Examination Survey (NHANES 1999-2018). Chemicals were measured in blood or urine (198 chemicals, 17 families). Immune biomarkers included percentages of lymphocytes, neutrophils, monocytes, basophils, and eosinophils, and counts of red blood cells, white blood cells, and mean corpuscular volume. We conducted survey-weighted, multivariable linear regressions of log2-transformed chemicals on immune measures, adjusted for age, sex, race/ethnicity, poverty-income ratio, waist circumference, cotinine concentration, creatinine for urinary chemicals, and survey cycle. We accounted for multiple comparisons using a false discovery rate (FDR). Among 45,528 adult participants, using survey weights, the mean age was 45.7 years, 51.4% were female, and 69.3% were Non-Hispanic White. There were 65 chemicals associated with white blood cell count. For example, a doubling in the concentration of blood lead was associated with a decrease of 61 white blood cells per µL (95% CI: 23–99; FDR=0.005). 122 (61.6%) chemicals were associated with at least one of the eight immune biomarkers. Chemicals in the Metals family were associated with all eight immune measures. Concentrations of a wide variety of biomarkers of exposure to chemicals such as metals and smoking-related compounds, were highly associated with immune system biomarkers, with implications for immune function and toxicology. This environmental chemical-wide association study identified chemicals from multiple families for further toxicological and epidemiological investigation.
A self-amplifying RNA vaccine against COVID-19 with long-term room-temperature stability
Authors: Voigt Emily A. , Gerhardt Alana , Hanson Derek , Battisti Peter , Reed Sierra , Singh Jasneet , Mohamath Raodoh , Jennewein Madeleine F. , Bakken Julie , Beaver Samuel , Press Christopher , Soon-Shiong Patrick , Paddon Christopher J. , Fox Christopher B. , Casper Corey 
Published: March 2022

ABSTRACTmRNA vaccines were the first to be authorized for use against SARS-CoV-2 and have since demonstrated high efficacy against serious illness and death. However, limitations in these vaccines have been recognized due to their requirement for cold storage, short durability of protection, and lack of access in low-resource regions. We have developed an easily-manufactured, potent self-amplifying RNA (saRNA) vaccine against SARS-CoV-2 that is stable at room temperature. This saRNA vaccine is formulated with a nanostructured lipid carrier (NLC), providing enhanced stability, improved manufacturability, and protection against degradation. In preclinical studies, this saRNA/NLC vaccine induced strong humoral immunity, as demonstrated by high pseudovirus neutralization titers to the Alpha, Beta, and Delta variants of concern and induction of long-lived bone marrow-resident antibody secreting cells. Robust Th1-biased T-cell responses were also observed after prime or homologous prime-boost in mice. Notably, the saRNA/NLC platform demonstrated thermostability at room temperature for at least 6 months when lyophilized. Taken together, this saRNA delivered by NLC represents a potential improvement in RNA technology that could allow wider access to RNA vaccines for the current COVID-19 and future pandemics.