bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Desire to Avoid Pregnancy Scale: clinical considerations and comparison with other questions about pregnancy preferences
Authors: Hall Jennifer A , Barrett Geraldine , Stephenson Judith , Edelman Natalie , Rocca Corinne H 
Published: November 2022

ABSTRACTBackgroundClinicians and people of reproductive age would benefit from a reliable way to identify who is, or is not, likely to become pregnant in the next year, to direct health advice. The 14-item Desire to Avoid Pregnancy (DAP) Scale is predictive of pregnancy; this paper compares it with other ways of assessing pregnancy preferences to shortlist options for clinical implementation.MethodsA cohort of 994 UK women of reproductive age completed the DAP and other questions about pregnancy preferences, including the Attitude towards Potential Pregnancy Scale (APPS), at baseline, and reported on pregnancies quarterly for a year. For each question, DAP item, and combinations of DAP items, we examined the predictive ability, sensitivity, specificity, area under the receiver operating curve (AUROC), and positive and negative predictive values.ResultsThe AUROCs and predictive ability of the APPS and DAP single items were weaker than the full DAP, though all except one had acceptable AUROCs (>0.7). The most predictive individual DAP item was ‘It would be a good thing for me if I became pregnant in the next three months’, where women who strongly agreed had a 66.7% chance of pregnancy within 12months and the AUROC was acceptable (0.77).ConclusionWe recommend exploring the acceptability to women and healthcare professionals of asking a single DAP item (‘I wouldn’t mind if I became pregnant in the next three months’), possibly in combination with additional DAP items. This will help to guide the provision of information and services to support reproductive preferences.Key messagesClinicians do not currently have a valid and reliable way of asking people about their pregnancy preferences.A single item from the Desire to Avoid Pregnancy Scale is effective at identifying who is likely to become pregnant in the next year; other questions, including the APPS, are less discriminative but may be more acceptable.The acceptability to women and health professionals of different ways of asking people about their pregnancy preferences in health care settings should be explored.
Genomic Characterization of Dengue Virus Outbreak in 2022 from Pakistan
Authors: Umair Massab , Rehman Zaira , Haider Syed Adnan , Ali Qasim , Jamal Zunera , Ammar Muhammad , Hakim Rabia , Bibi Shaheen , Sagheer Rida , Salman Muhammad , Ikram Aamer 
Published: November 2022

AbstractPakistan, a dengue endemic country has encountered several outbreaks during the past decade. The current study aimed to explore the serotype and genomic diversity of dengue virus responsible for the 2022 outbreak in Pakistan. During August-October 2022, blood samples (n=436) were collected from dengue patients, among which 64.4% (n=281) were positive based on RT-PCR. A subset of DENV-2 and DENV-1 samples were further subjected to whole-genome sequencing. In terms of gender and age, dengue infection was more prevalent in male patients (62.9%) with more adults (77.5%) being infected. Moreover, serotyping revealed DENV-2 to be most predominant serotype (64%; n=180), followed by DENV-1 (35.2%; n=99) and DENV-3 (0.35%; n=1). Phylogenetic analysis of sequenced samples indicates that all the samples (n=8) belong to the DENV-2 Cosmopolitan genotype, falling within a single monophyletic clade that is closely related to sequences from China and Singapore in 2018. Dengue virus dynamics reported in the current study warrants large scale genomic surveillance in order to better respond to future outbreaks.
Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses
Authors: Spatola Marianna , Nziza Nadège , Jung Wonyeong , Deng Yixiang , Yuan Dansu , Dinoto Alessandro , Bozzetti Silvia , Chiodega Vanessa , Ferrari Sergio , Lauffenburger Douglas A , Mariotto Sara , Alter Galit 
Published: November 2022

ABSTRACTCoronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health emergency. Although SARS-CoV-2 is primarily a respiratory pathogen, extra-respiratory organs, including the central nervous system (CNS), can also be affected. Neurologic symptoms have been observed not only during acute SARS-CoV-2 infection, but also at distance from respiratory disease, also known as long-COVID or neurological post-acute sequelae of COVID-19 (neuroPASC). The pathogenesis of neuroPASC is not well understood, but hypotheses include SARS-CoV-2-induced immune dysfunctions, hormonal dysregulations, and persistence of SARS-CoV-2 reservoirs. In this study, we used a high throughput systems serology approach to dissect the humoral response to SARS-CoV-2 (and other common Coronaviruses - 229E, HKU1, NL63, OC43) in the serum and cerebrospinal fluid (CSF) from 112 infected individuals who developed or did not develop neuroPASC. Unique SARS-CoV-2 humoral profiles were observed in the CSF of neuroPASC. All antibody isotypes (IgA, IgM, IgA) and subclasses (IgA1-2; IgG1-4) were detected in serum, whereas CSF was characterized by focused IgG1 (and absence of IgM). These data argue in favor of compartmentalized brain-specific responses against SARS-CoV-2 through selective transfer of antibodies from the serum to the CSF across the blood-brain-barrier, rather than intrathecal synthesis, where more diversity in antibody classes/subclasses would be expected. Moreover, compared to individuals who did not develop post-acute neurological complications following infection (n=94), those with neuroPASC (n=18) exhibited attenuated systemic antibody responses against SARS-CoV-2, characterized by decreased capacity to activate antibody-dependent complement deposition (ADCD), NK cell activation (ADNKA) and to bind Fcγ receptors. However, surprisingly, neuroPASC showed significantly expanded antibody responses to other common Coronaviruses, including 229E, HKU1, NL63, and OC43. This biased humoral activation across coronaviruses was particularly enriched in neuroPASC individuals with poor outcome, suggesting anoriginal antigenic sin(or immunologic imprinting), where pre-existing immune responses against related viruses shape the response to current infection, as a key prognostic marker of neuroPASC disease. Overall, these findings point to a pathogenic role for compromised anti-SARS-CoV-2 responses in the CSF, likely resulting in incomplete virus clearance from the brain and persistent neuroinflammation, in the development of post-acute neurologic complications of SARS-CoV-2 infection.
Mapping the electrophysiological structure of dystonic Globus Pallidus pars interna through intraoperative microelectrode recordings
Authors: Kaymak Ahmet , Vissani Matteo , Rinaldo Sara , Eleopra Roberto , Romito Luigi , Mazzoni Alberto 
Published: November 2022

AbstractObjectiveThe Globus Pallidus pars interna (GPi) is one of the main targets for Deep Brain Stimulation (DBS) therapies for dystonia and other movement disorders. Still, a complete picture of the spiking dynamics of the nucleus is far from being achieved. Microelectrode recordings (MER) provide a unique brain window opportunity to shed light on GPi organization, which might support intraoperative DBS target localization, as previously done for the Subthalamic nucleus (STN).ApproachHere we propose a novel procedure to analyze explorative MERs from DBS implants in dystonic patients. The procedure identifies the neural activity markers discriminating neurons in the GPi from those in the neighbouring structures, as well as the markers discriminating neurons located in different regions within the GPi.Main resultsThe identification of the borders of the GPi based on neural markers was a difficult task, due to internal inhomogeneities in GPi firing dynamics. However, the procedure was able to exploit these inhomogeneities to characterize the internal electrophysiological structure of the GPi. In particular, we found a reliable dorsolateral gradient in firing activity and regularity.SignificanceOverall, we characterized the spatial distribution of neural activity markers in the dystonic GPi, paving the way for the use of these markers for DBS target localization. The procedure we developed to achieve this result could be easily extended to MER performed for other disorders and in other areas.
Assessing the accuracy of California county level COVID-19 hospitalization forecasts to inform public policy decision making
Authors: White Lauren A. , McCorvie Ryan , Crow David , Jain Seema , León Tomás M. 
Published: November 2022

AbstractBackgroundThe COVID-19 pandemic has highlighted the role of infectious disease forecasting in informing public policy. However, significant barriers remain for effectively linking infectious disease forecasts to public health decision making, including a lack of model validation. Forecasting model performance and accuracy should be evaluated retrospectively to understand under which conditions models were reliable and could be improved in the future.MethodsUsing archived forecasts from the California Department of Public Health’s California COVID Assessment Tool(https://calcat.covid19.ca.gov/cacovidmodels/), we compared how well different forecasting models predicted COVID-19 hospitalization census across California counties and regions during periods of Alpha, Delta, and Omicron variant predominance.ResultsBased on mean absolute error estimates, forecasting models had variable performance across counties and through time. When accounting for model availability across counties and dates, some individual models performed consistently better than the ensemble model, but model rankings still differed across counties. Local transmission trends, variant prevalence, and county population size were informative predictors for determining which model performed best for a given county based on a random forest classification analysis. Overall, the ensemble model performed worse in less populous counties, in part because of fewer model contributors in these locations.ConclusionsEnsemble model predictions could be improved by incorporating geographic heterogeneity in model coverage and performance. Consistency in model reporting and improved model validation can strengthen the role of infectious disease forecasting in real-time public health decision making.
Physical inactivity among corporate bank workers in Accra, Ghana: Implications for health promotion
Authors: Nketiah George B. , Odoi-Agyarko Kwasi , Ndanu Tom A , Hayford Frank E. A. , Amoh Gordon , Lawson Henry J. 
Published: November 2022

AbstractIntroductionIt is common knowledge that any activity that results in caloric expenditure has the potential to prevent cardiovascular diseases, nonetheless, most people are physically inactive, especially office workers. This study sort to evaluate at baseline, the extent of physical inactivity and its determinants among staff of selected banks in Accra, Ghana.MethodsThis was a cross-sectional study involving 219 banking staff randomly selected from five commercial banking institutions in Accra, Ghana. Demographic data was collected with a structured questionnaire. Physical inactivity was assessed using the Global Physical Activity Questionnaire. Study associations were determined using univariate analysis, and multivariate logistic regression models with adjusted odds ratio (AOR) and 95% confidence intervals (CI) estimated.ResultsOf the 219 participants studied, the male to female ratio was 1.3:1.0 and the mean age (± SD) was 40.0±7.9 years. Overall, 165 (75.3%) of the study participants indulged in some form of physical activity, however, only 40 (18.3%) achieved the recommended levels. Physical inactivity was observed in 179 (81.7%) participants. The following were independently associated with physical inactivity: travel-related activities (AOR, 0.151; 95% CI, 0.059-0.384; p<0.001); working in the bank for 6-10 years (AOR, 4.617; 95% CI, 1.590-13.405; p=0.005); and working in the bank for 11 years and above (AOR, 2.816; 95% CI, 1.076-7.368; p=0.035).ConclusionPhysical inactivity was very high among bankers. Travel-related activities and working at the bank for more than six years were associated with physical inactivity. Thus, promoting regular physical activity, frequent monitoring, and implementation of other appropriate healthy lifestyle intervention strategies are vital to reduce risk of early onset disease conditions associated with physical inactivity in this population.
The interface between SARS-CoV-2 and non-communicable diseases (NCDs) in a high HIV/TB burden district level hospital setting, Cape Town, South Africa
Authors: Mnguni Ayanda Trevor , Schietekat Denzil , Ebrahim Nabilah , Sonday Nawhaal , Boliter Nicholas , Schrueder Neshaad , Gabriels Shiraaz , Cois Annibale , Tamuzi Jacques L. , Tembo Yamanya , Davies Mary-Ann , English Rene , Nyasulu Peter S. ,   the COVID-19 Research Response Collaboration.
Published: November 2022

AbstractBackgroundCOVID-19 experiences on noncommunicable diseases (NCDs) from district-level hospital settings during waves I and II are scarcely documented. The aim of this study is to investigate the NCDs associated with COVID-19 severity and mortality in a district-level hospital with a high HIV/TB burden.MethodsThis was a retrospective observational study that compared COVID-19 waves I and II at Khayelitsha District Hospital in Cape Town, South Africa. COVID-19 adult patients with a confirmed SARS-CoV-2 polymerase chain reaction (PCR) or positive antigen test were included. In order to compare the inter wave period, clinical and laboratory parameters on hospital admission of noncommunicable diseases, the Student t-test or Mann-Whitney U for continuous data and the X2 test or Fishers’ Exact test for categorical data were used. The role of the NCD subpopulation on COVID-19 mortality was determined using latent class analysis (LCA).FindingsAmong 560 patients admitted with COVID-19, patients admitted during wave II were significantly older than those admitted during wave I. The most prevalent comorbidity patterns were hypertension (87%), diabetes mellitus (65%), HIV/AIDS (30%), obesity (19%), Chronic Kidney Disease (CKD) (13%), Congestive Cardiac Failure (CCF) (8.8%), Chronic Obstructive Pulmonary Disease (COPD) (3%), cerebrovascular accidents (CVA)/stroke (3%), with similar prevalence in both waves except HIV status [(23% vs 34% waves II and I, respectively), p = 0.022], obesity [(52% vs 2.5%, waves II and I, respectively), p <0.001], previous stroke [(1% vs 4.1%, waves II and I, respectively), p = 0.046]. In terms of clinical and laboratory findings, our study found that wave I patients had higher haemoglobin and HIV viral loads. Wave II, on the other hand, had statistically significant higher chest radiography abnormalities, fraction of inspired oxygen (FiO2), and uraemia. The adjusted odds ratio for death vs discharge between waves I and II was similar (0.94, 95%CI: 0.84-1.05). Wave I had a longer average survival time (8.0 vs 6.1 days) and a shorter average length of stay among patients discharged alive (9.2 vs 10.7 days). LCA revealed that the cardiovascular phenotype had the highest mortality, followed by diabetes and CKD phenotypes. Only Diabetes and hypertension phenotypes had the lowest mortality.ConclusionEven though clinical and laboratory characteristics differed significantly between the two waves, mortality remained constant. According to LCA, the cardiovascular, diabetes, and CKD phenotypes had the highest death probability.
An image cryptography method in highly error-prone DNA storage channel
Authors: Zan Xiangzhen , Xie Ranze , Chu Ling , Su Yanqing , Yao Xiangyu , Xu Peng , Liu Wenbin 
Published: November 2022

AbstractRapid development in synthetic technologies has boosted DNA as a potential medium for large-scale data storage. Meanwhile, how to implement data security in DNA storage system is still an unsolved problem. In this paper, we propose an image encryption method based on the modulation-based storage architecture. The key idea is to take advantage of the unpredictable modulation signals to encrypt image in highly error-prone DNA storage channel. Numerical results demonstrate that our image encryption method is feasible and effective with excellent security against various attacks (statistical, differential, noise and data loss, etc.). Compared with other methods by DNA molecules hybridization reaction, the proposed method is more reliable and feasible for large-scale applications.
Demographic Reporting and Phenotypic Exclusion in fNIRS
Authors: Kwasa Jasmine , Peterson Hannah M , Jones Lietsel , Karrobi Kavon , Parker Termara , Nickerson Nia , Wood Sossena 
Published: November 2022

1.ABSTRACTFunctional near-infrared spectroscopy (fNIRS) promises to be a leading non-invasive neuroimaging method due to its portability and low cost. However, concerns are rising over its inclusivity of all skin tones and hair types (Parker and Ricard 2022, Webb et al 2022). Functional NIRS relies on direct contact of light-emitting optodes to the scalp, which can be blocked more by longer, darker, and especially curlier hair. Additionally, NIR light can be attenuated by melanin, which is accounted for in neither fNIRS hardware nor analysis methods. Recent work has shown that overlooking these considerations in other modalities like EEG leads to the disproportionate exclusion of individuals with these phenotypes – especially Black people – in both clinical and research literature (Bradford et al 2022, Choy 2020). In this article, we sought to determine if (1) biomedical optics developers and researchers report fNIRS performance variability between skin tones and hair textures, (2a) fNIRS neuroscience practitioners report phenotypic and demographic details in their articles, and thus, (2b) is a similar pattern of participant exclusion found in EEG also present in the fNIRS literature. We present a literature review of top Biomedical Optics and Human Neuroscience journals, showing that demographic and phenotypic reporting is unpopular in both fNIRS development and neuroscience applications. We conclude with a list of recommendations to the fNIRS community including examples of Black researchers addressing these issues head-on, inclusive best practices for fNIRS researchers, and recommendations to funding and regulatory bodies to achieve an inclusive neuroscience enterprise in fNIRS and beyond.
Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight
Authors: Zhou Mingqi , Riva Alberto , Gauthier Marie-Pierre L. , Kladde Michael P. , Ferl Robert J. , Paul Anna-Lisa 
Published: November 2022

AbstractThe Advanced Plant Experiment-04 - Epigenetic Expression (APEX04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines ofArabidopsis thaliana, wild-type Col-0 and the mutantelp2-5,which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to examine specific space- altered methylation at single molecule resolution to associate specific changes over large regions of spaceflight related genes. Therefore flap-enabled next-generation capture (FENGC), a novel targeted multiplexed DNA capture and enrichment technique allowing cleavage at any specified sites, was applied to survey spaceflight-altered DNA methylation at the single-molecule level. The FENGC capture panel contained 108 targets ranging from 509 to 704 nt within the promoter or gene body regions of gene targets derived from spaceflight whole-genome data sets. In addition to genes with significant changes in expression and average methylation levels between spaceflight and ground control, targets without differentially methylated WGBS but with space- altered distributions of the proportion of methylated cytosines per molecule were further identified. Moreover, trends of co-methylation of different cytosine contexts were exhibited in the same DNA molecules. We further identified significant DNA methylation changes in three previously biological process-unknown genes, and two of them showed enhanced root growth rate in loss-of-function mutants (named asELP2- regulated Methylation in Orbit 1and2). FENGC makes multiplexed targeted single- molecule profiling of methylation simple and cost-effective, which provides an additional power to population-based data for methylation analysis and identification of epigenetically modified substrates in plants. This case study has revealed regional spaceflight-altered methylation in selected targets, which were not identified by short- read methods in spaceflight plants. The newly identifiedEMO1andEMO2are root growth regulators, which can be epigenetically involved in plant adaptation to spaceflight.
The structural, dynamical and biochemical characterizations ofVerticillium dahliaepectate lyase, VdPelB, highlight its specificities
Authors: Safran Josip , Ung Vanessa , Bouckaert Julie , Habrylo Olivier , Molinié Roland , Fontaine Jean-Xavier , Lemaire Adrien , Voxeur Aline , Pilard Serge , Pau-Roblot Corinne , Mercadante Davide , Pelloux Jérôme , Sénéchal Fabien 
Published: November 2022

AbstractPectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by β-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB fromVerticillium dahliae, a plant pathogen. We first solved the crystal structure of VdPelB at 1.2Å resolution showing that it is a right-handed parallel β-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. VdPelB was most active on non-methylesterified pectins, at pH 8 in presence of Ca2+ions. VdPelB-G125R mutant was most active at pH 9 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released fromVerticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.