bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-Term Pediatric Acclimatization to Adaptive Hearing Aid Technology
Authors: Pinkl Joseph , Cash Erin K. , Evans Tommy C. , Neijman Timothy , Hamilton Jean W. , Ferguson Sarah D. , Martinez Jasmin L. , Rumley Johanne , Hunter Lisa L. , Moore David R. , Stewart Hannah J. 
Published: September 2020

AbstractPurposeThis pilot study assessed the perceptual, cognitive and academic learning effects of an adaptive integrated directionality and noise reduction hearing aid program in pediatric users.MethodsFifteen pediatric hearing aid users (6 to 12 years old) participated in a hearing aid pilot with pre- to post-comparisons. Participants received new bilateral, individually fitted Oticon OPN hearing aids programmed with OpenSound Navigator (OSN) processing. Word recognition in noise, sentence repetition in quiet, nonword repetition, vocabulary learning, selective attention, executive function, memory, reading and mathematical abilities were measured within one week of the initial hearing aid fitting and two months post-fit. Caregivers completed questionnaires assessing their child’s listening and communication abilities prior to study enrollment and after two months of using the study hearing aids.ResultsCaregiver reporting indicated significant improvements in speech and sound perception, spatial sound awareness and the ability to participate in conversations. However, there was no positive change in performance in any of the measured skills. Mathematical scores significantly declined after two months.ConclusionsOSN provided a perceived improvement in functional benefit, compared to their previous hearing aids, as reported by caregivers. However, there was no positive change in listening skills, cognition and academic success after two months of using OSN. Findings may have been impacted by reporter bias, limited sample size and a relatively short trial period. This study took place during the summer when participants were out of school which may have influenced the decline in mathematical scores. The results support further exploration with age and audiogram-matched controls, larger sample sizes, and longer test-retest intervals that correspond to the academic school year.
Serum SARS-CoV-2 nucleocapsid antigen detection is essential for primary diagnostics of SARS-CoV-2-associated pneumonia
Authors: Lebedin Yuri S. , Lyang Olga V. , Galstyan Anaida G. , Panteleeva Anna V. , Belousov Vsevolod V. , Rebrikov Denis V. 
Published: September 2020

AbstractThe article highlights the diagnostic value of SARS-CoV-2 seroconversion in patients with pneumonia based on the results of a retrospective study conducted at the height of the COVID-19 pandemic in Moscow, Russia.
Accessioning and automation compatible anterior nares swab design
Authors: Pettit Mary E. , Boswell Sarah A. , Qian Jason , Novak Richard , Springer Michael 
Published: September 2020

ABSTRACTThe COVID-19 pandemic has resulted in an unparalleled need for viral testing capacity across the world and is a critical requirement for successful re-opening of economies. The logistical barriers to near-universal testing are considerable. We have designed an injection molded polypropylene anterior nares swab, the RHINOstick, with a screw cap integrated into the swab handle that is compatible with fully automated sample accessioning and processing. The ability to collect and release both human and viral material is comparable to that of several commonly used swabs on the market. SARS-CoV-2 is stable on dry RHINOstick swabs for at least 3 days, even at 42°C, and elution can be achieved with small volumes. The swab and barcoded tube set can be produced, sterilized, and packaged at < 2 USD per unit and can easily be adopted by large research institutes to increase throughput and dramatically reduce the cost of a standard SARS-CoV-2 detection pipeline.
Implications of Monsoon Season & UVB Radiation for COVID-19 in India Manuscript
Authors: Kalippurayil Moozhipurath Rahul , Kraft Lennart 
Published: September 2020

AbstractBackgroundIndia has recorded 66,333 deaths over 36 administrative regions placing India third in the world after the US and Brazil for COVID-19 deaths as of 2 September 2020. Studies indicate that south-west monsoon season plays a role in the dynamics of contagious diseases, which tend to peak post-monsoon season. Recent studies show that vitamin D and its primary source Ultraviolet-B radiation (UVB) may play a protective role in mitigating COVID-19 deaths. However, the combined roles of the monsoon season and UVB in COVID-19 in India are still unclear. In this observational study, we empirically study the respective roles of monsoon season and UVB, whilst further exploring, whether monsoon season negatively impacts the protective role of UVB in COVID-19 deaths in India.MethodsWe use a log-linear Mundlak model to a panel dataset of 36 administrative regions in India from 14 March 2020 - 8 August 2020 (n=4005). We use the cumulative COVID-19 deaths as the dependent variable. We isolate the association of monsoon season and UVB as measured by Ultraviolet Index (UVI) from other confounding time-constant and time-varying region-specific factors.FindingsAfter controlling for various confounding factors, we observe that the monsoon season and a unit increase in UVI are separately associated with 12.8 percentage points and 2.0 percentage points decline in growth rates of COVID-19 deaths in the long run. These associations translate into substantial relative changes. For example, the current monsoon season, that has been going on for two weeks, is associated with a reduction in growth rates of COVID-19 deaths of 59%, whereas a permanent unit increase of UVI is associated with a reduction in growth rates of COVID-19 deaths of 37%. However, the current monsoon season, also reduces the protective role of UVI by 16.3% [0.33 percentage points], plausibly due to lower UVB exposure.InterpretationWe find independent protective roles of both the monsoon season and UVI in mitigating COVID-19 deaths. Furthermore, we find evidence that monsoon season is associated with a significant reduction in the protective role of UVI. The protective role of monsoon season is plausibly due to limited outdoor activities of people. Our study outlines the role of the monsoon season and UVB in COVID-19 in India and supports health-related policy decision making in India.
Clinical manifestations along with biochemical and psychological outcomes of COVID-19 cases in diabetic individuals in Bangladesh
Authors: Akter Farhana , Mannan Adnan , Mehedi H. M. Hamidullah , Rob Abdur , Ahmed Shakeel , Salauddin Asma , Hossain Md. Shakhawat , Hasan Md Mahbub 
Published: September 2020

AbstractBackground and aimsThis study investigated the clinical manifestations, outcomes and long-term complications of COVID-19 inpatients in Bangladesh while emphasizing on individuals having diabetes.MethodsA cross-sectional study was conducted for a sample of COVID-19 inpatients across four different hospitals of Bangladesh between April 1st and June 30, 2020. Variation in clinical characteristics, contact history, comorbidities, treatment pattern, and long-term complications were investigated.ResultsThere were 734 COVID-19 presentations in this study of which 19.8% of patients had diabetes. 76% were male and 85% of the patients had been administered with all vaccine doses during childhood. The most frequently occurring blood groups among patients with diabetes were B (+) ve (35%) and O (+) ve (31%). Among biochemical parameters, glucose, D-dimer, C-reactive protein (CRP) and Troponin levels were significantly elevated amidst the cohort with diabetes. The frequency of insulin dependent individuals increased three-fold during COVID-19. A number of COVID-19 patients with diabetes have been suffering from long term complications post recovery including pain, discomfort, memory loss and sleep disturbance.ConclusionIndividuals with diabetes have experienced severe manifestation of COVID-19 and post disease complications. Further in-depth studies focused on larger sample sizes are entailed to assess the relationships elaborately.
NeuroPM toolbox: integrating Molecular, Neuroimaging and Clinical data for Characterizing Neuropathological Progression and Individual Therapeutic Needs
Authors: Iturria-Medina Yasser , Carbonell Félix , Assadi Atousa , Adewale Quadri , Khan Ahmed F. , Baumeister Robert , Sanchez-Rodriguez Lazaro ,   for the Alzheimer’s Neuroimaging Initiative
Published: September 2020

AbstractThere is a critical need for a better multiscale and multifactorial understanding of neurological disorders, covering from genes to neuroimaging to clinical factors and treatments effects. Here we present NeuroPM-box, a cross-platform, user-friendly and open-access software for characterizing multiscale and multifactorial brain pathological mechanisms and identifying individual therapeutic needs. The implemented methods have been extensively tested and validated in the neurodegenerative context, but there is not restriction in the kind of disorders that can be analyzed. By using advanced analytic modeling of molecular, neuroimaging and/or cognitive/behavioral data, this framework allows multiple applications, including characterization of: (i) the series of sequential states (e.g. transcriptomic, imaging or clinical alterations) covering decades of disease progression, (ii) intra-brain spreading of pathological factors (e.g. amyloid and tau misfolded proteins), (iii) synergistic interactions between multiple brain biological factors (e.g. direct tau effects on vascular and structural properties), and (iv) biologically-defined patients stratification based on therapeutic needs (i.e. optimum treatments for each patient). All models’ outputs are biologically interpretable. A 4D-viewer allows visualization of spatiotemporal brain (dis)organization. Originally implemented in MATLAB, NeuroPM-box is compiled as standalone application for Windows, Linux and Mac environments: neuropm-lab.com/software. In a “regular” workstation, it can analyze over 150 subjects per day, reducing the need for using clusters or High-Performance Computing (HPC) for large-scale datasets. This open-access tool for academic researchers may significantly contribute to a better understanding of complex brain processes and to accelerating the implementation of Precision Medicine (PM) in neurology.
Outcomes associated with SARS-CoV-2 viral clades in COVID-19
Authors: Nakamichi Kenji , Shen Jolie Z. , Lee Cecilia S. , Lee Aaron , Roberts Emma A. , Simonson Paul D. , Roychoudhury Pavitra , Andriesen Jessica , Randhawa April K. , Mathias Patrick C. , Greninger Alex L. , Jerome Keith R. , Van Gelder Russell N. 
Published: September 2020

AbstractBackgroundThe COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system.MethodsWhole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline medical data along with outcomes of hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death.FindingsFull length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction.ConclusionSARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.FundingSupported by NIH P30EY001730, the Mark J. Daily, MD Research Fund (RVG), the Alida and Christopher Latham Research Fund (RVG, AYL, CSL), NIH K23EY029246 (AYL), US Food and Drug Administration (QYL)
Psychological preparedness for pandemic (COVID-19) management: Perceptions of nurses and nursing students in India
Authors: Gandhi Sailaxmi , Sahu Maya , Radhakrishnan G , Nattala Prasanthi , Sudhir Paulomi M. , Balachandran Rathi 
Published: September 2020

AbstractIntroductionThe growing COVID-19 pandemic has posed a great threat to millions of people worldwide. Nurses and nursing students are an important group of health professionals who are most likely to face many challenges in this unprecedented scenario. The present study aimed at exploring the perception of nurses and nursing students regarding psychological preparedness for the pandemic (COVID-19) management.Materials & MethodsThe study employed a quantitative cross-sectional online survey research design. Purposive sampling was used with an attempt to represent the entire nurses (i.e. nursing officers, nurse administrators and nursing teachers) and nursing students group of India. The survey link was shared to their email ID and they were invited to participate in the study. Data were collected using Psychological Preparedness for Disaster Threat Scale (PPDTS)-Modified, General Self Efficacy (GSE) Scale, Optimism Scale and Brief Resilient Coping Scale (BRS). Totally 685 responses were received and 676 forms were completed which were analyzed using SPSS software (version 24).ResultsThe mean age of the subjects was 31.72 (SD=9.58) years. Around 20% of the subjects previously had some kind of psychological training and 4% of the subjects had taken care of persons with COVID-19. Findings revealed that mean score for PPDTS, GSE, BRCS and Optimism was 73.44 (SD=10.82, 33.19 (SD=5.23), 16.79 (SD=2.73) and 9.61 (SD=2.26) respectively indicating that the subjects had moderate level of psychological preparedness, self-efficacy and resilience but higher level of optimism. Psychological preparedness, self-efficacy, optimism and resilience were positively correlated to each other. Self-efficacy, optimism, and resilience emerged as predictors of psychological preparedness.ConclusionThe findings suggested that self-efficacy, optimism and resilience can be considered as predictors for psychological preparedness in pandemic management. Appropriate training could influence self-efficacy while programs addressing resilience and coping may strengthen psychological preparedness which can help in further management of ongoing pandemic.
Reproductive Maternal and Newborn Health providers assessment of facility preparedness and its Determinants during the COVID-19 pandemic in Lagos, Nigeria
Authors: Charles Ameh , Aduragbemi Banke-Thomas , Mobolanle Balogun , Chigozie Makwe Christian , Bukola Afolabi Bosede 
Published: September 2020

AbstractThe global COVID-19 pandemic is predicted to compromise the achievement of global reproductive, maternal and newborn health (RMNH) targets. The objective of this study was to determine the health facility (HF) preparedness for RMNH service delivery during the outbreak from the perspective of RMNH providers and to determine what factors significantly predict this. An anonymous cross-sectional online survey of RMNH providers was conducted from 1st to 21st July 2020 in Lagos state Nigeria. We conducted a descriptive and ordinal regression analysis, with RMNH worker perception of HF preparedness for RMNH service delivery during the outbreak as the dependent variable.Two hundred and fifty-six RMNH workers participated, 35.2% reported that RMNH services were unavailable at some time since March 2020, 39% felt moderate or extreme work-related burnout, 84% were moderately or extremely concerned about the availability of PPE and related guidelines, and only 11.7% were extremely satisfied with the preparedness of their HFs. Our final model was a statistically significant predictor of RMNH worker perception of HF preparedness explaining 54.7% of the variation in the outcome variable. A one-unit increase in the level of satisfaction with the communication from HF management and level of concern about the availability of PPE and COVID-19 guidelines would increase the odds of observing a higher category of satisfaction with HF COVID-19 preparedness (OR 0.79-2.92, p<0.001 and 0.02-0.15 p<0.001 respectively).Adequate support of RMNH providers particularly provision of PPE and guidelines, appropriate communications about COVID- 19 should be prioritised as part of health system preparedness.
NMJ-Analyser: high-throughput morphological screening of neuromuscular junctions identifies subtle changes in mouse neuromuscular disease models
Authors: Maza Alan Mejia , Jarvis Seth , Lee Weaverly Colleen , Cunningham Thomas J. , Schiavo Giampietro , Secrier Maria , Fratta Pietro , Sleigh James N. , Sudre Carole H. , Fisher Elizabeth M.C. 
Published: September 2020

AbstractThe neuromuscular junction (NMJ) is the peripheral synapse formed between a motor neuron axon terminal and a muscle fibre. NMJs are thought to be the primary site of peripheral pathology in many neuromuscular diseases, but innervation/denervation status is often assessed qualitatively with poor systematic criteria across studies, and separately from 3D morphological structure. Here, we describe the development of ‘NMJ-Analyser’, to comprehensively screen the morphology of NMJs and their corresponding innervation status automatically. NMJ-Analyser generates 29 biologically relevant features to quantitatively define healthy and aberrant neuromuscular synapses and applies machine learning to diagnose NMJ degeneration. We validated this framework in longitudinal analyses of wildtype mice, as well as in four different neuromuscular disease models: three for amyotrophic lateral sclerosis (ALS) and one for peripheral neuropathy. We showed that structural changes at the NMJ initially occur in the nerve terminal of mutant TDP43 and FUS ALS models. Using a machine learning algorithm, healthy and aberrant neuromuscular synapses are identified with 95% accuracy, with 88% sensitivity and 97% specificity. Our results validate NMJ-Analyser as a robust platform for systematic and structural screening of NMJs, and pave the way for transferrable, and cross-comparison and high-throughput studies in neuromuscular diseases.
Pentapeptide repeat proteins QnrB1 and AlbG require ATP hydrolysis to rejuvenate poisoned gyrase complexes
Authors: Mazurek Łukasz , Ghilarov Dmitry , Michalczyk Elizabeth , Pakosz Zuzanna , Czyszczoń Wojciech , Wawro Karolina , Behroz Iraj , Süssmuth Roderich D. , Heddle Jonathan G. 
Published: September 2020

ABSTRACTDNA gyrase, a type II topoisomerase found predominantly in bacteria, is the target for a variety of “poisons”, namely natural product toxins (e.g. albicidin. microcin B17) and clinically important synthetic molecules (e.g. fluoroquinolones). Resistance to both groups can be mediated by pentapeptide repeat proteins (PRPs). Despite long-term studies, the mechanism of action of these protective PRPs is not known. We compared activities of two such proteins, QnrB1 and AlbGin vitro. Each of them provided specific protection against its cognate toxin (fluoroquinolone or albicidin), which strictly required ATP hydrolysis by gyrase. Through a combination of fluorescence anisotropy, pull-downs and photocrosslinking we show that QnrB1 binds to the GyrB protein. We further probed the QnrB1 binding site using site-specific incorporation of a photoreactive amino acid and mapped strong and specific crosslinks to the N-terminal ATPase/transducer domain. We propose a model in which protective PRPs bind to the enzyme as T-segment DNA mimics to promote dissociation of the bound poison molecule.
Systematic analysis of key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria
Authors: Gorrie Claire L , Da Silva Anders Goncalves , Ingle Danielle J , Higgs Charlie , Seemann Torsten , Stinear Timothy P , Williamson Deborah A , Kwong Jason C , Grayson M Lindsay , Sherry Norelle L , Howden Benjamin P 
Published: September 2020

ABSTRACTBackgroundPairwise single nucleotide polymorphisms (SNPs) are a cornerstone for genomic approaches to multidrug-resistant organisms (MDROs) transmission inference in hospitals. However, the impact of key analysis parameters on these inferences has not been systematically analysed.MethodsWe conducted a multi-hospital 15-month prospective study, sequencing 1537 MDRO genomes for comparison; methicillin-resistantStaphylococcus aureus, vancomycin-resistantEnterococcus faecium, and extended-spectrum beta-lactamase-producingEscherichia coliandKlebsiella pneumoniae. We systematically assessed the impact of sample and reference genome diversity, masking of prophage and regions of recombination, cumulative genome analysis compared to a three-month sliding-window, and the comparative effects each of these had when applying a SNP threshold for inferring likely transmission (≤15 SNPs forS. aureus, ≤25 for other species).FindingsAcross the species, using a reference genome of the same sequence type provided a greater degree of pairwise SNP resolution, compared to species and outgroup-reference alignments that typically resulted in inflated SNP distances and the possibility of missed transmission events. Omitting prophage regions had minimal impacts, however, omitting recombination regions a highly variable effect, often inflating the number of closely related pairs. Estimating pairwise SNP distances was more consistent using a sliding-window than a cumulative approach.InterpretationThe use of a closely-related reference genome, without masking of prophage or recombination regions, and a sliding-window for isolate inclusion is best for accurate and consistent MDRO transmission inference. The increased stability and resolution provided by these approaches means SNP thresholds for putative transmission inference can be more reliably applied among diverse MDROs.FundingThis work was supported by the Melbourne Genomics Health Alliance (funded by the State Government of Victoria, Department of Health and Human Services, and the ten member organizations); an National Health and Medical Research Council (Australia) Partnership grant (GNT1149991) and individual grants from National Health and Medical Research Council (Australia) to NLS (GNT1093468), JCK (GNT1008549) and BPH (GNT1105905).