bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental impact of Personal Protective Equipment supplied to health and social care services in England in the first six months of the COVID-19 pandemic
Authors: Rizan Chantelle , Reed Malcolm , Bhutta Mahmood F 
Published: September 2020

ABSTRACTObjectivesUse of Personal Protective Equipment (PPE) has been central to controlling spread of SARS-CoV2. This study aims to quantify the environmental impact of this, and to model strategies for its reduction.MethodsLife cycle assessment was used to determine environmental impacts of PPE supplied to health and social care in England during the first six months of the COVID-19 pandemic. The base scenario assumed all products were single-use, air freighted, and disposed via clinical waste. Scenario modelling was used to determine the effect of 1) switching mode of, or eliminating, international travel during supply, 2) reducing glove use 3) using reusable alternatives, 4) maximal recycling.ResultsThe carbon footprint of PPE supplied during the study period totalled 158,838 tonnes CO2e, with greatest contributions from gloves, aprons, face shields, and Type IIR surgical masks. The estimated damage to human health was 314 DALYs (disability adjusted life years), impact on ecosystems was 0.67 species.year (loss of local species per year), and impact on resource depletion costing US $ 20.4 million.Scenario modelling indicated one-third of the carbon footprint could be avoided through switching to shipping, and by 41% through manufacturing PPE in the UK. The carbon footprint was reduced by 83% compared with the base scenario through a combination of UK manufacturing, reducing glove use, using reusable gowns and reuse of face shields, and maximal recycling, estimated to save 259 DALYS, 0.54 species.year, and US $ 15 million due to resource depletion.ConclusionsThe environmental impact of PPE could be reduced through shipping supplies or domestic manufacture, rationalising glove use, using reusables where possible, and optimising waste management.SUMMARY BOXWhat is already known on this topicThe current COVID-19 pandemic has seen a massive global increase in the use and manufacture of PPE which has contributed, with other measures, to the reduction in transmission of the virus in many countries.What this study addsThe carbon footprint of PPE supplied to health and social care in England in the first six months of the COVD-19 pandemic was 158,848 tonnes CO2e, equivalent to around 65,500 return flights from London to New York.The environmental impact of PPE could be reduced through shipping supplies or domestic manufacture, rationalising glove use, using reusables where possible, and optimising waste processing.
Multivariate GWAS elucidates the genetic architecture of alcohol consumption and misuse, corrects biases, and reveals novel associations with disease
Authors: Mallard Travis T , Savage Jeanne E , Johnson Emma C , Huang Yuye , Edwards Alexis C , Hottenga Jouke J , Grotzinger Andrew D , Gustavson Daniel E , Jennings Mariela V , Anokhin Andrey , Dick Danielle M , Edenberg Howard J , Kramer John R , Lai Dongbing , Meyers Jacquelyn L , Pandey Ashwini K , Harden Kathryn Paige , Nivard Michel G , de Geus Eco JC , Boomsma Dorret I , Agrawal Arpana , Davis Lea K , Clarke Toni-Kim , Palmer Abraham A , Sanchez-Roige Sandra 
Published: September 2020

ABSTRACTGenome-wide association studies (GWASs) of the Alcohol Use Disorder Identification Test (AUDIT), a ten-item screener for alcohol use disorder (AUD), have elucidated novel loci for alcohol consumption and misuse. However, these studies also revealed that GWASs can be influenced by numerous biases (e.g., measurement error, selection bias), which have led to inconsistent genetic correlations between alcohol involvement and AUD, as well as paradoxically negative genetic correlations between alcohol involvement and psychiatric disorders/medical conditions. To explore these unexpected differences in genetic correlations, we conducted the first item-level and largest GWAS of AUDIT items (N=160,824), and applied a multivariate framework to mitigate previous biases. In doing so, we identified novel patterns of similarity (and dissimilarity) among the AUDIT items, and found evidence of a correlated two-factor structure at the genetic level (Consumption and Problems, rg=.80). Moreover, by applying empirically-derived weights to each of the AUDIT items, we constructed an aggregate measure of alcohol consumption that is strongly associated with alcohol dependence (rg=.67) and several other psychiatric disorders, and no longer positively associated with health and positive socioeconomic outcomes. Lastly, by performing polygenic analyses in three independent cohorts that differed in their ascertainment and prevalence of AUD, we identified novel genetic associations between alcohol consumption, alcohol misuse, and human health. Our work further emphasizes the value of AUDIT for both clinical and genetic studies of AUD, and the importance of using multivariate methods to study genetic associations that are more closely related to AUD.
Insufficient Eye Tracking Data Leads to Errors in Evaluating Typical and Atypical Fixation Preferences
Authors: Reimann Gabrielle E. , Walsh Catherine , Csumitta Kelsey D. , McClure Patrick , Pereira Francisco , Martin Alex , Ramot Michal 
Published: September 2020

AbstractEye tracking provides insights into social processing and its deficits in disorders such as autism spectrum disorder (ASD), especially in conjunction with dynamic, naturalistic stimuli. However, reliance on manual stimuli segmentation severely limits scalability. We assessed how the amount of available data impacts individual reliability of fixation preference for different facial features, and the effect of this reliability on between-group differences. We trained an artificial neural network to segment 22 Hollywood movie clips (7410 frames). We then analyzed fixation preferences in typically developing participants and participants with ASD as we incrementally introduced movie data for analysis. Although fixations were initially variable, results stabilized as more data was added. Additionally, while those with ASD displayed significantly fewer face-centered fixations (p<.001), they did not differ in eye or mouth fixations. Our results highlight the validity of treating fixation preferences as a stable individual trait, and the risk of misinterpretation with insufficient data.
ANNAVP, using neural networks to predict neutralization efficiency of antibodies against viral strains and to cluster strains by protein sequence
Authors: Cristian Ghiță Iulian 
Published: September 2020

AbstractStudying viral antibody neutralization data is a complex task and knowledge relating to the effectiveness of a particular antibody to particular strains of viruses cannot easily be extrapolated to other new, related strains. We have developed ANNAVP, a software that uses neural networks to model viral protein data. ANNAVP uses supervised or unsupervised learning and viral protein sequence data to form correlations between different strains and to predict the effectiveness of neutralizing agents against them.
Temporal dynamics of functional networks in long-term infant scalp EEG
Authors: Smith Rachel J. , Alipourjeddi Ehsan , Garner Cristal , Maser Amy L. , Shrey Daniel W. , Lopour Beth A. 
Published: September 2020

AbstractHuman functional connectivity networks are modulated on time scales ranging from milliseconds to days. Rapid changes in connectivity over short time scales are a feature of healthy cognitive function, and variability over long time scales can impact the likelihood of seizure occurrence. However, relatively little is known about modulation of healthy functional networks over long time scales. To address this, we analyzed functional connectivity networks calculated from long-term EEG recordings from 19 healthy infants. Networks were subject-specific, as inter-subject correlations between weighted adjacency matrices were low. However, within individual subjects, both sleep and wake networks were stable over time, with stronger functional connectivity during sleep than wakefulness. This enabled automatic separation of wakefulness and sleep states via principle components analysis of the functional network time series, with median classification accuracy of 91%. Lastly, we found that network strength, degree, clustering coefficient, and path length significantly varied with time of day, when measured in both wakefulness and sleep. Together, these results suggest that modulation of healthy functional networks occurs over long timescales and is robust and repeatable. Accounting for such temporal periodicities may improve the physiological interpretation and use of functional connectivity analysis to investigate brain function in health and disease.
College Openings in the United States Increased Mobility and COVID-19 Incidence
Authors: Andersen Martin S. , Bento Ana I. , Basu Anirban , Marsicano Christopher R. , Simon Kosali I. 
Published: September 2020

ABSTRACTSchool and college reopening-closure policies are considered one of the most promising non-pharmaceutical interventions for mitigating infectious diseases. Nonetheless, the effectiveness of these policies is still debated, largely due to the lack of empirical evidence on behavior during implementation. We examined U.S. college reopenings’ association with changes in human mobility within campuses and in COVID-19 incidence in the counties of the campuses over a twenty-week period around college reopenings in the Fall of 2020. We used an integrative framework, with a difference-in-differences design comparing areas with a college campus, before and after reopening, to areas without a campus and a Bayesian approach to estimate the daily reproductive number (Rt). We found that college reopenings were associated with increased campus mobility, and increased COVID-19 incidence by 3.4 cases per 100,000 (95% confidence interval [CI]: 1.5 – 5.4), or a 25% increase relative to the pre-period mean. This reflected our estimate of increased transmission locally after reopening. A greater increase in county COVID-19 incidence resulted from campuses that drew students from counties with high COVID-19 incidence in the weeks before reopening (χ2(2) = 10.19, p = 0.006). Even by Fall of 2021, large shares of populations remained unvaccinated, increasing the relevance of understanding non-pharmaceutical decisions over an extended period of a pandemic. Our study sheds light on movement and social mixing patterns during the closure-reopening of colleges during a public health threat, and offers strategic instruments for benefit-cost analyses of school reopening/closure policies.
Phylogenetic analysis of streptococci in samples taken from the throat cultures of children in Turkey and the presence of mef(A), mef(E), erm(B) and erm(TR) genes in patients withStreptococcus pyogenes
Authors: Balkan Çiğdem Eda , Bozkurt Hayrunisa Bekis , Öziç Cem 
Published: September 2020

AbstractObjectiveFailure to achieve success with penicillin treatment in some cases observed in the pediatric group and the decrease in macrolide activity have brought about the necessity of a new study aiming to differentiate bacteria at the species level in throat infections. Antibiotic resistance studies are of great importance for the treatment of bacterial infections in terms of public health and rational antibiotic use. For this purpose, we aimed to perform a species-level differentiation of streptococci isolated from the throat cultures of pediatric patients presenting to our hospital, to determine their antibiotic susceptibility, and to identify the macrolide resistance genes of mef(A), mef(E), erm(B) and erm(TR) in patients withStreptococcus pyogenes. The study included 51 samples taken from pediatric cases presenting with a sore throat as the patient group and 36 samples from children without this complaint as the control group.Material and MethodThe throat culture samples taken from 51 children presenting to the hospital with the complaint of sore throat were evaluated in the laboratory, and streptococcus was diagnosed using tests; gram staining, catalase and PYR, and the susceptibility profile was determined with the Kirby-Bauer disk-diffusion method. Bacteria were identified at the species level according to 16srRNA sequences, and possible macrolide resistance genes of mef(A), mef(E), erm(B) and erm(TR) were determined by PCR in species detected to haveS. pyogenes.ResultsOur antibiotic susceptibility results were consistent with the general results reported in Turkey. The sequence analysis of bacteria was performed according to 16srRNA sequences, andS. pyogenes, Streptococcus pneumoniae, Streptococcus anginosus, Streptococcus agalactiae, andStreptococcus dysgalactiaewere isolated. In patients withS. pyogenes, the genetic determinants of macrolide resistance, mef(A), mef(E), erm(B) and erm(TR), were investigated with the PCR method using primers specific to each gene. Different levels of expression were observed in five patients. Macrolide resistance inS. pyogenes, which is reported at various percentages in the world, was found to be 9.8% in our study.DiscussionThe results of our study show that penicillin resistance genes were found in five of the patients evaluated. When the anamnesis of these patients was examined, it was determined that there were patients that frequently presented to the hospital with throat infections and experienced re-infection within a few weeks after receiving treatment. The common discourse of clinicians is that there may be an unknown resistance development. Therefore, our research should be supported by new hypotheses and studies that are open to development.
Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area
Authors: Long S. Wesley , Olsen Randall J. , Christensen Paul A. , Bernard David W. , Davis James J. , Shukla Maulik , Nguyen Marcus , Saavedra Matthew Ojeda , Yerramilli Prasanti , Pruitt Layne , Subedi Sishir , Kuo Hung-Che , Hendrickson Heather , Eskandari Ghazaleh , Nguyen Hoang A. T. , Long J. Hunter , Kumaraswami Muthiah , Goike Jule , Boutz Daniel , Gollihar Jimmy , McLellan Jason S. , Chou Chia-Wei , Javanmardi Kamyab , Finkelstein Ilya J. , Musser James M. 
Published: September 2020

ABSTRACTWe sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCEThere is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, Texas, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture, evolution, and relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our study provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
Sox2-RNA mechanisms of chromosome topological control in developing forebrain
Authors: Cajigas Ivelisse , Chakraborty Abhijit , Lynam Madison , Swyter Kelsey R , Bastidas Monique , Collens Linden , Luo Hao , Ay Ferhat , Kohtz Jhumku D. 
Published: September 2020

SummaryPrecise regulation of gene expression networks requires the selective targeting of DNA enhancers. The Evf2 long non-coding RNA regulates Dlx5/6 ultraconserved enhancer(UCE) interactions with long-range target genes, controlling gene expression over a 27Mb region in mouse developing forebrain. Here, we show that Evf2 long range gene repression occurs through multi-step mechanisms involving the transcription factor Sox2, a component of the Evf2 ribonucleoprotein complex (RNP). Evf2 directly interacts with Sox2, antagonizing Sox2-dependent Dlx5/6UCE activation. Evf2 regulates Sox2 binding at key sites, including the Dlx5/6eii shadow enhancer and Dlx5/6UCE interaction sites. Evf2 differentially targets RNP-associated Sox2 protein pools (PPs), redirecting Sox2-PPs to one repressed gene at the expense of the other. Co-regulation of Dlx5/6UCEintrachromosomal interactions by Evf2 and Sox2 reveals a role for Sox2 in chromosome topology. We propose that RNA organizes RNPs in a subnuclear domain, regulating both long-range UCE targeting and activity through Sox2-RNP sequestration and recruitment.
Eugenol induces potent vasorelaxation in uterine arteries from pregnant goats – A promising natural therapeutic agent for hypertensive disorders of pregnancy
Authors: Parija SC , Jandhyam H , Mohanty BP , Parasar P , Nayak NR 
Published: September 2020

AbstractHypertensive disorders of pregnancy, including preeclampsia, affect about 8-13% of pregnancies and are the leading causes of pregnancy related maternal mortality worldwide. Poorly controlled high blood pressure during pregnancy increases the risk of pregnancy complications and development of future cardiovascular diseases. However, the choice for antihypertensive therapy during pregnancy has been limited due to side effects of many commonly used antihypertensive drugs and lack of other proven safe treatment options. Eugenol is a natural phenolic compound and the main component of clove oil. It is known for its antioxidant, anti-inflammatory and vasorelaxant actions. These beneficial effects of eugenol make it as an excellent therapeutic candidate for treatment of hypertensive disorders of pregnancy. Thus, as a first step, we compared the vasorelaxant effect of eugenol on the middle uterine arterial (MUA) rings from pregnant and nonpregnant goats. Additionally, we examined the potential involvement of the transient receptor potential channel 1 (TRPV1) in mediating the actions of eugenol and compared the effects with a known TRPV1 channel agonist, capsaicin. Isometric tension was measured in MUA rings from endometrial-myometrial junctions of pregnant and nonpregnant goats precontracted with phenylephrine, using a highly sensitive isometric force transducer and an automatic organ bath. The concentration-dependent contractile response curves of eugenol were compared to capsaicin, with and without pre-incubation of the MUA rings with a selective and non-selective TRPV1 antagonists, capsazepine (CAPZ) and Ruthenium Red (RR), respectively. Capsaicin induced concentration-dependent vasorelaxation in nonpregnant PE precontracted MUA rings and the concentration-response curve shifted to the right with significantly reduced pIC50 and Rmax values in the presence of CAPZ and RR. The effects were similar in MUA rings from pregnant animals, except that there was a moderate increase in pIC50 values in the presence of RR. Similarly, eugenol induced concentration-dependent vasorelaxation in both nonpregnant and pregnant PE precontracted MUA rings and the effects were markedly antagonized by CAPZ and RR. However, compared to capsaicin, the Rmax of eugenol was increased 31.25% in nonpregnant and 97.99% in pregnant MUA rings. These results suggest that eugenol has highly potent vasorelaxant effect in MUAs and its effect is partly mediated through activation of the TRPV1 channel. Most importantly, its vasorelaxant effect is about three-fold augmented in pregnancy, suggesting its potential value as a nutraceutical agent and therapeutic candidate for treatment of hypertensive disorders of pregnancy.
Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew,Plasmopara viticola
Authors: Fontaine Michael C. , Labbé Frédéric , Dussert Yann , Delière Laurent , Richart-Cervera Sylvie , Giraud Tatiana , Delmotte François 
Published: September 2020

AbstractEurope is the historical cradle of viticulture, but grapevines have been increasingly threatened by pathogens of American origin. The invasive oomycetePlasmopara viticolacauses downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. Comprehensive population genetic analyses of ~2000 samples from the most important wine-producing countries revealed very low genetic diversity in invasive downy mildew populations worldwide. All the populations originated from one of five native North American lineages, the one parasitizing wild summer grape. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa and, twice independently, Australia. Invasion of Argentina probably represents a tertiary introduction from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. It will help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.
Heterogeneity and ‘memory’ in stem cell populations
Authors: Stumpf Patrick S. , Arai Fumio , MacArthur Ben D. 
Published: September 2020

ABSTRACTModern single cell experiments have revealed unexpected heterogeneity in apparently functionally ‘pure’ cell populations. However, we are still lacking a conceptual framework to understand this heterogeneity. Here, we propose that cellular memories – the ability of individual cells to record their developmental past and adapt their response to their environment accordingly – are an essential ingredient in any such theory. We illustrate this idea by considering a simple age-structured model of stem cell proliferation. Using this model we argue that heterogeneity is central to stem cell population function, and memories naturally explain why stem cell numbers increase through life, yet regenerative potency simultaneously declines.