bluuebunny/crossref_metadata_2025_split huggingface dataset:
First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes
Authors: Van Patrick Tran , Anselmetti Yoann , Bast Jens , Dumas Zoé , Galtier Nicolas , Jaron Kamil S. , Martens Koen , Parker Darren J. , Robinson-Rechavi Marc , Schwander Tanja , Simion Paul , Schön Isa 
Published: December 2020

ABSTRACTSOstracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of non-marine ostracods; two with obligate sexual reproduction (Cyprideis torosaandNotodromas monacha) and the putative ancient asexualDarwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96%, and thus exceed the quality of several other published crustacean genomes obtained with similar techniques. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from non-marine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
Efficacy of lysophosphatidylcholine as direct treatment in combination with colistin againstAcinetobacter baumanniiin murine severe infections models
Authors: Miró-Canturri A , Ayerbe-Algaba R , Jiménez-Mejías ME , Pachón J , Smani Y 
Published: December 2020

ABSTRACTObjectivesThe stimulation of the immune response to prevent the progression of the infection may be an adjuvant to antimicrobial treatment. Previously, we showed that preemptive treatment with lysophosphatidylcholine (LPC) in combination with colistin improved the therapeutic efficacy of colistin against MDRAcinetobacter baumannii. In this study, we aimed to evaluate the efficacy of direct treatment with LPC in combination with colistin in murine experimental models of severe infections byA. baumannii.MethodsWe usedA. baumanniistrain Ab9, which is susceptible to colistin and most of the antibiotics used in clinical settings, andA. baumanniistrain Ab186, which is susceptible to colistin but presents a MDR pattern. The therapeutic efficacies of one and two doses of LPC (25 mg/kg/d) and colistin (20 mg/kg/8h), alone or in combination, were assessed against Ab9 and Ab186 in murine peritoneal sepsis and pneumonia models.ResultsOne and two doses of LPC in combination with colistin and colistin monotherapy enhanced bacterial clearance of Ab9 and Ab186 from spleen, lungs and blood and reduced mortality rates compared with those of the non-treated mice group in both experimental models (P<0.05). Moreover, one and two doses of LPC reduced the bacterial concentration in tissues and blood in both models, and increased mice survival in peritoneal sepsis model for both strains compared with those of colistin monotherapy group.ConclusionsLPC used as an adjuvant of colistin treatment may be helpful to reduce the severity and the resolution of the infection by MDRA. baumannii.
Free testosterone and malignant melanoma risk in men: prospective analyses of testosterone and SHBG with 19 cancers in men and postmenopausal women UK Biobank
Authors: Watts Eleanor L. , Perez-Cornago Aurora , Knuppel Anika , Tsilidis Konstantinos K. , Key Timothy J. , Travis Ruth C. 
Published: December 2020

AbstractWe investigated the associations of estimated free and total circulating testosterone and sex hormone-binding globulin (SHBG) with cancer risk in men and postmenopausal women, using a pan-cancer approach, including 19 cancers in UK Biobank.Risk was estimated using multivariable-adjusted Cox regression in up to 182,608 men and 122,112 postmenopausal women who were cancer-free at baseline. Participants diagnosed with cancer within two years of baseline were excluded. Hazard ratios (HRs) and confidence intervals (CIs) were corrected for regression dilution bias using repeat measurements. We accounted for multiple testing using the false discovery rate.In men, higher free testosterone was associated with higher risks of melanoma and prostate cancer (HR per 50 pmol/L increase=1.35, 95% CI 1.14-1.61 and 1.10,1.04-1.18, respectively). Higher total testosterone was associated with an elevated risk of liver cancer (HR per 5 nmol/L=2.45,1.56-3.84), and higher SHBG was associated with a higher risk of liver cancer (HR per 10 nmol/L=1.56,1.31-1.87) and a lower risk of prostate cancer (0.93,0.91-0.96); associations with liver cancer were attenuated after excluding early follow-up. In postmenopausal women, higher free and total testosterone and lower SHBG were associated with elevated risks of endometrial (HR per 10 pmol/L=1.59,1.32-1.90; HR per 0.5 nmol/L=1.34,1.18-1.52 and HR per 25 nmol/L=0.78,0.67-0.91, respectively) and breast cancer (1.32,1.22-1.43;1.24,1.17-1.31 and 0.88,0.83-0.94, respectively).We report a novel association of free testosterone with malignant melanoma in men; our findings also support known associations between sex hormones and risks for prostate, breast and endometrial cancers. The association with liver cancer in men may be attributable to reverse causation.
Cortical Mechanisms of Visual Hypersensitivity in Women at Risk for Chronic Pelvic Pain
Authors: Kmiecik Matthew J. , Tu Frank F. , Silton Rebecca L. , Dillane Katlyn E. , Roth Genevieve E. , Harte Steven E. , Hellman Kevin M. 
Published: December 2020

AbstractMultisensory hypersensitivity (MSH), which refers to persistent discomfort across sensory modalities, is a risk factor for chronic pain. Developing a better understanding of the neural contributions of disparate sensory systems to MSH may clarify its role in the development of chronic pain. We recruited a cohort of women (n=147) enriched with participants with menstrual pain at risk for developing chronic pain. Visual sensitivity was measured using a periodic pattern-reversal stimulus during EEG. Self-reported visual unpleasantness ratings were also recorded. Bladder pain sensitivity was evaluated with an experimental bladder-filling task associated with early clinical symptoms of chronic pelvic pain. Visual stimulation induced unpleasantness was associated with bladder pain and evoked primary visual cortex excitation; however, the relationship between unpleasantness and cortical excitation was moderated by bladder pain. Thus, future studies aimed at reversing the progression of MSH into chronic pain should prioritize targeting of cortical mechanisms responsible for maladaptive sensory input integration.
Why simple face masks are unexpectedly efficient in reducing viral aerosol transmissions
Authors: Freitag Steffen , Howell Steven G. , Jim Kevin T. C. 
Published: December 2020

SummaryDuring the current pandemic and in the past, shortages of high quality respirators have forced people to protect themselves with homemade face masks that filter poorly in comparison to N95 respirators 1–4 and are often designed in ways that makes them susceptible to leaks 5,6. Nevertheless, there is compelling epidemiological 7,8 and laboratory evidence 9–12 that face masks can be effective in impeding the spread of respiratory viruses such as influenza and SARS-CoV-2. Here we show that this apparent inconsistency can be resolved with a simple face mask model that combines our filtration efficiency measurements of various mask materials with existing data on exhaled aerosol characteristics. By reanalyzing these data we are able to reconcile the vastly different aerosol size distributions reported 13–19 and derive representative volume distributions for speech and breath aerosol. Multiplying filtration efficiency by those aerosol volumes, which are proportional to emitted viral load, shows that electrostatically charged materials perform the best but that even most uncharged fabrics remove > 85 % of breath and > 99 % of speech aerosol volume for exhaled particles < 10 µm in diameter. A leak model we develop shows the best uncharged fabric masks are made of highly air-permeable and often thin materials reducing viral load by up to 45 % and 50 % for breath and speech, respectively. Less permeable materials provide reduced protection because unfiltered air is forced through the leak. This can even render some charged materials inferior to uncharged household materials. Our model also shows that thin fabric masks provide protection for the wearer from aerosols expelled by another person reducing inhaled viral load by up to 20 % and 50 % and if leaks are avoided up to 35 % and 90 % for breath and speech, respectively.
Isolation and Characterization of Human Adipocyte-derived Extracellular Vesicles Using Filtration and Ultracentrifugation
Authors: Akbar Naveed , Pinnick Katherine E. , Paget Daan , Choudhury Robin P. 
Published: December 2020

ABSTRACTExtracellular vesicles (EVs) are lipid enclosed envelopes that carry biologically active material such as proteins, RNA, metabolites and lipids. EVs can modulate the cellular status of other cells locally in tissue microenvironments or through liberation into peripheral blood. Adipocyte- derived EVs are elevated in the peripheral blood and show alterations in their cargo (RNA and protein) during metabolic disturbances including, obesity and diabetes. Adipocyte-derived EVs can regulate the cellular status of neighboring vascular cells, such as endothelial cells and adipose tissue resident macrophages to promote adipose tissue inflammation. Investigating alterations in adipocyte-derived EVs in vivo is complex because EVs derived from peripheral blood are highly heterogenous and contain EVs from other sources, namely platelets, endothelial cells, erythrocytes and muscle. Therefore, the culture of human adipocytes provides a model system for the study of adipocyte derived EVs. Here, we provide a detailed protocol for the extraction of total small EVs from cell culture media of human gluteal and abdominal adipocytes using filtration and ultracentrifugation. We further demonstrate the use of Nanoparticle Tracking Analysis (NTA) for quantification of EV size and concentration and show the presence of EV-protein tumor susceptibility gene 101 (TSG101) in the gluteal and abdominal adipocyte derived-EVs. Isolated EVs from this protocol can be used for downstream analysis including, transmission electron microscopy, proteomics, metabolomics, small RNA-sequencing, microarray and utilized in functional in vitro/in vivo studies.SUMMARYWe describe the isolation of human adipocyte-derived extracellular vesicles (EVs) from gluteal and abdominal adipose tissue using filtration and ultracentrifugation. We characterize the isolated adipocyte-derived EVs by determining their size and concentration by Nanoparticle Tracking Analysis and by western blotting for the presence of EV-protein tumor susceptibility gene 101 (TSG101).
Systematic review and meta-analysis of the calibration of confidence judgments in individuals with schizophrenia spectrum disorders
Authors: Rouy Martin , Saliou Pauline , Nalborczyk Ladislas , Pereira Michael , Roux Paul , Faivre Nathan 
Published: December 2020

AbstractBackgroundMetacognitive deficits are well documented in schizophrenia spectrum disorders as a decreased capacity to adjust confidence to first-order performance in a cognitive task. Because metacognitive ability directly depends on first-order performance, observed metacognitive deficits might be driven by lower first-order performance. We aimed to determine the extent to which individuals with schizophrenia experience specific deficits when producing confidence judgments and examined whether studies controlling for first-order performance found metacognitive deficits of smaller magnitude.MethodElectronic databases were searched for studies published until April 24th2020. We conducted a Bayesian meta-analysis of 43 studies comparing the calibration of confidence in 1458 individuals with schizophrenia compared to 1337 matched controls. Group analyses and meta-regressions quantified how metacognitive deficits depended on task performance, cognitive domains, clinical severity, and antipsychotic dosage.OutcomesWe found a global metacognitive deficit in schizophrenia (g = -0.57, 95% CrI [-0.71, -0.43]), which was driven by studies which did not equate first-order performance between groups (g = -0.64, 95% CrI [-0.77, -0.51]), and inconclusive among controlled-studies (g = -0.28, 95% CrI [-0.63, 0.07], BF01= 1.3). Plus, the metacognitive deficit in non-controlled studies was correlated with first-order performance. No correlation was found between metacognitive deficit and clinical features of schizophrenia.InterpretationWe provide evidence for the existence of a deficit in the calibration of confidence judgments in schizophrenia, which is inflated due to non-equated first-order performance. Thus, efforts should be made to develop experimental protocols accounting for lower first-order performance in schizophrenia.
Screening for SARS-CoV-2 infection in asymptomatic individuals using the Panbio™ COVID-19 Antigen Rapid Test (Abbott) compared to RT-qPCR
Authors: Winkel Beatrice M.F. , Schram Emma , Gremmels Hendrik , Debast Sylvia B. , Schuurman Rob , Wensing Annemarie M.J. , Bonten Marc J.M. , Goedhart Edwin , Hofstra L. Marije ,   Antigen Rapid Test Validation Group
Published: December 2020

AbstractBackgroundAntigen-based point of care tests for identification of SARS-CoV-2 may markedly enhance effectiveness of population-based controlling strategies. Previous studies have demonstrated acceptable sensitivity and high specificity compared to RT-qPCR in symptomatic individuals, but test performance for asymptomatic individuals is unknown.MethodsTest performance of the Panbio™ COVID-19 Ag Rapid Test (Abbott) was compared to RT-qPCR in a longitudinal cohort study of asymptomatic football players and staff members of professional football clubs. Based on timing of symptoms and prior and subsequent test results, positive RT-qPCR tests were categorized as pre-symptomatic, early or late infection or persistent RNA shedding.Findings2425 tests were performed in 824 individuals, of which 52 (6.3%) were SARS-CoV-2 positive based on RT-qPCR. There were 2406 paired sets from asymptomatic subjects for analysis. Sixteen Panbio™ tests were inconclusive, for which sensitivity analyses were performed (considering results as either positive or negative or being excluded). Sensitivity of Panbio™ ranged from 61.76% (95% CI 49.2-73.3) to 69.12% (95% CI: 56.7-79.8) and specificity from 99.53% (95% CI: 99.2-99.8) to 100% (95% CI: 99.8-100). Sensitivity of Panbio™ to detect subjects with pre-symptomatic/early infection (n= 42) ranged from 81.82% (95% CI: 67.3-91.8) to 90.91% (95% CI: 78.3-97.5) with specificity always above 99%.InterpretationIn asymptomatic subjects the Panbio™ COVID-19 Ag Rapid Test had sensitivity of 81.82% to 90.91% and specificity above 99% for identifying pre-symptomatic and early SARS-CoV-2 infection.FundingThis study was funded by the executing institutes. The Panbio™ COVID-19 Ag Rapid Tests were provided by the Ministry of Health, Welfare and Sport (VWS).
Racial and Ethnic Disparities in COVID-19 Infection and Mortality in the United States: A state-wise update
Authors: Xian Zhaoying , Saxena Anshul , Javed Zulqarnain , Jordan John E. , Alkarawi Safa , Khan Safi U , Shah Karan , Vahidy Farhaan , Nasir Khurram , Dubey Prachi 
Published: December 2020

AbstractObjectivesTo evaluate COVID-19 infection and mortality in ethnic and racial sub-groups across all states in the United States.MethodsPublicly available data from “The COVID Tracking Project at The Atlantic” was accessed between 09/09/2020 and 09/14/2020. For each state and the District of Columbia, % infection, % death, % population proportion for subgroups of race (African American (AA), Asian, American Indian or Alaska Native, (AI/AN) and White), and ethnicity (Hispanic/Latino, and non-Hispanic), were recorded. Absolute and relative excess infection (AEI and REI) and mortality (AEM and REM) were computed as absolute and relative difference between % infection or % mortality and % population proportion for each state. Median (IQR) REI is provided below.ResultsThe Hispanic population had a median of 158% higher COVID-19 infection relative to their % population proportion (median REI 158%, [IQR: 100% to 200%]). This was followed by AA, with 50% higher COVID-19 infection relative to their % population proportion (median REI, 50% [IQR 25% to 100%]). The AA population had the most disproportionate mortality with a median of 46% higher mortality than % population proportion, (median REM 46% [IQR, 18% to 66%]). Disproportionate impact of COVID-19 was also seen in AI/AN and Asian population with ≥100% excess infections than % population proportion seen in 35 states for Hispanic, 14 states for AA, 9 states for AIAN, and 7 states for Asian populations. There was no disproportionate impact in the white population in any state.ConclusionsRacial/ethnic minorities (AA, Hispanic, AIAN and Asian populations) are disproportionately affected by COVID 19 infection and mortality across the nation. These findings underscore the potential role of social determinants of health in explaining the disparate impact of SARS-CoV-2 on vulnerable demographic groups, as well as the opportunity to improve outcomes in chronically marginalized populations.
OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England
Authors:   The OpenSAFELY Collaborative, Curtis Helen J , MacKenna Brian , Walker Alex J , Croker Richard , Mehrkar Amir , Morton Caroline E , Bacon Seb , Hickman George , Inglesby Peter , Bates Chris , Evans David , Ward Tom , Cockburn Jonathan , Davy Simon , Bhaskaran Krishnan , Schultze Anna , Rentsch Christopher T , Williamson Elizabeth , Hulme William , McDonald Helen I , Tomlinson Laurie , Mathur Rohini , Drysdale Henry , Eggo Rosalind M , Wing Kevin , Wong Angel YS , Forbes Harriet , Parry John , Hester Frank , Harper Sam , Evans Stephen JW , Douglas Ian J , Smeeth Liam , Goldacre Ben 
Published: December 2020

BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring.ObjectiveTo describe which people were switched from warfarin to DOACs; identify potentially unsafe co-prescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic.MethodsWorking on behalf of NHS England we conducted a population cohort based study using routine clinical data from >17 million adults in England.Results20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420).ConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.
Factors associated with decision making on COVID-19 vaccine acceptance among college students in South Carolina
Authors: Tam Cheuk Chi , Qiao Shan , Li Xiaoming 
Published: December 2020

AbstractBackgroundCOVID-19 vaccination could be a promising approach in controlling the pandemic, but its success strongly relies on the acceptance of vaccines among various populations including young adults who are especially vulnerable to COVID-19 due to their active lifestyle and perception of invulnerability. Vaccine acceptance decisions can be influenced by multiple factors and people may weigh these factors differently in their decision making. The current study aims to explore COVID-19 vaccine acceptance among college students in South Carolina and examine how they weigh these factors according to their levels of COVID-19 vaccine acceptance (i.e., acceptance, hesitance, refusal).MethodsOnline survey data were collected from 1062 college students in South Carolina between September and October 2020. Multivariate analysis of covariance was used to compare perceived importance of 12 factors affecting levels of vaccine acceptance, controlling for key demographic variables.ResultsAbout 60.6% of the college students reported they would definitely or likely take COVID-19 vaccine when available. Duration of vaccine protection, vaccine accessibility, and authoritative advice (e.g., if vaccination is recommended by school, government, or doctors) were considered important among the acceptance group; Negative consequences of vaccination and vaccine characteristics (i.e., ways the vaccine will be administered, and where the vaccine is made) were considered important by the refusal group; The hesitance group considered the same factors important as the refusal group did but also considered duration of vaccine protection and recommendation by school or doctors important.ConclusionOur findings suggest relatively low vaccine acceptance among college students in South Carolina and different factors that play a role in their vaccine uptake decision according to their levels of acceptance. Tailored vaccine promotion messages should address specific concerns among the refusal and hesitancy groups. School could play a positive role in vaccine campaign since the reluctancy group considered that recommendation by their school was important in their decision making. Health educators also need to pay particular attention to the refusal group who do not value duration of protection or authoritative advice as much as their counterparts in their vaccine decision making.