bluuebunny/crossref_metadata_2025_split huggingface dataset:
End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments
Authors: Parker Ceth W. , Singh Nitin , Tighe Scott , Blachowicz Adriana , Wood Jason M. , Seuylemezian Arman , Vaishampayan Parag , Urbaniak Camilla , Hendrickson Ryan , Laaguiby Pheobe , Clark Kevin , Clement Brian G. , O’Hara Niamh B. , Couto-Rodriguez Mara , Bezdan Daniela , Mason Chris , Venkateswaran Kasthuri 
Published: August 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019, is a respiratory virus primarily transmitted from person to person through inhalation of droplets or aerosols, laden with viral particles. However, as some studies have shown, virions can remain infectious for up to 72 hours on surfaces, which can lead to transmission through contact. For this reason, a comprehensive study was conducted to determine the efficiency of protocols to recover SARS-CoV-2 from surfaces in built environments. This end-to-end (E2E) study showed that the effective combination of monitoring SARS-CoV-2 on surfaces include using an Isohelix swab as a collection tool, DNA/RNA Shield as a preservative, an automated system for RNA extraction, and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) as the detection assay. Using this E2E approach, this study showed that, in some cases, SARS-CoV-2 viral standards were still recovered from surfaces as detected by RT-qPCR for as long as eight days even after bleach treatment. Additionally, debris associated with specific built environment surfaces appeared to negatively impact the recovery of RNA, with Amerstat inhibition as high as 90% when challenged with an inactivated viral control. Overall, it was determined that this E2E protocol required a minimum of 1,000 viral particles per 25 cm2 to successfully detect virus from test surfaces. When this method was employed to evaluate 368 samples collected from various built environmental surfaces, all samples tested negative, indicating that the surfaces were either void of virus or below the detection limit of the assay.ImportanceThe ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (the virus responsible for coronavirus disease 2019; COVID-19) pandemic has led to a global slow down with far reaching financial and social impacts. The SARS-CoV-2 respiratory virus is primarily transmitted from person to person through inhalation of infected droplets or aerosols. However, some studies have shown virions can remain infectious on surfaces for days, and can lead to human infection from contact with infected surfaces. Thus, a comprehensive study was conducted to determine the efficiency of protocols to recover SARS-CoV-2 from surfaces in built environments. This end-to-end study showed that the effective combination of monitoring SARS-CoV-2 on surfaces required a minimum of 1,000 viral particles per 25 cm2 to successfully detect virus from surfaces. This comprehensive study can provide valuable information regarding surface monitoring of various materials as well as the capacity to retain viral RNA and allow for effective disinfection.
Acute Peritoneal Dialysis During the COVID-19 Pandemic at Bellevue Hospital in New York City
Authors: Caplin Nina J. , Zhdanova Olga , Tandon Manish , Thompson Nathan , Patel Dhwanil , Soomro Qandeel , Ranjeeta Fnu , Joseph Leian , Scherer Jennifer , Joshi Shivam , Dyal Betty , Chawla Harminder , Iyer Sitalakshmi , Bails Doug , Benstein Judith , Goldfarb David S. , Gelb Bruce , Amerling Richard , Charytan David M. 
Published: August 2020

AbstractThe COVID-19 pandemic created an unprecedented strain on hospitals in New York City. Although practitioners focused on the pulmonary devastation, resources for the provision of dialysis proved to be more constrained. To deal with these shortfalls, NYC Health and Hospitals/Bellevue, NYU Brooklyn, NYU Medical Center and the New York Harbor VA Healthcare System, put together a plan to offset the anticipated increased needs for kidney replacement therapy.Prior to the pandemic, peritoneal dialysis was not used for acute kidney injury at Bellevue Hospital. We were able to rapidly establish an acute peritoneal dialysis program at Bellevue Hospital for acute kidney injury patients in the intensive care unit. A dedicated surgery team was assembled to work with the nephrologists for bedside placement of the peritoneal dialysis catheters. A multi-disciplinary team was trained by the lead nephrologist to deliver peritoneal dialysis in the intensive care unit. Between April 8, 2020 and May 8, 2020, 39 peritoneal dialysis catheters were placed at Bellevue Hospital. 38 patients were successfully started on peritoneal dialysis. As of June 10, 2020, 16 patients recovered renal function. One end stage kidney disease patient was converted to peritoneal dialysis and was discharged. One catheter was poorly functioning, and the patient was changed to hemodialysis before recovering renal function. There were no episodes of peritonitis and nine incidents of minor leaking, which resolved. Some patients received successful peritoneal dialysis while being ventilated in the prone position.In summary, despite severe shortages of staff, supplies and dialysis machines during the COVID-19 pandemic, we were able to rapidly implement a de novo peritoneal dialysis program which enabled provision of adequate kidney replacement therapy to all admitted patients who needed it. Our experience is a model for the use of acute peritoneal dialysis in crisis situations.
Hypertension among people living with HIV/AIDS in Cameroon: A cross-sectional analysis from Central Africa International Epidemiology Databases to Evaluate AIDS
Authors: Dzudie Anastase , Hoover Don , Kim Hae-Young , Ajeh Rogers , Adedimeji Adebola , Shi Qiuhu , Yone Walter Pefura , Nforniwe Denis Nsame , Njie Kinge Thompson , Kengne Andre Pascal , Ebasone Vanes Peter , Barche Blaise , Cecile Zoung-Kany Bisseck Anne , Nash Denis , Yotebieng Marcel , Anastos Kathryn 
Published: August 2020

AbstractBackgroundAntiretroviral therapy (ART) success has led people to live longer with HIV/AIDS (PLWH) and thus be exposed to increasing risk of cardiovascular diseases (CVD). Hypertension (HTN), the biggest contributor to CVD burden, is a growing concern among PLWH. The current report describes the prevalence and predictors of HTN among PLWH in care in Cameroon.MethodsThis cross-sectional study included all PLWH aged 20 years and above who received care between 2016 and 2019 at one of the three Central Africa International Epidemiology Databases to Evaluate AIDS (CA-IeDEA) sites in Cameroon (Bamenda, Limbe, and Yaoundé). HTN was defined as blood pressure (BP) ≥140/90 mm Hg or self-reported use of antihypertensive medication. Logistic regressions models examined the relationship between HTN and clinical characteristics, and HIV-related factors.ResultsAmong 9,839 eligible PLWH, 66.2% were female and 25.0% had prevalent HTN [age-standardized prevalence 23.9% (95% CI: 22.2–25.6)], among whom 28 (1.1%) were on BP lowering treatment, and 6 of those (21.4%) were at target BP levels. Median age (47.4 vs. 40.5 years), self-reported duration of HIV infection (5.1 vs 2.8 years), duration of ART exposure (4.7 vs 2.3 years), and CD4 count (408 vs 359 cell/mm3) were higher in hypertensives than non-hypertensives (all p< 0.001). Age and body mass index (BMI) were independently associated with higher prevalent HTN risk. PLWH starting ART had a 30% lower risk of prevalent HTN, but this advantage disappeared after a cumulative 2-year exposure to ART. There was no significant association between other HIV predictive characteristics and HTN.ConclusionAbout a quarter of these Cameroonian PLWH had HTN, driven among others by age and adiposity. Appropriate integration of HIV and NCDs services is needed to improve early detection, treatment and control of common comorbid NCD risk factors like hypertension and safeguard cardiovascular health in PLWH.
Longitudinal SARS-CoV-2 serosurveillance of over ten thousand health care workers in the Providence Oregon cohort
Authors: Leidner Rom , Frary Angi , Cramer Julie , Ball David , Weerasinghe Roshanthi , Schmidt Mark , Jin Justin , Luzzi Veronica , Saitman Alec , Young Jeffrey A. , Leidner David , Sawa Kendall , Marsal Scott , Olson Kevin , Frisco Nancy , Compton-Phillips Amy , Urba Walter , Piening Brian , Bifulco Carlo 
Published: August 2020

AbstractFrontline healthcare workers (HCW) are a high-risk population for SARS-CoV-2 infection. Here we present results from a large serosurveillance study of 10,019 asymptomatic HCW conducted during April-May 2020, in eight hospital medical centers across the state of Oregon, USA during the initial peak of the pandemic. Free and voluntary testing was performed at 14 +/− 3 day intervals, over a 4-week window at each site, utilizing a lab-developed ELISA based on the Epitope Diagnostics COVID-19 nucleocapsid IgG detection Kit. We identified 253 SARS-CoV-2 IgG seropositive individuals among 10,019 total participants, representing a cross-sectional seroprevalence of 2.53%. Subgroup analysis identified differential seropositivity by job role, ranging from 8.03% among housekeepers, odds ratio 3.17 (95% CI 1.59–5.71), to 0.00% among anesthesiologists, odds ratio 0.00 (95% CI 0–0.26), both of which were significant. Over the course of the study, 17 seroconversions (0.25%) and 101 seroreversions (1.50%) were identified. Self-reported SARS-CoV-2 swab qPCR testing, when compared with subsequent serology on study, showed only modest agreement, κ = 0.47 (95% CI 0.32–0.62). Overall, these findings demonstrate relatively low seroprevalence and very low seroconversion rates among HCW in Oregon, USA, over a period in which aggressive social distancing measures were in place. The high rate of seroreversion observed in this cohort, and the relatively high discordance between SARS-CoV-2 serology and swab qPCR, highlight limitations of current detection methods, and stress the need for development of novel assessment methodologies to more accurately identify exposure (and/or immunity) to SARS-CoV-2 in this population.
Single-cell analysis identifies TCF4 and ID3 as a molecular switch of mammary epithelial stem cell differentiation
Authors: Yan Koon-Kiu , Nekritz Erin , Ju Bensheng , Dong Xinran , Werner Rachel , Alsina-Beauchamp Dayanira , Rosencrance Celeste , Mukhopadhyay Partha , Pan Qingfei , Gorbatenko Andrej , Ding Liang , Wang Yanyan , Qian Chenxi , Shi Hao , Shaner Bridget , Natarajan Sivaraman , Chi Hongbo , Easton John , Silva Jose , Yu Jiyang 
Published: August 2020

ABSTRACTIt is well known that the expansion of the mammary epithelium during the ovarian cycles in female mammals is supported by the transient increase in mammary epithelial stem cells (MaSCs). However, dissecting the molecular mechanisms that govern MaSC function and differentiation is poorly understood due to the lack of standardized methods for their identification and isolation.The development of robust single-cell mRNA sequencing () technologies and the computational methods to analyze them provides us with novel tools to approach the challenge of studying MaSCs in a completely unbiased way without. Here, we have performed the largest scRNA-seq analysis of individual mammary epithelial cells (~70,000 cells). Our study identified a distinct cell population presenting molecular features of MaSCs.Importantly, further purification and additional in-depth single-cell analysis of these cells revealed that they are not a fully homogenous entity. Instead, we identified three subpopulations representing early stages of lineage commitment. By tracking their molecular evolution through single-cell network analysis we found that one of these subpopulations represents bipotent MaSCs from which luminal and basal lineages diverge. Importantly, we also confirmed the presence of these cells in human mammary glands. Finally, through expression and network analysis studies, we have uncovered transcription factors that are activated early during lineage commitment. These data identified E2-2 (Tcf4) and ID3 as a potential molecular switch of mammary epithelial stem cell differentiation.
Illegal hunting threatens the establishment of a lynx population and highlights the need of a centralized judiciary approach
Authors: Arlettaz Raphaël , Chapron Guillaume , Kéry Marc , Klaus Elisabeth , Mettaz Stéphane , Roder Stefanie , Vignali Sergio , Zimmermann Fridolin , Braunisch Veronika 
Published: August 2020

AbstractIllegal hunting (poaching) represents a major threat to the conservation of large predators. Yet, its impact remains difficult to quantify as there are strong incentives to conceal this criminal activity. Attributing changes in the population status of large carnivores in part to poaching is therefore an important conservation challenge.We present a case study of lynx (Lynx lynx) in southwestern Switzerland (canton of Valais) where the current distribution range is much smaller than it was in the recent past and population density is now >80% lower than in other lynx populations in the Swiss Alps, particularly in the adjacent Pre-Alps. We tested four hypotheses to explain this far lower density: 1) a too low density of trail camera-traps deployed for lynx surveys in Valais compared to the Pre-Alps (i.e. a methodological artefact); 2) less favourable environmental conditions around the camera-trap sites; 3) lower densities of the main prey; and 4) poaching.We estimated lynx and ungulate densities and environmental conditions at trail camera sites, and were able to clearly reject the first three hypotheses: 1) the monitoring protocol was similarly effective; 2) environmental conditions around the trapping sites in Valais were even more favourable to lynx detection than in the Pre-Alps; and 3) prey supply was even larger. Concerning hypothesis 4, we discovered a local, but dense network of 17 illegal lynx traps in the narrow main immigration corridor into Valais from the thriving adjacent lynx population in the Pre-Alps, suggesting intense local poaching.Our findings substantiate the suspicions of long-lasting lynx poaching as a threat to the establishment and survival of the Valais population. The fact that instances of poaching were publicly known since 1995 but remained unabated for at least two decades, until a first conviction occurred, questions the commitment of local authorities to address this case of wildlife crime. Our study shows that inquiries about wildlife crime such as top predator poaching may need to be carried out at the highest levels of jurisdiction to avoid any risk of collusion between law enforcement agents and poachers.
INFLUENCE OF SOME LEGUMINOUS TREES AND ARBUSCULAR MYCORRHIZAL FUNGI ON THE PHYSIOLOGY AND YIELD OF DIOSCOREA ROTUNDATA -POIR
Authors: Afolayan Ezekiel Taiwo 
Published: August 2020

AbstractThis work compares the physiological and yield characteristics of white yam (Dioscorea rotundata – Poir) under Arbuscular mycorrhizal fungi (AMF) inoculation, green manures of Gliricidia sepium, Leucaena leucocephala and other soil amendments. The experiment was conducted on the plot of land that had been overcropped, located at the back of the male Hostel, Federal College of Education, Abeokuta, Ogun State, Nigeria. The land was cleared and heaped at 1m x 1m apart. The experimental design employed was a complete randomized design in 5 replicates. The treatments were Glomus deserticola (GD), Glomus fasciculatum (GF), Gliricidia sepium (GS), Leucaena leucocephala (LL), Poultry manure (PM) and NPK fertilizers. Soils were dug from the heaps, 20 g of the inoculums of AMF (GD/ GF) were poured into the dug hole, seeds were laid on it and covered with soil (for GD & GF treatments). Others were applied at one week after sprouting. Growth and yield Parameters were determined at harvest while relative water and chlorophyll contents were measured forth nightly from 10 weeks after treatment. Data obtained were subjected to ANOVA while means were separated by Duncan multiple range test at P> 0.05. Results showed that growth, yield and physiological characters were enhanced in GD, GD+GF, GS and PM treated plants more than in inorganic fertilizers treated plants. There was a positive significant relationship between white yam’s growth, physiology and tuber yield. The study justifies the use of plant/animal manures and Arbuscular mycorrhizal fungi in place of inorganic fertilizers.
Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations
Authors: Nelson Thomas C. , Muir Christopher D. , Stathos Angela M. , Vanderpool Daniel D. , Anderson Kayli , Angert Amy L. , Fishman Lila 
Published: August 2020

ABSTRACTPREMISEAcross taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments.METHODSWe used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (Mimulus cardinalis).RESULTSWe mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats.CONCLUSIONSOur results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates.
Inconsistent effects of urbanization on amphibian genetic diversity
Authors: Schmidt Chloé , Garroway Colin J 
Published: August 2020

AbstractHabitat loss and fragmentation are leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing population sizes in human transformed habitats. With time this can lead to reduced effective population size and genetic diversity which restricts the ability of wildlife to cope with environmental change through genetic adaptation. However, it is not well understood whether these effects are generally applicable across taxa. Here, we repurposed and synthesized raw microsatellite data from online repositories from 19 amphibian species sampled at 554 sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density and the Human Footprint Index, we tested for generalizable effects of human land use on amphibian genetic diversity. We found no consistent relationships for any of our genetic metrics. While we did not detect directional effects for most species, a few generalist species responded positively to urbanization. These results contrast with consistent negative effects of urbanization in mammals and species specific positive and negative effects in birds. In the context of widespread amphibian declines, our results suggest that habitat loss in human transformed habitats is a more immediate concern than declining genetic diversity in populations that persist.
Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family
Authors: Guo Xiaohu , Söderholm Annika , Kanchugal P Sandesh , Isaksen Geir Villy , Warsi Omar , Eckhard Ulrich , Trigüis Silvia , Gogoll Adolf , Jerlström-Hultqvist Jon , Åqvist Johan , Andersson Dan I. , Selmer Maria 
Published: August 2020

AbstractThe first SAM degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as an S-adenosyl-L-methionine (SAM) hydrolase forming 5’-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha-beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography and NMR spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis,in vitroandin vivomutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.
Structural defects caused by Acrodermatitis Enteropathica mutations in the extracellular domain account for mistrafficking and malfunction of ZIP4
Authors: Kuliyev Eziz , Zhang Chi , Sui Dexin , Hu Jian 
Published: August 2020

AbstractZIP4 is a representative member of the Zrt-/Irt-like protein (ZIP) transporter family and responsible for zinc uptake from diet. Loss-of-function mutations of human ZIP4 (hZIP4) drastically reduce zinc absorption, causing a life-threatening autosomal recessive disorder, Acrodermatitis Enteropathica (AE). Although the zinc transport machinery is located in the transmembrane domain conserved in the entire ZIP family, half of the missense mutations occur in the extracellular domain (ECD) of hZIP4, which is only present in a fraction of mammalian ZIPs. How the AE-causing mutations in the ECD lead to ZIP4 malfunction has not be fully clarified. In this work, we characterized all the seven confirmed AE-causing missense mutations in hZIP4-ECD and found that the variants exhibited completely abolished zinc transport activity measured in a cell-based transport assay. Although the variants were able to be expressed in HEK293T cells, they failed to traffic to cell surface and were largely retained in the ER with immature glycosylation. When the corresponding mutations were introduced in the ECD of ZIP4 from Pteropus Alecto, a close homolog of hZIP4, the variants exhibited impaired protein folding and reduced thermal stability, which likely account for intracellular mistrafficking of the AE-associated variants and as such a total loss of zinc uptake in cells. This work provides a molecular pathogenic mechanism for AE, which lays out a basis for potential therapy using small molecular chaperones.