bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of various decontamination procedures on disposable N95 mask integrity and SARS-CoV-2 infectivity
Authors: Smith Jeffrey S. , Hanseler Haley , Welle John , Rattray Rogan , Campbell Mary , Brotherton Tacy , Moudgil Tarsem , Pack Thomas F. , Wegmann Keith , Jensen Shawn , Jin Justin , Bifulco Carlo B. , Prahl Scott A. , Fox Bernard A. , Stucky Nicholas L. 
Published: April 2020

AbstractThe COVID-19 pandemic has created a high demand on personal protective equipment, including disposable N95 masks. Given the need for mask reuse, we tested the feasibility of vaporized hydrogen peroxide (VHP), ultraviolet light (UV), and ethanol decontamination strategies on N95 mask integrity and the ability to remove the infectious potential of SARS-CoV-2. FIT test data showed functional degradation by both ethanol and UV decontamination to different degrees. VHP treated masks showed no significant change in function after two treatments. We also report a single SARS-CoV-2 virucidal experiment using Vero E6 cell infection. We hope our data will guide further research for evidenced-based decisions for disposable N95 mask reuse and help protect caregivers from SARS-CoV-2 and other pathogens.
Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection
Authors: Kojima N , Turner F , Slepnev V , Bacelar A , Deming L , Kodeboyina S , Klausner JD 
Published: April 2020

AbstractBackgroundCurrently, there is a pandemic caused by the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes Covid-19. We wanted to compare specimen types and collection methods to explore if a simpler to collect specimen type could expand access to testing.MethodsWe recruited individuals recently tested for SARS-CoV-2 infection through a “drive-through” testing program. In participants’ homes, we assessed the performance of self-collected oral fluid swab specimens with and without clinician supervision, clinician-supervised self-collected mid-turbinate (nasal) swab specimens, and clinician-collected nasopharyngeal swab specimens. We tested specimens with a validated reverse transcription-quantitative polymerase chain reaction assay for the detection of SARS-CoV-2 and measured cycle threshold values. Symptom status and date of onset of symptoms was also recorded for each participant.ResultsWe recruited 45 participants. The median age of study participant was 42 years old (Interquartile range, 31 to 52 years). Of the participants, 29 had at least one specimen test positive for SARS-CoV-2. Of those, 21 (73%) of 29 reported active symptoms. By specimen type and home-based collection method, clinician-supervised self-collected oral fluid swab specimens detected 26 (90%) of 29 infected individuals, clinician-supervised self-collected nasal swab specimens detected 23 (85%) of 27, clinician-collected posterior nasopharyngeal swab specimens detected 23 (79%) of 29, and unmonitored self-collected oral fluid swab specimens detected 19 (66%) of 29. Despite nasopharyngeal swabs being considered the gold standard, 4 participants tested negative by clinician-collected nasopharyngeal swab and positive by the 3 other specimen types. Additionally, false negative results by each sample type were seen to generally not overlap.ConclusionsSupervised self-collected oral fluid and nasal swab specimens performed similarly to, if not better than clinician-collected nasopharyngeal swab specimens for the detection of SARS-CoV-2 infection. No sample type captured all SARS-CoV-2 infections, suggesting potential heterogeneity in the distribution of viral load in different parts of the respiratory tract between individuals. Supervised self-collection performed comparably to clinician collection and would allow for rapid expansion of testing capacity in the United States by reducing the need for trained healthcare workers, reducing exposure of healthcare workers, and reducing the amount of PPE (personal protective equipment) being used for testing during a critical shortage.
Prevalence and spectrum of diabetic peripheral neuropathy and its correlation with insulin resistance - An experience from eastern India
Authors: Majumdar Manidipa , Banerjee Mainak , Sengupta Jinesh , Deb Soudeep , Jana Chanchal Kr. , Roy Biman Kanti 
Published: April 2020

ABSTRACTAIMSDiabetes mellitus is a public health problem worldwide, with diabetic neuropathy (DN) being a common complication. Studies indicate that, neurons can develop insulin resistance (IR) and cannot respond to the neurotrophic properties of insulin. Although studies exist on the relation between DN and glycemic exposure index (GEi), papers about correlation of DN with IR is rare. This study focused on the prevalence of neuropathies in DM patients and usefulness of IR as a marker of DN.METHODSA cross sectional observational study was done. All patients satisfying American Diabetes Association criteria and none of the exclusion criteria were included. Total sample size was 142. Main parameters studied were glycemic status, neurological examination and nerve conduction study findings. Dyck grading was used for severity of distal symmetric polyneuropathy (DSPN). For statistical analysis, logistic and ordinal logistic regressions were used as appropriate.RESULTS34.5% of the sample had DN, the commonest type being DSPN (72.9%). The study population was equally divided in terms of gender and 88.7% were type 2 diabetic. About 62.5% neuropathic cases were asymptomatic. Occurrence of DN correlated significantly with duration of diabetes, FBS and IR. Age, when adjusted for other risk factors was not significantly correlated to neuropathy. The severity of DSPN correlated significantly with GEi but not with IR.CONCLUSIONSThe prevalence of neuropathy was found to be similar to earlier western studies. This paper further establishes IR as a significant predictor for existence of DN, but it may not affect the progress of the neuropathy.
The clinical characteristics and mortal causes analysis of COVID-19 death patients
Authors: Guo Ao-Xiang , Cui Jia-Jia , OuYang Qian-Ying , He Li , Guo Cheng-Xian , Yin Ji-Ye 
Published: April 2020

AbstractPurposeCurrently, COVID-19 is causing a large number of deaths globally. However, few researches focused on the clinical features of death patients. This study conducted a retrospective analysis of clinical characteristics and mortal causes in Chinese COVID-19 death patients.Patients and methodsThe clinical characteristics of death patients were collected from publicized by local health authorities in China. Expressions of virus targets in human organs were obtained from GTEx database.Results159 patients from 24 provinces in China were recruited in our study, including 26 young patients under 60 and 133 aged 60 or older. The median age was 71 years, which indicated that most death patients were elderly. More male patients died of COVID-19 than females (1.65 fold). Hypertension was the most common coexisting disorder and respiratory failure was the most common direct cause of death. Fever (71.19%) and cough (55.08%) were the predominant presenting symptoms. There was one asymptomatic patient. In addition, by comparing young and old patients, heart disease was identified as an important risk factor for death in the aged patients. ACE2 and TMPRSS2 were the targets of SARS-CoV-2, we analyzed their expression in different organs. TMPRSS2 and ACE2 had a high expression in the organs which had corresponding clinical features in death patients.ConclusionMale, age and heart disease were the main risk factors of death. Beside, asymptomatic patients with serious coexisting disorders may also die of SARS-CoV-2. Thus, more attention should be paid to the old patients with heart disease and asymptomatic patients in the treatment.
Clinical characteristics of 34 COVID-19 patients admitted to ICU in Hangzhou, China
Authors: Zheng Yi , Sun Lijun , Xu Mi , Pan Jian , Zhang Yuntao , Fang Xueling , Fang Qiang , Cai Hongliu 
Published: April 2020

AbstractIntroductionThe purpose of the study was to summarize the clinical and laboratory characteristics of the coronavirus disease 2019 patients admitted to intensive care unit.MethodsWe tracked the data until March 5, 2020. The cases in our cohort were divided into cases only received noninvasive ventilation (NIV) and cases required invasive mechanical ventilation (IMV). The characteristics between the two groups were compared.Results34 cases were included in the study. The complications rate (including, acute liver injury, acute cardiac injury and acute kidney injury) were higher in IMV cases. Lymphocytopenia and neutrophilia occurred in most cases in both groups on the admission day, however, lymphocyte levels dropped progressively and more severe lymphopenia occurred in IMV group. Increased amounts of plasma IL-6 and IL-10 were found in both groups on the admission day, the progressive decrease of which occurred in NIV cases rather than IMV cases, and the levels were higher in IMV cases during hospitalization.ConclusionsLymphocytopenia, neutrophilia, and increase of IL-6 and IL-10 occurred in SARS-CoV-2 infected patients in ICU, however, the dynamics of those were significantly different in IMV cases and NIV cases during hospitalization.
Deflating the RNA Mg2+bubble. Stereochemistry to the rescue!
Authors: Auffinger Pascal , Ennifar Eric , D’Ascenzo Luigi 
Published: April 2020

AbstractProper evaluation of the ionic structure of biomolecular systems remains challenging in X-ray and cryo-EM techniques but is essential for advancing our understanding of complex structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+in the deposited structures and underrate the importance of stereochemical rules to correctly assign these ions. Herein, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure and establish that stereochemical principles should always be considered when evaluating ion binding features, even when K+anomalous signals are available as it is the case for 6QNR. Assignment errors can result in misleading conceptions of the solvent structure of ribosomes and other RNA systems and should therefore be avoided. Our analysis resulted in a significant decrease of bound Mg2+ions in the 6QNR structure, suggesting that K+and not Mg2+is the prevalent ion in the ribosome 1stsolvation shell. We stress that the use of proper stereochemical guidelines is critical for deflating the current Mg2+bubble witnessed in many ribosome and other RNA structures. Herewith, we would like to draw the attention of the researchers interested in the ionic structure of biomolecular systems on the importance and complementarity of stereochemistry and other ion identification techniques such as those pertaining to the detection of anomalous signals of transition metals and K+. We also stress that for the identification of lighter ions such as Mg2+, Na+, …, stereochemistry coupled with high resolution structures remain the best currently available option.
Induction of long-lived potential aestivation states in laboratoryAn. gambiaemosquitoes
Authors: Krajacich Benjamin J. , Sullivan Margery , Faiman Roy , Veru Laura , Graber Leland , Lehmann Tovi 
Published: April 2020

AbstractBackgroundHowAnophelinemosquitoes persist through the long dry season in Africa remains a gap in our understanding of these malaria vectors. To span this period in locations such as the Sahelian zone of Mali, mosquitoes must either migrate to areas of permanent water, recolonize areas as they again become favorable, or survive in harsh conditions including high temperatures, low humidity, and an absence of surface water (required for breeding). Adult mosquitoes surviving through this season must dramatically extend their typical lifespan (averaging 2-3 weeks) to 7 months. Previous work has found evidence that the malaria mosquitoAn. coluzzii, survives over 200 days in the wild between rainy seasons in a presumed state of aestivation (hibernation), but this state has so far not been replicated in laboratory conditions. The inability to recapitulate aestivation in the lab hinders addressing key questions such as how this state is induced, how it affects malaria vector competence, and its impact on disease transmission.MethodsWe compared survivorship of mosquitoes in climate-controlled incubators that adjusted humidity (40-85% RH), temperature (18-27 °C), and light conditions (8-12 hours of light). A range of conditions were chosen to mimic the late rainy and dry seasons as well as relevant extremes these mosquitoes may experience during aestivation.ResultsWe found that by priming mosquitoes in conditions simulating the late wet season in Mali, and maintaining mosquitoes in reduced light/temperature, mean mosquito survival increased from 18.34 +/− 0.65 to 48.02 +/− 2.87 days, median survival increased from 19 (95% CI: 17-21) to 50 days (95% CI: 40-58), and the maximum longevity increased from 38 to 109 days (p-adj < 0.001). While this increase falls short of the 200+ day survival seen in field mosquitoes, this extension is substantially higher than previously found through environmental or dietary modulation and is hard to reconcile with states other than aestivation. Future work will expand on these findings, looking to further extend the gains in life span while also investigating transcriptional changes in genes affecting aging, metabolism, and epigenetic regulation; hormone and nutrient levels; and vector competence for malaria causing parasites.Abstract Figure
Using coverage-based rarefaction to infer non-random species distributions
Authors: Engel Thore , Blowes Shane A. , McGlinn Daniel J. , May Felix , Gotelli Nicholas J. , McGill Brian J. , Chase Jonathan M. 
Published: April 2020

AbstractUnderstanding how species are non-randomly distributed in space, as well as how the resulting spatial structure of diversity responds to ecological, biogeographic and anthropogenic drivers is a critical piece of the biodiversity puzzle. However, most metrics that quantify the spatial structure of diversity (i.e., community differentiation), such as Whittaker’s classical β-diversity metric are influenced by sampling effects. As a result, these measures are influenced by species pool size, species abundance distributions and numbers of individuals. Null models have been proposed to evaluate the degree of differentiation among communities due to spatial structuring relative to that expected from sampling effects. However, to date, these null models do not accommodate the influence of sample completeness (i.e. the proportion of the species pool in the sample). Here, we develop an approach that makes use of individual- and coverage-based rarefaction and extrapolation. Using spatially explicit simulations, we show that our derived metric,βC, captures changes in intraspecific aggregation independently of changes in the species pool size. We then provide two case studies examining spatial structure in forest plots spanning latitudinal gradients: (1) a re-analysis of the “Gentry” plot dataset, and (2) comparing a high diversity plot in Barro Colorado Island, Panama with a low diversity plot in Harvard Forest, Massachusetts, USA. We find no evidence for systematic changes in spatial structure with latitude in these datasets. As it is rooted in biodiversity sampling theory and explicitly controls for sample completeness, our approach represents an important advance over existing null models for spatial aggregation. Potential applications of the approach range from better descriptors of biogeographic diversity patterns to the consolidation of local and regional diversity trends in the current biodiversity crisis.Open research statementThe novel code for the calculation ofβCcan be found in supplementary material S4. Empirical data sets utilized for this research are as follows: Phillips & Miller (2002), Orwig et al. (2015), Condit et al. (2019). Our research repository including the novel code is also available athttps://github.com/t-engel/betaCand will be uploaded to Zenodo upon acceptance of this manuscript.
Cold acclimation has a differential effect on leaf vascular bundle structure and carbon export rates in natural Arabidopsis accessions originating from southern and northern Europe
Authors: Schneider Katja , Abazaj Lorena , Niemann Cornelia , Schröder Laura , Nägele Thomas 
Published: April 2020

AbstractAcclimation to low but non-freezing temperature represents an ecologically important process forArabidopsis thalianabut also for many other plant species from temperate regions. Cold acclimation comprises and affects numerous molecular and physiological processes and the maintenance of sugar supply of sink tissue by photosynthetically active source tissue is preliminary for plant survival. Here, we analysed the correlation of changes in vascular bundle structure at the leaf petiole and sucrose exudation rates before and after cold acclimation. We compared six natural Arabidopsis accessions originating from southern and northern Europe. Photosynthetic capacities, i.e. maximum and effective quantum yield of photosystem II, revealed a significant effect of condition but not of genotype. Only for northern accessions we observed a highly significant negative correlation between leaf sucrose exudation rates, xylem and petiole cross section areas. Further, only for northern accessions we observed a significant increase of vascular bundle and leaf petiole cross section area during cold acclimation. In contrast, variance of cross section areas of cold acclimated southern accessions was strongly reduced compared to control plants while mean areas remained similar under both conditions. In summary, our findings suggest that natural Arabidopsis accessions from northern Europe significantly adjust sink strength and leaf vascular bundle structure to stabilize plant growth and photosynthesis for survival under low and freezing temperature.
Single-cell transcriptomic profiling maps monocyte/macrophage transitions after myocardial infarction in mice
Authors: Rizzo Giuseppe , Vafadarnejad Ehsan , Arampatzi Panagiota , Silvestre Jean-Sébastien , Zernecke Alma , Saliba Antoine-Emmanuel , Cochain Clément 
Published: April 2020

AbstractRationaleMonocytes and macrophages have a critical and dual role in post-ischemic cardiac repair, as they can foster both tissue healing and damage. To decipher how monocytes/macrophages acquire heterogeneous functional phenotypes in the ischemic myocardium, we profiled the gene expression dynamics at the single-cell level in circulating and cardiac monocytes/macrophages following experimental myocardial infarction (MI) in mice.Methods and resultsUsing time-series single-cell transcriptome and cell surface epitope analysis of blood and cardiac monocytes/macrophages, as well as the integration of publicly available and independently generated single-cell RNA-seq data, we tracked the transitions in circulating and cardiac monocyte/macrophage states from homeostatic conditions up to 11 days after MI in mice. We show that MI induces marked and rapid transitions in the cardiac mononuclear phagocyte population, with almost complete disappearance of tissue resident macrophages 1 day after ischemia, and rapid infiltration of monocytes that locally acquire discrete and time-dependent transcriptional states within 3 to 7 days. Ischemic injury induced a shift of circulating monocytes towards granulocyte-like transcriptional features (Chil3, Lcn2, Prtn3). Trajectory inference analysis indicated that while conversion to Ly6Clowmonocytes appears as the default fate of Ly6Chimonocytes in the blood, infiltrated monocytes acquired diverse gene expression signatures in the injured heart, notably transitioning to two main MI-associated macrophage populations characterized by MHCIIhiandTrem2hiIgf1higene expression signatures. Minor ischemia-associated macrophage populations with discrete gene expression signature suggesting specialized functions in e.g. iron handling or lipid metabolism were also observed. We further identified putative transcriptional regulators and new cell surface markers of cardiac monocyte/macrophage states.ConclusionsAltogether, our work provides a comprehensive landscape of circulating and cardiac monocyte/macrophage states and their regulators after MI, and will help to further understand their contribution to post-myocardial infarction heart repair.
The global population of SARS-CoV-2 is composed of six major subtypes
Authors: Júnior Ivair José Morais , Polveiro Richard Costa , Souza Gabriel Medeiros , Bortolin Daniel Inserra , Sassaki Flávio Tetsuo , Lima Alison Talis Martins 
Published: April 2020

AbstractThe World Health Organization characterized the COVID-19 as a pandemic in March 2020, the second pandemic of the 21stcentury. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-stranded RNA betacoronavirus of the familyCoronaviridae. Expanding virus populations, as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for a robust clustering. Here, we proposed the subdivision of the global SARS-CoV-2 population into sixteen well-defined subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3,nsp4,nsp6,nsp12,nsp13 andnsp14) cistrons, structural (spikeandnucleocapsid) and accessory (ORF8) genes. Six virus subtypes were predominant in the population, but all sixteen showed amino acid replacements which might have phenotypic implications. We hypothesize that the virus subtypes detected in this study are records of the early stages of the SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world, a typical founder effect. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing the candidate vaccines or drugs.
Actin binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II
Authors: Hayakawa Yuuki , Takaine Masak , Ngo Kien Xuan , Imai Taiga , Yamada Masafumi D. , Behjat Arash Badami , Umeda Kenichi , Hirose Keiko , Yurtsever Ayhan , Kodera Noriyuki , Tokuraku Kiyotaka , Numata Osamu , Fukuma Takeshi , Ando Toshio , Nakano Kentaro , Uyeda Taro Q.P. 
Published: April 2020

AbstractSubstoichiometric binding of certain actin-binding proteins induces conformational changes in a disproportionally large number of actin protomers in actin filaments. Here, we report a case in which such conformational changes in actin filaments have profound functional consequences. Rng2 is an IQGAP protein implicated in the assembly and contraction of contractile rings inSchizosaccharomyces pombe. We found that the calponin-homology actin-binding domain of Rng2 (Rng2CHD) strongly inhibits the motility of actin filaments on myosin IIin vitro.On skeletal muscle myosin II-coated surfaces, Rng2CHD halved the sliding speed of actin filaments at a binding ratio of 1.3% (=1/77), and virtually stopped movement at a binding ratio of 11% (=1/9). Rng2CHD also inhibited actin movements onDictyosteliummyosin II, but in this case by inducing the detachment of actin filaments from myosin II-coated surfaces. Rng2CHD induced cooperative structural changes of actin filaments accompanied by shortening of the filament helical pitch, and reduced the affinity between actin filaments and subfragment 1 (S1) of muscle myosin II in the presence of ADP. Intriguingly, actin-activated ATPase of S1 was hardly inhibited by Rng2CHD. We suggest that sparsely bound Rng2CHD induces global structural changes of actin filaments and interferes with the force generation by actin-myosin II.