bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sports Related Concussion Impacts Speech Rate and Muscle Function
Authors: Banks Russell E. , Beal Deryk S. , Hunter Eric J. 
Published: June 2020

ABSTRACTObjectiveTo examine speech rate and muscle function in athletes with and without sports related concussion (SRC).MethodsWe recruited 30 athletes aged 19-22 years-old who had sustained a SRC within the past 2 years and 30 pair-wise matched controls with no history of SRC from the student community at Michigan State University. Speech rate and muscle function were evaluated during diadochokinetic (DDK) tasks. Speech rate was measured via average time per syllable, average unvoiced time per syllable, and expert perceptual judgement. Speech muscle function was measured via surface electromyography over the obicularis oris, masseter, and segmental triangle. Group differences were assessed using MANOVA, bootstrapping and predictive ROC analyses.ResultsAthletes with SRC had slower speech rates during DDK tasks than controls as evidenced by longer average time per syllable (F(1, 52) = 11.072, p =.002, [95% CI : .01 to .04]), longer average unvoiced time per syllable (F(1, 52) = 16.031, p < .000, [95% CI : .01 to .029] and expert judgement of slowed rate (F(1, 22) = 9.782, p = .005, [95% CI : .163 to .807]). Rate measures were predictive of concussion history. Further, athletes with SRC required more speech muscle activation than controls to complete the DDK tasks (F(1, 3) = 17.12, p =.000, [95% CI: .003 to .006]).ConclusionWe found clear evidence of slowed speech and increased muscle activation during the completion of DDK tasks in athletes with SRC histories relative to controls. Speech rate and muscle assessment should be incorporated into clinical evaluation of concussion.
An Extended Laboratory Validation Study and Comparative Performance Evaluation of the Abbott ID NOW™ COVID-19 Assay in a Coastal California Tertiary Care Medical Center
Authors: Comer Stewart , Fisk David 
Published: June 2020

AbstractThe Abbott ID NOW™ COVID-19 assay is a rapid molecular diagnostic test particularly designed for on-site, rapid turnaround point of care (POC) testing. The utilization of rapid diagnostic tests is integral to optimizing workflow within the hospital and/or procedural-based clinics. The capability to provide both rapid disposition and correct patient classification during this COVID-19 pandemic is critically important with broad infection control implications for both patients and healthcare staff. A tightly controlled, extended laboratory validation was performed at our medical center to determine the negative test agreement of the Abbott ID NOW™ compared with the BD MAX™ analyzer, a laboratory-based, two target, molecular analyzer with a sensitive cycle threshold (Ct) positive cutoff value of ≤ 42. There was strict adoption of the procedures listed in the Abbott ID NOW™ Instruction for Use (IFU)1 insert delineating preferred practices for “optimal test performance.” Under these conditions, our institution demonstrated a significant negative percent agreement with 116 out of 117 patients correlating, which equates to a 99.1% concordance similar to a recently reported correlation study2.
Impact of weather indicators on the COVID-19 outbreak: A multi-state study in India
Authors: Singh Kuldeep , Agarwal Aryan 
Published: June 2020

AbstractThe present study examines the impact of weather indicators on the COVID-19 outbreak in the majorly affected states of India. In this study, we hypothesize that the weather indicators could significantly influence the impact of the corona virus. The Kendall and Spearman rank correlation tests were chosen to conduct the statistical analysis. In this regard, we compiled a daily dataset including confirmed case counts, Recovered case counts, Deceased cases, Average Temperature, Maximum Relative Humidity, Maximum Wind Speed for six most affected states of India during the period of March 25, 2020 to April 24, 2020. We investigated that the average Humidity and Average Temperature seven days ago play a significant role in the recovery of coronavirus cases. The rise in average temperature will improve the recovery rate in the days to come. The cities with very high humidity levels or dry weather conditions have high probabilities of recovery from COVID-19. The findings of this research will help the policymakers to identify risky geographic areas and enforce timely preventive measures.
Risk factors for critical-ill events of patients with COVID-19 in Wuhan, China: a retrospective cohort study
Authors: Yang Sen , Ma Le , Wang Yu-Lan , Wang Qian , Tong Qiang , Chen Miao , Zhang Hua , Yu De-Hua , Dai Sheng-Ming , Cui Ran 
Published: June 2020

AbstractBackgroundLittle is known about the risk factors for critical-ill events (intensive care, invasive ventilation, or death) in patients with COVID-19.MethodsPatients with laboratory-confirmed COVID-19 admitted to the Wuhan Leishenshan Hospital from February 13 to March 14 was retrospectively analyzed. Demographic data, symptoms, laboratory values at baseline, comorbidities, treatments and clinical outcomes were extracted from electronic medical records and compared between patients with and without critical-ill events. The least absolute shrinkage and selection operator (LASSO) and multivariate logistic regression models were developed to explore the risk factors for critical-ill events. A risk nomogram was established to predict the probability for the critical-ill events. Survival analysis of patients with critical-ill events was performed by the Kaplan-Meier method.Results463 COVID-19 patients were included in this study, of whom 397 were non-critically ill and 66 were critically ill (all from the intensive care unit). The LASSO regression identified four variables (hypersensitive cardiac troponin I, blood urea nitrogen, haemoglobin, and interleukin-6) contributing to the critical-ill events. Multivariable regression showed increasing odds of in-hospital critical-ill events associated with hypersensitive cTnI greater than 0.04 ng/mL (OR 20.98,95% CI 3.51-125.31), blood urea nitrogen greater than 7.6 mmol/L (OR 5.22, 95% CI 1.52-17.81, decreased haemoglobin (OR 1.06, 95% CI 1.04-1.10), and higher interleukin-6 (OR 1.05, 95% CI 1.02-1.08) on admission.ConclusionsHypersensitive cTnI greater than 0.04 ng/mL, blood urea nitrogen greater than 7.6 mmol/L, decreased haemoglobin, and high IL-6 were risk factors of critical-ill events in patients with COVID-19.Main pointHypersensitive cTnI greater than 0.04 ng/mL, BUN greater than 7.6 mmol/L, decreased haemoglobin, and high IL-6 were risk factors of critical-ill events (intensive care, invasive ventilation, or death) in patients with COVID-19.
Innate immune signaling in the olfactory epithelium reduces odorant receptor levels: modeling transient smell loss in COVID-19 patients
Authors: Rodriguez Steven , Cao Luxiang , Rickenbacher Gregory T. , Benz Eric G. , Magdamo Colin , Gomez Liliana Ramirez , Holbrook Eric H. , Albers Alefiya D. , Gallagher Rose , Westover M. Brandon , Evans Kyle E. , Tatar Daniel J. , Mukerji Shibani , Zafonte Ross , Boyer Edward W , Yu C. Ron , Albers Mark W. 
Published: June 2020

AbstractPost-infectious anosmias typically follow death of olfactory sensory neurons (OSNs) with a months-long recovery phase associated with parosmias. While profound anosmia is the leading symptom associated with COVID-19 infection, many patients regain olfactory function within days to weeks without distortions. Here, we demonstrate that sterile induction of anti-viral type I interferon signaling in the mouse olfactory epithelium is associated with diminished odor discrimination and reduced odor-evoked local field potentials. RNA levels of all class I, class II, and TAAR odorant receptors are markedly reduced in OSNs in a non-cell autonomous manner. We find that people infected with COVID-19 rate odors with lower intensities and have odor discrimination deficits relative to people that tested negative for COVID-19. Taken together, we propose that inflammatory-mediated loss of odorant receptor expression with preserved circuit integrity accounts for the profound anosmia and rapid recovery of olfactory function without parosmias caused by COVID-19.
Long time frames to detect the impact of changing COVID-19 control measures
Authors: Stockdale Jessica E , Doig Renny , Min Joosung , Mulberry Nicola , Wang Liangliang , Elliott Lloyd T , Colijn Caroline 
Published: June 2020

AbstractBackgroundMany countries have implemented population-wide interventions such as physical distancing measures, in efforts to control COVID-19. The extent and success of such measures has varied. Many jurisdictions with declines in reported COVID-19 cases are moving to relax measures, while others are continuing to intensify efforts to reduce transmission.AimWe aim to determine the time frame between a change in COVID-19 measures at the population level and the observable impact of such a change on cases.MethodsWe examine how long it takes for there to be a substantial difference between the cases that occur following a change in control measures and those that would have occurred at baseline. We then examine how long it takes to detect a difference, given delays and noise in reported cases. We use changes in population-level (e.g., distancing) control measures informed by data and estimates from British Columbia, Canada.ResultsWe find that the time frames are long: it takes three weeks or more before we might expect a substantial difference in cases given a change in population-level COVID-19 control, and it takes slightly longer to detect the impacts of the change. The time frames are shorter (11-15 days) for dramatic changes in control, and they are impacted by noise and delays in the testing and reporting process, with delays reaching up to 25-40 days.ConclusionThe time until a change in broad control measures has an observed impact is longer than is typically understood, and is longer than the mean incubation period (time between exposure than onset) and the often used 14 day time period. Policy makers and public health planners should consider this when assessing the impact of policy change, and efforts should be made to develop rapid, consistent real-time COVID-19 surveillance.
First SARS-CoV-2 detection in river water: implications in low sanitation countries
Authors: Guerrero-Latorre Laura , Ballesteros Isabel , Villacrés Irina M. , Granda M. Genoveva , Freire Byron P. , Ríos-Touma Blanca 
Published: June 2020

AbstractSince the beginning of SARS-CoV-2 pandemic studies on viral shedding have reported that this virus is excreted in feces in most patients. High viral loads are found at the sewage pipeline or at the entrance of wastewater treatment plants from cities where the number of COVID-19 cases are significant. In Quito (Ecuador) as in many other cities worldwide, wastewater is directly discharged into natural waters. The aim of this study was to evaluate SARS-CoV-2 presence in urban streams from a low sanitation context. Three river locations along the urban rivers of Quito were sampled on the 5th of June during a peak of COVID-19 cases. River samples were evaluated for water quality parameters and afterwards, concentrated for viral analysis using skimmed milk flocculation method. The viral concentrates were quantified for SARS-CoV-2 (N1 and N2 genes) and Human Adenovirus as a human viral indicator. The results showed that SARS-CoV-2 was detected for both target genes in all samples analyzed in a range of 2,91E+05 to 3,19E+06 GC/L for N1 and from 2,07E+05 to 2,22E+06 GC/L for N2. The high values detected in natural waters from a low sanitation region have several implications in health and ecology that should be further assessed.
stLFRsv: a germline SV analysis pipeline using co-barcoded reads
Authors: Guo Junfu , Shi Chang , Chen Xi , Wang Ou , Liu Ping , Yang Huanming , Xu Xun , Zhang Wenwei , Zhu Hongmei 
Published: June 2020

AbstractCo-barcoded reads originated from long DNA fragment (mean length larger than 50Kbp) with barcodes, maintain both single base level accuracy and long range genomic information. We propose a pipeline stLFRsv to detect structure variation using co-barcoded reads. stLFRsv identifies abnormally large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structure variations. The barcodes enabled co-barcoded reads phasing increases the signal to noise ratio and barcode sharing profiles are used to filter out false positives. We integrate the short reads SV caller smoove for smaller variations with stLFRsv. The integrated pipeline was evaluated on the well characterized genome HG002/NA24385 and obtained precision and recall rate of 74.2% and 22.3% for deletion on the whole genome. stLFR found some large variations not included in the benchmark set and verified by means of long reads or assembly. Our work indicates that co-barcoded reads technology has the potential to improve genome completeness.
Modulation of Aplnr signaling is required during the development and maintenance of the hematopoietic system
Authors: Jackson Melany , Fidanza Antonella , Taylor A. Helen , Rybtsov Stanislav , Axton Richard , Kydonaki Maria , Meek Stephen , Burdon Tom , Medvinsky Alexander , Forrester Lesley M. 
Published: June 2020

ABSTRACTApelin receptor (Aplnr/Agtrl1/Apj) marks a transient cell population during the differentiation of hematopoietic progenitor cells (HPCs) from pluripotent stem cells but the function of this signalling pathway during hematopoietic development both in vitro and in vitro is poorly understood. We generated an Aplnr-null mouse embryonic stem cell (mESC) line and demonstrated that they are significantly impaired in the production of HPCs indicating that the Aplnr pathway is required for their formation. Using Aplnr-tdTomato reporter mESCs we demonstrated that is expressed in a population of differentiating mesodermal cells committed to a hematopoietic and endothelial fate. Activation of this signaling pathway by the addition of the Apelin ligand to differentiating ESCs has no effect on the production of HPCs but the addition toex vivoAGM cultures impaired the generation of long term reconstituting hematopoietic stem cells and appeared to drive myeloid differentiation. Taken together, our data suggest that the Aplnr pathway is required for the generation of cells that give rise to HSCs during development but its subsequent down regulation is required for their maintenance.HIGHLIGHTSHematopoietic differentiation is impaired in Aplnr-null ESCsAplnr-tdTomato reporter marks a subpopulation of ESC-derived mesoderm.Aplnr signaling drives the maturation of lineage-committed myeloid progenitorsIn AGM explant cultures HSC activity is reduced in the presence of Aplnr ligands.
Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution
Authors: Overholt Kalon J. , Krog Jonathan R. , Bryson Bryan D. 
Published: June 2020

ABSTRACTAs the global COVID-19 pandemic continues to escalate, no effective treatment has yet been developed for the severe respiratory complications of this disease. This may be due in large part to the unclear immunopathological basis for the development of immune dysregulation and acute respiratory distress syndrome (ARDS) in severe and critical patients. Specifically, it remains unknown whether the immunological features of the disease that have been identified so far are compartment-specific responses or general features of COVID-19. Additionally, readily detectable biological markers correlated with strata of disease severity that could be used to triage patients and inform treatment options have not yet been identified. Here, we leveraged publicly available single-cell RNA sequencing data to elucidate the common and compartment-specific immunological features of clinically severe COVID-19. We identified a number of transcriptional programs that are altered across the spectrum of disease severity, few of which are common between the lung and peripheral immune environments. In the lung, comparing severe and moderate patients revealed severity-specific responses of enhanced interferon, A20/IκB, IL-2, and IL-6 pathway signatures along with broad signaling activity ofIFNG, SPP1, CCL3, CCL8, andIL18across cell types. These signatures contrasted with features unique to ARDS observed in the blood compartment, which included depletion of interferon and A20/IκB signatures and a lack of IL-6 response. The cell surface markerS1PR1was strongly upregulated in patients diagnosed with ARDS compared to non-ARDS patients in γδ T cells of the blood compartment, and we nominate S1PR1 as a potential marker for immunophenotyping ARDS in COVID-19 patients using flow cytometry.HIGHLIGHTSCOVID-19 disease severity is associated with a number of compositional shifts in the cellular makeup of the blood and lung environments.Transcriptional data suggest differentially expressed cell surface proteins as markers for COVID-19 immunophenotyping from BALF and PBMC samples.Severity-specific features COVID-19 manifest at the pathway level, suggesting distinct changes to epithelia and differences between local and systemic immune dynamics.Immune-epithelial cellular communication analysis identifies ligands implicated in transcriptional regulation of proto-oncogenes in the lung epithelia of severe COVID-19 patients.Network analysis suggests broadly-acting dysregulatory ligands in the pulmonary microenvironment as candidate therapeutic targets for the treatment of severe COVID-19.
Hypoxia induced sex-difference in zebrafish brain proteome profile reveals the crucial role of H3K9me3 in recovery from acute hypoxia
Authors: Das Tapatee , Kamle Avijeet , Kumar Arvind , Chakravarty Sumana 
Published: June 2020

ABSTRACTUnderstanding the molecular basis of sex differences in neural response to acute hypoxic insult has profound implications for the effective prevention and treatment of ischemic stroke. Global hypoxic-ischemic induced neural damage has been studied recently under the well-controlled, non-invasive, reproducible conditions using zebrafish model. Our earlier report on sex difference in global acute hypoxia induced neural damage and recovery in zebrafish prompted us for comprehensive study on the mechanisms underlying the recovery. An omics approach for studying quantitative changes in brain proteome upon hypoxia insult following recovery was undertaken using iTRAQ-based LC-MS/MS approach. The results shed light on altered expression of many regulatory proteins in zebrafish brain upon acute hypoxia following recovery. The sex difference in differentially expressed proteins along with the proteins expressed in uniform direction in both the sexes was studied. Core expression analysis by Ingenuity Pathway analysis (IPA) showed a distinct sex difference in the disease function heatmap. Most of the upstream regulators obtained through IPA were validated at the transcriptional level. Translational upregulation of H3K9me3 in male led us to elucidate the mechanism of recovery by confirming transcriptional targets through ChIP-qPCR. The upregulation of H3K9me3 level in male at 4 hr post-hypoxia appears to affect the early neurogenic markers nestin, klf4 and sox2, which might explain the late recovery in male, compared to female. Acute hypoxia-induced sex-specific comparison of brain proteome led us to reveal many differentially expressed proteins, which can be further studied for the development of novel targets for better therapeutic strategy.
Age-related dedifferentiation and hyperdifferentiation of perceptual and mnemonic representations
Authors: Deng Lifu , Davis Simon W. , Monge Zachary A. , Wing Erik A. , Geib Benjamin R. , Raghunandan Alex , Cabeza Roberto 
Published: June 2020

AbstractPreliminary evidence indicates that occipito-temporal activation patterns for different visual stimuli are less distinct in older (OAs) than younger (YAs) adults, suggesting a dedifferentiation of visual representations with aging. Yet, it is unclear if this deficit (1) affects only sensory or also categorical aspects of representations during visual perception (perceptual representations), and (2) affects only perceptual or also mnemonic representations. To investigate these issues, we fMRI-scanned YAs and OAs viewing and then remembering visual scenes. First, using representational similarity analyses, we distinguished sensory vs. categorical features of perceptual representations. We found that, compared to YAs, sensory features in early visual cortex were less differentiated in OAs (i.e., age-related dedifferentiation), replicating previous research, whereas categorical features in anterior temporal lobe (ATL) were more differentiated in OAs. This is, to our knowledge, the first report of anage-related hyperdifferentiation. Second, we assessed the quality of mnemonic representations by measuring encoding-retrieval similarity (ERS) in activation patterns. We found that aging impaired mnemonic representations in early visual cortex and hippocampus but enhanced mnemonic representations in ATL. Thus, both perceptual and mnemonic representations in ATL were enhanced by aging. In sum, our findings suggest that aging impairs visual and mnemonic representations in posterior brain regions but enhances them in anterior regions.
An Atlas of Phosphorylation and Proteolytic Processing Events During Excitotoxic Neuronal Death Reveals New Therapeutic Opportunities
Authors: Ameen S. Sadia , Dufour Antoine , Hossain M. Iqbal , Hoque Ashfaqul , Sturgeon Sharelle , Nandurkar Harshal , Draxler Dominik , Medcalf Robert , Kamaruddin Mohd Aizuddin , Lucet Isabelle S. , Leeming Michael G. , Liu Dazhi , Dhillon Amardeep , Lim Jet Phey , Zhu Hong-Jian , Bokhari Laita , Roulston Carli , Kleifeld Oded , Giuseppe D. Ciccotosto , Williamson Nicholas A. , Ang Ching-Seng , Cheng Heung-Chin 
Published: June 2020

SummaryExcitotoxicity, a neuronal death process in neurological disorders, is initiated by over-stimulation of neuronal ionotropic glutamate receptors. The over-stimulated receptors dysregulate proteases, protein kinases and phosphatases, which in turn modify target neuronal proteins to induce cell death. To decipher this cell death mechanism, we used quantitative proteomics, phosphoproteomics and N-terminomics to identify modified proteins in excitotoxic neurons. Data, available in ProteomeXchange (identifiers: PXD019527 and PXD019211), enabled us to identify over one thousand such proteins with calpains, cathepsins and over twenty protein kinases as their major modifiers. These protein modification events can potentially perturb signalling pathways governing cell survival, synaptogenesis, axonal guidance and mRNA processing. Importantly, blocking the modification of Src protein kinase, a signalling hub in excitotoxic neurons, protected against neuronal lossin vivoin a rat model of neurotoxicity. Besides offering new insights into excitotoxic neuronal death mechanism, our findings suggest potential neuroprotective therapeutic targets for treating neurological disorders.Graphical abstractHighlightsMulti-dimensional proteomic analysis identified proteins modified by proteolysis and altered phosphorylation in neurons undergoing excitotoxic cell death.Calpains, cathepsins and over twenty protein kinases are major modifiers of these proteins.These protein modification events are predicted to impact cell survival, axonal guidance, synaptogenesis and mRNA processing.Blocking modification of an identified protein Src, which acts as a major signalling hub in neurons, was protective against excitotoxic injuryin vivo.In BriefUsing multidimensional proteomic approaches, Ameen,et al. mapped the changes of proteome, phosphoproteome and N-terminome of cultured primary neurons during excitotoxicity, a crucial neuronal death process in neurological disorders. These proteomic changes document new excitotoxicity-associated molecular events, and offer insights into how these events are organized to induce neuronal death. Potential therapeutic relevance of these molecular events is illustrated by the demonstration thatin vivoblockade of one of these events could protect against excitotoxic neuronal loss.