bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive and analysis of COVID-19 cases cumulative total: ARIMA model based on machine learning
Authors: Yan Zehui , Wang Yanding , Yang Meitao , Li Zhiqiang , Gong Xinran , Wu Di , Zhang Wenyi , Wang Yong 
Published: January 2022

AbstractAt present, COVID-19 poses a serious threat to global human health, and the cumulative confirmed cases in America, Brazil and India continue to grow rapidly. Therefore, the prediction models of cumulative confirmed cases in America, Brazil and India from August 1, 2021 to December 31, 2021 were established. In this study, the prevalence data of COVID-19 from 1 August 2021 to 31 December 2021 were collected from the World Health Organization website. Several ARIMA models were formulated with different ARIMA parameters. ARIMA (7,2,0), ARIMA (3,2,1), and ARIMA (10,2,4) models were selected as the best models for America, Brazil, and India, respectively. Initial combinations of model parameters were selected using the automated ARIMA model, and the optimized model parameters were then found based on Bayesian information criterion (BIC). The analytical tools autocorrelation function (ACF), and partial autocorrelation function (PACF) were used to evaluate the reliability of the model. The performance of different models in predicting confirmed cases from January 1, 2022 to January 5, 2022 was compared by using root mean square error (RMSE), mean absolute error (MAE), and mean absolute percentage error (MAPE). This study shows that ARIMA models are suitable for predicting the prevalence of COVID-19 in the future. The results of the analysis can shed light on understanding the trends of the outbreak and give an idea of the epidemiological stage of these regions. Besides, the prediction of COVID-19 prevalence trends of America, Brazil, and India can help take precautions and policy formulation for this epidemic in other countries.
The effect of COVID-19 mRNA vaccine on human lung carcinoma cells in vitro by means of Raman spectroscopy and imaging
Authors: Abramczyk Halina , Surmacki Jakub 
Published: January 2022

AbstractThe effect of COVID-19 mRNA vaccine on human lung carcinoma epithelial cells (A549) in vitro as a convenient preclinical model has been studied by means of Raman spectroscopy and imaging. The paper focuses on Raman imaging as a tool to explore apoptosis and oxidative phosphorylation in mitochondrial dysfunctions. The Raman results demonstrate alterations in the oxidation-reduction pathways associated with cytochrome c. We found that the COVID-19 mRNA vaccine downregulates the concentration of cytochrome c upon incubation with tumorous lung cells. Concentration of oxidized form of cytochrome c in mitochondria of lung cells decreases upon incubation the COVID-19 mRNA vaccine. Lower concentration of oxidized cytochrome c in mitochondria illustrates lower effectiveness of oxidative phosphorylation (respiration), reduced apoptosis and lessened ATP production. Moreover, mRNA vaccine increases significantly de novo lipids synthesis in lipid droplets up to 96 hours and alterations in biochemical composition. It seems that lipid composition of cells returns to the normal level for longer incubation time (14 days). In cell nucleus the mRNA vaccine does not produce statistically significant changes. The observed alterations in biochemical profiles upon incubation with mRNA vaccine in the specific organelles of the tumorous lung cells are similar to those we observe for other types of cancers, particularly brain glial cells.
Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export
Authors: Gomez-Martinez Ismael , Bliton R. Jarrett , Breau Keith A. , Czerwinski Michael J. , Williamson Ian A. , Wen Jia , Rawls John F. , Magness Scott T. 
Published: January 2022

AbstractBackground & AimsAbsorption, metabolism, and export of dietary lipids occurs in the small intestinal epithelium. Caco-2 and organoids have been used to study these processes but are limited in physiological relevance or preclude simultaneous apical and basal access. Here, we develop a high-throughput planar human absorptive enterocyte (AE) monolayer system for investigating lipid-handling, then evaluate the role of fatty acid oxidation (FAO) in fatty acid (FA) export, using etomoxir, C75, and anti-diabetic drug, metformin.MethodsSingle-cell RNA-sequencing (scRNAseq), transcriptomics, and lineage trajectory was performed on primary human jejunum.In vivoAE maturational states informed conditions used to differentiate human intestinal stem cells (ISCs) that mimicin vivoAE maturation. The system was scaled for high-throughput drug screening. Fatty acid oxidation (FAO) was pharmacologically modulated and BODIPY™ (B)-labelled FAs were used to evaluate FA-handling via fluorescence and thin layer chromatography (TLC).ResultsscRNAseq shows increasing expression of lipid-handling genes as AEs mature. Culture conditions promote ISC differentiation into confluent AE monolayers. FA-handling gene expression mimicsin vivomaturational states. FAO inhibitor, etomoxir, decreased apical-to-basolateral export of medium-chain B-C12 and long-chain B-C16 FAs whereas CPT1 agonist, C75, and antidiabetic drug, metformin, increased apical-to-basolateral export. Short-chain B-C5 was unaffected by FAO inhibition and diffused through AEs.ConclusionsPrimary human ISCs in culture undergo programmed maturation. AE monolayers demonstratein vivomaturational states and lipid-handling gene expression profiles. AEs create strong epithelial barriers in 96-Transwell format. FA export is proportional to FAO. Metformin enhances FAO and increases basolateral FA export, supporting an intestine-specific role.
Human sialomucin CD164 is an essential entry factor for lymphocytic choriomeningitis virus
Authors: Liu Jamin , Knopp Kristeene A. , Rackaityte Elze , Wang Chung Yu , Laurie Matthew T. , Sunshine Sara , Puschnik Andreas S , DeRisi Joseph L 
Published: January 2022

AbstractLymphocytic choriomeningitis virus (LCMV) is a well-studied mammarenavirus that can be fatal in congenital infections. However, our understanding of LCMV and its interactions with human host factors remain incomplete. Here, host determinants affecting LCMV infection were investigated through a genome-wide CRISPR knockout screen in A549 cells, a human lung adenocarcinoma line. We identified and validated a variety of novel host factors that play a functional role in LCMV infection. Among these, knockout of the sialomucin CD164, a heavily glycosylated transmembrane protein, was found to ablate infection with multiple LCMV strains but not other hemorrhagic mammarenaviruses, in several cell types. Further characterization revealed a dependency of LCMV entry on the cysteine-rich domain of CD164, including a N-linked glycosylation site at residue 104 in that region. Given the documented role of LCMV with respect to transplacental human infections, CD164 expression was investigated in human placental tissue and placental cell lines. CD164 was found to be highly expressed in the cytotrophoblast cells, an initial contact site for pathogens within the placenta, and LCMV infection in placental cells was effectively blocked using a monoclonal antibody specific to the cysteine-rich domain of CD164. Together, this study identifies novel factors associated with LCMV infection of human tissues, and highlights the importance of CD164, a sialomucin that has previously not been associated with viral infection.
Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium
Authors: Doing Georgia , Lee Alexandra J. , Neff Samuel L. , Holt Jacob D. , Stanton Bruce A. , Greene Casey S. , Hogan Deborah A. 
Published: January 2022

AbstractOver the past two decades, thousands of RNA sequencing (RNA-seq) gene expression profiles of Pseudomonas aeruginosa have been made publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In the work we present here, we draw on over 2,300 P. aeruginosa transcriptomes from hundreds of studies performed by over seventy-five different research groups. We first developed a pipeline, using the Salmon pseudo-aligner and two different P. aeruginosa reference genomes (strains PAO1 and PA14), that transformed raw sequence data into a uniformly processed data in the form of sample-wise normalized counts. In this workflow, P. aeruginosa RNA-seq data are filtered using technically and biologically driven criteria with characteristics tailored to bacterial gene expression and that account for the effects of alignment to different reference genomes. The filtered data are then normalized to enable cross experiment comparisons. Finally, annotations are programmatically collected for those samples with sufficient meta-data and expression-based metrics are used to further enhance strain assignment for each sample. Our processing and quality control methods provide a scalable framework for taking full advantage of the troves of biological information hibernating in the depths of microbial gene expression data. The re-analysis of these data in aggregate is a powerful approach for hypothesis generation and testing, and this approach can be applied to transcriptome datasets in other species.SignificancePseudomonas aeruginosa causes a wide range of infections including chronic infections associated with cystic fibrosis. P. aeruginosa infections are difficult to treat and people with CF-associated P. aeruginosa infections often have poor clinical outcomes. To aid the study of this important pathogen, we developed a methodology that facilitates analyses across experiments, strains, and conditions. We aligned, filtered for quality and normalized thousands of P. aeruginosa RNA-seq gene expression profiles that were publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The workflow that we present can be efficiently scaled to incorporate new data and applied to the analysis of other species.
Characterization and identification of a novel daidzein reductase involved in (S)-equol biosynthesis in Clostridium C1
Authors: Hu Yun-fei , Yang Chun-Fang , Song Can , Zhong Wei-Xuan , Li Bai-yuan , Cao Lin-yan , Chen Hua-hai , Zhao Chang-Hui , Yin Ye-shi 
Published: January 2022

Abstract(S)-equol is an isoflavone with high estrogen-like activity and no toxic effects in the human body, and is only produced by some gut bacteria in vivo. It plays an important role in maintaining individual health, however, the dearth of resources associated with (S)-equol-producing bacteria has seriously restricted the production and application of (S)-equol. We report here a novel functional gene C1-07020 that was identified from a chick (S)-equol-producing bacterium (Clostridium C1). We found that recombinant protein of C1-07020 possessed similar function to daidzein reductase (DZNR), which can convert daidzein (DZN) into R/S-dihydrodaidzein (R/S-DHD). Interestingly, C1-07020 can reverse convert (R/S)-DHD (DHD oxidases) into DZN even without cofactors or anaerobic conditions. Additionally, high concentrations of (S)-equol can directly promote DHD oxidase but inhibit DZNR activity. Molecular docking and site-directed mutagenesis revealed that the amino acid Arg 75 was the active site of DHD oxidases. Subsequently, an engineered E. coli strain based on C1-07020 was constructed and showed higher yield of (S)-equol than the engineered bacteria from our previous work. Metagenomics analysis and PCR detection surprisingly revealed that C1-07020 and related bacteria may be prevalent in the gut of humans and animals and their (S)-equol production state may cause differed between (S)-equol producer and non-producer. Overall, a novel DZNR from Clostridium C1 was found and identified in this study, and its bidirectional enzyme activities and wide distribution in the gut of humans and animals provide alternative strategies for revealing the individual regulatory mechanisms of (S)-equol-producing bacteria.Importance(S)-equol is a final product of DZN that metabolized by some enteric bacteria. Although (S)-equol played very important roles in maintaining human health, larger differences in equol production varied between different populations. Here, a novel DZNR gene C1-07020, which related to (S)-equol production, was reported. The bidirectional enzyme functions and wide distribution of C1-07020 in human and animal gut provided additional insights into the metabolic regulation of (S)-equol. Additionally, C1-07020 can be used for improving the production of (S)-equol in vitro.
Lung Perfusion Disturbances Detected with MRI in Non-Hospitalized Post-COVID-19 Individuals with Dyspnea 3 -13 Months after the Acute Disease
Authors: Yu Jimmy , Granberg Tobias , Shams Roya , Petersson Sven , Sköld Magnus , Nyrén Sven , Lundberg Johan 
Published: January 2022

AbstractBackgroundDyspnea is a prevalent symptom in the post-COVID-19 condition, though its mechanisms are largely unknown. Lung perfusion abnormalities have been reported in acute COVID-19 and could be suspected in patients with lingering dyspnea after the acute phase.ObjectivesTo detect pulmonary perfusion disturbances in non-hospitalized post-COVID condition with persistent dyspnea 4-13 months after the disease onset.MethodsNon-hospitalized individuals reporting persistent dyspnea after COVID-19 and matched healthy controls were prospectively recruited between October 2020 and May 2021 to undergo pulmonary dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), six-minute walk test, and self-reported scales questionnaires on dyspnea and physical activity. The DCE-MRI perfusion images were quantified into two parametric values: mean time-to-peak (TTP) and TTP ratio.ResultsTwenty-eight persons with post-COVID condition and persistent dyspnea (mean age 46.5±8.0 years, 75% women) and 22 healthy controls (mean age 44.1±10.8 years, 73% women) were included. The post-COVID group had higher mean pulmonary TTP (0.43±0.04 vs. 0.41±0.03, P=0.011) and higher TTP ratio (0.096±0.052 vs. 0.068±0.027, P=0.032). Notably, post-COVID males had the highest values (mean TTP 0.47±0.02, TTP ratio 0.160±0.039, P<0.001 for both values compared to male controls and post-COVID females). Correlation between dyspnea and perfusion parameters was demonstrated in the males (r=0.83, P<0.001 for mean TTP; r=0.76, P=0.003 for TTP ratio), but not in females.ConclusionsLung perfusion disturbances were detected in males reporting post-COVID dyspnea using perfusion parameters from DCE-MRI. The distinct sex difference has implications for understanding the perplexing post-COVID pathophysiology and warrants future studies. DCE-MRI could provide biomarkers for such studies.
Comparative immunogenicity of heterologous versus homologous 3rd SARS-CoV-2 vaccine doses in kidney transplant recipients
Authors: Thomson Tina , Prendecki Maria , Gleeson Sarah , Martin Paul , Spensley Katrina , Seneschall Charlotte , Gan Jaslyn , Clarke Candice L. , Lewis Shanice , Pickard Graham , Thomas David , McAdoo Stephen P. , Lightstone Liz , Cox Alison , Kelleher Peter , Willicombe Michelle 
Published: January 2022

AbstractBackgroundSolid organ transplant recipients have attenuated immune responses to SARS-CoV-2 vaccines. Emerging evidence suggests at least equivalent immunogenicity of heterologous compared with homologous vaccine regimens in the general population. In this study, we report on immune responses to 3rd dose BNT162b2 vaccines in transplant recipients either primed with ChAdOx1 or BNT162b2.Methods700 kidney transplant recipients were prospectively screened for serological responses (median time of 33 (21-52) days) following 3 primary doses of a SARS-CoV2 vaccine. All vaccine doses were received post-transplant, and all 3rd doses were BNT162b2. All participants had serological testing performed post-2nd vaccination at a median time of 34 (IQR 26-46) days following the 2nd inoculation, and at least once prior to their 1st dose of vaccine.Results366/700 (52.3%) participants were primed with BNT162b2, whilst 334/700 (47.7) had received ChAdOx1. Overall, 139/700 (19.9%) participants had evidence of prior infection. Of 561 infection naïve participants, 263 (46.9%) had no detectable anti-S following 2-doses of vaccine (V2). 134 (23.9%) participants remained seronegative post 3rd vaccine (V3); 54/291 (18.6%) and 79/270 (29.3%) of participants receiving BNT162b2 and ChAdOx1 respectively, p=0.0029. Median anti-S concentrations were significantly higher post-V3 in patients who had received BNT162b2 compared with ChAdOx1, at 612 (27-234) versus 122 (7.1-1111) BAU/ml respectively, p<0.0001.Cellular responses were investigated in 30 infection naïve participants at a median time of 35 (24-46) days post-V3. Eighteen of 30 (60.0%) participants had undetectable T-cell responses. There were neither qualitative or quantitative differences in T-cell responses between those patients who received BNT162b2 or ChAdOx1 as their first 2-doses, with 10/16 (62.5%) and 8/14 (57.1%) respectively having undetectable T-cell responses, p=0.77.ConclusionA significant proportion of transplant recipients remain seronegative following 3 doses of SARS-CoV-2 vaccines, with anti-S concentrations lower in patients receiving heterologous versus homologous vaccinations.
Incontinence and Healthcare Utilization of Medicare Patients
Authors: Duncan Ian , Stocking Andrew , Fitzner Karen , Ahmed Tamim , Huynh Nhan 
Published: January 2022

AbstractPurposeClaims data are used to directly measure the prevalence of incontinence and incontinence-related events within a large Medicare population.DesignRetrospective analysis.Subjects and SettingsThe study relied on administrative claims data from the CMS Medicare Limited Data Set (5% sample) in 2018. The analysis was limited to fee-for-service (FFS) Medicare beneficiaries with minimum of 3-month enrollment in Parts A & B and at least 65 years old.MethodsWe used diagnosis codes to identify members with incontinence in their 2018 claims experience and grouped these members into 3 categories (urinary incontinent only, fecal incontinent only, and dual incontinent (DI)) and four sites-of-service (nursing home, Skilled-nursing Facility (SNF), home health, and self-care). We then determined the incidence of four types of incontinence-related events for each cohort: 1) Urinary Tract Infections (UTIs), 2) Incontinence-Associated Dermatitis (IAD), 3) Slips and falls, and 4) Behavioral disruptions.ResultsWe found that 11.2 percent of Medicare members had a claims-based diagnosis of incontinence in 2018. This result falls below the estimated share of the over-65 population who are incontinent, as reported in the literature. The prevalence of the four incontinence-related events is significantly higher (between 2 percentage points to 17 percentage points) for members who experience dual incontinence relative to those with only urinary incontinence. On average, those diagnosed with incontinence experienced 5 times more UTIs, two times as many dermatitis events, more than twice as many slips and falls, and 2.8 times more behavior disruptions compared to those without an incontinence diagnosis.ConclusionsAlthough we find that the prevalence of incontinence is under-reported relative to the literature, our results show that those who are diagnosed as incontinent experience a much higher prevalence of UTIs, IAD, slips and falls, and behavioral deterioration compared to those who are not diagnosed as incontinent. Our results suggest that incontinence may be an important indicator diagnosis of many other conditions and, if not well-managed, may challenge the desire for those who are incontinent to age at home.
Pharmacological treatment for connective tissue disease-associated interstitial lung involvement: Protocol for an overview of systematic reviews and meta-analyses
Authors: Karassa Fotini B. , Bougioukas Konstantinos I. , Pelechas Eleftherios , Skalkou Anastasia , Argyriou Evangelia , Haidich Anna-Bettina 
Published: January 2022

AbstractBackgroundInterstitial lung disease (ILD) is the most important pulmonary manifestation of the connective tissue diseases (CTDs) since it is associated with high morbidity and mortality. However, there is uncertainty on what constitutes the optimal treatment options from a variety of competing interventions. The aim of the overview is to summarize existing evidence of the effectiveness and harm of pharmacological therapies for adults with CTD-ILD.MethodsA literature search will be conducted in MEDLINE, the Cochrane Database of Systematic Reviews, DARE, the Centre for Reviews and Dissemination Health Technology Assessment database, Epistemonikos.org, KSR Evidence, and PROSPERO. We will search for systematic reviews and meta-analyses that examine pharmacological treatment for CTD-ILD. Updated supplemental search will also be undertaken to identify additional randomized controlled trials. The primary outcomes will be changes in lung function measures and adverse events. Methodological quality of the included reviews will be assessed using the AMSTAR 2 tool. The overall quality of the evidence will be evaluated using the GRADE rating. Summarized outcome data extracted from systematic reviews will be described in narrative form or in tables. For each meta-analysis we will estimate the summary effect size by use of random-effects and fixed-effects models with 95% confidence intervals, the between-study heterogeneity expressed by I2, and the 95% prediction interval. If feasible, given sufficient data, network meta-analysis will be conducted to combine direct and indirect evidence of class and agent comparisons.DiscussionWhile many factors are crucial in selecting an appropriate treatment for patients with CTD-ILD, evidence for the efficacy and safety of a drug is essential in guiding this decision. Thus, this overview will aid clinicians in balancing risks versus benefits of the available therapies by providing high-quality evidence to support informed decision making and may contribute to future guideline development.Systematic review registrationpending
Mitigating isolation: further comparing the effect of LFD testing for early release from self-isolation for COVID-19 cases
Authors: Bays Declan , Whiteley Timothy , Williams Hannah , Finnie Thomas , Gent Nick 
Published: January 2022

AbstractIn a recent paper, we described how lateral flow device (LFD) testing might be used to reduce the amount of excess time individuals spend in isolation following confirmation of a COVID-19 infection. Through the work presented here, we look to expand upon this and explore in more detail the benefit that such an approach might provide. We use our previously described model to study scenarios through the metrics “proportion released still infectious”, “excess time spent in isolation” (time isolated while no longer infectious), and “time spent infectious after early release”. We also look to consider the effect on these metrics by comparing values obtained when a single negative LFD test is required for early release, versus requiring two and three sequential negative LFD tests. Results show that jointly employing self-isolation and LFD testing may deliver sizeable reductions to the proportion of individuals being release while still infection, the average amount of excess time spent in isolation by those no longer a public health threat, and the average amount of time spent infectious by those released early. These effects considered in conjunction could provide a considerable decrease in the public health risk posed by still infectious individuals being released back into the population by actively monitoring their infection status throughout their isolation period. Such an approach could also help lighten the impact incurred on the individual by reducing the amount of time spent in isolation while posing no further public health risk, in addition to alleviating pressures on the economy and in healthcare settings caused by mass isolation in times of high prevalence.