bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of the COVID-19 epidemic on the department of stomatology in a tertiary hospital: a case study in the General Hospital of the Central Theater Command, Wuhan, China
Authors: Dong Qingshan , Kuria Angelica , Weng Yanming , Liu Yu , Cao Yang 
Published: September 2020

AbstractObjectivesThe aim of this study is to depict the impacts of COVID-19 pandemic on the clinical services and academic activities in the department of stomatology of a tertiary hospitals in Wuhan, China.MethodsWe obtained historical data of the Department of Stomatology from the Health Information System of the General Hospital of Central Theater Command, Wuhan, China between January 2018 and June 2020. Line plots were used to illustrate temporal trend of the variables. Mean ± standard deviation and median with interquartile range were used to summarize the variables. The Kruskal-Wallis equality-of-populations rank test was used to compare the difference between groups.ResultsA significant decrease was noted in the monthly average number of patients seeking the outpatient services for the year 2020. The monthly numbers of patients seeking outpatient services were decreased by two thirds from 2018 to 2020. The number of emergency cases also decreased significantly by 64% in 2020. The monthly number of teaching hours decreased from 3.8 ± 1.5 in 2018 and 4.7 ± 1.4 in 2019 to 1.7 ± 1.9 in 2020. The number of interns also decreased more than 70% in 2020.ConclusionsThe impacts of COVID 19 in the stomatology clinic were significant with notable decreases in clinical services and education offered to the stomatology students. We must find solutions to keep as many as needed dental profession stay on thriving and to remain on the frontline of healthcare.
Effects of an Innovative Training Program for New Graduate Registered Nurses: a Comparison Study
Authors: Xu Fengqin , Wang Yinhe , Ma Liang , Yu Jiang , Li Dandan , Zhou Guohui , Xu Yuzi , Zhang Hailin , Cao Yang 
Published: September 2020

AbstractNew graduate registered nurses (NGRNs) face great challenge during the transition from school to clinical practice. The aim of the study is to evaluate the effects of a new training mode for newly recruited NGRNs in a Chinese teaching hospital. This is a quasi-randomized controlled study. One hundred and fifty NGRNs were randomly selected from a teaching hospital and assigned into two groups. The conventional training and a new training program were taken for the control group and the research group respectively. At the end of training, the two groups were evaluated and compared for theoretical knowledge and operation skills using a self-assessment questionnaire and the Chinese Registered Nurse Core Competency Scale. The theoretical knowledge (88.4 vs. 81.7, p< 0.001), operation skills (94.8 vs. 90.3, p< 0.001), and total core competencies scores (156.2 vs. 148.8, p< 0.05) in the research group were significantly higher than those in the control group. Compared to the control group, the research group had statistically significantly higher scores in education and consultation (2.47 vs. 2.40), clinical nursing (2.87 vs. 2.62), interpersonal relationship (2.56 vs. 2.43), and critical thinking and scientific research (2.78 vs. 2.61). The innovative pre-job training program for NGRNs conducted in Chinese clinical nursing skill training bases could significantly improve the training effect and is worthy of broader implementation.
Smartphone overuse and visual impairment in children and young adults: a systematic review and meta-analysis
Authors: Wang Jian , Li Mei , Zhu Daqiao , Cao Yang 
Published: September 2020

AbstractBackgroundSmartphone overuse has been cited as a potentially modifiable risk factor that can result in visual impairment. However, associations between smartphone overuse and visual impairment have not been consistently reported.ObjectiveThe aim of this systematic review is to determine the association between smartphone overuse and visual impairment, including myopia, blurred vision, and poor vision, in children and young adults.MethodsWe conducted a systematic search in the Cochrane Library, Pubmed, EMBASE, Web of Science Core Collection, and ScienceDirect since the beginning of the databases to June 2020. Fourteen eligible studies (ten cross-sectional studies and four controlled trials) were identified, which included a total of 27110 subjects with mean ages ranging from 9.5 to 26.0 years. We used a random-effects model in the ten cross-sectional studies (n= 26962) and a fixed-effects model in the four controlled trials (n= 148) to combine odds ratios (OR) and effect sizes (ES). TheI2statistics was used to assess heterogeneity.ResultsA pooled OR of 1.05 (95% CI: 0.98, 1.13;p= 0.159) from cross-sectional studies suggests that smartphone overuse is not statistically significantly associated with myopia, poor vision, or blurred vision, however these visual impairments together are more apparent in children (OR = 1.06, 95% CI: 0.99, 1.14; p = 0.087) than in young adults (OR = 0.91, 95% CI: 0.57, 1.46; p = 0.707). In all the controlled trials, the smartphone overuse groups showed worse visual function scores compared with the less-use groups. The pooled ES is 0.76 (95% CI: 0.53, 0.99) and statistically significant (p< 0.001).ConclusionsOur results indicate that longer smartphone use may increase the likelihood of ocular symptoms including myopia, asthenopia, and/or ocular surface disease, especially in children. Thus, regulating use time and restricting the prolonged use of smartphones may prevent ocular and visual symptoms. Further research on the patterns of use, with longer follow-up on the longitudinal associations will help inform detailed guidelines and recommendations for smartphone use in children and young adults.
A novel sample pooling strategy and its application for mass screening of SARS-CoV-2 in an outbreak of COVID-19 in Vietnam
Authors: Thanh Ton That , Nhan Nguyen Thi Thanh , Mai Huynh Kim , Trieu Nguyen Bao , Huy Le Xuan , Thuy Ho Thi Thanh , Chung Le Thanh , Anh Nguyen Ngoc , Hong Nguyen Thi Thu , Thang Bui Duc , Thu Nguyen Thi Hoai , Chi Le Thi Kim , Hanh Nguyen Thi , Hoang Nguyen Huy , Van Vinh Chau Nguyen , Thwaites Guy , Hung Do Thai , Van Tan Le , Yen Ngo Thi Kim 
Published: September 2020

ABSTRACTWe present a sample pooling approach and the results of its application for mass screening of SARS-CoV-2 in >96,000 asymptomatic individuals. Our approach did not compromise the sensitivity of PCR, while increasing the throughput and reducing 77% of the costs. 22/32 asymptomatic cases would have been missed without mass screening.
Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance
Authors:   REACT Study Investigators:, Riley Steven , Ainslie Kylie E. C. , Eales Oliver , Walters Caroline E. , Wang Haowei , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul 
Published: September 2020

SummaryBackgroundBased on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease.MethodsWe report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected.FindingsOver all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber.InterpretationAlthough low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.
Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France
Authors: Germain Nicolas , Herwegh Stéphanie , Hatzfeld Anne-Sophie , Bocket Laurence , Prévost Brigitte , Danze Pierre-Marié , Marchetti Philippe 
Published: September 2020

BackgroundThe COVID-19 pandemic has altered organ and tissue donations as well as transplantation practices. SARS-CoV-2 serological tests could help in the selection of donors. We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA.Methods235 tissue donors at the Lille Tissue bank between November 1, 2019 and March 16, 2020 were included. Archived serum samples were tested for SARS-CoV-2 antibodies using two FDA-approved kits.Results: Most donors were at higher risks for severe COVID-19 illness including age over 65 years (142/235) and/or presence of co-morbidities (141/235). According to the COVID-19 risk assessment of transmission, 183 out of 235 tissue donors presented with a low risk level and 52 donors with an intermediate risk level of donor derived infection. Four out of the 235 (1.7%) tested specimens were positive for anti-SARS-CoV-2 antibodies: 2 donors with anti-N protein IgG and 2 other donors with anti-S protein total Ig. None of them had both type of antibodies. Conclusion: Regarding the seroprevalence among tissue donors, we concluded that the transmission probability to recipient via tissue products was very low at the beginning of the outbreak.
Mortality associated with third generation cephalosporin-resistance in Enterobacteriaceae infections: a multicentre cohort study in Southern China
Authors: Wang Jiancong , Zhou Mouqing , Hesketh Therese , Kritsotakis Evangelos I. 
Published: September 2020

ABSTRACTBackgroundEmerging third generation cephalosporin-resistant Enterobacteriaceae (3GCR-EB) pose a global healthcare concern. We assessed excess mortality in patients infected with 3GCR-EB compared to patients infected with third-generation cephalosporin-susceptible Enterobacteriaceae (3GCS-EB).MethodsThe study cohort comprised all inpatients with a community-onset or healthcare-associated infection caused by Enterobacteriaceae in three tertiary-care public hospitals in 2017. Excess in-hospital mortality was assessed using competing risk survival models, adjusting for baseline patient characteristics.ResultsOf 2,343 study patients (median age 60 years; 45.2% male), 1,481 (63.2%) had 3GCS-EB and 862 (36.8%) 3GCR-EB infection. 494 (57.0%) 3GCR-EB isolates were co-resistant to fluoroquinolones and 15 (1.7%) co-resistant to carbapenems. In-hospital mortality was similar in the 3GCS-EB and 3GCR-EB groups (2.4% vs. 2.8%; p=0.601). No increase in the hazard of in-hospital mortality was detected for 3GCR-EB infections compared to 3GCS-EB infections (sub-distribution hazard ratio [HR] 0.80; 95%CI, 0.41 - 1.55) in multivariable analysis adjusting for patient age, sex, intensive care admission, origin of infection and site of infection. Analysis of cause-specific hazards showed that 3GCR-EB infections significantly decreased the daily rate of hospital discharge (cause-specific HR=0.84; 95%CI, 0.76 - 0.92) thereby leading to lengthier hospitalizations.ConclusionThird-generation cephalosporin resistance in Enterobacteriaceae infection per se was not associated with increased in-hospital mortality in this study. However, 3GCR-EB infections were seen to place significant healthcare burden by increasing the length of hospitalization compared to 3GCS-EB infections.
NGPINT: A Next-generation protein-protein interaction software
Authors: Banerjee Sagnik , Velásquez-Zapata Valeria , Fuerst Gregory , Elmore J. Mitch , Wise Roger P. 
Published: September 2020

ABSTRACTMapping protein-protein interactions at a proteome scale is critical to understanding how cellular signaling networks respond to stimuli. Since eukaryotic genomes encode thousands of proteins, testing their interactions one-by-one is a challenging prospect. High-throughput yeast-two hybrid (Y2H) assays that employ next-generation sequencing to interrogate cDNA libraries represent an alternative approach that optimizes scale, cost, and effort. We present NGPINT, a robust and scalable software to identify all putative interactors of a protein using Y2H in batch culture. NGPINT combines diverse tools to align sequence reads to target genomes, reconstruct prey fragments and compute gene enrichment under reporter selection. Central to this pipeline is the identification of fusion reads containing sequences derived from both the Y2H expression plasmid and the cDNA of interest. To reduce false positives, these fusion reads are evaluated as to whether the cDNA fragment forms anin-frametranslational fusion with the Y2H transcription factor. NGPINT successfully recognized 95% of interactions in simulated test runs. As proof of concept, NGPINT was tested using published data sets and recognized all validated interactions. NGPINT can be used in any organism with an available reference, thus facilitating the discovery of protein-protein interactions in non-model organisms.
Single-cell RNA sequencing of Tocilizumab-treated peripheral blood mononuclear cells as an in vitro model of inflammation
Authors: Zarinsefat Arya , Hartoularos George , Chandran Sindhu , Yee Chun J. , Vincenti Flavio , Sarwal Minnie M. 
Published: September 2020

AbstractCOVID-19 has posed a significant threat to global health. Early data has revealed that IL-6, a key regulatory cytokine, plays an important role in the cytokine storm of COVID-19. Multiple trials are therefore looking at the effects of Tocilizumab, an IL-6 receptor antibody that inhibits IL-6 activity, on treatment of COVID-19, with promising findings. As part of a clinical trial looking at the effects of Tocilizumab treatment on kidney transplant recipients with subclinical rejection, we performed single-cell RNA sequencing of comparing stimulated PBMCs before and after Tocilizumab treatment. We leveraged this data to create an in vitro cytokine storm model, to better understand the effects of Tocilizumab in the presence of inflammation. Tocilizumab-treated cells had reduced expression of inflammatory-mediated genes and biologic pathways, particularly amongst monocytes. These results support the hypothesis that Tocilizumab may hinder the cytokine storm of COVID-19, through a demonstration of biologic impact at the single-cell level.
NHR-49 Acts in Distinct Tissues to Promote Longevity versus Innate Immunity
Authors: Naim Nikki , Amrit Francis RG , Ratnappan Ramesh , DelBuono Nicholas , Loose Julia A , Ghazi Arjumand 
Published: September 2020

ABSTRACTAging and immunity are inextricably linked and many genes that extend lifespan also enhance immunoresistance. However, it remains unclear if longevity-enhancing factors modulate immunity and longevity by distinct or shared mechanisms. Here, we demonstrate that theCaenorhabditis eleganspro-longevity factor, NHR-49, also promotes resistance againstPseudomonas aeruginosa, but modulates immunity and longevity by spatially and mechanistically distinct mechanisms. Fenofibrate, an agonist of NHR-49’s mammalian functional homolog, PPARα, enhanced worm immunoresistance in an NHR-49-dependent manner. NHR-49 expression is increased by germline ablation, an intervention that extends lifespan, but lowered by pathogen exposure. NHR-49 acted in multiple somatic tissues to promote longevity, whereas, it’s pro-immunity function was mediated by neuronal expression. The canonical NHR-49 target genes,acs-2andfmo-2, were upregulated by germline loss, but infection triggeredfmo-2downregulation andacs-2upregulation. Interestingly, neither gene conferred resistance against Gram-negativePseudomonas, unlike their reported roles in immunity against Gram-positive pathogens. Thus, NHR-49 is differentially regulated by interventions that bring about long-term changes (lifespan extension) vs. short-term stress (pathogen exposure) and in response it orchestrates distinct outputs, including pathogen-specific transcriptional programs. Overall, our study demonstrates the independent control of immunity and longevity by a conserved regulatory protein.
Orphan G protein-coupled receptor, GPR37L1: pharmacological toolbox empty once again
Authors: Ngo Tony , Wilkins Brendan P. , So Sean S. , Keov Peter , Chahal Kirti K. , Finch Angela M. , Coleman James L.J. , Kufareva Irina , Smith Nicola J. 
Published: September 2020

AbstractOrphan G protein-coupled receptors (GPCRs) are largely intractable therapeutic targets, owing to the lack of chemical tools for exploring their pharmacology. The discovery of such tools, however, is hampered by a number of unknowns, such as effector coupling and appropriate positive controls. In our 2017 Nature Chemical Biology paper1, we developed a computational chemical tool discovery approach called GPCR Contact-Informed Neighboring Pocket (GPCR-CoINPocket). This method predicted pharmacological similarity of GPCRs in a ligand- and structure-independent manner, to enable the discovery of off-target activities of known compounds at orphan GPCRs and hence the identification of so-called surrogate ligands. Our orphan GPCR target for prospective surrogate ligand discovery efforts was GPR37L1, a brain-specific receptor linked to cerebellar development2and seizures3. We had previously demonstrated that GPR37L1 constitutively coupled to Gαs and generated ligand-independent increases in intracellular cAMP4§. Thus, the inverse agonist activities of computationally predicted surrogates were tested in the cAMP response element luciferase (CRE-luc) reporter gene assay in human embryonic kidney (HEK293) cells expressing either vector control or what we thought was untagged GPR37L1 in pcDNA3.1. However, we recently discovered that the GPR37L1 construct used in that study was incorrect: instead of pcDNA3.1, it carried the receptor inserted backwards into a yeast p426GPD vector (hereafter referred to as p426-r37L1). Here, we correct the cloning error and describe our subsequent unsuccessful efforts to re-test the computationally predicted GPR37L1 ligands (triggering an author-initiated retraction of1).NoteWe, the authors, are working with the Nature Chemical Biology Editors to retract our 2017 paper ‘Orphan receptor ligand discovery by pickpocketing pharmacological neighbors’1. The present manuscript is under review at Nature Chemical Biology as a Matters Arising accompaniment to the anticipated author-initiated retraction. We initiated the steps towards the retraction upon discovering a regrettable cloning error that put into question the in vitro findings reported in1. This action was unanimously agreed upon by all authors. The computational aspects of the original manuscript1are unaffected by this error.
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors
Authors: Hoffmann H.-Heinrich , Schneider William M. , Sánchez-Rivera Francisco J. , Luna Joseph M. , Ashbrook Alison W. , Soto-Feliciano Yadira M. , Leal Andrew A. , Le Pen Jérémie , Ricardo-Lax Inna , Michailidis Eleftherios , Hao Yuan , Stenzel Ansgar F. , Peace Avery , Allis C. David , Lowe Scott W. , MacDonald Margaret R. , Poirier John T. , Rice Charles M. 
Published: September 2020

SUMMARYThe ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen four related coronaviruses (HCoV-229E, HCoV-NL63, HCoV-OC43 and SARS-CoV-2) at two physiologically relevant temperatures (33 °C and 37 °C), allowing us to probe this interactome at a much higher resolution relative to genome scale studies. This approach yielded several new insights, including unexpected virus and temperature specific differences in Rab GTPase requirements and GPI anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating COVID-19, and help prepare for future coronavirus outbreaks.HIGHLIGHTSFocused CRISPR screens targeting host factors in the SARS-CoV-2 interactome were performed for SARS-CoV-2, HCoV-229E, HCoV-NL63, and HCoV-OC43 coronaviruses.Focused interactome CRISPR screens achieve higher resolution compared to genome-wide screens, leading to the identification of critical factors missed by the latter.Parallel CRISPR screens against multiple coronaviruses uncover host factors and pathways with pan-coronavirus and virus-specific functional roles.The number of host proteins that interact with a viral bait protein is not proportional to the number of functional interactors.Novel SARS-CoV-2 host factors are expressed in relevant cell types in the human airway.