bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study
Authors: Stirrup Oliver , Blackstone James , Mapp Fiona , MacNeil Alyson , Panca Monica , Holmes Alison , Machin Nicholas , Shin Gee Yen , Mahungu Tabitha , Saeed Kordo , Saluja Tranprit , Taha Yusri , Mahida Nikunj , Pope Cassie , Chawla Anu , Cutino-Moguel Maria-Teresa , Tamuri Asif , Williams Rachel , Darby Alistair , Robertson David , Flaviani Flavia , Nastouli Eleni , Robson Samuel , Smith Darren , Loose Matthew , Laing Kenneth , Monahan Irene , Kele Beatrix , Haldenby Sam , George Ryan , Bashton Matthew , Witney Adam , Byott Matthew , Coll Francesc , Chapman Michael , Peacock Sharon ,   COG-UK HOCI Investigators,   The COVID-19 Genomics UK (COG-UK) consortium, Hughes Joseph , Nebbia Gaia , Partridge David G , Parker Matthew , Price James , Peters Christine , Roy Sunando , Snell Luke B , de Silva Thushan I , Thomson Emma , Flowers Paul , Copas Andrew , Breuer Judith 
Published: February 2022

AbstractIntroductionViral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.MethodsWe conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of ‘rapid’ (<48h) and 4 weeks of ‘longer-turnaround’ (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.ResultsA total of 2170 HOCI cases were recorded from October 2020-April 2021, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (IRR 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a per-protocol sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days.ConclusionWhile we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.
Excess COVID-19-associated deaths among the unvaccinated population ≥18 years old in the United States, May 30 – December 4, 2021
Authors: Jia Katherine M. , Hanage William P. , Lipsitch Marc , Swerdlow David L. 
Published: February 2022

AbstractVaccines against SARS-CoV-2 were authorized at the end of 2020 and are effective in preventing deaths; however, many persons remain unvaccinated. Using weekly publicly available CDC data of COVID-19-associated death rates by age and vaccination status from 26 US jurisdictions, we estimated the number of excess deaths that might have been averted by vaccination among unvaccinated persons ≥ 18 years old from May 30 to December 4, 2021. We subtracted the death rate in the vaccinated from rates in the unvaccinated to estimate the death rate each week that could be attributable to non-vaccination and multiplied this rate difference by the number of people in the unvaccinated group for each age group and each week, to estimate the excess mortality among the unvaccinated. Then, we extrapolated the number of deaths due to non-vaccination in the 26 jurisdictions to the whole US population using 2020 census estimates. In the 26 participating jurisdictions there were an estimated 83,400 excess deaths among the unvaccinated from May 30 to December 4, 2021. The largest number of excess deaths occurred in those 65–79 years old (n=28,900; 34.7% of total), followed by those 50-64 years old (n=25,900; 31.1%). Extrapolated to the US population we estimated approximately 135,000 excess deaths during the study period in persons ≥18 years old. Our estimates are an underestimate of all excess deaths that have occurred since vaccine became available because our analysis period was limited to May 30 to December 4, 2021, and many excess deaths occurred before and after this period. In summary, we used retrospective data to estimate the substantial number of COVID-19-associated deaths among the unvaccinated illustrating the importance of vaccination to prevent further unnecessary mortality during this pandemic.
Correlation between post-vaccination titres of combined IgG, IgA, and IgM anti-Spike antibodies and protection against breakthrough SARS-CoV-2 infection: a population-based longitudinal study (COVIDENCE UK)
Authors: Vivaldi Giulia , Jolliffe David A , Faustini Sian , Holt Hayley , Perdek Natalia , Talaei Mohammad , Tydeman Florence , Chambers Emma S , Cai Weigang , Li Wenhao , Gibbons Joseph M , Pade Corinna , McKnight Áine , Shaheen Seif O , Richter Alex G , Martineau Adrian R 
Published: February 2022

AbstractIn this population-based cohort of 7530 adults, combined IgG/A/M anti-Spike titres measured after SARS-CoV-2 vaccination were predictive of protection against breakthrough SARS-CoV-2 infection. Discrimination was significantly improved by adjustment for factors influencing risk of SARS-CoV-2 exposure including household overcrowding, public transport use, and visits to indoor public places.
Clinico epidemiological profile of Omicron variant of SARS CoV2 in Rajasthan
Authors: Sharma Ravi Prakash , Gautam Swati , Sharma Pratibha , Singh Ruchi , Sharma Himanshu , Parsoya Dinesh , Deba Farah , Bhomia Neha , pal Nita , Potdar Varsha A , Yadav Pragya D , Gupta Nivedita , Bhandari Sudhir , Malhotra Bharti 
Published: February 2022

AbstractBackgroundOmicron a new variant of SARS COV2 was first detected in November 2021. This was believed to be highly transmissible and evade immunity as a result urgent need was felt to screen all positive, identify Omicron cases and isolate them to prevent spread of infection and study their clinico-epidemiological profile.MethodologyAll positive cases detected in state of Rajasthan during November to January beginning were selected for next generation sequencing. Processing was done as per protocol on Ion Torrent S5 system for 1210 samples and bioinformatics analysis was done.ResultsAmong the 1210 samples tested 762(62.9%) were Delta/Delta like and other lineages, 291(24%) were Omicron and 157(12.9%) were invalid or repeat samples. Within a month the proportion of Delta and other variants was reversed, from zero omicron became 81% and delta and other variants 19%, initially all omicron cases were international travelers and their contacts but soon community transmission was seen. Majority of omicron patients were asymptomatic (56.7%) or had mild disease (33%), 9.2% had moderate symptoms and 2(0.7%) had severe disease requiring hospitalization, of which one (0.3%) died and rest (99.7%) recovered. History of vaccination was seen in 81.1%, of previous infection in 43.2%. Among the Omicron cases BA.1 (62.8%) was the predominant lineage followed by BA.2(23.7%) and B.1.529 (13.4%), however rising trends were seen initially for BA.1 and later for BA.2 also.ConclusionIn very short time Omicron has spread in community and has taken over the preexisting Delta/Delta like and other lineages, it evades immunity, but the good part is most of the cases were asymptomatic or had mild disease and mortality rate was very low.
Socio-economic deprivation and cancer incidence in England: Quantifying the role of smoking
Authors: Payne Nick W. S. , Brown Katrina F. , Delon Christine , Kotrotsios Yannis , Soerjomataram Isabelle , Shelton Jon 
Published: February 2022

AbstractBackgroundMore deprived populations typically experience higher cancer incidence rates and smoking prevalence compared to less deprived populations. We calculated the proportion of cancer cases attributable to smoking by socio-economic deprivation in England and estimated the impact smoking has on the deprivation gap for cancer incidence.MethodsData for cancer incidence (2013-2017), smoking prevalence (2003-2007) and population estimates (2013-2017) were split by sex, age-group and deprivation quintile. Relative risk estimates from meta-analyses were used to estimate the population attributable fraction (PAF) for 15 cancer types associated with smoking. The deprivation gap was calculated using age-specific incidence rates by deprivation quintile.ResultsSmoking-related cancer PAFs in England are 2.2 times larger in the most deprived quintile compared to the least deprived quintile (from 9.7% to 21.1%). If everyone had the same smoking prevalence as the least deprived quintile, 20% of the deprivation gap in cancer incidence could have been prevented. If nobody smoked, 61% of the deprivation gap could have been prevented.ConclusionsThe majority of the deprivation gap in cancer incidence could have been prevented in England between 2013-2017 if nobody had smoked. Policy makers should ensure that tobacco control policies reduce overall smoking prevalence by tackling smoking inequalities.
Persistence of SARS-CoV-2 immunity, Omicron’s footprints, and projections of epidemic resurgences in South African population cohorts
Authors: Sun Kaiyuan , Tempia Stefano , Kleynhans Jackie , Gottberg Anne von , McMorrow Meredith L , Wolter Nicole , Bhiman Jinal N. , Moyes Jocelyn , Plessis Mignon du , Carrim Maimuna , Buys Amelia , Martinson Neil A , Kahn Kathleen , Tollman Stephen , Lebina Limakatso , Wafawanaka Floidy , du Toit Jacques D. , Gómez-Olivé Francesc Xavier , Mkhencele Thulisa , Viboud Cécile , Cohen Cheryl ,   the PHIRST group
Published: February 2022

AbstractUnderstanding the build-up of immunity with successive SARS-CoV-2 variants and the epidemiological conditions that favor rapidly expanding epidemics will facilitate future pandemic control. High-resolution infection and serology data from longitudinal household cohorts in South Africa reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the cohort’s history of past exposures to different SARS-CoV-2 variants and vaccination, we use mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modelling suggests the Omicron wave infected a large fraction of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. Future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.One Sentence SummaryClosely monitored population in South Africa reveal high cumulative infection rates and durable protection by prior infection against pre-Omicron variants. Modelling indicates that a large fraction of the population has been infected with Omicron; yet epidemic resurgences are plausible under a wide range of epidemiologic scenarios.
Development and validation of radiomics nomograms for preoperative prediction of characteristics in non-small cell lung cancer and circulating tumor cells
Authors: Wang Yang , Zhu Junkai , Cheng Wenxuan , Xu Li , Wang Xin , Wang Jian , Yang Jun , Niu Fengnan , li Wenyi , Wen Zhibo , Lu Xiaofan , Yan Fangrong 
Published: February 2022

ABSTRACTPurposeTo develop and validate three radiomics nomograms for preoperative prediction of pathological and progression diagnosis in non-small cell lung cancer (NSCLC) as well as circulating tumor cells (CTCs).Patients and methodsA total of 224 and 134 patients diagnosed with NSCLC were respectively gathered in 2018 and 2019 in this study. There were totally 1,197 radiomics features that were extracted and quantified from the images produced by computed tomography (CT). Then we selected the radiomics features with predictive value by LASSO and combined them into radiomics signature. Logistic regression models were built using radiomics signature as the only predictor, which were then converted to nomograms for individualized predictions. Finally, the performance of the nomograms was assessed on both two cohorts.ResultsAs for discrimination, the AUC of pathological diagnosis nomogram and progression diagnosis nomogram in NSCLC were both higher than 90% in the training cohort and higher than 80% in the validation cohort. The performance of the CTC-diagnosis nomogram was somehow unexpected where the AUC were range from 60% to 70% in both two cohorts. As for calibration, nonsignificant statistics (p>0.05) yielded by Hosmer-Lemeshow tests suggested no departure between model prediction and perfect fit. Additionally, decision curve analyses demonstrated the clinically usefulness of the nomograms.ConclusionWe developed radiomics-based nomograms for pathological, progression and CTC diagnosis prediction in NSCLC, respectively. Nomograms for pathological and progression diagnosis were demonstrated well performed to facilitate the preoperative individualized prediction, while the nomogram for CTC-diagnosis prediction needed improvement.
Food intake patterns, social determinants and emotions during COVID-19 confinement
Authors: Rios Maritza , Subinas Jon , Delgado Celestina , Torres Eliecer , Goodridge Amador , Cubilla-Batista Idalina 
Published: February 2022

ABSTRACTObjectiveThe COVID-19 pandemic was accompanied by varying movement restriction measures across populations worldwide. These restrictions altered daily activities at all levels, including food access and intake, as well as psychological feelings during lockdown. The main objective of the present study was to evaluate health, and nutrition behaviors during confinement during the first wave of the COVID-19 pandemic.MethodWe conducted a cross-sectional study using an online survey for data collection; a total of 1,561 surveys were validated.ResultsThe majority of respondents were women (74.2%) between 18 and 49 years old. Among the respondents, 83.3% indicated a university education level, and 49.9% reported a monthly family income equal to or less than 1,000 USD. In addition, more than 50% self-reported overweight or obesity. Responses were analyzed using k-means algorithms to identify food intake patterns; we found three patterns: a healthy food intake pattern, a non-healthy food intake pattern and a mixed food intake pattern. The respondents with healthy food intake and non-healthy food intake patterns reported better socioeconomic conditions. Individuals classified as having mixed food intake patterns had lower incomes, less education and higher unemployment rates. Regarding emotions, we found that women experienced more negative emotions, such as fear, worry and anxiety, during the lockdown period.ConclusionsTaken together, these results suggest that the mobility restriction measures imposed during the COVID-19 pandemic affected food intake patterns by exacerbating existing inequalities. We believe that directing resources towards strategies with the greatest positive impacts on public health remains key, especially in critical situations such as the COVID-19 pandemic.
Omicron-Specific and Bivalent Omicron-Containing Vaccine Candidates Elicit Potent Virus Neutralisation in the Animal Model
Authors: Abdoli Asghar , Jamshidi Hamidreza , Taqavian Mohammad , Baghal Mehdi Lari , Jalili Hasan 
Published: February 2022

AbstractBackgroundOmicron variant (B. 1.1.529) is able to escape from naturally acquired and vaccine-induced immunity, which mandates updating the current COVID-19 vaccines. Here, we investigated and compared the neutralising antibody induction of the ancestral variant-based BIV1-CovIran vaccine, the Omicron variant-based BIV1-CovIran Plus vaccine, and the novel bivalent vaccine candidate, BBIV1-CovIran, against the Omicron and ancestral Wuhan variants on the rat model.MethodsViruses were isolated from a clinical specimen and virus characterisation performed. After inactivating the viral particles, the viruses were purified and formulated. Bivalent vaccines were a composition of 2.5 μg (5 μg total) or 5 μg (10 μg total) doses of each ansectral-based and Omicron-based monovalent vaccine. Subsequently, the potency of the monovalent and bivalent vaccines was investigated using the virus neutralisation test (VNT).ResultsThe group that received three doses of the Omicron-specific vaccine demonstrated neutralisation activity against the Omicron variant with a geometric mean titer of 337.8. However, three doses of the Wuhan variant-specific vaccine could neutralise the Omicron variant at a maximum of 1/32 serum dilution. The neutralisation activity of the Omicron-specific vaccine, when administered as the booster dose after two doses of the Wuhan variant-specific vaccine, was 100% against the Omicron variant and the Wuhan variant at 1/64 and 1/128 serum dilution, respectively. Three doses of 5 μg bivalent vaccine could effectively neutralise both variants at the minimum of 1/128 serum dilution. The 10 μg bivalent vaccine at three doses showed even higher neutralisation titers: geometric mean titer of 338.0 against Omicron and 445.7 against Wuhan).ConclusionIt is shown that the candidate bivalent vaccine could elicit a potent immune response against both Wuhan-Hu-1 and Omicron BA.1 variants. Therefore, we plan to evaluate the updated vaccine in the clinical trial setting.
Workplace infection control measures and romantic activities of workers during COVID-19 pandemic: a prospective cohort study in Japan
Authors: Fujino Yoshihisa , Okawara Makoto , Hino Ayako , Muramatsu Keiji , Nagata Tomohisa , Ikegami Kazunori , Tateishi Seiichiro , Tsuji Mayumi , Ishimaru Tomohiro ,   the CORoNaWork project
Published: February 2022

AbstractBackgroundDue to the COVID-19 pandemic, non-married people are at high risk of loneliness. With social interactions restricted, it is important for non-married people to acquire a new romantic partner for their mental health and quality of life. We hypothesized that infection control efforts in the workplace influence people’s social interactions, including romantic activities.MethodsWe conducted an internet-based prospective cohort study from December 2020 (baseline) to December 2021, using self-administered questionnaires. Briefly, 27,036 workers completed the questionnaires at baseline, and when followed up after one year, 18,560 (68.7%) participated. A total of 6,486 non-married individuals with no romantic relationship at baseline were included in the analysis. At baseline they were asked about the implementation of infection control measures in the workplace, and at follow-up they were asked about activities they performed with a view to romantic relationships during the period from baseline to follow-up.ResultsCompared to workers in workplaces with no infection control measures, the OR associated with romance-related activities for those in workplaces with seven or more infection control measures was 1.90 (95% CI: 1.45-2.48, p<0.001), and the OR associated with having a new romantic partner was 1.79 (95% CI: 1.20-2.66, p=0.004).ConclusionsUnder the COVID-19 pandemic, the implementation of infection control measures in the workplace and the expressed satisfaction with those measures promoted romantic relationships among non-married, single individuals.
CT-Guided Direct Current Cardioversion for Atrial Arrhythmias During the COVID-19 Pandemic
Authors: Veillet-Chowdhury Mahdi , Dabbagh Ghaith Sharaf , Benton Stewart M. , Hill April M. , Lee Jefferson H. , Singleton Matthew J. , Fazio Gregory P. , Harvey James E. , Samady Habib , Singh David , Khanji Mohammed Y. , Nazarian Saman , Pugliese Francesca , Obeng-Gyimah Edmond , Schuler Brian T. , Chahal C. Anwar A. 
Published: February 2022

ABSTRACTObjectiveTo assess left atrial appendage (LAA) thrombus detection using a novel cardiac computed tomography (CT) protocol specifically prior to direct current cardioversion (DCCV).BackgroundTransesophageal echocardiography (TEE) is the gold standard in evaluating the LAA prior to DCCV for atrial fibrillation (AF) or flutter (AFL). The COVID-19 pandemic has restricted availability of TEE and anesthesia support.MethodsProspective cohort of consecutive patients with uncontrolled AF/AFL referred for DCCV from March 2020 to March 2021 were enrolled. CT evaluation of LAA was performed with an initial arterial and subsequent 30-second delayed acquisition to exclude thrombus prior to DCCV. Primary end points were to assess safety and outcomes.ResultsA total of 161 patients were included; mean age 69.8 ± 11.1 years; mean CHA2DS2-VASc 3.4 ± 1.7; and HAS-BLED 1.8 ± 0.9. Median follow-up 175 (105-267) days with zero cardiac-related deaths, and no episodes of TIA or embolic stroke. There was no statistically significant change in mean glomerular filtration rate (GFR) in the study population between the pre- and post-GFR measurements (73.9 ± 21.0 vs 72.7 ± 20.3; p=0.104). Overall mean total dose length product (DLP) was 1042.8 ± 447.5 mGy*cm. Modifying the CT protocol to a narrower 8-cm axial coverage had a statistically significant decrease in total DLP (from 1130.6 ± 464.1 mGy*cm to 802.1 ± 286.4 mGy*cm; P<0.0001).ConclusionCardiac CT is both a safe and feasible alternative imaging to TEE for patients prior to DCCV.PerspectivesCompetency in Medical KnowledgeCardiac CT is a powerful tool for the evaluation of left atrial appendage and detection of thrombus prior to direct current cardioversion.Translational OutlookOur protocol was implemented with the restrictions during COVID-19 in mind, yet CT can be a viable tool beyond the pandemic; future randomized clinical trials can bridge the gap between CT and TEE in the setting of cardioversion and help elucidate its safety profile further.
SARS-CoV-2 Permissive Glioblastoma Cell Line for High Throughput Antiviral Screening
Authors: Vanhulle Emiel , Stroobants Joren , Provinciael Becky , Camps Anita , Noppen Sam , Maes Piet , Vermeire Kurt 
Published: February 2022

AbstractDespite the great success of the administered vaccines against SARS-CoV-2, the virus can still spread, as evidenced by the current circulation of the highly contagious Omicron variant. This emphasizes the additional need to develop effective antiviral countermeasures. In the context of early preclinical studies for antiviral assessment, robust cellular infection systems are required to screen drug libraries. In this study, we reported the implementation of a human glioblastoma cell line, stably expressing ACE2, in a SARS-CoV-2 cytopathic effect (CPE) reduction assay. These glioblastoma cells, designated as U87.ACE2+, expressed ACE2 and cathepsin B abundantly, but had low cellular levels of TMPRSS2 and cathepsin L. The U87.ACE2+ cells fused highly efficiently and quickly with SARS-CoV-2 spike expressing cells. Furthermore, upon infection with SARS-CoV-2 wild-type virus, the U87.ACE2+ cells displayed rapidly a clear CPE that resulted in complete cell lysis and destruction of the cell monolayer. By means of several readouts we showed that the U87.ACE2+ cells actively replicate SARS-CoV-2. Interestingly, the U87.ACE2+ cells could be successfully implemented in an MTS-based colorimetric CPE reduction assay, providing IC50 values for Remdesivir in the low nanomolar range. Lastly, the U87.ACE2+ cells were consistently permissive to all tested SARS-CoV-2 variants of concern, including the current Omicron variant. Thus, ACE2 expressing glioblastoma cells are highly permissive to SARS-CoV-2 with productive viral replication and with the induction of a strong CPE that can be utilized in high-throughput screening platforms.