bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-harm presentations to Emergency Departments and Place of Safety during the ‘first wave’ of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020
Authors: Nuzum Eleanor , Martin Evangelia , Morgan Gemma , Dutta Rina , Mueller Christoph , Polling Catherine , Pritchard Megan , Velupillai Sumithra , Stewart Robert 
Published: December 2020

AbstractThe lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the ‘first wave’ lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaM’s Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.
Current forecast of COVID-19: a Bayesian and Machine Learning approaches
Authors: Prieto Kernel 
Published: December 2020

AbstractWe address the estimation of the effective reproductive numberRtbased on serological data using Bayesian inference. We also explore the Bayesian learning paradigm to estimateRt. We calculateRtfor the top five most affected principal regions of Mexico. We present a forecast of the spread of coronavirus in Mexico based on a contact tracing model using Bayesian inference inspired in a data-driven approach. We investigate the health profile of individuals diagnosed with coronavirus in order to predict their type of patient care (inpatient or outpatient) and survival. Specifically, we analyze the comorbidity associated with coronavirus using Machine Learning. We implemented two classifiers, the first one, to predict the type of care procedure a diagnosed person with coronavirus presenting chronic diseases will obtain: outpatient or hospitalized. Second one, a classifier for the survival of the patient: survived or deceased. We present two techniques to deal with these kinds of unbalanced dataset related with outpatient/hospitalized and survived/deceased cases, occurring in general for these type coronavirus datasets in the world, in order obtain to a better performance for the classification.
Unique predictors of intended uptake of a COVID-19 vaccine
Authors: Lennon Robert P. , Small Meg L. , Smith Rachel A. , Van Scoy Lauren J. , Myrick Jessica G. , Martin Molly A. ,   Data4Action Research Group
Published: December 2020

AbstractIntroductionAn effective vaccine for COVID-19 is only of value if the public has confidence in taking it. There is little data on COVID-19-specific vaccine confidence or its determinants in the United States. The objective of this study was to determine public confidence in a COVID-19 vaccine.MethodsA cross-sectional survey of Pennsylvanian adults, August-October, 2020, to identify their likelihood of taking an approved, no-cost coronavirus vaccine, general vaccine acceptance, and sociodemographic traits to identify predictors of vaccine acceptance.ResultsOf the 950 respondents, 55% were “very likely”, 20% “somewhat likely”, 14% “unsure”, 4% “somewhat unlikely”, and 7% “very unlikely” to take a coronavirus vaccine, even though 70% had taken the flu vaccine since September 2019. The strongest predictors of vaccine acceptance were trust in the system evaluating vaccines and perceptions of local COVID-19 vaccination norms. The strongest predictors of negative vaccine intentions were worries about unknown side-effects and positive attitudes toward natural infection. Sociodemographic factors, political views, and religiosity did not predict vaccine intentions.ConclusionsFewer adults intend to take a coronavirus vaccine than currently take the flu vaccine. To overcome coronavirus vaccine hesitancy, information campaigns to reinforce positive predictors and overcome negative predictors are indicated.
COVID-19 in persons affected by Hansen’s disease in Brazil
Authors: Deps Patrícia D. , Repsold Taynah A. R. , Salgado Claudio G. , de Carvalho Bouth Raquel , Cerqueira Selma Regina Penha Silva , Brezinscki Marisa Simon , Peixoto Rebeca Ruppert Galarda Baptista , Barreto Jaison Antonio , Fonseca Andrea M. A. , Peixoto Marlene L. S. , Mendes Seyna Ueno R. , Mendes Rafael Pereira Rabelo , dos Santos Oliveira Pedro Paulo , Gomes Ciro Martins 
Published: December 2020

AbstractBackgroundHansen’s disease (HD) is endemic in Brazil, a country with the third highest number of COVID-19 cases in the world and the second highest number of COVID-19 deaths. COVID-19 in persons affected by HD has not been described at population level in this country.MethodsWe collated numbers of COVID-19 cases and deaths among patients who were receiving routine treatment for HD at six centres across Brazil (Belém, Bauru, Brasília, Vitória, Petrolina, Palmas) between 1st March and 10th December 2020.ResultsOf 1,333 HD patients receiving treatment, 70 (5.2%) reported having had COVID-19. Almost all patients (97% (1,296/1,333)) including all but one of the COVID-19 cases were receiving MDT comprising rifampicin (600mg once per month), dapsone (100mg daily), and clofazimine (50 mg daily plus 300 mg once per month). Four patients died, including a patient in their 30’s on MDT who had a severe type 2 HD reaction (erythema nodosum leprosum) and who was taking clofazimine 100mg daily.ConclusionsWe cannot determine from these preliminary data whether persons affected by Hansen’s disease have a higher or lower risk of COVID-19 and related mortality compared with the general population. We will continue to monitor the effects of COVID-19 in persons affected by and treated for HD and extend this to monitor SARS-CoV-2 vaccine effectiveness in this group of patients.
Clinical and Virological Characteristics of Hospitalized COVID-19 Patients in a German Tertiary Care Center during the First Wave of the SARS-CoV-2 Pandemic
Authors: Thibeault Charlotte , Mühlemann Barbara , Helbig Elisa T. , Mittermaier Mirja , Lingscheid Tilman , Tober-Lau Pinkus , Meyer-Arndt Lil A. , Meiners Leonie , Stubbemann Paula , Haenel Sascha S. , de Jarcy Laure Bosquillon , Lippert Lena , Pfeiffer Moritz , Stegemann Miriam S. , Roehle Robert , Wiebach Janine , Hippenstiel Stefan , Zoller Thomas , Müller-Redetzky Holger , Uhrig Alexander , Balzer Felix , von Kalle Christof , Suttorp Norbert , Jones Terry C. , Drosten Christian , Witzenrath Martin , Sander Leif E. ,   Pa-COVID Study Group, Corman Victor M. , Kurth Florian 
Published: December 2020

AbstractBackgroundAdequate patient allocation is pivotal for optimal resource management in strained healthcare systems, and requires detailed knowledge of clinical and virological disease trajectories.MethodsA cohort of 168 hospitalized adult COVID-19 patients enrolled in a prospective observational study at a large European tertiary care center was analyzed.ResultsForty-four percent (71/161) of patients required invasive mechanical ventilation (IMV). Shorter duration of symptoms before admission (aOR 1.22 per day less, 95%CI 1.10-1.37, p<0.01), age 60-69 as compared to 18-59 years (aOR 4.33, 95%CI 1.07-20.10, p=0.04), and history of hypertension (aOR 5.55, 95%CI 2.00-16.82, p<0.01) were associated with need for IMV. Patients on IMV had higher maximal concentrations, slower decline rates, and longer shedding of SARS-CoV-2 than non-IMV patients (33 days, IQR 26-46.75, vs 18 days, IQR 16-46.75, respectively, p<0.01). Median duration of hospitalization was 9 days (IQR 6-15.5) for non-IMV and 49.5 days (IQR 36.8-82.5) for IMV-patients.ConclusionOur results indicate a short duration of symptoms before admission as a risk factor for severe disease and different viral load kinetics in severely affected patients.
Decay of Fc-dependent antibody functions after mild to moderate COVID-19
Authors: Lee Wen Shi , Selva Kevin John , Davis Samantha K. , Wines Bruce D. , Reynaldi Arnold , Esterbauer Robyn , Kelly Hannah G. , Haycroft Ebene R. , Tan Hyon-Xhi , Juno Jennifer A. , Wheatley Adam K. , Hogarth P. Mark , Cromer Deborah , Davenport Miles P. , Chung Amy W. , Kent Stephen J. 
Published: December 2020

AbstractThe capacity of antibodies to engage with innate and adaptive immune cells via the Fc region is important in preventing and controlling many infectious diseases, and is likely critical in SARS-CoV-2 infection. The evolution of such antibodies during convalescence from COVID-19 is largely unknown. We developed novel assays to measure Fc-dependent antibody functions against SARS-CoV-2 spike (S)-expressing cells in serial samples from a cohort of 53 subjects primarily with mild-moderate COVID-19, out to a maximum of 149 days post-infection. We found that S-specific antibodies capable of engaging dimeric FcγRIIa and FcγRIIIa decayed linearly over time. S-specific antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent phagocytosis (ADP) activity within plasma declined linearly as well, in line with the decay of S-specific IgG. Although there was significant decay in S-specific plasma ADCC and ADP activity, they remained readily detectable by all assays in 94% of our cohort at the last timepoint studied, in contrast with neutralisation activity which was only detectable in 70% of our cohort by the last timepoint. Our results suggest that Fc effector functions such as ADCC and ADP could contribute to the durability of SARS-CoV-2 immunity, particularly late in convalescence when neutralising antibodies have waned. Understanding the protective potential of antibody Fc effector functions is critical for defining the durability of immunity generated by infection or vaccination.
Catechol-Containing Compounds are a Broad Class of Protein Aggregation Inhibitors: II. Rosmarinic Acid Potently Detoxifies Amylin Amyloid and Ameliorates Diabetic Pathology in HIP Rats
Authors: Wu Ling , Velander Paul , Brown Anne M. , Wang Yao , Liu Dongmin , Bevan David R. , Zhang Shijun , Xu Bin 
Published: December 2020

AbstractProtein aggregation is associated with a large number of human protein misfolding diseases, yet FDA-approved drugs are currently not available. Amylin amyloid and plaque depositions in the pancreas are hallmark features of type 2 diabetes. Moreover, these amyloid deposits are implicated in the pathogenesis of diabetic complications such as neurodegeneration. We recently discovered that catechols and redox-related quinones/ anthraquinones represent a broad class of protein aggregation inhibitors. Further screening of a targeted library of natural compounds in complementary medicine that were enriched with catechol-containing compounds identified rosmarinic acid as a potent inhibitor of amylin aggregation (estimated inhibitory concentration IC50= 200-300 nM). Structure-function relationship analysis of rosmarinic acid showed the additive effects of two catechol-containing components of the RA molecule. We further showed that RA does not reverse fibrillation back to monomeric amylin, but lead to non-toxic, remodeled protein aggregates. Rosmarinic acid has significantex vivoefficacy in reducing human amylin oligomer levels in HIP rat sera as well as in sera from diabetic patients.In vivoefficacy studies of rosmarinic acid treatment with the diabetic HIP rat model demonstrated significant reduction in amyloid islet deposition and strong mitigation of diabetic pathology. Our work provides newin vitromolecular mechanisms andin vivoefficacy insights for a model nutraceutical agent against type 2 diabetes and other aging-related protein misfolding diseases.
Rapid, point-of-care molecular diagnostics with Cas13
Authors: Agrawal Shreeya , Fanton Alison , Chandrasekaran Sita S. , Charrez Bérénice , Escajeda Arturo M. , Son Sungmin , Mcintosh Roger , Bhuiya Abdul , de León Derby María Díaz , Switz Neil A. , Armstrong Maxim , Harris Andrew R. , Prywes Noam , Lukarska Maria , Biering Scott B. , Smock Dylan C. J. , Mok Amanda , Knott Gavin J. , Dang Qi , Van Dis Erik , Dugan Eli , Kim Shin , Liu Tina Y. ,   IGI Testing Consortium, Harris Eva , Stanley Sarah A. , Lareau Liana F. , Tan Ming X. , Fletcher Daniel A. , Doudna Jennifer A. , Savage David F. , Hsu Patrick D. 
Published: December 2020

SummaryRapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/μL of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.
NOTCH3 variants are common in the general population and associated with stroke and vascular dementia: an analysis of 200,000 participants
Authors: Cho Bernard PH , Nannoni Stefania , Harshfield Eric L , Tozer Daniel J , Gräf Stefan , Bell Steven , Markus Hugh S 
Published: December 2020

ABSTRACTBackgroundCysteine-altering NOTCH3 variants identical to those causing the rare monogenic form of stroke, CADASIL, have been reported more common than expected in the general population, but their clinical significance and contribution to stroke and dementia risk in the community remains unclear.MethodsCysteine-altering NOTCH3 variants were identified in UK Biobank whole-exome sequencing data (N=200,632). Frequency of stroke, dementia and other clinical features of CADASIL, and MRI white matter hyperintensity volume were compared between variant carriers and non-carriers. MRIs from those with variants were visually rated, each matched with three controls.ResultsOf 200,632 participants with exome sequencing data available, 443 (∼1 in 450) carried 67 different cysteine-altering NOTCH3 variants. After adjusting for age, sex, and ancestry principal components, NOTCH3 variant carriers had increased risk of stroke (OR: 2.33, p=0.0003), and vascular dementia (OR: 5.03, p=0.007), and increased WMH volume (standardised difference: 0.52, p<0.001), and white matter ultrastructural damage on DTI-PSMD (standardised difference: 0.71, p<0.001). On visual analysis of MRIs from 47 carriers and 148 matched controls, variants were associated with presence of lacunes (OR: 4.83, p<0.001) and cerebral microbleeds (OR: 3.61, p<0.001). WMH prevalence was most increased in the anterior temporal lobes (OR: 6.92, p<0.001) and external capsule (OR: 12.44, p<0.001).ConclusionsCysteine-changing NOTCH3 variants are common in the general population and are risk factors for apparently “sporadic” stroke and vascular dementia. They are associated with MRI changes of SVD, in a distribution similar to that seen in CADASIL.
Excess mortality during the first ten months of COVID-19 epidemic at Jakarta, Indonesia
Authors: Elyazar Iqbal RF , Surendra Henry , Ekawati Lenny L , Djaafara Bimandra A. , Nurhasim Ahmad , Arif Ahmad , Hidayana Irma , Widyastuti  , Oktavia Dwi , Adrian Verry , Salama Ngabila , Hamdi Imam , Andrianto Adhi , Lina Rosa N , Lestari Karin D , Shankar Anuraj H , Hamers Raph L , Thwaites Guy , Baird J. Kevin 
Published: December 2020

AbstractExcess mortality during the COVID-19 epidemic is an important measure of health impacts. We examined mortality records from January 2015 to October 2020 from government sources at Jakarta, Indonesia: 1) burials in public cemeteries; 2) civil death registration; and 3) health authority death registration. During 2015-2019, an average of 26,342 burials occurred each year from January to October. During the same period of 2020, there were 42,460 burials, an excess of 61%. Burial activities began surging in early January 2020, two months before the first official laboratory confirmation of SARS-CoV-2 infection in Indonesia in March 2020. Analysis of civil death registrations or health authority death registration showed insensitive trends during 2020. Burial records indicated substantially increased mortality associated with the onset of and ongoing COVID-19 epidemic in Jakarta and suggest that SARS-CoV-2 transmission may have been initiated and progressing at least two months prior to official detection.Article summary lineAnalysis of civil records of burials in Jakarta, Indonesia showed a 61% increase during 2020 compared to the previous five years, a trend that began two months prior to first official confirmation of SARS-CoV-2 transmission in the city.
Are commercial antibody assays substantially underestimating SARS-CoV-2 ever infection? An analysis on a population-based sample in a high exposure setting
Authors: Nasrallah Gheyath K. , Dargham Soha R. , Shurrab Farah , Al-Sadeq Duaa W. , Al-Jighefee Hadeel , Chemaitelly Hiam , Kanaani Zaina Al , Khal Abdullatif Al , Kuwari Einas Al , Coyle Peter , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Yassine Hadi M. , Al Kuwari Mohamed G. , Qotba Hamda , Romaihi Hamad Eid Al , Tang Patrick , Bertollini Roberto , Al-Thani Mohamed , Althani Asmaa A. , Abu-Raddad Laith J. 
Published: December 2020

AbstractBackgroundPerformance of three automated commercial serological IgG-based assays was investigated for assessing SARS-CoV-2 ever (past or current) infection in a population-based sample in a high exposure setting.MethodsPCR and serological testing was performed on 394 individuals.ResultsSARS-CoV-2-IgG seroprevalence was 42.9% (95% CI 38.1%-47.8%), 40.6% (95% CI 35.9%-45.5%), and 42.4% (95% CI 37.6%-47.3%) using the CL-900i, VidasIII, and Elecsys assays, respectively. Between the three assays, overall, positive, and negative percent agreements ranged between 93.2%-95.7%, 89.3%-92.8%, and 93.8%-97.8%, respectively; Cohen kappa statistic ranged from 0.86-0.91; and 35 specimens (8.9%) showed discordant results. Among all individuals, 12.5% (95% CI 9.6%-16.1%) had current infection, as assessed by PCR. Of these, only 34.7% (95% CI 22.9%-48.7%) were seropositive by at least one assay. A total of 216 individuals (54.8%; 95% CI 49.9%-59.7%) had evidence of ever infection using antibody testing and/or PCR during or prior to this study. Of these, only 78.2%, 74.1%, and 77.3% were seropositive in the CL-900i, VidasIII, and Elecsys assays, respectively.ConclusionsAll three assays had comparable performance and excellent agreement, but missed at least 20% of individuals with past or current infection. Commercial antibody assays can substantially underestimate ever infection, more so when infection rates are high.
The Presence of Ambulatory Hypoxia as an Early Predictor of Moderate to Severe COVID-19 Disease
Authors: Bhasin Ajay , Bregger Melissa , Kluk Mark , Park Peter , Feinglass Joe , Barsuk Jeffrey 
Published: December 2020

AbstractBackgroundThe importance of ambulatory hypoxia without resting hypoxia in COVID-19 is unknown. Ambulatory hypoxia without resting hypoxia may help objectively identify high-risk patients hospitalized with COVID-19. Interventions may be initiated earlier with sufficient lead-time between development of ambulatory hypoxia and other outcome measures.MethodsWe performed a retrospective study of adult patients hospitalized with COVID-19 from March 1, 2020 to October 30, 2020 in ten hospitals in an integrated academic medical system in the Chicagoland area. We analyzed patients who had daily ambulatory oximetry measurements, excluding patients who had first ambulatory oximetry measurements after the use of oxygen therapies (nasal cannula or advanced oxygen therapies). We determined the association of ambulatory hypoxia without resting hypoxia with the eventual need for nasal cannula or advanced oxygen therapies (defined as high flow nasal cannula, Bi-PAP, ventilator, or extracorporeal membrane oxygenation). We also calculated the time between development of ambulatory hypoxia and the need for oxygen therapies.ResultsOf 531 patients included in the study, 132 (24.9%) had ambulatory hypoxia. Presence of ambulatory hypoxia was strongly associated with subsequent use of nasal cannula (OR 4.8, 95% CI 2.8 – 8.4) and advanced oxygen therapy (IRR 7.7, 95% CI 3.4 – 17.5). Ambulatory hypoxia preceded nasal cannula use by a median 12.5 hours [IQR 3.25, 29.25] and advanced oxygenation therapies by 54 hours [IQR 25, 82].ConclusionAmbulatory hypoxia without resting hypoxia may serve as an early, non-invasive physiologic marker for the likelihood of developing moderate to severe COVID-19 and help clinicians triage patients and initiate earlier interventions.
A Systematic High-throughput Phenotyping Assay for Sugarcane Stalk Quality Characterization by Near-infrared Spectroscopy
Authors: Wang Maoyao , Li Xinru , Shen Yinjuan , Adnan Muhammad , Mao Le , Lu Pan , Hu Qian , Jiang Fuhong , Khan Muhammad Tahir , Deng Zuhu , Huang Jiangfeng , Zhang Muqing 
Published: December 2020

AbstractStalk quality improvement is deemed a promising strategy to enhance sugarcane production. However, the lack of efficient approaches for a systematic evaluation of sugarcane germplasm limited stalk quality improvement. In this study, 628 sugarcane samples were employed to take a high-throughput assay for determining the sugarcane stalk quality. Based on the high-performance anion chromatography method, large sugarcane stalk quality variations were detected in biomass composition and the corresponding fundamental ratio values. Online and offline Near-infrared Spectroscopy (NIRS) modeling strategies were applied for multiple purpose calibration. Consequently, 25 equations were generated with the excellent determination coefficient (R2) and ratio performance deviation (RPD) values. Notably, for some observations, RPD values as high as 6.3 were observed that indicated their exceptional performance potential and prediction capacity. Hence, this study provides a feasible way for high-throughput assessment of stalk quality, permitting large-scale screening of optimal sugarcane germplasm.