bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Prevalence of Anti–Severe Acute Respiratory Syndrome Coronavirus 2 (Anti–SARS-CoV-2) Antibodies After the First Wave of Coronavirus Disease 2019 (COVID-19) in Kinshasa, Democratic Republic of the Congo: Results of a Cross-sectional Household-Based Survey
Authors: Nkuba Antoine N , Makiala Sheila M , Guichet Emilande , Tshiminyi Paul M , Bazitama Yannick M , Yambayamba Marc K , Kazenza Benito M , Kabeya Trésor M , Matungulu Elysee B , Baketana Lionel K , Mitongo Naomi M , Thaurignac Guillaume , Leendertz Fabian H , Vanlerberghe Veerle , Pelloquin Raphaël , Etard Jean-François , Maman David , Mbala Placide K , Ayouba Ahidjo , Peeters Martine , Muyembe Jean-Jacques T , Delaporte Eric , Ahuka Steve M 
Published: June 2021

Abstract

Background
In October 2020, after the first wave of coronavirus disease 2019 (COVID-19), only 8290 confirmed cases were reported in Kinshasa, Democratic Republic of the Congo, but the real prevalence remains unknown. To guide public health policies, we aimed to describe the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) antibodies in the general population in Kinshasa.

Methods
We conducted a cross-sectional, household-based serosurvey between 22 October 2020 and 8 November 2020. Participants were interviewed at home and tested for antibodies against SARS-CoV-2 spike and nucleocapsid proteins in a Luminex-based assay. A positive serology was defined as a sample that reacted with both SARS-CoV-2 proteins (100% sensitivity, 99.7% specificity). The overall weighted, age-standardized prevalence was estimated and the infection-to-case ratio was calculated to determine the proportion of undiagnosed SARS-CoV-2 infections.

Results
A total of 1233 participants from 292 households were included (mean age, 32.4 years; 764 [61.2%] women). The overall weighted, age-standardized SARS-CoV-2 seroprevalence was 16.6% (95% CI: 14.0–19.5%). The estimated infection-to-case ratio was 292:1. Prevalence was higher among participants ≥40 years than among those &lt;18 years (21.2% vs 14.9%, respectively; P &lt; .05). It was also higher in participants who reported hospitalization than among those who did not (29.8% vs 16.0%, respectively; P &lt; .05). However, differences were not significant in the multivariate model (P = .1).

Conclusions
The prevalence of SARS-CoV-2 is much higher than the number of COVID-19 cases reported. These results justify the organization of a sequential series of serosurveys by public health authorities to adapt response measures to the dynamics of the pandemic.
Reporting of Infectious Diseases in the United States During the Coronavirus Disease 2019 (COVID-19) Pandemic
Authors: Crane Matthew A , Popovic Aleksandra , Panaparambil Rohan , Stolbach Andrew I , Romley John A , Ghanem Khalil G 
Published: June 2021

Abstract
Reporting of infectious diseases other than COVID-19 has been greatly decreased throughout the COVID-19 pandemic. We find this decrease varies by routes of transmission, reporting state, and COVID-19 incidence at the time of reporting. These results underscore the need for continual investment in routine surveillance efforts despite pandemic conditions.
Overuse of Tuberculosis Surveillance Testing in Patients With Inflammatory Bowel Disease Compared to Non-IBD Patients on Biologic Therapy
Authors: Fine Sean , Vecchio Marc , Filipe Goncalves Monteiro Joao , Vecchio Eric , Mao Eric J 
Published: June 2021

Abstract

Background
Biologic treatment for moderate to severe inflammatory bowel disease (IBD) places patients at risk for infectious complications. Tuberculosis (TB) infection and reactivation can lead to serious morbidity and mortality for immunosuppressed patients. As a result, guidelines recommend screening for TB before starting biologic treatment, but a paucity of data remains on the utility of surveillance testing.

Methods
We performed a retrospective chart review at a single academic center evaluating both IBD and non-IBD patients on biologic therapy. The primary outcome was to determine the number of subsequent surveillance tests performed after initial screening for latent TB in both patient groups.

Results
A total of 188 patients (147 IBD and 41 non-IBD patients) on biologic therapy were included. Screening for TB before biologic treatment was performed in 56% of non-IBD patients versus 83% for patients with IBD (P = 0.0003). Of the total cohort, 65% had at least 2 follow-up surveillance tests for TB. Three or more surveillance tests were performed in 40% of patients with IBD versus only 13% for non-IBD patients (P = 0.0132). A total of 7 patients (4%) had an abnormal surveillance test. No patients were confirmed to have a diagnosis of TB or underwent treatment.

Conclusions
Patients on biologic therapy unnecessarily undergo surveillance testing for TB. Patients with IBD on biologic therapy are screened annually for TB at a higher rate compared to non-IBD patients. Standardization of care among patients on biologic therapy is necessary to avoid excessive testing in areas with a low incidence of TB.
Nest sanitation behavior does not increase the likelihood of parasitic egg rejection in herring gulls
Authors: Stratton James B , Dearborn Donald C 
Published: June 2021

AbstractBirds’ behavioral response to brood parasitism can be influenced not only by evolution but also by context and individual experience. This could include nest sanitation, in which birds remove debris from their nests. Ultimately, nest sanitation behavior might be an evolutionary precursor to the rejection of parasitic eggs. Proximately, the context or experience of performing nest sanitation behavior might increase the detection or prime the removal of parasitic eggs, but evidence to date is limited. We tested incubation-stage nests of herring gulls Larus argentatus to ask whether nest sanitation increased parasitic egg rejection. In an initial set of 160 single-object experiments, small, red, blocky objects were usually rejected (18 of 20 nests), whereas life-sized, 3D-printed herring gull eggs were not rejected whether red (0 of 20) or the olive-tan base color of herring gull eggs (0 of 20). Next, we simultaneously presented a red, 3D-printed gull egg and a small, red block. These nests exhibited frequent nest sanitation (small, red block removed at 40 of 48 nests), but egg rejection remained uncommon (5 of those 40) and not significantly different from control nests (5 of 49) which received the parasitic egg but not the priming object. Thus, performance of nest sanitation did not shape individuals’ responses to parasitism. Interestingly, parents were more likely to reject the parasitic egg when they were present as we approached the nest to add the experimental objects. Depending on the underlying mechanism, this could also be a case of experience creating variation in responses to parasitism.
Eight-year outcomes for patients with aortic valve stenosis at low surgical risk randomized to transcatheter vs. surgical aortic valve replacement
Authors: Jørgensen Troels Højsgaard , Thyregod Hans Gustav Hørsted , Ihlemann Nikolaj , Nissen Henrik , Petursson Petur , Kjeldsen Bo Juel , Steinbrüchel Daniel Andreas , Olsen Peter Skov , Søndergaard Lars 
Published: June 2021

Abstract

Aims
The aims of the study were to compare clinical outcomes and valve durability after 8 years of follow-up in patients with symptomatic severe aortic valve stenosis at low surgical risk treated with either transcatheter aortic valve implantation (TAVI) or surgical aortic valve replacement (SAVR).

Methods and results
In the NOTION trial, patients with symptomatic severe aortic valve stenosis were randomized to TAVI or SAVR. Clinical status, echocardiography, structural valve deterioration, and failure were assessed using standardized definitions. In total, 280 patients were randomized to TAVI (n = 145) or SAVR (n = 135). Baseline characteristics were similar, including mean age of 79.1 ± 4.8 years and a mean STS score of 3.0 ± 1.7%. At 8-year follow-up, the estimated risk of the composite outcome of all-cause mortality, stroke, or myocardial infarction was 54.5% after TAVI and 54.8% after SAVR (P = 0.94). The estimated risks for all-cause mortality (51.8% vs. 52.6%; P = 0.90), stroke (8.3% vs. 9.1%; P = 0.90), or myocardial infarction (6.2% vs. 3.8%; P = 0.33) were similar after TAVI and SAVR. The risk of structural valve deterioration was lower after TAVI than after SAVR (13.9% vs. 28.3%; P = 0.0017), whereas the risk of bioprosthetic valve failure was similar (8.7% vs. 10.5%; P = 0.61).

Conclusions
In patients with severe aortic valve stenosis at low surgical risk randomized to TAVI or SAVR, there were no significant differences in the risk for all-cause mortality, stroke, or myocardial infarction, as well as the risk of bioprosthetic valve failure after 8 years of follow-up.

Clinical trial registration
URL: http://www.ClinicalTrials.gov. Unique identifier: NCT01057173.
Antithrombotic therapies in aortic and peripheral arterial diseases in 2021: a consensus document from the ESC working group on aorta and peripheral vascular diseases, the ESC working group on thrombosis, and the ESC working group on cardiovascular pharmacotherapy
Authors: Aboyans Victor , Bauersachs Rupert , Mazzolai Lucia , Brodmann Marianne , Palomares José F Rodriguez , Debus Sebastian , Collet Jean-Philippe , Drexel Heinz , Espinola-Klein Christine , Lewis Basil S , Roffi Marco , Sibbing Dirk , Sillesen Henrik , Stabile Eugenio , Schlager Oliver , De Carlo Marco 
Published: June 2021

Abstract
The aim of this collaborative document is to provide an update for clinicians on best antithrombotic strategies in patients with aortic and/or peripheral arterial diseases. Antithrombotic therapy is a pillar of optimal medical treatment for these patients at very high cardiovascular risk. While the number of trials on antithrombotic therapies in patients with aortic or peripheral arterial diseases is substantially smaller than for those with coronary artery disease, recent evidence deserves to be incorporated into clinical practice. In the absence of specific indications for chronic oral anticoagulation due to concomitant cardiovascular disease, a single antiplatelet agent is the basis for long-term antithrombotic treatment in patients with aortic or peripheral arterial diseases. Its association with another antiplatelet agent or low-dose anticoagulants will be discussed, based on patient’s ischaemic and bleeding risk as well therapeutic paths (e.g. endovascular therapy). This consensus document aims to provide a guidance for antithrombotic therapy according to arterial disease localizations and clinical presentation. However, it cannot substitute multidisciplinary team discussions, which are particularly important in patients with uncertain ischaemic/bleeding balance. Importantly, since this balance evolves over time in an individual patient, a regular reassessment of the antithrombotic therapy is of paramount importance.
Understanding primary health care physicians’ perspective and approach to pre-conception care in Saudi Arabia
Authors: Alamer Ebtihal , Al-Watban Lemmese , Nafisah Faris Ibrahim 
Published: June 2021

AbstractBackgroundPre-conception care is well known as part of opportunistic, proactive, preventive care for men and women throughout their reproductive years; to lower behavioural, environmental and health-related factors that could lead to poor maternal and foetal outcomes. Many studies have been conducted on the delivery of pre-conception care worldwide. However, no studies were conducted in Saudi Arabia on this topic.ObjectiveTo explore knowledge, attitudes and practice of pre-conception care among primary health care physicians in Riyadh’s Ministry of Health primary care centres and identify barriers they may face.MethodsA phenomenological qualitative approach using in-depth interviews was conducted on participants recruited, between January 2019 and January 2020. Data collection and thematic analysis continued concurrently until maximum variation and theme saturation was achieved by the 10th interview.ResultsThree themes emerged from the data: interpretation of pre-conception care; pre-conception care initiative; and collaboration and education. Participants believed in the benefits of pre-conception care despite their expressed hesitancy in providing it. They expressed dissatisfaction with a few barriers to pre-conception care provision including time constraints in the clinical setting and cultural factors. However, they remained optimistic and motivated to implement changes to attain a higher quality of care.ConclusionsThe gained insight from the in-depth exploration of physicians’ perspectives on pre-conception care helps direct future resources and efforts to both team-based, multi-disciplinary preventative approaches, and population education on the importance of preparing for a pregnancy.
Alcohol use among adult men and its impact on personal and family life: findings of a community-based cross-sectional survey and focus groups discussions from a low alcohol taxed region, Puducherry, India
Authors: Olickal Jeby Jose , Selvaraj Ramya , Saya Ganesh Kumar , Chinnakali Palanivel 
Published: June 2021

Abstract

Background
There is limited published literature on the impact of alcohol use among alcohol dependents and their family members.

Objectives
To find the factors associated with alcohol use and explore the impact of alcohol use on alcohol dependents and their family members.

Methods
A cross-sectional analytical study was conducted among 316 men aged above 18 years, and four focus group discussions (FGDs) were conducted among alcohol dependents and their family members. A validated semi-structured questionnaire was used.

Results
The mean (SD) age of the study participants was 45.2 (15.1) years, and 276 of them (87.3%) were educated. The prevalence of alcohol use was found to be 38% [95% confidence interval (CI) = 32.8–43.4]. Older age [adjusted prevalence (APR) = 2.23 (95% CI = 1.17–4.27)], no formal education [APR = 1.20 (95% CI = 1.20–1.20)], rural residence [APR = 1.05 (95% CI = 1.05–1.05)], self-reported comorbidities [APR = 1.21 (95% CI = 1.21–1.21)], tobacco use [APR = 2.42 (95% CI = 1.98–2.97)] and individuals having a family history of alcohol use [APR = 2.42 (95% CI = 1.73–3.37)] were the factors associated with alcohol use. The family members of alcohol users suffer mainly mental, emotional and physical abuse. Abusive language used by the alcoholic father and family break-ups have an influence on children and in their schooling.

Conclusions
Prevalence of alcohol use in a low alcohol taxed region in India was high. The family members of alcohol users mainly suffer mental, emotional and physical abuse.
Ageism in COVID-Related Newspaper Coverage: The First Month of a Pandemic
Authors: Jen Sarah , Jeong Mijin , Kang Hyun , Riquino Michael 
Published: June 2021

AbstractObjectivesMedia sources have consistently described older adults as a medically vulnerable population during the coronavirus disease 2019 (COVID-19) pandemic, yet a lack of concern over their health and safety has resulted in dismissal and devaluation. This unprecedented situation highlights ongoing societal ageism and its manifestations in public discourse. This analysis asks how national news sources performed explicit and implicit ageism during the first month of the pandemic.MethodUsing content and critical discourse analysis methods, we analyzed 287 articles concerning older adults and COVID-19 published between March 11 and April 10, 2020, in 4 major U.S.-based newspapers.ResultsFindings indicate that while ageism was rarely discussed explicitly, ageist bias was evident in implicit reporting patterns (e.g., frequent use of the term “elderly,” portrayals of older adults as “vulnerable”). Infection and death rates and institutionalized care were among the most commonly reported topics, providing a limited portrait of aging during the pandemic. The older “survivor” narrative offers a positive alternative by suggesting exceptional examples of resilience and grit. However, the survivor narrative may also implicitly place blame on those unable to survive or thrive in later life.DiscussionThis study provides insight for policy makers, researchers, and practitioners exploring societal perceptions of older adults and how these perceptions are disseminated and maintained by the media.
Naturally Acquired SARS-CoV-2 Immunity Persists for Up to 11 Months Following Infection
Authors: De Giorgi Valeria , West Kamille A , Henning Amanda N , Chen Leonard N , Holbrook Michael R , Gross Robin , Liang Janie , Postnikova Elena , Trenbeath Joni , Pogue Sarah , Scinto Tania , Alter Harvey J , Cantilena Cathy Conry 
Published: June 2021

Abstract

Background
Characterizing the kinetics of the antibody response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of critical importance to developing strategies that may mitigate the public health burden of coronavirus disease 2019 (COVID-19). We conducted a prospective, longitudinal analysis of COVID-19 convalescent plasma donors at multiple time points over an 11-month period to determine how circulating antibody levels change over time following natural infection.

Methods
From April 2020 to February 2021, we enrolled 228 donors. At each study visit, subjects either donated plasma or had study samples drawn only. Anti–SARS-CoV-2 donor testing was performed using the VITROS Anti–SARS-CoV-2 Total and IgG assays and an in-house fluorescence reduction neutralization assay.

Results
Anti–SARS-CoV-2 antibodies were identified in 97% of COVID-19 convalescent donors at initial presentation. In follow-up analyses, of 116 donors presenting at repeat time points, 91.4% had detectable IgG levels up to 11 months after symptom recovery, while 63% had detectable neutralizing titers; however, 25% of donors had neutralizing levels that dropped to an undetectable titer over time.

Conclusions
Our data suggest that immunological memory is acquired in most individuals infected with SARS-CoV-2 and is sustained in a majority of patients for up to 11 months after recovery.
Clinical Trials Registration. NCT04360278.
dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering
Authors: Ambrose Stephanie J , Hall Ruth M 
Published: June 2021

Abstract
To track the spread of antibiotic resistance genes, accurate identification of individual genes is essential. Acquired trimethoprim resistance genes encoding trimethoprim-insensitive homologues of the sensitive dihydrofolate reductases encoded by the folA genes of bacteria are increasingly found in genome sequences. However, naming and numbering in publicly available records (journal publications or entries in the GenBank non-redundant DNA database) has not always been unambiguous. In addition, the nomenclature has evolved over time. Here, the changes in nomenclature and the most commonly encountered problems and pitfalls affecting dfrA gene identification arising from historically incorrect or inaccurate numbering are explained. The complete set of dfrA genes/DfrA proteins found in Gram-negative bacteria for which readily searchable sequence information is currently available has been compiled using less than 98% identity for both the gene and the derived protein sequence as the criteria for assignment of a new number. In most cases, trimethoprim resistance has been demonstrated. The gene context, predominantly in a gene cassette or near the ori end of CR1 or CR2, is also covered. The RefSeq database that underpins the programs used to automatically identify resistance genes in genome data sets has been curated to assign all sequences listed to the correct number. This led to the assignment of corrected or new gene numbers to several mis-assigned sequences. The unique numbers assigned for the dfrA/DfrA set are now listed in the RefSeq database, which we propose provides a way forward that should end future duplication of numbers and the confusion that causes.
Application of natural language processing techniques to identify off-label drug usage from various online health communities
Authors: Dreyfus Brian , Chaudhary Anuj , Bhardwaj Parth , Shree V Karthikhaa 
Published: June 2021

Abstract

Objective
Outcomes mentioned on online health communities (OHCs) by patients can serve as a source of evidence for off-label drug usage evaluation, but identifying these outcomes manually is tedious work. We have built a natural language processing model to identify off-label usage of drugs mentioned in these patient posts.

Materials and Methods
Single patient posts from 4 major OHCs were considered for this study. A text classification model was built to classify the posts as either relevant or not relevant based on patient experience. The relevant posts were passed through a spelling correction tool, CSpell, and then medications and indications from these posts were identified using cTAKES (clinical Text Analysis and Knowledge Extraction System), a named entity recognition tool. Drug and indication pairs were identified using a dependency parser. Finally, if the paired indication was not mentioned on the label of the drug approved by U.S. Food and Drug Administration, it was tagged as off-label use of that drug.

Results
Using this algorithm, we identified 289 off-label indications, achieving a recall of 76%.

Conclusions
The method designed in this study identifies and extracts the semantic relationship between drugs and indications from demotic posts in OHCs. The results demonstrate the feasibility of using natural language processing techniques in identifying off-label drug usage across online health forums for a variety of drugs. Understanding patients’ off-label use of drugs may be able to help manufacturers innovate to better address patients’ needs and assist doctors’ prescribing decisions.
MT-clinical BERT: scaling clinical information extraction with multitask learning
Authors: Mulyar Andriy , Uzuner Ozlem , McInnes Bridget 
Published: June 2021

Abstract

Objective
Clinical notes contain an abundance of important, but not-readily accessible, information about patients. Systems that automatically extract this information rely on large amounts of training data of which there exists limited resources to create. Furthermore, they are developed disjointly, meaning that no information can be shared among task-specific systems. This bottleneck unnecessarily complicates practical application, reduces the performance capabilities of each individual solution, and associates the engineering debt of managing multiple information extraction systems.

Materials and Methods
We address these challenges by developing Multitask-Clinical BERT: a single deep learning model that simultaneously performs 8 clinical tasks spanning entity extraction, personal health information identification, language entailment, and similarity by sharing representations among tasks.

Results
We compare the performance of our multitasking information extraction system to state-of-the-art BERT sequential fine-tuning baselines. We observe a slight but consistent performance degradation in MT-Clinical BERT relative to sequential fine-tuning.

Discussion
These results intuitively suggest that learning a general clinical text representation capable of supporting multiple tasks has the downside of losing the ability to exploit dataset or clinical note-specific properties when compared to a single, task-specific model.

Conclusions
We find our single system performs competitively with all state-the-art task-specific systems while also benefiting from massive computational benefits at inference.