bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparison of Less Invasive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Diagnostic Specimens in Nursing Home Residents—Arkansas, June–August 2020
Authors: Gable Paige , Huang Jennifer Y , Gilbert Sarah E , Bollinger Susan , Lyons Amanda K , Sabour Sarah , Surie Diya , Biedron Caitlin , Haney Tafarra , Beshearse Elizabeth , Gregory Christopher J , Seely Kathryn A , Clemmons Nakia S , Patil Naveen , Kothari Atul , Gulley Trent , Garner Kelley , Anderson Karen , Thornburg Natalie J , Halpin Alison L , McDonald L Clifford , Kutty Preeta K , Brown Allison C ,   Centers for Disease Control and Prevention COVID-19 Laboratory Task Force, Ramachandran Sumathi , Hughes Holly , Bohannon Caitlin , Sexton D Joseph , Lonsway David , Bhatnagar Amelia , Breaker Erin , Adamczyk Michelle , McAllister Gillian A , Campbell Davina , Houston Hollis , Perry-Dow K Allison , Reese Natashia , Paulick Ashley , Spicer Lori , Harcourt Jennifer L , Coughlin Melissa M , Tamin Azaibi , Whitaker Brett , Stumpf Megan M , Mills Lisa , Ata Ur Rasheed Mohammad 
Published: April 2021

Abstract

Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing remains essential for early identification and clinical management of cases. We compared the diagnostic performance of 3 specimen types for characterizing SARS-CoV-2 in infected nursing home residents.

Methods
A convenience sample of 17 residents were enrolled within 15 days of first positive SARS-CoV-2 result by real-time reverse transcription polymerase chain reaction (RT-PCR) and prospectively followed for 42 days. Anterior nasal swabs (AN), oropharyngeal swabs (OP), and saliva specimens (SA) were collected on the day of enrollment, every 3 days for the first 21 days, and then weekly for 21 days. Specimens were tested for presence of SARS-CoV-2 RNA using RT-PCR and replication-competent virus by viral culture.

Results
Comparing the 3 specimen types collected from each participant at each time point, the concordance of paired RT-PCR results ranged from 80% to 88%. After the first positive result, SA and OP were RT-PCR-positive for ≤48 days; AN were RT-PCR–positive for ≤33 days. AN had the highest percentage of RT-PCR–positive results (21/26 [81%]) when collected ≤10 days of participants’ first positive result. Eleven specimens were positive by viral culture: 9 AN collected ≤19 days following first positive result and 2 OP collected ≤5 days following first positive result.

Conclusions
AN, OP, and SA were effective methods for repeated testing in this population. More AN than OP were positive by viral culture. SA and OP remained RT-PCR-positive longer than AN, which could lead to unnecessary interventions if RT-PCR detection occurred after viral shedding has likely ceased.
Estimating Population-Level Effects of the Acellular Pertussis Vaccine Using Routinely Collected Immunization Data
Authors: Rane Madhura S , Halloran M Elizabeth 
Published: April 2021

Abstract

Background
Measuring and reporting the different population-level effects of the acellular pertussis vaccine on pertussis disease in addition to direct effects can increase the cost-effectiveness of a vaccine.

Methods
We conducted a retrospective cohort study of children born between 1 January 2008 and 31 December 2017, in King County, Washington, who were enrolled in the Washington State Immunization Information System. Diphtheria, tetanus toxoids, and acellular pertussis (DTaP) vaccination data from in the Washington State Immunization Information System was linked with pertussis case data from Public Health Seattle and King County. Census-level vaccination coverage was estimated as proportion of age-appropriately vaccinated children residing in it. Direct vaccine effectiveness was estimated by comparing pertussis risk in fully vaccinated and undervaccinated children. Population-level vaccine effectiveness (VE) measures were estimated by comparing pertussis risk in census tracts in the highest quartile for vaccination coverage with that in the lowest quartile.

Results
For direct protection, estimated VE was 76% (95% confidence interval, 63%–84%) in low-vaccination-coverage clusters, and it decreased to 47% (13%–68%) in high-coverage clusters, after adjustment for potential confounders. The estimated indirect VE was 45.0% (95% confidence interval, 1%–70%), the total VE 93.9% (91%–96%), and the overall VE 42.2% (19%–60%).

Conclusion
Our findings suggest that DTaP vaccination provided direct as well as indirect protection in the highly immunized King County, Washington. Routine DTaP vaccination programs may have the potential to provide not only protection for vaccinated individuals but also for the undervaccinated individuals living in the same area.
Cis-epistasis at the LPA locus and risk of cardiovascular diseases
Authors: Zeng Lingyao , Moser Sylvain , Mirza-Schreiber Nazanin , Lamina Claudia , Coassin Stefan , Nelson Christopher P , Annilo Tarmo , Franzén Oscar , Kleber Marcus E , Mack Salome , Andlauer Till F M , Jiang Beibei , Stiller Barbara , Li Ling , Willenborg Christina , Munz Matthias , Kessler Thorsten , Kastrati Adnan , Laugwitz Karl-Ludwig , Erdmann Jeanette , Moebus Susanne , Nöthen Markus M , Peters Annette , Strauch Konstantin , Müller-Nurasyid Martina , Gieger Christian , Meitinger Thomas , Steinhagen-Thiessen Elisabeth , März Winfried , Metspalu Andres , Björkegren Johan L M , Samani Nilesh J , Kronenberg Florian , Müller-Myhsok Bertram , Schunkert Heribert 
Published: April 2021

Abstract

Aims
Coronary artery disease (CAD) has a strong genetic predisposition. However, despite substantial discoveries made by genome-wide association studies (GWAS), a large proportion of heritability awaits identification. Non-additive genetic effects might be responsible for part of the unaccounted genetic variance. Here, we attempted a proof-of-concept study to identify non-additive genetic effects, namely epistatic interactions, associated with CAD.

Methods and results
We tested for epistatic interactions in 10 CAD case–control studies and UK Biobank with focus on 8068 SNPs at 56 loci with known associations with CAD risk. We identified a SNP pair located in cis at the LPA locus, rs1800769 and rs9458001, to be jointly associated with risk for CAD [odds ratio (OR) = 1.37, P = 1.07 × 10−11], peripheral arterial disease (OR = 1.22, P = 2.32 × 10−4), aortic stenosis (OR = 1.47, P = 6.95 × 10−7), hepatic lipoprotein(a) (Lp(a)) transcript levels (beta = 0.39, P = 1.41 × 10−8), and Lp(a) serum levels (beta = 0.58, P = 8.7 × 10−32), while individual SNPs displayed no association. Further exploration of the LPA locus revealed a strong dependency of these associations on a rare variant, rs140570886, that was previously associated with Lp(a) levels. We confirmed increased CAD risk for heterozygous (relative OR = 1.46, P = 9.97 × 10−32) and individuals homozygous for the minor allele (relative OR = 1.77, P = 0.09) of rs140570886. Using forward model selection, we also show that epistatic interactions between rs140570886, rs9458001, and rs1800769 modulate the effects of the rs140570886 risk allele.

Conclusions
These results demonstrate the feasibility of a large-scale knowledge-based epistasis scan and provide rare evidence of an epistatic interaction in a complex human disease. We were directed to a variant (rs140570886) influencing risk through additive genetic as well as epistatic effects. In summary, this study provides deeper insights into the genetic architecture of a locus important for cardiovascular diseases.
Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition
Authors: Klie Adam , Tsui Brian Y , Mollah Shamim , Skola Dylan , Dow Michelle , Hsu Chun-Nan , Carter Hannah 
Published: April 2021

Abstract
High-quality metadata annotations for data hosted in large public repositories are essential for research reproducibility and for conducting fast, powerful and scalable meta-analyses. Currently, a majority of sequencing samples in the National Center for Biotechnology Information’s Sequence Read Archive (SRA) are missing metadata across several categories. In an effort to improve the metadata coverage of these samples, we leveraged almost 44 million attribute–value pairs from SRA BioSample to train a scalable, recurrent neural network that predicts missing metadata via named entity recognition (NER). The network was first trained to classify short text phrases according to 11 metadata categories and achieved an overall accuracy and area under the receiver operating characteristic curve of 85.2% and 0.977, respectively. We then applied our classifier to predict 11 metadata categories from the longer TITLE attribute of samples, evaluating performance on a set of samples withheld from model training. Prediction accuracies were high when extracting sample Genus/Species (94.85%), Condition/Disease (95.65%) and Strain (82.03%) from TITLEs, with lower accuracies and lack of predictions for other categories highlighting multiple issues with the current metadata annotations in BioSample. These results indicate the utility of recurrent neural networks for NER-based metadata prediction and the potential for models such as the one presented here to increase metadata coverage in BioSample while minimizing the need for manual curation.
Database URL: https://github.com/cartercompbio/PredictMEE
The Impact of Vedolizumab on COVID-19 Outcomes Among Adult IBD Patients in the SECURE-IBD Registry
Authors: Agrawal Manasi , Zhang Xian , Brenner Erica J , Ungaro Ryan C , Kappelman Michael D , Colombel Jean-Frederic 
Published: April 2021

Abstract

Background
The impact of immune-modifying therapies on outcomes of coronavirus disease 2019 [COVID-19] is variable. The purpose of this study was to determine the impact of vedolizumab [VDZ], a gut-selective anti-integrin, on COVID-19 outcomes in inflammatory bowel disease [IBD] patients.

Methods
Using data from the Surveillance of Coronavirus Under Research Exclusion for IBD [SECURE-IBD], an international registry of IBD patients with confirmed COVID-19, we studied the impact of VDZ on COVID-19 hospitalization and severe COVID-19 [intensive care unit stay, mechanical ventilation and/or death].

Results
Of 3647 adult patients on any IBD medication in the registry, 457 [12.5%] patients were on VDZ. On multivariable analyses using backward selection of covariates, VDZ use was not associated with hospitalization or severe COVID-19 when compared with patients on all other medications (adjusted odds ratio [aOR] 0.87; 95% confidence interval [CI] 0.71, 1.1 and aOR 0.95; 95% CI 0.53, 1.73, respectively). On comparing VDZ monotherapy to anti-tumour necrosis factor [anti-TNF] monotherapy, the odds for hospitalization, but not severe COVID-19, were higher [aOR CI 1.39; 95% CI 1.001, 1.90 and aOR 2.92; 95% CI 0.98, 8.71, respectively]. In an exploratory analysis, VDZ monotherapy, compared to anti-TNF monotherapy, was associated with new-onset gastrointestinal symptoms at the time of COVID-19, especially among patients whose IBD was in remission.

Conclusions
COVID-19 outcomes among IBD patients on VDZ are comparable to those on all other therapies. Hospitalization, but not severe COVID-19, is more likely with VDZ monotherapy than with anti-TNF monotherapy. Overall, VDZ appears to be safe in IBD patients with COVID-19.
Predictors of reoperation and mortality after complete atrioventricular septal defect repair
Authors: Fong Laura S , Betts Kim , Ayer Julian , Andrews David , Nicholson Ian A , Winlaw David S , Orr Yishay ,   the Australian CAVSD study group, Alphonso Nelson , Bell Douglas , Hu Thomas , Konstantinov Igor E , Radford Dorothy 
Published: April 2021

Abstract

OBJECTIVES
Previous studies investigating risk factors associated with reoperation or mortality after repair of complete atrioventricular septal defect (CAVSD) often have not included sizeable cohorts undergoing modified single-patch repair. Both double patch and modified single-patch techniques have been widely used in Australia since the 1990s. Using a large multi-institutional cohort, we aimed to identify risk factors associated with reoperation or mortality following CAVSD repair.

METHODS
Between January 1990 and December 2015, a total of 829 patients underwent biventricular surgical repair of CAVSD in Australia at 4 centres. Patients with associated tetralogy of Fallot and other conotruncal abnormalities were excluded. Demographic details, postoperative outcomes including reoperation and survival, and associated risk factors were analysed.

RESULTS
Fifty-six patients (6.8%) required early reoperation (≤30 days) for significant left atrioventricular valve regurgitation or residual septal defects. Freedom from reoperation at 10, 15 and 20 years was 82.7%, 81.1% and 77%, respectively. Patients without Down syndrome and moderate left atrioventricular valve regurgitation on postoperative echocardiogram were found to be independent risk factors for reoperation. Operative mortality was 3.3%. Overall survival at 10, 15 and 20 years was 91.7%, 90.7% and 88.7%, respectively. Prior pulmonary artery banding was a predictor for mortality, while later surgical era (2010–2015) was associated with a reduction in mortality risk.

CONCLUSIONS
Improved survival in the contemporary era is in keeping with improvements in surgical management and higher rates of primary CAVSD repair over time. The presence of residual moderate left atrioventricular valve regurgitation on postoperative echocardiography is an important factor associated with reoperation and close surveillance is essential to allow timely reintervention. Primary CAVSD repair at age &lt;3 months should be preferenced to palliation with pulmonary artery banding due to the association of pulmonary artery banding with mortality in the long-term.
Intermediate-term neurodevelopmental outcomes and quality of life after arterial switch operation beyond early neonatal period
Authors: Ramanan Sowmya , Sundaram Soumya , Gopalakrishnan Arun , Anija D V , Sandhya P , Jose Dhiya Susan , Baruah Sudip Dutta , Menon Sabarinath , Dharan Baiju S 
Published: April 2021

Abstract

OBJECTIVES
The study objective was to evaluate the cardiac, neurodevelopmental, psycho-social and health-related quality of life (HRQOL) outcomes of children who underwent an arterial switch operation (ASO).

METHODS
Children who underwent ASO were evaluated on follow-up at 3–5 years with cardiovascular, neurodevelopmental and HRQOL assessment using validated tools. Children with developmental delay, attention-deficit hyperactivity disorder, autism spectrum disorder, neuromotor and speech and language impairment were considered to have neurodevelopmental disorder (NDD). The impact of socioeconomic status (Kuppuswamy classification), perioperative cardiac, nutritional and psycho-social factors on outcomes was analysed.

RESULTS
There were 61 (89.7%) survivors at a mean follow-up of 50.9 ± 7.6 months. The median age at surgery was 41 days (22–74.5). One-third of patients had growth restriction. Two children had residual cardiovascular lesions requiring intervention. The mean HRQOL score was &gt;90 in all scales of the Paediatric Quality of Life Inventory™ 3.0 Cardiac Module. Neurological abnormalities were seen in 19 patients (31.1%) of whom 17 (27.9%) patients had NDD and 12 had developmental delay. Speech and language impairment, attention-deficit hyperactivity disorder, and neuromotor impairment were found in 16.4%, 3.3% and 6.7% patients, respectively. On multivariate analysis, increasing time to lactate normalization and low socioeconomic status were associated with developmental delay after ASO.

CONCLUSIONS
While intermediate-term cardiac outcomes and HRQOL after ASO were fairly satisfactory, NDD was identified in one-fourth of these children. Increasing time to lactate normalization after ASO and low socioeconomic status were associated with suboptimal intermediate neurodevelopment outcomes after ASO.
Serial right ventricular assessment in patients with hypoplastic left heart syndrome: a multiparametric cardiovascular magnetic resonance study
Authors: Sobh Mohamed , Freitag-Wolf Sandra , Scheewe Jens , Kanngiesser Luca M , Uebing Anselm S , Gabbert Dominik D , Voges Inga 
Published: April 2021

Abstract

OBJECTIVES
The aim of this study was to assess single right ventricular (RV) function in a large cohort of hypoplastic left heart syndrome (HLHS) patients after the completion of total cavopulmonary connection by analysing serial cardiovascular magnetic resonance (CMR) studies.

METHODS
CMR studies from 95 HLHS patients were analysed. RV end-diastolic and end-systolic volumes (RVEDV, RVESV), ejection fraction (RVEF) and long-axis strain (LAS) were measured from cine images.

RESULTS
All 95 patients had at least 2 CMR scans and 35 patients had 3 CMR scans. The median age (first quartile–third quartile) at the 3 examinations was 4.2 (3.3–6.1), 9.4 (6.1–11.4) and 14.6 (11.8–16.8) years. RV indexed volumes (RVEDVi and RVESVi) increased from first to the second and from the first and second examination to the third examination in patients with &gt;10 years of age (P &lt; 0.05). There was a slight decrease in RVEF and LAS throughout the examinations, but this was not statistically significant. Correlations were found between RVEF and LAS (r = −0.23; P &lt; 0.01). Both RVEF and LAS correlated with RVEDVi and RVESVi (r = −0.17 to 0.43; P &lt; 0.05).

CONCLUSIONS
Serial assessment of CMR studies in HLHS patients after total cavopulmonary connection completion demonstrate an increase in indexed RV volumes in older HLHS patients but only mild reduction in RVEF and LAS. The correlation of indexed RV volumes with RVEF and LAS together with the significant increase in RV volumes over time suggests that indexed RV volumes might be superior to RV functional markers to monitor the RV in HLHS patients.
Morphological alterations, activity, mRNA fold changes, and aging changes before and after orthodontic force application in young and adult human-derived periodontal ligament cells
Authors: Mohanakumar Aravind , Vijay Geethu L , Vijayaraghavan Nandakumar , Rajendran Rahul S , Chandran Madhav B , Thulasidharan Midhun U , Damodaran Deepak R , Sreekumar Chandrima , Krishnan Vinod 
Published: April 2021

AbstractBackgroundThe response of periodontal ligament cells (PDLC) from adult subjects in comparison to those obtained from younger ones to mechanical forces has been a matter of interest recently because of induced senescent changes. This study evaluated and compared cell surface changes and activity, integrin beta 1, and β-actin mRNA fold changes as well as klotho protein secretion capabilities of PDLC from young and adult donors before and after subjecting to orthodontic forces.MethodsA total of 40 subjects with bimaxillary dentoalveolar protrusion requiring extraction of first premolars for orthodontic treatment were selected and divided into two groups. Force ranging from 80 to 90 g was applied to maxillary first premolars and extraction was carried out at two different time periods—pre-treatment (control group) and 28 days after force application (experimental group). Periodontal ligament was obtained, and cell surface changes and activity were observed with atomic force microscopy (AFM) and fluorescent tagging. mRNA fold change of integrin beta-1 and β-actin mRNA, as well as beta-galactosidase assay, was performed, and levels of klotho protein were evaluated.ResultsAFM nanoindentation and fluorescent tagging indicated increased surface morphological changes in younger cells compared to adult ones. We observed a decrease in integrin beta 1 but an increase in β-actin mRNA levels in PDLC obtained from younger subjects compared to adults, while an increase was observed in SA-β-GAL from adult cells. The level of klotho protein was lower in adult cells in comparison to younger ones.LimitationsLarge sample studies are required to find out a variation in aging characteristics between young and adult PDLC.ConclusionsThe study observed significant differences between PDLC obtained from younger and adult subjects in response to orthodontic force application.
Contingent valuation of landowner demand for forest amenities: application in Andalusia, Spain
Authors: Oviedo José L , Campos Pablo , Caparrós Alejandro 
Published: April 2021

AbstractWe applied discrete choice contingent valuation to the amenities consumed by non-industrial private forest owners in Andalusia (Spain) in a survey of 765 landowners. The landowners’ median willingness to accept compensation from an alternative investment for giving up land amenity consumption is EUR 387.8 per hectare yearly. The preferred model shows diminishing marginal values of amenity consumption with property size, negative effects of eucalyptus and Aleppo pine presence and positive effects of distance to urban centres. We discuss the performance of the question formats and models employed and recommend the single-bounded format in this valuation context.
Effects of environmental factors on sensitivity of Cryptococcus neoformans to fluconazole and amphotericin B
Authors: Carlson Tyler , Lupinacci Emily , Moseley Katie , Chandrasekaran Srikripa 
Published: April 2021

ABSTRACT
Cryptococcus neoformans is a leading cause of fungal meningitis in immunocompromized populations. Amphotericin B (AMB) and fluconazole (FLC) are common anticryptococcal agents. AMB treatment leads to severe side-effects. In contrast, FLC-based therapy is relatively safe, although C. neoformans often develops resistance to this drug. C. neoformans must adapt to the challenging environment of the human host. Environmental effects on potency of AMB and FLC and development of drug resistance remain poorly characterized. Here, the effects of nutrients, temperature and antioxidants on susceptibility of C. neoformans towards FLC and AMB were investigated. Limited nutrients led to a decrease and an increase of sensitivity towards FLC and AMB, respectively. Co-treatment with various antioxidants also demonstrated reciprocal effects on susceptibility towards FLC and AMB. In contrast, elevated temperature increased the efficacy of both drugs, although the effect on FLC was more drastic as compared to that of AMB. In addition, temperatures of 37°C and above prevented development of FLC resistance. Our study pointed to a critical role of the environment on susceptibility towards AMB and FLC and revealed reciprocal effects towards these antifungal drugs, reflecting contrasting modes of action of AMB and FLC.
Screening of probiotic candidates in a simulated piglet small intestine in vitro model
Authors: Hansen L H B , Cieplak T , Nielsen B , Zhang Y , Lauridsen C , Canibe N 
Published: April 2021

ABSTRACT
The CoMiniGut in vitro model mimicking the small intestine of piglets was used to evaluate four probiotic strains for their potential as a preventive measure against development of diarrhea in weaned pigs. In the in vitro system, piglet digesta was inoculated with pathogenic enterotoxigenic Escherichia coli F4 (ETEC F4), and the short-chain fatty acid profile and the gut microbiota composition were assessed. A total of four probiotic strains were evaluated: Enterococcus faecium (CHCC 10669), Lactobacillus rhamnosus (CHCC 11994), Bifidobacterium breve (CHCC 15268) and Faecalibacterium prausnitzii (CHCC 28556). The significant differences observed in metabolite concetration and bacterial enumeration were attributed to variation in inoculating material or pathogen challenge rather than probiotic treatment. Probiotic administration influenced the microbiota composition to a small extend. Learnings from the present study indicate that the experimental setup, including incubation time and choice of inoculating material, should be chosen with care.