bluuebunny/crossref_metadata_2025_split huggingface dataset:
Information Avoidance, Self-affirmation, and Intentions to Receive Genomic Sequencing Results Among Members of an African Descent Cohort
Authors: Peterson Emily B , Taber Jennifer M , Klein William M P 
Published: June 2021

Abstract

Background
Information avoidance tendencies have been found to be associated with lower intentions to pursue medically actionable genomic sequencing results, but less so among individuals who engage more in spontaneous self-affirmation. Yet these results were obtained with a largely non-Hispanic White, high-SES cohort.

Purpose
To assess these variables, their magnitude, and their associations in an African-descent cohort as part of the same ClinSeq® exome sequencing program.

Methods
Participants reported levels of spontaneous self-affirmation, information avoidance, and intentions to receive three types of results – medically actionable, non-medically actionable, and carrier status as part of a baseline survey.

Results
Relative to the original, non-Hispanic White cohort, those in the African-descent cohort had higher levels of spontaneous self-affirmation and lower intentions of learning about carrier genomic results; they reported comparable levels of information avoidance and intentions to receive other results. Information avoidance was negatively associated with intention to receive non-actionable results in the African-descent cohort, as found in the initial cohort, with no moderating effect of spontaneous self-affirmation. Information avoidance, spontaneous self-affirmation, and their interaction were not associated with intentions to receive actionable results (contrary to findings in the initial cohort), or carrier results.

Conclusions
Individuals of African descent may engage in relatively more spontaneous self-affirmation, and do not appear to engage in more information avoidance. Their information avoidance tendencies were associated with pursuit of non-actionable sequencing results, with no moderating effect of self-affirmation, and were not associated with pursuit of actionable results or carrier results.
Invited Commentary: Is the Long Shadow of Childhood Disadvantage on Lifelong Health Getting Worse Over Time?
Authors: Melchior Maria 
Published: June 2021

AbstractSocial inequalities in health and their early-life origins have been extensively documented. Although the complex direct and intermediate mechanisms linking early-life disadvantage to later health are not yet fully understood, new findings on biological markers distinctly related with early-life experiences suggest a causal relationship. In this issue, Fuller-Rowell et al. (Am J Epidemiol. 2021:190(11):2284–2293) step back to examine the role of childhood disadvantage in the United States in different periods, observing that the relationship with later health seems to have strengthened over time. The main explanation the authors bring up has to do with increased income segregation and changes in labor market composition that limit opportunities for persons with low educational attainment. In other words, while the rich get richer, the poor get poorer, the middle class shrinks, and there are fewer interactions across different socioeconomic groups and the social ladder is blocked. Other evidence suggests that investments in children, through early education and academic support programs, could help reduce the consequences of childhood disadvantage on long-term health.
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
Authors: Roncoroni Miguel , Droesbeke Bert , Eguinoa Ignacio , De Ruyck Kim , D’Anna Flora , Yusuf Dilmurat , Grüning Björn , Backofen Rolf , Coppens Frederik 
Published: June 2021

Abstract

Summary
Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatics knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment.

Availability and implementation
CLI ENA upload tool is available at github.com/usegalaxy-eu/ena-upload-cli (DOI 10.5281/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu/view/iuc/ena_upload/382518f24d6d and github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload (development); and ENA upload Galaxy container at github.com/ELIXIR-Belgium/ena-upload-container (DOI 10.5281/zenodo.4730785).
EchoNavigator® technology facilitates transapical mitral paravalvular leak closure: a case report
Authors: Buzaev Igor Vyacheslavovich , Khalikova Gulchachak , Plechev Vladimir Vyacheslavovich , Onorato Eustaquio Maria 
Published: June 2021

Abstract

Background
Catheter-based closure has emerged as a less invasive alternative to surgery in high-risk patients with paravalvular leak (PVL) and clinically significant regurgitation with feasibility and efficacy demonstrated in multiple studies.

Case summary
A 72-year-old female with a past history of long-standing rheumatic heart disease underwent mechanical mitral valve replacement in 2008. Ten years later, redo surgery was performed due to a worsening mitral PVL and the leakage was closed by direct pledget-supported sutures, preserving the mechanical valve. She was recently admitted again for haemolytic anaemia and congestive heart failure (New York Heart Association Classes III–IV) due to a recurrent mitral PVL. We report our initial clinical experience using a novel software solution (EchoNavigator®-system) for intuitive guidance during a catheter-based transapical mitral PVL closure.

Discussion
Transapical mitral PVL closure with a specifically designed device demonstrated in our case to be a better option than redo surgery. Recently introduced fusion imaging modalities enhanced visualization of soft tissue anatomy and device location improving enormously the results of this challenging intervention.
Potential for optimizing management of obesity in the secondary prevention of coronary heart disease
Authors: De Bacquer Dirk , Jennings Catriona S , Mirrakhimov Erkin , Lovic Dragan , Bruthans Jan , De Smedt Delphine , Gotcheva Nina , Dolzhenko Maria , Fras Zlatko , Pogosova Nana , Lehto Seppo , Hasan-Ali Hasan , Jankowski Piotr , Kotseva Kornelia , De Backer Guy , Wood David , Rydén Lars 
Published: June 2021

Abstract

Aims
Prevention guidelines have identified the management of obese patients as an important priority to reduce the burden of incident and recurrent cardiovascular disease. Still, studies have demonstrated that over 80% of patients with coronary heart disease (CHD) fail to achieve their weight target. Here, we describe advice received and actions reported by overweight CHD patients since being discharged from hospital and how weight changes relate to their risk profile.

Methods and results
Based on data from 10 507 CHD patients participating in the EUROASPIRE IV and V studies, we analysed weight changes from hospital admission to the time of a study visit ≥6 and &lt;24 months later. At hospitalization, 34.9% were obese and another 46.0% were overweight. Obesity was more frequent in women and associated with more comorbidities. By the time of the study visit, 19.5% of obese patients had lost ≥5% of weight. However, in 16.4% weight had increased ≥5%. Weight gain in those overweight was associated with physical inactivity, non-adherence to dietary recommendations, smoking cessation, raised blood pressure, dyslipidaemia, dysglycaemia, and lower levels of quality of life. Less than half of obese patients was considering weight loss in the coming month.

Conclusions
The management of obesity remains a challenge in the secondary prevention of CHD despite a beneficial effect of weight loss on risk factor prevalences and quality of life. Cardiac rehabilitation programmes should include weight loss interventions as a specific component and the incremental value of telehealth intervention as well as recently described pharmacological interventions need full consideration.
Coffee cell walls—composition, influence on cup quality and opportunities for coffee improvements
Authors: Li Zheng , Zhang Chuntang , Zhang Yuan , Zeng Wei , Cesarino Igor 
Published: June 2021

AbstractThe coffee beverage is the second most consumed drink worldwide after water. In coffee beans, cell wall storage polysaccharides (CWSPs) represent around 50 per cent of the seed dry mass, mainly consisting of galactomannans and arabinogalactans. These highly abundant structural components largely influence the organoleptic properties of the coffee beverage, mainly due to the complex changes they undergo during the roasting process. From a nutritional point of view, coffee CWSPs are soluble dietary fibers shown to provide numerous health benefits in reducing the risk of human diseases. Due to their influence on coffee quality and their health-promoting benefits, CWSPs have been attracting significant research attention. The importance of cell walls to the coffee industry is not restricted to beans used for beverage production, as several coffee by-products also present high concentrations of cell wall components. These by-products include cherry husks, cherry pulps, parchment skin, silver skin, and spent coffee grounds, which are currently used or have the potential to be utilized either as food ingredients or additives, or for the generation of downstream products such as enzymes, pharmaceuticals, and bioethanol. In addition to their functions during plant development, cell walls also play a role in the plant’s resistance to stresses. Here, we review several aspects of coffee cell walls, including chemical composition, biosynthesis, their function in coffee’s responses to stresses, and their influence on coffee quality. We also propose some potential cell wall–related biotechnological strategies envisaged for coffee improvements.
Personal Network Bridging Potential Across Geographic Context
Authors: Roth Adam R , Peng Siyun , Perry Brea L 
Published: June 2021

Abstract

Objectives
Personal networks play a fundamental role in the daily lives of older adults. Although many studies examine how life course factors and personal preferences shape network formation, fewer consider how the places in which older adults live present opportunities and obstacles to cultivate social relationships. In the present study, we explore how geographic context is associated with the ability to bridge social ties within one’s personal network.

Methods
We use data from the Person-to-Person Health Interview Survey (N = 709), a representative sample of Indiana residents. Personal network data were collected using 4 name-generating prompts. Logistic regression models and linear regression models were used to assess 2 measures of network bridging.

Results
A minority of respondents reported the ability to bridge ties within their networks. Respondents residing in rural and mixed counties were less likely than urban respondents to have at least one member of their network who was completely disconnected from all other members.

Discussion
These findings suggest that the communities in which older adults live condition opportunities for accessing unique network resources. Additional research adopting a network perspective is needed to provide insight into geographic disparities occurring among the older population.
Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice
Authors: Yoshioka Hiroki , Li Aimin , Suzuki Akiko , Ramakrishnan Sai Shankar , Zhao Zhongming , Iwata Junichi 
Published: June 2021

Abstract
The etiology of cleft lip with/without cleft palate (CL/P), one of the most frequent craniofacial birth defects worldwide, is complicated by contributions of both genetic and environmental factors. Understanding the etiology of these conditions is essential for developing preventive strategies. This study thus aims to identify regulatory networks of microRNAs (miRNAs), transcriptional factors (TFs) and non-TF genes associated with cleft lip (CL) that are conserved in humans and mice. Notably, we found that miR-27b, miR-133b, miR-205, miR-376b and miR-376c were involved in the regulation of CL-associated gene expression in both humans and mice. Among the candidate miRNAs, the overexpression of miR-27b, miR-133b and miR-205, but not miR-376b and miR-376c, significantly inhibited cell proliferation through suppression of CL-associated genes (miR-27b suppressed PAX9 and RARA; miR-133b suppressed FGFR1, PAX7, and SUMO1; and miR-205 suppressed PAX9 and RARA) in cultured human and mouse lip mesenchymal cells. Taken together, our results suggest that elevated expression of miR-27b, miR-133b and miR-205 may play a crucial role in CL through the suppression of genes associated with CL.
Impact of an educational intervention on WHO surgical safety checklist and pre-operative antibiotic use at a referral hospital in southwestern Uganda
Authors: Ngonzi Joseph , Bebell Lisa M , Boatin Adline A , Owaraganise Aspihas , Tiibajuka Leevan , Fajardo Yarine , Lugobe Henry Mark , Wylie Blair J , Jacquemyn Yves , Obua Celestino , Haberer Jessica E , Geertruyden Jean-pierre van 
Published: June 2021

Abstract

Introduction
The World Health Organization (WHO) recommends adherence to its surgical safety checklist (SSC) to optimize patient safety and reduce cesarean surgical site infection (SSI). Educational interventions combined with audit and feedback mechanisms on the checklist use by clinicians have the potential to improve adherence and clinical outcomes. Despite the increase in cesarean delivery rates, there is a paucity of data on how such interventions can improve adherence in resource-limited settings.

Objective
We performed a quality improvement project to measure the impact of an educational intervention with daily audit and feedback procedures on rates of WHO SSC adherence, including pre-operative antibiotic administration and SSI at Mbarara Regional Referral Hospital maternity ward in Uganda.

Methods
The study involved chart abstraction of WHO SSC and pre-operative antibiotic use during cesarean deliveries and signs of subsequent SSI in three phases. First, we conducted a retrospective review of all charts from May to June 2018 (pre-intervention phase). Second, we instituted an educational intervention on the WHO SSC and pre-operative antibiotics use, followed by a daily audit of charts and feedback to clinicians from July to August 2018 (the intervention phase). Third, we reviewed charts from September to October 2018 (the post-intervention phase). The WHO SSC adherence, pre-operative antibiotic administration and SSI rates were measured as the proportion of the total cesarean deliveries per study phase and then compared across the three phases.

Results
We reviewed 678 patients’ charts (200 in the pre-intervention phase, 230 in the intervention phase and 248 in the post-intervention phase). The mean patient age was 25 years. The use of the WHO SSC was 7% in the pre-intervention phase compared to 92% in the intervention phase (P &lt; 0.001), and 77% in the post-intervention phase (P &lt; 0.001). Pre-intervention antibiotic receipt was 18% compared to 90% in the intervention phase (P &lt; 0.001) and 84% in the post-intervention phase (P &lt; 0.001). The documented SSI rate in the pre-intervention phase was 15% compared to 7% in the intervention phase (P = 0.02) and 11% in the post-intervention phase (P = 0.20).

Conclusions
An educational intervention, daily audit and feedback to clinicians increased the use of the WHO SSC and prophylactic antibiotics for cesarean delivery—although the rates waned with time. Research to understand factors influencing the checklist use and antibiotic prophylaxis including prescriber knowledge, motivation and clinical process is required. Implementation interventions to sustain usage and impact on clinical outcomes need to be explored.
Trading off accuracy and explainability in AI decision-making: findings from 2 citizens’ juries
Authors: van der Veer Sabine N , Riste Lisa , Cheraghi-Sohi Sudeh , Phipps Denham L , Tully Mary P , Bozentko Kyle , Atwood Sarah , Hubbard Alex , Wiper Carl , Oswald Malcolm , Peek Niels 
Published: June 2021

Abstract

Objective
To investigate how the general public trades off explainability versus accuracy of artificial intelligence (AI) systems and whether this differs between healthcare and non-healthcare scenarios.

Materials and Methods
Citizens’ juries are a form of deliberative democracy eliciting informed judgment from a representative sample of the general public around policy questions. We organized two 5-day citizens’ juries in the UK with 18 jurors each. Jurors considered 3 AI systems with different levels of accuracy and explainability in 2 healthcare and 2 non-healthcare scenarios. Per scenario, jurors voted for their preferred system; votes were analyzed descriptively. Qualitative data on considerations behind their preferences included transcribed audio-recordings of plenary sessions, observational field notes, outputs from small group work and free-text comments accompanying jurors’ votes; qualitative data were analyzed thematically by scenario, per and across AI systems.

Results
In healthcare scenarios, jurors favored accuracy over explainability, whereas in non-healthcare contexts they either valued explainability equally to, or more than, accuracy. Jurors’ considerations in favor of accuracy regarded the impact of decisions on individuals and society, and the potential to increase efficiency of services. Reasons for emphasizing explainability included increased opportunities for individuals and society to learn and improve future prospects and enhanced ability for humans to identify and resolve system biases.

Conclusion
Citizens may value explainability of AI systems in healthcare less than in non-healthcare domains and less than often assumed by professionals, especially when weighed against system accuracy. The public should therefore be actively consulted when developing policy on AI explainability.
Improving domain adaptation in de-identification of electronic health records through self-training
Authors: Liao Shun , Kiros Jamie , Chen Jiyang , Zhang Zhaolei , Chen Ting 
Published: June 2021

Abstract

Objective
De-identification is a fundamental task in electronic health records to remove protected health information entities. Deep learning models have proven to be promising tools to automate de-identification processes. However, when the target domain (where the model is applied) is different from the source domain (where the model is trained), the model often suffers a significant performance drop, commonly referred to as domain adaptation issue. In de-identification, domain adaptation issues can make the model vulnerable for deployment. In this work, we aim to close the domain gap by leveraging unlabeled data from the target domain.

Materials and Methods
We introduce a self-training framework to address the domain adaptation issue by leveraging unlabeled data from the target domain. We validate the effectiveness on 4 standard de-identification datasets. In each experiment, we use a pair of datasets: labeled data from the source domain and unlabeled data from the target domain. We compare the proposed self-training framework with supervised learning that directly deploys the model trained on the source domain.

Results
In summary, our proposed framework improves the F1-score by 5.38 (on average) when compared with direct deployment. For example, using i2b2-2014 as the training dataset and i2b2-2006 as the test, the proposed framework increases the F1-score from 76.61 to 85.41 (+8.8). The method also increases the F1-score by 10.86 for mimic-radiology and mimic-discharge.

Conclusion
Our work demonstrates an effective self-training framework to boost the domain adaptation performance for the de-identification task for electronic health records.
Urinary Pharmacokinetic Profile of Cannabidiol (CBD), Δ9-Tetrahydrocannabinol (THC) and Their Metabolites following Oral and Vaporized CBD and Vaporized CBD-Dominant Cannabis Administration
Authors: Sholler Dennis J , Spindle Tory R , Cone Edward J , Goffi Elia , Kuntz David , Mitchell John M , Winecker Ruth E , Bigelow George E , Flegel Ronald R , Vandrey Ryan 
Published: June 2021

Abstract
The market for products containing cannabidiol (CBD) is booming globally. However, the pharmacokinetics of CBD in different oral formulations and the impact of CBD use on urine drug testing outcomes for cannabis (e.g., 11-nor-9-carboxy-Δ9-tetrahydrocannabinol (Δ9-THCCOOH)) are understudied. This study characterized the urinary pharmacokinetics of CBD (100 mg) following vaporization or oral administration (including three formulations: gelcap, pharmacy-grade syrup and or Epidiolex) as well as vaporized CBD-dominant cannabis (containing 100 mg CBD and 3.7 mg Δ9-THC) in healthy adults (n = 18). A subset of participants (n = 6) orally administered CBD syrup following overnight fasting (versus low-fat breakfast). Urine specimens were collected before and for 58 h after dosing on a residential research unit. Immunoassay (IA) screening (cutoffs: 20, 50 and 100 ng/mL) for Δ9-THCCOOH was performed, and quantitation of cannabinoids was completed via LC–MS-MS. Urinary CBD concentrations (ng/mL) were higher after oral (mean Cmax: 734; mean Tmax: 4.7 h, n = 18) versus vaporized CBD (mean Cmax: 240; mean Tmax: 1.3 h, n = 18), and oral dose formulation significantly impacted mean Cmax (Epidiolex = 1,274 ng/mL, capsule = 776 ng/mL, syrup = 151 ng/mL, n = 6/group) with little difference in Tmax. Overnight fasting had limited impact on CBD excretion in urine, and there was no evidence of CBD conversion to Δ8- or Δ9-THC in any route or formulation in which pure CBD was administered. Following acute administration of vaporized CBD-dominant cannabis, 3 of 18 participants provided a total of six urine samples in which Δ9-THCCOOH concentrations ≥15 ng/mL. All six specimens screened positive at a 20 ng/mL IA cutoff, and two of six screened positive at a 50 ng/mL cutoff. These data show that absorption/elimination of CBD is impacted by drug formulation, route of administration and gastric contents. Although pure CBD is unlikely to impact drug testing, it is possible that hemp products containing low amounts of Δ9-THC may produce a cannabis-positive urine drug test.