bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictors of non-participation in a cardiac telerehabilitation programme: a prospective analysis
Authors: Brouwers Rutger Willem Maurice , Brini Alberto , Kuijpers Robin Wilhelmus Franciscus Henricus , Kraal Jozua Johannes , Kemps Hareld Marijn Clemens 
Published: December 2021

AbstractAims Current cardiac telerehabilitation (CTR) interventions are insufficiently tailored to the preferences and competences of individual patients, which raises the question whether their implementation will increase overall participation and adherence to cardiac rehabilitation (CR). However, research on patient-specific factors that influence participation and adoption of CTR interventions is scarce. The aim of this study was to evaluate which patient-related characteristics influence participation in a novel CTR intervention in patients with coronary artery disease.Methods and results This prospective observational substudy of the SmartCare-CAD randomized controlled trial evaluated patient characteristics of study participants as proxy for participation in a CTR intervention. We compared demographic, geographic, and health-related characteristics between trial participants and non-participants to determine which characteristics influenced trial participation. A total of 699 patients (300 participants and 399 non-participants; 84% male, mean age 64.3 ± 10.5 years) were included. Most of the non-participants refused participation because of insufficient technical skills or lack of interest in digital health (26%), or preferred centre-based CR (21%). Variables independently associated with non-participation included: higher age, lower educational level, shorter travelling distance, smoking, positive family history for cardiovascular disease, having undergone coronary artery bypass grafting; and a higher blood pressure, worse exercise capacity, and higher risk of depression before the start of CR.ConclusionParticipation in CTR is strongly influenced by demographic and health-related factors such as age, educational level, smoking status, and both physical and mental functioning. Cardiac telerehabilitation interventions should therefore be redesigned with the involvement of these currently underrepresented patient subgroups.
No Evidence That Genetic Variation at the Klotho Locus Is Associated With Longevity in Caucasians from the Newcastle 85+ Study and the UK Biobank
Authors: Amin Hasnat A , Cordell Heather J , Martin-Ruiz Carmen , Robinson Louise , Kirkwood Tom , Blakemore Alexandra I , Drenos Fotios 
Published: December 2021

Abstract
The demographics of Western populations are changing, with an increase in the proportion of older adults. There is evidence to suggest that genetic factors may influence the aging process: studying these may lead to interventions to help individuals live a longer and healthier life. Evidence from several groups indicates that Klotho (KL), a gene encoding a single-pass transmembrane protein that acts as an FGF23 co-receptor, may be associated with longevity and healthy aging. We aimed to explore this area further by comparing the genotype counts in 642 long-lived individuals from the Newcastle 85+ Study with 18 295 middle-aged Newcastle-based controls from the UK Biobank to test whether variants at the KL gene locus are over- or under-represented in older individuals. If KL is associated with longevity, then we would expect the genotype counts to differ between the 2 cohorts. We found that the rs2283368 CC genotype and the rs9536338 C allele, but not the KL-VS haplotype, were associated with reaching very old age. However, these associations did not replicate in the remainder of the UK Biobank cohort. Thus, our results do not reliably support the role of KL as a longevity factor.
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects
Authors: Sheffield Nathan C , Stolarczyk Michał , Reuter Vincent P , Rendeiro André F 
Published: December 2021

Abstract

Background
Organizing and annotating biological sample data is critical in data-intensive bioinformatics. Unfortunately, metadata formats from a data provider are often incompatible with requirements of a processing tool. There is no broadly accepted standard to organize metadata across biological projects and bioinformatics tools, restricting the portability and reusability of both annotated datasets and analysis software.

Results
To address this, we present the Portable Encapsulated Project (PEP) specification, a formal specification for biological sample metadata structure. The PEP specification accommodates typical features of data-intensive bioinformatics projects with many biological samples. In addition to standardization, the PEP specification provides descriptors and modifiers for project-level and sample-level metadata, which improve portability across both computing environments and data processing tools. PEPs include a schema validator framework, allowing formal definition of required metadata attributes for data analysis broadly. We have implemented packages for reading PEPs in both Python and R to provide a language-agnostic interface for organizing project metadata.

Conclusions
The PEP specification is an important step toward unifying data annotation and processing tools in data-intensive biological research projects. Links to tools and documentation are available at http://pep.databio.org/.
A high-throughput multiplexing and selection strategy to complete bacterial genomes
Authors: Arredondo-Alonso Sergio , Pöntinen Anna K , Cléon François , Gladstone Rebecca A , Schürch Anita C , Johnsen Pål J , Samuelsen Ørjan , Corander Jukka 
Published: December 2021

Abstract

Background
Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections.

Results
Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library.

Conclusions
The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.
Long-term Disease Behavior and Surgical Intervention Analysis in Hospitalized Patients With Crohn’s Disease in China: A Retrospective Cohort Study
Authors: Bai Xiaoyin , Zhang Huimin , Ruan Gechong , Lv Hong , Li Yue , Li Ji , Tan Bei , Zheng Weiyang , Jin Meng , Xu Hui , Yang Hong , Qian Jiaming 
Published: December 2021

Abstract

Background
There is lack of real-world data for disease behavior and surgery of Crohn’s disease (CD) from large-scale Chinese cohorts.

Methods
Hospitalized patients diagnosed with CD in our center were consecutively included from January 2000 to December 2018. Disease behavior progression was defined as the initial classification of B1 to the progression of B2 or B3. Clinical characteristics including demographics, disease classification and activity, medical therapy, development of cancers, and death were collected.

Results
Overall, 504 patients were included. Two hundred thirty-one (45.8%) patients were initially classified as B1; 30 (13.0%), 71 (30.7%), and 95 (41.1%) of them had disease progression at the 1-year follow-up, 5-year follow-up, and overall, respectively. Patients without location transition before behavior transition were less likely to experience behavior progression. However, patients without previous exposure to a corticosteroid, immunomodulator, or biological agent had a greater chance of experiencing behavior progression. When the long-term prognosis was evaluated, 211 (41.9%) patients underwent at least 1 CD-related surgery; 108 (21.4%) and 120 (23.8%) of these patients underwent surgery before and after their diagnosis, respectively. An initial classification as B1, no behavior transition, no surgery prior to diagnosis, and previous corticosteroid exposure during follow-up were associated with a lower risk of undergoing surgery.

Conclusions
This study depicts the clinical features and factors associated with behavior progression and surgery among hospitalized CD patients in a Chinese center. Behavior progression is associated with a higher probability of CD-related surgery, and strengthened therapies are necessary for them in the early phase.
Treatment Decision-making in Chinese Inflammatory Bowel Disease Patients
Authors: Yang Li , Song Xiaomei , Chen Yan , Li Yue , Gu Yubei , Wang Xinying , Zhu Liangru , Zhi Min , Ouyang Chunhui , Guo Hong 
Published: December 2021

Abstract

Background
Inflammatory bowel disease (IBD) is rising in China, and the tendency for lifelong recurrence decreases patients’ quality of life. However, no studies on treatment decision-making in Chinese patients with IBD exist. Thus, this study aimed to determine the actual and ideal decision-making, as well as factors affecting decision-making in Chinese IBD patients.

Methods
A multicenter online questionnaire was distributed among patients diagnosed with IBD. To assess factors that influence treatment decision-making, univariate and multivariate logistic regression analyses were performed.

Results
From March 20, 2018, to May 20, 2018, a total of 866 patients completed the questionnaires, including 222 patients with ulcerative colitis, 588 patients with Crohn’s disease, and 56 patients with unclassified IBD. There was a significant difference between ideal and actual decision-making in Chinese IBD patients (P &lt; .005). The factors affecting ideal decision-making included income, education, illness severity, religiosity, the importance of the treatment decision, the employment situation, and occupation area. The factors affecting actual decision-making included age, illness severity, religiosity, the employment situation, economic anxiety, concern about the side effects, and the importance of the treatment decision.

Conclusions
There is a significant difference between ideal and actual decision-making in IBD patients in China. That is, the economy, religiosity, illness severity, and concern about the side effects of treatment are the most important factors affecting treatment decisions in Chinese IBD patients.
Maternal respiratory health and intrauterine exposure-driven birthweight: a two-sample Mendelian randomization study
Authors: He Baoting , Kwok Man Ki , Chan Io Ieong , Schooling C Mary 
Published: December 2021

Abstract

Background
Observationally, poorer maternal respiratory health is associated with poorer birth outcomes, possibly confounded by socioeconomic position and other maternal attributes. We used multivariable Mendelian randomization (MR) to obtain unconfounded estimates of effect of maternal lung function on birthweight, independent of maternal height.

Methods
Single nucleotide polymorphisms (SNPs) for forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) in women were obtained from publicly available summary statistics from the UK Biobank. SNPs for asthma were obtained from the Trans-National Asthma Genetic consortium. SNPs for height in women were obtained from the Genetic Investigation of Anthropometric Traits consortium and the genetic estimates were obtained the UK Biobank. The genetic associations with maternally-driven birthweight were obtained from the Early Growth Genetics consortium. Multivariable MR estimates were obtained using inverse variance weighting with multivariable MR-Egger as sensitivity analysis.

Results
Maternal lung capacity, as indicated by FVC, was positively associated with maternally-driven birthweight (0.08 per standard deviation, 95% confidence interval 0.01 to 0.15) independent of maternal height, whereas no clear such associations were shown for maternal airway function, indicated by FEV1 and peak expiratory flow, or for asthma, on maternally-driven birthweight. Similar findings were shown using MR-Egger.

Conclusions
These findings suggest that maternal lung function, especially lung capacity independent of maternal height, is directly associated with maternally-driven birthweight, and highlights the importance of maternal respiratory health in fetal growth.
Soybean-BioCro: a semi-mechanistic model of soybean growth
Authors: Matthews Megan L , Marshall-Colón Amy , McGrath Justin M , Lochocki Edward B , Long Stephen P 
Published: December 2021

Abstract
Soybean is a major global source of protein and oil. Understanding how soybean crops will respond to the changing climate and identifying the responsible molecular machinery are important for facilitating bioengineering and breeding to meet the growing global food demand. The BioCro family of crop models are semi-mechanistic models scaling from biochemistry to whole crop growth and yield. BioCro was previously parameterized and proved effective for the biomass crops Miscanthus, coppice willow and Brazilian sugarcane. Here, we present Soybean-BioCro, the first food crop to be parameterized for BioCro. Two new module sets were incorporated into the BioCro framework describing the rate of soybean development and carbon partitioning and senescence. The model was parameterized using field measurements collected over the 2002 and 2005 growing seasons at the open air [CO2] enrichment (SoyFACE) facility under ambient atmospheric [CO2]. We demonstrate that Soybean-BioCro successfully predicted how elevated [CO2] impacted field-grown soybean growth without a need for re-parameterization, by predicting soybean growth under elevated atmospheric [CO2] during the 2002 and 2005 growing seasons, and under both ambient and elevated [CO2] for the 2004 and 2006 growing seasons. Soybean-BioCro provides a useful foundational framework for incorporating additional primary and secondary metabolic processes or gene regulatory mechanisms that can further aid our understanding of how future soybean growth will be impacted by climate change.
Identifying Pathways to Peace: How International Support Can Help Prevent Conflict Recurrence
Authors: Mross Karina , Fiedler Charlotte , Grävingholt Jörn 
Published: December 2021

AbstractThis article provides new evidence on how the international community can effectively foster peace after civil war. It expands the current literature's narrow focus on either peacekeeping or aggregated aid flows, adopting a comprehensive, yet disaggregated, view on international peacebuilding efforts. We distinguish five areas of peacebuilding support (peacekeeping, nonmilitary security support, support for politics and governance, for socioeconomic development, and for societal conflict transformation) and analyze which types or combinations are particularly effective and in which context. Applying configurational analysis (qualitative comparative analysis) to all thirty-six post-civil war peace episodes between 1990 and 2014, we find that (1) peacekeeping is only one important component of effective post-conflict support, (2) the largest share of peaceful cases can be explained by support for politics and governance, (3) only combined international efforts across all types of support can address difficult contexts, and (4) countries neglected by the international community are highly prone to experiencing conflict recurrence. Three case studies shed light on underlying causal mechanisms.
Validation of the RIDASCREEN® Peanut for Determination of Peanut Protein in Cookies, Milk Chocolate, Ice Cream, Trail Mix, Puffed Rice Cereals, and Granola Bar: AOAC Performance Tested MethodSM 112102
Authors: Lacorn Markus , Dubois Tina , Gößwein Christian , Kredel Rebecca , Ferkinghoff Bianca , Brunelle Sharon , Théolier Jérémie , Dominguez Silvia , Weiss Thomas 
Published: December 2021

Abstract

Background
Regulations in many countries worldwide prescribe that peanut must be listed on food labels as a cause of food allergies. Re-evaluated voluntary incidental trace allergen labelling (VITAL) values for peanut revealed the eliciting dose (ED01) value—at which 99% of all peanut-allergic individuals will not react—is 0.2 mg peanut protein.

Objective
Validation of a sandwich ELISA based on monoclonal antibodies to detect peanut proteins.

Methods
Non-processed and processed samples are extracted by an easy procedure at 60°C within 10 min. The measurement range is between 0.75 and 6 mg/kg peanut using a national institute of standards and technology (NIST) reference material as calibrator.

Results
The system shows no cross-reactivity against 91 different food commodities. The LOD was 0.15 mg/kg for food matrixes such as cookies, milk chocolate, ice cream, trail mix, puffed rice cereal, and granola bar. LOQ was verified at a level of 0.75 mg/kg. Recovery studies with incurred milk chocolate and ice cream revealed consistent recoveries between 67 and 85%. Mean recoveries for incurred cookies depend on the baking temperature and time and ranged from 60 to 109%. Repeatability was between 5.2 and 12.3%, whereas relative intermediate precision was between 6.4 and 13.0%. The results for incurred cookies and milk chocolate in the independent laboratory study showed mean recoveries between 99 and 104% with RSDs between 3.56 and 19.5% under repeatability conditions.

Conclusion
The results from the in-house validation study and the independent lab confirmed that the method is accurate and in accordance with requirements laid down in Standard Method Performance Requirement 2017.020.

Highlights
RIDASCREEN® Peanut quantifies proteins from peanut in a wide range of food categories.
Socioeconomic Features of Burn Injuries in Southern Iran: A Cross-sectional Study
Authors: Mohammadi Ali Akbar , Hoghoughi Mohammad Ali , Karoobi Mohammadreza , Ranjbar Keivan , Shahriarirad Reza , Erfani Amirhossein , Modarresi Mahboobeh-Sadat , Zardosht Mitra 
Published: December 2021

Abstract
Burn injuries are among the most traumatic incidences which could be associated with substantial morbidity and mortality. The incidence of these injuries differs based on population socioeconomic characteristics. In this study, we aim to evaluate the distribution of burn injuries based on socioeconomic and causative factors. Relative features from the targeted population were obtained and evaluated. Data were extracted in August 2019 and statistical analysis of the data was conducted from February 2020 to April 2020. This cross-sectional record-based study was conducted from 2008 to 2016 in a main referral center for burn injuries in the southern Iran. Participants included burn survivors and burn patients who were registered as outpatients or inpatients. A total of 4919 burn cases with a mean age of 31.91 ± 17.33, including 2926 (59.5%) males and 1993 (40.5%) females was reported. The majority of our cases had an educational level of under diploma (40.72%). A significant correlation between age, gender, and percentage of burn with the level of education was recorded (P &lt; .001). The most frequent cause of burn injuries was flame with 2537 (51.9%) cases. The most susceptible population to burn injuries were reported to be poorly educated individuals, which emphasizes the preventive role of education.
Interference of Lactiplantibacillus plantarum With Pseudomonas aeruginosa on the Infected Burns in Wistar Rats
Authors: Abootaleb Mohammad , Mohammadi Bandari Narjes , Arbab Soleimani Nazila 
Published: December 2021

Abstract
Burns are the most prevalent type of trauma in the world, and they have a high fatality rate. For cutaneous wound healing, modern and natural therapies, particularly probiotic supplements, have lately been considered. The goal of this study was to see how Lactiplantibacillus plantarum affected wound healing as well as the antibacterial activity of probiotic lactobacilli against Pseudomonas aeruginosa. The glass slide method was used to assess anti-adhesion activity, and the high-performance liquid chromatography method was used to quantify anti-adhesion chemicals in cell-free supernatant. Multidrug-resistant (MDR) P. aeruginosa was administered subcutaneously directly on the burn after induction of second-degree wounds. Three groups of animals were created. Every day, the supernatants were sprayed for therapy, and the wound healing was monitored. Lactobacilli bacteria had good anti-adhesion effects on P. aeruginosa, according to our findings, and high-performance liquid chromatography research revealed that their inhibitory effect could be attributable to four main organic acids: lactic acid, acetic acid, citric acid, and succinic acid. When the effect of treatments on fibroblastic cells was examined, it was discovered that the group treated with L. plantarum supernatants had the most fibroblastic cells when compared to the nontreated group. Furthermore, the bacteria increased the number of fibroblastic cells, re-epithelialization in the wound area, and the thickness of the epidermis and dermis layers. Lactobacilli bacteria’s antimicrobial activity against MDR P. aeruginosa was determined by prevents infection. These findings revealed that L. plantarum can treat a P. aeruginosa infection in a second-degree burn and can significantly reduce inflammation.
Influential Factors in the Recovery Process of Burn Survivors in a Predominately Rural State: A Qualitative Study
Authors: Dukes Kimberly , Baldwin Stephanie , Assimacopoulos Evangelia , Grieve Brian , Hagedorn Joshua , Wibbenmeyer Lucy 
Published: December 2021

Abstract
Navigating the recovery journey following a burn injury can be challenging. Survivor stories can help define recovery constructs that can be incorporated into support programs. We undertook this study to determine themes of recovery in a predominately rural state. Eleven purposefully selected burn survivors were interviewed using a semi-structured format. Consensus coding of verbatim transcriptions was used to determine themes of successful recovery. Four support-specific themes were identified. These included: using active coping strategies, expressing altruism through helping others, finding meaning and acceptance, and the active seeking and use of support. These themes could be incorporated into support programming and would help guide future survivors through the recovery period.