bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of Body Mass Index & Spine Flexibility on Surgical Outcomes for Patients with Adolescent Idiopathic Scoliosis
Authors: Linden Gabriel S. , Hresko M. Timothy , Cook Danielle , Birch Craig M. , Hedequist Daniel J. , Hogue Grant D. 
Published: August 2022

Study Design.
Retrospective cohort study.

Objective.
To investigate the relationship between body mass index (BMI), spine flexibility index (FI), and their combined effects on adolescent idiopathic scoliosis (AIS) surgical outcomes.

Background.
BMI and FI are two factors considered during pre-surgical planning for AIS correction, but there is sparse research about their relationship. We hypothesize that AIS patients with increased BMI may be associated with decreased FI - a combination which could lead to worsened surgical outcomes.

Methods.
AIS patients ages 11-19 at surgery, who underwent posterior fusion at a single-center from 2011-2017, were reviewed. Patients without proper radiographs to assess FI, or a previous spine surgical history, were excluded. FI was categorized as stiff (FI<50) or flexible (FI≥50), and patients were separated by major curve region. BMI was categorized as underweight (<5th percentile), healthy-weight (5th-85th percentile), overweight (85th-95th percentile), or obese (>95th percentile). Regression analysis was conducted to test BMI and FI’s effects on intraoperative, immediate postoperative, and two-year postoperative outcomes.

Results.
543 patients (82% female), with an average age of 14.9 years, were included. 346 patients had available two-year data. A 10% increase in BMI was associated with a 1.3% decrease in FI for patients with major thoracolumbar/lumbar curves (P=0.01). Obese patients were most likely to have a postoperative complication (P=0.003) or two-year complication (P=0.04). Revision surgery occurred after 58% of postoperative complications (15/26) and 80% of two-year complications (4/5). FI was negatively associated with initial curve magnitude (P<0.001), operative time (P=0.02), and blood loss (P=0.02). Overweight patients with flexible curves were 10.0 times more likely to sustain a postoperative complication than healthy-weight patients with stiff curves (P=0.001).

Conclusion.
Elevated BMI was associated with decreased FI in patients with major thoracolumbar/lumbar curves. Patients with a high BMI and high FI were associated with the greatest risk of postoperative complication.
Efficacy of pharmacologic treatment for treating gastrointestinal angiodysplasias-related bleeding: a systematic review and meta-analysis
Authors: Gkolfakis Paraskevas , Fostier Romane , Tziatzios Georgios , Lazaridis Nikolaos , Fernandez Y Viesca Michael , Facciorusso Antonio , Despott Edward , Triantafyllou Konstantinos , Devière Jacques , Arvanitakis Marianna 
Published: August 2022

Introduction
We evaluated the efficacy of pharmacologic treatments for patients with overt or occult bleeding due to gastrointestinal angiodysplasias (GIADs).

Methods
A systematic computer-aided literature search across Medline, Cochrane, Scopus and Embase databases was performed. Studies evaluating pharmacologic treatments for patients presenting with GIADs-related overt or occult bleeding were included. Post-treatment rebleeding was the primary outcome. Need for red blood cells (RBC) transfusion, post-treatment hemoglobin levels and adverse events rate comprised secondary outcomes. Results are presented as odds ratio (OR), mean difference (MD) or pooled rates (%) with 95% confidence intervals (95%CI).

Results
Four types of pharmacologic treatment were identified (25 studies): somatostatin analogs, hormonal therapy, thalidomide and angiogenesis inhibitors. Pharmacologic treatment of any kind led to significantly reduced bleeding episodes [OR (95% CI), 0.08 (0.04–0.18)]. No pharmacologic treatment was superior to others (P = 0.46). Overall, pooled rebleeding rate post-treatment was 34% (26–43%). Similarly, significantly fewer patients required RBC transfusion during the post-treatment period [0.03 (0.03–0.07)], with no differences among various treatments (P = 0.83), yielding an overall pooled transfusion rate of 33% (19–46%). Administration of pharmacological treatment led to significant improvement in terms of hemoglobin levels [MD (95% CI), 3.21 g/dL (2.42–3.99)]. The pooled rate of adverse events was 32% (22–42%).

Conclusion
In patients with GIADs administration of any pharmacologic treatment significantly decreases rebleeding episodes and transfusions leading to higher hemoglobin values. One-third of them experience at least one adverse event related to the treatment.
Genomic ascertainment for UBA1 variants and VEXAS syndrome: a population-based study
Authors: Beck David B. , Bodian Dale L. , Shah Vandan , Mirshahi Uyenlinh L. , Kim Jung , Ding Yi , Strande Natasha T. , Cantor Anna , Haley Jeremy S. , Cook Adam , Hill Wesley , Grayson Peter C. , Ferrada Marcela A. , Kastner Daniel L. , Carey David J. , Stewart Douglas R. 
Published: August 2022

AbstractImportanceVEXAS (vacuoles, E1-ubiquitin-activating enzyme, X-linked, autoinflammatory, somatic) syndrome is a disease with rheumatologic and hematologic features caused by somatic variants in UBA1. Pathogenic variants are associated with a broad spectrum of clinical manifestations. Knowledge of prevalence, penetrance, and clinical characteristics of this disease have been limited by ascertainment biases based on known phenotypes. This study used a genomic ascertainment approach to overcome these limitations and better define UBA1-related disease.ObjectiveDetermine the prevalence of pathogenic variants in UBA1 and associated clinical manifestations in an unselected population using a genomic ascertainment approach.Design, Setting and ParticipantsThis cohort study evaluated UBA1 variants in exome data from 163,096 participants within the Geisinger MyCode Community Health Initiative. Clinical phenotypes were determined from Geisinger electronic health record (EHR) data up to January 1st, 2022.Main outcomes and measuresPrevalence of somatic UBA1 variation; presence of rheumatologic, hematologic, pulmonary, dermatologic, and other symptoms in individuals with somatic UBA1 variation; structured and manual review of EHR; review of bone marrow biopsies; survival in carriers of somatic UBA1 variation.ResultsIn a retrospective study of 163,096 participants (mean age 52.8 years; 94% of European ancestry, 61% female), 11 individuals harbored somatic, known pathogenic UBA1 variants, with 100% having clinical manifestations consistent with VEXAS syndrome. We found a previously unreported UBA1 variant (c.1861A>T; p.Ser621Cys) in a symptomatic patient. Disease-causing UBA1 variants were found in ∼1 in 14,000 unrelated individuals, and ∼1 in 4,000 men >50 years old. A disease-causing UBA1 variant confers a ∼ 6.6 higher probability of mortality vs. age-, sex-, and BMI-matched non-carriers. The majority (7, 58%) of individuals did not meet criteria for rheumatologic and hematologic diagnoses previously associated with VEXAS syndrome, however all individuals had anemia (mean 7.8 g/dL, median 7.5g/dL), mostly macrocytic (91%) with concomitant thrombocytopenia (91%). Finally, we identified a pathogenic variant in one male prior to onset of VEXAS-related signs or symptoms and two females had disease with heterozygous variants.Conclusions and relevanceThis cohort study showed that the prevalence, penetrance, and expressivity of pathogenic UBA1 variants were higher than expected. More expansive UBA1 testing will lead to molecular diagnoses and improved treatment for patients.
Evidence to inform effective alcohol pricing policies in the European Union
Authors: Angus Colin 
Published: August 2022

AbstractAimTo map current alcohol pricing policies across the European Union and United Kingdom and review the latest evidence on their effectivenessDesignCurrent policies were mapped using publicly available data. Evidence was systematically reviewed using a three-stage approach: a) a systematic search for published studies in PubMed and Google Scholar, b) a snowball search of grey literature and hand-searching the references of existing reviews and c) consultation with topic experts.SettingAny appraisal or evaluation on the impact of an alcohol pricing policy in an EU or UK nation that reported alcohol consumption or health outcomes.ParticipantsThe general populationMeasurementsAny reported measures of alcohol consumption or alcohol-related health outcomes.FindingsThe mapping exercise found that there is substantial variation in both the levels and structures of alcohol taxation across Europe. The review found 83 studies, consisting of 34 prospective modelling studies and 49 retrospective evaluations. These came primarily from the UK and Scandinavia. The majority of studies looked at the impact of changes to alcohol taxation, although a substantial minority looked at the impacts of Minimum Unit Pricing for alcohol. Studies consistently fond that increases in taxation, or the introduction of Minimum Unit Pricing, have led to reductions in alcohol consumption and improvements in public health and, in spite of concerns about cross-border sales moderating these benefits, there is little evidence to support these concerns in practice.ConclusionThere is ample evidence to show that alcohol pricing policies can and have worked across Europe and are likely to form a key part of any effective policy approach to reduce alcohol-related harm.
Identify Non-Mutational p53 Functional Deficiency in Human Cancers
Authors: Li Qianpeng , Zhang Yang , Luo Sicheng , Zhang Zhang , Oberg Ann L. , Kozono David E. , Lu Hua , Sarkaria Jann N. , Ma Lina , Wang Liguo 
Published: August 2022

AbstractAn accurate assessment ofTP53’s functional status is critical for cancer genomic medicine. However, there is a significant challenge in identifying tumors with non-mutational p53 inactivations that are not detectable through DNA sequencing. These undetected cases are often misclassified as p53-normal, leading to inaccurate prognosis and downstream association analyses. To address this issue, we build the support vector machine (SVM) models to systematically reassess p53’s functional status inTP53wild-type (TP53WT) tumors from multiple TCGA cohorts. Cross-validation demonstrates the excellent performance of the SVM models with a mean AUC of 0.9822, precision of 0.9747, and recall of 0.9784. Our study reveals that a significant proportion (87-99%) ofTP53WTtumors actually have compromised p53 function. Additional analyses uncovered that these genetically intact but functionally impaired (termed as predictively reduced function of p53 orTP53WT-pRF) tumors exhibit genomic and pathophysiologic features akin to p53 mutant tumors: heightened genomic instability and elevated levels of hypoxia. Clinically, patients withTP53WT-pRF tumors experience significantly shortened overall survival or progression-free survival compared to those withTP53WT-pN (predictive normal function of p53) tumors, and these patients also display increased sensitivity to platinum-based chemotherapy and radiation therapy.
Inferring Single-Molecule Chromatin Interactions via Online Convex Network Dictionary Learning
Authors: Peng Jianhao , Pan Chao , Lyu Hanbaek , Kim Minji , Cheng Albert , Milenkovic Olgica 
Published: August 2022

ABSTRACTMotivationGenomes of multicellular systems are compartmentalized and dynamically folded within the three-dimensional (3D) confines of the nucleus in order to facilitate gene regulation. Among the 3D-genome mapping technologies currently in use, droplet-based, barcode-linked sequencing (ChIA-Drop) has the unique capability to capture complex multi-way chromatin interactions at the single-molecule level. ChIA-Drop data gives rise to higher-order interaction networks in which nodes represent genomic fragments while (hyper)edges capture observed physical contacts. The problem of interest is to use this data to create a “dictionary” of interaction patterns (subnetworks) that accurately describe all global chromatin structures and associate dictionary elements with cellular functions.ResultsTo construct interpretable chromatin dictionaries, we introduce a new algorithm termed online convex network dictionary learning (online cvxNDL). Unlike classical dictionary learning for image or text processing, online cvxNDL uses special subgraph sampling methods and produces interpretable subnetwork representatives corresponding to “convex mixtures” of patterns observed in real data. To demonstrate the utility of the method, we perform an in-depth study of RNAPII-enriched ChIA-Drop data from Drosophila Melanogaster S2 cell lines. Our results are two-fold: First, we show that online cvxNDL allows for accurate reconstruction of the original interaction network data using only a collection of roughly 25 dictionary elements and their “representatives” directly observed in the data. Second, we identify collections of interaction patterns of chromatin elements shared by related processes on different chromosomes and those unique to certain chromosomes. This is accomplished through Gene Ontology (GO) enrichment analysis that allows us to associate dictionary element representatives with functional properties of their corresponding chromatin region and in the process, determine what we call the “span” and “density” of chromatin interaction patterns.Availability and ImplementationThe code and dataset are available at: https://github.com/jianhao2016/online_cvxNDL/Contactmilenkov@illinois.edu
Reference BioImaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae
Authors: Peters Kristian , König-Ries Birgitta 
Published: August 2022

AbstractMacro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as for assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic attributes of the species belonging to the family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable meta-data using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.
Efficient sampling designs to assess biodiversity spatial autocorrelation : should we go fractal ?
Authors: Laroche F. 
Published: August 2022

AbstractQuantifying the autocorrelation range of species distribution in space is necessary for applied ecological questions, like implementing protected area networks or monitoring programs. However, the power of spatial sampling designs to estimate this range is negatively related with other objectives such as estimating environmental effects acting upon species distribution. Mixing random sampling points and systematic grid (‘hy-brid’ designs) is a classic solution to make a trade-off. However, fractal designs (i.e. self-similar designs with well-identified scales) could make an even better compromise, because they cover a wide array of possible autocorrelation range values across scales. Using maximum likelihood estimation in an optimal design of experiments approach, we compared errors of hybrid and fractal designs when simultaneously estimating an effect acting upon a response variable and the residual autocorrelation range. We found that Pareto-optimal sampling strategies depended on the feasible grid mesh size (FGMS) over the study area, given the sampling budget. When the FMGS was shorter than expected autocorrelation range values, grid design was the best option on all criteria. When the FMGS was around or larger than expected autocorrelation range values, the choice of designs depended on the effect under study. Fractal designs outperformed hybrid designs when studying the effect of a monotonic environmental gradient across space, while grid design was more efficient for other types of question. Beyond the niche identified in our analysis, fractal designs may also appear interesting when studying response variables with more heterogeneous spatial structure across scales, and when considering more practical criteria of performance such as the distance needed to cover the design.
Candidate proteins associated with popping expansion capacity of popcorn
Authors: Gemelli Talita Mayara de Campos Jumes , Romani Isaac , Dos Santos Natália Ferreira , Machado Maria de Fátima P.S. , Scapim Carlos Alberto , Domont Gilberto Barbosa , Nogueira Fábio César Sousa , Gonela Adriana 
Published: August 2022

AbstractThe mechanical resistance of the popcorn pericarp has a positive and direct relationship to its expansion volume. It allows enough time for the endosperm to gelatinize completely before its extravasation. Expansion is a polygenic trait that has been extensively studied. However, no records in the literature indicate proteins that directly affect pericarp thickness and integrity. Therefore, the present work aimed to identify candidate pericarp proteins associated with the expansion capacity of popcorn kernels using the shotgun proteomic approach. The analyses were carried out in the pericarp of two popcorn inbred lines, P11 (expansion volume of 30 mL g-1) and P16 (expansion volume of 14 mL g-1), in two developmental stages (15 and 25 DAP). A total of 803 non-redundant proteins were identified. Most of them were involved in key processes associated with pericarp development and thickening. Two candidate proteins stood out among the differentially abundant proteins. Peroxidase was up-accumulated in P11/25 DAP (high popping expansion) and was 1.498 times more abundant in this inbred line, while xyloglucan endotransglucosylase/hydrolase was more abundant in P16 (low popping expansion) in both developmental stages. Thus, the peroxidase protein increases expandability, whereas xyloglucan endotransglucosylase/hydrolase decreases it, even though its specific role has not been elucidated. These proteins should be further investigated, as they may be used to improve expansion capacity in popcorn breeding programs.
Glasses Against transmission of SARS-CoV-2 in the community (GLASSY): a pragmatic randomized trial
Authors: Fretheim Atle , Elgersma Ingeborg Hess , Helleve Arnfinn , Elstrøm Petter , Kacelnik Oliver , Hemkens Lars G. 
Published: August 2022

AbstractBackgroundObservational studies have reported an association between use of eye protection and reduced risk of SARS-CoV-2 infection and other respiratory viruses, but as for most non-pharmaceutical interventions for infection control, no randomized trials have been conducted. We conducted a randomized trial to evaluate the effectiveness of recommending the use of glasses in public as protection against being infected with SARS-CoV-2 and other respiratory viruses.Methods and findingsThis was a pragmatic, randomized, trial in Norway from 2 February to 24 April 2022 where all adult members of the public who did not regularly wear glasses, had no symptoms of COVID-19 and no COVID-19 in the last 6 weeks, were eligible. Participants randomized to the intervention group were asked to wear glasses (e.g. sunglasses) for 2 weeks when close to others in public spaces. The primary outcome was positive COVID-19 test result notified to the Norwegian Surveillance System for Communicable Diseases (MSIS). Secondary outcomes included positive COVID-19 test result based on self-report and episode of respiratory infection based on self-report of symptoms. We randomized 3717 participants. All were identified and followed up in the registries and 87% responded to the end of study-questionnaire. The proportions with a notified positive COVID-19 test in the national registry were 3.7% in the intervention group (68/1852) and 3.5% (65/1865) in the control group (95% CI for risk difference -1.0% to 1.4%; relative risk 1.10, 95% CI 0.75 to 1.50). The proportions with a positive COVID-19 test based on self-report were 9.6% and 11.5% (95% CI for risk difference -3.9% to 0.1%; relative risk 0.83, 95% CI 0.69 to 1.00). The risk of respiratory infections based on self-reported symptoms was lower in the intervention group (31% vs. 34%; 95% CI for risk difference -3.3% to -0.3%; relative risk 0.90, 95% CI 0.82 to 0.99).ConclusionsOur results indicate that asking people to wear glasses may protect the public against respiratory infections, but the findings are not certain, and the study needs replication. Although the evidence is uncertain, and the effect probably modest at best, wearing glasses may be worth considering as one component in the infection control toolbox since it is a simple, low burden, and low-cost intervention, with few negative consequences.Trial registrationClinicalTrials.gov Identifier: NCT05217797FundingThe costs of running the trial were covered by the Centre for Epidemic Interventions Research (CEIR), Norwegian Institute of Public Health. The authors received no specific funding for this work