bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clues to mortality trends and their related factors in IgG4-related disease: A Japanese single-centre retrospective study
Authors: Kawahara Hiroyuki , Mizushima Ichiro , Tsuge Shunsuke , Shin Seung , Yoshinobu Takahiro , Hoshiba Ryohei , Nishioka Ryo , Zoshima Takeshi , Hara Satoshi , Ito Kiyoaki , Kawano Mitsuhiro 
Published: October 2022

ABSTRACT

Objectives
This study aimed to clarify mortality trends and their related factors in immunoglobulin G4-related disease (IgG4-RD) with various organ involvement.

Methods
We retrospectively reviewed the medical records of patients with IgG4-RD at a single rheumatology centre in Japan. We calculated the standardized mortality ratio using Japanese national mortality statistics. Cox regression analyses were also performed to assess mortality-related factors.

Results
A total of 179 patients with IgG4-RD were included with a median follow-up period of 47 months. The standardized mortality ratio in our cohort was 0.86 (95% confidence interval 0.41–1.59). Univariate Cox regression analyses indicated that the number of affected organs at diagnosis (hazard ratio 1.45, 95% confidence interval 1.02–2.05), estimated glomerular infiltration rate &lt;45 ml/min/1.73 m2 at diagnosis (vs. ≥45, hazard ratio 8.48, 95% confidence interval 2.42–29.79), and the presence of malignancy during the clinical course (hazard ratio 5.85, 95% confidence interval 1.62–21.15) had a significant impact on the time to death.

Conclusions
Our findings suggest that in the rheumatology department, IgG4-RD does not significantly affect long-term patient survival. However, multi-organ involvement, renal dysfunction, and malignancy may be associated with higher mortality trends in IgG4-RD. Early detection and appropriate management of risk factors may improve the long-term prognosis of patients with IgG4-RD.
IAnimal: a cross-species omics knowledgebase for animals
Authors: Fu Yuhua , Liu Hong , Dou Jingwen , Wang Yue , Liao Yong , Huang Xin , Tang Zhenshuang , Xu JingYa , Yin Dong , Zhu Shilin , Liu Yangfan , Shen Xiong , Liu Hengyi , Liu Jiaqi , Yang Xin , Zhang Yi , Xiang Yue , Li Jingjin , Zheng Zhuqing , Zhao Yunxia , Ma Yunlong , Wang Haiyan , Du Xiaoyong , Xie Shengsong , Xu Xuewen , Zhang Haohao , Yin Lilin , Zhu Mengjin , Yu Mei , Li Xinyun , Liu Xiaolei , Zhao Shuhong 
Published: October 2022

AbstractWith the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for the interpretation of gene regulation mechanisms and the comprehensive analyses of biological systems. IAnimal (https://ianimal.pro/), a cross-species, multi-omics knowledgebase, was developed to improve the utilization of massive public data and simplify the integration of multi-omics information to mine the genetic mechanisms of objective traits. Currently, IAnimal provides 61 191 individual omics data of genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq) and genome annotation information for 21 species, such as mice, pigs, cattle, chickens, and macaques. The scale of its total clean data has reached 846.46 TB. To better understand the biological significance of omics information, a deep learning model for IAnimal was built based on BioBERT and AutoNER to mine ‘gene’ and ‘trait’ entities from 2 794 237 abstracts, which has practical significance for comprehending how each omics layer regulates genes to affect traits. By means of user-friendly web interfaces, flexible data application programming interfaces, and abundant functional modules, IAnimal enables users to easily query, mine, and visualize characteristics in various omics, and to infer how genes play biological roles under the influence of various omics layers.
Animal-SNPAtlas: a comprehensive SNP database for multiple animals
Authors: Gao Yingjie , Jiang Guanghui , Yang Wenqian , Jin Weiwei , Gong Jing , Xu Xuewen , Niu Xiaohui 
Published: October 2022

Abstract
Single-nucleotide polymorphisms (SNPs) as the most important type of genetic variation are widely used in describing population characteristics and play vital roles in animal genetics and breeding. Large amounts of population genetic variation resources and tools have been developed in human, which provided solid support for human genetic studies. However, compared with human, the development of animal genetic variation databases was relatively slow, which limits the genetic researches in these animals. To fill this gap, we systematically identified ∼ 499 million high-quality SNPs from 4784 samples of 20 types of animals. On that basis, we annotated the functions of SNPs, constructed high-density reference panels and calculated genome-wide linkage disequilibrium (LD) matrixes. We further developed Animal-SNPAtlas, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/) which includes high-quality SNP datasets and several support tools for multiple animals. In Animal-SNPAtlas, users can search the functional annotation of SNPs, perform online genotype imputation, explore and visualize LD information, browse variant information using the genome browser and download SNP datasets for each species. With the massive SNP datasets and useful tools, Animal-SNPAtlas will be an important fundamental resource for the animal genomics, genetics and breeding community.
KEGG for taxonomy-based analysis of pathways and genomes
Authors: Kanehisa Minoru , Furumichi Miho , Sato Yoko , Kawashima Masayuki , Ishiguro-Watanabe Mari 
Published: October 2022

Abstract
KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
Extrapolated longer-term effects of the DAPA-CKD trial: a modelling analysis
Authors: McEwan Phil , Boyce Rebecca , Sanchez Juan Jose Garcia , Sjöström C David , Stefansson Bergur , Nolan Stephen , Correa-Rotter Ricardo , Rossing Peter , Chertow Glenn M , McMurray John J V , Wheeler David C , Heerspink Hiddo J L 
Published: October 2022

ABSTRACT

Background
The Dapagliflozin and Prevention of Adverse Outcomes in Chronic Kidney Disease (DAPA-CKD) trial assessed dapagliflozin versus placebo, in addition to standard therapy, in patients with chronic kidney disease (CKD) and albuminuria, and was terminated prematurely due to overwhelming efficacy. The study objective was to model the long-term clinical outcomes of DAPA-CKD beyond the trial follow-up.

Methods
A Markov model extrapolated event incidence per 1000 patients and CKD progression rates for patients receiving dapagliflozin or placebo over a 10-year time horizon. We derived treatment-specific CKD stage transition matrices using DAPA-CKD trial data. We extrapolated relevant efficacy endpoints using parametric survival equations for all-cause mortality and generalized estimating equations for recurrent events.

Results
When extrapolated over a 10-year period, patients randomized to dapagliflozin spent more time in CKD stages 1–3 and less in stages 4–5 than placebo [0.65 (95% CrI 0.41, 0.90) and –0.23 (95% CrI -0.45, 0.00) years per patient, respectively]. Dapagliflozin prevented an estimated 83 deaths and 51 patients initiating kidney replacement therapy per 1000 patients over 10 years. Predicted rates of hospitalized heart failure and abrupt declines in kidney function were reduced (19 and 39 estimated events per 1000 patients, respectively).

Conclusions
Adding dapagliflozin to standard therapeutic management of CKD is expected to have long-term cardiorenal benefit beyond what has been demonstrated in the DAPA-CKD trial, with patients predicted to live longer with fewer complications.
Measuring the impact of state and local Tobacco 21 policies in the United States: A longitudinal study of youth and young adults ages 15–21
Authors: Patel Minal , Simard Bethany J , Benson Adam F , Donovan Emily M , Pitzer Lindsay 
Published: October 2022

AbstractIntroductionTobacco 21 (T21) policies, which prohibit tobacco sales to individuals under 21, aim to reduce youth tobacco use by limiting youth access to these products. Little, however, is known about the longitudinal effect of T21 policies on youth tobacco use behaviors at the national level.MethodsParticipants aged 15–21 years from a longitudinal study conducted between May 2014 and May 2019 (n = 13,990) were matched to geocoded T21 policies. Generalized linear mixed models examined the association of direct and bordering T21 policy exposure and cigarette and e-cigarette use and intention to use, accounting for individual characteristics.ResultsControlling for sociodemographic and psychosocial covariates, there were statistically significant positive associations between T21 exposure and e-cigarette use (OR = 1.45 [1.03,2.06], p &lt; .003) and intention to use e-cigarettes (OR = 1.54 [1.05,2.26], p &lt; .027). We found no association between T21 policy exposure and cigarette use or intention to use cigarettes. Furthermore, exposure to T21 policies did not significantly modify the relationship between age and either cigarette outcome.ConclusionsThis is the first longitudinal study to evaluate state and local T21 policies at the national level. Our analyses demonstrate that existing T21 policies are not sufficient to reduce youth tobacco use and intentions to use, and suggest that T21 policies need to be a part of a comprehensive tobacco policy landscape. Our findings suggest further research is warranted on state and local T21 policy enforcement and implementation, including how T21 may differentially impact cigarette and e-cigarette use, and may have implications for the federal T21 policy.ImplicationsThis research evaluates state and local T21 policies in the United States longitudinally, finding that T21 policies are not sufficient to stem e-cigarette use among adolescents and young adults. These findings support further policy action and suggest that local and state T21 policies are not sufficient to reduce tobacco use and rather, need to be part of a broader, more comprehensive set of tobacco control policies. Further research on enforcement and implementation challenges of T21 policies and the impacts of the new federal T21 policy is warranted.
Health Care Utilization and Costs in Systemic Therapies for Metastatic Melanoma from 2016 to 2020
Authors: Qian Mollie F , Betancourt Nicolas J , Pineda Alain , Maloney Nolan J , Nguyen Kevin A , Reddy Sunil A , Hall Evan T , Swetter Susan M , Zaba Lisa C 
Published: October 2022

AbstractBackgroundWidespread implementation of immune checkpoint inhibitors (ICI) and targeted therapies for metastatic melanoma has led to a decline in melanoma-related mortality but increased healthcare costs. We aimed to determine how healthcare utilization varied by systemic, non-adjuvant melanoma treatment from 2016 to 2020.Patients and MethodsAdults with presumed stage IV metastatic melanoma receiving systemic therapy from 2016 to 2020 were identified in Optum, a nationwide commercial claims database. Treatment groups were nivolumab, pembrolizumab, ipilimumab+nivolumab (combination-ICI), or BRAF+MEK inhibitor (BRAFi+MEKi) therapy. Outcomes included hospitalizations, days hospitalized, emergency room (ER) visits, outpatient visits, and healthcare costs per patient per month (pppm). Multivariable regression models were used to analyze whether cost and utilization outcomes varied by treatment group, with nivolumab as reference.ResultsAmong 2018 adult patients with metastatic melanoma identified, mean (SD) age was 67 (15) years. From 2016 to 2020, nivolumab surpassed pembrolizumab as the most prescribed systemic melanoma therapy while combination-ICI and BRAFi+MEKi therapies remained stable. Relative to nivolumab, all other therapies were associated with increased total healthcare costs (combination-ICI: β = $47 600 pppm, 95%CI $42 200-$53 100; BRAFi+MEKi: β = $3810, 95%CI $365-$7260; pembrolizumab: β = $6450, 95%CI $4420-$8480). Combination-ICI and BRAFi+MEKi therapies were associated with more inpatient hospital days.ConclusionsAmid the evolving landscape of systemic therapy for advanced melanoma, nivolumab monotherapy emerged as the most used and least costly systemic treatment from 2016 to 2020. Its sharp increase in use in 2018 and lower costs relative to pembrolizumab may in part be due to earlier adoption of less frequent dosing intervals.
Measurement Properties of the Timed Functional Arm and Shoulder Test in Patients With Shoulder Problems
Authors: Safford Daniel W , Shah Kshamata M , Turner Jeffrey A , McClure Philip W 
Published: October 2022

Abstract

Objective
The purpose of this study was to determine the feasibility, reliability, validity, and responsiveness of the Timed Functional Arm and Shoulder Test (TFAST) in patients with shoulder problems.

Methods
This study was a repeated-measures clinical measurement observational cohort study. A total of 104 patients who were symptomatic participated in this study. The TFAST was collected as part of an patient’s outpatient physical therapist care at 6 different sites. The test and data collection were performed at 3 time points: baseline (initial evaluation), follow-up at the patient’s first return visit within 7 days of evaluation, and discharge at the patient’s final visit for care.

Results
All participants were able to perform the TFAST at baseline, with 1 exception, and 67 participants completed data collection at all 3 time points. There were no adverse effects in any participant related to performing the TFAST. Intrarater intersession reliability, reported as ICC(2,1), was 0.91 (95% CI = 0.79–0.95). The mean difference in TFAST scores for the affected arm was 23.2 repetitions (77.4 at baseline to 100.6 at discharge). The Cohen d effect size was 1.02, and the standardized response mean was 0.95. The minimal clinically important difference was determined to be 21 repetitions.

Conclusion
The TFAST seems to be feasible and appropriate for use in a wider population than other existing shoulder performance measures. The TFAST has demonstrated adequate reliability, validity, and responsiveness in patients with shoulder problems. Clinicians may consider using the TFAST to objectively assess patient performance.

Impact
The TFAST may be used to expand measurement of objective shoulder performance in a wide population of patients with shoulder problems. This test may provide information beyond an patient’s self-report and contribute to clinical decision-making.
Treatment for Mild Chronic Hypertension During Pregnancy
Authors: Tita Alan T. , Szychowski Jeff M. , Boggess Kim , Dugoff Lorraine , Sibai Baha , Lawrence Kirsten , Hughes Brenna L. , Bell Joseph , Aagaard Kjersti , Edwards Rodney K. , Gibson Kelly , Haas David M. , Plante Lauren , Metz Torri , Casey Brian , Esplin Sean , Longo Sherri , Hoffman Matthew , Saade George R. , Hoppe Kara K. , Foroutan Janelle , Tuuli Methodius , Owens Michelle Y. , Simhan Hyagriv N. , Frey Heather , Rosen Todd , Palatnik Anna , Baker Susan , August Phyllis , Reddy Uma M. , Kinzler Wendy , Su Emily , Krishna Iris , Nguyen Nicki , Norton Mary E. , Skupski Daniel , El-Sayed Yasser Y. , Ogunyemi Dotum , Galis Zorina S. , Harper Lorie , Ambalavanan Namasivayam , Geller Nancy L. , Oparil Suzanne , Cutter Gary R. , Andrews William W. 
Published: October 2022

(Abstracted from N Engl J Med 2022;386:1781–1792)
Chronic hypertension affects >2% of pregnancies in the United States and disproportionately affects Black women. The condition is also associated with an increased risk of adverse neonatal outcomes, including preeclampsia, placental abruption, preterm birth, small for gestational age (SGA), or perinatal death, and maternal outcomes, including maternal death, heart failure, stroke, pulmonary edema, or acute kidney injury.
Fifteen Years of Autologous Oocyte Thaw Outcomes From a Large University-Based Fertility Center
Authors: Cascante Sarah Druckenmiller , Blakemore Jennifer K. , DeVore Shannon , Hodes-Wertz Brooke , Fino M. Elizabeth , Berkeley Alan S. , Parra Carlos M. , McCaffrey Caroline , Grifo James A. 
Published: October 2022

(Abstracted from Fertil Steril 2022;118:158–166)
Changes in social norms have resulted in a trend toward motherhood at a later age in the United States. Oocyte preservation (OC) is now a widely used methodology of fertility preservation used to offset the age-related fertility decline related to decreased oocyte quantity and quality.
The complement system in antineutrophil cytoplasmic antibody-associated vasculitis: pathogenic player and therapeutic target
Authors: Mazzariol Martina , Manenti Lucio , Vaglio Augusto 
Published: October 2022

Purpose of review
The purpose of this review is to discuss the role of the complement system in the pathogenesis of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) as well as the employment of complement inhibitors in AAV treatment.

Recent findings
AAV has traditionally been considered a pauci-immune disease until recent findings demonstrated the pathogenic role of the complement system. The complement alternative pathway is crucial in AAV, and C5a seems to be a key molecule for AAV to develop. Avacopan, a C5a-receptor (C5aR) antagonist, proved effective in achieving AAV remission and ameliorating kidney function.

Summary
The increased circulating levels of some complement components – as well as the consumption of others – in patients with AAV suggested a systemic activation of the complement system. Low C3 levels correlate with a more aggressive disease and a worse renal prognosis. In ANCA-associated glomerulonephritis, renal deposits of C3d and properdin, suggestive of local alternative pathway activation, correlate with glomerular crescents and proteinuria. The interaction between C5a and neutrophil triggers alternative pathway activation, suggesting the central role of C5a in AAV pathogenesis. Avacopan, a C5aR inhibitor, showed beneficial effects in AAV and represents a promising therapy to achieve sustained remission and to spare glucocorticoids.
Descriptive Epidemiology of Isolated Distal Radius Fractures in Children: Results From a Prospective Multicenter Registry
Authors: Shah Apurva S. , Guzek Ryan H. , Miller Mark L. , Willey Michael C. , Mahan Susan T. , Bae Donald S. ,   the Pediatric Distal Radius Fracture (PDRF) Study Group
Published: October 2022

Introduction:
More than 1 in 4 pediatric fractures involves the distal radius. Most prior epidemiologic studies are limited to retrospective, single center investigations, and often include adults. This study aims to describe the contemporary epidemiology of pediatric distal radius fractures using prospectively collected data from a multicenter Pediatric Distal Radius Fracture Registry.

Methods:
Patients aged 4 to 18 years diagnosed with a distal radius fracture from June 2018 through December 2019 at 4 tertiary care pediatric centers were screened and enrolled in this prospective longitudinal cohort study. Patients were excluded if they presented with bilateral distal radius fractures, polytrauma, or re-fracture. Demographic information, mechanism of injury, fracture characteristics, associated injuries, and procedural information were recorded. All radiographs were reviewed and measured. Descriptive statistics and bivariate analyses were performed.

Results:
A total of 1951 patients were included. The mean age was 9.9±3.3 years, and 61.3% of patients were male (P<0.001). Most injuries occurred during a high-energy fall (33.5%) or sports participation (28.4%). The greatest proportion of fractures occurred during the spring months (38.5%). Torus fractures (44.0%) were more common than bicortical (31.3%) or physeal (21.0%) fractures. Of the physeal fractures, 84.3% were Salter-Harris type II. Associated ulnar fractures were observed in 51.2% of patients. The mean age at injury was higher for patients with physeal fractures (11.6±2.9 y) than patients with torus or bicortical fractures (9.4±3.1 and 9.6±3.1 y, respectively; P<0.001). Thirty-six percent of distal radius fractures underwent closed reduction and 3.3% underwent surgical fixation. Patients treated with closed reduction were more likely to be male (68.7% vs. 57.2%; P<0.001), obese (25.3% vs. 17.2%; P<0.001), and have bicortical fractures (62.2% vs. 14.5%; P<0.001).

Conclusions:
Distal radius fractures in children have a male preponderance and are most likely to occur in the spring months and during high-energy falls and sports. Physeal fractures tend to occur in older children while torus and bicortical fractures tend to occur in younger children.

Level of Evidence:
Level I—prognostic.
Clinical Outcomes of Single Versus Double Anaerobic Coverage for Intra-abdominal Infections
Authors: Raymond Lendelle , Cani Eris , Zeana Cosmina , Lois William , Park Tae Eun 
Published: October 2022

Abstract

Background
Double anaerobic coverage is often used for intra-abdominal infections postoperatively. The primary objective of this study was evaluating length of hospital stay, in-hospital postoperative complications, and readmission within 30 days of discharge due to postoperative complications in patients who received piperacillin/tazobactam versus piperacillin/tazobactam plus metronidazole for intra-abdominal infections. The secondary objective was comparing in-hospital mortality and hospital-associated Clostridioides difficile infection between the 2 groups.

Methods
This retrospective cohort study included adults, who received either single or double anaerobic coverage postoperatively for at least 48 hours between January 1, 2016, and June 30, 2019. Statistical analysis involved matching patients 1:1 between the 2 groups based on Charlson Comorbidity Index, American Society of Anesthesiologists physical status classification, and surgical wound classification. Descriptive statistics and logistic regression were used to analyze the outcomes.

Results
Of 163 patients, 134 were matched 1:1 into single and double anaerobic coverage groups. The baseline characteristics of each group were similar except for diagnosis. Double anaerobic coverage was more often used for gastrointestinal perforations (38.8% vs 16.4%, P = 0.004) and single anaerobic coverage for acute cholecystitis (37.3% vs 9%, P < 0.001). In a multivariate analysis, double anaerobic coverage was associated with longer length of hospital stay (P = 0.003) compared with single anaerobic coverage. In-hospital mortality (6%) and hospital-associated C. difficile (1.5%) infection were only observed in the double anaerobic coverage group.

Conclusions
Double anaerobic coverage is associated with longer length of hospital stay and in-hospital postoperative complications.