bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis
Authors: Wang Shixiang , Tao Ziyu , Wu Tao , Liu Xue-Song 
Published: October 2020

Abstract

Summary
Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. Sigflow pipeline can be applied to both human and mouse genomes.

Availability and implementation
Sigflow is an open source software under academic free license v3.0 and it is freely available at https://github.com/ShixiangWang/sigflow or https://hub.docker.com/r/shixiangwang/sigflow.

Supplementary information
Supplementary data are available at Bioinformatics online.
Hourly modelling of Thermal Hydrogen electricity markets
Authors: Moore Jared , Meeks Noah 
Published: October 2020

Abstract
The hourly operation of Thermal Hydrogen electricity markets is modelled. The economic values for all applicable chemical commodities are quantified (syngas, ammonia, methanol and oxygen) and an hourly electricity model is constructed to mimic the dispatch of key technologies: bi-directional power plants, dual-fuel heating systems and plug-in fuel-cell hybrid electric vehicles. The operation of key technologies determines hourly electricity prices and an optimization model adjusts the capacity to minimize electricity prices yet allow all generators to recover costs. We examine 12 cost scenarios for renewables, nuclear and natural gas; the results demonstrate emissions-free, ‘energy-only’ electricity markets whose supply is largely dominated by renewables. The economic outcome is made possible in part by seizing the full supply-chain value from electrolysis (both hydrogen and oxygen), which allows an increased willingness to pay for (renewable) electricity. The wholesale electricity prices average $25–$45/MWh, or just slightly higher than the assumed levelized cost of renewable energy. This implies very competitive electricity prices, particularly given the lack of need for ‘scarcity’ pricing, capacity markets, dedicated electricity storage or underutilized electric transmission and distribution capacity.
Marmoset Brain ISH Data Revealed Molecular Difference Between Cortical Folding Patterns
Authors: Li Xiao , Liu Tao , Li Yujie , Li Qing , Wang Xianqiao , Hu Xintao , Guo Lei , Zhang Tuo , Liu Tianming 
Published: October 2020

AbstractLiterature studies have demonstrated the structural, connectional, and functional differences between cortical folding patterns in mammalian brains, such as convex and concave patterns. However, the molecular underpinning of such convex/concave differences remains largely unknown. Thanks to public access to a recently released set of marmoset whole-brain in situ hybridization data by RIKEN, Japan; this data’s accessibility empowers us to improve our understanding of the organization, regulation, and function of genes and their relation to macroscale metrics of brains. In this work, magnetic resonance imaging and diffusion tensor imaging macroscale neuroimaging data in this dataset were used to delineate convex/concave patterns in marmoset and to examine their structural features. Machine learning and visualization tools were employed to investigate the possible transcriptome difference between cortical convex and concave patterns. Experimental results demonstrated that a collection of genes is differentially expressed in convex and concave patterns, and their expression profiles can robustly characterize and differentiate the two folding patterns. More importantly, neuroscientific interpretations of these differentially expressed genes, as well as axonal guidance pathway analysis and gene enrichment analysis, offer novel understanding of structural and functional differences between cortical folding patterns in different regions from a molecular perspective.
Association Between Minimum Inhibitory Concentration, Beta-lactamase Genes and Mortality for Patients Treated With Piperacillin/Tazobactam or Meropenem From the MERINO Study
Authors: Henderson A , Paterson D L , Chatfield M D , Tambyah P A , Lye D C , De P P , Lin R T P , Chew K L , Yin M , Lee T H , Yilmaz M , Cakmak R , Alenazi T H , Arabi Y M , Falcone M , Bassetti M , Righi E , Rogers B A , Kanj S S , Bhally H , Iredell J , Mendelson M , Boyles T H , Looke D F M , Runnegar N J , Miyakis S , Walls G , Khamis M A I , Zikri A , Crowe A , Ingram P R , Daneman N , Griffin P , Athan E , Roberts L , Beatson S A , Peleg A Y , Cottrell K , Bauer M J , Tan E , Chaw K , Nimmo G R , Harris-Brown T , Harris P N A ,   MERINO Trial Investigators and the Australasian Society for Infectious Disease Clinical Research Network (ASID-CRN), Newton Peter , Wren Heather , Graham Maryza , Korman Tony , Aljohani Sameera M , Alalwan Bassam , Sultana Khizra , Sartor Assunta , Welch Darren , Kahlmeter Gunnar 
Published: October 2020

Abstract

Introduction
This study aims to assess the association of piperacillin/tazobactam and meropenem minimum inhibitory concentration (MIC) and beta-lactam resistance genes with mortality in the MERINO trial.

Methods
Blood culture isolates from enrolled patients were tested by broth microdilution and whole genome sequencing at a central laboratory. Multivariate logistic regression was performed to account for confounders. Absolute risk increase for 30-day mortality between treatment groups was calculated for the primary analysis (PA) and the microbiologic assessable (MA) populations.

Results
In total, 320 isolates from 379 enrolled patients were available with susceptibility to piperacillin/tazobactam 94% and meropenem 100%. The piperacillin/tazobactam nonsusceptible breakpoint (MIC &gt;16 mg/L) best predicted 30-day mortality after accounting for confounders (odds ratio 14.9, 95% confidence interval [CI] 2.8–87.2). The absolute risk increase for 30-day mortality for patients treated with piperacillin/tazobactam compared with meropenem was 9% (95% CI 3%–15%) and 8% (95% CI 2%–15%) for the original PA population and the post hoc MA populations, which reduced to 5% (95% CI −1% to 10%) after excluding strains with piperacillin/tazobactam MIC values &gt;16 mg/L. Isolates coharboring extended spectrum β-lactamase (ESBL) and OXA-1 genes were associated with elevated piperacillin/tazobactam MICs and the highest risk increase in 30-day mortality of 14% (95% CI 2%–28%).

Conclusions
After excluding nonsusceptible strains, the 30-day mortality difference from the MERINO trial was less pronounced for piperacillin/tazobactam. Poor reliability in susceptibility testing performance for piperacillin/tazobactam and the high prevalence of OXA coharboring ESBLs suggests that meropenem remains the preferred choice for definitive treatment of ceftriaxone nonsusceptible Escherichia coli and Klebsiella.
Low Health Literacy Exists in the Inflammatory Bowel Disease (IBD) Population and Is Disproportionately Prevalent in Older African Americans
Authors: Dos Santos Marques Isabel C , Theiss Lauren M , Baker Samantha J , Liwo Amandiy , Wood Lauren N , Cannon Jamie A , Morris Melanie S , Kennedy Gregory D , Fouad Mona N , Davis Terry C , Chu Daniel I 
Published: October 2020

Abstract

Background
Low health literacy is common in general populations, but its prevalence in the inflammatory bowel disease (IBD) population is unclear. The objective of this study was to assess the prevalence of low health literacy in a diverse IBD population and to identify risk factors for low health literacy.

Methods
Adult patients with IBD at a single institution from November 2017 to May 2018 were assessed for health literacy using the Newest Vital Sign (NVS). Demographic and socioeconomic data were also collected. Primary outcome was the prevalence of low health literacy. Secondary outcomes were length-of-stay (LOS) and 30-day readmissions after surgical encounters. Bivariate comparisons and multivariable regression were used for analyses.

Results
Of 175 IBD patients, 59% were women, 23% were African Americans, 91% had Crohn disease, and mean age was 46 years (SD = 16.7). The overall prevalence of low health literacy was 24%. Compared to white IBD patients, African Americans had significantly higher prevalence of low health literacy (47.5% vs 17.0%, P &lt; 0.05). On multivariable analysis, low health literacy was associated with older age and African American race (P &lt; 0.05). Of 83 IBD patients undergoing abdominal surgery, mean postoperative LOS was 5.5 days and readmission rate was 28.9%. There was no significant difference between LOS and readmissions rates by health literacy levels.

Conclusions
Low health literacy is present in IBD populations and more common among older African Americans. Opportunities exist for providing more health literacy-sensitive care in IBD to address disparities and to benefit those with low health literacy.
Linker histone H1.5 is an underestimated factor in differentiation and carcinogenesis
Authors: Behrends Marthe , Engmann Olivia 
Published: October 2020

Abstract
Human histone H1.5, in mice called H1b, belongs to the family of linker histones (H1), which are key players in chromatin organization. These proteins sit on top of nucleosomes, in part to stabilize them, and recruit core histone modifying enzymes. Through subtype-specific deposition patterns and numerous post-translational modifications, they fine-tune gene expression and chromatin architecture, and help to control cell fate and homeostasis. However, even though it is increasingly implicated in mammalian development, H1.5 has not received as much research attention as its relatives. Recent studies have focused on its prognostic value in cancer patients and its contribution to tumorigenesis through specific molecular mechanisms. However, many functions of H1.5 are still poorly understood. In this review, we will summarize what is currently known about H1.5 and its function in cell differentiation and carcinogenesis. We will suggest key experiments that are required to understand the molecular network, in which H1.5 is embedded. These experiments will advance our understanding of the epigenetic reprogramming occurring in developmental and carcinogenic processes.
Cross-Sectional Examination of Musculoskeletal Pain and Physical Function in a Racially and Socioeconomically Diverse Sample of Adults
Authors: Sardina Angie L , Gamaldo Alyssa A , Andel Ross , Johnson Shanthi , Baker Tamara A , Thorpe Roland J , McEvoy Cathy , Evans Michele K , Zonderman Alan B 
Published: October 2020

Abstract

Background
Musculoskeletal pain alters physiological function, which may be evidenced as early as middle age. Previous research has concluded that middle-aged adults are a high-risk group for musculoskeletal pain and report functional limitations similar to older adults. However, few studies have examined the relationships between musculoskeletal pain and physical function, using objective performance measures in a sample of racially and socioeconomically diverse adults. Thus, this study examined musculoskeletal pain in relation to physical function in middle-aged (30–64 years) White and Black adults and investigated whether the relationship varied by sociodemographic characteristics.

Methods
This cross-sectional examination incorporated data from the Healthy Aging in Neighborhoods of Diversity across the Life-Span Study. Participants (n = 875) completed measures of musculoskeletal pain and objective measures of physical performance (ie, lower and upper body strength, balance, and gait abnormalities). Physical performance measures were standardized to derive a global measure of physical function as the dependent variable.

Results
Approximately, 59% of participants identified at least 1 pain sites (n = 518). Multivariable regression analyses identified significant relationships between greater musculoskeletal pain and poorer physical function (β = −0.07, p = .031), in mid midlife (β = −0.04, p = .041; age 40–54) and late midlife (β = −0.05, p = .027; age 55–64).

Conclusions
This study observed that musculoskeletal pain was associated with poorer physical function within a diverse group of middle-aged adults. Future research should longitudinally explore whether chronic musculoskeletal pain identified at younger ages is associated with greater risk for functional limitation and dependence in later life.
Social Vulnerability and Medical Complexity Among Medicare Beneficiaries Receiving Home Health Without Prior Hospitalization
Authors: Burgdorf Julia G , Mroz Tracy M , Wolff Jennifer L 
Published: October 2020

AbstractBackground and ObjectivesRecent Medicare home health payment changes reduce reimbursement for care provided to patients without a preceding hospitalization. Beneficiaries may enter home health without a preceding hospitalization via referral from a community provider or through incurring multiple episodes of home health care. We assess potential implications of this change by examining the characteristics of patients accessing Medicare home health through each of these pathways.Research Design and MethodsNationally representative retrospective cohort study of 1,224 (weighted n = 5,913,080) older adults who participated in the National Health and Aging Trends Study between 2011 and 2015 and received Medicare-funded home health within 1 year of interview. Patient characteristics before home health were drawn from the National Health and Aging Trends Study, while characteristics during home health, referral source, and number of episodes incurred were drawn from linked Outcomes and Assessment Information Set and Medicare claims. We tested for differences in characteristics by referral source and number of episodes using weighted chi-square tests and t tests.ResultsPatients referred to home health from the community were more than twice as likely to be Medicaid-enrolled (24.0% vs 12.5%, p &lt; .001), have dementia (29.5% vs 12.4%, p &lt; .001), and have received 80 or more hours/month of family caregiver assistance (20.7% vs 10.1%, p &lt; .001) prior to home health entry compared to those referred from a hospital or skilled nursing facility. Patients who incurred multiple episodes in a spell of home health care were more likely to have high clinical severity during home health (48.3% vs 28.1%, p &lt; .001), compared to those with a single episode.Discussion and ImplicationsGreater social vulnerability and care needs before home health were associated with community referral, while greater clinical severity during home health was associated with incurring multiple episodes of care. Findings suggest that recent payment changes may threaten home health access among beneficiaries with greater social vulnerability and/or medical complexity.
Between Social Inclusion and Exclusion: Integration of Daycare Guests in the Nursing Home Setting
Authors: Hämel Kerstin , Röhnsch Gundula 
Published: October 2020

AbstractBackground and ObjectivesIn integrated daycare, community-dwelling older people in need of care join existing groups in residential care facilities during the day. This study focuses on how nursing home residents experience the integrative care approach, exploring opportunities for social inclusion and mechanisms of exclusion.Research Design and MethodsA purposive sample of residents differing in cognitive capacity and level of (non)conflictual interaction with daycare guests was selected. Episodic interviews with residents (N = 10) and close relatives (N = 2) were conducted in 3 pilot facilities in Germany and analyzed using thematic coding.ResultsThe analysis revealed different orientation patterns towards the presence of daycare guests: respondents (a) demonstrated indifference to the daycare guests, (b) saw bonding with guests as a means to connect to the outside world, and (c) perceived incompatibility between in-group and out-group. Criticisms included disruption of daily routines and loss of privacy. Most interviewees came to terms with the care situation using rational and moral arguments.Discussion and ImplicationsThe study reveals the importance of residents’ participation when integrating daycare guests. Institutional procedures are required to prevent exclusion of daycare guests and avoid overtaxing residents.
Are there causal relationships between attention-deficit/hyperactivity disorder and body mass index? Evidence from multiple genetically informed designs
Authors: Liu Chao-Yu , Schoeler Tabea , Davies Neil M , Peyre Hugo , Lim Kai-Xiang , Barker Edward D , Llewellyn Clare , Dudbridge Frank , Pingault Jean-Baptiste 
Published: October 2020

Abstract

Background
Attention-deficit/hyperactivity disorder (ADHD) and body mass index (BMI) are associated. However, it remains unclear whether this association reflects causal relationships in either direction or confounding. Here, we implemented genetically informed methods to examine bidirectional causality and potential confounding.

Methods
Three genetically informed methods were employed: (i) cross-lagged twin-differences analyses to assess bidirectional effects of ADHD symptoms and BMI at ages 8, 12, 14 and 16 years in 2386 pairs of monozygotic twins from the Twins Early Development Study (TEDS); (ii) within- and between-family ADHD and BMI polygenic score (PS) analyses in 3320 pairs of dizygotic TEDS twins; and (iii) two-sample bidirectional Mendelian randomization (MR) using summary statistics from genome-wide association studies (GWAS) on ADHD (N = 55,374) and BMI (N = 806,834).

Results
Mixed results were obtained across the three methods. Twin-difference analyses provided little support for cross-lagged associations between ADHD symptoms and BMI over time. PS analyses were consistent with bidirectional relationships between ADHD and BMI, with plausible time-varying effects from childhood to adolescence. MR findings also suggested bidirectional causal effects between ADHD and BMI. Multivariable MR indicated the presence of substantial confounding in bidirectional relationships.

Conclusions
The three methods converged to highlight multiple sources of confounding in the association between ADHD and BMI. PS and MR analyses suggested plausible causal relationships in both directions. Possible explanations for mixed causal findings across methods are discussed.
Finiteness of Isomorphism Classes of Hyperbolic Polycurves with Prescribed Fundamental Groups
Authors: Sawada Koichiro 
Published: October 2020

AbstractIn the present paper, we show that there are at most finitely many isomorphism classes of hyperbolic polycurves (i.e., successive extensions of families of hyperbolic curves) over certain types of fields whose étale fundamental group is isomorphic to a prescribed profinite group.
Q-Systems and Extensions of Completely Unitary Vertex Operator Algebras
Authors: Gui Bin 
Published: October 2020

AbstractComplete unitarity is a natural condition on a CFT-type regular vertex operator algebra (VOA), which ensures that its modular tensor category (MTC) is unitary. In this paper we show that any CFT-type unitary (conformal) extension $U$ of a completely unitary VOA $V$ is completely unitary. Our method is to relate $U$ with a Q-system $A_U$ in the $C^*$-tensor category $\textrm{Rep}^{\textrm{u}}(V)$ of unitary $V$-modules. We also update the main result of [ 30] to the unitary cases by showing that the tensor category $\textrm{Rep}^{\textrm{u}}(U)$ of unitary $U$-modules is equivalent to the tensor category $\textrm{Rep}^{\textrm{u}}(A_U)$ of unitary $A_U$-modules as unitary MTCs. As an application, we obtain infinitely many new (regular and) completely unitary VOAs including all CFT-type $c&lt;1$ unitary VOAs. We also show that the latter are in one-to-one correspondence with the (irreducible) conformal nets of the same central charge $c$, the classification of which is given by [ 29].
Advanced Oxidation Protein Product (AOPP) Levels in Second- and Third-Degree Thermal Burns
Authors: Mert Handan , Açikkol Suat , Çalli İskan , Çibuk Salih , Keskin Sıddık , Mert Nihat 
Published: October 2020

AbstractBurn is a systemic injury affecting the entire organism according to its etiology and severity. The aim of this study was to investigate plasma AOPP levels before and after treatment of second- and third-degree thermal burn patients and determine the changes in this parameter, and also, to find out the relationship between AOPP level and hospitalization period and total body surface area (TBSA). The study material consisted of pediatric patients with the complaint of second- and third-degree thermal burns aged between 1 and 18 years, with a burn area exceeding 10%. Blood samples were taken twice before and after treatment. AOPP level in blood plasma was measured in ELISA. It was observed that in the second-degree thermal burn group, AOPP level was 25.85 ± 2.82 ng/ml before the treatment decreased to 22.16 ± 3.62 ng/ml after treatment, whereas in the third-degree thermal burn group before the treatment AOPP was 25.96 ± 3.49 ng/ml, and after the treatment dropped to 21.70 ± 3.79 ng/ml, decreases were significantly important (P &lt; .05). There was no statistically significant difference between the two groups in terms of AOPP levels (P &gt; .05). Correlation analyses in the second- and third-degree thermal burn group did not show any correlation between AOPP levels and burn area and length of hospitalization period. As a result, AOPP level has been studied, for the first time, in burn cases. In both groups, the level of AOPP increased due to oxidative stress before treatment and decreased after treatment.
A botanical collector abroad: contextualizing Thomas Penny’s travels in Switzerland and France, 1565–1568
Authors: Addyman Marie 
Published: October 2020

Abstract
Between 1565 and 1568 Thomas Penny travelled in Switzerland and France. The material he gathered and recorded served as annotations to Conrad Gessner’s plant records. The intention to publish these edited notes as a collection was never realized, but Penny’s journey clarifies many of the material circumstances under which collecting was undertaken.