bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rewards versus Imprisonment
Authors: Mungan Murat C 
Published: October 2021

Abstract
This article considers the possibility of simultaneously reducing crime, prison sentences, and the tax burden of financing the criminal justice system by introducing rewards, which operate by increasing quality of life outside of prison. Specifically, it proposes a procedure wherein a part of the imprisonment budget is redirected towards financing rewards. The feasibility of this procedure depends on how effectively the marginal imprisonment sentence reduces crime, the crime rate, the effectiveness of rewards, and how accurately the government can direct rewards towards individuals who are most responsive to such policies. A related welfare analysis reveals an advantage of rewards: they operate by transferring or creating wealth, whereas imprisonment destroys wealth. Thus, the conditions under which rewards are optimal are broader than those under which they can be used to jointly reduce crime, sentences, and taxes. With an exogenous [resp. endogenous] budget for law enforcement, it is optimal to use rewards when the imprisonment elasticity of crime is small [resp. the marginal cost of public funds is not high]. These conditions hold, implying that using rewards is optimal, in numerical examples generated by using estimates for key values from the empirical literature.
The moss traits that rule cyanobacterial colonization
Authors: Liu Xin , Rousk Kathrin 
Published: October 2021

Abstract

Background and Aims
Cyanobacteria associated with mosses represent a main nitrogen (N) source in pristine, high-latitude and -altitude ecosystems due to their ability to fix N2. However, despite progress made regarding moss–cyanobacteria associations, the factors driving the large interspecific variation in N2 fixation activity between moss species remain elusive. The aim of the study was to identify the traits of mosses that determine cyanobacterial colonization and thus N2 fixation activity.

Methods
Four moss species varying in N2 fixation activity were used to assess cyanobacterial abundance and activity to correlate it with moss traits (morphological, chemical, water-balance traits) for each species.

Key Results
Moss hydration rate was one of the pivotal traits, explaining 56 and 38 % of the variation in N2 fixation and cyanobacterial colonization, respectively, and was linked to morphological traits of the moss species. Higher abundance of cyanobacteria was found on shoots with smaller leaves, and with a high frequency of leaves. High phenol concentration inhibited N2 fixation but not colonization. These traits driving interspecific variation in cyanobacterial colonization, however, are also affected by the environment, and lead to intraspecific variation. Approximately 24 % of paraphyllia, filamentous appendages on Hylocomium splendens stems, were colonized by cyanobacteria.

Conclusions
Our findings show that interspecific variations in moss traits drive differences in cyanobacterial colonization and thus, N2 fixation activity among moss species. The key traits identified here that control moss-associated N2 fixation and cyanobacterial colonization could lead to improved predictions of N2 fixation in different moss species as a function of their morphology.
Decolonization, Language, and Race in Applied Linguistics and Social Justice
Authors: Rosa Jonathan , Flores Nelson 
Published: October 2021

Abstract
While applied linguistics research can serve as an important site for understanding and contributing to efforts toward challenging historical and contemporary power structures, it is also crucial to interrogate how numerous normative concepts and logics within the field of applied linguistics both reflect and reenact dominant power structures. Centering colonialism and racism in our analysis, this commentary considers how applied linguistics often focuses on modest reforms supporting affirmation and inclusion of marginalized populations and practices, rather than on fundamental institutional changes required to eradicate the forces that produce marginalization. As applied linguists grapple with questions surrounding the extent to which their work contributes in substantive ways to social justice struggles, we are inspired by collaborations that challenge us to reconsider normative assumptions about both language and justice. These collaborations demand a comprehensive reckoning that frames social justice not as a normative reality that can be achieved through modest reforms to liberal governance, but rather as an existential horizon that necessitates a fundamental reimagination of communication’s role in narrating and creating decolonial worlds that sustain collective well-being.
GraphCDR: a graph neural network method with contrastive learning for cancer drug response prediction
Authors: Liu Xuan , Song Congzhi , Huang Feng , Fu Haitao , Xiao Wenjie , Zhang Wen 
Published: October 2021

Abstract
Predicting the response of a cancer cell line to a therapeutic drug is an important topic in modern oncology that can help personalized treatment for cancers. Although numerous machine learning methods have been developed for cancer drug response (CDR) prediction, integrating diverse information about cancer cell lines, drugs and their known responses still remains a great challenge. In this paper, we propose a graph neural network method with contrastive learning for CDR prediction. GraphCDR constructs a graph neural network based on multi-omics profiles of cancer cell lines, the chemical structure of drugs and known cancer cell line-drug responses for CDR prediction, while a contrastive learning task is presented as a regularizer within a multi-task learning paradigm to enhance the generalization ability. In the computational experiments, GraphCDR outperforms state-of-the-art methods under different experimental configurations, and the ablation study reveals the key components of GraphCDR: biological features, known cancer cell line-drug responses and contrastive learning are important for the high-accuracy CDR prediction. The experimental analyses imply the predictive power of GraphCDR and its potential value in guiding anti-cancer drug selection.
Machine learning meets omics: applications and perspectives
Authors: Li Rufeng , Li Lixin , Xu Yungang , Yang Juan 
Published: October 2021

AbstractThe innovation of biotechnologies has allowed the accumulation of omics data at an alarming rate, thus introducing the era of ‘big data’. Extracting inherent valuable knowledge from various omics data remains a daunting problem in bioinformatics. Better solutions often need some kind of more innovative methods for efficient handlings and effective results. Recent advancements in integrated analysis and computational modeling of multi-omics data helped address such needs in an increasingly harmonious manner. The development and application of machine learning have largely advanced our insights into biology and biomedicine and greatly promoted the development of therapeutic strategies, especially for precision medicine. Here, we propose a comprehensive survey and discussion on what happened, is happening and will happen when machine learning meets omics. Specifically, we describe how artificial intelligence can be applied to omics studies and review recent advancements at the interface between machine learning and the ever-widest range of omics including genomics, transcriptomics, proteomics, metabolomics, radiomics, as well as those at the single-cell resolution. We also discuss and provide a synthesis of ideas, new insights, current challenges and perspectives of machine learning in omics.
vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA
Authors: Vogt Frank , Shirsekar Gautam , Weigel Detlef 
Published: October 2021

Abstract

Motivation
Genome-wide association study (GWAS) requires a researcher to perform a multitude of different actions during analysis. From editing and formatting genotype and phenotype information to running the analysis software to summarizing and visualizing the results. A typical GWAS workflow poses a significant challenge of utilizing the command-line, manual text-editing and requiring knowledge of one or more programming/scripting languages, especially for newcomers.

Results
vcf2gwas is a package that provides a convenient pipeline to perform all of the steps of a traditional GWAS workflow by reducing it to a single command-line input of a Variant Call Format file and a phenotype data file. In addition, all the required software is installed with the package. vcf2gwas also implements several useful features enhancing the reproducibility of GWAS analysis.

Availability and implementation
The source code of vcf2gwas is available under the GNU General Public License. The package can be easily installed using conda. Installation instructions and a manual including tutorials can be accessed on the package website at https://github.com/frankvogt/vcf2gwas.

Supplementary information
Supplementary data are available at Bioinformatics online.
The associations between poverty and social–emotional outcomes among children in Japan
Authors: Lee Kyunghee 
Published: October 2021

AbstractThe current study examined the impacts of poverty on children’s socio-emotional outcomes among Japanese children. Children of 325 Japanese families were identified based on the Japan Household Panel Study and Japan Child Panel Survey. Poverty was examined in four non-linear income to needs ratio categories and the poverty status, poverty and non-poverty. Compared to children who were in the lowest income to needs ratios, children in the upper categories had less fewer behavioural problems. Children in poverty had significantly lower physical health, emotional well-being, self-esteem, family, friends and school relationship than those children not in poverty. Children’s time spent on academics and family support significantly affected children’s social outcomes. Child poverty and its adverse impacts on children’s mental health should be considered in the ecological framework that incorporates children, family, community and policy.This study examined the associations between poverty and socio-emotional developments among children in Japan. Children and parents of 325 Japanese families participated and provided data on the household poverty status and children’s socio-emotional outcomes. Children’s socio-emotional outcomes included in the study were behavioural difficulties (strength/weakness) reported by parents and social adaptability (six indicators on the quality of life) measured by children’s self-report. Findings indicated that poverty has significant adverse impacts on Japanese children’s mental health. The adverse impact of poverty became more prevalent as families’ income decreased. Among children living in poverty, self-reported mental health problems were significantly higher than those reported by parents. Other factors such as grade level (upper grade), less time spent on academics and a larger household size negatively affected mental health. Findings suggest for policy interventions with increased expenditures on income assistance programmes for families with children in Japan. In addition, social workers or other service providers in Japan should facilitate matching low-income families with children to available social service programmes. Poverty and its adverse impacts on children’s mental health should be considered in an ecological framework that incorporates children, family, community and policy.
ECCO Guidelines on Therapeutics in Ulcerative Colitis: Surgical Treatment
Authors: Spinelli Antonino , Bonovas Stefanos , Burisch Johan , Kucharzik Torsten , Adamina Michel , Annese Vito , Bachmann Oliver , Bettenworth Dominik , Chaparro Maria , Czuber-Dochan Wladyslawa , Eder Piotr , Ellul Pierre , Fidalgo Catarina , Fiorino Gionata , Gionchetti Paolo , Gisbert Javier P , Gordon Hannah , Hedin Charlotte , Holubar Stefan , Iacucci Marietta , Karmiris Konstantinos , Katsanos Konstantinos , Kopylov Uri , Lakatos Peter L , Lytras Theodore , Lyutakov Ivan , Noor Nurulamin , Pellino Gianluca , Piovani Daniele , Savarino Edoardo , Selvaggi Francesco , Verstockt Bram , Doherty Glen , Raine Tim , Panis Yves 
Published: October 2021

Abstract
This is the second of a series of two articles reporting the European Crohn’s and Colitis Organisation [ECCO] evidence-based consensus on the management of adult patients with ulcerative colitis [UC]. The first article is focused on medical management, and the present article addresses medical treatment of acute severe ulcerative colitis [ASUC] and surgical management of medically refractory UC patients, including preoperative optimisation, surgical strategies, and technical issues. The article provides advice for a variety of common clinical and surgical conditions. Together, the articles represent an update of the evidence-based recommendations of the ECCO for UC.
MiR-1-3p and MiR-124-3p Synergistically Damage the Intestinal Barrier in the Ageing Colon
Authors: Sun Ting-yi , Li Ya-qi , Zhao Fu-qian , Sun Hai-mei , Gao Yang , Wu Bo , Yang Shu , Ji Feng-qing , Zhou De-shan 
Published: October 2021

Abstract

Background and Aims
Disruption of the intestinal barrier of the digestive tract is a common pathophysiological change in the elderly, which may partly contribute to gut dysfunction and inflammatory bowel disease [IBD]. This study aimed to discover new interactive epigenetic regulation patterns involved in intestinal barrier dysfunction and colitis in elderly populations.

Methods
Intestinal barrier function and structure were evaluated in naturally ageing mice and elderly people. High-throughput analysis was performed on colonic tissues from humans and mice. The synergistic roles of miR-1-3p and miR-124-3p were identified using microRNA mimic/agomirs. Related genes were examined in biopsies of old IBD patients.

Results
A defective mucus barrier was observed before mucosal microstructural damage during ageing. Elevated miR-1-3p expression in the colons of older individuals impaired the mucus barrier by directly targeting T-synthase, similarly to the mechanism of miR-124-3p, which we reported previously. Importantly, the synergistic effect of a half dose of each microRNA supplement on T-synthase and CDK4/6 was stronger than that of a full dose of miR-1-3p or miR-124-3p alone, and mice co-treated with two microRNAs showed greater susceptibility to chemical-induced colitis than mice treated with either microRNA alone. These two microRNAs were up-expressed in old IBD patients.

Conclusions
The slight increases in miR-1-3p and miR-124-3p expression with ageing may be important contributors to the breakdown of intestinal homeostasis by targeting divergent genes in different cells. These data reveal the potential ability of multiple microRNAs to exert synergistic effects to damage the intestinal barrier and promote inflammatory bowel disease development in elderly populations.
Optimal Heart Team Protocol to Improve Revascularization Decisions in Patients with Complex Coronary Artery Disease: A Sequential Mixed Method Study
Authors: Ma Hanping , Lin Shen , Li Xi , Dou Kefei , Yang Weixian , Feng Wei , Liu Sheng , Wu Yuan , Peng Boshizhang , Zheng Zhe 
Published: October 2021

Abstract

Aims
Current guidelines recommend a heart team in the decision-making for patients with complex coronary artery disease (CAD). However, the decision-making stability of these teams has not been evaluated and the optimum protocol is unknown. We assessed inter-team agreement for revascularization decision-making and influencing factors to inform the development of a heart team protocol.

Methods and results
This sequential, explanatory mixed methods study included (i) a cross-sectional quantitative study to assess inter-team agreement on treatment strategy for retrospectively enrolled complex CAD patients and (ii) a qualitative study that used semi-structured interviews with heart team members to identify factors influencing decision-making discrepancy. We randomly selected 101 complex CAD patients. Sixteen specialists were randomly assigned to four heart teams to make decisions for these patients. The primary outcome kappa of inter-team decision-making agreement was moderate (kappa 0.58). Factors influencing decision-making were generated through inductive thematic analysis and were summarized by 3 themes (specialist quality, team composition, and meeting process) and 10 subthemes. Recommendations of heart team implementation were generated based on qualitative and quantitative data at five levels: specialist selection, specialist training, team composition, team training, and meeting process. A detailed protocol on the integration of guidelines, previous experience, and recommendations was generated to establish and deploy a qualified heart team.

Conclusion
Agreement between heart teams for revascularization decision-making in complex CAD patients was moderate. Potential factors associated with decision discrepancies were summarized and recommendations were generated. A detailed heart team protocol was designed and should be validated in future.
Effect of coronary artery bypass grafting on quality of life: a meta-analysis of randomized trials
Authors: Creber Ruth Masterson , Dimagli Arnaldo , Spadaccio Cristiano , Myers Annie , Moscarelli Marco , Demetres Michelle , Little Matthew , Fremes Stephen , Gaudino Mario 
Published: October 2021

Abstract

Aims
We conducted a systematic review and meta-analysis to evaluate temporal trends in quality of life (QoL) after coronary artery bypass grafting (CABG) surgery in randomized clinical trials, and a quantitative comparison from before surgery to up to 5 years after surgery.

Methods and results
We searched MEDLINE, CINAHL, EMBASE, Cochrane Library, and PsycINFO from 2010 to 2020 to identify studies that included the measurement of QoL in patients undergoing CABG. The primary outcome was the Seattle Angina Questionnaire (SAQ), and secondary outcomes were the 36-item Short Form Health Survey (SF-36) and EuroQol Questionnaire (EQ-5D). We pooled the means and the weighted mean differences over the follow-up period. In the meta-analysis, 2586 studies were screened and 18 full-text studies were included. There was a significant trend towards higher QoL scores from before surgery to 1 year post-operatively for the SAQ angina frequency (AF), SAQ QoL, SF-36 physical component (PC), and EQ-5D, whereas the SF-36 mental component (MC) did not improve significantly. The weighted mean differences from before surgery to 1 year after was 24 [95% confidence interval (CI): 21.6–26.4] for the SAQ AF, 31 (95% CI: 27.5–34.6) for the SAQ QoL, 9.8 (95% CI: 7.1–12.8) for the SF-36 PC, 7.1 (95% CI: 4.2–10.0) for the SF-36 MC, and 0.1 (95% CI: 0.06–0.14) for the EQ-5D. There was no evidence of publication bias or small-study effect.

Conclusion
CABG had both short- and long-term improvements in disease-specific QoL and generic QoL, with the largest improvement in angina frequency.
Sadler Saddled: Reconciliation and Recrimination in a Restoration Parish
Authors: Legon Ed 
Published: October 2021

Abstract
The Surrey town of Mitcham attracted national attention in 1665 when a brief pamphlet war erupted between its vicar, Anthony Sadler, and his parishioners. In this testy public altercation, Sadler accused his patron, the local landowner Robert Cranmer, not only of neglecting his duty to maintain the ruinous vicarage and of misusing tithes, but also of disloyalty and nonconformity. Cranmer was vindicated in print by a neighbour who dismissed and ridiculed Sadler, pointing to the patron’s presentation of future Anglicans to the vicarage during the Interregnum. This article uses a remarkable body of evidence from ecclesiastical court records and elsewhere to unpick these claims and counter-claims to conformity and loyalty. In doing so, it demonstrates that the protracted dispute between Sadler and his parishioners, of which the pamphlets of 1665 were only one manifestation, was borne along by the development of equally strong but opposing positions with respect to the thorny issue of how to bridge the divisions of civil war and revolution. Moreover, the article demonstrates that this positioning had the effect of prolonging the dispute until Sadler resigned from the parish in 1669, and bringing it into several other venues of conflict resolution. This episode sheds light on several features of English society in the decades immediately before and after the Restoration, especially change and continuity in a parish within a shifting national political and religious context; the participation of men and women in law and religion; and the enduring and volatile legacy of civil conflict.
Comprehensive Study of Heart Rate Recovery and Altered Ventilatory Response to Exercise in Patients with Obstructive Sleep Apnea
Authors: Banawan Laila Abd Elhaleem , Daabis Rasha Galal , Eshmawey Heba Ahmed , Elhaleim Hend Ramadan Attia Abd 
Published: October 2021

Abstract

Background
Obstructive sleep apnea (OSA) is a chronic disorder that results in many cardiovascular disorders including hypertension, arrhythmias and congestive heart failure (CHF). Polysomnography is the gold standard for diagnosis of OSA, even though up to 93% of women and 82% of men with moderate to severe OSA still remain undiagnosed. Cardiopulmonary exercise testing (CPXT) has been conventionally used for evaluation of coronary artery diseases and rehabilitation of cardiac patients. Modern systems allow for the analysis of gas exchange at rest, during exercise, and during recovery and also yield measures of oxygen uptake (V O2), carbon dioxide output (V CO2), and minute ventilation (V E) together with heart rate, blood pressure, electrocardiography findings, and symptoms. This may have clinical utility if added to the available screening tools used to identify OSA.

Aim of study
To assess altered ventilatory response and heart rate recovery in response to exercise in patients with obstructive sleep apnea and their relation to its severity.

Methods and Results
Case control study was enrolled including 30 patients with obstructive sleep apnea (OSA) divided according to severity (5 mild, 8 moderate and 17 severe) and 15 control healthy overweight with sedentary lifestyle individuals. The two groups underwent cardiopulmonary exercise testing and different pulmonary and cardiac parameters were calculated. Greater VE, VE/VCO2, VE/VO2 ratios and VE/VCO2 slope were statistically significant regarding the patients group (P &lt; 0.001, F = 69.053, 104.381, 140.806 and 68.010 respectively according to ANOVA test). OSA patients had a reduced maximal exercise capacity expressed as lower VO2 peak, decreased breathing reserve (BR) and VO2 at anaerobic threshold compared to control group (P &lt; 0.001, F = 22.597, 68.773 and 82.90 respectively). Delayed heart rate recovery (HRR) and weaker chronotropic response (CR) in patients with OSA than in controls with negative relationship to severity of OSA were proved (p &lt; 0.001, F = 119.493 and 91.271 respectively). The study revealed elevated maximal systolic BP (max SBP), diastolic BP (max DBP) and recovery SBP in the following 2 minutes after exercise in patients with OSA relative to their healthy controls with positive relationship to the severity of OSA (P &lt; 0.001, F = 37.129, 169.275 and 244.609 respectively).

Conclusion
Patients with OSA demonstrated exaggerated ventilatory response to exercise and autonomic dysfunction reflected by measurement of heart rate variability and reduced maximal exercise capacity than healthy controls.

Abbreviations
OSA, CHF, CPXT, VO2, VCO2, VE, VE/VCO2, VE/VO2, VE/VCO2, BR, CR, HRR, max SBP and max DBP.