bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motivations behind complementary and alternative medicine use in patients with Crohn’s disease and ulcerative colitis
Authors: Klemm Natasha , Trasolini Roberto , Bressler Brian , Rosenfeld Gregory , Almasan Gina , Leung Yvette 
Published: August 2024

Abstract

Background
Complementary and alternative medicine (CAM) use is common in inflammatory bowel disease (IBD) patients and impacts compliance with conventional treatment. Gastroenterologists should understand the motivational factors of CAM use—factors that push patients away from standard therapy or pull towards CAM. Our study describes the motivations behind CAM use for IBD and evaluates differences between Crohn’s disease (CD) and ulcerative colitis (UC) patients.

Methods
Retrospective cohort survey of patients over 18 years old with IBD, evaluated by gastroenterologists at a tertiary care referral centre from January 1 to December 31, 2019. Only patients who reported CAM use were included. Chi-square and independent t-tests were performed and P-value &lt;0.05 was significant.

Results
Of the 230 completed surveys, 193 reported CAM use (CD: 57.5% vs UC: 42.5%). Demographics, disease duration, and hospitalizations were similar, but CD patients had lower SIBDQ scores (CD: 48.1 vs UC: 53.5, P &lt; 0.001). Both groups were largely influenced by their social network to use CAM (CD: 33% vs UC: 31.3%) and did not feel well informed about CAM (87.4%). CD and UC patients had similar push and pull factors. Push factors included lack of improvement (39%) and side effects (20%) with conventional treatment. Pull factors included the desire for a holistic approach (21%) and to improve mood (35%). UC patients wanted a natural approach to treat their IBD, which nearly reached significance (P = 0.049). Most patients hoped fatigue 62.7%, and diarrhoea 61.7% would improve with CAM, but more CD patients wanted to improve their appetite (P = 0.043).

Conclusion
Despite differences in QoL, push and pull motivations for CAM use did not differ between CD and UC patients. Most users do not feel well informed of CAM and ongoing dialogue is important for patient-centred care.
When criminality begets crime: the role of elected politicians in India
Authors: Prakash Nishith , Sahoo Soham , Saraswat Deepak , Sindhi Reetika 
Published: August 2024

Abstract
This article examines the effect of electing criminally accused politicians on crime in India, considering the severity of their alleged offenses. Employing an instrumental variable approach that exploits the quasi-random variation in outcomes of close elections between candidates with and without criminal accusations, we find that a standard deviation (SD) increase in the share of criminally accused leaders in institutionally weaker states leads to a 0.05 SD rise in yearly reported crimes. Leaders accused of serious crimes have a more pronounced effect on crime outcomes, including crimes against women. Crucially, leaders accused of serious crimes also exert a negative influence on female labor force participation, underlining their detrimental impact on socioeconomic welfare. Our findings highlight the significance of considering the nature and severity of criminal accusations when evaluating the impact of criminally accused politicians on crime and society.
Social vulnerability and survival in 112 000 adolescents and young adults with cancer: a population-based study
Authors: Tortolero Guillermo A , Betts Andrea C , Suragh Tiffany A , Pruitt Sandi L , Roth Michael E , Murphy Caitlin C 
Published: August 2024

Abstract
Evidence suggests neighborhood-level factors contribute to cancer outcomes, although most research focuses on pediatric and adult populations. Using population-based data from the Texas Cancer Registry, we examined neighborhood-level social vulnerability, a composite measure of 14 census tract-level social risk factors, and survival among 112 142 adolescents and young adults with cancer (AYAs, age 15-39 years). We estimated 1-, 5-, and 10-year overall survival by quintile of social vulnerability and used Cox proportional hazards models (2-sided significance testing) to estimate the association between social vulnerability and all-cause mortality. Survival decreased as social vulnerability increased; for example, 5-year survival was 86.5% (95% confidence interval [CI] = 85.1 to 87.0) in the least vulnerable quintile compared to 74.0% (95% CI = 73.4 to 74.5) in the most vulnerable quintile. Social vulnerability was associated with all-cause mortality in adjusted models (highest vs lowest quintile: adjusted hazard ratio [aHR] = 1.55, 95% CI = 1.48 to 1.63). Achieving equity in AYAs’ survival requires interventions to address neighborhood disparities.
The transcription factor EjNAC5 regulates loquat fruit chilling lignification
Authors: Huang Yiqing , Liang Zihao , Lu Jiao , Zhang Mengxue , Cao Xizhi , Hu Ruoqian , Li Dongdong , Grierson Donald , Chen Wenbo , Zhu Changqing , Wu Di , Shi Yanna , Chen Kunsong 
Published: August 2024

Abstract
Changes in both lignin biosynthesis and DNA methylation have been reported to be associated with chilling stress in plants. When stored at low temperatures, red-fleshed loquat is prone to lignification, with increased lignin content and fruit firmness, which has deleterious effects on taste and eating quality. Here, we found that 5 °C storage mitigated the increasing firmness and lignin content of red-fleshed ‘Dahongpao’ (‘DHP’) loquat fruit that occurred during 0 °C storage. EjNAC5 was identified by integrating RNA sequencing with whole-genome bisulfite sequencing analysis of ‘DHP’ loquat fruit. The transcript levels of EjNAC5 were positively correlated with changes in firmness and negatively correlated with changes in DNA methylation level of a differentially methylated region in the EjNAC5 promoter. In white-fleshed ‘Baisha’ (‘BS’) loquat fruit, which do not undergo chilling-induced lignification at 0 °C, the transcripts of EjNAC5 remained low and the methylation level of the differentially methylated region in the EjNAC5 promoter was higher, compared with ‘DHP’ loquat fruit. Transient overexpression of EjNAC5 in loquat fruit and stable overexpression in Arabidopsis and liverwort led to an increase in lignin content. Furthermore, EjNAC5 interacts with EjERF39 and EjHB1 and activates the transcription of Ej4CL1 and EjPRX12 genes involved in lignin biosynthesis. This regulatory network involves different transcription factors from those involved in the lignification pathway. Our study indicates that EjNAC5 promoter methylation modulates EjNAC5 transcript levels and identifies novel EjNAC5–EjERF39–Ej4CL1 and EjNAC5–EjHB1–EjPRX12 regulatory modules involved in chilling induced-lignification.
The evolution of ovarian somatic cells characterized by transcriptome and chromatin accessibility across rodents, monkeys, and humans
Authors: Zhang Qiancheng , Sun Fengyuan , Zhang Ruifeng , Zhao Donghong , Zhu Ran , Cheng Xin , Long Xin , Hou Xinling , Yan Rui , Cao Yu , Guo Fan , Yan Long , Hu Yuqiong 
Published: August 2024

Abstract
The ovary plays a crucial role in the reproductive system of female mammals by producing mature oocytes through folliculogenesis. Non-human model organisms are extensively utilized in research on human ovarian biology, thus necessitating the investigation of conservation and divergence in molecular mechanisms across species. In this study, we employed integrative single-cell analysis of transcriptome and chromatin accessibility to identify the evolutionary conservation and divergence patterns of ovaries among humans, monkeys, mice, rats, and rabbits. Our analyses revealed that theca cells exhibited the most significant changes during evolution based on scRNA-seq and scATAC-seq datasets. Furthermore, we discovered common cis-regulatory architectures in theca cells across species by conducting joint analyses of scRNA-seq and scATAC-seq datasets. These findings have potential applications in non-human biomedical and genetic research to validate molecular mechanisms found in human organisms. Additionally, our investigation into non-coding genomic regions identified intergenic highly transcribed regions (igHTRs) that may contribute to the evolution of species-specific phenotypic traits. Overall, our study provides valuable insights into understanding the molecular characteristics of adult ovaries while offering new perspectives for studying human ovarian physiology and diseases.
Degrees of truthlikeness, independence, equality and order in probabilistic propositional knowledge representation
Authors: Kuipers Theo A F 
Published: August 2024

Abstract
Probabilistic propositional knowledge representation, as here conceived, deals with knowledge representation in the form of probabilistic (p-)valuations of the atomic propositions of a propositional language, of probability (p-)distributions over propositional state descriptions and with their relation. The aim of the paper is conceptual: introducing and illustrating a number of related, normalized concepts regarding both valuations and distributions: degrees of truthlikeness, (internal) independence, equality and order. The backbone of these concepts is the relevant sum of absolute distances. All degrees are in the unit interval and will be illustrated at the relevant place by data about the co-morbidity of psychiatric syndromes (Van Loo et al., 2016). In a new section we illustrate all concepts by an example of weather conditions, to be precise: (not) windy, (not) hot, (not) rainy days in March 2023, in De Bilt (NL). We also briefly discuss some other approaches: other distance measures, covariance as a measure of mutual dependence and various degrees of equality. In the final section we enlist several further research questions and issues, among which the question whether this paper is relevant for propositional probability logics. The paper is highly inspired by the rich paper of Gustavo Cevolani and Roberto Festa (2021).
Introductory Information for Therapists
Authors: Smits Jasper A. J. , Otto Michael W. 
Published: August 2024

Abstract
This chapter provides a brief background on integrating exercise-based interventions into mental-health care. It explains how the therapist guide works hand in hand with the client workbook. Due to the obvious benefits of exercise for stress, mood, anxiety, habit control, and cognition, there is a clear need for the adoption of exercise-based interventions across the range of settings where clients seek help. The chapter then provides an overview of the scope of the issue concerning mood and anxiety disorders. It emphasizes that exercise interventions may be an acceptable treatment modality for individuals who are unwilling to commit to psychotherapy or pharmacotherapy.
Exercise for Stress, Worry, and Panic
Authors: Smits Jasper A. J. , Otto Michael W. 
Published: August 2024

Abstract
This chapter focuses on exercise programs for clients with stress, worry, and panic. It discusses strategies to complement and fine-tune the exercise prescription to help target these core features of anxiety disorders. According to research, individuals who have a high level of anxiety sensitivity respond to benign bodily sensations with fear because they are concerned that these sensations have harmful consequences. Thus, targeting anxiety sensitivity may be critical to overcoming panic disorder. The chapter suggests educating clients about the roles of fears of anxiety sensations in panic disorder and the efficacy of exposure to bodily sensations through exercise in an effort to overcome anxiety sensitivity.
Exercise to Enhance Resilience
Authors: Smits Jasper A. J. , Otto Michael W. 
Published: August 2024

Abstract
This chapter focuses on how exercise programs can be used in the transdiagnostic task of enhancing psychological resilience. The term “psychological resilience” primarily refers to a person’s ability to recover from stress and adversity. Exercise prescriptions can serve as a tool to help insulate individuals from some of the emotional and physical sequelae of stressors. Exercise programs to enhance resilience can also be introduced as part of the relapse-prevention phase of treatment. The chapter introduces the notion of mind/body balance as a way to generalize interventions to broader well-being, focusing on feeling mentally fit in order to better manage stressors.
Intervention Issues
Authors: Smits Jasper A. J. , Otto Michael W. 
Published: August 2024

Abstract
This chapter examines the issues of long term maintenance of an exercise program. It offers recommendations for helping clients develop a cognitive style for noticing and positively interpreting their exercise experiences and working to eliminate the barriers that arise during an exercise program. Cognitive coaching refers to an adaptive style of self-talk designed to direct attention to the most pleasurable aspects of exercise and exercise-related achievements during and after exercise. The chapter covers the therapist’s role in working to overcome barriers to the regular adoption of exercise and helping clients develop a self-coaching style to deal with lapses and exercise over the long term. It emphasizes that the management of self-coaching is vital in maintaining early exercise efforts.
Exercising over the Long Term
Authors: Otto Michael W. , Smits Jasper A. J. 
Published: August 2024

Abstract
This chapter highlights the impact of exercising over the long term. It emphasizes that variety is important in maintaining a strong exercise habit over time. One way to keep exercise interesting over the long term is for clients to allow their goals for exercise to change. Additionally, keeping a log of moods and exercise can help the client to keep track of the nature and quality of the exercise program while simultaneously providing the client with space for coaching toward new exercise goals. The chapter warns about the possibility of lapses in exercise habits before offering advice on how to do self-coaching regardless of the level of motivation.
Diasporic Somali migration to Turkey: Exploring the intersection of mobility, place, and geopolitics
Authors: Abdi Ayan Yasin , Galal Lise Paulsen 
Published: August 2024

Abstract
This article explores the recent migration of diasporic Somalis to Turkey. Drawing on ethnographic studies, we examine the interplay between mobility and place within this context. Through an analysis of historical ties, geographical location, and geopolitical implications, we investigate how diasporic Somalis’ sense of Turkey as a place emerges as a preferred destination. We argue that Turkey's engagement with Somalia and its growing presence in the region have not only been valued but also highly regarded, thus motivating diasporic Somalis to choose Turkey as their new migration destination. However, the issue of diasporic Somalis' migration to Turkey extends beyond its perceived moral and strategic appeal, encompassing aspects of neo-colonialism and a place of exclusion. In conclusion, this article highlights the complex interplay of political and geopolitical factors that contribute to the uncertain future of diasporic Somalis in Turkey.
A novel interaction between the 5′ untranslated region of the Chikungunya virus genome and Musashi RNA binding protein is essential for efficient virus genome replication
Authors: Sun Kaiwen , Appadoo Francesca , Liu Yuqian , Müller Marietta , Macfarlane Catriona , Harris Mark , Tuplin Andrew 
Published: August 2024

Abstract
Chikungunya virus (CHIKV) is a re-emerging, pathogenic alphavirus that is transmitted to humans by Aedesspp. mosquitoes—causing fever and debilitating joint pain, with frequent long-term health implications and high morbidity. The CHIKV replication cycle is poorly understood and specific antiviral therapeutics are lacking. In the current study, we identify host cell Musashi RNA binding protein-2 (MSI-2) as a proviral factor. MSI-2 depletion and small molecule inhibition assays demonstrated that MSI-2 is required for efficient CHIKV genome replication. Depletion of both MSI-2 and MSI-1 homologues was found to synergistically inhibit CHIKV replication, suggesting redundancy in their proviral function. Electromobility shift assay (EMSA) competition studies demonstrated that MSI-2 interacts specifically with an RNA binding motif within the 5′ untranslated region (5′UTR) of CHIKV and reverse genetic analysis showed that mutation of the binding motif inhibited genome replication and blocked rescue of mutant virus. For the first time, this study identifies the proviral role of MSI RNA binding proteins in the replication of the CHIKV genome, providing important new insight into mechanisms controlling replication of this significant human pathogen and the potential of a novel therapeutic target.
Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability
Authors: Wulff Thomas F , Hahnke Karin , Lécrivain Anne-Laure , Schmidt Katja , Ahmed-Begrich Rina , Finstermeier Knut , Charpentier Emmanuelle 
Published: August 2024

Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA in Escherichia coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogen Streptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome of S. pyogenes SF370 and demonstrate that the adaptation of S. pyogenes TadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing in S. pyogenes and provide novel insights into the plasticity of the editome and its regulation in bacteria.
CRISPR perfect adaptation for robust control of cellular immune and apoptotic responses
Authors: Zhang Yichi , Zhang Shuyi 
Published: August 2024

Abstract
A central challenge in the quest for precise gene regulation within mammalian cells is the development of regulatory networks that can achieve perfect adaptation—where outputs consistently return to a set baseline post-stimulus. Here, we present such a system that leverages the CRISPR activation (CRISPRa) and anti-CRISPR proteins as two antithetic elements to establish perfect adaptation in mammalian cells and dynamically regulate gene expression. We demonstrate that this system can maintain stable expression levels of target genes in the face of external perturbations, thus providing a robust platform for biological applications. The versatility of our system is further showcased through its integration with endogenous regulatory mechanisms in T cells, such as the NF-κB-mediated immune response, and its ability to program apoptosis responses for precise spatial and temporal control of cellular growth and death. This study not only advances our understanding of gene regulation in mammalian cells but also opens new avenues for therapeutic intervention, particularly in diseases characterized by dysregulated gene expression.
CytoCellDB: a comprehensive resource for exploring extrachromosomal DNA in cancer cell lines
Authors: Fessler Jacob , Ting Stephanie , Yi Hong , Haase Santiago , Chen Jingting , Gulec Saygin , Wang Yue , Smyers Nathan , Goble Kohen , Cannon Danielle , Mehta Aarav , Ford Christina , Brunk Elizabeth 
Published: August 2024

Abstract
Recently, the cancer community has gained a heightened awareness of the roles of extrachromosomal DNA (ecDNA) in cancer proliferation, drug resistance and epigenetic remodeling. However, a hindrance to studying ecDNA is the lack of available cancer model systems that express ecDNA. Increasing our awareness of which model systems express ecDNA will advance our understanding of fundamental ecDNA biology and unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations for cell lines within the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). We identify 139 cell lines that express ecDNA, a 200% increase from what is currently known. We expanded the total number of cancer cell lines with ecDNA annotations to 577, which is a 400% increase, covering 31% of cell lines in CCLE/DepMap. We experimentally validate several cell lines that we predict express ecDNA or homogeneous staining regions (HSRs). We demonstrate that CytoCellDB can be used to characterize aneuploidy alongside other molecular phenotypes, (gene essentialities, drug sensitivities, gene expression). We anticipate that CytoCellDB will advance cytogenomics research as well as provide insights into strategies for developing therapeutics that overcome ecDNA-driven drug resistance.
Analysis of the discontinuation and nonpublication of neurooncological randomized clinical trials
Authors: Butler Molly , Mehra Mehul , Chandasir Abdullah , Kaoutzani Lydia , Vale Fernando L 
Published: August 2024

Abstract

Background
Premature discontinuation and nonpublication of clinical trials contribute to research waste and compromise our ability to improve patient outcomes. However, the extent to which these problems exist in neurooncological randomized clinical trials (RCTs) is not known. This study aimed to evaluate the prevalence of discontinuation and nonpublication of neurooncological RCTs, identify contributing factors, and assess trial characteristics associated with each.

Methods
We performed a retrospective, cross-sectional study of neurooncological RCTs registered in Clinicaltrials.gov before March 7, 2023. Data were collected from Clinicaltrials.gov and associated publications were located. We attempted to contact authors for all trials without associated publications or an identified reason for discontinuation.

Results
Of 139 included RCTs, 57 (41%) were discontinued. The most common reason for discontinuation identified was slow enrollment or accrual (23%), though 30 trials (53%) were discontinued for unknown reasons. Trials funded by sources other than industry or the National Institutes of Health were more likely to be discontinued (odds ratio 4.2, 95% confidence interval 1.3–13.8). In total, 67 of the 139 (48%) RCTs were unpublished, including 50 of the 57 (88%) discontinued studies and 17 of the 82 (21%) completed studies.

Conclusions
In our study, discontinuation of neurooncological clinical trials was common and often occurred for unknown reasons. Trials were also frequently unpublished, particularly those that were discontinued. Addressing these findings may provide an opportunity to reduce research waste and improve outcomes for patients with neurological cancers.