bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Meaning in the Retirement Transition: Scoping Review
Authors: Wood Rachel E , Pachana Nancy A 
Published: February 2025

Abstract

Background and Objectives
The retirement transition is a period of major change and instability, which may challenge a person’s sense of meaning in life. This scoping review sought to characterize the current research on the role of meaning in the retirement transition.

Research Design and Methods
This scoping review was conducted according to JBI and PRISMA reporting guidelines. Database searches of Scopus, PubMed, PsycINFO, and Social Science Database, and ProQuest Dissertations and Theses Global yielded 738 records (after duplicates removed). Accessory searches yielded an additional 286 records. Eligible articles included peer-reviewed literature and theses (qualitative and quantitative) that explored an aspect of meaning in the context of the retirement transition.

Results
A total of 30 studies (21 qualitative and nine quantitative) were included. These studies examined a broad range of research questions on different aspects of meaning – meaning in life, meaning making, meaningful engagement, and meaning of retirement. Most were single, stand-alone studies (not part of a broader research program) that included only a single time point. Only six studies were longitudinal.

Discussion and Implications
This review revealed a heterogeneous set of studies and identified gaps in reporting of important participant characteristics, lack of conceptual clarity in defining meaning, and few longitudinal studies. There is a need for more theoretically driven, programs of research that include longitudinal designs, ideally using mixed methods approaches, to build a richer understanding of the role of meaning during this major life transition.
Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl
Authors: Wang Gang , Zhang Xinye , Zhao Xiurong , Ren Xufang , Chen Anqi , Dai Wenting , Zhang Li , Lu Yan , Jiang Zhihua , Wang Huie , Liu Yong , Zhao Xiaoyu , Wen Junhui , Cheng Xue , Zhang Yalan , Ning Zhonghua , Ban Liping , Qu Lujiang 
Published: February 2025

Abstract

Introduction
The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation that causes the leucistic plumage of the blue peafowl (also called white peafowl) remains unknown.

Results
In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, and a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes, and 33 peafowl W chromosomes genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found 3 hybrid green peafowls in zoo samples rather than in the wild samples, with a blue peafowl genomic content of 16–34%. Maternal genetic analysis showed that 2 of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in 4 zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP3 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G&gt;A) in the EDNRB2 gene is the genetic causative mutation for leucistic plumage of blue peafowl, preventing melanocytes from being transported into plumage, thereby inhibiting melanin deposition.

Conclusion
Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide a valuable resource for blue peafowl genomics-assisted breeding.
VaxBot-HPV: a GPT-based chatbot for answering HPV vaccine-related questions
Authors: Li Yiming , Li Jianfu , Li Manqi , Yu Evan , Rhee Danniel , Amith Muhammad , Tang Lu , Savas Lara S , Cui Licong , Tao Cui 
Published: February 2025

Abstract

Objective
Human Papillomavirus (HPV) vaccine is an effective measure to prevent and control the diseases caused by HPV. However, widespread misinformation and vaccine hesitancy remain significant barriers to its uptake. This study focuses on the development of VaxBot-HPV, a chatbot aimed at improving health literacy and promoting vaccination uptake by providing information and answering questions about the HPV vaccine.

Methods
We constructed the knowledge base (KB) for VaxBot-HPV, which consists of 451 documents from biomedical literature and web sources on the HPV vaccine. We extracted 202 question-answer pairs from the KB and 39 questions generated by GPT-4 for training and testing purposes. To comprehensively understand the capabilities and potential of GPT-based chatbots, 3 models were involved in this study: GPT-3.5, VaxBot-HPV, and GPT-4. The evaluation criteria included answer relevancy and faithfulness.

Results
VaxBot-HPV demonstrated superior performance in answer relevancy and faithfulness compared to baselines. For test questions in KB, it achieved an answer relevancy score of 0.85 and a faithfulness score of 0.97. Similarly, it attained scores of 0.85 for answer relevancy and 0.96 for faithfulness on GPT-generated questions.

Discussion
VaxBot-HPV demonstrates the effectiveness of fine-tuned large language models in healthcare, outperforming generic GPT models in accuracy and relevance. Fine-tuning mitigates hallucinations and misinformation, ensuring reliable information on HPV vaccination while allowing dynamic and tailored responses. The specific fine-tuning, which includes context in addition to question-answer pairs, enables VaxBot-HPV to provide explanations and reasoning behind its answers, enhancing transparency and user trust.

Conclusions
This study underscores the importance of leveraging large language models and fine-tuning techniques in the development of chatbots for healthcare applications, with implications for improving medical education and public health communication.
Assessing the use of neonatal sepsis guidelines and antibiotic prescription with large-scale prospective data from Zimbabwe and Malawi
Authors: Khan Nushrat , Chimhini Gwendoline , Shrestha Som Kumar , Cortina-Borja Mario , Chimhuya Simbarashe , Zailani Gloria , Gannon Hannah , Mangiza Marcia , Fitzgerald Felicity , Heys Michelle , Chiume Msandeni 
Published: February 2025

Abstract

Background
Neonatal sepsis is a major cause of mortality in low-resource settings. We assessed how neonatal sepsis guidelines were used in two Zimbabwean hospitals and one Malawian hospital.

Methods
Using routine data collected with the digital health intervention, Neotree, we retrospectively reviewed doctors’ and nurses’ agreement with national and World Health Organization (WHO) guideline recommendations for antibiotic prescription for sepsis. We compared clinical features and outcomes of neonates who should have received antibiotics as per guideline with those who actually received them and fitted a logistic regression model to identify features associated with prescription.

Results
Data were collected between January 2021 and June 2022 from 10,868 neonates: 6,045 admitted to Sally Mugabe Central Hospital (SMCH), 1,094 to Chinhoyi Provincial Hospital (CPH) and 3,729 to Kamuzu Central Hospital (KCH). Complete implementation of national guidelines would increase antibiotics at admission: from 2,188 (38%) to 3,745 (64%) at SMCH, 472 (44%) to 852 (79%) at CPH, and 1,519 (41%) to 3,043 (82%) at KCH. Clinical features of sepsis were frequently not acted on, but the case-fatality rate was lower in those not prescribed antibiotics despite guideline recommendation. Application of WHO guidelines would increase antibiotic prescription to 91% at SMCH, 88% at CPH, and 77% in KCH. Maternal risk factors for sepsis, male gender, low birth weight, older age at admission, and spontaneous vaginal delivery were associated with higher rate of antibiotic prescription.

Conclusion
Guideline-recommended clinical signs for sepsis are inconsistently used, with clinicians using other features for antibiotic decision-making. Work is needed to revise clinical diagnostic algorithms in low-resource settings to ensure they are useful, usable and contextually appropriate.
Can we disentangle between the emission of an accretion disc around a single black hole and a circumbinary disc?
Authors: Varniere Peggy , Mignon-Risse Raphaël , Casse Fabien 
Published: February 2025

Abstract
The detection of gravitational waves from binary black holes (BBHs) started the hunt for their pre-merger electromagnetic emission. In that respect, numerical simulations have been looking for the ‘smoking gun’ signal that could help identify pre-merger systems. Here we study if any of the expected features of circumbinary discs, such as the periodic modulation from the orbiting ‘lump’, could be used to identify pre-merger BBHs or if they could be easily confused with other systems. Indeed, while the timing feature associated with the ‘lump’ seems to be present for a large part of the parameter space defined by the binary separation and mass ratio in circular binaries, it was recently proposed to form thanks to an instability occurring naturally at the edge of accretion discs around single black holes (SBH). In order to check if features of a circumbinary disc could be reproduced by a SBH system, we search for at least one SBH fit able to replicate the given synthetic observations of a circumbinary disc. We found that many of the features from a circumbinary disc can be reproduced by a SBH system with different masses, distances or inner disc positions. Interestingly, while we can always find a SBH model providing a good enough fit to the data, the presence of two variabilities, associated with the lump and the binary, or binary-lump beat, period, is a necessary condition for a wide range of BBH system parameters and should be used as a test to disqualify some BBH candidates.
Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time
Authors: Dong Xiaofeng , Matthews David A , Gallo Giulia , Darby Alistair , Donovan-Banfield I’ah , Goldswain Hannah , MacGill Tracy , Myers Todd , Orr Robert , Bailey Dalan , Carroll Miles W , Hiscox Julian A 
Published: February 2025

Abstract
In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been selected that are more transmissible and capable of partial immune escape. Currently, models for projecting the evolution of SARS-CoV-2 are based on using dominant genome sequences to forecast whether a known mutation will be prevalent in the future. However, novel variants of SARS-CoV-2 (and other viruses) are driven by evolutionary pressure acting on minor variant genomes, which then become dominant and form a potential next wave of infection. In this study, sequencing data from 96 209 patients, sampled over a 3-year period, were used to analyse patterns of minor variant genomes. These data were used to develop unsupervised machine learning clusters to identify amino acids that had a greater potential for mutation than others in the Spike protein. Being able to identify amino acids that may be present in future variants would better inform the design of longer-lived medical countermeasures and allow a risk-based evaluation of viral properties, including assessment of transmissibility and immune escape, thus providing candidates with early warning signals for when a new variant of SARS-CoV-2 emerges.
XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites
Authors: Lin Xiaohui , Leung Kay Sze Karina , Wolfe Kaitlynn F , Call Nicolas , Bhandari Seema Khattri , Huang Xiaoyu , Lee Brian J , Tomkinson Alan E , Zha Shan 
Published: February 2025

Abstract
Poly-ADP-ribose polymerases 1 and 2 (PARP1 and 2) are critical sensors of DNA-strand breaks and targets for cancer therapy. Upon DNA damage, PARP1 and 2 synthesize poly-ADP-ribose (PAR) chains on themselves and other substrates, facilitating DNA single-strand break repair by recruiting PAR-binding DNA repair factors, including X-ray repair cross-complementing group 1 (XRCC1) and aprataxin and polynucleotide kinase phosphatase-like factor (APLF). While diverse DNA lesions activate PARP1, PARP2 is selectively activated by 5′ phosphorylated nicks. They function independently and compensate for each other. Previous studies suggest that PARP1 and its PAR chains act upstream to recruit PARP2 to DNA damage sites. Here, we report that the scaffold protein XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to damage sites. XRCC1-deficiency causes hyperactivation of PARP1 while attenuating micro-irradiation-induced PARP2 foci. Mechanistically, the BRCT1 domain of XRCC1 binds to PAR, while its BRCT2 domain interacts with the PARP2 catalytic domain independently of the PARP2 enzymatic activity and the LIG3 BRCT domain via residues D575 and Y576. This mode of PARP2 enrichment is important for the recruitment of certain PAR-binding proteins, such as APLF, but dispensable for others, such as the XRCC1–BRCT1 domain. These findings highlight the distinct role of PARP1 and PARP2 in PAR synthesis and uncover unexpected hierarchical roles of PARP1 and XRCC1 upstream of PARP2.
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
Authors: Xu Zhiting , Lin Qing , Cai Xiaodian , Zhong Zhanming , Teng Jinyan , Li Bingjie , Zeng Haonan , Gao Yahui , Cai Zexi , Wang Xiaoqing , Shi Liangyu , Wang Xue , Wang Yi , Zhang Zipeng , Lin Yu , Liu Shuli , Yin Hongwei , Bai Zhonghao , Wei Chen , Zhou Jun , Zhang Wenjing , Zhang Xiaoke , Shi Shaolei , Wu Jun , Diao Shuqi , Liu Yuqiang , Pan Xiangchun , Feng Xueyan , Liu Ruiqi , Su Zhanqin , Chang Chengjie , Zhu Qianghui , Wu Yuwei , Zhou Zhongyin , Bai Lijing , Li Kui , Wang Qishan , Pan Yuchun , Xu Zhong , Peng Xianwen , Mei Shuqi , Mo Delin , Liu Xiaohong , Zhang Hao , Yuan Xiaolong , Liu Yang , Liu George E , Su Guosheng , Sahana Goutam , Lund Mogens Sandø , Ma Li , Xiang Ruidong , Shen Xia , Li Pinghua , Huang Ruihua , Ballester Maria , Crespo-Piazuelo Daniel , Amills Marcel , Clop Alex , Karlskov-Mortensen Peter , Fredholm Merete , Tang Guoqing , Li Mingzhou , Li Xuewei , Ding Xiangdong , Li Jiaqi , Chen Yaosheng , Zhang Qin , Zhao Yunxiang , Zhao Fuping , Fang Lingzhao , Zhang Zhe 
Published: February 2025

Abstract
Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology. Here, we conducted a comprehensive genome-wide association studies (GWAS) followed by cross-breed meta-analysis for 232 complex traits and within-breed meta-analysis for 12 traits, using 28.3 million imputed sequence variants in 70 328 animals across 14 pig breeds. We identified 6 878 quantitative trait loci (QTL) for 139 complex traits. Leveraging the Pig Genotype-Tissue Expression (PigGTEx) resource, we systematically investigated the biological context and regulatory mechanisms behind these trait-QTLs, ultimately prioritizing 14 829 variant-gene-tissue-trait regulatory circuits. For instance, rs344053754 regulates UGT2B31 expression in the liver and intestines, potentially by modulating enhancer activity, ultimately influencing litter weight at weaning in pigs. Furthermore, we observed conservation of certain genetic and regulatory mechanisms underlying complex traits between humans and pigs. Overall, our cross-breed meta-GWAS in pigs provides invaluable resources and novel insights into the genetic regulatory and evolutionary mechanisms of complex traits in mammals.
Financial incentives for substance abstinence: a systematic review and meta-analysis
Authors: Phillips-Chantelois Damon , Sharrad Kelsey , Perveen Shagufta , Gammatopoulos Tahlia , Usmani Nawal , Szumlinski Karen , Carson-Chahhoud Kristin 
Published: February 2025

Abstract

Introduction
Substance Use Disorder (SUD) increased by 45% globally in the past 10 years, representing one of the largest increases in risk factors for disease. Financial incentives (FI) are a promising tool to promote health behavior change, including substance abstinence. We aim to address a 10-year gap in the evidence and identify key characteristics for optimal treatment.

Methods
A meta-analysis of randomized controlled trials (RCTs) was undertaken per Cochrane guidelines and the PRISMA 2020 checklist. Medline, PsycINFO, and EMBASE were searched up to 11th September 2024. Included studies offered FI to substance users in exchange for substance abstinence compared to an alternative intervention control. The primary outcome extracted was substance abstinence at latest follow-up. Secondary outcomes such as cost-effectiveness, adverse events, and motivational assessments were also extracted. Risk of bias was analyzed using the RoB 1 tool.

Results
Of 5,042 studies identified, 246 were shortlisted for full-text review and included 39 RCTs (N = 27,845) for meta-analysis. SUD categories spanning nicotine (n = 30, OR = 1.83; 95%CI = 1.65-2.03, p &lt; .001), alcohol (n = 3, OR = 4.69, 95%CI = 1.59-13.86, p = .005), stimulants (n = 2, OR = 3.52; 95%CI = 0.36-34.18, p = 0.28), and polydrug (n = 2, OR = 3.11, 95%CI = 0.53-18.25, p = 0.21) were meta-analyzed for improving abstinence rates. Cannabis and opioid sub-groups could not be meta-analyzed. Overall effectiveness was significant for FI improving substance abstinence rates (OR=1.93, 95%CI=1.66-2.24, p&lt;.001) with continued significance through 12-month or longer follow-ups (OR=1.78; 95%CI=1.50-2.12, p&lt;.001).

Conclusions
Findings from this meta-analysis suggest that FI are an effective tool for increasing substance abstinence, particularly nicotine and alcohol, however, future research is recommended for other substances such as stimulants and opioids.

Implications
This systematic review and meta-analysis exploring the use of financial incentives for substance use disorders provides the first update on trends in this field since 2014 and the first meta-analysis since 2006. Notably, this review challenges the concerns of sustainability and effects on motivation which have withheld the clinical application of financial incentives for substance use disorders.
Embedded structure in quantum theory, functional operator and multiverse
Authors: Kawamura Yoshiharu 
Published: February 2025

Abstract
We explore a wider theoretical framework that has quantum field theory built-in, taking the fact that quantum mechanics is reconstructed from quantum field theory as a hint. We formulate a quantum theory with an embedded structure by introducing functional operators, and we find that it could describe the level II multiverse. Topics related to a beginning of the universe such as an inflation, the third quantization and the landscape are discussed in our formulation.
Biomaterials for neuroengineering: applications and challenges
Authors: Wu Huanghui , Feng Enduo , Yin Huanxin , Zhang Yuxin , Chen Guozhong , Zhu Beier , Yue Xuezheng , Zhang Haiguang , Liu Qiong , Xiong Lize 
Published: February 2025

Abstract
Neurological injuries and diseases are a leading cause of disability worldwide, underscoring the urgent need for effective therapies. Neural regaining and enhancement therapies are seen as the most promising strategies for restoring neural function, offering hope for individuals affected by these conditions. Despite their promise, the path from animal research to clinical application is fraught with challenges. Neuroengineering, particularly through the use of biomaterials, has emerged as a key field that is paving the way for innovative solutions to these challenges. It seeks to understand and treat neurological disorders, unravel the nature of consciousness, and explore the mechanisms of memory and the brain’s relationship with behavior, offering solutions for neural tissue engineering, neural interfaces and targeted drug delivery systems. These biomaterials, including both natural and synthetic types, are designed to replicate the cellular environment of the brain, thereby facilitating neural repair. This review aims to provide a comprehensive overview for biomaterials in neuroengineering, highlighting their application in neural functional regaining and enhancement across both basic research and clinical practice. It covers recent developments in biomaterial-based products, including 2D to 3D bioprinted scaffolds for cell and organoid culture, brain-on-a-chip systems, biomimetic electrodes and brain–computer interfaces. It also explores artificial synapses and neural networks, discussing their applications in modeling neural microenvironments for repair and regeneration, neural modulation and manipulation and the integration of traditional Chinese medicine. This review serves as a comprehensive guide to the role of biomaterials in advancing neuroengineering solutions, providing insights into the ongoing efforts to bridge the gap between innovation and clinical application.
Effects of psychological stress on inflammatory bowel disease via affecting the microbiota–gut–brain axis
Authors: Chen Yuhan , Chen Xiaofen , Lin Suqin , Huang Shengjun , Li Lijuan , Hong Mingzhi , Li Jianzhou , Ma Lili , Ma Juan 
Published: February 2025

Abstract
Inflammatory bowel disease (IBD) is an idiopathic intestinal inflammatory condition with chronic and relapsing manifestations and is characterized by a disturbance in the interplay between the intestinal microbiota, the gut, and the brain. The microbiota–gut–brain axis involves interactions among the nervous system, the neuroendocrine system, the gut microbiota, and the host immune system. Increasing published data indicate that psychological stress exacerbates the severity of IBD due to its negative effects on the microbiota–gut–brain axis, including alterations in the stress response of the hypothalamic–pituitary–adrenal (HPA) axis, the balance between the sympathetic nervous system and vagus nerves, the homeostasis of the intestinal flora and metabolites, and normal intestinal immunity and permeability. Although the current evidence is insufficient, psychotropic agents, psychotherapies, and interventions targeting the microbiota–gut–brain axis show the potential to improve symptoms and quality of life in IBD patients. Therefore, further studies that translate recent findings into therapeutic approaches that improve both physical and psychological well-being are needed.