bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mailed smoking cessation support for Aboriginal and Torres Strait Islander people who smoke: protocol for a hybrid type 1 effectiveness – implementation trial
Authors: Bryant Jamie , Roberts-Barker Kayden , Mills Zabowie , Booth Kade , Foster Joley , Mersha Amanual Getnet , Maddox Raglan , Chamberlain Catherine , Bonevski Billie , Segan Cathy , Taylor Nathan , Kennedy Michelle 
Published: December 2024

IntroductionSmoking is the leading preventable cause of death and the single most significant risk behaviour contributing to adverse health conditions among Aboriginal and Torres Strait Islander people. There is an urgent need for innovative approaches to support reductions in smoking prevalence. This study will assess the implementation and effectiveness of a mailed smoking cessation support programme that includes nicotine replacement therapy (NRT) (Which Way Quit Pack) for Aboriginal and Torres Strait Islander people.Methods and analysisA hybrid type 1 effectiveness—implementation trial will be conducted in Australia from 2023 to 2025. A sample of 500 Aboriginal and Torres Strait Islander people aged over 16 who smoke will be recruited using social media. All participants will: (a) receive a mailedWhich Way Quit Packthat includes pamphlets and resources on quitting, information about quit smoking support options (MyQuitBuddy App) and a selection of merchandise; (b) be offered a referral to Aboriginal Quitline; and (c) be offered a free 12-week mail out course of combination NRT. Outcome data will be obtained using quantitative surveys and qualitative Yarning. Effectiveness outcomes will include assessment of 7-day point prevalence, continuous abstinence and quit attempts at 3- and 6-month follow-up. Implementation outcomes will include assessment of recruitment and retention rates, intervention uptake and adherence, and intervention acceptability.Cessation data will be analysed using an intention-to-treat principle with all individuals lost to follow-up considered as smoking. Yarns will be analysed by Aboriginal and Torres Strait Islander members of the research team privileging Collaborative Yarning, with the support of a reflexive thematic analysis approach that will identify themes while also reflecting potential biases and perspectives of the researcher throughout the analysis process.Ethics and disseminationEthics approvals were obtained from Aboriginal Health and Medical Research Council Ethics Committee of NSW (1894/21) and the University of Newcastle (H-2022-0174). Findings will be disseminated through publications, conference presentations and sharing with relevant government bodies.Trial registration numberAustralian New Zealand Clinical Trials Registry (ACTRN12623001021662).
Cohort profile: Health and Attainment of Pupils in a Primary Education National Cohort (HAPPEN) – a hybrid total population cohort in Wales, UK
Authors: Locke Amy , Jones Hope , James Michaela , Marchant Emily , Kennedy Jonathan L , Burdett David W E , Bandyopadhyay Amrita , Stratton Gareth , Brophy Sinead 
Published: December 2024

PurposeHealth and Attainment of Pupils in a Primary Education National (HAPPEN) is a primary school national cohort which brings together education, health and well-being research in line with the Curriculum for Wales framework. Health, education and social care data are linked and held in the Secure Anonymised Information Linkage (SAIL) Databank. In addition, school-aged children complete the HAPPEN Survey to inform the design and implementation of the Health and Well-being curriculum. Over 600 schools take part in the HAPPEN Survey. Linkage of health and education records from the HAPPEN national cohort with HAPPEN Survey responses gives enriched cohort detail which can be used to extrapolate to other schools in Wales. We present the descriptive data available in HAPPEN, and the future expansion plans.ParticipantsThe HAPPEN cohort includes 37 902 primary-aged school children from 2016 to July 2023. Of this number, 28 019 can be linked in SAIL with their anonymised linkage field. In addition, to date (May 2024), HAPPEN Survey data have been captured from over 45 000 children, which can be linked to the electronic data. The survey continues to rise by 7000–8000 responses annually.Findings to dateThe cohort is 49% girls, 47% boys (3% prefer not to state their gender and 1% of this data is missing) and 14% are from an ethnic minority background (10% prefer not to state their ethnicity). Initial findings have explored the impact of COVID-19 on well-being and play opportunities, along with a longitudinal exploration of well-being throughout the years.Future plansHAPPEN is an ongoing dynamic cohort of data collection. Access to the cohort is available through SAIL. Ongoing research includes the evaluation of interventions for primary school children such as natural experiment methods, free school meal roll-out in Wales, interventions to improve physical literacy including changes to the built environment and interventions to improve the health and well-being of primary school children.
Understanding barriers and facilitators to non-pharmaceutical chronic pain research engagement among people living with chronic pain in the UK: a two-phase mixed-methods approach
Authors: Hansford Kirralise , Crossland Anna E , Baker Daniel , Preston Catherine , McKenzie Kirsten J 
Published: December 2024

ObjectivesChronic pain treatment engagement is dominated by pharmaceutical methods, while previous research has assessed barriers to uptake of non-pharmaceutical treatments, there has not been research one step earlier in the treatment development pipeline; assessing barriers to take part in research that develops non-pharmaceutical chronic pain treatment methods.DesignA two-phase approach was used to assess barriers and facilitators to research participation for people living with chronic pain. Online focus groups were run in phase 1, generating qualitative data, while phase 2 used the themes identified within phase 1 to assess agreement and disagreement.SettingParticipants consisted of people with chronic pain across the UK.Participants36 participants with chronic pain conditions (defined as any pain lasting or recurring for more than 3 months) were recruited for phase 1. Seven participants could not attend their focus group or a subsequent session, leaving a final sample size of 29 participants (83% female, 17% male; age=20–78 years, M=44.3 years). Phase 2 consisted of 103 participants (89% female, 10% male, 1% prefer not to say; age=20–80 years, M=46.6 years).ResultsPhase 1 identified the largest barrier to be ‘distrust’, relating to a distrust of medical and research professionals, distrust of confidentiality assurances and distrust that the research would have an impact. The greatest facilitator identified was ‘improved accessibility’, which related to the accessibility of the research environment, the type of research being conducted and accessible advertisement of the research within trusted settings. Phase 2 found around 80% agreement with all facilitator themes and a mix of opinions regarding barrier themes, highlighting the individuality of barriers experienced when living with chronic pain.ConclusionsAddressing the barriers and implementing the facilitators identified here ensures that patient participants are comfortable and safe within research environments. Furthermore, this project provides recommendations for researchers to follow to help increase patient engagement in research studies.
Pranayama (yogic breathing practices) in Parkinson’s disease: protocol for a scoping review of literature
Authors: Rao Prajwal , Agarwal Dhiraj , Rohatgi Shalesh , Chaturvedi Sarika 
Published: December 2024

IntroductionParkinson’s disease is a neurodegenerative disorder that presents with motor symptoms such as tremors, slowness and gait difficulties, in addition to various non-motor symptoms such as anxiety, depression and autonomic and sleep disturbances. Pranayama (yogic breathing practices) has been studied as a part of yoga interventions in Parkinson’s disease. Previous systematic reviews and meta-analyses have not detailed the pranayama practices used in clinical studies, and there is no clarity on the pranayama practices that would be most beneficial for Parkinson’s disease. This scoping review aims to map the available scientific evidence on the effect of pranayama interventions for Parkinson’s disease and identify the potential gaps in the literature.Methods and analysisA literature search will be conducted in major databases (JBI evidence synthesis, MEDLINE, Cochrane Library, including Cochrane Complimentary Medicine, and Scopus) from 1990 to date. Relevant grey literature will be searched. Two independent reviewers will initially review the extracted articles and will be further adjudicated by two independent reviewers. Data management will be done using Rayyan software throughout the review. Data extracted will include specific details of the population, concept, context and study methods specific to the scoping review objectives. The extracted data will be presented in tabular/diagrammatic form, reporting on items aligning with the review objectives, such as details of the pranayama intervention and its clinical outcomes. A narrative summary will accompany the tabulated results, identifying the gaps in evidence and areas for future research.Ethics and disseminationEthics approval is not required for this scoping review. The findings will be disseminated through publications in peer-reviewed journals and conference presentations.Trial registration numberProtocol Registration in Open Science Framework -https://osf.io/jdwga/?view_only=82aa5afd46974416a402fa1a0ac39fce
Experience, access and utilisation of fertility care for infertile men within the biomedical sector in urban Bangladesh: protocol for a qualitative study
Authors: Nahar Papreen , Shafique Sohana , Satalkar-Götz Priya , Sultana Foyjunnaher , Mburu Gitau 
Published: December 2024

IntroductionOne in six people of reproductive age experience infertility in their lifetime throughout the world, often with devastating consequences. Men are often invisible in infertility research and services, yet masculinity and reproductive agency intersect within social, cultural and religious contexts to shape their experiences of infertility and masculine expression. This study aims to provide insights into the lived experience of male infertility, the availability and access of infertility services for men within the biomedical sector in Bangladesh and the potential willingness of men to use home-based semen testing.Methods and analysisThis qualitative study will be conducted in Dhaka and Khulna districts in Bangladesh over 18 months (late 2023–2025). A total of 35 biomedically diagnosed infertile men will be selected for interview using convenience sampling. Additionally, 25 key informants, including healthcare providers from public and private fertility clinics and health policymakers, will be interviewed. Service availability will be documented by creating a list of fertility clinics and cataloguing services offered in a selection of these clinics. Both inductive and deductive thematic analysis will be used.Ethics and disseminationThe study has been reviewed and approved by the Brighton and Sussex Medical School’s Research and Governance Ethics Committee (RGEC: ER/BSMS9E3G/1), Institutional Review Board of icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh) and the WHO Ethics Review Committee (WHO ERC, AID: A66040). A comprehensive participant information sheet containing the study aims, objectives and data collection procedures will be provided to eligible participants and informed consent obtained. Two dissemination workshops will be held, one with the community at the field level and another with the key stakeholders, that is policymakers, health service and clinical stakeholders to disseminate the results of the study and its implications for fertility care for men with infertility in Bangladesh and other low- and middle-income countries. Scientific manuscripts will be published in open-access journals to inform the global community.
Negotiation of new international health law on intellectual property, technology transfer, open science and pathogen access and benefit sharing: a textual and contextual analysis
Authors: de Beer Jeremy , De Koker Rosa 
Published: December 2024

IntroductionThis original research article reframes new international law and policy developments at the intersections of open science, technology transfer, intellectual property and access and sharing the benefits of biomedical innovation in the context of global pandemics.MethodsThrough textual and contextual analysis, using the lens of national experiences and negotiating positions of one high-income country, Canada, it traces the evolution of legal normative developments from a proposed waiver of aspects of the World Trade Organisation Agreement on Trade-Related Aspects of Intellectual Property Rights through a forum shift to negotiate a new agreement for pandemic preparedness and response (the Pandemic Agreement) at the WHO.ResultsThe analysis shows a significant evolution of treaty provisions on R&D, sustainable and diversified production of pandemic-related products, transfer of technology and know-how and access and benefit sharing. Juxtaposed against a Canadian parliamentary report, stakeholder consultations and Canada’s stated commitment to equity, the negotiating texts reflect major compromises on the key issues. High-income countries sought open access to pathogen gene sequence data crucial for pandemic prevention, preparedness and response while resisting measures other than voluntarily licensing on mutually agreed terms of private intellectual property rights derived from the use of such data or other publicly funded research. Low- and middle-income countries, meanwhile, were offered diluted language on technology transfer in exchange for a new pathogen access and benefit-sharing scheme.ConclusionsThe practical effects of these compromises remain to be seen, but they risk exacerbating rather than ameliorating global health inequities.
Preclinical model for evaluating human TCRs against chimeric syngeneic tumors
Authors: Semilietof Aikaterini , Stefanidis Evangelos , Gray-Gaillard Elise , Pujol Julien , D'Esposito Alessia , Reichenbach Patrick , Guillaume Philippe , Zoete Vincent , Irving Melita , Michielin Olivier 
Published: December 2024

BackgroundThe adoptive cell transfer (ACT) of T cell receptor (TCR)-engineered T cells targeting the HLA-A2-restricted epitope NY-ESO-1157-165(A2/NY) has yielded important clinical responses against several cancers. A variety of approaches are being taken to augment tumor control by ACT including TCR affinity-optimization and T-cell coengineering strategies to address the suppressive tumor microenvironment (TME). Most TCRs of clinical interest are evaluated in immunocompromised mice to enable human T-cell engraftment and do not recapitulate the dynamic interplay that occurs with endogenous immunity in a treated patient. A variety of humanized mouse models have been described but they have limitations in immune reconstitution and are technically challenging to implement. Here, we have developed a chimeric syngeneic tumor model in which A2Kb transgenic C57BL/6 mice are engrafted with B16 expressing A2Kb:NY as a single chain trimer (SCT) and treated by ACT with murine T cells expressing A2/NY TCRs comprising human variable fused to mouse constant regions.MethodsWe compared the function of a supraphysiological affinity A2/NY TCR (wtc51m), a computationally designed TCR in an optimal affinity range (DMβ), and a near non-binding TCR (V49I), engineered in both primary human and murine T cells by lentiviral and retroviral transduction, respectively. We evaluated a variety of strategies to stably express A2Kb:NY on the surface of mouse tumor cell lines including B16 melanoma, ultimately achieving success with an SCT comprising human β2m fused by GS linkers to both the NY-peptide and to α1 of the HLA complex. ACT studies were performed in B16-A2Kb:NY tumor-bearing, non-preconditioned immune-competent HLA-A*0201/H-2Kb (A2Kb) transgenic C57BL/6 mice and tumors characterized post-transfer.ResultsWe observed significantly improved function of DMβ-T cells as well as superior infiltration and tumor control upon ACT as compared to the control TCR-T cells. Moreover, with our chimeric syngeneic tumor model, we were able to track dynamic and favorable changes in the TME upon DMβ-T cell transfer.ConclusionsWe have developed a robust, simple, and inexpensive preclinical strategy for evaluating human TCRs in the context of a fully competent murine immune system that can aid in the development of coengineered TCR-T cells and combination treatments translated to the clinic.
From Triumph to Uncertainty: The Journey of Software Engineering in the AI Era
Authors: Mastropaolo Antonio , Escobar-Velásquez Camilo , Linares-Vásquez Mario 
Published: December 2024

Over the last ten years, the realm of Artificial Intelligence (AI) has experienced an explosion of revolutionary breakthroughs, transforming what seemed like a far-off dream into a reality that is now deeply embedded in our everyday lives. AI’s widespread impact is revolutionizing virtually all aspects of human life, and software engineering (SE) is no exception. As we explore this changing landscape, we are faced with questions about what the future holds for SE and how AI will reshape the roles, duties, and methodologies within the field. The introduction of these groundbreaking technologies highlights the inevitable shift towards a new paradigm, suggesting a future where AI’s capabilities may redefine the boundaries of SE, potentially even more than human input.
In this paper, we aim at outlining the key elements that, based on our expertise, are vital for the smooth integration of AI into SE, all while preserving the intrinsic human creativity that has been the driving force behind the field. First, we provide a brief description of SE and AI evolution. Afterward, we delve into the intricate interplay between AI-driven automation and human innovation, exploring how these two components can work together to advance SE practices to new methods and standards.
Effect of Calcium Hydroxide Versus Double Antibiotic Paste on Endodontic Treatment Outcomes in Teeth With Large Periapical Lesions: A Triple‐Blind Randomized Clinical Trial
Authors: Rahmati Afsaneh , Seyedein Farshad , Dianat Omid , Saedi Sara , Rostami Golriz , Akbarzadeh Baghban Alireza , Sabertahan Shima , Kazem Majid 
Published: December 2024

Objective: The successful management of necrotic pulps and apical periodontitis poses a tough challenge in endodontic therapy, as it involves addressing compromised tooth vitality and microbial invasion of root canal systems. Failure to effectively treat these conditions can lead to persistent infection and severe patient discomfort. The efficacy of double antibiotic paste (DAP), a mixture of ciprofloxacin and metronidazole, was evaluated and compared to calcium hydroxide (CH) by assessing radiographic and clinical outcomes of nonsurgical endodontic treatment in cases with necrotic pulps and the presence of apical periodontitis.Methods: Thirty maxillary anterior teeth with necrotic pulps and apical periodontitis (periapical index [PAI] = 5) were divided randomly into two experimental groups. The first group received CH dressing, while the other group filled with DAP as intracanal medicament. After 3 weeks, medicaments were removed, and teeth were obturated in both groups. Teeth were assessed clinically and radiographically at 6‐month and 12‐month follow‐ups. A chi‐square test was performed to compare the outcome between the groups.Results: None of the teeth showed complete healing in a 6‐month follow‐up. At the 12‐month follow‐up, six samples in the DAP group showed complete healing of the periapical (PA) lesion, while none of the samples in the CH group were completely healed. The PA healing outcome was as follows: in the DAP group, 40% of cases were healed, 60% healing, and 0% diseased, while in the CH group, 0% healed, 93.3% healing, and 6.7% diseased. The results of the two experimental groups in 12 months differed significantly (p  < 0.05).Conclusion: DAP group has shown significantly better outcomes compared to CH as intracanal medicament in the treatment of teeth with PA lesions. This finding suggests that DAP may offer a more effective therapeutic approach in managing necrotic pulps and apical periodontitis, potentially improving patient outcomes and treatment success rates.Trial Registration: Clinical Trial Registry identifier: IRCT2015060822615N1
Longitudinal Glioma Monitoring via Cerebrospinal Fluid Cell-Free DNA
Authors: Riviere-Cazaux Cecile , Dong Xiaoxi , Mo Wei , Kumar Rahul , Dai Chao , Carlstrom Lucas P. , Munoz-Casabella Amanda , Ghadimi Keyvan , Nesvick Cody L. , Andersen Katherine M. , Hoplin Matthew D. , Canaday Nicholas , Jusue-Torres Ignacio , Malik Noor , Campian Jian L. , Ruff Michael W. , Uhm Joon H. , Eckel Passow Jeanette E. , Kaufmann Timothy J. , Routman David M. , Kizilbash Sani H. , Sener Ugur , Warrington Arthur E. , Jenkins Robert B. , Du Pan , Jia Shidong , Burns Terry C. 
Published: December 2024

Abstract

Purpose:
Current methods for glioma response assessment are limited. This study aimed to assess the technical and clinical feasibility of molecular profiling using longitudinal intracranial cerebrospinal fluid (CSF) from patients with gliomas.

Experimental Design:
Adults with gliomas underwent longitudinal intracranial CSF collection via Ommaya reservoirs or ventriculoperitoneal shunts. Cell-free DNA (cfDNA) was extracted and analyzed using PredicineCARE for cancer variant profiling and/or PredicineSCORE for low-pass whole-genome sequencing.

Results:
Five patients (two females and three males; median age, 40 years; range, 32–64 years) underwent longitudinal intracranial CSF collection via Ommaya reservoirs (n = 4) or ventriculoperitoneal shunts (n = 1). In total, 47 CSF samples were obtained (median volume, 4.00 mL; 0.5–5 mL). Forty-one samples (87.2%) yielded sufficient cfDNA for testing. Patient-specific tumor-associated variant allelic frequencies (VAF), and thus tumor fraction, decreased in pre- versus postchemoradiation samples, including through pseudoprogression. These also increased with radiographic progression in three patients, although identifying the time of definitive disease progression from MRIs was a significant limitation. In two patients with isocitrate dehydrogenase (IDH)–mutant gliomas, decreasing IDH1 VAF after resection and chemoradiation correlated with decreased CSF D-2-hydroxyglutarate levels (0.64× and 0.62×, respectively, for the first patient and 0.01× and 0.07× for the other patient), although D-2-hydroxyglutarate and IDH1 VAF were not concordant in one patient thereafter. Moreover, the copy-number burden decreased below the limit of quantification during treatment and increased above the limit at progression.

Conclusions:
Longitudinal intracranial CSF cfDNA can be obtained in patients with gliomas during their disease course. However, before deploying this technique, numerous questions and challenges should be answered.