bluuebunny/crossref_metadata_2025_split huggingface dataset:
“We’re here to help them if they want to come”: A qualitative exploration of hospital staff perceptions and experiences with outpatient non-attendance
Authors: Selim Shayma Mohammed , McPhail Steven M , Carter Hannah E , Malatzky Christina , Kularatna Sanjeewa , Naicker Sundresan 
Published: September 2024

AbstractBackgroundPatient non-attendance remains a major challenge for health services. Few studies have examined how health service providers think about, potentially address, and prioritise non-attendance within the scope of their practice. This study aimed to (1) explore healthcare professionals’ perspectives, beliefs, and opinions about the impact of patient non-attendance within a publicly-funded outpatient physiotherapy clinic context; (2) explore perceived barriers and facilitators associated with the implementation of non-attendance mitigation strategies; and (3) identify health service staff generated solutions to address perceived barriers and enhance facilitators.MethodsA focus group discussion and semi-structured interviews were conducted between June 2023 to January 2024 with 27 physiotherapy department clinic outpatient staff involved in operationalising clinic referral processing, appointment scheduling, or providing care to patients. Data was analysed using a hybrid inductive/deductive framework analysis approach.ResultsParticipants indicated that non-attendance had predominantly negative implications for the health service, healthcare provider, and patient. The interconnected issue of non-attendance encompassed multiple areas and were broadly categorised into five inductively identified themes: impact of non-attendance, perceptions of value, material deprivation, service delivery and built environment, and professional role and identity. Non-attendance mitigation strategies generated by participants were deductively mapped to the theoretical domains framework (TDF) to explore behavioural determinants that may influence successful implementation. This included knowledge, reinforcement, goals, optimism, memory, attention and decision-making, environmental resources and context, and emotions.ConclusionsStaff identified multiple strategies for reducing non-attendance; implementing many of these strategies would require additional resourcing. Research determining the effectiveness of such strategies both in the short-term and long-term following implementation into practice remains a priority for future investigation.
CelloType: A Unified Model for Segmentation and Classification of Tissue Images
Authors: Pang Minxing , Roy Tarun Kanti , Wu Xiaodong , Tan Kai 
Published: September 2024

AbstractCell segmentation and classification are critical tasks in spatial omics data analysis. We introduce CelloType, an end-to-end model designed for cell segmentation and classification of biomedical microscopy images. Unlike the traditional two-stage approach of segmentation followed by classification, CelloType adopts a multi-task learning approach that connects the segmentation and classification tasks and simultaneously boost the performance of both tasks. CelloType leverages Transformer-based deep learning techniques for enhanced accuracy of object detection, segmentation, and classification. It outperforms existing segmentation methods using ground-truths from public databases. In terms of classification, CelloType outperforms a baseline model comprised of state-of-the-art methods for individual tasks. Using multiplexed tissue images, we further demonstrate the utility of CelloType for multi-scale segmentation and classification of both cellular and non-cellular elements in a tissue. The enhanced accuracy and multi-task-learning ability of CelloType facilitate automated annotation of rapidly growing spatial omics data.
Plaintiff experiences of the medico-legal environment in Ireland
Authors: McCarthy Suzanne , Donnelly Mary , Joy Aislinn , Lehane Elaine , O’Sullivan Peter , Spain Eimear 
Published: September 2024

AbstractIntroductionThe recent surge in clinical claims in Ireland has sparked concerns about the unsustainable trajectory of medical negligence litigation. Current evaluations have primarily focused on the financial and temporal aspects of litigation, leaving a gap in understanding the experiences of plaintiffs within the adversarial system. This study aims to fill this gap by critically exploring the experiences of those affected by medical negligence and the ensuing legal process.MethodsA qualitative descriptive approach was employed to explore the experiences of plaintiffs following patient safety incidents and their interactions with the legal process. Semi-structured, open-ended interviews were conducted with participants who had been involved in medical negligence litigation in Ireland. Participants were eligible for inclusion if they were aged 18 years or over and were involved in medical negligence litigation in Ireland (as a plaintiff), whether the case was resolved by negotiated settlement, a form of alternative dispute resolution (e.g. mediation), or trial hearing. Maximum variation sampling was used to capture a diverse range of experiences, with sample size determined by the concept of ‘information power.’ Recruitment was facilitated by the Health Service Executive (HSE) through invitations sent by The National Open Disclosure Office. Interviews were conducted in-person or online, recorded, transcribed, and analysed thematically. Ethical approval was obtained from the Social Research Ethics Committee of University College Cork.FindingsThis research presents the views and experiences of fifteen participants; eleven participants shared their experiences relating to an adverse event which impacted a family member (one participant spoke about two family members), nine of whom were children (including both minors and adult children), and three were a spouse. Of the twelve individuals discussed, eight were deceased. Five main themes were identified from the analysis: i) Navigating the aftermath of a patient safety event: Communication, Support and Abandonment; ii) The pathway from adverse event to litigation; iii) Experiences of the Legal System; iv) Emotional and Mental Health Impact of Litigation on Plaintiffs; v) Advocating for Change: Participant Recommendations.DiscussionThis research highlights the profound impact of actions taken after a patient safety event on patients, families, healthcare professionals, and organisations, and the importance of Open Disclosure in meeting ethical obligations and ensuring healthcare accountability. It explores the complex relationships between financial compensation, justice-seeking, and the healthcare and legal systems. The findings contribute significant insights to the discourse on medical negligence in Ireland.
Access to Allogeneic Cell Transplantation Based on Donor Search Prognosis: An Interventional Trial
Authors: Dehn Jason G. , Logan Brent , Shaw Bronwen E. , Devine Steven , Ciurea Stefan O. , Horowitz Mary , He Naya , Pusic Iskra , Srour Samer A. , Arai Sally , Juckett Mark , Uberti Joseph , Hill LaQuisa , Vasu Sumithira , Hogan William J. , Hayes-Lattin Brandon , Westervelt Peter , Bashey Asad , Farhadfar Nosha , Grunwald Michael R. , Leifer Eric , Symons Heather , Saad Ayman , Vogel Jenny , Erickson Connor , Buck Kelly , Lee Stephanie J. , Pidala Joseph 
Published: September 2024

ABSTRACTImportancePatients requiring allogeneic hematopoietic cell transplantation have variable likelihoods of identifying an 8/8 HLA-matched unrelated donor. A Search Prognosis calculator can estimate the likelihood.ObjectiveTo determine if using a search algorithm based on donor search prognosis can result in similar incidence of transplant between patients Very Likely (>90%) vs Very Unlikely (<10%) to have a matched unrelated donor.DesignThis interventional trial utilized a Search Prognosis-based biologic assignment algorithm to guide donor selection. Trial enrollment from June 13, 2019-May 13, 2022; analysis of data as of September 7, 2023 with median follow-up post-evaluability of 14.5 months.SettingsNational multi-center Blood and Marrow Transplantation Clinical Trials Network 1702 study of US participating transplant centers.ParticipantsAcute myeloid and lymphoid leukemias, myelodysplastic syndrome, Hodgkin’s and non-Hodgkin’s lymphomas, severe aplastic anemia, and sickle cell disease patients referred to participating transplant centers were invited to participate. 2225 patients were enrolled and 1751 were declared evaluable for this study. Patients were declared evaluable once it was determined no suitable HLA-matched related donor was available.InterventionPatients assigned to the Very Likely arm were to proceed with matched unrelated donor, while Very Unlikely were to utilize alternative donors. A third stratum, Less Likely (∼25%) to find a matched unrelated donor, were observed under standard center practices, but were not part of the primary objective.Main OutcomeCumulative incidence of transplantation by Search Prognosis armResultsEvaluable patients included 1751 of which 413 (24%) were from racial/ethnic minorities. Search prognosis was 958 (55%) Very Likely, 517 (30%) Less Likely and 276 (16%) Very Unlikely. 1171 (67%) received HCT, 384 (22%) died without HCT, and 196 (11%) remained alive without HCT. Among the 1,234 patients, the adjusted cumulative incidence (95% CI) of HCT at 6-months was 59.8% (56.7-62.8) in the Very Likely group versus 52.3% (46.1-58.5) in the Very Unlikely (P=0.113).ConclusionsA prospective Search Prognosis-based algorithm can be effectively implemented in a national multicenter clinical trial. This approach resulted in rapid alternative donor identification and comparable rates of HCT in patients Very Likely and Very Unlikely to find a matched unrelated donor.Trial Registration:NCT#03904134
No Increased Risk of Major Adverse Cardiovascular Events following Nicotinamide Exposure
Authors: Wheless Lee , Guennoun Ranya , Michalski-McNeely Basia , Gonzalez Katlyn M , Weiss Rachel , Zhang Siwei , Yao Lydia , Madden Chris , Chen Hua-Chang , Triozzi Jefferson L , Tao Ran , Wilson Otis , Wells Quinn S , Hung Adriana , Bibee Kristin , Hartman Rebecca I , Xu Yaomin ,   VA Million Veteran Program
Published: September 2024

ABSTRACTIMPORTANCENicotinamide metabolites have recently been implicated in increased risk of major cardiovascular events (MACE). Supportive data about clinical risk of MACE for nicotinamide users is lacking.OBJECTIVETo determine whether nicotinamide use results in an increase of MACE.DESIGN, SETTING, PARTICIPANTSRetrospective cohort study of two patient cohorts, Vanderbilt University Medical Center (VUMC) and Military Veteran Program (MVP). The risk of MACE in patients exposed to nicotinamide was compared to the risk of MACE in unexposed patients. In the VUMC cohort, 1228 patients were exposed to nicotinamide based on keyword entry for “nicotinamide” or “niacinamide” and hand-review of charts, while 253 were unexposed but had documented recommendation for use. In the MVP cohort, there were 1594 with exposure to nicotinamide propensity score matched to 2694 without exposure.EXPOSURESThe primary exposure for the VUMC cohort was a confirmed exposure to nicotinamide in chart review. The primary exposure for the MVP cohort was medication entry for “nicotinamide” or “niacinamide”.MAIN OUTCOME(S) AND MEASURE(S)The primary outcome was development of MACE based on a validated phenotype.RESULTSBetween both cohorts, 6039 patients were included, of whom 5125 were male with a mean age of 63.2 years. Neither cohort had significant differences in mean age, sex, race and ethnicity between the nicotinamide exposed and unexposed groups. In the VUMC cohort, there was no significant association between nicotinamide exposure and the primary outcome of MACE (HR 0.76, 95% CI 0.46 – 1.25, p = 0.28). MACE prior to nicotinamide exposure was strongly associated with subsequent MACE (HR 9.01, 95% CI 5.90 – 13.70, p < 0.001). In the MVP cohort, we adjusted for MACE risk factors as potential confounding variables and saw no significant association between nicotinamide exposure and MACE (HR 1.00 95% CI 0.75 – 1.32), while history of prior MACE remained strongly associated with subsequent MACE (HR 9.50, 95% CI 6.38 – 14.1).CONCLUSIONS AND RELEVANCEIn this retrospective cohort study of 6039 adults from two different patient populations, we found no increased risk of MACE in patients with nicotinamide exposure.
Biological markers of brain network connectivity and pain sensitivity distinguish low coping from high coping Veterans with persistent post-traumatic headache
Authors: Monroe Katrina S. , Schiehser Dawn M. , Parr Aaron W. , Simmons Alan N. , Hays Weeks Chelsea C. , Bailey Barbara A. , Shahidi Bahar 
Published: September 2024

AbstractHeadache is the most common type of pain following mild traumatic brain injury. Roughly half of those with persistent post-traumatic headache (PPTH) also report neck pain which is associated with greater severity and functional impact of headache. This observational cohort study aimed to identify biological phenotypes to help inform mechanism-based approaches in the management of PPTH with and without concomitant neck pain. Thirty-three military Veterans (mean (SD) = 37±16 years, 29 males) with PPTH completed a clinical assessment, quantitative sensory testing, and magnetic resonance imaging of the brain and cervical spine. Multidimensional phenotyping was performed using a Random Forest analysis and Partitioning Around Medoids (PAM) clustering of input features from three biologic domains: 1) resting state functional connectivity (rsFC) of the periaqueductal gray (PAG), 2) quality and size of cervical muscles, and 3) mechanical pain sensitivity and central modulation of pain. Two subgroups were distinguished by biological features that included forehead pressure pain threshold and rsFC between the PAG and selected nodes within the default mode, salience, and sensorimotor networks. Compared to the High Pain Coping group, the Low Pain Coping group exhibited higher pain-related anxiety (p=0.009), higher pain catastrophizing (p=0.004), lower pain self-efficacy (p=0.010), and greater headache-related disability (p=0.012). Findings suggest that greater functional connectivity of pain modulation networks involving the PAG combined with impairments in craniofacial pain sensitivity, but not cervical muscle health, distinguish a clinically important subgroup of individuals with PPTH who are less able to cope with pain and more severely impacted by headache.
Explicit solution of the SVIR (Susceptible-Vaccinated-Infectious-Recovered) epidemic model
Authors: Yoshida Norio 
Published: September 2024

AbstractAn explicit solution of an initial value problem for the Susceptible-Vaccinated-Infectious-Recovered (SVIR) epidemic model is obtained, and various properties of the explicit solution are investigated. It is shown that the parametric form of the explicit solution satisfies some linear differential system including a positive solution of an integral equation. In this paper integral equations play an important role in establishing the explicit solution of the SVIR epidemic model, in particular, the number of infected individuals can be represented in a simple form by using a positive solution of an integral equation. Uniqueness of positive solutions of the SVIR epidemic model is also investigated, and it is shown that the explicit solution is a unique solution in the class of positive solutions.
Sidechain chemistry-encoded solid/liquid phase transitions of condensates
Authors: Chen Feipeng , Han Yongxu , Li Xiufeng , Guo Wei , Wu Changjin , Xia Jiang , Zeng Xiangze , Shum Ho Cheung 
Published: September 2024

AbstractNature effectively leverages multivalent interactions among fundamental building blocks in solvents to create remarkable materials for various purposes. One prominent example is the formation of biomolecular condensates through the phase separation of proteins and nucleic acids. In particular, these condensates play crucial roles in regulating cellular functions and constructing natural materials. During the phase separation, solvents not only provide liquid environments for solvating molecules but play crucial roles in affecting the material properties of condensates. However, it remains controversial in the literature that alcohol molecules, as one type of solvents, can solidify some condensates while also melting others, leading to liquid-to-solid phase transition (LSPT) or solid-to-liquid phase transitions (SLPT), respectively. The mechanism underlying the alcohol-induced solid/liquid phase transitions of condensates remains poorly understood. Here, we combine systematic experimental characterizations with molecular dynamics simulations to demonstrate that the phase transitions of condensates depend on their sidechain chemistry and dominant molecular interactions. Specifically, “hydrophilic” condensates, which consist of many charged sidechains, undergo LSPT by adding alcohols due to strengthened electrostatic interactions. In contrast, “hydrophobic” condensates comprised of abundant aromatic sidechains undergo SLPT with the addition of alcohols because of weakened cation-π and π-π interactions. Importantly, these findings are generally applicable for predicting phase transitions of a wide range of condensates formed by synthetic polyelectrolytes and intrinsically disordered proteins based on their sidechain hydrophobicity or amino acid compositions. Our work not only reconciles a conundrum in the literature but provides a fundamental framework for understanding the responsiveness of condensates to environmental stimuli. These insights are instrumental for developing therapeutic drugs to treat pathological aggregates and engineering stimuli-responsive biomaterials from the perspective of sidechain chemistry and molecular interactions.
A single ancestralANP32locus in ticks creates multiple protein variants that all support the Thogoto virus polymerase
Authors: Zhang Zhenyu , Nipper Thomas , Aziati Ishmael D. , Boon Adrianus C. M. , Mehle Andrew 
Published: September 2024

AbstractViral polymerases rely on cellular cofactors to support efficient transcription of viral genes and replication of the viral genome. The RNA-dependent RNA polymerase of influenza virus, an orthomyxovirus, requires cellular ANP32A or ANP32B proteins for genome replication. However, little is known about whether ANP32 proteins are required by other orthomyxoviruses like the tick-borne thogotoviruses. Recent structural studies coupled with functional assays suggested that the Thogoto virus polymerase uses both ANP32A and ANP32B from brown dog ticks. We clarify here that this tick vector encodes a singleANP32locus corresponding toANP32A. This single gene produces multiple protein variants through alternative splicing and start-site selection, all of which enhance Thogoto virus polymerase. Thogoto virus polymerase activity is also enhanced by human and chicken ANP32 proteins. Thus, ANP32A is a deeply conserved pro-viral cofactor and Thogoto virus shows remarkable plasticity utilizing ANP32 homologues separated by almost 1 billion years of evolution.
Engineering Rubisco Condensation in Chloroplasts to Manipulate Plant Photosynthesis
Authors: Chen Taiyu , Hojka Marta , Davey Philip , Sun Yaqi , Zhou Fei , Lawson Tracy , Nixon Peter J. , Lin Yongjun , Liu Lu-Ning 
Published: September 2024

AbstractAlthough Rubisco is the most abundant enzyme globally, it is inefficient for carbon fixation because of its low turnover rate and limited ability to distinguish CO2and O2, especially under high O2conditions. To address these limitations, phytoplankton, including cyanobacteria and algae, have evolved CO2-concentrating mechanisms (CCM) that involve compartmentalizing Rubisco within specific structures, such as carboxysomes in cyanobacteria or pyrenoids in algae. Engineering plant chloroplasts to establish similar structures for compartmentalizing Rubisco has attracted increasing interest for improving photosynthesis and carbon assimilation in crop plants. Here, we present a method to effectively induce the condensation of endogenous Rubisco within tobacco (Nicotiana tabacum) chloroplasts by genetically fusing superfolder green fluorescent protein (sfGFP) to the tobacco Rubisco large subunit (RbcL). By leveraging the intrinsic oligomerization feature of sfGFP, we successfully created pyrenoid-like Rubisco condensates that display dynamic, liquid-like properties within chloroplasts without affecting Rubisco assembly and catalytic function. The transgenic tobacco plants demonstrated comparable autotrophic growth rates and full life cycles in ambient air relative to the wild-type plants. Our study offers a promising strategy for modulating endogenous Rubisco assembly and spatial organization in plant chloroplasts via phase separation, which provides the foundation for generating synthetic organelle-like structures for carbon fixation, such as carboxysomes and pyrenoids, to optimize photosynthetic efficiency.
Causal associations between plasma proteins and prostate cancer: a Proteome-Wide Mendelian Randomization
Authors: Lin Chen , Zhuona Rong , Yanlun Gu , Yuke Chen , Wei Yu , Ying Zhou , Xiaocong Pang 
Published: September 2024

AbstractBackgroundDue to the limitations in specificity of current diagnostic methods for prostate cancer (PCa), more reliable biomarkers are needed to explore for improving early detection. Plasma proteins represent a promising source of biomarkers, therefore understanding the causal relationships between specific plasma proteins and PCa could be conductive to identify novel biomarkers and therapeutic targets for PCa prevention and treatment.MethodsWe performed a meta-analysis of two independent genome-wide association studies (GWASs) including 94,397 individuals with PCa and 192,372 controls. A mendelian randomization (MR) supplemented by colocalization analysis was conducted, usingcis-acting variants on 4,907 plasma proteins from deCODE Genetics (N=35,559) and 2,940 plasma proteins from UK Biobank Pharma Proteomics Project (UKB-PPP) (N=54,219). Then, the biological pathway analysis and druggability evaluation of the risk proteins were further performed.ResultsFive possible susceptibility loci (JAZF1, PDILM5, WDPCP, EEFSEC, and TNS3) for PCa were identified through the meta-analysis of GWASs. Among 3,722 plasma proteins, 193 proteins were associated with PCa risk, of which 20 high-risk proteins, including KLK3, were validated in both the deCODE and UKB-PPP cohorts. Functional annotation of these genes encoding proteins confirmed enrichment of immune response, inflammatory response, cell-cell interaction and so on. Genetic colocalization and druggable genome analyses also identified several potential drug targets for PCa, such as HSPB1, RRM2B and PSCA.ConclusionsWe identified novel variants as well as several protein biomarkers linked to PCa risk and indicated pathways associated with PCa, which offered new insights into PCa etiology and contributed to development of novel biomarkers for early detection and potential therapeutic interventions.FundingThis work was supported by grants from Beijing Municipal Natural Science Foundation (grant No. JQ24059, No. L234038) and National Natural Science Foundation of China (grant No. 82274015).Graphical abstractA comprehensive study design summarized as follows.Abstract Figure