bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piloting a minimum data set for older people living in care homes in England: a developmental study
Authors: Gordon Adam L , Rand Stacey , Crellin Elizabeth , Allan Stephen , Tracey Freya , De Corte Kaat , Lloyd Therese , Brine Richard , Carroll Rachael E , Towers Ann-Marie , Burton Jennifer Kirsty , Akdur Gizdem , Hanratty Barbara , Webster Lucy , Palmer Sinead , Jones Liz , Meyer Julienne , Spilsbury Karen , Killett Anne , Wolters Arne T , Peryer Guy , Goodman Claire 
Published: January 2025

Abstract

Background
We developed a prototype minimum data set (MDS) for English care homes, assessing feasibility of extracting data directly from digital care records (DCRs) with linkage to health and social care data.

Methods
Through stakeholder development workshops, literature reviews, surveys and public consultation, we developed an aspirational MDS. We identified ways to extract this from existing sources, including DCRs and routine health and social care datasets. To address gaps, we added validated measures of delirium, cognitive impairment, functional independence and quality of life to DCR software. Following routine health and social care data linkage to DCRs, we compared variables recorded across multiple data sources, using a hierarchical approach to reduce missingness where appropriate. We reported proportions of missingness, mean and standard deviation (SD) or frequencies (%) for all variables.

Results
We recruited 996 residents from 45 care homes in three English Integrated Care Systems. 727 residents had data included in the MDS. Additional data were well completed (&lt;35% missingness at wave 1). Competition for staff time, staff attrition and software-related implementation issues contributed to missing DCR data. Following data linkage and combining variables where appropriate, missingness was reduced (≤4% where applicable).

Discussion
Integration of health and social care is predicated on access to data and interoperability. Despite governance challenges we safely linked care home DCRs to statutory health and social care datasets to create a viable prototype MDS for English care homes. We identified issues around data quality, governance, data plurality and data completion essential to MDS implementation going forward.
Diagnostic utility of lymphocyte enhancer factor 1 in aggressive B-cell lymphoma with MYC rearrangement
Authors: Wang Xin , Faraz Maria , Chen Anne , Nazeer Tipu , Huang Xiaoyan 
Published: January 2025

Abstract

Objectives
We sought to investigate the diagnostic value of lymphocyte enhancer factor 1 (LEF1) expression in aggressive B-cell lymphomas (BCL) with MYC gene rearrangement (MYC-R).

Methods
Sixty-seven cases of BCL were studied and included Burkitt lymphoma (BL) (23 cases); diffuse large B-cell lymphoma (DLBCL), not otherwise specified (NOS) with MYC-R (13 cases); and DLBCL/high-grade B-cell lymphoma with MYC, BCL2, and/or BCL6 rearrangements (double-hit [DH] or triple-hit [TH], 17 cases). Random DLBCL-NOS (14 cases) without MYC-R was recruited as a control group. By immunohistochemical stains, 3 patterns of LEF1 staining were recorded as pattern 0 (negative), pattern 1 (weak and heterogeneous staining, &lt;80%), and pattern 2 (moderate/strong and uniform staining, ≥80%).

Results
Pattern 1 can be seen in all BCLs with MYC-R included in this study and more commonly seen in DLBCL without MYC-R (8/14 cases). Pattern 2 is characteristic (positive predictive value = 86%) for Epstein-Barr virus (EBV)–negative BL, while pattern 0 was seen in 22 (76%) of 29 cases of DLBCL-MYC-R/DH/TH (P &lt; .001). Seven of 8 EBV-positive BL cases showed pattern 0, which was completely opposite to the common pattern 2 in EBV-negative BL (12/15 cases). Pattern 2 was not detected in all DH/TH cases.

Conclusions
Weak and heterogeneous staining of LEF1 can be seen in all the BCLs with and without MYC-R. Strong and uniform staining of LEF1 is highly characteristic of EBV-negative BL among all aggressive BCLs with MYC-R, while the negative staining of LEF1 is mostly suggestive of DLBCL-MYC-R/DH/TH. Lymphocyte enhancer factor 1 provides additional diagnostic value in the differentiation of BL from other aggressive BCLs with MYC-R, especially in a limited specimen.
On brain stimulation in epilepsy
Authors: Trevelyan Andrew J , Marks Victoria S , Graham Robert T , Denison Timothy , Jackson Andrew , Smith Elliot H 
Published: January 2025

Abstract
Brain stimulation has, for many decades, been considered as a potential solution for the unmet needs of the many people living with drug-resistant epilepsy. Clinically, there are several different approaches in use, including vagus nerve stimulation, deep brain stimulation of the thalamus, and responsive neurostimulation. Across populations of patients, all deliver reductions in seizure load and sudden unexpected death in epilepsy risk, yet do so variably, and the improvements seem incremental rather than transformative. In contrast, within the field of experimental neuroscience, the transformational impact of optogenetic stimulation is evident; by providing a means to control subsets of neurons in isolation, it has revolutionized our ability to dissect out the functional relations within neuronal microcircuits. It is worth asking, therefore, how preclinical optogenetics research could advance clinical practice in epilepsy?
Here, we review the state of the clinical field, and the recent progress in preclinical animal research. We report various breakthrough results, including the development of new models of seizure initiation, its use for seizure prediction, and for fast, closed-loop control of pathological brain rhythms, and what these experiments tell us about epileptic pathophysiology. Finally, we consider how these preclinical research advances may be translated into clinical practice.
Incidence and Outcome of Hepatitis D Virus Infection in People With Human Immunodeficiency Virus (HIV) and Hepatitis B Virus Coinfection in the Era of Tenofovir-Containing Antiretroviral Therapy
Authors: Huang Yu-Shan , Sun Hsin-Yun , Ho Shu-Yuan , Lin Kuan-Yin , Liu Wang-Da , Sheng Wang-Huei , Hsieh Szu-Min , Chuang Yu-Chung , Su Li-Hsin , Su Yi-Ching , Liu Wen-Chun , Chang Sui-Yuan , Hung Chien-Ching 
Published: January 2025

Abstract

Background
Tenofovir-containing antiretroviral therapy (ART) improves survival in hepatitis B virus (HBV)–coinfected people with HIV (PWH). We investigated the incidence of hepatitis D virus (HDV) infection and its clinical impact in HBV-coinfected PWH in the era of tenofovir-containing ART.

Methods
Between 2011 and 2022, HBV-coinfected PWH were included and followed until December 2023. Anti-HDV antibody screening was performed using sequentially archived blood samples. Timing of incident HDV infection was estimated as the midpoint between the last timepoint of anti–HDV-negative samples and the first timepoint of anti–HDV-positive samples. Differences in survival and liver-related outcomes between HDV-infected and -uninfected PWH were analyzed.

Results
534 HBV-coinfected PWH were included; 36 (6.7%) tested HDV-seropositive at baseline. During 3987.78 person-years of follow-up (PYFU), 50 (10.0%) of 498 anti–HDV-negative PWH seroconverted for HDV, with an overall incidence rate of 12.54 per 1000 PYFU; 88.0% (44/50) of HDV seroconverters were men who have sex with men. After a median follow-up of 10.2 years (84.7% of the follow-up period covered by tenofovir-containing ART), all-cause mortality was 4.7% (25/534). PWH with HDV had significantly higher rates of liver-related mortality (3.5% vs 0.4%, P = .032), cirrhosis (11.3% vs 3.6%, P = .008), and hepatitis flare (28.2% vs 14.2%, P = .001) than HDV-uninfected PWH. In multivariate Cox analysis, HDV infection was associated with liver-related mortality (adjusted HR, 9.696; 95% CI, 1.284–73.222, P = .028). Risk of hepatocellular carcinoma was similar for HDV-infected and HDV-uninfected PWH.

Conclusions
HBV-coinfected PWH remain at risk of HDV superinfection and HDV infection is associated with liver-related death in the era of tenofovir-containing ART.
Iron management and exercise training in individuals with chronic kidney disease: lived experiences
Authors: Lightfoot Courtney J , Greenwood Sharlene A , Asgari Elham , Banerjee Debasish , Bhandari Sunil , Burton James O , Kalra Philip A , McCafferty Kieran , Oliveira Benjamin A , Reid Chante , Swift Pauline A , Wheeler David C , Wilkinson Thomas J , Bramham Kate , Smith Alice C 
Published: January 2025

ABSTRACT

Background
Non-anaemic iron deficiency is highly prevalent in people living with chronic kidney disease (CKD) but is underdiagnosed and undertreated, especially in earlier stages of CKD. A multicentre trial assessing the effect of intravenous iron supplementation in iron-deficiency but not anaemic people with CKD included a qualitative sub-study that aimed to explore the patient experience and psychosocial impact of living with CKD and iron deficiency, and the experience of the therapeutic intervention (intravenous iron and exercise).

Methods
Semi-structured interviews were conducted with 23 trial participants blinded to treatment. Topics explored included experiences of living with CKD and iron deficiency, symptoms, social and leisure activities, quality of life, and participants’ views and experiences of receiving the therapeutic intervention. Thematic analysis was used to identify and report themes.

Results
Six overarching themes were identified: lack of awareness of iron deficiency; overwhelming feelings of tiredness; feeling limited; balancing emotions; perceptions and experiences of therapeutic treatment received; and impact of trial participation on life participation. Trial participation, specifically the exercise training, was perceived to be beneficial, with improvements in life participation and psychological wellbeing experienced. However, there were no clear differences between treatment groups, with mixed perceptions about which therapeutic treatment was received.

Conclusions
The impact of tiredness on individuals with CKD is profound and can result in reduced vitality, impaired ability to engage in life activities and emotional conflict. Improved communication and support about psychosocial impact and management of symptoms, particularly fatigue, for people with CKD may be required, alongside effective therapeutic interventions, to improve symptom management and quality of life.
Fostering consensus for the implementation of a clinical pharmacy specialization: a nominal group technique approach with pharmacy stakeholders
Authors: Moura Laura , Steurbaut Stephane , Mota Filipe Helder , Alves da Costa Filipa 
Published: January 2025

Abstract

Objectives
To explore the need for a specialization in clinical pharmacy and the model to be adopted, as perceived by Portuguese stakeholders.

Methods
A nominal group technique through two online meetings addressed four questions: pros and cons of specialization models used internationally; preferred model for Portugal; and success factors for implementation.

Key findings
All nine stakeholders recognized the need to train pharmacists in clinical pharmacy and agreed specialization is essential, through a model including strong clinical undergraduate education, supplemented with postgraduate training. The postgraduate component considered most suited comprised a balanced approach to theoretical and practical training, where the relative weigh of theory (20%–60%) could progressively decrease with the implementation of the European directive 2024/782 establishing the minimum training requirements for the professions of pharmacists, where the clinical pharmacy is to be strengthened at the undergraduate level. Success factors for implementing this model include, establishing a regulatory framework for the career and the desired characteristics of the graduates from the postgraduate programme.

Conclusions
This study led to a consensus among key Portuguese stakeholders on the model to be adopted for a clinical pharmacy specialization in Portugal and, the information gathered will be used to guide future implementation.
Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island
Authors: Pick Kat , Stadel Lauren , Raivio Tracy L 
Published: January 2025

Abstract
In this study, we identify and characterize a novel phage-inducible chromosomal island (PICI) found in commensal Escherichia coli MP1. This novel element, EcCIMP1, is induced and mobilized by the temperate helper phage vB_EcoP_Kapi1. EcCIMP1 contributes to superinfection immunity against its helper phage, impacting bacterial competition outcomes. Genetic analysis of EcCIMP1 led us to uncover a putative transcriptional repressor, which silences virulence gene expression in the murine pathogen Citrobacter rodentium. We also found a putative excisionase encoded by EcCIMP1 which paradoxically does not promote excision of EcCIMP1 but rather supports excision of the helper phage. Another putative excisionase encoded by a presumed integrative conjugative element can also support the excision of vB_EcoP_Kapi1, demonstrating crosstalk between excisionases from multiple classes of mobile genetic elements within the same cell. Although phylogenetically distant from other characterized PICIs, EcCIMP1 and EcCIMP1-like elements are prevalent in both pathogenic and commensal isolates of E. coli from around the world, underscoring the importance of characterizing these abundant genetic elements.
Effect of growing season length on gross primary productivity increased in the Jinsha River watershed
Authors: Li Ming-Wei , Zhang Jing , Wu Zhao-Fei , Fu Yong-Shuo H 
Published: January 2025

Abstract
Climate change has significantly altered the carbon and water cycles of terrestrial ecosystems. Climate change and the extended vegetation growing season enhanced ecosystem gross primary production (GPP). However, the relative contributions of climate drivers and vegetation phenology to GPP remain unclear. Based on satellite-derived vegetation phenology and GPP datasets from 1982 to 2018, we investigated the spatiotemporal patterns of GPP and its drivers in the Jinsha River Watershed. We found that the growing season GPP significantly increased from 1982 to 2018, which was primarily attributed to changes in the growing season length (GSL) and temperature. The effect of GSL on GPP is highest (r = 0.34), with its effect being larger than that of temperature, precipitation, and radiation in 41% of the watershed. Importantly, the area where GPP was predominantly influenced by GSL increased by 12% in grid cells during the period of 2001–2018 compared to 1982–2000, indicating that GSL is playing an increasingly important role in driving GPP. Our findings highlight the dynamic responses of GPP to climate change and the associated phenological variations, which is crucial for improving the understanding of the terrestrial carbon balance.
Clinical Integration and Application of the 2022 WHO Pituitary Tumor Classification
Authors: Asa Sylvia L , Ezzat Shereen , Mete Ozgur 
Published: January 2025

Abstract
The pituitary is a complex endocrine organ that gives rise to adenohypophysial epithelial neuroendocrine tumors, to hypothalamic neuroendocrine neuronal neoplasms, to non-endocrine glial-related pituicytomas and to Rathke’s pouch-derived craniopharyngiomas and pituitary blastomas. The past 30 years have seen significant advances in the classification of these tumors based on cell lineages, molecular alterations and biomarker features that distinguish tumor types and their subtypes. Adenohypophysial cells give rise to pituitary neuroendocrine tumors (PitNETs) that usually follow one of three cell differentiation pathways. Pituicytomas have multiple morphologic variants and hypothalamic neuronal tumors can be gangliocytomas composed of magnocellular neurons or neurocytomas composed of small neurocytes. Craniopharyngiomas have two distinct families, papillary and adamantinomatous, with different alterations in signaling pathways. Pituitary blastomas are primitive tumors composed of an admixture of immature elements of Rathke’s pouch with immature but differentiated hormone-secreting adenohypophysial cells. These various tumors are associated with specific clinical manifestations, creating a complex clinico-radiologic-pathologic classification that has both important clinical distinctions but also predictive therapeutic value. Syndromic disease has allowed the identification of genes that may be implicated in the development of these tumors, but the majority are sporadic tumors that, with a few exceptions, have no recurrent genetic alterations. The structure-function correlations that have been elucidated are critical to allow subclassification of clinical disorders that will pave the way for further advances in understanding genetic predisposition and environmental factors that alter epigenetic profiles of pituitary cells.
Circulating PD-1hi CXCR5– and CXCR5+ CD4 T cells are elevated in patients with newly diagnosed giant cell arteritis, and predict relapse
Authors: Monjo-Henry Irene , Nieto-Carvalhal Beatriz , Uyaguari Mariela , García-Carazo Sara , Balsa Alejandro , de Miguel Eugenio , Miranda-Carús María-Eugenia 
Published: January 2025

Abstract

Objectives
GCA is a large/medium-vessel granulomatous vasculitis, and the Programmed Cell Death 1/Programmed Cell Death-ligand-1 (PD-1/PD-L1) coinhibitory pathway seems to be implicated in its pathogenesis. CD4 T cells expressing high PD-1 levels, CD4+CXCR5–PD-1hi peripheral helper (Tph) and CD4+CXCR5+PD-1hi follicular helper T cells (Tfh) are key mediators of autoimmunity. Their frequencies are elevated in the peripheral blood of subjects with several autoimmune conditions but have not been investigated in GCA. Our objective was to study the frequency of circulating Tph (cTph) and Tfh (cTfh) in patients with newly diagnosed GCA (nGCA).

Methods
Prospective, non-interventional study on consecutive patients referred to our US GCA fast-track clinic over a period of 24 months. Peripheral blood was drawn immediately upon initial diagnosis. For each patient, an age- and gender-matched healthy control (HC) was included. Peripheral blood mononuclear cells isolated by Ficoll-Hypaque were examined by cytometry. Patients were subsequently treated with standard therapy according to the updated 2018 EULAR recommendations.

Results
Sixty-five nGCA patients were included. As compared with HC, nGCA patients presented at baseline with an increased frequency of cTph and cTfh cells. Among the 46 patients who could be followed up for 12 months, 19 experienced a relapse. The baseline frequency of cTph and cTfh cells had been significantly lower in patients who relapsed as compared with those who did not. A cTph cell frequency &lt;1.0 predicted relapse with a sensitivity of 90% and specificity of 93%.

Conclusion
nGCA patients demonstrate increased baseline cTph and cTfh cell frequencies. Lower baseline proportions of cTph and cTfh cells associate with relapse.
Phellodendrine inhibits oxidative stress and promotes autophagy by regulating the AMPK/mTOR pathway in burn sepsis-induced intestinal injury
Authors: Ding Wei , Qian Kun , Bao Wenxiu , Wang Zhen 
Published: January 2025

Abstract
Intestinal injury is an important complication of burn sepsis with limited therapeutic choices. Phellodendrine is a promising compound for gastrointestinal inflammatory diseases and is extracted from the traditional Chinese medicine phellodendron bark. The study aimed to explore the role of phellodendrine against oxidative stress and autophagy in burn sepsis-induced intestinal injury. A mouse model of burn sepsis model was established by intraperitoneally injecting 10 mg/kg lipopolysaccharide (LPS) to mice burned by boiled water. Phellodendrine (30 mg/kg) was injected into mice in the drug group after scalding and before LPS injection. Hematoxylin and eosin staining was performed to observe histopathological changes in murine small intestines. TdT-mediated dUTP Nick-End Labeling (TUNEL) assay was performed to evaluate intestinal cell apoptosis. Immunofluorescence staining was performed to measure the expression and distribution of autophagy markers, light chain 3II (LC3II) and p62 in intestinal tissues. Oxidative stress indicators were detected using corresponding commercial kits. Protein levels of apoptotic markers, autophagy markers, and factors involved in adenosine monophosphate-activated protein kinase (AMPK)/mechanistic target of rapamycin (mTOR) pathway in intestines were quantified by western blotting. Phellodendrine attenuated bun sepsis-induced intestinal pathological changes. Meanwhile, aggravated cell apoptosis, reduction of antioxidant enzymes, and downregulation of autophagy markers in intestinal tissues of burn sepsis group were all improved by phellodendrine. In addition, phellodendrine activated the phosphorylation (p) of AMPK and inhibited p-mTOR signaling in intestines of burn septic mice. In conclusion, phellodendrine suppresses oxidative stress and activates autophagy in burn sepsis-induced intestinal injury by activating AMPK and inhibiting mTOR signaling.
Driver injury severity analysis of work zone crashes: A Bayesian hierarchical generalized ordered probit approach
Authors: Huang Peng , Xiong Yanwen , Tang Shijiang , Wang Shaohua , Zeng Qiang , Lee Jaeyoung Jay 
Published: January 2025

Abstract
Highway work zones are locations where severe traffic crashes tend to occur. Most of the extant research on work zone crash severity neglects the discrepancy in the injuries sustained by different drivers involved in the same crash. Admittedly, it is essential to analyze crash-level factors to their highest injury severity; but it is equally important to understand driver-level contributing factors to their injury severity to establish effective safety countermeasures to minimize drivers’ injury severity. Thus, this research aims to identify the factors with significant impacts on driver injury severity of work zone crashes and estimate their effects on each severity level. Data of 3,880 drivers involved in 2,134 work zone crashes are obtained from the Crash Report Sampling System (CRSS) database of the United States and employed for the empirical investigation. A Bayesian hierarchical generalized ordered probit model is advocated for analyzing the driver injury severity. Model performance indices suggest that the advocated hierarchical model is superior to the generalized ordered probit model, and considerable within-crash correlation is found across the observed driver injury severity. The estimated parameters show that driver age and gender, alcohol use, vehicle age and type, speeding and speed limit, weather condition, lighting condition, and crash type have significant effects on the driver injury severity in work zone crashes. Marginal effects of the significant factors on each divided injury severity level are also estimated. Countermeasures are proposed from the results to reduce severe injuries sustained by drivers involved in work zone crashes.