bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a nurse-driven protocol for indwelling urinary catheter removal and novel utilization dashboard: a pre/postintervention observational study
Authors: Kamel Michelle , Harris Nichole , Berry Andrew , Warsavage Theodore , Bessesen Mary T. , Kon Shelley E. 
Published: February 2025

Background: Nurse-driven protocols (NDPs) for urinary catheter removal are proven tools for decreasing catheter-associated urinary tract infections (CAUTIs); however, they are not used consistently in acute care settings. Objective: To determine the impact of a NDP for urinary catheter removal on CAUTI rates and device utilization ratio. Design: Pre/postintervention, observational study at a 160-bed, level 1a academically affiliated Veterans Affairs (VA) hospital. Methods: CAUTI rates and device utilization ratios were examined before and after implementation of the NDP. Results: The CAUTI rate decreased from 0.99 per 1,000 urinary catheter days in the preintervention period to 0.27 per 1000 urinary catheter days in the postintervention period. The device utilization ratio (catheter days/patient days) decreased from 14% in the preintervention period to 12% in the postintervention period. Conclusion: The NDP reduced the CAUTI rate and the device utilization ratio. A multidisciplinary project team and use of a data visualization dashboard may be valuable implementation strategies to increase utilization of NDPs such as HOUDINI.
Retinitis linked to human herpesvirus type 6: a case study in a splenectomised patient
Authors: Santos-Oliveira Joana , Cunha Ana Maria , Moleiro Ana Filipa , Ribeiro Margarida , Torres-Costa Sónia , Oliveira-Ferreira Cláudia , Pedrosa Ana Catarina , Araújo Joana , Figueira Luís , Silva Marta 
Published: February 2025

Abstract
Human herpesvirus-6 (HHV-6) is a member of the HHV family and is a rare cause of infectious uveitis. We report a case of a splenectomised patient, hospitalised due to invasive pneumococcal disease, who was diagnosed with retinitis in the right eye, with good visual acuity (0.1 LogMAR). Given the presence of HHV-6 Polymerase chain reaction (PCR) in the cerebrospinal fluid and the serum and the coexistence of a severe central nervous system infection, the ophthalmological features were attributed to the HHV-6 infection. He was treated with topical corticosteroid eyedrops, cyclopentolate, and prednisolone acetate ointment and systemically with intravenous ganciclovir 5 mg/kg bid for 14 days and then oral valganciclovir 900 mg bid for 4 weeks. The diagnosis was promptly presumed, enabling the early initiation of appropriate treatment and contributing to the preservation of the good visual acuity initially observed.
Tumor secretome shapes the immune landscape during cancer progression
Authors: Yang Jianqiang , Tang Sijia , Saba Nabil F. , Shay Chloe , Teng Yong 
Published: February 2025

Abstract
The focus of cancer immunotherapy has traditionally been on immune cells and tumor cells themselves, often overlooking the tumor secretome. This review provides a comprehensive overview of the intricate relationship between tumor cells and the immune response in cancer progression. It highlights the pivotal role of the tumor secretome - a diverse set of molecules secreted by tumor cells - in significantly influencing immune modulation, promoting immunosuppression, and facilitating tumor survival. In addition to elucidating these complex interactions, this review discusses current clinical trials targeting the tumor secretome and highlights their potential to advance personalized medicine strategies. These trials aim to overcome the challenges of the tumor microenvironment by designing therapies tailored to the secretome profiles of individual cancer patients. In addition, advances in proteomic techniques are highlighted as essential tools for unraveling the complexity of the tumor secretome, paving the way for improved cancer treatment outcomes.
Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci
Authors: Shi Chenfu , Zhao Danyun , Butler Jake , Frantzeskos Antonios , Rossi Stefano , Ding James , Ferrazzano Carlo , Wynn Charlotte , Hum Ryan Malcolm , Richards Ellie , Gupta Muskan , Patel Khadijah , Yap Chuan Fu , Plant Darren , Grencis Richard , Martin Paul , Adamson Antony , Eyre Stephen , Bowes John , Barton Anne , Ho Pauline , Rattray Magnus , Orozco Gisela 
Published: February 2025

Abstract

Background
Genome-wide association studies (GWAS) have uncovered the genetic basis behind many diseases and conditions. However, most of these genetic loci affect regulatory regions, making the interpretation challenging. Chromatin conformation has a fundamental role in gene regulation and is frequently used to associate potential target genes to regulatory regions. However, previous studies mostly used small sample sizes and immortalized cell lines instead of primary cells.

Results
Here we present the most extensive dataset of chromatin conformation with matching gene expression and chromatin accessibility from primary CD4+ and CD8+ T cells to date, isolated from psoriatic arthritis patients and healthy controls. We generated 108 Hi-C libraries (49 billion reads), 128 RNA-seq libraries and 126 ATAC-seq libraries. These data enhance our understanding of the mechanisms by which GWAS variants impact gene regulation, revealing how genetic variation alters chromatin accessibility and structure in primary cells at an unprecedented scale. We refine the mapping of GWAS loci to implicated regulatory elements, such as CTCF binding sites and other enhancer elements, aiding gene assignment. We uncover BCL2L11 as the probable causal gene within the rheumatoid arthritis (RA) locus rs13396472, despite the GWAS variants’ intronic positioning relative to ACOXL, and we identify mechanisms involving SESN3 dysregulation in the RA locus rs4409785.

Conclusions
Given these genes’ significant role in T cell development and maturation, our work deepens our comprehension of autoimmune disease pathogenesis, suggesting potential treatment targets. In addition, our dataset provides a valuable resource for the investigation of immune-mediated diseases and gene regulatory mechanisms.
BNT162b2 mRNA vaccination affects the gut microbiome composition of patients with follicular lymphoma and chronic lymphocytic leukemia
Authors: Chiarenza Annalisa , Aluisio Gaia Vertillo , Parrinello Nunziatina Laura , Marino Sara , Corsale Anna Maria , Privitera Grete Francesca , Azgomi MojtabaShekarkar , La Spina Enrico , Cambria Daniela , Curtopelle Angelo , Isola Gaetano , Botta Cirino , Di Raimondo Francesco , Romano Alessandra , Santagati Maria 
Published: February 2025

Abstract

Background
In both chronic lymphatic leukemia (CLL) and follicular lymphoma (FL) immunotherapy determines B-depletion that leads to temporary suppression of humoral immunity, which is clinically relevant especially during the COVID-19 pandemic, when most patients in the first wave received the BNT162b2 vaccine during anti-neoplastic treatment.

Methods
To capture changes in the immunome and microbiome composition in CLL and FL patients upon mRNA-based vaccination, we designed a prospective, longitudinal study to profile both the humoral and the cellular response after exposure to the BNT162b2 COVID-19 vaccine.

Results
In both CLL patients and FL patients, the second and third administrations of the BNT162b2 vaccine increased the titer of specific antibodies against SARS-CoV-2. In FL patients, vaccination induced expansion of central memory CD8 + CD57dim CD279 + T cells and reduction of the neutrophil subset myeloid 1 (CD14−CD15+CD16dimCD64+CD33−CD38+PDL1+HLA-DR−); in both cohorts, CD45RA + CD27 + CD279 + NK cells were expanded after a full cycle of vaccination. After vaccination, the genera Collinsella, Gemmiger, Lachnospiraceae, Blautia, Ruminococcus and Lactobacillus increased in both CLL patients and FL patients, whereas Faecalibacterium, Enterobacteriacae, and Enterococcus decreased. Multivariate analysis failed to identify factors associated with changes in microbiome communities among the CLL and FL cohorts, considering age, sex, exposure to anti-CD20 therapy and disease activity. Only in FL patients, alpha diversity was negatively correlated with neutrophil subsets myeloid 1 e 5 at baseline and positively correlated with neutrophil subset 6 after vaccination. PICRUSt2 analysis showed how microbiome can also affect the host health promoting chronic inflammation. The L-lysine biosynthesis pathway was more represented in CLL patients, whereas the L-valine degradation pathway and the anaerobic degradation of purine nucleobases were overrepresented in the FL cohort.

Conclusions
Taken together, our findings reveal the effect of the BNT162b2 vaccine in shaping the microbiome composition in CLL and FL patients, despite receiving treatment for their underlying active disease, and highlight the importance of a comprehensive analysis of the immunome and microbiome profiling to understand immune function in these cohorts of patients.
Citronellol inhibits the activity of AtSRT1 to increase IAA content and signal transduction, promoting the growth of A. thaliana
Authors: Wen Jin-Rui , Nie Hong-Yan , Liao Hong-Xin , Xu Fu-Rong , Liu Xiao-Yun , Dong Xian 
Published: February 2025

Abstract
Histone acetylation is a key epigenetic modification involved in plant development. Although histone deacetylase inhibitors (HDACi) are commonly studied in human diseases, their role in regulating histone deacetylation in plants remains unclear. This study explores the function of Citronellol, a volatile small molecule, as a plant-derived HDACi using Arabidopsis thaliana (L.) Heynh (A. thaliana) as a model. Citronellol at concentrations of 3 and 6 mM enhanced both root development and aboveground growth. Enzyme activity assays, molecular docking, and molecular dynamics simulations showed that Citronellol binds to specific residues (PHE:64, ARG:65, MET:1, and ILE:214) of the histone deacetylase AtSRT1 in Arabidopsis, inhibiting its activity and elevating H3K9ac levels. Integrated RNA-seq and ChIP-seq analyses revealed that Citronellol increased the expression of genes linked to growth and development, including ATCTH, CPL3, IBR5, TCP4, and KUA1, through enhanced histone acetylation and activation of plant hormone signaling pathways. These findings provide new insights into the epigenetic regulation of plant growth by Citronellol, identifying it as a novel HDACi. Citronellol could serve as an effective plant growth regulator, offering valuable applications for agricultural development.

Graphical Abstract
The dynamics of frequency connectedness between technology ETFs and uncertainty indices under extreme market conditions
Authors: Ozcelebi Oguzhan , McIver Ronald , Kang Sang Hoon 
Published: February 2025

Abstract
We examine technology ETF and uncertainty index (VIX, GVZ, and OVZ) spillover dynamics and quantile frequency interconnectedness across market states. This study is the first to use quantile-frequency spillover, quadruple wavelet coherence, and wavelet quantile correlation methodologies to facilitate these analyses. The total connectedness index value is 70%, which is much higher in both the upper and lower quantiles. Under normal market conditions, short-term connectedness significantly exceeds long-term connectedness. Levels of ETF-uncertainty indicator connectedness increase under extreme market conditions; most technology ETFs are net spillover transmitters and uncertainty indices net spillover receivers, indicating the contagion risk of ETF investments. We show that while greater ETF-uncertainty index connectedness may benefit portfolio diversification, large fluctuations in technology EFTs can result in financial instability due to high market volatility. In the long term, the joint effects of uncertainty indices on ETFs are significant, with negative correlations between ETFs and uncertainties at different frequencies, supporting the potential role of uncertainty indices in hedging technology ETF portfolio risks. Dynamic portfolio rebalancing, scenario analysis, and stress testing may help to manage the effects of high connectedness.
PROMIS-9 UE physical function demonstrates moderate responsiveness for patients following upper limb prosthesis intervention
Authors: Castleberry Todd J. , England Dwiesha L. , Fylstra Bretta L. , Stevens Phillip M. , Todd Amy E. , Mandacina Stephen A. , Wurdeman Shane R. 
Published: February 2025

Abstract

Background
Upper extremity physical function is an essential health domain in the rehabilitation care for patients with upper limb amputation or absence. The PROMIS-9 UE Physical Function short form is a recently established instrument designed for individuals with upper limb amputation or absence. The instrument’s responsiveness to changes after receiving a prosthesis has not been investigated. The current study aimed to evaluate the ability of the PROMIS-9 UE to detect changes in bimanual (two-handed) functional capacity after patients’ receipt of a prosthesis.

Methodology
A retrospective chart review was conducted on the longitudinal PROMIS-9 UE outcome measure scores completed between April 2016 and February 2024. Participants included individuals with an outcome collected before and after prosthesis receipt.

Results
The final sample size included 124 individuals (91 male, 33 female; 43.4 ± 15.0 years old, 34.4 ± 103.0 months since amputation, and 62.9% injury etiology). Analyses found significant improvement across all patients in the PROMIS-9 UE scores from baseline to post prosthesis intervention (baseline: 25.3 ± 8.6, post: 29.5 ± 9.6; p < 0.001). The PROMIS-9 UE demonstrated a moderate responsiveness (Standardized Response Mean = 0.6) to prosthetic intervention. This was a directional change consistent with subjective patient reports of increased functionality. Furthermore, findings from the linear mixed model demonstrated significant responsiveness for the PROMIS-9 UE instrument to detect post-intervention changes after controlling for potential confounding effects (p < 0.001).

Conclusions
These findings suggest the PROMIS-9 UE Physical Function instrument demonstrates moderate clinical utility in capturing patient progress following upper limb prosthesis intervention.
Insights into geminiviral pathogenesis: interaction between βC1 protein and GLABROUS1 enhancer binding protein (GeBP) in Solanaceae
Authors: Zhao Meisheng , Li Mingjun , Zhang Liping , Wu Nan , Tang Xinyue , Yang Xiaolong , Ghanem Hussein , Wu Menglin , Wu Gentu , Qing Ling 
Published: February 2025

Abstract
Transcription factors (TFs) play crucial roles in plant development and pathogen defense. However, plant viruses can exploit TFs to facilitate their infection or transmission. In this study, we confirmed the βC1 proteins, encoded by tobacco curly shoot virus (TbCSV)- and tomato yellow leaf curl China virus (TYLCCNV)-associated betasatellites, interacted with GLABROUS1 enhancer binding protein (GeBP) TFs from solanaceous plants including Nicotiana benthamiana, Solanum lycopersicum, S. tuberosum, and Capsicum annuum. Further analysis verified the nuclear localization, homodimerization, and DNA-binding ability of the GeBP TFs, along with its interaction with βC1 in the nucleus. PVX-mediated overexpression of NbGeBP showed no effect on the accumulation of viral and betasatellite DNAs in N. benthamiana plants after infection with TbCSV and its heterologous betasatellite, malvastrum yellow vein virus associated betasatellite (MaYVB), or its homologous betasatellite, TbCSB. However, both TbCSV and MaYVV caused a decrease in NbGeBP expression during the early stages of infection, regardless of the presence of homologous or heterologous betasatellites, implying that NbGeBP might play a role in virus infection. TbCSV/TbCSB and TYLCCNV/TYLCCNB infect many solanaceous plants, and solanaceous GeBP proteins interact with βC1 proteins from TbCSB and TYLCCNB. The yeast two-hybrid and bimoleccular fluorescence complementation assays showed that AtGeBP from Arabidopsis thaliana could not interact with TbCSB βC1, revealing that the GeBP-βC1 interactions might only exist in GeBP proteins from solanaceous plants. Importantly, the βC1 protein from MaYVB, which was almost not reported on natural infection in solanaceous plants, could not interact with GeBP, suggesting the potential roles of GeBP in monopartite begomovirus infection of solanaceous plants.
The use of an intra-aortic balloon pump in patients with cardiogenic shock secondary to acute myocardial infarction
Authors: Qutub Mohammed A. 
Published: February 2025

Abstract

Background
Cardiogenic shock secondary to acute myocardial infarction (AMI-CS) is associated with high mortality despite advances in therapy. The intra-aortic balloon pump (IABP) is used to support hemodynamics in these patients, but its efficacy remains debated. This study aimed to evaluate the outcomes of IABP use in patients with AMI complicated by CS.

Results
This retrospective cohort study included 95 patients with AMI-CS treated at a tertiary referral center from January 2020 to December 2022. Patients were divided into two groups: those receiving IABP (n = 72) and those not receiving IABP (n = 23). Baseline characteristics revealed that patients who received IABP had more advanced shock [SCAI stage E 25% vs. 9%, P < 0.01], an increased prevalence of cardiac arrest at presentation [31% vs. 4%, P = 0.01], and required more aggressive hospital interventions, including vasopressor support [97% vs. 39%, P < 0.01], mechanical ventilation [90% vs. 30%, P < 0.01], and renal replacement therapy [42% vs. 9%, P < 0.01]. The IABP group had significantly higher in-hospital mortality [69% vs. 30%, P < 0.01]. IABP was associated with increased in-hospital mortality in patients with cardiac arrest [OR 27, P < 0.01], but in patients without cardiac arrest, IABP use reduced mortality [OR 0.15, P = 0.02]. There were no significant differences in cerebrovascular accident, bleeding, and length of stay between groups. No significant differences in long-term survival were observed between the groups [log-rank P = 0.44].

Conclusions
IABP use in AMI-CS patients was associated with higher in-hospital mortality, reflected by the more critical clinical status of these patients at baseline. IABP may offer in-hospital survival benefits in patients without cardiac arrest but does not improve long-term outcomes. Further research is needed to refine its role in clinical practice.
Testosterone Treatment and Sexual Function in Men: Secondary Analysis of the T4DM (Testosterone for Diabetes) Trial
Authors: Wittert Gary A , Robledo Kristy P , Handelsman David J , Inder Warrick J , Stuckey Bronwyn G A , Yeap Bu B , Bracken Karen , Allan Carolyn A , Jesudason David , Jenkins Alicia , Januszewski Andrzej S , Grossmann Mathis 
Published: February 2025

Abstract

Context
The combined effects of testosterone treatment and lifestyle intervention on sexual function in men at high risk of type 2 diabetes are unclear.

Objective
To assess the effect of testosterone treatment with a lifestyle intervention in men aged 50 to 74 years at high risk of, or newly diagnosed with, type 2 diabetes (via oral glucose tolerance test).

Design
A secondary analysis of the Testosterone for the Prevention of Type 2 Diabetes trial, a double-blind, placebo-controlled trial conducted across 6 Australian centers.

Interventions
Intramuscular testosterone undecanoate (1000 mg) or placebo, 3 monthly for 2 years alongside a community-based lifestyle program.

Main outcomes
Sexual function measured using the International Index of Erectile Function (IIEF)-15 questionnaire.

Results
Of 1007 participants, 792 (79%) had complete International Index of Erectile Function-15 data. Baseline domain scores were inversely related to age and waist circumference, but unrelated to serum testosterone or estradiol levels. Testosterone treatment improved all 5 International Index of Erectile Function-15 domain scores, with stronger effects on sexual desire and orgasmic function in older men, and sexual desire in men with higher depression scores. Testosterone had no impact on depression. Independent of treatment, reductions in waist circumference were associated with improved erectile function, and reductions in depression scores correlated with better sexual function. Clinically significant improvement in erectile function and sexual desire occurred in 3% and 10% of men, respectively, and was inversely related to baseline function. Clinically significant improvement improvements in erectile function and sexual desire were greater in younger and older men respectively.

Conclusion
Testosterone treatment enhanced sexual desire and, to a lesser extent, erectile function, particularly in older men and those with higher waist circumference or depressive symptoms. Reduced waist circumference and depression independently improved sexual function.
The COVID-19 pandemic and its impact on mental health. Causes and consequences - an overview
Authors: Cioch Michał Jakub , Kaczmarska Urszula , Woźniak Aleksandra , Nowak Julia , Hermanowicz Kamil , Doman Katarzyna , Najdek Agnieszka , Oleksy Daria , Mycyk Marcin , Komada Dawid 
Published: February 2025

Introduction:This article provides an overview of the COVID-19 pandemic, which lasted from 2019 to 2023, and its impact on mental health. It will discuss risk factors leading to mental health disorders during the pandemic. Attention will also be given to the risk factors and possible causes, groups most affected and the ways to deal with mental disorders during a pandemic will also be discussed. Aim of study:The aim of the study is to assess the impact of the COVID-19 pandemic on mental health, identify risk factors and possible causes of mental disorders during this period, and identify groups that are particularly vulnerable to the negative psychological effects of the pandemic.Materials and methods:A comprehensive literature review was conducted using the PubMed database, focusing on articles published up to the end of 2024. The search included the keywords “COVID-19”, “mental health”, “pandemic”, “depression” in different combinations. Relevant studies were selected based on criteria such as causes and risk factors. Special attention was paid to vulnerable groups (e.g., children and the elderly, etc.) and how changes in the pandemic (e.g., social isolation) affected mental health. Conclusion:The pandemic of COVID-19 has affected not only people's physical health but also their mental health. Studies indicate that during the COVID-19 pandemic, the incidence of mental illnesses increased, and the symptoms of people with mental disorders were exacerbated including symptoms of general anxiety, sleep disorders, depressive disorders, etc. The study discussed risk factors such as social isolation, etc. and how they caused an increase in mental disorders