bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclosporine A alleviates colitis by inhibiting the formation of neutrophil extracellular traps via the regulating pentose phosphate pathway
Authors: Xu Chenjing , Ye Ziping , Jiang Wenyu , Wang Shu , Zhang Hongjie 
Published: December 2023

Abstract
Background
The aberrant formation of neutrophil extracellular traps (NETs) has been implicated in ulcerative colitis (UC), a chronic recurrent intestinal inflammation. Cyclosporine A (CsA) is now applied as rescue therapy for acute severe UC. In addition, it has been certained that CsA inhibits the formation of NETs in vitro and the mechanism of which was still vague. The study aimed to explore the mechanism CsA inhibits the NETs formation of colitis in vivo and in vitro.

Methods
NETs enrichment in clinical samples was analyzed using databases from Gene Expression Omnibus and verified in our center. Dextran sulfate sodium (DSS)-induced acute colitis mice model was used to investigate the effect of CsA on NETs of colonic tissue expression. To clarify the mechanism, intracellular energy metabolites were examined by Liquid Chromatograph Mass Spectrometer, and reactive oxygen species (ROS) levels were examined by fluorescence intensity in neutrophils treated with CsA after LPS stimulation. The transcriptional level and activity of G6PD of neutrophils were also assessed using qRT-PCR and WST-8. RNA Sequencing was used to detect differentially expressed genes of neutrophils stimulated by LPS with or without CsA. The expression levels of related proteins were detected by western blot.

Results
NETs enrichment was especially elevated in moderate-to-severe UC patients compared to HC. NETs expression in the colon from DSS colitis was decreased after CsA treatment. Compared with neutrophils stimulated by LPS, NETs formation and cellular ROS levels were decreased in LPS + CsA group. Cellular ribulose 5-phosphate and NADPH/NADP + related to the pentose phosphate pathway (PPP) were reduced in LPS + CsA group. In addition, CsA could decrease G6PD activity in neutrophils stimulated with LPS, and the results were further verified by inhibiting G6PD activity. At last, P53 protein was highly expressed in LPS + CsA group compared with the LPS group. Intracellular G6PD activity, ROS level and NETs formation, which were downregulated by CsA, could be reversed by a P53 inhibitor.

Conclusion
Our results indicated CsA could alleviate the severity of colitis by decreasing the formation of NETs in vivo. In vitro, CsA reduced ROS-dependent NETs release via downregulating PPP and cellular ROS levels by decreasing G6PD activity directly by activating the P53 protein.
Molecular mechanism and therapeutic potential of HDAC9 in intervertebral disc degeneration
Authors: Lei Ming , Lin Hui , Shi Deyao , Hong Pan , Song Hui , Herman Bomansaan , Liao Zhiwei , Yang Cao 
Published: December 2023

Abstract
Background
Intervertebral disc degeneration (IVDD) is the major cause of low-back pain. Histone deacetylase 9 (HDAC9) was dramatically decreased in the degenerative nucleus pulposus (NP) samples of patients with intervertebral disc degeneration (IVDD) according to bioinformatics analysis of Gene Expression Omnibus (GEO) GSE56081 dataset. This study aims to investigate the role of HDAC9 in IVDD progression.

Methods
The contribution of HDAC9 to the progression of IVDD was assessed using HDAC9 knockout (HDAC9KO) mice and NP-targeted HDAC9-overexpressing mice by IVD injection of adenovirus-mediated HDAC9 under a Col2a1 promoter. Magnetic resonance imaging (MRI) and histological analysis were used to examine the degeneration of IVD. NP cells were isolated from mice to investigate the effects of HDAC9 on apoptosis and viability. mRNA-seq and coimmunoprecipitation/mass spectrometry (co-IP/MS) analysis were used to analyze the HDAC9-regulated factors in the primary cultured NP cells.

Results
HDAC9 was statistically decreased in the NP tissues in aged mice. HDAC9KO mice spontaneously developed age-related IVDD compared with wild-type (HDAC9WT) mice. In addition, overexpression of HDAC9 in NP cells alleviated IVDD symptoms in a surgically-induced IVDD mouse model. In an in vitro assay, knockdown of HDAC9 inhibited cell viability and promoted cell apoptosis of NP cells, and HDAC9 overexpression had the opposite effects in NP cells isolated from HDAC9KO mice. Results of mRNA-seq and co-IP/MS analysis revealed the possible proteins and signaling pathways regulated by HDAC9 in NP cells. RUNX family transcription factor 3 (RUNX3) was screened out for further study, and RUNX3 was found to be deacetylated and stabilized by HDAC9. Knockdown of RUNX3 restored the effects of HDAC9 silencing on NP cells by inhibiting apoptosis and increasing viability.

Conclusion
Our results suggest that HDAC9 plays an important role in the development and progression of IVDD. It might be required to protect NP cells against the loss of cell viability and apoptosis by inhibiting RUNX3 acetylation and expression during IVDD. Together, our findings suggest that HDAC9 may be a potential therapeutic target in IVDD.

Graphical Abstract
Short-time allowances in times of crisis: a survey experiment
Authors: Stephan Gesine , Dütsch Matthias , Osiander Christopher 
Published: December 2023

AbstractDuring the COVID-19 pandemic, many countries used short-time work schemes, i.e., subsidies for temporary working hours reductions due to production drops. In Germany, regulations on entitlements and benefits have been much more generous during the pandemic than they were in noncrisis times. This paper conducts a factorial survey experiment among the workforce to investigate which amounts of short-time benefits and which associated replacement rates were perceived as appropriate during the pandemic. We interpret our findings in the context of the deservingness theory. Our results show that the assessments are partly consistent with the legal design features in Germany. One of our key findings is that, according to respondents, the short-time allowance should decrease slightly with an increasing duration of short-time work. In Germany, however, with the onset of the pandemic, a rule was temporarily implemented that step-wise increased short-time work benefits with the duration of short-time work.
PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data
Authors: Hu Xiaojun , Hurtado-Gonzales Oscar P. , Adhikari Bishwo N. , French-Monar Ronald D. , Malapi Martha , Foster Joseph A. , McFarland Clint D. 
Published: December 2023

Abstract
Background
Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-throughput sequencing (HTS) has been applied successfully for plant pathogen discovery, leading to its current application in routine pathogen detection. However, the analysis of massive amounts of HTS data has become one of the major challenges for the use of HTS more broadly as a rapid diagnostics tool. Several bioinformatics pipelines have been developed to handle HTS data with a focus on plant virus and viroid detection. However, there is a need for an integrative tool that can simultaneously detect a wider range of other plant pathogens in HTS data, such as bacteria (including phytoplasmas), fungi, and oomycetes, and this tool should also be capable of generating a comprehensive report on the phytosanitary status of the diagnosed specimen.

Results
We have developed an open-source bioinformatics pipeline called PhytoPipe (Phytosanitary Pipeline) to provide the plant pathology diagnostician community with a user-friendly tool that integrates analysis and visualization of HTS RNA-seq data. PhytoPipe includes quality control of reads, read classification, assembly-based annotation, and reference-based mapping. The final product of the analysis is a comprehensive report for easy interpretation of not only viruses and viroids but also bacteria (including phytoplasma), fungi, and oomycetes. PhytoPipe is implemented in Snakemake workflow with Python 3 and bash scripts in a Linux environment. The source code for PhytoPipe is freely available and distributed under a BSD-3 license.

Conclusions
PhytoPipe provides an integrative bioinformatics pipeline that can be used for the analysis of HTS RNA-seq data. PhytoPipe is easily installed on a Linux or Mac system and can be conveniently used with a Docker image, which includes all dependent packages and software related to analyses. It is publicly available on GitHub at https://github.com/healthyPlant/PhytoPipe and on Docker Hub at https://hub.docker.com/r/healthyplant/phytopipe.
Profiles of global mutations in the human intercellular adhesion molecule-1 (ICAM-1) shed light on population-specific malaria susceptibility
Authors: Gill Jasmita , Singh Himmat , Sharma Amit 
Published: December 2023

AbstractPlasmodium falciparum is responsible for malaria-related morbidity and mortality. PfEMP1 (P. falciparum erythrocyte membrane protein 1) mediates infected erythrocytes adhesion to various surface vascular receptors, including intercellular adhesion molecule-1 (ICAM-1), associating this interaction with severe malaria in several studies. Genetic variation in host ICAM-1 plays a significant role in determining susceptibility to malaria infection via clinical phenotypes such as the ICAM-1Kilifi variant which has been reported to be associated with susceptibility in populations. Our genomic and structural analysis of single nucleotide polymorphisms (SNPs) in ICAM-1 revealed 9 unique mutations each in its distinct A-type and BC-type PfEMP1 DBLβ-interacting regions. These mutations are noted in only a few field isolates and mainly in the African/African American population. The ICAM-1Kilifi variant lies in a flexible loop proximal to the DBLβ-interacting region. This analysis will assist in establishing functional correlations of reported global mutations via experimental and clinical studies and in the tailored design of population-specific genetic surveillance studies. Understanding host polymorphism as an evolutionary force in diverse populations can help to predict predisposition to disease severity and will contribute towards laying the framework for designing population-specific personalized medicines for severe malaria.
Cognitive dysfunction in systemic lupus erythematosus is associated with disease activity and oxidative stress: a comparative study with rheumatoid arthritis for identifying biomarkers
Authors: de Sousa Daniela Cabral , Sobreira Emmanuelle Silva Tavares , Feitosa Werbety Lucas Queiroz , Aires Ticiana Maria Pinto Moreira , Araújo Leticia Pastuszka Paz , Silva Andressa Laura Castro , Joventino Caroline Brandão , Silveira Nathalia Maria Tomaz , Chaves-Filho Adriano José Maia , Macêdo Danielle Silveira , Braga-Neto Pedro 
Published: December 2023

Abstract
Background
The prevalence and pathophysiological mechanisms of cognitive deficits (CD) Systemic Lupus Erythematosus (SLE) and Rheumatoid arthritis (RA) are very heterogeneous and poorly understood. We characterized CD in patients with SLE compared with RA patients and healthy controls. We compared the neuropsychological profile of SLE and RA with patients’ oxidative/inflammatory biomarkers for CD.

Methods
We performed a cross-sectional study, including 50 SLE patients, 29 RA patients, and 32 healthy controls. SLEDAI and DAS28 assessed disease activity. SF-36 questionnaire and a battery of cognitive tests were applied to all participants. Blood samples were collected to determine IL-6, S100ß, myeloperoxidase (MPO), malondialdehyde and reduced glutathione (GSH) alterations.

Results
In the SLE group, higher GSH was associated with the absence of CD (With CD = 69 ± 49, Without CD = 112 ± 81, p = 0.030), while higher IL-6 was associated with the presence of CD in the RA group (With CD = 603 ± 173, Without CD = 431 ± 162, p = 0.032). Regarding specific cognitive domains, in SLE higher MPO was associated with poor performance in reasoning and abstraction (p = 0.039), higher IL-6 was associated with poor performance in inhibitory control and attention (p = 0.031), and higher GSH was associated with better performance in memory(p = 0.021). Higher SLEDAI was associated with poor performance in semantic fluency(p = 0.031), inhibitory control, and attention in the SLE group(p = 0.037). In the RA group, higher DAS-28 was associated with poor performance in executive functions(p = 0.016) and phonemic fluency (p = 0.003).

Conclusion
SLE patients’ disease activity, inflammatory state, and oxidative stress were associated with CD. In RA patients, CD was associated with disease activity and inflammatory state. These results encourage further studies with larger samples aiming to confirm oxidative stress parameters as biomarkers of CD in SLE patients.
Serum magnesium level and cardiac valve calcification in hemodialysis patients
Authors: Tsai Shihming , Li Yuehong , Wu Xianglan 
Published: December 2023

Abstract
Introduction
Cardiac valve calcification is closely related to cardiovascular disease. The aim of this study was to investigate the magnesium level and cardiac valve calcification in hemodialysis patients.

Methods
A cross-sectional study was conducted in 105 maintenance hemodialysis patients with complete follow-up data from June 2020 to May 2021 in Beijing Tsinghua Changgung Hospital, Tsinghua University. Baseline data, including sex, age, primary disease, liver and kidney function, electrolytes and parathyroid hormone, were recorded. According to their echocardiograms, patients were divided into a cardiac valve calcification group and a noncardiac valve calcification group, and the correlations between valve calcification and clinical data were analyzed.

Results
Of 105 patients under hemodialysis, 60 (56.6%) were male, with an average age of 62.1 ± 13.5 years and a mean dialysis duration of 58.8 ± 45.4 months. The majority of primary renal diseases were diabetic nephropathy (55, 51.9%). Approximately 64.8% of the 105 maintenance hemodialysis patients had cardiac valve calcification, and 35.2% were in the noncardiac valve calcification group. The independent t test and the chi-square test analysis showed that the cardiac valve calcification group had older age, higher smoking rate, diabetes mellitus, lower extremity arterial occlusion, coronary heart disease, and coronary artery calcification ratio but lower parathyroid hormone, serum calcium, serum magnesium, albumin, prealbumin, and high-density lipoprotein cholesterol levels (P < 0.05). Logistic regression analysis showed that age, diabetes mellitus, coronary artery calcification, lower serum magnesium, lower serum calcium, and lower parathyroid hormone levels were associated with valve calcification.

Conclusion
The presence of cardiac valve calcification was associated with age, calcium, phosphorus and lower magnesium level. These factors we should pay more attention in clinical practice.
The endorsement of general and artificial intelligence reporting guidelines in radiological journals: a meta-research study
Authors: Zhong Jingyu , Xing Yue , Lu Junjie , Zhang Guangcheng , Mao Shiqi , Chen Haoda , Yin Qian , Cen Qingqing , Jiang Run , Hu Yangfan , Ding Defang , Ge Xiang , Zhang Huan , Yao Weiwu 
Published: December 2023

Abstract
Background
Complete reporting is essential for clinical research. However, the endorsement of reporting guidelines in radiological journals is still unclear. Further, as a field extensively utilizing artificial intelligence (AI), the adoption of both general and AI reporting guidelines would be necessary for enhancing quality and transparency of radiological research. This study aims to investigate the endorsement of general reporting guidelines and those for AI applications in medical imaging in radiological journals, and explore associated journal characteristic variables.

Methods
This meta-research study screened journals from the Radiology, Nuclear Medicine & Medical Imaging category, Science Citation Index Expanded of the 2022 Journal Citation Reports, and excluded journals not publishing original research, in non-English languages, and instructions for authors unavailable. The endorsement of fifteen general reporting guidelines and ten AI reporting guidelines was rated using a five-level tool: “active strong”, “active weak”, “passive moderate”, “passive weak”, and “none”. The association between endorsement and journal characteristic variables was evaluated by logistic regression analysis.

Results
We included 117 journals. The top-five endorsed reporting guidelines were CONSORT (Consolidated Standards of Reporting Trials, 58.1%, 68/117), PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses, 54.7%, 64/117), STROBE (STrengthening the Reporting of Observational Studies in Epidemiology, 51.3%, 60/117), STARD (Standards for Reporting of Diagnostic Accuracy, 50.4%, 59/117), and ARRIVE (Animal Research Reporting of In Vivo Experiments, 35.9%, 42/117). The most implemented AI reporting guideline was CLAIM (Checklist for Artificial Intelligence in Medical Imaging, 1.7%, 2/117), while other nine AI reporting guidelines were not mentioned. The Journal Impact Factor quartile and publisher were associated with endorsement of reporting guidelines in radiological journals.

Conclusions
The general reporting guideline endorsement was suboptimal in radiological journals. The implementation of reporting guidelines for AI applications in medical imaging was extremely low. Their adoption should be strengthened to facilitate quality and transparency of radiological study reporting.
Exploring stakeholders’ experiences of comprehensive geriatric assessment in the community and out-patient settings: a qualitative evidence synthesis
Authors: Hayes Christina , Fitzgerald Christine , O’Shaughnessy Íde , Condon Brian , Leahy Aoife , O’Connor Margaret , Manning Molly , Griffin Anne , Glynn Liam , Robinson Katie , Galvin Rose 
Published: December 2023

Abstract
Background
Comprehensive Geriatric Assessment (CGA) is a multidimensional interdisciplinary process that addresses an older adult’s biopsychosocial capabilities to create an integrated and co-ordinated plan of care. While quantitative evidence that demonstrates the positive impacts of CGA on clinical and process outcomes has been synthesised, to date qualitative research reporting how older adults and service providers experience CGA has not been synthesised. This study aimed to systematically review and synthesise qualitative studies reporting community-dwelling older adults’, caregivers’ and healthcare professionals’ (HCP) experiences of CGA in the primary care and out-patient (OPD) setting.

Method
We systematically searched five electronic databases including MEDLINE, CINAHL, PsycINFO, PsycARTICLES and Social Sciences Full Text targeting qualitative or mixed methods studies that reported qualitative findings on older adults’, caregivers’ and HCPs’ experiences of CGA in primary care or out-patient settings. There were no language or date restrictions applied to the search. The protocol was registered with the PROSPERO database (Registration: CRD42021283167). The methodological quality of the included studies was appraised using the Critical Appraisal Skills Programme checklist for qualitative research. Results were synthesised according to Noblit and Hare’s seven-step approach to meta-ethnography, which involves an iterative and inductive process of data synthesis.

Results
Fourteen studies were included where CGA was completed in the home, general practice, out-patient setting in acute hospitals and in hybrid models across the community and hospital-based OPD settings. Synthesis generated four key themes: (1) CGA is experienced as a holistic process, (2) The home environment enhances CGA, (3) CGA in the community is enabled by a collaborative approach to care, and (4) Divergent experiences of the meaningful involvement of older adults, caregivers and family in the CGA process.

Conclusion
Findings demonstrate that CGA in a home-based or OPD setting allows for a holistic and integrated approach to care for community-dwelling older adults while increasing patient satisfaction and accessibility of healthcare. Healthcare professionals in the community should ensure meaningful involvement of older adults and their families or caregivers in the CGA process. Further robustly designed and well reported trials of different models of community-based CGA informed by the findings of this synthesis are warranted.
Diagnostic value of 3D volume measurement of central pulmonary artery based on CTPA images in the pulmonary hypertension
Authors: Zhao Wanwan , Guo Jialing , Dong Ningli , Hei Huanhuan , Duan Xiaoyi , Shen Cong 
Published: December 2023

Abstract
Background
This retrospective study aims to evaluate the diagnostic value of volume measurement of central pulmonary arteries using computer tomography pulmonary angiography (CTPA) for predicting pulmonary hypertension (PH).

Methods
A total of 59 patients in our hospital from November 2013 to April 2021 who underwent both right cardiac catheterization (RHC) and CTPA examination were included. Systolic pulmonary artery pressure (SPAP), mean PAP (mPAP), and diastolic PAP (DPAP) were acquired from RHC testing. Patients were divided into the non-PH group (18 cases) and the PH group (41 cases). The diameters of the main pulmonary artery (DMPA), right pulmonary artery (DRPA), and left pulmonary artery (DLPA) were measured manually. A 3D model software was used for the segmentation of central pulmonary arteries. The cross-sectional areas (AMPA, ARPA, ALPA) and the volumes (VMPA, VRPA, VLPA) were calculated. Measurements of the pulmonary arteries derived from CTPA images were compared between the two groups, and correlated with the parameters of RHC testing. ROC curves and decision curve analysis (DCA) were used to evaluate the benefit of the three-dimensional CTPA parameters for predicting PH. A multiple linear regression model with a forward-step approach was adopted to integrate all statistically significant CTPA parameters for PH prediction.

Results
All parameters (DMPA, DRPA, DLPA, AMPA, ARPA, ALPA, VMPA, VRPA, and VLPA) of CTPA images exhibited significantly elevated in the PH group in contrast to the non-PH group (P < 0.05), and showed positive correlations with the parameters of RHC testing (mPAP, DPAP, SPAP) (r ranged 0.586~0.752 for MPA, 0.527~0.640 for RPA, and 0.302~0.495 for LPA, all with P < 0.05). For the MPA and RPA, 3D parameters showed higher correlation coefficients compared to their one-dimensional and two-dimensional counterparts. The ROC analysis indicated that the VMPA showed higher area under the curves (AUC) than the DMPA and AMPA without significance, and the VRPA showed higher AUC than the DRPA and ARPA significantly (DRPA vs. VRPA, Z = 2.029, P = 0.042; ARPA vs. VRPA, Z = 2.119, P = 0.034). The DCA demonstrated that the three-dimensional parameters could provide great net benefit for MPA and RPA. The predictive equations for mPAP, DPAP, and SPAP were formulated as [8.178 + 0.0006 * VMPA], [1.418 + 0.0005 * VMPA], and [-11.137 + 0.0006*VRPA + 1.259 * DMPA], respectively.

Conclusion
The 3D volume measurement of the MPA and RPA based on CTPA images maybe more informative than the traditional diameter and cross-sectional area in predicting PH.