bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated connectivity risk ranking for phosphorus and nitrogen along agricultural open ditches to inform targeted and specific mitigation management
Authors: Opoku D. G. , Healy M. G. , Fenton O. , Daly K. , Condon T. , Tuohy P. 
Published: February 2024

Introduction: On dairy farms with poorly drained soils and high rainfall, open ditches receive nutrients from different sources along different pathways which are delivered to surface water. Recently, open ditches were ranked in terms of their hydrologic connectivity risk for phosphorus (P) along the open ditch network. However, the connectivity risk for nitrogen (N) was not considered in that analysis, and there remains a knowledge gap. In addition, the P connectivity classification system assumes all source–pathway interactions within open ditches are active, but this may not be the case for N. The objective of the current study, conducted across seven dairy farms, was to create an integrated connectivity risk ranking for P and N simultaneously to better inform where and which potential mitigation management strategies could be considered.Methods: First, a conceptual figure of known N open ditch source–pathway connections, developed using both the literature and observations in the field, was used to identify water grab sampling locations on the farms. During fieldwork, all open ditch networks were digitally mapped, divided into ditch sections, and classified in terms of the existing P connectivity classification system.Results and Discussion: The results showed that not all source–pathway connections were present across ditch categories for all species of N. This information was used to develop an improved open ditch connectivity classification system. Farmyard-connected ditches were the riskiest for potential point source losses, and outlet ditches had the highest connectivity risk among the other ditch categories associated with diffuse sources. Tailored mitigation options for P and N speciation were identified for these locations to intercept nutrients before reaching receiving waters. In ditches associated with diffuse sources, nitrate was introduced by subsurface sources (i.e., in-field drains and groundwater interactions from springs, seepage, and upwelling) and ammonium was introduced through surface connectivity pathways (i.e., runoff from internal roadways). On similar dairy farms where open ditches are prevalent, the integrated classification system and mapping procedure presented herein will enable a targeted and nutrient-specific mitigation plan to be developed. The same methodology may be applied to develop a bespoke integrated connectivity risk ranking for P and N along agricultural open ditches in other areas.
Single-cell RNA sequencing reveals cell type-specific immune regulation associated with human neuromyelitis optica spectrum disorder
Authors: Jiang Yushu , Dai Shuhua , Pang Rui , Qin Lingzhi , Zhang Milan , Liu Huiqin , Wang Xiaojuan , Zhang Jiewen , Peng Gongxin , Wang Yongchao , Li Wei 
Published: February 2024

IntroductionOne rare type of autoimmune disease is called neuromyelitis optica spectrum disorder (NMOSD) and the peripheral immune characteristics of NMOSD remain unclear.MethodsHere, single-cell RNA sequencing (scRNA-seq) is used to characterize peripheral blood mononuclear cells from individuals with NMOSD.ResultsThe differentiation and activation of lymphocytes, expansion of myeloid cells, and an excessive inflammatory response in innate immunity are observed. Flow cytometry analyses confirm a significant increase in the percentage of plasma cells among B cells in NMOSD. NMOSD patients exhibit an elevated percentage of CD8+ T cells within the T cell population. Oligoclonal expansions of B cell receptors are observed after therapy. Additionally, individuals with NMOSD exhibit elevated expression of CXCL8, IL7, IL18, TNFSF13, IFNG, and NLRP3.DiscussionPeripheral immune response high-dimensional single-cell profiling identifies immune cell subsets specific to a certain disease and identifies possible new targets for NMOSD.
Impacts of systemic inflammation response index on the prognosis of patients with ischemic heart failure after percutaneous coronary intervention
Authors: Ma Meishi , Wu Kang , Sun Tienan , Huang Xin , Zhang Biyang , Chen Zheng , Zhao Zehao , Zhao Jiajian , Zhou Yujie 
Published: February 2024

BackgroundAtherosclerosis and cardiovascular diseases are significantly affected by low-grade chronic inflammation. As a new inflammatory marker, the systemic inflammation response index (SIRI) has been demonstrated to be associated with several cardiovascular disease prognoses. This study aimed to investigate the prognostic impact of SIRI in individuals having ischemic heart failure (IHF) following percutaneous coronary intervention (PCI).MethodsThis observational, retrospective cohort study was conducted at a single site. Finally, the research involved 1,963 individuals with IHF who underwent PCI, with a 36-month follow-up duration. Based on the SIRI quartiles, all patients were classified into four groups. Major adverse cardiovascular events (MACEs) were the primary outcomes. Every element of the main endpoint appeared in the secondary endpoints: all-cause mortality, non-fatal myocardial infarction (MI), and any revascularization. Kaplan–Meier survival analysis was conducted to assess the incidence of endpoints across the four groups. Multivariate Cox proportional hazards analysis confirmed the independent impact of SIRI on both the primary and secondary endpoints. The restricted cubic spline (RCS) was used to assess the nonlinear association between the SIRI and endpoints. Subgroup analysis was performed to confirm the implications of SIRI on MACE in the different subgroups.ResultsThe main outcome was much more common in patients with a higher SIRI. The Kaplan–Meier curve was another tool that was used to confirm the favorable connection between SIRI and MACE. SIRI was individually connected to a higher chance of the main outcome according to multivariate analyses, whether or not SIRI was a constant [SIRI, per one−unit increase, hazard ratio (HR) 1.04, 95% confidence interval (95% CI) 1.01–1.07, p = 0.003] or categorical variable [quartile of SIRI, the HR (95% CI) values for quartile 4 were 1.88 (1.47–2.42), p &lt;0.001, with quartile 1 as a reference]. RCS demonstrated that the hazard of the primary and secondary endpoints generally increased as SIRI increased. A non-linear association of SIRI with the risk of MACE and any revascularization (Non-linear P &lt;0.001) was observed. Subgroup analysis confirmed the increased risk of MACE with elevated SIRI in New York Heart Association (NYHA) class III–IV (P for interaction = 0.005).ConclusionIn patients with IHF undergoing PCI, increased SIRI was a risk factor for MACE independent of other factors. SIRI may represent a novel, promising, and low-grade inflammatory marker for the prognosis of patients with IHF undergoing PCI.
CD274 (PD-L1) negatively regulates M1 macrophage polarization in ALI/ARDS
Authors: Tang Nana , Yang Yang , Xie Yifei , Yang Guohui , Wang Qin , Li Chang , Liu Zeyi , Huang Jian-an 
Published: February 2024

BackgroundAcute lung injury (ALI)/severe acute respiratory distress syndrome (ARDS) is a serious clinical syndrome characterized by a high mortality rate. The pathophysiological mechanisms underlying ALI/ARDS remain incompletely understood. Considering the crucial role of immune infiltration and macrophage polarization in the pathogenesis of ALI/ARDS, this study aims to identify key genes associated with both ALI/ARDS and M1 macrophage polarization, employing a combination of bioinformatics and experimental approaches. The findings could potentially reveal novel biomarkers for the diagnosis and management of ALI/ARDS.MethodsGene expression profiles relevant to ALI were retrieved from the GEO database to identify co-upregulated differentially expressed genes (DEGs). GO and KEGG analyses facilitated functional annotation and pathway elucidation. PPI networks were constructed to identify hub genes, and differences in immune cell infiltration were subsequently examined. The expression of hub genes in M1 versus M2 macrophages was evaluated using macrophage polarization datasets. The diagnostic utility of CD274 (PD-L1) for ARDS was assessed by receiver operating characteristic (ROC) analysis in a validation dataset. Experimental confirmation was conducted using two LPS-induced M1 macrophage models and an ALI mouse model. The role of CD274 (PD-L1) in M1 macrophage polarization and associated proinflammatory cytokine production was further investigated by siRNA-mediated silencing.ResultsA total of 99 co-upregulated DEGs were identified in two ALI-linked datasets. Enrichment analysis revealed that these DEGs were mainly involved in immune-inflammatory pathways. The following top 10 hub genes were identified from the PPI network: IL-6, IL-1β, CXCL10, CD274, CCL2, TLR2, CXCL1, CCL3, IFIT1, and IFIT3. Immune infiltration analysis revealed a significantly increased abundance of M1 and M2 macrophages in lung tissue from the ALI group compared to the control group. Subsequent analysis confirmed that CD274 (PD-L1), a key immunological checkpoint molecule, was highly expressed within M1 macrophages. ROC analysis validated CD274 (PD-L1) as a promising biomarker for the diagnosis of ARDS. Both in vitro and in vivo experiments supported the bioinformatics analysis and confirmed that the JAK-STAT3 pathway promotes CD274 (PD-L1) expression on M1 macrophages. Importantly, knockdown of CD274 (PD-L1) expression potentiated M1 macrophage polarization and enhanced proinflammatory cytokines production.ConclusionThis study demonstrates a significant correlation between CD274 (PD-L1) and M1 macrophages in ALI/ARDS. CD274 (PD-L1) functions as a negative regulator of M1 polarization and the secretion of proinflammatory cytokines in macrophages. These findings suggest potential new targets for the diagnosis and treatment of ALI/ARDS.
Neoadjuvant Immune Checkpoint Inhibitors in hepatocellular carcinoma: a meta-analysis and systematic review
Authors: Tian Chunhong , Yu Yifan , Wang Yuqing , Yang Lunwei , Tang Ying , Yu Chengyang , Feng Gaofei , Zheng Dayong , Wang Xiongwen 
Published: February 2024

BackgroundNeoadjuvant immunotherapy has demonstrated beneficial outcomes in various cancer types; however, standardized protocols for neoadjuvant immunotherapy in hepatocellular carcinoma (HCC) are currently lacking. This systematic review and meta-analysis aims to investigate the reliability of neoadjuvant immunotherapy’s efficacy and safety in the context of HCC.MethodsA systematic search was conducted across PubMed (MEDLINE), EMBASE, the Web of Science, the Cochrane Library, and conference proceedings to identify clinical trials involving resectable HCC and neoadjuvant immunotherapy. Single-arm meta-analyses were employed to compute odds ratios and 95% confidence intervals (CIs). Heterogeneity analysis, data quality assessment, and subgroup analyses based on the type of immunotherapy drugs and combination therapies were performed. This meta-analysis is registered in PROSPERO (identifier CRD42023474276).ResultsThis meta-analysis included 255 patients from 11 studies. Among resectable HCC patients, neoadjuvant immunotherapy exhibited an overall major pathological response (MPR) rate of 0.47 (95% CI 0.31-0.70) and a pathological complete response (pCR) rate of 0.22 (95% CI 0.14-0.36). The overall objective response rate (ORR) was 0.37 (95% CI 0.20-0.69), with a grade 3-4 treatment-related adverse event (TRAE) incidence rate of 0.35 (95% CI 0.24-0.51). Furthermore, the combined surgical resection rate was 3.08 (95% CI 1.66-5.72). Subgroup analysis shows no significant differences in the efficacy and safety of different single-agent immunotherapies; the efficacy of dual ICIs (Immune Checkpoint Inhibitors) combination therapy is superior to targeted combined immunotherapy and monotherapy, while the reverse is observed in terms of safety.DiscussionNeoadjuvant immunotherapy presents beneficial outcomes in the treatment of resectable HCC. However, large-scale, high-quality experiments are warranted in the future to provide robust data support.
Quality of life and quality of education among physiotherapy students in Europe
Authors: Schramlová Michaela , Řasová Kamila , Jonsdottir Johanna , Pavlíková Markéta , Rambousková Jolana , Äijö Marja , Šlachtová Martina , Kobesová Alena , Žiaková Elena , Kahraman Turhan , Pavlů Dagmar , Bermejo-Gil Beatriz María , Bakalidou Daphne , Billis Evdokia , Georgios Papagiannis , Alves-Guerreiro José , Strimpakos Nikolaos , Příhoda Aleš , Kiviluoma-Ylitalo Marika , Lähteenmäki Marja-Leena , Koišová Jana , Berisha Gentiana , Hagovská Magdalena , Arca Anna Laura , Cortés-Amador Sara 
Published: February 2024

BackgroundThe study of physiotherapy is challenging and can affect the students’ well-being and quality of life. The aim of this study was to describe and compare factors that could affect well-being among students across Europe.MethodsIn this descriptive cross-sectional study using an online questionnaire survey, students of bachelor’s physiotherapy programs from 23 European faculties, from 8 countries, were interviewed on mental health and stress burden, sleep quality, dietary habits, and physical activity.ResultsAlthough 75% of students rated their quality of life positively and 47% were satisfied with their mental health, 65% showed higher levels of stress and 51% described impaired sleep quality. The minimum physical activity of 150 min weekly was described by 79% of students, within which 67% engaged in strengthening twice a week. Students with a higher stress load/worse psychological health also showed worse sleep quality and lower amount of physical activity, women were significantly worse off. In terms of physical activity and sleep quality, students from Finland and Kosovo achieved the best results, while students from Italy, Greece, and Portugal achieved the worst. Students from Italy indicated the greatest dissatisfaction with the organisation of the study system and communication with teachers, while in Kosovo students rated the communication and study organisation the highest. All students had a problem with adhering to nutritional habits. Students from Italy and Spain, with the lowest body mass indexes and weight averages, were closest to the nutrition recommendations.ConclusionWe demonstrated that physiotherapy students are burdened with stress, suffer from sleep disorders, and do not follow the recommendations regarding nutrition nor physical activity. There are significant differences between universities and countries in some aspects.
Distinct characteristics and prognosis of IgA nephropathy patients with nephrotic syndrome: a propensity score-matched cohort study
Authors: Jiang Yuanyuan , Chen Pei , Zhao Wenjing , Liu Lijun , Shi Sufang , Lv Jicheng , Zhang Hong 
Published: February 2024

IntroductionIgA nephropathy (IgAN) is the most prevalent primary glomerulonephritis globally. While nephrotic syndrome (NS) is uncommon in IgAN, its significance remains unclear.MethodsWe conducted a retrospective analysis of 170 IgAN patients, classifying them into NS (n = 85) and non-NS (n = 85) groups. Our study aims to compare their clinical characteristics, treatment responses, and prognoses. Patients were selected based on renal biopsy from 2003 to 2020. Propensity score matching ensured comparability. Clinical, pathological, and immunological data were analyzed. Composite endpoints were defined as end-stage kidney disease (ESKD) or a 30% decline in estimated glomerular filtration rate (eGFR).ResultsNS patients showed higher eGFR (74.3 ± 36.8 vs. 61.5 ± 33.6 mL/min.1.73 m2, p = 0.02), severe hematuria (35.0 (4.7,147.5) vs. 4.0 (1.8,45,0) cells/μl, p &lt; 0.001), severe foot process effacement (p = 0.01), and lower C3 levels (1.0 ± 0.3 vs. 1.1 ± 0.2 g/L, p = 0.03). In contrast, the non-NS group had higher BMI (24.3 ± 4.0 vs. 26.8 ± 3.7 kg/m2, p &lt; 0.001) and elevated serum uric acid levels (376 (316,417) vs. 400 (362, 501) mmol/L, p = 0.001), suggesting metabolic factors might contribute to their condition. Both groups exhibited similar MESTC scores. NS patients had higher complete remission rates (26.2% vs. 14.1%, p = 0.04). Cox regression revealed NS independently associated with a higher risk of composite endpoints (HR = 1.97, 95% CI 1.05–3.72, p = 0.04). Linear mixed models did not show significant eGFR trajectory differences.DiscussionThis study has established that IgAN patients with NS exhibit distinct characteristics, including active disease and increased complement activation. NS is independently associated with a poorer prognosis, emphasizing the need for targeted interventions in this subgroup.
Germline RECQL gene mutations in Chinese patients with breast cancer
Authors: Hu Jun , Shen Yong , Zhang Kun , Chen Yiding 
Published: February 2024

IntroductionBreast cancer is the most common malignant tumor in women, seriously threatening health and survival. TP-dependent DNA helicase Q1 (RECQL) is a breast cancer susceptibility gene with possible familial links. However, RECQL gene mutations among Chinese women with breast cancer have not been evaluated. Therefore, this study assessed RECQL mutations and their relationships with clinicopathological and epidemiological characteristics in Chinese women with breast cancer.MethodClinical information was also obtained via the hospital information system and a follow-up questionnaire. Peripheral venous blood (2 mL) was extracted from all patients and stored at –80°C for future use; the early venous blood samples were from our hospital’s sample bank. RECQL gene sequencing were performed by the Shanghai Aishe Gene Company (China).ResultsWe found that a RECQL mutation is a susceptibility factor for breast cancer. Moreover, patients with RECQL mutations were more likely to have a family history of breast cancer than those without. Also, patients with RECQL variants of uncertain significance (VUS) were less likely to develop invasive ductal carcinoma than those without. In addition, unexplained RECQL mutations occurred more often in patients with human epidermal growth factor receptor 2+ breast cancer than in those with other subtypes.DiscussionThese results provide a basis for creating screening criteria specific to Chinese women. However, the frequency of RECQL mutations was low, and the number of pathogenic mutations was too small and could not be analyzed. Thus, more extensive, long-term studies that include other functional experiments are needed to verify these results.
Prevalence of Mycobacterium kansasii in clinical and environmental isolates, a systematic review and meta-analysis
Authors: Narimisa Negar , Bostanghadiri Narjess , Goodarzi Forough , Razavi Shabnam , Jazi Faramarz Masjedian 
Published: February 2024

BackgroundMycobacterium kansasii infection is one of the most common causes of non-tuberculosis mycobacterial (NTM) disease worldwide. However, accurate information on the global prevalence of this bacterium is lacking. Therefore, this study was conducted to investigate the prevalence of M. kansasii in clinical and environmental isolates.MethodsDatabases, including PubMed, Scopus, and the Web of Science, were utilized to gather articles on the prevalence of M. kansasii in clinical and environmental isolates. The collected data were analyzed using Comprehensive Meta-Analysis software.ResultsA total of 118 and 16 studies met the inclusion criteria and were used to analyze the prevalence of M. kansasii in clinical and environmental isolates, respectively. The prevalence of M. kansasii in NTM and environmental isolates were 9.4 and 5.8%, respectively. Subsequent analysis showed an increasing prevalence of M. kansasii over the years. Additionally, the results indicated a significant difference in the prevalence of this bacteria among different regions.ConclusionThe relatively high prevalence of M. kansasii among NTM isolates suggests the need for further implementation of infection control strategies. It is also important to establish appropriate diagnostic criteria and management guidelines for screening this microorganism in environmental samples in order to prevent its spread, given its high prevalence in environmental isolates.
In vitro anti-Helicobacter pylori activity and the underlining mechanism of an empirical herbal formula – Hezi Qingyou
Authors: Feng Zhong , Li Hui , Hao Yajie , Peng Chang , Ou Ling , Jia Junwei , Xun Mingjin , Zou Yuanjing , Chen Meiyun , Zhang Guimin , Yao Meicun 
Published: February 2024

BackgroundHelicobacter pylori (H. pylori) is thought to primarily colonize the human stomach and lead to various gastrointestinal disorders, such as gastritis and gastric cancer. Currently, main eradication treatment is triple or quadruple therapy centered on antibiotics. Due to antibiotic resistance, the eradication rate of H. pylori is decreasing gradually. Therefore, searching for anti-H. pylori drugs from herbal sources has become a strategy for the treatment. Our team proposed a Hezi Qingyou Formula (HZQYF), composed of Chebulae Fructus, Ficus hirta Vahl and Cloves, and studied its anti-H. pylori activity and mechanism.MethodsChemical components of HZQYF were studied using UHPLC–MS/MS and HPLC. Broth microdilution method and agar dilution method were used to evaluate HZQYF’s antibacterial activity. The effects of HZQYF on expression of adhesion genes (alpA, alpB, babA), urease genes (ureE, ureF), and flagellar genes (flaA, flaB) were explored using Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) technology. Effects on morphology and permeability of the extracellular membrane were studied using scanning electron microscopy (SEM) and N-phenylnaphthalen-1-amine (NPN) uptake. Effect on urease activity was studied using a urease kinetics analysis in vitro. Immunofluorescence staining method was used to examine the effect on adhesion. Western blot was used to examine the effect on cagA protein.ResultsMinimum inhibitory concentration (MIC) values of the formula against H. pylori clinical strains and standard strains were 80–160 μg/mL, and minimum bactericidal concentration (MBC) values were 160–320 μg/mL. The formula could down-regulate the expression of adhesion genes (alpA, alpB, babA), urease genes (ureE, ureF) and flagellar genes (flaA, flaB), change the morphology of H. pylori, increase its extracellular membrane permeability, and decrease its urease activity.ConclusionPresent studies confirmed that HZQYF had promising in vitro anti-H. pylori activities and demonstrated its possible mechanism of action by down-regulating the bacterial adhesion, urease, and flagellar gene expression, which provided scientific bases for further clinical investigations.