bluuebunny/crossref_metadata_2025_split huggingface dataset:
Therapeutic effects of platelet-derived extracellular vesicles on viral myocarditis correlate with biomolecular content
Authors: Beetler Danielle J. , Giresi Presley , Di Florio Damian N. , Fliess Jessica J. , McCabe Elizabeth J. , Watkins Molly M. , Xu Vivian , Auda Matthew E. , Bruno Katelyn A. , Whelan Emily R. , Kocsis Stephen P. C. , Edenfield Brandy H. , Walker Sierra A. , Macomb Logan P. , Keegan Kevin C. , Jain Angita , Morales-Lara Andrea C. , Chekuri Isha , Hill Anneliese R. , Farres Houssam , Wolfram Joy , Behfar Atta , Stalboerger Paul G. , Terzic Andre , Cooper Leslie T. , Fairweather DeLisa 
Published: January 2025

IntroductionExtracellular vesicles (EVs) can potently inhibit inflammation yet there is a lack of understanding about the impact of donor characteristics on the efficacy of EVs. The goal of this study was to determine whether the sex and age of donor platelet-derived EVs (PEV) affected their ability to inhibit viral myocarditis.MethodsPEV, isolated from men and women of all ages, was compared to PEV obtained from women under 50 years of age, which we termed premenopausal PEV (pmPEV). Because of the protective effect of estrogen against myocardial inflammation, we hypothesized that pmPEV would be more effective than PEV at inhibiting myocarditis. We injected PEV, pmPEV, or vehicle control in a mouse model of viral myocarditis and examined histology, gene expression, protein profiles, and performed proteome and microRNA (miR) sequencing of EVs.ResultsWe found that both PEV and pmPEV significantly inhibited myocarditis; however, PEV was more effective, which was confirmed by a greater reduction of inflammatory cells and proinflammatory and profibrotic markers determined using gene expression and immunohistochemistry. Proteome and miR sequencing of EVs revealed that PEV miRs specifically targeted antiviral, Toll-like receptor (TLR)4, and inflammasome pathways known to contribute to myocarditis while pmPEV contained general immunoregulatory miRs.DiscussionThese differences in EV content corresponded to the differing anti-inflammatory effects of the two types of EVs on viral myocarditis.
The emergence of DNAM-1 as the facilitator of NK cell-mediated killing in ovarian cancer
Authors: Pounds Rachel , Croft Wayne , Pearce Hayden , Hossain Tasnia , Singh Kavita , Balega Janos , Jeevan David N. , Sundar Sudha , Kehoe Sean , Yap Jason , Moss Paul , Zuo Jianmin 
Published: January 2025

IntroductionOvarian cancer (OC) is the sixth most common malignancy in women and the poor 5-year survival emphasises the need for novel therapies. NK cells play an important role in the control of malignant disease but the nature of tumour-infiltrating and peripheral NK cells in OC remains unclear.MethodsUsing flow cytometric analysis, we studied the phenotype and function of NK cells in blood, primary tumour and metastatic tissue in 80 women with OC. The cell type contexture of metastatic OC tissue was explored utilising scRNAseq analysis, with a focus on portraying an immunogenic tumour microenvironment and determining the characteristics of a dysfunctional NK cell population.ResultsThe proportion of peripheral NK cells was markedly elevated with a highly activated profile and increased cytotoxicity. In contrast, NK cell numbers in primary tumour and metastasis were substantially reduced, with downregulation of activatory receptors together with elevated PD-1 expression. scRNA-Seq identified 5 NK cell subpopulations along with increased exhausted and immature NK cells within tumour tissue compared to normal tissue. These features were attenuated following chemotherapy where higher levels of activated and cytotoxic NK cells associated with improved disease-free survival. Correlation of NK cell phenotype with clinical outcomes revealed high levels of DNAM-1 expression on tissue-localised and peripheral NK cells to be associated with reduced survival. Expression of PVR, the DNAM-1 ligand, was significantly increased on tumours and DNAM-1 mediated NK cell lysis of primary tumour tissue was observed in vitro.DiscussionThese findings reveal profound modulation of the tumour tissue and systemic profile of NK cells which likely contributes to the high rates of local progression and metastasis seen with OC. Immunotherapeutic approaches that overcome local immune suppression and enhance DNAM-1-targeted lysis of OC offer the potential to improve disease control.
SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells
Authors: Bernhardt Melissa , Rech Anne , Berthold Marion , Lappe Melina , Herbel Jan-Niklas , Erhard Florian , Paschen Annette , Schilling Bastian , Schlosser Andreas 
Published: January 2025

BackgroundThe immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It is highly dynamic and reflects the current cellular state, enabling the immune system to recognize abnormal cellular conditions, such as those present in cancer cells. To precisely determine how changes in cellular processes, such as those induced by drug treatment, affect the immunopeptidome, quantitative immunopeptidomics approaches are essential.MethodsTo meet this need, we developed a pulsed SILAC-based method for quantitative immunopeptidomics. Metabolic labeling with lysine, arginine, and leucine enabled isotopic labeling of nearly all HLA peptides across all allotypes (&gt; 90% on average). We established a data analysis workflow that integrates the de novo sequencing-based tool Peptide-PRISM for comprehensive HLA peptide identification with MaxQuant for accurate quantification.ResultsWe employed this strategy to explore the modulation of the immunopeptidome upon MAPK pathway inhibition (MAPKi) and to investigate alterations associated with early cellular responses to inhibitor treatment and acquired resistance to MAPKi. Our analyses demonstrated significant changes in the immunopeptidome early during MAPKi treatment and in the resistant state. Moreover, we identified putative tumor-specific cryptic HLA peptides linked to these processes that might represent exploitable targets for cancer immunotherapy.ConclusionsWe have developed a new mass spectrometric approach that allowed us to investigate the effects of common MAPK inhibitors on the immunopeptidome of melanoma cells. This finally led to the discovery of new potential targets for cancer immunotherapy.
Extracellular acyl-CoA-binding protein as an independent biomarker of COVID-19 disease severity
Authors: Isnard Stephane , Mabanga Tsoarello , Royston Léna , Berini Carolina A. , Bu Simeng , Aiyana Orthy , Feng Hansen , Lebouché Bertrand , Costiniuk Cecilia T. , Cox Joseph , Kroemer Guido , Durand Madeleine , Routy Jean-Pierre ,   the Biobanque Québécoise de la COVID-19 (BQC-19)
Published: January 2025

BackgroundFactors leading to severe COVID-19 remain partially known. New biomarkers predicting COVID-19 severity that are also causally involved in disease pathogenesis could improve patient management and contribute to the development of innovative therapies. Autophagy, a cytosolic structure degradation pathway is involved in the maintenance of cellular homeostasis, degradation of intracellular pathogens and generation of energy for immune responses. Acyl-CoA binding protein (ACBP) is a key regulator of autophagy in the context of diabetes, obesity and anorexia. The objective of our work was to assess whether circulating ACBP levels are associated with COVID-19 severity, using proteomics data from the plasma of 903 COVID-19 patients.MethodsSomalogic proteomic analysis was used to detect 5000 proteins in plasma samples collected between March 2020 and August 2021 from hospitalized participants in the province of Quebec, Canada. Plasma samples from 903 COVID-19 patients collected during their admission during acute phase of COVID-19 and 295 hospitalized controls were assessed leading to 1198 interpretable proteomic profiles. Levels of anti-SARS-CoV-2 IgG were measured by ELISA and a cell-binding assay.ResultsThe median age of the participants was 59 years, 46% were female, 65% had comorbidities. Plasma ACBP levels correlated with COVID-19 severity, in association with inflammation and anti-SARS-CoV-2 antibody levels, independently of sex or the presence of comorbidities. Samples collected during the second COVID-19 wave in Quebec had higher levels of plasma ACBP than during the first wave. Plasma ACBP levels were negatively correlated with biomarkers of T and NK cell responses interferon-γ, tumor necrosis factor-α and interleukin-21, independently of age, sex, and severity.ConclusionsCirculating ACBP levels can be considered a biomarker of COVID-19 severity linked to inflammation. The contribution of extracellular ACBP to immunometabolic responses during viral infection should be further studied.
Gut microbiota and inflammasome-mediated pyroptosis: a bibliometric analysis from 2014 to 2023
Authors: Zhang Hang , Zhao Tian , Gu Juan , Tang Fushan , Zhu Lei 
Published: January 2025

BackgroundThe role of gut microbiota in inflammatory disease development and progression has been recognized more recently. Inflammasome-mediated pyroptosis in involved in these diseases. This complex relationship between gut microbiota and inflammasome-mediated pyroptosis provides an important field of research. Bibliometric analysis provides a comprehensive understanding of this relationship, offering valuable insights into emerging research trends.Materials and methodsLeveraging data spanning from 2014 to 2023 sourced from the Web of Science Core Collection, our analysis was conducted using advanced tools such as SCImago Graphica, VOSviewer, and CiteSpace software. Visualizations were created using GraphPad Prism software. We explored the nuanced aspects of research hotspots, collaborative networks, and developing trends in this field.ResultsA global bibliometric analysis identified 520 relevant studies spanning 41 countries and 887 institutions. Over the past decade, publication trends have shown consistent growth, with China and the United States leading the research output. Southern Medical University and Nanjing Medical University in China emerged as leading institutions in this filed. Prominent contributors include Jia Sun, Yuan Zhang, Wei Chen, Jing Wang, and Hongtao Liu from China, alongside Eicke Latz from Germany. High-impact journals such as Frontiers in Immunology and Nature Communications have been pivotal in disseminating research in this domain. Keyword analysis highlighted a primary focus on gut microbiota, NLRP3 inflammasome, pyroptosis pathways, and inflammatory diseases, themes that persist in recent studies. Furthermore, burst keyword analysis identified “butyrate” as the sole term currently experiencing a marked increase in research interest.ConclusionResearch has been deeply focused on the gut microbiota and inflammasome triggered pyroptosis in years. Over the past decade, the exploration of how gut microbiota and NLRP3 or NLRP6 inflammasome-mediated pyroptosis has been an area of interest. Future investigations in this filed may primarily revolve around understanding the correlation between butyrate and NLRP3 inflammasome induced pyroptosis in relation to conditions. However, an in-depth analysis, through studies is crucial to uncover and elucidate the complex mechanisms linking these elements.
The response of soil microbial community to application of organic amendment to saline land
Authors: Cong Peifei , Huang Pengfei , Huang Zhisheng 
Published: January 2025

IntroductionThe salinization of coastal soils is a primary cause of global land degradation. The aim of this study was to evaluate the effect of organic amendment on the soil microbial community within a saline gradient.MethodsThe study was designed with five levels of electrical conductivity (EC): 0.33, 0.62, 1.13, 1.45 and 2.04 ds m−1. By conducting indoor potted plant experiments, determine the effects of applying microbial organic fertilizer on the physicochemical properties of soil and the structure of soil microbial communities under different salinity concentrations.ResultsCompared with the control, higher OM content, total N, and higher crop biomass were observed in samples with organic amendment at the same salinity level. At the same salinity levels, the mean bacterial activity (AUC) and the mean number of substrates were higher than in the soil without organic amendment according to analyses by means of Biolog ECO MicroPlate. The results of canonical correspondence analysis indicate that after the application of organic amendments, the composition of loam and clay replaces soil pH, and aboveground biomass replaces root biomass as key indicators closely monitoring Community level physiological profiling (CLPP). In soil with the same salinity level, the application of microbial organic fertilizer led to an increase in the proportion of Actinobacteriota and a decrease in the proportion of Chloroflexi. In 0.3dS m-1 soil, the abundance of actinomycetes increased from 23% to 27% after application of microbial organic fertilizer, while the abundance of basidiomycetes decreased from 20% to 6%. In addition, after the application of microbial organic fertilizer, RB41, blastococcus and solirubrobacter significantly increased, while Melothermus and Herpetosiphon significantly decreased.DiscussionThis study provides a strong theoretical basis for using microbial organic fertilizers to improve saline-alkali soil.
Applicability of a serodiagnostic line blot for idiopathic inflammatory myopathy: the muscle biopsy is not all
Authors: Fontana Pedro Nogueira , da Silva Vinícius Gomes , Corazzini Roseli , Athayde Natália Merten , Ferreira da Silva Ana Marina Dutra , Brockhausen Igor , Correia Carolina da Cunha , Sobreira Cláudia Ferreira da Rosa , Tomaselli Pedro José , Petean Flávio , de Oliveira Rodrigo , Feitoza Pablo Vinícius , Moraes Soane Michel , Saraiva Natália , Hidalgo Rafaela , Fideles Cláudia , Feder David , Carvalho Alzira Alves de Siqueira 
Published: January 2025

IntroductionDifferential diagnosis of rare idiopathic inflammatory myopathies (IIM) is mainly based on clinical aspects, muscle biopsy analysis, and auxiliary assays that determine myositis-specific and associated autoantibodies (MSA and MAA). While MSAs are considered specific for their respective IIM subclass, MAAs can be present in more than one subclass and in other conditions. This study compares results of a multispecific line blot assay with the final diagnosis of IIM patients based on clinical features and muscle biopsy to draw conclusions for the test's applicability in the diagnostic workflow.MethodsSamples from patients (n = 50) diagnosed with various forms of IIM, including patients (n = 5) with other myopathies, were analyzed using the EUROLINE Autoimmune Inflammatory Myopathies 16 Ag (IgG), an anti-HMGCR (IgG) line blot, and the Anti-cN-1A ELISA (IgG, all EUROIMMUN).ResultsMSA and MAA were detected in 74.0% (37/50) of sera and were concordant with the final diagnosis in 64.8% (24/37), discordant in 16.2% (6/37) and not evaluable in 18.9% (7/37) of cases. In 100% (5/5) of patients with other myopathies, no MSA was found. MSA/MAA-co-positivity was observed in 18.0% (9/50) of patients. In 30.0% (15/50) of cases, the muscle biopsy analysis was essential to establish the final diagnosis.ConclusionThe agreement between serodiagnostic results and final diagnosis highlights the applicability of the EUROIMMUN myositis-related diagnostic test as first line diagnostic tool in the IIM diagnosis workflow and suggests morphological analysis in cases of inconclusive or negative serology. However, results of diagnostic assays shall always be interpreted in combination with clinical features.
Alternations of interhemispheric functional connectivity in patients with acute acquired concomitant esotropia: a resting state fMRI study using voxel-mirrored homotopic connectivity
Authors: Chen Jiayu , Hao Jie , Liu Jiawen , Li Huijian , Meng Zhaojun , Fu Jing 
Published: January 2025

PurposeTo investigate the changes in cerebral hemispheric functional connections in patients with acute acquired concomitant esotropia (AACE) and their relationship with clinical manifestations, utilizing voxel-mirrored homotopic connectivity (VMHC).MethodsA prospective, observational study was conducted involving 32 AACE patients and 31 age-, sex-, and education-matched healthy controls (HC). The resting-state functional magnetic resonance imaging (rs-fMRI) signals, binocular vision function, and psychometric scale scores were collected rs-fMRI data and structural image data were analyzed for VMHC, and a two-sample t-test was used to analyze the differences in VMHC between groups. Spearman correlation analysis evaluated the relationship between fMRI indicators and clinical features.ResultsThere was no statistical difference between the two groups concerning sex, age, height and weight. VMHC levels in the superior frontal gyrus and anterior cingulate were significantly lower in the AACE group (p &lt; 0.05). In the AACE group, the VMHC values of the left caudate positively correlated with near vision work duration (r = 0.381, p = 0.034), the deviation angles at near (r = 0.428, p = 0.015) and at distance (r = 0.416, p = 0.018). The VMHC values in the bilateral olfactory cortex also positively correlated with the near vision work duration (Right: r = 0.389, p = 0.031; Left: r = 0.372, p = 0.039) while Beck Depression Inventory (BDI) scores negatively correlated with the VMHC values of the left olfactory cortex (r = −0.359, p = 0.048).ConclusionThe dysfunction of the medial frontal gyrus and anterior cingulate gyrus is the underlying neuropathological mechanism of AACE, and these dysfunctions may be related to poor eye habits and the severity of deviation.
Comparative efficacy of neuroprotective agents for improving neurological function and prognosis in acute ischemic stroke: a network meta-analysis
Authors: Wang Yuchen , Li Mengqi , Jiang Yuye , Ji Qiuhong 
Published: January 2025

BackgroundIschemic stroke is the second leading cause of death and the third leading cause of combined disability and mortality globally. While reperfusion therapies play a critical role in the management of acute ischemic stroke (AIS), their applicability is limited, leaving many patients with significant neurological deficits and poor prognoses. Neuroprotective agents have garnered attention for their potential as adjunct therapies; however, their relative efficacy remains unclear. This study utilized a network meta-analysis (NMA) to systematically compare the efficacy of neuroprotective agents in improving neurological function and prognosis in stroke patients.MethodsThis study adhered to PRISMA guidelines and the Cochrane Handbook for systematic reviews. Randomized controlled trials (RCTs) were identified through comprehensive searches of the PubMed, Embase, and Cochrane Library databases. Two independent reviewers conducted the selection process, data extraction, and quality assessment. Outcomes included 90-day modified Rankin Scale (90d-mRS), change of National Institutes of Health Stroke Scale score from baseline to 90-day/14-day/7-day (90d/14d/7d-NIHSS) and 90-day/14-day Barthel Index (90d/14d-BI). Data analyses were performed using RevMan 5.4 and Stata 14.0.ResultsA total of 42 RCTs involving 12,210 participants were included in this analysis. The interventions assessed included Cerebrolysin, Citicoline, Edaravone, Edaravone Dextranol, Human urinary kallidinogenase, Minocycline, Nerinetide, Butylphthalide, Vinpocetine, and Control. The NMA results demonstrated that NBP ranked highest for the 90d-mRS, 90d-NIHSS, 14d-NIHSS, and 14d-BI outcomes. Edaravone was found to be the most effective intervention for the 7d-NIHSS and 90d-BI outcomes.ConclusionThe findings of this study indicate that different neuroprotective agents exhibit distinct advantages at specific stages of recovery. NBP showed outstanding performance in improving 90d-mRS and 90d-NIHSS, underscoring its potential in long-term rehabilitation. Edaravone demonstrated significant superiority in 7d-NIHSS scores, highlighting its role in early neuroprotection. These results provide valuable insights for individualized clinical treatment. To further validate the efficacy and safety of neuroprotective agents, future studies should involve larger sample sizes and conduct multicenter, large-scale randomized controlled trials.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?RecordID=601346, identifier CRD42024601346.
Effect of gestational age on clinical features in necrotizing enterocolitis-associated intestinal perforation
Authors: Chen Minming , Feng Wei , Hou Jinping , Die Xiaohong , Guo Zhenhua , Wang Yi 
Published: January 2025

PurposeTo investigate the clinical features of necrotizing enterocolitis-associated intestinal perforation (NEC-IP) in neonates with different gestational ages (GAs). Furthermore, we also want to identify the risk factors of poor prognosis for these patients.MethodsThe retrospective study of patients with NEC-IP was conducted with basic information, comorbidity, intraoperative findings, related treatment, and prognosis. According to the GA, patients were divided into three groups: early (GA: 28–&lt;32 weeks, Group 1), mid-term (GA: 32–&lt;34 weeks, Group 2), and late (GA: 34–&lt;37 weeks, Group 3). The clinical features of the three groups were analyzed, and risk factors for poor prognosis were identified.ResultsOf the 113 cases, the number of cases in Groups 1 to 3 was 36 (31.9%), 44 (38.9%), and 33 (29.2%), respectively; and the overall proportion of poor prognosis was 19.4% (22/113). For basic information, the birth weight of Group 1 was lower than that of Group 2 and Group 3, while the postnatal day at the time of surgery of NEC and the onset age were higher than that of Group 2 (onset age: G1 12.0[7.00;20.5], G2 9.00[4.00;13.0]; postnatal day at the time of surgery: G1 22.0[13.8;27.2], G2 13.0[8.00;21.0]) (P &lt; 0.016). For comorbidity, the incidence of sepsis, coagulopathy, type of (congenital heart disease) CHD, and hypoproteinemia in Group 1 was higher than that in Group 2 (all P &lt; 0.016), and the incidence of respiratory failure, hypoproteinemia in Group 1 was higher than that in Group 3 (all P &lt; 0.016). For related treatment, the usage rate of vasoactive substances and mechanical ventilation in Group 1 was higher than that of Group 2 and Group 3 (all P &lt; 0.016). By Lasso and Logistic regression analysis, we found that GA (OR: 0.274, 95%CI: 0.078–0.796), sepsis (OR: 7.955, 95%CI: 1.424–65.21), coagulopathy (OR: 19.51, 95%CI: 3.393–179.1), CHD (OR: 6.99, 95%CI: 1.418–54.83) and diseased bowel segment (OR: 2.804, 95%CI: 1.301–7.316) were the independent factors for poor prognosis (all P &lt; 0.05).ConclusionsThe clinical features of NEC-IP patients differ based on GA, particularly in terms of CHD type, postnatal day at the time of surgery, utilization of vasoactive substances, and prognosis. Furthermore, GA, sepsis, coagulopathy, CHD, and diseased bowel segment are independent factors for poor prognosis of patients with NEC-IP.