bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustering and machine learning-based integration identify cancer associated fibroblasts genes’ signature in head and neck squamous cell carcinoma
Authors: Wang Qiwei , Zhao Yinan , Wang Fang , Tan Guolin 
Published: March 2023

Background: A hallmark signature of the tumor microenvironment in head and neck squamous cell carcinoma (HNSCC) is abundantly infiltration of cancer-associated fibroblasts (CAFs), which facilitate HNSCC progression. However, some clinical trials showed targeted CAFs ended in failure, even accelerated cancer progression. Therefore, comprehensive exploration of CAFs should solve the shortcoming and facilitate the CAFs targeted therapies for HNSCC.Methods: In this study, we identified two CAFs gene expression patterns and performed the single‐sample gene set enrichment analysis (ssGSEA) to quantify the expression and construct score system. We used multi-methods to reveal the potential mechanisms of CAFs carcinogenesis progression. Finally, we integrated 10 machine learning algorithms and 107 algorithm combinations to construct most accurate and stable risk model. The machine learning algorithms contained random survival forest (RSF), elastic network (Enet), Lasso, Ridge, stepwise Cox, CoxBoost, partial least squares regression for Cox (plsRcox), supervised principal components (SuperPC), generalised boosted regression modelling (GBM), and survival support vector machine (survival-SVM).Results: There are two clusters present with distinct CAFs genes pattern. Compared to the low CafS group, the high CafS group was associated with significant immunosuppression, poor prognosis, and increased prospect of HPV negative. Patients with high CafS also underwent the abundant enrichment of carcinogenic signaling pathways such as angiogenesis, epithelial mesenchymal transition, and coagulation. The MDK and NAMPT ligand–receptor cellular crosstalk between the cancer associated fibroblasts and other cell clusters may mechanistically cause immune escape. Moreover, the random survival forest prognostic model that was developed from 107 machine learning algorithm combinations could most accurately classify HNSCC patients.Conclusion: We revealed that CAFs would cause the activation of some carcinogenesis pathways such as angiogenesis, epithelial mesenchymal transition, and coagulation and revealed unique possibilities to target glycolysis pathways to enhance CAFs targeted therapy. We developed an unprecedentedly stable and powerful risk score for assessing the prognosis. Our study contributes to the understanding of the CAFs microenvironment complexity in patients with head and neck squamous cell carcinoma and serves as a basis for future in-depth CAFs gene clinical exploration.
A novel lysosome-related gene signature coupled with gleason score for prognosis prediction in prostate cancer
Authors: Huang Ying , Yang Fan , Zhang Wenyi , Zhou Yupeng , Duan Dengyi , Liu Shuang , Li Jianmin , Zhao Yang 
Published: March 2023

Background: Prostate cancer (PCa) is highly heterogeneous, which makes it difficult to precisely distinguish the clinical stages and histological grades of tumor lesions, thereby leading to large amounts of under- and over-treatment. Thus, we expect the development of novel prediction approaches for the prevention of inadequate therapies. The emerging evidence demonstrates the pivotal role of lysosome-related mechanisms in the prognosis of PCa. In this study, we aimed to identify a lysosome-related prognostic predictor in PCa for future therapies.Methods: The PCa samples involved in this study were gathered from The Cancer Genome Atlas database (TCGA) (n = 552) and cBioPortal database (n = 82). During screening, we categorized PCa patients into two immune groups based on median ssGSEA scores. Then, the Gleason score and lysosome-related genes were included and screened out by using a univariate Cox regression analysis and the least absolute shrinkage and selection operation (LASSO) analysis. Following further analysis, the probability of progression free interval (PFI) was modeled by using unadjusted Kaplan–Meier estimation curves and a multivariable Cox regression analysis. A receiver operating characteristic (ROC) curve, nomogram and calibration curve were used to examine the predictive value of this model in discriminating progression events from non-events. The model was trained and repeatedly validated by creating a training set (n = 400), an internal validation set (n = 100) and an external validation (n = 82) from the cohort.Results: Following grouping by ssGSEA score, the Gleason score and two LRGs—neutrophil cytosolic factor 1 (NCF1) and gamma-interferon-inducible lysosomal thiol reductase (IFI30)—were screened out to differentiate patients with or without progression (1-year AUC = 0.787; 3-year AUC = 0.798; 5-year AUC = 0.772; 10-year AUC = 0.832). Patients with a higher risk showed poorer outcomes (p &lt; 0.0001) and a higher cumulative hazard (p &lt; 0.0001). Besides this, our risk model combined LRGs with the Gleason score and presented a more accurate prediction of PCa prognosis than the Gleason score alone. In three validation sets, our model still achieved high prediction rates.Conclusion: In conclusion, this novel lysosome-related gene signature, coupled with the Gleason score, works well in PCa for prognosis prediction.
Transcriptomic analysis reveals shared gene signatures and molecular mechanisms between obesity and periodontitis
Authors: Cai Yisheng , Zuo Xuemei , Zuo Yuyang , Wu Shuang , Pang Weiwei , Ma Keqiang , Yi Qiaorong , Tan Lijun , Deng Hongwen , Qu Xiaochao , Chen Xiangding 
Published: March 2023

BackgroundBoth obesity (OB) and periodontitis (PD) are chronic non-communicable diseases, and numerous epidemiological studies have demonstrated the association between these two diseases. However, the molecular mechanisms that could explain the association between OB and PD are largely unclear. This study aims to investigate the common gene signatures and biological pathways in OB and PD through bioinformatics analysis of publicly available transcriptome datasets.MethodsThe RNA expression profile datasets of OB (GSE104815) and PD (GSE106090) were used as training data, and GSE152991 and GSE16134 as validation data. After screening for differentially expressed genes (DEGs) shared by OB and PD, gene enrichment analysis, protein-protein interaction (PPI) network construction, GeneMANIA analysis, immune infiltration analysis and gene set enrichment analysis (GSEA) were performed. In addition, receiver operating characteristic (ROC) curves were used to assess the predictive accuracy of the hub gene. Finally, we constructed the hub gene-associated TF-miRNA-mRNA regulatory network.ResultsWe identified a total of 147 DEGs shared by OB and PD (38 down-regulated and 109 up-regulated). Functional analysis showed that these genes were mainly enriched in immune-related pathways such as B cell receptor signalling, leukocyte migration and cellular defence responses. 14 hub genes (FGR, MNDA, NCF2, FYB1, EVI2B, LY86, IGSF6, CTSS, CXCR4, LCK, FCN1, CXCL2, P2RY13, MMP7) showed high sensitivity and specificity in the ROC curve analysis. The results of immune infiltration analysis showed that immune cells such as macrophages, activated CD4 T cells and immune B cells were present at high infiltration levels in both OB and PD samples.The results of GeneMANIA analysis and GSEA analysis suggested that five key genes (FGR, LCK, FYB1, LY86 and P2RY13) may be strongly associated with macrophages. Finally, we constructed a TF-miRNA-mRNA regulatory network consisting of 233 transcription factors (TFs), 8 miRNAs and 14 mRNAs based on the validated information obtained from the database.ConclusionsFive key genes (FGR, LCK, FYB1, LY86, P2RY13) may be important biomarkers of OB and PD. These genes may play an important role in the pathogenesis of OB and PD by affecting macrophage activity and participating in immune regulation and inflammatory responses.
The effect of combined knockdowns of Attacins on survival and bacterial load in Tenebrio molitor
Authors: Keshavarz Maryam , Zanchi Caroline , Rolff Jens 
Published: March 2023

IntroductionUpon infection, insect hosts simultaneously express a cocktail of antimicrobial peptides (AMPs) which can impede pathogen colonization and increase host fitness. It has been proposed that such a cocktail might be adaptive if the effects of co-expressed AMPs are greater than the sum of individual activities. This could potentially prevent the evolution of bacterial resistance. However, in vivo studies on AMPs in combination are scarce. Attacins are one of the relatively large AMP families, which show anti-Gram-negative activity in vitro.Material and methodsHere, we used RNA interference (RNAi) to silence three members of the Attacin family genes in the mealworm beetle, Tenebrio molitor: (TmAttacin1a (TmAtt1a), TmAttacin1b (TmAtt1b), and TmAttacin2 (TmAtt2) both individually and in combination. We then infected T. molitor with the Gram negative entomopathogen Pseudomonas entomophila.ResultsWe found that survival of the beetles was only affected by the knockdown of TmAttacin1b, TmAttacin2 and the knockdown of all three Attacins together. Triple knockdown, rather than individual or double knockdowns of AMPs, changes the temporal dynamics of their efficiency in controlling the colonization of P. entomophila in the insect body.DiscussionMore precisely, AMP gene expression influences P. entomophila load early in the infection process, resulting in differences in host survival. Our results highlight the importance of studying AMP-interactions in vivo.
Evaluation of preclinical efficacy of human umbilical cord mesenchymal stem cells in ankylosing spondylitis
Authors: Shen Danpeng , Wang Zhiqiang , Wang Hongwei , Zhu Hongyan , Jiang Cuibao , Xie Fan , Zhang Hongpeng , Lv Qian , Liu Qi , Qi Nianmin , Wang Hao 
Published: March 2023

ObjectiveUmbilical cord mesenchymal stem cells (UCMSCs) have significant regenerative, tissue repair, and immunomodulatory properties that can help reduce inflammatory responses in patients with ankylosing spondylitis (AS). In this study, we used a combination of bovine proteoglycan and dimethyldioctadecylammonium (DDA) to establish a mouse model of proteoglycan-induced spondylitis (PGISp). To evaluate the therapeutic effects of UCMSCs, we treated PGISp mice with different doses of hUCMSCs via tail vein injection.MethodsAt week 13, the PGISp mice exhibited thickened, erythematous paws, erythema in the extremities, and lameness. CT scans revealed necrotic lysis of chondrocytes, formation of fissures, visible hemorrhage, connective tissue hyperplasia, and focal infiltration of lymphocytes in the intervertebral discs. At week 14, the PGISp mice were randomly divided into three groups and administered different doses of hUCMSCs (0.25, 0.5, and 1.0×107 cells/kg, iv, QOW×2, n=10). To assess the therapeutic effects of hUCMSCs, we evaluated Th cell subsets in the spleen, spleen and thymus coefficients, peripheral blood inflammatory factors, and pathological and imaging observations of the spines and lumbar spines in the PGISp mice.ResultsThe results demonstrated that injection of hUCMSCs shifted the balance axis between Th1 and Th2 cells in the spleen towards Th2 cells. Moreover, the spleen coefficient and levels of inflammatory cytokines (TNF-α and CCL-2) in the serum decreased after hUCMSC injection. CT imaging and pathological analysis indicated that hUCMSC treatment inhibited ectopic osteogenesis and maintained clear small joint gaps, which slowed down the progression of structural lesions in the disc, nucleus pulposus, fibrous ring, and cartilage in PGISp mice.ConclusionAdministering hUCMSCs at the 14th week after modeling proved to be an effective treatment for PGISp mice. This experiment offers a valuable reference for the pre-clinical use of hUCMSCs in the treatment of AS.
Alterations in the gut virome in patients with ankylosing spondylitis
Authors: Li Chen , Zhang Yan , Yan Qiulong , Guo Ruochun , Chen Changming , Li Shenghui , Zhang Yue , Meng Jinxin , Ma Jie , You Wei , Wu Zhisong , Sun Wen 
Published: March 2023

IntroductionAnkylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.MethodsTo investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.ResultsAS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.DiscussionThis work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.
The impact of persistent precarity on patients’ capacity to manage their treatment burden: A comparative qualitative study between urban and rural patients with multimorbidity in South Africa
Authors: van Pinxteren Myrna , Mbokazi Nonzuzo , Murphy Katherine , Mair Frances S. , May Carl , Levitt Naomi 
Published: March 2023

BackgroundPeople living with multimorbidity in low-and middle-income countries (LMICs) experience a high workload trying to meet the demands of self-management. In an unequal society like South Africa, many people face continuous economic uncertainty, which can impact on their capacity to manage their illnesses and lead to poor health outcomes. Using precariousness – the real and perceived impact of uncertainty – as a lens, this paper aims to identify, characterise, and understand the workload and capacity associated with self-management amongst people with multimorbidity living in precarious circumstances in urban and rural South Africa.MethodsWe conducted qualitative semi-structured interviews with 30 patients with HIV and co-morbidities between February and April 2021. Patients were attending public clinics in Cape Town (Western Cape) and Bulungula (Eastern Cape). Interviews were transcribed and data analysed using qualitative framework analysis. Burden of Treatment Theory (BoTT) and the Cumulative Complexity Model (CuCoM) were used as theoretical lenses through which to conceptualise the data.ResultsPeople with multimorbidity in rural and urban South Africa experienced multi-faceted precariousness, including financial and housing insecurity, dangerous living circumstances and exposure to violence. Women felt unsafe in their communities and sometimes their homes, whilst men struggled with substance use and a lack of social support. Older patients relied on small income grants often shared with others, whilst younger patients struggled to find stable employment and combine self-management with family responsibilities. Precariousness impacted access to health services and information and peoples’ ability to buy healthy foods and out-of-pocket medication, thus increasing their treatment burden and reducing their capacity.ConclusionThis study highlights that precariousness reduces the capacity and increases treatment burden for patients with multimorbidity in low-income settings in South Africa. Precariousness is both accumulative and cyclic, as financial insecurity impacts every aspect of peoples’ daily lives. Findings emphasise that current models examining treatment burden need to be adapted to accommodate patients’ experiences in low-income settings and address cumulative precariousness. Understanding treatment burden and capacity for patients in LMICs is a crucial first step to redesign health systems which aim to improve self-management and offer comprehensive person-centred care.
The application of data altruism in clinical research through empirical and legal analysis lenses
Authors: Lalova-Spinks Teodora , Meszaros Janos , Huys Isabelle 
Published: March 2023

BackgroundThe legal framework for clinical research in the EU is complex and the lack of harmonization of the relevant legal and ethical rules remains one of the main challenges for stakeholders in the field. The recently adopted Data Governance Act (DGA) and the proposal for a European Health Data Space (EHDS) promise to solve the existing challenges with respect to access to and (re)use of personal data for research, but also risk to further complexify the field. The DGA introduced a novel mechanism – data altruism. Data altruism is understood as the voluntary sharing of personal and non-personal data, based on the consent of data subjects or the permission of natural and legal persons, without seeking a reward and for objectives of general interest. This study aimed to gain insights into the opinion of clinical research stakeholders on data altruism, and to critically discuss key issues pertaining to the application of data altruism from a legal point of view.MethodsSemi-structured interviews with (1) data protection officers (DPOs) and legal experts working with commercial and academic sponsors of clinical trials, (2) investigators, and (3) members of research ethics committees. Data underwent framework analysis. The legal discussion was comprised of legal doctrinal research with focus on the DGA, EHDS proposal, and the interplay with the EU General Data Protection Regulation (GDPR).ResultsFourteen experts took part in the interviews, more than half of which were DPOs/legal experts. Interviewees were based in seven EU Member states and the United Kingdom. The majority of participants were critical towards the data altruism mechanism and pointed out challenges and risks associated with its application.ConclusionAlthough data altruism holds the potential to facilitate data sharing, its application in clinical research at the moment is still riddled with uncertainties. The interplay of the DGA rules with the provisions of the GDPR and the EHDS proposal are insufficiently clear and further efforts from the legislator are required to build a working, patient-centered, and research fostering data altruism system.
Targeted plasma metabolomics combined with machine learning for the diagnosis of severe acute respiratory syndrome virus type 2
Authors: Le Anthony T. , Wu Manhong , Khan Afraz , Phillips Nicholas , Rajpurkar Pranav , Garland Megan , Magid Kayla , Sibai Mamdouh , Huang ChunHong , Sahoo Malaya K. , Bowen Raffick , Cowan Tina M. , Pinsky Benjamin A. , Hogan Catherine A. 
Published: March 2023

IntroductionThe routine clinical diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely restricted to real-time reverse transcription quantitative PCR (RT-qPCR), and tests that detect SARS-CoV-2 nucleocapsid antigen. Given the diagnostic delay and suboptimal sensitivity associated with these respective methods, alternative diagnostic strategies are needed for acute infection.MethodsWe studied the use of a clinically validated liquid chromatography triple quadrupole method (LC/MS–MS) for detection of amino acids from plasma specimens. We applied machine learning models to distinguish between SARS-CoV-2-positive and negative samples and analyzed amino acid feature importance.ResultsA total of 200 samples were tested, including 70 from individuals with COVID-19, and 130 from negative controls. The top performing model overall allowed discrimination between SARS-CoV-2-positive and negative control samples with an area under the receiver operating characteristic curve (AUC) of 0.96 (95%CI 0.91, 1.00), overall sensitivity of 0.99 (95%CI 0.92, 1.00), and specificity of 0.92 (95%CI 0.85, 0.95).DiscussionThis approach holds potential as an alternative to existing methods for the rapid and accurate diagnosis of acute SARS-CoV-2 infection.
Creatine in the fetal brain: A regional investigation of acute global hypoxia and creatine supplementation in a translational fetal sheep model
Authors: Tran Nhi T. , Muccini Anna M. , Hale Nadia , Tolcos Mary , Snow Rod J. , Walker David W. , Ellery Stacey J. 
Published: March 2023

BackgroundCreatine supplementation during pregnancy is a promising prophylactic treatment for perinatal hypoxic brain injury. Previously, in near-term sheep we have shown that fetal creatine supplementation reduces cerebral metabolic and oxidative stress induced by acute global hypoxia. This study investigated the effects of acute hypoxia with or without fetal creatine supplementation on neuropathology in multiple brain regions.MethodsNear-term fetal sheep were administered continuous intravenous infusion of either creatine (6 mg kg–1 h–1) or isovolumetric saline from 122 to 134 days gestational age (dGA; term is approx. 145 dGA). At 131 dGA, global hypoxia was induced by a 10 min umbilical cord occlusion (UCO). Fetuses were then recovered for 72 h at which time (134 dGA) cerebral tissue was collected for either RT-qPCR or immunohistochemistry analyses.ResultsUCO resulted in mild injury to the cortical gray matter, thalamus and hippocampus, with increased cell death and astrogliosis and downregulation of genes involved in regulating injury responses, vasculature development and mitochondrial integrity. Creatine supplementation reduced astrogliosis within the corpus callosum but did not ameliorate any other gene expression or histopathological changes induced by hypoxia. Of importance, effects of creatine supplementation on gene expression irrespective of hypoxia, including increased expression of anti-apoptotic (BCL-2) and pro-inflammatory (e.g., MPO, TNFa, IL-6, IL-1β) genes, particularly in the gray matter, hippocampus, and striatum were identified. Creatine treatment also effected oligodendrocyte maturation and myelination in white matter regions.ConclusionWhile supplementation did not rescue mild neuropathology caused by UCO, creatine did result in gene expression changes that may influence in utero cerebral development.