bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell profiling reveals distinct immune response landscapes in tuberculous pleural effusion and non-TPE
Authors: Yang Xinting , Yan Jun , Xue Yu , Sun Qing , Zhang Yun , Guo Ru , Wang Chaohong , Li Xuelian , Liang Qingtao , Wu Hangyu , Wang Chong , Liao Xinlei , Long Sibo , Zheng Maike , Wei Rongrong , Zhang Haoran , Liu Yi , Che Nanying , Luu Laurence Don Wai , Pan Junhua , Wang Guirong , Wang Yi 
Published: June 2023

BackgroundTuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb) and remains a major health threat worldwide. However, a detailed understanding of the immune cells and inflammatory mediators in Mtb-infected tissues is still lacking. Tuberculous pleural effusion (TPE), which is characterized by an influx of immune cells to the pleural space, is thus a suitable platform for dissecting complex tissue responses to Mtb infection.MethodsWe employed singe-cell RNA sequencing to 10 pleural fluid (PF) samples from 6 patients with TPE and 4 non-TPEs including 2 samples from patients with TSPE (transudative pleural effusion) and 2 samples with MPE (malignant pleural effusion).ResultCompared to TSPE and MPE, TPE displayed obvious difference in the abundance of major cell types (e.g., NK, CD4+T, Macrophages), which showed notable associations with disease type. Further analyses revealed that the CD4 lymphocyte population in TPE favored a Th1 and Th17 response. Tumor necrosis factors (TNF)-, and XIAP related factor 1 (XAF1)-pathways induced T cell apoptosis in patients with TPE. Immune exhaustion in NK cells was an important feature in TPE. Myeloid cells in TPE displayed stronger functional capacity for phagocytosis, antigen presentation and IFN-γ response, than TSPE and MPE. Systemic elevation of inflammatory response genes and pro-inflammatory cytokines were mainly driven by macrophages in patients with TPE.ConclusionWe provide a tissue immune landscape of PF immune cells, and revealed a distinct local immune response in TPE and non-TPE (TSPE and MPE). These findings will improve our understanding of local TB immunopathogenesis and provide potential targets for TB therapy.
AATF/Che-1 RNA polymerase II binding protein overexpression reduces the anti-tumor NK-cell cytotoxicity through activating receptors modulation
Authors: Caforio Matteo , Tumino Nicola , Sorino Cristina , Manni Isabella , Di Giovenale Stefano , Piaggio Giulia , Iezzi Simona , Strimpakos Georgios , Mattei Elisabetta , Moretta Lorenzo , Fanciulli M. , Vacca Paola , Locatelli Franco , Folgiero Valentina 
Published: June 2023

IntroductionAATF/Che-1 over-expression in different tumors is well known and its effect on tumorigenicity is mainly due to its central role demonstrated in the oncogenic pathways of solid tumors, where it controls proliferation and viability. The effect exerted by tumors overexpressing Che-1 on the immune response has not yet been investigated.MethodsStarting from ChIP-sequencing data we confirmed Che-1 enrichment on Nectin-1 promoter. Several co-cultures experiments between NK-cells and tumor cells transduced by lentiviral vectors carrying Che-1-interfering sequence, analyzed by flow-cytometry have allowed a detailed characterization of NK receptors and tumor ligands expression.ResultsHere, we show that Che-1 is able to modulate the expression of Nectin-1 ligand at the transcriptional level, leading to the impairment of killing activity of NK-cells. Nectin-1 down-modulation induces a modification in NK-cell ligands expression able to interact with activating receptors and to stimulate NK-cell function. In addition, NK-cells from Che-1 transgenic mice, confirming a reduced expression of activating receptors, exhibit impaired activation and a preferential immature status.DiscussionThe critical equilibrium between NK-cell ligand expression on tumor cells and the interaction with NK cell receptors is affected by Che-1 over-expression and partially restored by Che-1 interference. The evidence of a new role for Che-1 as regulator of anti-tumor immunity supports the necessity to develop approaches able to target this molecule which shows a dual tumorigenic function as cancer promoter and immune response modulator.
Immunological modifications following chemotherapy are associated with delayed recurrence of ovarian cancer
Authors: Adzibolosu Nicholas , Alvero Ayesha B. , Ali-Fehmi Rouba , Gogoi Radhika , Corey Logan , Tedja Roslyn , Chehade Hussein , Gogoi Vir , Morris Robert , Anderson Matthew , Vitko Julie , Lam Clarissa , Craig Douglas B. , Draghici Sorin , Rutherford Thomas , Mor Gil 
Published: June 2023

IntroductionOvarian cancer recurs in most High Grade Serous Ovarian Cancer (HGSOC) patients, including initial responders, after standard of care. To improve patient survival, we need to identify and understand the factors contributing to early or late recurrence and therapeutically target these mechanisms. We hypothesized that in HGSOC, the response to chemotherapy is associated with a specific gene expression signature determined by the tumor microenvironment. In this study, we sought to determine the differences in gene expression and the tumor immune microenvironment between patients who show early recurrence (within 6 months) compared to those who show late recurrence following chemotherapy.MethodsPaired tumor samples were obtained before and after Carboplatin and Taxol chemotherapy from 24 patients with HGSOC. Bioinformatic transcriptomic analysis was performed on the tumor samples to determine the gene expression signature associated with differences in recurrence pattern. Gene Ontology and Pathway analysis was performed using AdvaitaBio’s iPathwayGuide software. Tumor immune cell fractions were imputed using CIBERSORTx. Results were compared between late recurrence and early recurrence patients, and between paired pre-chemotherapy and post-chemotherapy samples.ResultsThere was no statistically significant difference between early recurrence or late recurrence ovarian tumors pre-chemotherapy. However, chemotherapy induced significant immunological changes in tumors from late recurrence patients but had no impact on tumors from early recurrence patients. The key immunological change induced by chemotherapy in late recurrence patients was the reversal of pro-tumor immune signature.DiscussionWe report for the first time, the association between immunological modifications in response to chemotherapy and the time of recurrence. Our findings provide novel opportunities to ultimately improve ovarian cancer patient survival.
Sex-differences in the longitudinal recovery of neuromuscular function in COVID-19 associated acute respiratory distress syndrome survivors
Authors: Lulic-Kuryllo Tea , Benedini Marco , Cogliati Marta , Cudicio Alessandro , Guarneri Bruno , Gazzina Stefano , Piva Simone , Latronico Nicola , Orizio Claudio , Negro Francesco 
Published: June 2023

IntroductionPatients admitted to the intensive care unit (ICU) following severe acute respiratory syndrome 2 (SARS-CoV-2) infection may have muscle weakness up to 1 year or more following ICU discharge. However, females show greater muscle weakness than males, indicating greater neuromuscular impairment. The objective of this work was to assess sex differences in longitudinal physical functioning following ICU discharge for SARS-CoV-2 infection.MethodsWe performed longitudinal assessment of physical functioning in two groups: 14 participants (7 males, 7 females) in the 3-to-6 month and 28 participants (14 males, 14 females) in the 6-to-12 month group following ICU discharge and assessed differences between the sexes. We examined self-reported fatigue, physical functioning, compound muscle action potential (CMAP) amplitude, maximal strength, and the neural drive to the tibialis anterior muscle.ResultsWe found no sex differences in the assessed parameters in the 3-to-6-month follow-up, indicating significant weakness in both sexes.Sex differences emerged in the 6-to-12-month follow-up. Specifically, females exhibited greater impairments in physical functioning, including lower strength, walking lower distances, and high neural input even 1 year following ICU-discharge.DiscussionFemales infected by SARS-CoV-2 display significant impairments in functional recovery up to 1 year following ICU discharge. The effects of sex should be considered in post-COVID neurorehabilitation.
Epidemiology and risk factors of respiratory syncytial virus associated acute respiratory tract infection in hospitalized children younger than 5 years from Sri Lanka
Authors: Divarathna Maduja V. M. , Rafeek Rukshan A. M. , Morel Adrian J. , Aththanayake Chathuri , Noordeen Faseeha 
Published: June 2023

BackgroundRespiratory syncytial virus (RSV) is the leading cause of acute respiratory tract infections (ARTI) and a major cause of morbidity and mortality in children worldwide.AimThis study aimed to describe the prevalence and seasonal patterns of RSV and to determine the actual and predictive association of RSV-associated ARTI and clinical, socio-demographic, and climatic risk factors in children &lt; 5 years.MethodsNasopharyngeal aspirates were collected from 500 children &lt; 5 years admitted to the Kegalle General Hospital, Sri Lanka between May 2016 to July 2018. RSV and RSV subtypes were detected using immunofluorescence assay and real time RT-PCR, respectively. Descriptive and inferential statistics were done for the data analysis using Chi-square, Fisher’s exact, Kruskal–Wallis test, and multiple binary logistic regression in the statistical package for social sciences (SPSS), version 16.0.ResultsPrevalence of RSV-associated ARTI was 28% in children &lt; 5 years. Both RSV subtypes were detected throughout the study period. RSV-B was the dominant subtype detected with a prevalence of 72.14%. RSV infection in general caused severe respiratory disease leading to hypoxemia. Compared to RSV-B, RSV-A infection had more symptoms leading to hypoxemia. Factors increasing the risk of contracting RSV infection included number of people living (n &gt; 6), having pets at home and inhaling toxic fumes. The inferential analysis predicts RSV infection in children &lt; 5 years with ARTI, with a 75.4% probability with clinical and socio-demographic characteristics like age &lt; 1 year, fever for &gt; 4 days, cough, conjunctivitis, stuffiness, fatigue, six or more people at home, having pets at home and inhaling toxic fumes. Climatic factors like increases in temperature (°C), wind speed (Km/h), wind gust (Km/h), rainfall (mm) and atmospheric pressure (mb) showed a strong correlation with the RSV infection in children.
Identification of diagnostic biomarkers in Alzheimer’s disease by integrated bioinformatic analysis and machine learning strategies
Authors: Jin Boru , Cheng Xiaoqin , Fei Guoqiang , Sang Shaoming , Zhong Chunjiu 
Published: June 2023

BackgroundAlzheimer’s disease (AD) is the most prevalent form of dementia, and is becoming one of the most burdening and lethal diseases. More useful biomarkers for diagnosing AD and reflecting the disease progression are in need and of significance.MethodsThe integrated bioinformatic analysis combined with machine-learning strategies was applied for exploring crucial functional pathways and identifying diagnostic biomarkers of AD. Four datasets (GSE5281, GSE131617, GSE48350, and GSE84422) with samples of AD frontal cortex are integrated as experimental datasets, and another two datasets (GSE33000 and GSE44772) with samples of AD frontal cortex were used to perform validation analyses. Functional Correlation enrichment analyses were conducted based on Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Reactome database to reveal AD-associated biological functions and key pathways. Four models were employed to screen the potential diagnostic biomarkers, including one bioinformatic analysis of Weighted gene co-expression network analysis (WGCNA)and three machine-learning algorithms: Least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) analysis. The correlation analysis was performed to explore the correlation between the identified biomarkers with CDR scores and Braak staging.ResultsThe pathways of the immune response and oxidative stress were identified as playing a crucial role during AD. Thioredoxin interacting protein (TXNIP), early growth response 1 (EGR1), and insulin-like growth factor binding protein 5 (IGFBP5) were screened as diagnostic markers of AD. The diagnostic efficacy of TXNIP, EGR1, and IGFBP5 was validated with corresponding AUCs of 0.857, 0.888, and 0.856 in dataset GSE33000, 0.867, 0.909, and 0.841 in dataset GSE44770. And the AUCs of the combination of these three biomarkers as a diagnostic tool for AD were 0.954 and 0.938 in the two verification datasets.ConclusionThe pathways of immune response and oxidative stress can play a crucial role in the pathogenesis of AD. TXNIP, EGR1, and IGFBP5 are useful biomarkers for diagnosing AD and their mRNA level may reflect the development of the disease by correlation with the CDR scores and Breaking staging.
Case report: Anti septin-5-encephalitis as a treatable cause of cerebellar ataxia and psychiatric symptoms
Authors: Wischmann Johannes , Borowski Kathrin , Havla Joachim , Thaler Franziska S. , Winkler Tobias , Jung Tobias , Straube Andreas , Masouris Ilias 
Published: June 2023

ObjectivesAnti-septin-5 encephalitis is a rare disease with only few published cases, mainly based on retrospective CSF and serum analyses. Predominant symptoms are cerebellar ataxia and oculomotor abnormalities. Due to the rareness of the disease, treatment recommendations are scarce. Herein, we prospectively describe the clinical course of a female patient with anti-septin-5 encephalitis.MethodsWe describe diagnostic workup, treatment and follow-up of a 54-year-old patient presenting with vertigo, unsteady gait, lack of drive and behavioral changes.ResultsClinical examination revealed severe cerebellar ataxia, saccadic smooth pursuit, upbeat-nystagmus, and dysarthria. Additionally, the patient presented with a depressive syndrome. MRI of the brain and spinal cord were normal. CSF analysis showed lymphocytic pleocytosis (11 cells/μl). Extensive antibody testing revealed anti septin-5 IgG in both CSF and serum without coexisting anti-neuronal antibodies. PET/CT detected no signs of malignancy. Corticosteroids, plasma exchange, and rituximab led to transient clinical improvement followed by relapse. Re-applied treatment with plasma exchange followed by bortezomib resulted in moderate but sustained clinical improvement.DiscussionAnti septin-5 encephalitis represents a rare but treatable and therefore relevant differential diagnosis in patients with cerebellar ataxia. Psychiatric symptoms can be observed in anti septin-5 encephalitis. Immunosuppressive treatment including bortezomib is moderately effective.
Ameliorative effects of Kyung-Ok-Ko and its mixture with Pueraria lobata Ohwi on postmenopausal osteoporosis by promoting phytoestrogenic activity in rats
Authors: Kim Minseo , Kim Hyun-Sook , Oh Joohee , Zhou Xiangqin , Ahn SongHee , Koo Youngtae , Kim Hyun-Jung , Jang Jiwon 
Published: June 2023

IntroductionKyung-Ok-Ko (KOK) is a popular traditional medicine used as a natural alternative to hormone replacement therapy for treating postmenopausal symptoms in Asia. Pueraria lobata Ohwi (P. lobata) is rich in isoflavones and has been traditionally used in combination with other herbs to produce synergistic and pharmaceutical effects via a multi-target approach for disease treatment. We aimed to investigate the phytoestrogenic effects of KOK extract against postmenopausal symptoms in ovariectomized (OVX) rats and confirm its efficacy by mixing KOK and P. lobata extracts.MethodsOVX rats were daily oral administrated with KOK and KOK + P. lobata mixture extracts (300–400 mg/kg) and their body weight and tail temperature were monitored for 12 weeks. The biochemical parameters, estradiol levels, and bone turnover markers were measured in the serum samples. Moreover, the estrogen receptor, ER-α and ER-β expression in the uterus and the uterus morphology were evaluated. AMPK, ATG1/ULK1, and mTOR protein expression in the liver were assessed.ResultsThe 12-week treatment with KOK and KOK + P. lobata mixture extracts did not cause liver damage or hormonal changes in the OVX rats. The treatments reduced the high lipid accumulation-related body weight gain and the tail temperature increase that was induced by ovariectomy. Further, it exhibited protective effects against hyperlipidemia and osteoporosis. No significant difference was observed in uterine weight compared to the OVX-treated group, while endometrial thickness reduction inhibition was observed due to ovariectomy. Bone mineral density (BMD) and serum osteocalcin levels, which decreased in OVX rats, increased with both treatments. Western blotting analysis showed that ER-α and ER-β were not expressed in the treated rats, whereas these proteins were expressed in Sham-operated rats. No significant differences in the phosphorylation of AMPK were observed; however, the ATG1/ULK1 and mTOR protein phosphorylation levels were upregulated and downregulated in the treated rats compared to those of OVX rats, respectively.ConclusionThis is the first in vivo study observing the efficacy and synergistic effects of the mixture of KOK and P. lobata. Our results suggest the potential of KOK and KOK + P. lobata mixture as an alternative therapy for alleviating menopausal symptoms.
Thermal ablation as an alternative to liver transplantation for hepatocellular carcinoma with clinically significant portal hypertension: propensity score matching study
Authors: Long Yinglin , Yang Zhou , Zeng Qingjing , Liu Zhongqi , Xu Erjiao , He Xuqi , Yuan Lianxiong , Fu Binsheng , Li Kai 
Published: June 2023

PurposeThe objectives were to investigate the safety and efficacy of thermal ablation as an alternative to liver transplantation for hepatocellular carcinoma patients with clinically significant portal hypertension (CSPH).Materials and MethodsFrom July 2016 to September 2019, hepatocellular carcinoma patients with CSPH treated by liver transplantation (N=37) or thermal ablation (N=114) were enrolled. Cumulative intrahepatic recurrence, overall survival and major complications were compared by propensity score matching.ResultsIn the two matched groups, the 1-, 2-, and 3-year intrahepatic recurrence rates for the ablation group (22.3%, 50.0%, and 50.0%, respectively) were significantly higher than those for the transplantation group (4.5%, 4.5%, and 4.5%, respectively) (P=0.016). The 1-, 2-, and 3-year overall survival rates were comparable between the two groups [96.1%, 88.7%, and 88.7%, respectively (ablation group) vs. 84.6%, 76.2%, and 76.2%, respectively (transplantation group)] (P=0.07). The major complication rate for the ablation group [4.8% (3/62)] was significantly lower than that for the transplantation group [36.0% (9/25)] (P&lt;0.001).ConclusionsThermal ablation is a safe and effective alternative for hepatocellular carcinoma patients with CSPH.
Individual risk and prognostic value prediction by machine learning for distant metastasis in pulmonary sarcomatoid carcinoma: a large cohort study based on the SEER database and the Chinese population
Authors: Yi Xinglin , Xu Wenhao , Tang Guihua , Zhang Lingye , Wang Kaishan , Luo Hu , Zhou Xiangdong 
Published: June 2023

BackgroundThis study aimed to develop diagnostic and prognostic models for patients with pulmonary sarcomatoid carcinoma (PSC) and distant metastasis (DM).MethodsPatients from the Surveillance, Epidemiology, and End Results (SEER) database were divided into a training set and internal test set at a ratio of 7 to 3, while those from the Chinese hospital were assigned to the external test set, to develop the diagnostic model for DM. Univariate logistic regression was employed in the training set to screen for DM-related risk factors, which were included into six machine learning (ML) models. Furthermore, patients from the SEER database were randomly divided into a training set and validation set at a ratio of 7 to 3 to develop the prognostic model which predicts survival of patients PSC with DM. Univariate and multivariate Cox regression analyses have also been performed in the training set to identify independent factors, and a prognostic nomogram for cancer-specific survival (CSS) for PSC patients with DM.ResultsFor the diagnostic model for DM, 589 patients with PSC in the training set, 255 patients in the internal and 94 patients in the external test set were eventually enrolled. The extreme gradient boosting (XGB) algorithm performed best on the external test set with an area under the curve (AUC) of 0.821. For the prognostic model, 270 PSC patients with DM in the training and 117 patients in the test set were enrolled. The nomogram displayed precise accuracy with AUC of 0.803 for 3-month CSS and 0.869 for 6-month CSS in the test set.ConclusionThe ML model accurately identified individuals at high risk for DM who needed more careful follow-up, including appropriate preventative therapeutic strategies. The prognostic nomogram accurately predicted CSS in PSC patients with DM.
Modality-based attention and dual-stream multiple instance convolutional neural network for predicting microvascular invasion of hepatocellular carcinoma
Authors: Li Zhi , Wang Yutao , Zhu Yuzhao , Xu Jiafeng , Wei Jinzhu , Xie Jiang , Zhang Jian 
Published: June 2023

Background and purposeThe presence of microvascular invasion (MVI) is a crucial indicator of postoperative recurrence in patients with hepatocellular carcinoma (HCC). Detecting MVI before surgery can improve personalized surgical planning and enhance patient survival. However, existing automatic diagnosis methods for MVI have certain limitations. Some methods only analyze information from a single slice and overlook the context of the entire lesion, while others require high computational resources to process the entire tumor with a three-dimension (3D) convolutional neural network (CNN), which could be challenging to train. To address these limitations, this paper proposes a modality-based attention and dual-stream multiple instance learning(MIL) CNN.Materials and methodsIn this retrospective study, 283 patients with histologically confirmed HCC who underwent surgical resection between April 2017 and September 2019 were included. Five magnetic resonance (MR) modalities including T2-weighted, arterial phase, venous phase, delay phase and apparent diffusion coefficient images were used in image acquisition of each patient. Firstly, Each two-dimension (2D) slice of HCC magnetic resonance image (MRI) was converted into an instance embedding. Secondly, modality attention module was designed to emulates the decision-making process of doctors and helped the model to focus on the important MRI sequences. Thirdly, instance embeddings of 3D scans were aggregated into a bag embedding by a dual-stream MIL aggregator, in which the critical slices were given greater consideration. The dataset was split into a training set and a testing set in a 4:1 ratio, and model performance was evaluated using five-fold cross-validation.ResultsUsing the proposed method, the prediction of MVI achieved an accuracy of 76.43% and an AUC of 74.22%, significantly surpassing the performance of the baseline methods.ConclusionOur modality-based attention and dual-stream MIL CNN can achieve outstanding results for MVI prediction.