bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of a novel redox- related differentially expressed lncRNA prognostic signature for predicting clinical immunotherapy response in gastric cancer
Authors: Peng Guisen , Wu Di , Shan Lidong , Lu Weicheng , Hu Mingjie , Liu Mulin , Wu Huazhang 
Published: May 2023

Abstract
Redox responses modulated by intracellular long noncoding RNA (lncRNA) can be involved in tumorigenesis and progression. However, the role of redox-related lncRNAs (RRlncRNAs) in gastric cancer (GC) development remains mostly unknown. Our research aims to establish and validate novel prognostic and immune infiltration markers for GC by constructing a prognostic model of RRlncRNAs. We downloaded the transcriptomic and mutational data for 407 GC pa-tients from The Cancer Genome Atlas (TCGA) database and randomized them 1:1 into a training and validation set to show that redox-related lncRNAs affect GC patients' prognosis. Subse-quently, the prognostic model was constructed for the screened RRlncRNAs using the Least Absolute Shrinkage and Selection Operator (LASSO) and the multivariate COX regression algo-rithm. Then, Survival analyses were performed on the train and test sets. The overall survival rate of GC patients was significantly correlated with the signatures of eight RRlncRNAs, including AC103702.2, AL138756.1, AL356417.2, CFAP61-AS1, RHPN1-AS1, CDK6-AS1, LINC02864, and AL355574.1. Meanwhile, we validated the model's accuracy through nomograms, Decision Curve Analysis (DCA), and comparisons using models from other studies. The results demonstrated that our model is more effective and outperforms the signature of Jiang et al. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of gene enrichment in high-risk patients shows significant enrichment in immune-related pathways. Waterfall plots of gene mutations, tumor mutation burden (TMB), and tumor immune dysfunction and exclusion (TIDE) showed significant differences in immune function between high- and low-risk groups. Then, we divided the 407 GC patients into two clusters using a consensus clustering algorithm and found significant differences in their immune microenvironment through immune cell difference anal-ysis, ESTIMATEScore, and gene set enrichment analysis (GSEA). Taken together, we conclude that the prognostic model constructed by RRlncRNAs can significantly affect the prognosis of GC patients and may alter their tumor progression by modulating the immune microenvironment in vivo. Our study found eight RRlncRNA-associated signatures, representing promising new markers for immunotherapy and diagnosis in GC patients.
miR-17~92 suppresses proliferation and invasion of cervical cancer cells by inhibiting cell cycle regulator Cdt2
Authors: Singh Garima , Sharma Sonika Kumari , Dorata Aastha , Singh Samarendra Kumar 
Published: May 2023

Abstract

Cervical cancer (CC) is the 4th most leading cause of death among women worldwide, and if diagnosed in late stages the treatment options are almost negligible. 99% of CC is caused by high-risk human papilloma viruses (HR-HPV). Upon integration into human genome, the encoded viral proteins mis-regulate various onco-suppressors and checkpoint factors including cell cycle regulators. One such protein is cell cycle S phase licensing factor, CDC-10 dependent transcript-2 (Cdt2) which has been reported to be highly upregulated in various cancers including CC. Also, in CC cells, several tumor suppressor miRNAs are suppressed, including miR-17 ~ 92 cluster. In this study, we report that miR-17 ~ 92 directly recruits to 3’UTR of Cdt2 and downregulates this oncogene which suppresses the proliferation, migration and invasion capabilities of the CC cell lines without effecting non-cancerous cells. We further show that suppression of Cdt2 by miR-17 ~ 92, blocks the cancerous cells in S phase and induces apoptosis, eventually leading to their death. Hence, our work for the first time, mechanistically shows how miR-17 ~ 92 could work as tumor suppressor in cervical cancer cells, opening up the potential of miR-17 ~ 92 to be used in developing therapy for cervical cancer treatment.
Nomogram for predicting of postoperative delirium in elderly patients undergoing radical esophagectomy
Authors: ✝ Ming-fangYan , Xu Yi-ping , Lin Zhen-meng , Chen Han-shen , Ke Jianfang , Zheng Hui-zhe , Luo Hui-yu 
Published: May 2023

Abstract
Background Postoperative delirium (POD) commonly occurs in elderly patients with esophageal cancer after curative surgery and is associated with serious outcomes. This study aimed to construct and validate a nomogram to predict POD after esophagectomy for carcinoma.Methods 1107 patients who underwent esophageal cancer surgery at the Fujian Cancer Hospital from January 2018 to September 2022 were retrospectively enrolled from a prospective database as the training cohort. The least absolute shrinkage and selection operator (LASSO) method was performed to screen the potential risk factors. Multivariate logistic regression was used to identify the independent predictors and to develop the the nomogram in the training cohort. The receiver operating characteristic (ROC) curve, calibration plot, and decision curve analysis (DCA) plots were adopted to assess the predictive accuracy of the nomogram. The validation cohort consisted of 338 patients treated at First Affiliated Hospital of Fujian Medical University was performed to externally validate the nomogram.Results The rate of POD was 16.6%(184/1107) in the training cohort. Age, diabetes mellitus, ASA classification, albumin level and surgical approach were identified as independent predictors for POD in multivariate analyses. The nomogram yielded great discrimination, with the area under the ROC curve were 0.788(95%CI: 0.752, 0.824) and 0.812(95%CI: 0.762, 0.862) in the training cohort and the validation cohort, respectively. The calibration plots and Hosmer–Lemeshow tests demonstrated a good correlation between the nomogram prediction and actual observation. The DCA further illustrated a high clinical application value of the model.Conclusions This study established a reliable nomogram based on five clinical parameters that could can be accurate and applicable in the probability of POD in elderly patients undergoing esophageal cancer surgery.
Discovery and Characterization of Genes Conferring Natural Resistance to the Antituberculosis Antibiotic Capreomycin
Authors: Chang Chin-Yuan , Ing Toh , Keisha Johan Elaine , Wang Yung-Lin , Pan Yi-Chi , Jhu Yu-Heng , Hsiao Po-Yun , Liao Wen-Ting , Chen Po-Yuan , Ko Tai-Ming 
Published: May 2023

Abstract
Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistant genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network analysis classified 353 Cph homologues into five major clusters. We examined the function and targeted antibiotics of three putative resistance proteins in cluster I via bioinformatics, biochemical, and protein structural analysis. We found that the proteins in cluster I are from various species and indeed confer resistance to CMN. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.
Development and validation of asthma diagnostic scale for Chinese children under 6 years old
Authors: Bai Shasha , zhang pingbo , liu quanhua , Chen Mengxue , Zhong Wenwei , Ma Yan , Zhang Jianhua , Hua Li , Bao Yixiao 
Published: May 2023

Abstract
Background: There is no diagnostic criteria for asthma in children under 6 years of age up to now.
Objective: To construct an asthma diagnostic scale for children (< 6 years old) to improve the diagnosis of asthma in China.
Methods: Electronic medical record database of a hospital was used to develop the scale. Item pool was established through literature survey and expert opinion, the screening and optimization of items were conducted by using Delphi method, t-test, reactivity analysis, Pearson correlation coefficient, factor analysis, reliability and validity test. The predictive probability of asthma was calculated using the logistic regression, and the receiver operating characteristic (ROC) curve evaluated the diagnostic efficiency of the scale. Another childhood asthma database validated the scale.
Results: The asthma diagnostic scale for children (< 6 years old) included five dimensions: dimension 1 (shortness of breath, three concave sign, cyanosis, moist rale, heart rhythm, heart sound and dyspnea), dimension 2 (respiratory sound, cough, sputum), dimension 3 (frequency of wheezing, allergic rhinitis, history of allergy in one or both parents), dimension 4 (gender, wheezing sound, atopic dermatitis), and dimension 5 (reversible airflow, positive in vitroor in vivo allergy test). Cronbach’s α coefficients for the five dimensions were 0.846, 0.459, 0.019, 0.202, and 0.024. The area under the ROC curve (AUC), sensitivity, and specificity were 0.737, 59.1%, and 81.2%. AUC, sensitivity, and specificity of the validation data were 0.614, 76.2%, and 46.7%.
Conclusion:The asthma diagnostic scale for children (< 6 years old) had certain reliability, validity, and diagnostic efficiency.
Plastic bronchitis in children：a review of 55 cases over a 10-year period
Authors: Chen Xiaowen , Wu Shangzhi , Huang Zhanhang , Lin Yuneng , Xu Jiaxing , Xu Qingyun , Chen Dehui 
Published: May 2023

Abstract
Objective To summarize the clinical characteristics and treatment experiences of patients with plastic bronchitis (PB).Methods All patients who were diagnosed with PB by bronchoscopic removal of tree-like casts at a single institution from January 2012 to May 2022 were retrospectively reviewed. Demographic and clinical data were retrieved from electronic patient records༎Results A total of 55 patients, with a median age of 5.3 years, were eligible for the study. Nineteen cases had underlying diseases, among which asthma was the most common. Clinical symptoms were characterized by cough and fever, while moist rales (78.2%) and dyspnea (61.8%) were the most common signs. The most common laboratory finding was elevated C-reactive protein (58.2%). Patchy exudation was the most frequent radiographic finding (81.2%), followed by consolidation (60.0%) and pleural effusion (43.6%). Respiratory pathogens were detected in 41 cases, and M. pneumoniae was the most common one (41.8%), followed by adenovirus (20.0%) and influenza B virus (10.9%). The casts were removed by alveolar lavage, combined with ambroxol immersion (63.6%) and forceps (30.9%). Patients received an average of 2.3 bronchoscopies, and the median time for the first procedure was 3 days after admission. Antibiotics were given to all patients, methylprednisolone to 33 (60.0%), and gamma globulin to 25 (45.5%). A total of 53 cases were improved with an overall mortality rate of 3.6%.Conclusions PB in children is characterized by airway obstruction, mostly caused by respiratory infections, and timely removal of the cast by bronchoscopy is the most effective treatment.
Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting
Authors: Yisimayi Ayijiang , Song Weiliang , wang jing , Jian Fanchong , Yu Yuanling , Chen Xiaosu , Xu Yanli , Yang Sijie , Niu Xiao , Xiao Tianhe , Wang Jing , An Ran , Zhang Na , Wang Yao , Wang Peng , Zhao Lijuan , Sun Haiyan , Yu Lingling , Gu Qingqing , Shao Fei , Jin Ronghua , Shen Zhongyang , Xie Xiaoliang , Wang Youchun , Cao Yunlong 
Published: May 2023

Abstract
The continuous emergence of highly immune evasive SARS-CoV-2 variants, like XBB.1.5 and XBB.1.16, highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by wildtype (WT)-based vaccination would compromise the antibody response to Omicron-based boosters. Vaccination strategies that can counter immune imprinting are critically needed. In this study, we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. By isolating 781 RBD-targeting mAbs from repeated Omicron infection cohorts, we revealed that double Omicron exposure alleviates immune imprinting by generating a large proportion of highly matured and potent Omicron-specific antibodies. Importantly, epitope characterization using deep mutational scanning (DMS) showed that these Omicron-specific antibodies target distinct RBD epitopes compared to WT-induced antibodies, and the bias towards non-neutralizing epitopes observed in single Omicron exposures due to imprinting was largely restored after repeated Omicron stimulation, together leading to a substantial neutralizing epitope shift. Based on the DMS profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated the combinations of these mutations could further boost XBB.1.5’s immune-evasion capability while maintaining high ACE2 binding affinity. Our findings suggest the WT component should be abandoned when updating COVID-19 vaccine antigen compositions to XBB lineages, and those who haven't been exposed to Omicron yet should receive two updated vaccine boosters.
Construction and Drug Screening of 3D Co-culture System Using Extrahepatic Cholangiocarcinoma Organoids and Tumor-associated Macrophages
Authors: Guo Yinghao , Li Jiangtao , Ye Qinghuang , Li Qi , Jin Yun , Yu Yuanquan , Zhang Xiaoxiao , Xi Longfu , Wang Yihang , Wu Di , Pan Yanzhi , Wei Shumei , Li Qingyong , Wang Huiquan 
Published: May 2023

Abstract
Background: Tumor-associated macrophages (TAMs) play a key role in cholangiocarcinoma, but research has been hindered by the lack of highly reductive tumor models. Organoids are a type of three-dimensional (3D) cell-culture technology derived from tumor stem cells in vitro. Although organoids are appropriate experimental models for tumor research, they cannot reflect the crosstalk that occurs between cancer cells and TAMs in the tumor microenvironment (TME).Methods: We successfully established a tumor model by co-culturing organoids and TAMs from 6 cases of primary extrahepatic cholangiocarcinoma (eCCA) through Transwell culture systems, and we explored the interactions between cells.Result: Our comprehensive analysis and comparison of histopathology, genomics, and multiomics outcomes confirmed that this co-culture model can better capture intra- and inter-tumor heterogeneity. Drug sensitivity data in vitro revealed that gemcitabine and cisplatin are effective drugs for cholangiocarcinoma, and TAMs in the tumor microenvironment promote organoids growth and chemotherapy resistance.Conclusion: In conclusion, our organoid model of cholangiocarcinoma co-cultured with TAMs highly simulates source specimens and is a promising preclinical tumor model.
Semi-solid plasticity and deformation control of superalloy investment casting
Authors: Ding Zhengyi , Wang Donghong , Guan Bang , Cui Jiayu , Shu Da , Sun Baode 
Published: May 2023

Abstract
The deformation in superalloy investment casting under thermal-mechanical coupled stress is causing huge waste of materials and energy. Mechanical models of both alloy and shell are essential to predict the deformation of castings accurately. The elastoplastic behavior of superalloy in semi-solid zone is critical to the deformation during solidification. In this paper, the deformation of ring-to-ring castings with Ni-based superalloy K4169 is researched. To obtain the thermal-mechanical behavior of K4169 from solid region to semi-solid zone, physical simulated uniaxial compression is performed. Yield stress and plastic modulus from the measurement are imported into the database for numerical simulation. Different thermal-mechanical models of both alloy and shell are compared. With elastoplastic model for alloy, considering the deformability of shell with elastic model, the accuracy of prediction is within CT4 level, with a maximum error of 0.39mm. The deformation of reaches the minimum when the initial temperature of alloy and shell are 1500℃ and 900℃. The research on semi-solid performance of alloy and thermal-mechanical models can provide theoretical guidance for deformation prediction. The method of this research is promising in dimensional control of castings, and can be transported to dimensional control problems upon solidification process with different kinds of materials and castings.
Knowledge of spawning phenology may enhance selective barrier passage for wetland obligate fishes
Authors: Piczak Morgan , Theÿsmeÿer Tys , Doka Susan E. , Midwood Jonathan D. , Cooke Steve J. 
Published: May 2023

Abstract
Within the Laurentian Great Lakes, many native fishes use wetlands for spawning; however, these areas are also used by non-native common carp (Cyprinus carpio) that may impart negative ecological impacts. There is interest to manage common carp using barriers to decrease passage to specific habitats (e.g., their spawning sites), but these barriers could also exclude native wetland obligate spawners such as largemouth bass (Micropterus salmoides) and northern pike (Esox lucius). Our objective was to determine if differences in phenologies, specifically, spawning movements could be exploited in shallow areas to operate seasonal barriers that are opened and closed to promote selective fragmentation. Using a long-term dataset from the Cootes Paradise Marsh fishway (Hamilton, Ontario), we generated predictive models based on cumulative growing degree day (CGDD) for all three fishes. These models successfully predicted earlier arrival by all species in a warmer year and delayed spawning movements during a cold year, supporting the role of temperature as a driver of interannual variation in spawning movements. We then compared the fishway model predictions to movement timing to spawning habitat within nearby Toronto Harbour; movement data was derived from acoustic telemetry information. We found that the models performed well and predictions were correlated with movements of all three species, but performance was weakest for northern pike. It is our hope that managers could use these predictive models to assist in the operation of seasonal barriers to optimize control of non-native common carp, while minimizing negative impacts for native species that require access to coastal wetlands.
In vitro Comparative Quality Assessment of Different Brands of Hydrochlorothiazide Tablets Marketed in Northeast Ethiopia
Authors: Teshome Yehualashet , Kassahun Haile , Said Yimer , Wondesen Abate , Ayenew Kassahun Dires , Berihun Samuel , Linger Bedilu 
Published: May 2023

Abstract
Background This study aimed to evaluate the quality and physicochemical bioequivalence of commercially available brands of hydrochlorothiazide 25mg tablets in community pharmacies in Dessie town, Northeast Ethiopia.Methods Experimental-based cross-sectional study design was applied using disintegration, identification, friability, uniformity, hardness, and assay test methods as described in the USP. Difference (f1) and similarity (f2) factor values were calculated to assess in vitro bioequivalence of generic products with the comparator.Result The study revealed that all investigated brands of hydrochlorothiazide tablets contain a genuine active pharmaceutical ingredient (API) in their formulations. The friability test result was concordant with the USP (< 1%) in eight of the investigated brands. Whereas the result of the hardness limit was concordant (39.23N, USP 2019) in only six of those brands. The weight variation test result indicated that all samples complied with USP specification limits. The quantitative assay result of API was within the limit of USP (90% up to 110%). Similarly, all samples meet the disintegration time limit (i.e, ≤ 30 minutes) and drug-releasing tolerance limit (API released more than 60% within 60 minutes). The f2 values were > 50 & f1 values were ˂15 for all sampled brands of hydrochlorothiazide tablet formulations.Conclusion The majority of sampled brands of hydrochlorothiazide 25 mg tablets met the quality requirements as per USP official test specifications limit. From similarity factor (f2) and difference factor (f1) values, all studied brands were equivalent to the comparator and can interchangeably use in the clinical area.
Identification of mRNA and lncRNA profiles and potential targeted agents for fibrolamellar carcinoma based on RNA-sequencing data
Authors: Kim Janghyun , Kim Young , Lee Bora 
Published: May 2023

Abstract
Background: Fibrolamellar carcinoma (FLC) is a rare type of liver cancer that primarily affects adolescents and young adults without prior liver disease or virus infections. Patients with FLC often have non-specific symptoms and are often diagnosed at a later stage with a higher frequency of metastases compared to other liver cancers. A fusion transcript of DNAJB1 and PRKACA has been identified in all FLC patients, which can lead to increased activity of PKA and cellular proliferation, although the exact mechanism through which FLC develops remains unclear. In this study, we investigated common mRNA and lncRNA profiles in various FLC samples using bioinformatics analysis.
Methods: We analyzed differentially expressed mRNAs and lncRNAs from three different public datasets. We performed Gene Ontology (GO), KEGG, and Protein-Protein Interaction (PPI) Network analyses with the differentially expressed (DE) mRNAs of FLC. Using DE mRNAs and lncRNAs, we predicted potential lncRNA target genes and screened for small molecule compounds for the FLC.
Results: We identified 912 differentially expressed mRNAs and 308 differentially expressed lncRNAs from RNA sequencing analysis. GO analysis showed that the upregulated mRNAs in FLC were enriched in collagen fibril and extracellular matrix organization, while the downregulated mRNAs were enriched in xenobiotic metabolic and exogenous drug catabolic process. Furthermore, the upregulated mRNAs were enriched in PI3k-Akt signaling pathway based on KEGG pathway analysis, and in epithelial mesenchymal transition from GSEA analysis. we performed trans-target prediction analysis and identified 454 co-expressed pairs in FLC. Lastly, we screened and obtained potential therapeutic small molecule compounds using hub genes of FLC we identified.
Conclusions: Our study revealed common mRNA and lncRNA expression profiles in FLC, and identified hub genes of DE mRNAs and lncRNA target genes, as well as small molecular compounds that could potentially be used as treatments. These results could contribute to further understanding of FLC and provides potential avenues for diagnosis and treatment.