bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of lncRNAs expression profile related to goat skeletal muscle at different development stages
Authors: Han Haiyin , Li Wentao , Liu Jiannan , Fan Yekai , Zhang Hui , Yang Junqi , Gao Yahui , Liu Yufang 
Published: April 2022

Abstract
Background
Long noncoding RNAs (lncRNAs) act vital roles in muscle growth and development, however, the reports of their expression characteristics and effects in goat skeletal muscle growth are few.
Result
Here, the RNA sequencing reads of goat longissimus doris tissues collected from kid (1 month old) and youth (9 months old) were mapped to the reference genome. As a result, we obtained an average of ~ 14.58 Gb high-quality clean reads. A total of 3,441 lncRNAs were identified, including 1,281 lincRNAs, 805 antisense lncRNAs and 1,355 sense_overlapping lncRNAs. These lncRNAs shared some properties in goat, such as shorter transcript length, fewer exons and shorter open reading frame (ORF). Among them, 36 differentially expressed lncRNAs (DE lncRNA) were identified, of which 10 lncRNAs were randomly selected to validate by RT-qPCR. Moreover, 79 co-location interactions were found between 26 lncRNAs and 71 genes by co-location analysis and functional annotation, and these genes were functionally involved in skeletal muscle related biological processes, such as skeletal system development, negative regulation of G1/S transition of mitotic cell cycle, negative regulation of cell cycle G1/S phase transition, myoblast fate determination and myosin complex. Additionally, trans regulation analysis suggested 36 lncRNAs and 2,684 mRNAs were included in co-expression networks. These co-expressed mRNAs were significantly enriched in muscle development related GO terms. The key lncRNA-mRNA interactions could reveal the function of lncRNA in goat and may be valuable in regulating skeletal muscle growth and development. In the last, the ceRNA (lncRNA-miRNA-mRNA) networks containing 4 lncRNAs, 3 miRNAs, and 8 mRNAs were constructed. Importantly, muscle development related mRNAs were included in the ceRNA networks, such as IFRD1, NKX2-5 and other genes.
Conclusion
This study revealed the lncRNAs expression profile in skeletal muscle growth and development and can facilitate further study on their function in goat muscle biology.
Fragment-Based Design of SARS-CoV-2 Mpro inhibitors
Authors: Teli Divya Madhukarbhai , Patel Bansari , Chhabria Mahesh T. 
Published: April 2022

Abstract
SARS-CoV-2 virus has been identified as a causative agent has been identified for COVID19 pandemic. Till date, about more than 6.1 million deaths have been reported due to COVID-19 across the globe. Looking into the current outbreak, there is an urgent need to identify the potential treatment for the disease. The prominence of main protease in the life cycle of virus shapes the main protease as a viable target for design and development of antiviral agents to combat COVID-19. The current study presents the fragment linking strategy to design the novel Mpro inhibitors for COVID-19. Total 2,93,451 fragments from diversified libraries have been screened for their binding affinity towards Mpro enzyme. The best 1600 fragment hits were subjected to fragment joining to achieve 100 new molecules using Schrödinger software. The resulting molecules were further screened for their Mpro binding affinity, ADMET and drug-likeness features. Best 13 molecules were selected and best compound was investigated for its ligand-receptor complex stability through molecular dynamics study using GROMACS software. The resulting molecules have the potential to be further evaluated for COVID-19 drug discovery.
Early-life origin of prostate cancer through deregulation of miR-206 networks in maternally malnourished offspring rats
Authors: Portela Luiz , Constantino Flavia , Camargo Ana , Santos Sergio , Colombelli Ketlin , Fioretto Matheus , Barata Luisa , Ramos Erick , Scarano Wellerson , Moreno Carlos , Justulin Luis A 
Published: April 2022

Abstract
The Developmental Origins of Health and Disease (DOHaD) has provided the framework to assess how early life experiences can shape health and disease throughout the life course. While maternal malnutrition has been proposed as a risk factor for the developmental programming of prostate cancer (PCa), the molecular mechanisms remain poorly understood. Here, we found an association between deregulation of steroidogenesis and impairment of the ventral prostate (VP) growth in young offspring rats exposed to maternal low protein diet (LPD) during gestation and lactation. Reanalysis of RNA-seq data demonstrated that miR-206 was upregulated in the VP of young maternally malnourished offspring. Target prediction and in vitro studies identified Plasminogen (PLG) as a direct target of miR-206. To give further insights into the participation of the miR-206-PLG network in prostate carcinogenesis in the progeny submitted to maternal LPD. RT-qPCR analysis revealed deregulation of the miR-206-PLG network in the VP of older rats that developed prostate carcinoma in situ. Furthermore, mimic studies revealed a negative correlation between miR-206 and estrogen receptor α (ESR1) expression in PNT2 cells. Together, we demonstrate that early life estrogenization associated with deregulation of miR-206-networks can contribute to the developmental origins of PCa in maternally malnourished offspring. Understanding the molecular mechanisms by which early life malnutrition affects offspring health can encourage the adoption of a governmental policy for the prevention of non-communicable chronic diseases related to the DOHaD concept.
Continuous Glucose Monitoring and 1-hour Plasma Glucose Identifies Glycemic Variability and Dysglycemia in High-Risk Individuals with HbA1c &lt;5.7%
Authors: Dorcely Brenda , Sifonte Eliud , Popp Collin , Divakaran Anjana , Katz Karin , Musleh Sarah , Jagannathan Ram , Curran Margaret , Sevick Mary Ann , Aleman Jose O. , Goldberg Ira J. , Bergman Michael 
Published: April 2022

Abstract
Purpose: Although commonly used, HbA1c is insensitive for diagnosing prediabetes and diabetes. Glycemic variability (GV) or a 1-hour plasma glucose level (1-h PG) ≥ 155 mg/dL (8.6 mmol/L) during a 75-gram oral glucose tolerance test (OGTT) better identifies individuals with dysglycemia. The objectives were to (1) compare continuous glucose monitoring (CGM) with the OGTT for detecting dysglycemia in high-risk subjects with HbA1c < 5.7% (39 mmol/mol), and (2) correlate the 1-h PG with CGM-derived GV indices. Research Design and Methods: Subjects (n=15) with a HbA1c < 5.7% (39 mmol/mol) and at least one other risk factor for type 2 diabetes such as overweight, obesity, hypertension, or hyperlipidemia were recruited. A 2-h OGTT was performed within 3-7 days of CGM insertion, which was worn up to 14 days. Results: The average age was 50 ± 14 years, with the majority of participants being men (80%) and Caucasian (67%). The mean HbA1c was 5.3±0.2% (34 mmol/mol). The 1-h PG was highly correlated with 1-h CGM glucose levels (ρ=0.881, p<0.001) as well GV indices: mean amplitude of glucose excursions (ρ =0.67, p<0.01), standard deviation (ρ=0.79, p<0.01), and lability index (ρ =0.64, p=0.001). Conclusion: 1-h interstitial CGM glucose and 1-h PG can detect dysglycemia in high-risk subjects with HbA1c < 5.7% (39 mmol/mol). CGM may be an alternative screening tool for glucose disorders.
Multisystem injury by Intrauterine Device: a report of five cases and literature review
Authors: Sun Junyi , Tang Qiao , Zhang Xiangyang 
Published: April 2022

Abstract
BackgroundIUD placement is a widely used method of contraception in China and is currently recommended by the World Health Organization as a first-line contraceptive program，Intrauterine Device Migration can cause multiple system damage，Experts other than urologists and gynecologists often ignore this trigger.We aim to summarize cases and provide clinicians with more appropriate treatment options.Case presentationWe reported five cases of ectopic IUDs and its effect on multiple systems, 2 cases underwent laparoscopic treatment, 2 cases underwent hysteroscopy, and one case underwent laparoscopic free ectopic contraceptive ring removal and ureter-bladder replantation, with no surgery post-complication difference. Combining the five cases in our hospital, researchers searched PubMed, and other databases in the last 10 years to determine similar studies. A total of 48 cases were ectopic to the urinary system, including ectopic to bladder (42 cases 87.5%), ureter (5 cases 10.4%), urethra (1 case 2.0%); ectopic to digestive system, 41 cases;20 cases from ectopic to reproductive system,65 cases underwent laparoscopic technology (50.7%), endoscopy (15.6%), and open surgery accounted for only 9%. Discussion and Conclusions Specialists other than urologists and gynecologists should not ignore injuries caused by Intrauterine Device Migration. Clinicians should choose the appropriate surgical plan according to the position of the ectopic to relieve the complications.
Peptide inhibition of the mTORC1 signaling: A trend in Cancer Therapeutics
Authors: Tiwari Ashok , Kumar Anuj , R Rachana 
Published: April 2022

Abstract
Cancer is the second most leading cause of deaths in the world and has been manifested by various hallmarks including uncontrolled cell proliferation, increased cell survival, abnormal angiogenesis, eluding of antitumor immunity and acquisition of metabolic processes unique to cancers. Interestingly, mTOR signaling is found to be associated with all of these hallmarks which makes it the most appropriate choice for target therapies against cancer. Inhibition of the target protein by peptides designed by using the interfacial amino acids of its interacting partner is one of the approaches of target therapies. The same approach has been engaged here to inhibit association of the mTOR kinase and RHEB. The sequential amino acids of the mTOR kinase were utilized to design three different native peptides which were further modified by incorporating evolutionary changes as the mutations. All the peptides were tested for their affinity with the RHEB by performing protein-peptide docking on the HADDOCK 2.4 docking interface and the binding energy calculation on the FoldX5.0 interface. Also, the interactions were analyzed using the ligplot+ tool. The peptide H2P1 and H3P1 showed good binding energies (-14.28 kcal/mol and − 14.53 kcal/mol, respectively) in comparison to the entire mTOR-RHEB complex (-15.83 kcal/mol). This was also supported by a good number of Hydrogens bonds and other positive interactions. All these evidences support their potency to interrupt the mTORC1 signaling which can be further established based on these shreds of evidences.
Whole-exome sequencing analysis of mutation characteristics in recurrent or metastatic gastrointestinal stromal tumors
Authors: Wang Lingquan , Liang Yingchao , Zhang Wenjing , Wang Xufeng , Ni Zhentian , Mei Yu , Yan Chao , Li Chen , Xie Jing , Yan Min , Yang Liang , Zhu Zhenggang , Liu Wentao 
Published: April 2022

Abstract
Purpose: Surgical resection for the metastasis and recurrence of gastrointestinal stromal tumors (GISTs) is controversial. Therefore, it is increasingly important to identify clinical factors related to survival and explore the driver genes and mutations in GIST. Patients and Methods: GIST patients who received two surgeries for primary and recurrent and/or metastatic tumors between January 2003 and December 2018 were reviewed. Paired PT (primary tumor), RMT (recurrent and/or metastatic tumor), and normal DNA were whole-exome sequenced to generate comparable data in eight GIST cases.
Results: We identified 39 eligible patients with a median overall survival time of 56.7 months (IQR: 9.6-190.3 months). Regular TKI (Imatinib) treatment after primary tumor resection was associated with better OS, while presence of liver metastasis was prognostic for worse OS in GIST patients who received re-surgery due to recurrent and/or metastatic tumors. Compared with normal tissue, mutation of the MUC family in eight PTs and seven RMTs among the eight patients was detected. In the irregular (TKI) group, correlations and differences were noted in KIT mutations between the PT and RMT, while its influence was lower in the other cases. We also found that the mutation signature and subclone indicated the spatial and temporal heterogeneity of the tumor.
Conclusions: MUC mutations may be a potential predictor of recurrent and/or metastatic GIST. Treatment with TKI influenced KIT mutations in RMT of GIST patients. Due to the heterogeneity in the PT and RMT, the direction of tumor evolution and progression were not stable and regular.
SMARCA4-deficient undifferentiated uterine sarcoma: A Case Report and Literature Review
Authors: Fan Ruirui , Gao Jie , Chen Dahong , Hou Jinlin , Chen Hanlin , Lu Mingzhi 
Published: April 2022

Abstract
SMARCA4-deficient undifferentiated uterine sarcoma (SDUS) is a highly invasive single-gene malignant tumour caused by mutations in the SMARCA4 gene. SDUS has a poor prognosis and has no established treatment scheme at present. What's more, there is no relevant research on the role of immune microenvironment analysis in SDUS worldwide. Here, we report a case of SDUS that combined examinations via morphology, immunohistochemistry, immunofluorescence, and molecular detection and analysed the immune microenvironment of SDUS for the first time. Therefore, our report will help in the diagnostic awareness of SDUS.
NAPSB as a predictive marker for prognosis and therapy associated with an immuno-hot tumor microenvironment in hepatocellular carcinoma NAPSB predicts prognosis and therapy in HCC
Authors: Ning Yu-Mei , Lin Kun , Liu Xiao-Ping , Ding Yang , Jiang Xiang , Zhang Zhang , Xuan Yu-Ting , Dong Li , Liu Lan , Wang Fan , Zhao Qiu , Wang Hai-Zhou , Fang Jun 
Published: April 2022

Abstract
Background
Napsin B Aspartic Peptidase, Pseudogene (NAPSB) was associated with CD4 + T cell infiltration in pancreatic ductal adenocarcinoma. But the biological role of NAPSB in hepatocellular carcinoma (HCC) remains to be determined.
Methods
The expression of NAPSB in pan-cancer and HCC as well as its clinicopathological association were analyzed using data from several public datasets. qRT-PCR was used to verify the relative expression of NAPSB in HCC using Zhongnan cohort. Kaplan-Meier analyses, univariate and multivariate Cox regression were conducted to determine the predictive value of NAPSB on HCC prognosis. Then enrichment analyses were performed to identify the possible biological functions of NAPSB. Subsequently, the immunological characteristics of NAPSB in the HCC tumor microenvironment (TME) were demonstrated comprehensively. The role of NAPSB in predicting hot tumors and its impact on immunotherapy and chemotherapy responses was also analyzed.
Results
NAPSB was downregulated in HCC and high NAPSB expression showed an improved survival outcome. Enrichment analyses showed that NAPSB was related to immune activation. NAPSB was positively correlated with immunomodulators, tumor-infiltrating immune cells (TIICs), T cell inflamed score, and cancer immunity cycles and highly expressed in immuno-hot tumors. High expression of NAPSB was sensitive to immunotherapy and chemotherapy, possibly due to its association with pyroptosis, apoptosis and necrosis (PANoptosis).
Conclusions
NAPSB was correlated with an immuno-hot and inflamed TME and tumor cell death. It can be utilized as a promising predictive marker for prognosis and therapy in HCC.
Description of Pseudocapillaria (Discocapillaria) trilobularis n. sp. (Capillariidae) and redescription of Heliconema alatum (Majumdar, 1965) (Physalopteridae), two nematodes parasitising synbranchiform fishes in India
Authors: Moravec František , Chaudhary Anshu , Kashyap Deepa , Singh Suhani , Kumar Yougesh 
Published: April 2022

Abstract
One new nematode species is described and another one, already known species is redescribed based on specimens collected from synbranchiform fishes of the River Ganga, India, in 2021 and 2022: Pseudocapillaria (Discocapillaria) trilobularis n. sp. (Capillariidae) from the intestine of cuchia, Monopterus cuchia (Hamilton) (Synbranchidae), is mainly characterised by the presence of the large ventral postcloacal lobe in the male, the spicule length 351 µm, the size of eggs 60–69 × 30–36 µm (with protruding polar plugs) and by the body length (male 10.50 mm, females 11.02–12.44 mm). It is the fourth species of this genus recorded from fishes in India. The species name Heliconema alatum (Majumdar, 1965) (Physalopteridae) is resurrected. This nematode is redescribed from specimens collected from the intestine of zig-zag eel, Mastacembelus armatus (Lacepède) (Mastacembelidae). The examination by SEM revealed some previously not reported morphological features in this nematode species, e.g., the presence of cephalic papillae or a lateroterminal depression and two inner flat dorsoventral teeth on each pseudolabium. Based on these findings, H. monopteri Moravec, Chaudhary & Singh, 2019 is considered a junior synonym of H. alatum.
Genes associated with situs inversus in patients with primary ciliary dyskinesia are identified by the weighted gene correlation network analysis
Authors: Xia Pengcheng , Chen Jing , Liu Yingchao , Cui Xiaolin , Wang Cuicui , Zong Shuai , Wang Le , Lu Zhiming 
Published: April 2022

Abstract
Background.
Primary ciliary dyskinesia (PCD) is an autosomal recessive disorder characterized by immotile and dysmotile cilia or absence of cilia. Situs inversus (SI) is one of the phenomena frequently observed in PCD. However, little is known about the association between SI with PCD.
Material and Methods.
The microarray data of PCD were retrieved from the Gene Expression Omnibus (GEO) database to construct the co-expression network by the weighted gene co-expression network analysis (WGCNA). R software package Limma was used to perform the differential analysis. The gene network modules associated with SI screened with the common genes were further annotated based on Gene Ontology (GO) database and enriched based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Gene Set Enrichment Analysis (GSEA) was applied to identify the significant pathways. CIBERSORT was used to perform the correlation analysis of immune cells. The protein-protein interaction (PPI) network was constructed based on STRING database to identify the hub genes in the network.
Results.
Genes involved in PCD were identified related to SI. The results of the correlation analysis of immune cells showed that there were significant differences in the activated contents of dendritic cells. The WGCNA analysis revealed a total of 8 hub genes (i.e., ATP5A1, NDUFS3, NDUFV2, PSMC3, UBE2M, ALDH18A1, DBT, FOXRED1). Based on the GO annotations of hub genes, a group of GO terms were revealed to show significant difference, including mitochondrial part, oxidoreductase complex, cytosol, mitochondrial respiratory chain complex I, NADH dehydrogenase complex, respiratory chain complex I, catalytic complex, mitochondrial envelope, respiratory chain complex, and mitochondrial respiratory chain. KEGG enrichment analysis of hub genes identified a group of metabolic pathways showing significant difference, including Propanoate metabolism, beta-Alanine metabolism, Fatty acid degradation, Valine, leucine and isoleucine degradation, Huntington disease, Carbon metabolism, Fatty acid metabolism, Lysine degradation, Butanoate metabolism, and Metabolic pathways.
Conclusion.
Our study identified the variations in immune cells in PCD patients. The hub genes provide novel therapeutic targets for the diagnosis and treatment of PCD and SI.
Changes in the transcriptome of thyroid cancer cell lines after radiotherapy and analysis of the potential mechanisms regulating radiotherapy sensitivity
Authors: Zhao Yinlong , Liu Yu , Zhong Lili , Ji Jianfeng , Yi Heqing 
Published: April 2022

Abstract

Background 131Iodine (131I) is an important method for the treatment of thyroid cancer. However, resistance to 131I therapy in some patients results in treatment failure due to the mechanisms involving iodine metabolism and radiotherapy sensitivity. At present, the mechanism of radiosensitivity of 131I treatment for thyroid cancer is not sufficiently documented. Methods Time course data on transcriptome differential expression were obtained by next-generation sequencing after administration of high-dose radiation therapy to thyroid cancer cell lines (treated vs. control). Based on the fuzzy clustering algorithm, the time course data were analyzed with the Mfuzz software package, and then the series of clusters reflecting the differential expression trend of the transcriptome was obtained. Bioinformatics was used to construct ceRNA-miRNA-mRNA networks, protein-protein interaction (PPI) networks, survival analysis, and Cox regression analysis to identify competing endogenous RNA (ceRNA) pathways associated with radiosensitivity.Results Six time-course clusters with differentiated changing trends are obtained after radiation therapy. Six ceRNA networks are constructed from the 6 time-course clusters transcriptome data, and the hub genes are screened out. After survival analysis and Cox regression analysis, a total of six genes, BNIP3L, TP53INP2, CHAF1A, KDM6B, NUP153, and DCBLD, and their ceRNA pathways were screened. These ceRNA pathways are mainly involved in mitophagy, autophagy, apoptosis, proliferation, DNA damage, and repair, and are closely related to the mechanisms of radio-sensitivity. Conclusion We identified several ceRNA pathways potentially involved in the regulation of thyroid cancer radiosensitivity, which provides important clues for the mechanistic study of thyroid cancer radiosensitivity. To our knowledge, this is the first systematic and comprehensive analysis of transcriptome alteration trends in thyroid cancer cells after radiation and the prediction of pathways associated with sensitivity to radiotherapy.
Partially linear additive hazards regression for clustered and right censored data
Authors: Chen Wei , Ren Fengling 
Published: April 2022

Abstract
For analyzing clustered survival data, a flexible partially linear additive hazards model is proposed. To accommodate the nonlinear effects, the unknown regression function is approximated by B-splines. All regression coefficients are estimated through a system of pseudo-score functions. Under certain conditions, the proposed estimators are shown to be asymptotically normal, where a consistent estimator of the covariance matrix is given. Simulation studies are also conducted to evaluate the finite sample performance of the proposed method, which is illustrated using a real data set from an AIDS clinical trial.