bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upregulation of miR-205 induces CHN1 expression, which is associated with the aggressive behaviour of cervical cancer cells and correlated with lymph node metastasis
Authors: liu jianbing , li yunfeng , chen xihua , xu xiangbo , zhao haoqi , wang shufang , hao jianqing , he bin , liu shuyan , wang jiedong 
Published: September 2020

Abstract
Background: Cervical cancer is the leading cause of cancer-related death in women worldwide. However, the mechanisms mediating the development and progression of cervical cancer are unclear. In this study, we aimed to elucidate the roles of microRNAs and a1-chimaerin (CHN1) protein in cervical cancer progression. Methods: The expression of miR-205 and CHN1 protein was investigated by in situ hybridisation and immunohistochemistry. We predicted the target genes of miR-205 using software prediction and dual luciferase assays. The expression of mRNAs and proteins was tested by qRT-PCR and western blotting respectively. The ability of cell growth, migration and invasion was evaluated by CCK-8 and transwell. Cell apoptosis was analysed by flow cytometry analysis. Results: We found that miR-205 and CHN1 were highly expressed in human cervical cancer tissue compared with paired normal cervical tissues. The CHN1 gene was shown to be targeted by miR-205 in HeLa cells. Interestingly, transfection with miR-205 mimic upregulated CHN1 mRNA and protein, while miR-205 inhibitor downregulated CHN1 in high-risk and human papilloma virus (HPV)-negative human cervical cancer cells in vitro,. These data suggested that miR-205 positively regulated the expression of CHN1. Furthermore, the miR-205 mimic promoted cell growth, apoptosis, migration, and invasion in high-risk and HPV-negative cervical cancer cells, while the miR-205 inhibitor blocked these biological processes. Knockdown of CHN1 obviously reduced the aggressive cellular behaviours induced by upregulation of miR-205, suggesting that miR-205 positively regulated CHN1 to mediate these cell behaviours during the development of cervical cancer. Furthermore, CHN1 was correlated with lymph node metastasis in clinical specimens. Conclusions: Our findings showed that miR-205 positively regulated CHN1 to mediate cell growth, apoptosis, migration, and invasion during cervical cancer development, particularly for high-risk HPV-type cervical cancer. These findings suggested that dysregulation of miR-205 and subsequent abnormalities in CHN1 expression promoted the oncogenic potential of human cervical cancer.
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients
Authors: LOU Shaoke , Li Tianxiao , Spakowicz Daniel , Yan Xiting , Chupp Geoffrey Lowell , Gerstein Mark 
Published: September 2020

Abstract
Background: The pathogenesis of asthma is a complex process involving multiple genes and pathways. Identifying biomarkers from asthma datasets, especially those that include heterogeneous subpopulations, is challenging. Potentially, autoencoders provide ideal frameworks for such tasks as they can embed complex, noisy high-dimensional gene expression data into a low-dimensional latent space in an unsupervised fashion, enabling us to extract distinguishing features from expression data.Results: Here, we developed a framework combining a denoising autoencoder and a supervised learning classifier to identify gene signatures related to asthma severity. Using the trained autoencoder with 50 hidden units, we found that hierarchical clustering on the low-dimensional embedding corresponds well with previously defined and clinically relevant clusters of patients. Moreover, each hidden unit has contributions from each of the genes, and pathway analysis of these contributions shows that the hidden units are significantly enriched in known asthma-related pathways. We then used genes that contribute most to the hidden units to develop a secondary random-forest classifier for directly predicting asthma severity. The feature importance metric from this classifier identified a signature based on 50 key genes, which are associated with severity. Furthermore, we can use these key genes to successfully estimate FEV1/FVC ratios across patients, via support-vector-machine regression. Conclusion: We found that the denoising autoencoder framework can extract meaningful patterns corresponding to functional gene groups and patient clusters from the gene expression of asthma patients.
Association between physical activity and conversion from mild cognitive impairment to dementia
Authors: Kim Yeo Jin , Han Kyung-Do , Baek Min Seok , Cho Hanna , Lee Eun Joo , Lyoo Chul Hyoung 
Published: September 2020

Abstract
Background: Physical activity has been suggested to prevent the conversion of mild cognitive impairment (MCI) to dementia in patients. We investigated the association between the continuance and regularity of physical activity and the risk of developing dementia in patients with MCI.Methods: We analyzed 6-year followed up data for 247,149 individuals in the National Health Insurance Service (NHIS) cohort of Korea who were enrolled between January 1, 2009 and December 31, 2015. The patients were divided into four groups: those who did not engage in physical activity consistently (Never-PA group), those who initiated physical activity (Initiation-PA group), those who ceased physical activity (Withdrawal-PA group), and those who performed physical activity consistently (Maintenance-PA group). We also divided the patients into two groups: those who engaged in physical activity irregularly (Irregular-PA) and those who undertook physical activity regularly (Regular-PA).Results: When the risk for the Never-PA group was set as the benchmark (ref=1), the Maintenance-PA group had the lowest incidence of dementia of the Alzheimer type (DAT) compared to the other groups (HR= 0.82, 95% CI 0.79-0.86). The DAT risk of Initiation-PA group (HR = 0.89, 95% CI 0.85-0.93) was lower than the Never-PA group. In addition, compared to the Irregular-PA group, the Regular-PA group had a 15% reduced risk for developing DAT.Conclusions: Although no causal inference could be made, continued regular physical activity in patients with MCI is associated with a protective effect against developing DAT. Moreover, ceasing physical activity could halt this protective effect.
SisterC: A novel 3C-technique to detect chromatin interactions between and along sister chromatids
Authors: Oomen Marlies E. , Hedger Adam K. , Watts Jonathan K. , Dekker Job 
Published: September 2020

Abstract
Current chromosome conformation capture techniques are not able to distinguish sister chromatids. Here we describe the protocol of SisterC1: a novel Hi-C technique that leverages BrdU incorporation and UV/Hoechst-induced single strand breaks to identify interactions along and between sister chromatids. By synchronizing cells, BrdU is incorporated only on the newly replicated strand, which distinguishes the two sister chromatids2,3. This is followed by Hi-C4 of cells that can be arrested in different stages of the cell cycle, e.g. in mitosis. Before final amplification of the Hi-C library, strands containing BrdU are specifically depleted by UV/Hoechst treatment. SisterC libraries are then sequenced using 50bp paired end reads, followed by mapping using standard Hi-C processing tools. Interactions can then be assigned as inter- or intra-sister interactions based on read orientation.
KIAA0101 and UbcH10 interact to regulate non-small cell lung cancer cell proliferation by disrupting the function of the spindle assembly checkpoint
Authors: Lei Han , Wang Kun , Jiang Tongying , Lu Jingjing , Dong Xue , Wang Feilong , Li Qiang , Zhao Liming 
Published: September 2020

Abstract
Background: Chromosome mis-segregation caused by spindle assembly checkpoint (SAC) dysfunction during mitosis is an important pathogenic factor in cancer, and modulating SAC function has emerged as a potential novel therapy for non-small cell lung cancer (NSCLC). UbcH10 is considered to be associated with SAC function and the pathological types and clinical grades of NSCLC. KIAA0101, which contains a highly conserved proliferating cell nuclear antigen (PCNA)-binding motif that is involved in DNA repair in cancer cells, plays an important role in the regulation of SAC function in NSCLC cells, and bioinformatics predictions showed that this regulatory role is related to UbcH10. We hypothesized KIAA0101 and UbcH10 interact to mediate SAC dysfunction and neoplastic transformation during the development of USCLC. Methods: NSCLC cell lines were used to investigate the spatial-temporal correlation between UbcH10 and KIAA0101 expression and the downstream effects of modulating their expression were evaluated. Further immunoprecipitation assays were used to investigate the possible mechanism underlying the correlation between UbcH10 and KIAA0101. Eventually, the effect of modulating UbcH10 and KIAA010 on tumor growth and its possible mechanisms were explored through in vivo tumor-bearing models.Results: In this study, we demonstrated that both UbcH10 and KIAA0101 were upregulated in NSCLC tissues and cells and that their expression levels were correlated in a spatial and temporal manner. Importantly, UbcH10 and KIAA0101 coordinated to mediate the premature degradation of various SAC components to cause further SAC dysfunction and neoplastic proliferation. Moreover, tumor growth in vivo was significantly inhibited by silencing UbcH10 and KIAA0101 expression. Conclusions: KIAA0101 and UbcH10 interact to cause SAC dysfunction, chromosomal instability and malignant proliferation in NSCLC, suggesting that UbcH10 and KIAA0101 are potential therapeutic targets for the treatment of NSCLC by ameliorating SAC function.
Inducing multiple antibodies to treat squamous cell esophageal carcinoma
Authors: Hoshino Isamu , Nabeya Yoshihiro , Takiguchi Nobuhiro , Gunji Hisashi , Ishige Fumitaka , Iwatate Yosuke , Kuwajima Akiko , Shiratori Fumiaki , Okada Rei , Shimada Hideaki 
Published: September 2020

Abstract
Background: The positive response and the clinical usefulness of 14 serum antibodies in patients with esophageal squamous cell carcinoma (ESCC) were examined in this study. The Cancer Genome Atlas (TCGA) was used to investigate the frequency of gene expressions, mutations, and amplification of these 14 antigens and also the possible effects of antibody induction. Methods: Blood serum derived from 85 patients with ESCC was collected and analyzed for the 14 antibodies using ELISA. The prognosis between positive and negative antibodies were then compared. The antibody panel included galectin1, HCA25a, HCC-22-5, and HSP70. Results: Patient serum was positive for all antibodies, except VEGF, with the positive rates ranging from 1.18% to 10.59%. Positive rates for galectin1, HCA25a, HCC-22-5, and HSP70 were >10%. TCGA data revealed that all antigen-related genes had little or no mutation or amplification, and hence an increase in gene expression affected antibody induction. The positive results from the panel accounted for the positive rate comparable to the combination of CEA and SCC. No significant association was observed between the presence of antibodies and disease prognosis. Conclusions: The detection rates of galectin1, HCA25a, HCC-22-5, and HSP70 were 10% higher in patients with ESCC. Gene overexpression may be involved in such antibody production. These four antibodies were applied as a panel in comparison with conventional tumor markers. Moreover, it was confirmed that the combination of this panel and the conventional tumor markers significantly improved the positive rate.
A one-year cohort study of complications, continuation, and failure rates of postpartum TCu380A in Tanzania
Authors: Rwegoshora France John , Muganyizi Projestine Selestine , Kimario Grasiana Festus , Paul Ponsian Patrick , Makins Anita 
Published: September 2020

Abstract
Background Less than 1% of married women in Tanzania use an Intrauterine Contraceptive Device (IUD) for contraception. An initiative by the International Federation of Gynecology and Obstetrics (FIGO) has been in progress since 2015 resulting in escalated method uptake in implementing hospitals. This study investigates failure rate, complications, and risk factors for one-year continuation of TCu380A IUD when used for immediate postpartum contraception under the initiative in Tanzania Methodology A prospective cohort study of women who had TCu380A insertion within 48 hours of delivery in 6 hospitals in Tanzania between 1st December 2017 and 18th April 2018 was conducted. Face to face post insertion interviews were made with 1114 clients before discharge and later through phone calls up to the beginning of 13th month postpartum. Postpartum Intrauterine Device (PPIUD) continuation status, complications, duration of time they stayed with the IUD and the currently used method if PPIUD was discontinued were enquired. The outcome variable was PPIUD continuation at one year of IUD insertion. Data were analyzed using Statistical Product and Service Solutions software (SPSS) for Windows version 20 (IBM SPSS Statistics, Chicago, IL, USA). Results In total 511(45.8%)clients had consented and availed to complete the one-year follow-up. Out of these, 440 still had IUD, giving a one-year continuation rate of 86.1%. Most (63%) IUD discontinuations occurred in the period between 7th week and 6 months of insertion. One-year method expulsion rate was 2.1%. There was one reported pregnancy that gives a method failure rate of about 2 per 1000. The independent risk factors in favor of method continuation at one year were absence of medical or social problem, being a youth (16-24 years), and delivery by Cesarean section. Conclusions The continuation rate when CuT380A is used for immediate postpartum contraception is high, with low complication and failure rates. Some medical and social factors are important for method continuation, hence the need to consider in training, counselling and advocacy.
Increased E2F2 predicts poor prognosis in patients with HCC based on TCGA data
Authors: Zeng Zhili , Cao Zebiao , Tang Ying 
Published: September 2020

Abstract
Background: The E2F family of transcription factor 2 (E2F2) plays an important role in the development and progression of various tumors, but its association with hepatocellular carcinoma (HCC) remains unknown. Our study aimed to investigate the role and clinical significance of E2F2 in HCC.Methods: HCC raw data were extracted from The Cancer Genome Atlas (TCGA). Wilcoxon signed-rank test, Kruskal-Wallis test and logistic regression were applied to analyze the relationship between the expression of E2F2 and clinicopathologic characteristics. Cox regression and Kaplan-Meier were employed to evaluate the correlation between clinicopathologic features and survival. The biological function of E2F2 was annotated by Gene Set Enrichment Analysis (GSEA).Results: The expression of E2F2 was increased in HCC samples. The expression of elevated E2F2 in HCC samples was prominently correlated with histologic grade (OR =2.62 for G3-4 vs. G1-2, p=1.80E-05), clinical stage (OR =1.74 for III-IV vs. I-II, p=0.03), T (OR =1.64 for T3-4 vs.T1-2, p=0.04), tumor status (OR =1.88 for with tumor vs. tumor free, p= 3.79E-03), plasma alpha fetoprotein (AFP) value (OR =3.18 for AFP≥400 vs AFP＜20, p= 2.16E-04; OR=2.50 for 20≤AFP＜400 vs AFP＜20, p=2.56E-03). Increased E2F2 had an unfavorable OS (p=7.468e−05), PFI (p=3.183e−05), DFI (p=0.001), DSS (p=4.172e−05). Elevated E2F2 was independently bound up with OS (p =0.004, hazard ratio [HR]= 2.4 (95% CI [1.3-4.2])), DFI (P =0.029, hazard ratio [HR] = 2.0 (95% CI [1.1-3.7])) and PFI (P =0.005, hazard ratio [HR] = 2.2 (95% CI [1.3-3.9])). GSEA disclosed that cell circle, RNA degradation, pyrimidine metabolism, base excision repair, aminoacyl tRNA biosynthesis, DNA replication, p53 signaling pathway, nucleotide excision repair, ubiquitin-mediated proteolysis, citrate cycle TCA cycle were notably enriched in E2F2 high expression phenotype.Conclusions: Elevated E2F2 can be a promising independent prognostic biomarker and therapeutic target for HCC. Additionally, cell cycle, pyrimidine metabolism, DNA replication, p53 signaling pathway, ubiquitin-mediated proteolysis, the citrate cycle TCA cycle may be the key pathway by which E2F2 participates in the initial and progression of HCC.
Data Processing Scheme Based on Blockchain
Authors: Fu Jinhua , Xu Mixue , Huang Yongzhong , Si Xueming , Yuan Chao 
Published: September 2020

Abstract
In the white paper written on Bitcoin, a chain of blocks was proposed by Satoshi Nakamoto. Since then, blockchain has been rapidly developed. Blockchain is not only limited to the field of cryptocurrency but also has been extensively applied to the Internet of Things (IoT), supply chain finance, electronic evidence storage, data sharing, and e-government fields. Both the public chain and the alliance chain have been extensively developed. In the data processing field, blockchain has a particularly good application potential. The Square Kilometre Array (SKA) is a proposal consisting of a joint venture of more than ten countries, resulting in the world’s largest synthetic aperture radio telescope. In the SKA, the processing scale of the data is large, and it consists of several data processing nodes. The data will be processed in the cloud computing mode. Taking the SKA under consideration, this report proposes a data processing scheme based on blockchain for the anti-counterfeiting, anti-tampering and traceability of data. Furthermore, the authenticity and integrity of the data are assured. The primary aspects include data distribution, data operation and data sharing, which correspond to the data reception, data algorithm processing and result sharing of data operation in the SKA. With this process, the integrity, reliability and authenticity of the data are guaranteed. Additionally, smart contracts, homomorphic hashing, secure containers, aggregate signatures and one-way encrypted channels are implemented to ensure the intelligence, security and high performance of the process.
Adaptation and preliminary psychometric properties of three self-stigma outcome measures for people living with dementia
Authors: MSc Jemini Bhatt BSc , Stoner Charlotte R , Scior Katrina , Charlesworth Georgina 
Published: September 2020

Abstract
Background: A diagnosis of dementia presents individuals with both social and psychological challenges but research on self-stigma in dementia has been largely confined to qualitative approaches due to a lack of robust outcome measures that assess change. The Stigma Impact Scale (SIS) is the most commonly used measure of self-stigma in dementia but its suitability as a tool to assess change in a diverse UK population is unclear. Thus, the aim of this study was to identify, adapt and evaluate the acceptability and preliminary psychometric properties of self-stigma measures for people with dementia for use as measures of change. Method: A 4-step sequential design of identifying, selecting, adapting and testing psychometric measures as follows: 1) identification of stigma outcome measures through reviewing anti-stigma intervention literature, 2) selection of candidate measures through quality assessment (Terwee criteria) and expert consultation, 3) adaptation for UK dementia population (Stewart and colleagues Modification Framework) 4) testing of adapted measures in people living with dementia (N=40) to establish acceptability and preliminary reproducibility (test retest), criterion (concurrent with SIS) and construct (negative convergence with Rosenberg self-esteem scale) validity. Results: Seven measures were identified from the review, but most were poor quality (Terwee range: 0-4). Three measures were selected for modification: Stigma Stress Scale; Secrecy subscale of the Stigma Coping Orientation Scale; Disclosure Related Distress Scale. Internal consistency and test-retest reliability were acceptable (.866≤α≤ .938; ICC .721-.774), except for the Stigma Stress Scale (α= .643) for which the component subscales (perceived harm, ability to cope) had stronger psychometric properties. Concurrent validity with the SIS was not established (r<.7) although there were significant correlations between total SIS and perceived harm (r=.587) and between internalized shame and secrecy (r=.488). Relationships with self-esteem were in the hypothesized direction for all scales and subscales indicating convergent validity.Conclusion: Stigma scales from mental health are not readily adapted for use with people with dementia. However there is preliminary evidence for the acceptability, reliability and validity of measures of perceived harm, secrecy and stigma impact. Further conceptual and psychometric development is required.
CXCL1 contributes to IL-6 expression in osteoarthritis and rheumatoid arthritis synovial fibroblasts by CXCR2, c-Raf, MAPK and AP-1 pathway
Authors: Hou Sheng-Mou , Chen PoChun , Lin Chieh-Mo , Fang Mei-Ling , Chi Miao-Ching , Liu Ju-Fang 
Published: September 2020

Abstract
Background: Osteoarthritis (OA) and rheumatoid arthritis (RA) are common joint disorders that are considered to be different diseases due to their unique molecular mechanisms and pathogenesis. Chemokines and their corresponding receptors have been well-characterized in RA progression, but less so in OA pathogenesis.Methods: The human primary synovial fibroblasts (SFs) were obtained from human OA and RA tissue samples. The Western blot and qPCR were performed to analyze expression levels of CXCL1, as well as CXCL-promoted IL-6 expression in both OASFs and RASFs. The signal cascades that mediate the CXCL1-promoted IL-6 expression were identified by using chemical inhibitors, siRNAs and shRNAs.Results: Here, we found that both diseases feature elevated levels of CXCL1 and interleukin (IL)-6, an important proinflammatory cytokine that participates in OA and RA pathogenesis. In OASFs and RASFs, CXCL1 promoted IL-6 expression in a dose- and time-dependent manner. In OASFs and RASFs overexpressing CXCL1 or transduced with shRNA plasmid, IL-6 expression was markedly upregulated. CXCR2, c-Raf and MAPKs was found to regulate CXCL1-induced IL-6 expression in OASFs and RASFs. Finally, CXCL1 triggered the transcriptional activities of c-Jun (which regulates the expression of proinflammatory proteins) in OASFs and RASFs.Conclusions: Our present work suggests that the CXCL1/CXCR2 axis helps to orchestrate inflammatory responses in OA and RA SFs.