bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative physicochemical and evolutionary study of SARS-CoV-2 and SARS with special reference to salt bridge and their microenvironment: A plausible explanation for divergency, stability and severity of SARS-CoV-2
Authors: Mitra Debanjan , Pal Aditya K. , Mohapatra Pradeep Kumar Das 
Published: September 2020

Abstract
The occurrence of concentrated pneumonia cases in Wuhan city, Hubei province of China was first reported on December 30, 2019. Currently, it is known as COVID 19 and now it is a nightmare for the whole world. SARS CoV first reported in 2002, but not spread worldwide. After 18 years, in 2020 it reappears and spread worldwide as SARS-CoV-2 (COVID 19), the most dangerous virus creating disease in the world. Is it possible to create a favorable evolution within this short time? If possible, then what are those properties that are changed in SARS-CoV-2 to make it undefeated? What are the basic differences between SARS-CoV-2 and SARS? This study will find all those queries. Here, all protein sequences of SARS-CoV-2 and SARS are retrieved from the database to check their physicochemical, evolutionary and structural properties. Results showed that, charged residues are playing a key role in SARS-CoV-2 evolution. SARS-CoV-2 increases its polarity by the help of charged residues, not by the polar residues. Their divergence is also strictly restricted. Induction of salt bridges with their high energies makes it very stable in any extreme conditions. Microenvironment residues also play a very crucial role in its stability. Mostly residues are favorable and contribute high energies. These microenvironment residues help in protein engineering to reduce its stability and make them week. This comparative study will help to understand the evolution from SARS to SARS-CoV-2.
Hybrid Carcinoma of The Parotid Gland: A Report of Three Extremely Rare Cases with An Immunohistochemical Analysis and A Review of The Literature
Authors: Kusafuka Kimihide , Yamashita Masaru , Yamanaka Shoji , HIrata Kazuki , Kubota Aki , Murakami Akinori , Muramatsu Aya , Arai Kazumori , Suzuki Makoto 
Published: September 2020

Abstract
Background: Hybrid carcinoma (HC) of the salivary glands is defined as when two or more kinds of carcinoma exist at the same location in a single mass. Herein, we report 3 rare cases of salivary gland HC. Case Presentation: Case 1 involved an 86-year-old Japanese male. Case 2 involved a 70-year-old Japanese female. Case 3 involved a 66-year-old Japanese male. Histologically, case 1 involved a combination of salivary duct carcinoma (SDC) and squamous cell carcinoma (SqCC). Immunostaining indicated that the former was positive for gross cystic disease fluid protein (GCDFP)-15 and androgen receptor (AR), whereas the latter expressed cytokeratin (CK) 5/6 and p63. Case 2 involved a combination of SqCC and neuroendocrine carcinoma (NEC). Immunostaining indicated that the former was positive for CK5/6 and p40, whereas the latter was positive for synaptophysin and neural cell adhesion molecule. Case 3 involved a combination of SDC and epithelial-myoepithelial carcinoma (EMC). Immunostaining indicated that the former was positive for GCDFP-15 and AR, whereas the inner cells of the latter were positive for CK7, and the outer cells of the latter were positive for alpha-smooth muscle actin and p40. A transitional zone between the SDC and EMC existed in case 3. Conclusions: Therefore, we diagnosed them as parotid gland HC. This is the first report of a case of HC involving a combination of NEC and SqCC. In case 3, it was speculated that high-grade SDC arose from low-grade EMC. However, as HC is different from carcinoma with high-grade transformation, HC should be diagnosed carefully.
Identification and Validation of RNA&nbsp;Binding Protein-associated Prognostic Model for Neuroblastoma
Authors: YANG JUN , Zhou Jiaying , Li Cuili , Wang Shaohua 
Published: September 2020

Abstract
Background: The abnormal expression of RNA binding protein (RBP) may be related to the development and progress of cancer. However, little is known about the mechanism of RBP in neuroblastoma (NB). Methods: We downloaded the RNA expression data of NB and normal nervous tissues from the (TARGET) database and GTEx database, and determined the differential expression of RBP between normal and cancerous tissues. Then the function and prognostic value of these RBPs were systematically studied. Results: A total of 348 differentially expressed RBPs were identified, together with 166 up-regulated RBPs and 182 down-regulated RBPs. Two hub RBPs (CPEB3 and CTU1) were identified as prognostic-related genes and chose to build prognostic risk score models. Further analysis showed that based on this model, the overall survival rate of patients in the high-risk subgroup was lower (P=2.152e-04). The area under the curve(AUC) of the receiver-operator characteristic curve(ROC) of the prognostic model is 0.720 in the TARGET cohort. There is a significant difference in the survival rate of patients in the high and low risk subgroups in the validation data set GSE85047 (P = 0.1237e-08), the AUC is 0.730. Conclusions: RNA binding protein (CPEB3 and CTU1) can be used as molecular markers of NB.
USP39 Promotes Malignant Proliferation and Angiogenesis of Renal Cell Carcinoma by Inhibiting VEGF-A Alternative Splicing
Authors: Pan Xiu-wu , Xu Da , Chen Wenjin , Chen Jia-xin , Ye Jian-qing , Gan Si-shun , Zhou Wang , Xu Song , Shi Lei , Cui Xingang 
Published: September 2020

Abstract
Objective: To investigate the function and mechanism of USP39 in promoting malignant proliferation and angiogenesis of RCC.Methods: We applied ONCOMINE database to analyze the correlation between USP39 expression level and the clinical characteristics of RCC. The effect of USP39 on RCC was evaluated by MTT assay, cell cycle analysis, colony formation assay and tubule formation assay. The interaction between USP39 and VEGF-A alternative splicing was assessed by co-immunoprecipitation and Western blot assays. Results: The mRNA expression level of USP39 in RCC was significantly higher than that in normal renal tissue (P<0.001), and negatively correlated with the survival rate of RCC patients (P<0.01). Silencing of USP39 in 786-O and ACHN cells obviously inhibited cell proliferation and colony formation, and induced S phase arrest. USP39 overexpression significantly increased the number of tubules (P<0.05) and branches (P<0.01) formed by HUVEC cells, and USP39 knockdown produced an opposite effect (P<0.05). The USP39 (101-565) fragment directly mediated its binding to SRSF1 and SRPK1, and promoted the phosphorylation of SRSF1 to regulate VEGF-A alternative splicing. USP39 knockdown upregulated the expression of VEGF-A165b, and USP39 overexpression downregulated the expression of VEGF-A165b significantly (both P<0.05).Conclusion: USP39 acted as a pro-tumor factor by motivating the malignant biological processes of RCC, probably through promoting VEGF-A alternative splicing and regulating SRSF1 and SRPK1. USP39 may prove to be a potential therapeutic target for RCC.
Radiomics Model Based on Shear-Wave Elastography Can Predict the Axillary Lymph Node Status in Early-Stage Breast Cancer
Authors: Jiang Meng , Li Chang-Li , Chen Rui-Xue , Tang Shi-Chu , Luo Xiao-Mao , Chuan Zhi-Rui , Lv Wen-Zhi , Cui Xin-Wu , Dietrich Christoph F. 
Published: September 2020

Abstract
Background: Accurate prediction of axillary lymph node (ALN) involvement in early-stage breast cancer is important for determining appropriate axillary treatment and therefore avoiding unnecessary axillary surgery and complications. This study aimed to develop and validate an ultrasound radiomics nomogram for preoperative evaluation of the ALN burden. Methods: Data of 303 patients from Wuhan Tongji Hospital (training cohort) and 130 cases from Hunan Provincial Tumour Hospital (external validation cohort) between Jun 2016 and May 2019 were enrolled. Radiomic features were extracted from shear-wave elastography (SWE) and corresponding B-mode ultrasound (BMUS) images. Then, the minimum redundancy maximum relevance (MRMR) and least absolute shrinkage and selection operator (LASSO) algorithm were used to select ALN status-related features and construct the SWE and BMUS radiomic signatures. Proportional odds ordinal logistic regression was performed using the radiomic signature together with clinical data, and an ordinal nomogram was subsequently developed. We evaluated the performance of the nomogram using C-index, calibration, and compared it with clinical model.Results: Multivariate analysis indicated that SWE signature, US-reported LN status and molecular subtype were independent risk factors associated with ALN status. The radiomics nomogram based on these variables showed good calibration and discrimination in the training set (overall C-index: 0.842; 95%CI, 0.773–0.879) and the validation set (overall C-index: 0.822; 95%CI, 0.765–0.838). For discriminating between disease-free axilla (N0) and any axillary metastasis (N + (≥1)), it achieved C-index of 0.845 (95%CI, 0.777–0.914) for the training cohort and 0.817 (95%CI, 0.769–0.865) for the validation cohort. The tool could also discriminate between low (N + (1–2)) and heavy metastatic burden of ALN (N + (≥3)), with C-index of 0.827 (95%CI, 0.742–0.913) for the training cohort and 0.810 (95%CI, 0.755–0.864) for the validation cohort. Conclusions: The presented radiomics nomogram shows favourable predictive ability for ALN staging in patients with early-stage breast cancer, which could provide incremental information for preoperative decision-making.
MiR-24-3p Attenuates IL-1β-Induced Chondrocyte Injury Associated With Osteoarthritis by Targeting BCL2L12
Authors: Xu Jin , Qian Xiaozhong , Ding Ren 
Published: September 2020

Abstract
Background: Osteoarthritis (OA) is a chronic and degenerative joint disease prevalent in the elderly. MiR-24-3p has been reported to be involved in an OA-resembling environment. However, the functional role and underlying mechanism of miR-24-3p in chondrocyte injury associated with OA remains unknown. Methods: The expression of miR-24-3p was determined in OA cases and control patients, as well as IL-1β-stimulated chondrocyte cell line CHON-001 using reverse transcription quantitative PCR analysis. Cell viability was analyzed by CCK-8 assay. Apoptosis status was assessed by caspase-3 activity detection. The pro-inflammatory cytokines (TNF-α and IL-18) were determined using ELISA assay. The association between miR-24-3p and BCL2L12 was confirmed by luciferase reporter assay.Results: We first observed that miR-24-3p expression level was lower in the OA cases than in the control patients and IL-1β decreased the expression of miR-24-3p in the chondrocyte CHON-001. Functionally, overexpression of miR-24-3p significantly attenuated IL-1β-induced chondrocyte injury, as reflected by increased cell viability, decreased caspase-3 activity, pro-inflammatory cytokines (TNF-α and IL-18). Western blot analysis showed that overexpression of miR-24-3p weakened IL-1β-induced cartilage degradation, as reflected by reduction of MMP13 (Matrix Metalloproteinase-13) and ADAMTS5 (A Disintegrin And Metalloproteinase with Thrombospondin Motifs-5) protein expression, as well as markedly elevation of COL2A1 (collagen type II). Importantly, BCL2L12 was demonstrated to be a target of miR-24-3p. BCL2L12 knockdown imitated, while overexpression significantly abrogated the protective effects of miR-24-3p against IL-1β-induced chondrocyte injury.Conclusions: In conclusion, our work provides important insight into targeting miR-24-3p/BCL2L12 axis in OA therapy.
Effects of Neonicotinoid Seed Treatments on Phyllosphere and Soil Bacterial Communities Over Time
Authors: Parizadeh Mona , Mimee Benjamin , Kembel Steven W. 
Published: September 2020

Abstract
BackgroundThe phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices. Widespread pesticide application may have had non-target impacts on these beneficial microorganisms. Neonicotinoids are a family of systemic insecticides being vastly used to control soil and foliar pests in recent decades. A few studies have demonstrated the long-term and non-target effects of neonicotinoids on agroecosystem microbiota, but the generality of these findings remains unclear. In this study, we used 16S rRNA gene amplicon sequencing to characterize the effects of neonicotinoid seed treatment on soil and phyllosphere bacterial community diversity, composition and temporal dynamics in a three-year soybean/corn rotation in Quebec, Canada. Results We found that habitat, host species and time are stronger drivers of variation in bacterial composition than neonicotinoid application. They respectively explained 37.3%, 3.2% and 2.9% of the community variation. However, neonicotinoids did have an impact on bacterial community structure, especially on the taxonomic composition of soil communities (2.6%) and over time (2.4%). They also caused a decrease in soil alpha diversity in the middle of the growing season. While the neonicotinoid treatment favored some bacterial genera known as neonicotinoid biodegraders, there was a decline in the relative abundance of some potentially beneficial soil bacteria, such as the plant growth-promoting rhizobacteria and the bacteria involved in the nitrogen cycle, in response to the pesticide application.ConclusionsOur results indicate that neonicotinoids have non-target effects on phyllosphere and soil bacterial communities in a soybean-corn agroecosystem, especially potentially beneficial bacteria that are vital for plant growth and improve soil fertility. Exploring the interactions among bacteria and other organisms, as well as the bacterial functional responses to the pesticide treatment, may enhance our understanding of these non-target effects and help us adapt agricultural practices to control these impacts.
Inter-Rater Agreement and Test-Retest Reliability of the Performance and Fitness (PERF-FIT) Test Battery for Children: A Test for Motor Skill Related Fitness.
Authors: Smits-Engelsman Bouwien , Smit Eline , Doe-Asinyo Rosemary Xorlanyo , Lawerteh Stella Elikplim , Aertssen Wendy , Ferguson Gillian , Jelsma Dorothee L 
Published: September 2020

Abstract
Background: The Performance and Fitness (PERF-FIT) test battery for children is a recently developed, valid assessment tool for measuring motor skill-related physical fitness in 5 to 12-year-old children living in low-income settings. The aim of this study was to determine: (1) inter-rater agreement and (2) test-retest reliability of the PERF-FIT in children from 3 different countries (Ghana, South Africa and the Netherlands). Method: For inter-rater reliability 29 children, (16 boys and 13 girls, 6-10 years) were scored by 2 raters simultaneously. For test–retest reliability 72 children, (33 boys and 39 girls, 5-12 years) performed the test twice, minimally one week and maximally two weeks apart. Relative and absolute reliability indices were calculated. ANOVA was used to examine differences between the three assessor teams in the three countries.Results: The PERF-FIT demonstrated excellent inter-rater reliability (ICC, 0.99) and good test-retest reliability (ICC, ≥ 0.80) for 11 of the 12 tasks. a poor ICC was found for the Jumping item only, due to low spread in values. Overall, measurement error, Limits of Agreement and Coefficient of Variation had acceptable levels to support clinical use. No systematic differences were found between first and second measurement between the three countries but for one item (Overhead throw). Conclusions: The PERF-FIT can reliably measure motor skill related fitness in 5 to 12-year-old children in different settings and help clinicians monitor levels of power and agility, and fundamental motor skills (throwing, bouncing, catching, jumping, hopping and balance).
Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken
Authors: Cazals Anaïs , ESTELLÉ Jordi , BRUNEAU Nicolas , COVILLE Jean-Luc , MENANTEAU Pierrette , ROSSIGNOL Marie-Noëlle , JARDET Deborah , BEVILACQUA Claudia , RAU Andrea , BED’HOM Bertrand , VELGE Philippe , CALENGE Fanny 
Published: September 2020

Abstract
Background Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication through the consumption of contaminated poultry products. Genetic selection of animals more resistant to Salmonella carriage and the modulation of gut microbiota are two promising ways of decreasing individual Salmonella carriage. This study aims to identify the main genetic and microbial factors controlling the individual levels of Salmonella carriage in chickens (Gallus gallus) in controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines, N and 61, were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce the recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition through a 16S rRNA gene high-throughput sequencing approach. Results Results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Out of 617 Operational Taxonomic Units (OTUs), over 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between high and low Salmonella carriers, with 39 differentially abundant OTUs. Finally, via metagenome functional prediction based on 16S data, we identified several metabolic pathways potentially associated to microbiota taxonomic differences (e.g. butyrate metabolism) between high and low carriers. Conclusions Overall, this study demonstrates that the caecal microbiota composition of the N and 61 lines is influenced by the host genetics, which could be one of the reasons why these lines differ for their Salmonella carriage in experimental infection conditions.
The Study of Diagnostic Value of Bipolarity Index for Bipolar Disorder in China: Meta-analysis of Sensitivity and Specificity
Authors: Sun Fengli , Jianfeng Zhu , Hejian Tao , Weidong Jin 
Published: September 2020

Abstract
BackgroundThe diagnosis of bipolar disorder is still one of the key problems in psychiatric clinic. Although DSM-5 has made some important changes, it has not completely changed the missed diagnosis and misdiagnosis of bipolar disorder.It was very important that diagnostic scale was used in clinic.But the study results of assist diagnostic scale for bipolar disorder should been concluded and analyzed.Bipolarity index was one of assist diagnostic scale,which should be analyzed comprehensively.MethodsWe searched CBM, CNKI , WANFANG and CSSCI in Chinese to find literature from Julyr 31 2004 to July 31 2020 related to Bipolarity Index in diagnosis for bipolar disorder ,among which results such as comments, letters, reviews and case reports were excluded. The rate of sensitivity,specificity,accuracy,positive predictive value and negative predictive value in diagnosis was synthesized and discussed.ResultsA total of 1237 subjects were included in 5 studies. Random effect model is used to account for the data by Revman 5.2. The results showed that the sensitivity of BI in diagnostic was 0.93 (95% CI: 0.93–1.00), the specificity was 85% (95% CI: 0.69–0.96). the positive predict value was 74% (95% CI: 0.53–0.91).the negative predict value was 95% (95% CI: 0.81–1.00).and accuracy was 86% (95% CI: 0.77–0.93). Significant heterogeneity was detected across studies regarding these incidence estimates. ConclusionThe idea diagnostic value of BI was found. although the significant heterogeneity detected in studies.We must interpret the results with caution and also put attention to this result,which include comparison to other diagnostic scale,perfecting sue of BI in clinical psychiatry.
WITHDRAWN: Angelica Sinensis Extract Protects Against Memory Deficits by Promoting P38 MAPK–mediated Hippocampal Neurogenesis and Neuronal Survival in the Chronic Phase of Transient Global Cerebral Ischemia in Rats
Authors: Lee Yu-Chen , Huang Hui-Chi , Kao Shung-Te , Cheng Chin-Yi 
Published: September 2020

Abstract
Background: Reversible cardiac arrest and diseases related to reduced blood flow to the brain cause transient global cerebral ischemia (GCI), which may induce long-term cognitive deficits. In addition, hippocampal cornu ammonis 1 (CA1) pyramidal neurons are selectively vulnerable to ischemic insults and play an important role in memory. This study aimed to determine the effects of the Angelica sinensis (Oliv.) Diels (ASD) extract on ischemia-induced memory deficits at 28 d after transient global cerebral ischemia (GCI) and to investigate the precise mechanisms underlying the p38 mitogen-activated protein kinase (MAPK)-related signaling pathway’s involvement in hippocampal neurogenesis. Rats underwent 25 min of four-vessel occlusion. The ASD extract was intragastrically administered at doses of 0.25 g/kg (ASD-0.25 g), 0.5 g/kg (ASD-0.5 g), 1 g/kg (ASD-1 g), 1 g/kg after dimethyl sulfoxide administration (D+ASD-1 g), or 1 g/kg after SB203580 (a p38 MAPK inhibitor) administration (SB+ASD-1 g) at 1, 3, 7, 10, 14, 17, 21, and 24 d after transient GCI. Results: ASD-0.5 g, ASD-1 g, and D+ASD-1 g treatments effectively attenuated memory deficits and had the following effects: upregulation of bromodeoxyuridine (BrdU) and Ki67 expression, and BrdU/neuronal nuclei (NeuN) co-expression in the hippocampal dentate gyrus (DG); upregulation of microtubule-associated protein 2 /NeuN co-expression in the hippocampal CA1 region; upregulation of phospho-p38 MAPK (p-p38 MAPK), phospho-cAMP response element-binding protein (p-CREB), brain-derived neurotrophic factor (BDNF), glial cell line-derived neurotrophic factor (GDNF), and vascular endothelial growth factor A (VEGF-A) expression in the hippocampus. Furthermore, most BrdU-positive cells colocalized with NeuN and Ki67 in the hippocampal DG. SB+ASD-1 g treatment abrogated the effects of ASD-1 g on the expression of these proteins and exacerbated memory deficits. Conclusion: ASD-0.5 g and ASD-1 g treatments provided neuroprotective effects against memory deficits by enhancing hippocampal neurogenesis and dendritic stability. The effects of the ASD extract on hippocampal neurogenesis and neuronal survival are caused by the activation of p38 MAPK–mediated CREB/BDNF, GDNF, and VEGF-A signaling pathways in the hippocampus at 28 d after transient GCI.