bluuebunny/crossref_metadata_2025 huggingface dataset:
The Landscape of Glycosyltransferase Gene Signature for Overall Survival Prediction in Hepatocellular Carcinoma
Authors: Cai Qiang , Yu Shizhe , Zhao Jian , Ma Duo , Jiang Long , Zhang Xinyi , Yu Zhiyong
Published: December 2020

Background: Hepatocellular carcinoma (HCC) is heterogeneous disease occurring in the background of chronic liver diseases. The role of glycosyltransferase (GT) genes have recently been the focus of research associating with the development of tumors. However, the prognostic value of GT genes in HCC remains not elucidated. This study aimed to demonstrate the GT genes related to the prognosis of HCC through bioinformatics analysis.Methods: The GT genes signatures were identified from the training set of The Cancer Genome Atlas (TCGA) dataset using univariate and the least absolute shrinkage and selection operator (LASSO) Cox regression analyses. Then, we analyzed the prognostic value of GT genes signatures related to the overall survival (OS) of HCC patients. A prognostic model was constructed, and the risk score of each patient was calculated as formula, which divided HCC patients into high- and low-risk groups. Kaplan-Meier (K-M) and Receiver operating characteristic (ROC) curves were used to assess the OS of HCC patients. The prognostic value of GT genes signatures was further investigated in the validation set of TCGA database. Univariate and multivariate Cox regression analyses were performed to demonstrate the independent factors on OS. Finally, we utilized the gene set enrichment analysis (GSEA) to annotate the function of these genes between the two risk categories. Results: In this study, we identified and validated 4 GT genes as the prognostic signatures. The K-M analysis showed that the survival rate of the high-risk patients was significantly lower than that of the low-risk patients. The risk score calculated with 4 gene signatures could predict OS for 3-, 5-, and 7-year in patients with HCC, revealing the prognostic ability of these gene signature. In addition, Multivariate Cox regression analyses indicated that the risk score was an independent prognostic factor for HCC. Functional analysis further revealed that immune-related pathways were enriched, and immune status in HCC were different between the two risk groups.Conclusion: In conclusion, a novel GT genes signature can be used for prognostic prediction in HCC. Thus, targeting GT genes may be a therapeutic alternative for HCC.
Prognostic Role of DFNA5 in Head and Neck Squamous Cell Carcinoma Revealed by Systematic Expression Analysis
Authors: Liu Zhiguo , Liu Hongyan , Dong Qian , Li Hongyu , Zhang Bin , Liu Yufeng , Tang Haikuo
Published: December 2020

The gasdermin E gene (GSDME, also known as DFNA5) is mutated in familial aging-related hearing loss. Recent studies have also revealed that the expression of DFNA5 is suppressed in many cancer types; however, little is known about the function of DFNA5 in head and neck squamous cell carcinoma (HNSCC). Accordingly, the aim of the present study was to evaluate the expression of DFNA5 and explore its prognostic value in HNSCC. We used a set of bioinformatics tools, including Oncomine, TIMER, TISIDB, cBioPortal, and GEPIA, to analyze the expression of DFNA5 in patients with HNSCC from public databases. Kaplan-Meier plotter was used to evaluate the potential prognostic significance of DFNA5. DFNA5 mRNA levels were significantly higher in HNSCC tissues than in normal tissues, and high DFNA5 expression was correlated with worse survival. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that DFNA5 expression has a strong positive correlation with cell adhesion and the integrin signaling pathway, whereas its expression was negatively correlated with the levels of infiltrating B cells (cor = –0.223, P = 8.57e-07) and CD8 T cells (cor = –0.223, P = 2.99e-07). Overall, this study demonstrates that DFNA5 expression has prognostic value for HNSCC patients. Moreover, these results suggest that regulation of lymphocyte infiltration is the mechanism underlying the function of DFNA5 in HNSCC.
Spatial Ecological and Health Risk Assessment of Heavy Metal Contamination in Surface Soils From Lagos Lagoon Wetlands, Nigeria
Authors: Adesuyi Adeola Alex , Njoku Kelechi L. , Akinola Modupe O. , Olayinka Dupe N. , Jimoh Olalekan A.
Published: December 2020

Wetlands quality and spatial distribution are being threatened by anthropogenic drivers in addition to the emerging threats of climate change. In this study, selected heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) in soils from Lagos lagoon wetlands were investigated to assess spatial distribution, ecological and health risks. The data obtained were subjected to statistical analysis using GraphPad 7.0 and SPSS 22.0. Spatial distribution mapping of heavy metals was performed using ArcGIS10.0 (ESRI, Redlands, CA, USA) with Kriging interpolation. Results showed that heavy metals in the soil varied significantly (p<0.05). The contamination factors (CF) were generally low with the values for Cr, Ni, Cu, and Zn very low (<1). The CF values for some of the sampling points showed that the soils are generally moderately contaminated by Pb, Cd and Cu. The modified degree of contamination of Pb (2.35) indicates a moderate degree of contamination while that of Cd (12.60) indicates a high degree of contamination of these wetland soils. The potential ecological risk index (RI) of Pb, Cd, Cr, Ni, Cu and Zn were 70.40, 2264.40, 0.68, 1.55, 13.65, and 2.29, respectively. The RI for Pb, Cr, Ni, Cu and Zn were less than 100, hence, low, while the RI value of Cd was a very high risk (RI ≥ 400). Soils from this wetland’s areas show serious significant potential ecological risk due to Cd. Additionally, children were more susceptible to the potential health risk irrespective of the carcinogenic or non – carcinogenic risk. There were no significant carcinogenic and non – carcinogenic risks for adults and children. This wetland assessment provided important information for policymaking to reduce the potential effects of soil contamination on humans and the eco-environment.
Universal Fragment of mtDNA for Cervidae and Other Ungulate Species Identification
Authors: Filip Ewa , Strzała Tomasz , Stępień Edyta , Pizoń Klaudia
Published: December 2020

ObjectiveThe abundance of literature and many studies aimed at the identification of free-living animal species has helped to identify specific nucleotide marker sequences. In many cases, the best marker to distinguish species is the mitochondrial genome (mtDNA) or one of its fragments. In molecular analyses of Cervidae, biological material such as blood or muscle is easily obtained, as nearly all of these species are gaming animals.ResultsIn our research, we present the case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The proposed methodology is helpful as a routine identification procedure for a variety of tissue sources, even in cases where the samples are degraded. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base.
Deviations in the Gut Microbiota of Neonates Affected by Maternal Group B Streptococcus Infection
Authors: Li Yue-feng , Gong Xue-lei , Chen Su-xiang , Wang Ke-jian , Jiang Yan-hua
Published: December 2020

Background: Group B Streptococcus (GBS) infection is the leading cause of septicemia, meningitis, and pneumonia in neonates. Aberrant gut colonization in early life may predispose children to various diseases in adulthood. However, the associations between gut microbial changes and GBS infection is still unclear.Methods: We adopted a new microarray-based technique on neonatal meconium samples collected from 13 participants with mother’s GBS infection/colonization in vaginas and 73 uninfected controls.Results: The composition and diversity of meconium microbiota in GBS group were similar to that of healthy controls. However, we identified several specific taxa that were differentially abundant between the two groups (linear discriminant analysis (LDA) effect size (LEfSe): p<0.05, LDA>2.0). Particularly, the relative abundance of Lactobacillus paracasei was significantly reduced, indicating a role in GBS infection.Conclusions: Our study presented a series of bacterial species affected by GBS, thus providing novel evidence in support of initial intestinal microbiota dysbiosis in the neonates with mother’s GBS infection/colonization.
The Effect of Furanone on Enterotoxigenic Escherichia Coli (ETEC) O139 Transcriptome Was Analyzed Using RNA-seq
Authors: Li Jing-He , Yu Jia-Lin , An Qiang , Zhang Chun-Lei , Yi Peng-Fei
Published: December 2020

Background: In recent years, the effective ingredients of some medicine play an anti-infection role in inhibiting the formation of bacterial virulence factors and biofilm without affecting the growth of bacteria, which can reduce the survival pressure of bacteria and is not easy to develop drug resistance. It is considered to be a better way to control the infection of pathogenic microorganisms. Bacteria can produce signal molecules called auto-inducers (AIs) which can sense the bacteria density change. When auto-inducers accumulate to the threshold, they will regulate the bacteria biological behavior to adapt the changes of environment, including the formation of biofilm, virulence factors and bioluminescence. This is quorum sensing (QS).4-Hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) is a non-halogenated furanone found in strawberries, pineapples and other fruits and widely used as a safe food additive in beverages, ice cream and cigarettes. At present, there are lots of studies about furanone. Previous studies have shown that this kind of compound can compete with Acyl-homoserine lactone (AHL) in binding with its receptors, which inhibits the initiation of quorum sensing system. Results: In recent years, few studies about the transcriptome analysis of the furanone interacting with Enterotoxigenic Escherichia coli (ETEC) were reported. Therefore, we analyzed the effect of furanone on ETEC O139 transcriptome by RNA-seq. The result show that genes related to QS did not change after the interaction of 10μg/ml furanone and ETEC O139, while the expression of some genes related to the pathogenicity of ETEC O139 increased, such as flagellum assembly, biofilm formation and adhesion and so on.Conclusions: 10μg/ml furanone have no influence on QS system, but could contribute to adhesion, invasion, flagellum assembly and biofilm formation of ETEC O139.
Coalescence of Molecular Filaments
Authors: Kumar Nanda , Arzoumanian Doris , Men'shchikov Alexander , Palmeirim Pedro , Inutsuka Shu-Ichiro
Published: December 2020

Star-forming molecular filaments are found to display a spectrum of line-masses (mass per unit length)1. This spectrum is thought to influence key observational parameters of star formation2 including the core and stellar initial mass function1. The exact mechanism producing the wide-range of line-masses is unknown, even though, higher surface densities are often observed at the intersection of filaments in hub-filament systems3. Here we show that cascades of lower density filaments coalescing to form higher density filaments and eventually hubs. By performing a multi-scale decomposition of surface density maps of the MonR2 star-forming region, which displays a spiral-shaped hub-filament system4, the coalescence effect is detected in two consecutive cascading steps (the surface density jumps by an order of magnitude at each step) before merging at the central hub which is found to be a dense network of short high-density filaments (as opposed to its view as a massive clump). The radial density structure of the dense-gas component of the hub-filament system shows a power-law dependence of NH2 ∝ r−2 over the scale of ∼5 pc, a feature previously found only at scales of 0.1 pc in star-forming cores5. It appears that the hub-filament system is mimicking the radial profile of an isothermal sphere, at parsec scales, a feature not known until now. This behavior is not seen for the diffuse cloud (NH2 ∝ r−0.5) which holds nearly equal mass. The filamentary nature of the hub implies that only some (embedded in the filaments), and not all, stellar seeds within the hub can become massive stars.
Molecular Epidemiology of Cryptosporidium spp. in an Agricultural Area of Northern Vietnam: A Community Survey
Authors: Iwashita Hanako , Takemura Taichiro , Tokizawa Asako , Sugamoto Tetsuhiro , VU DINH THIEM , Nguyen Hai Tuan , PHAM Duc_Tho , Quynh Anh Pham Hong , Thi Hang Doan , Tran Na Ly , Yamashiro Tetsu
Published: December 2020

BackgroundCryptosporidium spp. is a protozoan parasite with worldwide distribution that causes cryptosporidiosis in humans and other animals. In the countryside of northern Vietnam, where free-roaming livestock are widespread, cryptosporidiosis is an important zoonotic disease. However, there have been few studies of cryptosporidiosis in Southeast Asia from the perspective of zoonotic disease epidemiology. The purpose of this study was to investigate the occurrence of Cryptosporidium infection in both humans and animals and to gain an awareness of the potential threat posed by this zoonotic infection in northern Vietnam.Methods We conducted a community survey to collect information about cases of diarrhea in an agricultural area of northern Vietnam. For this study, a total of 2715 samples (2120 human diarrheal samples, 471 non-diarrheal human samples, and 124 animal stool samples) were collected. A direct immunofluorescence assay (DFA) was used to detect Cryptosporidium spp. oocysts in concentrated stool samples by observation under a fluorescent microscope. DNA extraction, PCR amplification of the three genes (COWP, SSU-rRNA, and GP60), and sequencing analysis were performed to identify Cryptosporidium spp.Results Of 2715 samples, 15 samples (10 diarrheal samples, 2 non-diarrheal samples, and 3 animal stool samples) tested positive by PCR for the COWP gene. Three species of Cryptosporidium spp. were detected; C. canis (from six human diarrheal samples, two human non-diarrheal samples, and one dog sample); C. hominis (from four human diarrheal samples); and C. suis (from two pig samples). In terms of C. hominis, the GP60 subtype IeA12G3T3 was detected in all four human diarrheal samples.Conclusions Although the number of positive samples was very small, our epidemiological data showed that the emerging pattern of each of the three species (C. canis, C. hominis, and C. suis) was different at this study site. For example, zoonotic transmission of C. canis, between dogs and humans was suspected. Further studies are needed to assess the risk of oocyst contamination in the wider environment, including water, in this study area.
Network of “drug-target-SARS-CoV-2 Related Genes” Through Integrated Analysis of Pharmacology and Geo Database
Authors: Hou Jin ping , Wang Yong heng , Chen Yu meng , Chen Yi hao , Zhu Xiao , Qin Rui si , Chen Tingting
Published: December 2020

BackgroundCoronavirus Disease 2019 (COVID-19) respiratory disease rapidly caused a global pandemic and social and economic disruption. The combination of Traditional Chinese medicine (TCM) and Conventional Western medicine (CWM) is more effective for COVID-19 treatment. Moreover, TCM and CWM are important data source for developing new drug targets and promote strategies treat SARS-CoV-2 infections. However, many studies have analyzed the therapeutic mechanism of CWM or TCM alone for COVID-19, it is still unclear the interaction mechanism between TCM and CWM on COVID-19.MethodsThis paper integrates network pharmacology and GEO database to mine and identify COVID-19 molecular therapeutic targets, providing potential targets and new ideas for COVID-19 gene therapy and new drug development. It includes: 1) using TCMSP, TTD, PubChem and CTD databases to analyze drug interactions and associated phenotypes for SARS-CoV-2, to correlate drug and disease interaction mechanisms to screen key drug targets; 2) using GEO database to correlate differential genes and drug targets to screen potential antiviral gene therapy targets, to construct regulatory network and key points of SARS-CoV-2 therapeutic drugs; 3) using computer simulation of molecular docking to screen virus-related proteins for new drugs. ResultsIntegrated analysis of network pharmacology discovered that baicalein, estrone and quercetin are the pivotal active ingredients in TCM and CWM. Combining drug target genes in pharmacology database and virus induced genes in GEO database, the result showed the core hub genes related to COVID-19: STAT1, IL1B, IL6, IL8, PTGS2 and NFKBIA, and these genes were significantly downregulated in A549 and NHBE cells by SARS-CoV-2 infection. Moreover, chemical interaction and molecular docking analysis of hub genes showed that folic acid might as be potential therapeutic drug for COVID-19 treatment, and SARS-CoV-2 nucleocapsid phosphoprotein was a potential drug target. The network of “drug-target-SARS-CoV-2 related genes” provide noval potential compounds and targets for further studies of SARS-CoV-2.ConclusionsIntegrated analysis of network pharmacology and big data mining provided noval potential compounds and targets for further studies of SARS-CoV-2. Our research implied folic acid and SARS-CoV-2 N as therapeutic target in TCM and CWM. Our research also suggests that targeting SARS-CoV-2 N protein is likely to be a common mechanism of TCM and CWM. On the one hand, the identification of pivotal genes provides a target for COVID-19 molecular therapy, on the other hand, it provides ideas for the analysis of interaction mechanism between virus and host.
Paternal Obesity and Epigenetic Inheritance of Breast Cancer: The Role of Systemic Effects and Transmission to the Second Generation
Authors: Fontelles Camile C. , Cruz Raquel Santana da , Gonsiewski Alexandra K. , Barin Ersilia , Tekmen Volkan , Jin Lu , Cruz M. Idalia , Loudig Olivier , Warri Anni , Assis Sonia de
Published: December 2020

Background: While genetics explains some familial breast cancer cases, we showed that environmentally-induced epigenetic inheritance of breast cancer can also occur in rodent models. We previously reported that paternal consumption of a high-fat diet and ensuing obesity increased breast cancer susceptibility in the offspring (F1). Nevertheless, it is still unclear whether paternal-induced programming of breast cancer in daughters is associated with systemic alterations or mammary epithelium-specific factors. It also remains to be determined whether the ancestrally programmed breast cancer predisposition in F1 progeny can be transmitted to subsequent generations. Methods: Male mice (F0) were fed either a control (CO) diet or an obesity-inducing diet (OID) for seven weeks and then mated with female mice (F0) reared on a CO diet. The resulting offspring (F1), also exclusively fed CO diet, were either used for mammary gland and tumor transplantation surgeries or to generate the F2 generation. To induce the mammary tumors, female mice were treated with 7,12 dimethylbenz[a]anthracene (DMBA). Total RNA extracted from F0 or F1 males sperm was used for small RNA-Seq analysis. Results: Mammary glands from F1 CO female offspring exhibited enhanced development when transplanted into OID females [OID(CO-MG)], as shown by higher mammary gland area, epithelial branching and elongation, compared to CO females that received a CO mammary gland [CO(CO-MG)]. Similarly, mammary tumors from F1 CO female offspring transplanted into OID females [OID(CO.T)] displayed improved growth with a higher proliferation/apoptosis rate. We also found that granddaughters (F2) from the OID grand-paternal germline showed accelerated tumor growth compared to COxCO granddaughters (F2). Transmission of breast cancer predisposition to the F2 generation through OID male germline was associated with alterations in specific sperm tRNA fragments (tRF) in both F0 and F1 males.Conclusions: Our findings indicate that systemic metabolic and mammary stromal alterations are the most significant contributors to paternal programming of mammary gland development and cancer predisposition in female offspring rather than mammary epithelium confined factors. Our data also show breast cancer predisposition in OID daughters can be transmitted to subsequent generations and could explain some familial cancers, if confirmed in humans.
Laughter as a Paradigm of Socio-emotional Signal Processing in Dementia
Authors: Sivasathiaseelan Harri , Marshall Charles R , Benhamou Elia , Leeuwen Janneke EP van , Bond Rebecca L , Russell Lucy L , Greaves Caroline , Moore Katrina M , Ha Chris JD , Frost Chris , Rohrer Jonathan D , Scott Sophie K , Warren Jason D
Published: December 2020

Background: Laughter is a fundamental communicative signal in our relations with other people and is used to convey a diverse repertoire of social and emotional information. It is therefore potentially a useful probe of impaired socio-emotional signal processing in neurodegenerative diseases. Here we investigated the cognitive and affective processing of laughter systematically in patients representing all major syndromes of frontotemporal dementia, a disease spectrum characterised by severe socio-emotional dysfunction, as well as typical amnestic Alzheimer’s disease in relation to healthy age-matched individuals. Methods: We assessed cognitive labelling and valence rating of samples of spontaneous (mirthful and hostile) and volitional (posed) laughter versus two auditory control conditions (a synthetic laughter-like stimulus and spoken numbers) in 47 patients with frontotemporal dementia (22 with behavioural variant frontotemporal dementia, 12 with semantic variant primary progressive aphasia and 13 with nonfluent-agrammatic primary progressive aphasia), 15 patients with typical amnestic Alzheimer’s disease and 20 healthy age-matched individuals. Neuroanatomical associations of laughter processing were assessed using voxel-based morphometry of patients’ brain MR images. Results: While all dementia syndromes were associated with impaired identification of laughter subtypes relative to healthy controls, this was significantly more severe overall in frontotemporal dementia than in Alzheimer’s disease and particularly in the behavioural and semantic variants, which also showed abnormal affective evaluation of laughter. Certain striking syndromic signatures emerged, including enhanced liking for hostile laughter in behavioural variant frontotemporal dementia, impaired processing of synthetic laughter in the nonfluent-agrammatic variant (consistent with a generic complex auditory perceptual deficit) and ‘numerophilia’ in the semantic variant. Across the patient cohort, overall laughter identification accuracy correlated with regional grey matter in a core network encompassing inferior frontal and cingulo-insular cortices; and more specific correlates of laughter identification accuracy were delineated in cortical regions mediating affective disambiguation (identification of hostile and posed laughter in orbitofrontal cortex) and authenticity (social intent) decoding (identification of mirthful and posed laughter in anteromedial prefrontal cortex).Conclusions: These findings reveal a rich diversity of cognitive and affective laughter phenotypes in canonical dementia syndromes and suggest that laughter is an informative probe of neural mechanisms underpinning socio-emotional dysfunction in neurodegenerative disease.
Effect of Visual Feedback on Behavioral Control and Functional Activity During Bilateral Hand Movement
Authors: Guo Jing , Li Long , Zheng Yang , Quratul Ain , Liu Tian , Wang Jue
Published: December 2020

Background: Previous researches state vision as vital source of information for movement control and more precisely for accurate hand movement. Further, fine bimanual motor activity may be associated to various oscillatory activities within distinct brain areas and inter-hemispheric interactions. However, neural coordination among the distinct brain areas responsible to enhance motor accuracy is still not adequate.Methods: In the current study we investigated task-dependent modulation by simultaneously measuring high time resolution electroencephalogram (EEG), electromyogram (EMG) and force along with bi-maual and uni-manual motor tasks. The errors were controlled using visual feedback. In order to complete the uni-manual tasks, subject was asked to grip the strain gauge using index finger and thumb of right hand thereby exerting force on connected visual feedback system. Whereas the bi-manual task involved finger abduction of left index finger in two contractions along with visual feedback system and at the same time the right hand gripped using definite force on two conditions that whether visual feedback existed or not for right hand.Results: Primarily, the existence of visual feedback for right hand significantly decreased brain network global and local efficiency in theta and alpha band when compared with the elimination of visual feedback.Conclusions: Brain network activity in theta and alpha band coordinate to facilitate fine hand movement. The findings may provide a new neurological insight on virtual reality auxiliary equipment and subjects with neurological disorders that cause movement errors requiring accuracy motor training.
A Fatal Case of MSTN Mutation Calf Pancreatitis
Authors: Yang MiaoMiao , Wei Zhuying , Zhou Xinyu , Bai Chunling , Zhang Ying , Li Guangpeng
Published: December 2020

Background:Myostatin (MSTN) is related to growth and development. MSTN gene-mutated animals are prone to dystocia and fetus enlargement, but there is no report of pancreatitis. Pancreatitis is a disease of the pancreas caused by the self-digesting effect of trypsin. In animals, pancreatitis often occurs in dogs or cats and manifests as edema, congestion, bleeding, or necrosis of the pancreas. Clinically, symptoms such as abdominal pain, bloating, nausea, vomiting, and fever appear. Elevated levels of amylase in blood and urine. Pancreatitis is very dangerous to the survival of animals. We must pay attention to it.Case presentation: This is a fatal case report of a myostatin (MSTN) gene-mutated calf diagnosed with pancreatitis. Analyses of the blood biochemistry, blood routine, postmortem anatomy and tissue section of the 2-month old calf showed that the pancreatitis indexes α-amylase and serum lipase were higher than those of normal MSTN gene-mutated and wild-type cattle. The pancreas was found to be swollen, dark red and bloody. The structure of the acinar cells of the pancreas was unidentifiable, and massive coagulation necrosis and lysis necrosis filled in the lobules of the pancreas. The interlobular spaces became enlarged, the vessels among the lobules were dilated and congested with obvious edema and blood stasis.Conclusions: Evidence from anatomy, histology, blood physiology, and biochemistry parameters indicate that the myostatin mutated calf died of pancreatitis. There are few reports on the pathology of gene-mutated animals. This is the first case of MSTN gene-mutated bovine pancreatitis.
Association between changes in salivary microbiota with glucose levels during pregnancy – findings from a pilot study
Authors: Zhang Xin , Wang Pei , Ma Liangkun , Guo Rongjun , Zhang Yongjing , Wang Peng , Liu Juntao , Zhao Jizhi
Published: December 2020

Background : Microbial shifts that correspond to host variations during pregnancy are vital in health maintenance. Significant changes have been reported in the oral microbiota of pregnant women when compared with nonpregnant women, but little is known about the dynamic shifts in oral microbiota during the pregnancy course. Methods : In this study, changes in salivary microbiota in 81 healthy pregnant women throughout the early stage (G1: 9-14 weeks), middle stage (G2: 21-28 weeks), and late stage (G3: 31-38 weeks) were investigated with 16S rRNA sequencing techniques. Correlations between salivary microbiota and maternal characteristics, including fasting blood glucose (FBG) levels, were evaluated. Results : Alpha diversity indexes were stable throughout pregnancy, but significant changes were found in beta diversity measured by weighted and unweighted UniFrac distances. Fourteen dominant trimester-specific taxa were identified using the LEfSe method, including Bacteroidetes in G1, Proteobacteria in G2 and Firmicutes in G3 at the phylum level. Tax4Fun prediction analysis revealed significant changes in Genetic Information Processing, Environmental Information Processing, Unclassified and Human Diseases in G2 and in Metabolism in G3 when compared to G1. Significant correlations were found between FBG levels and microbial composition, and these correlations were independent of gestational diabetes mellitus (GDM) status. Conclusion : Within the limitations of this study, the dynamic changes in salivary microbiota during pregnancy were characterized, and beyond pregnancy, FBG was also involved in shaping the salivary microbiota.
The Effect of Changes in Cerebral Oximeter Values During Cardiac Surgery on the Incidence of Postoperative Cognitive Dysfunction (POCD): a Retrospective Study Based on Propensity Score Matched Analysis
Authors: Ahn Jin hee , Lee Eun kyung , Kim Doyeon , Kang Sehee , Choi Won-Jun , Byun Jae-hun , Shim Jae-Geum , Lee Sung Hyun
Published: December 2020

Background The occurrence of postoperative cognitive dysfunction(POCD) after major cardiac surgery is associated with an increase in perioperative mortality and morbidity. The increased regional cerebral oxygen saturation(rSO2) value is likely related to increased POCD due to oxidative stress. The incidence of POCD in relation to an increase in rSO2 values is not clinically known yet.Methods Among 3482 patients underwent cardiac surgery, 976 patients were allocated for this retrospective study. Of these, 230 patients (32.5%) were observed to have postoperative neurologic symptoms. After propensity score 1:2 ratio matching, a total of 690 patients were included in the analysis. Recorded data on occurrence of POCD from the postoperative period to predischarge were collected from the electronic records. Results The mean baseline rSO2 value was higher in the POCD (–) group than in the POCD (+) group (61.9 ± 9.6 vs 55.3 ± 11.4; P < 0.001). The mean overall minimum rSO2 value was lower in the POCD (+) group (52.2 ± 8.3 vs 48.3 ±10.5, P < 0.001). As compared with baseline, the POCD (+) group had significantly higher values in the CPB preweaning and CPB post-weaning periods (P < 0.001, respectively). There was a greater decrease in the overall minimum rSO2 values compared with baseline in the POCD (–) group (P < 0.001). The maximum mean rSO2 changes compared with baseline were higher in the POCD (+) group (adjusted odds ratio, 1.08; 95% confidence interval [CI], 1.04–1.11; P < 0.001). The AUROC for delta values of minimal compared with baseline values was 0.62 and the AUROC for the delta values of maximal compared with baseline values was 0.72.Conclusions Increased cerebral oximeter levels relative to baseline values has an effect on the development of POCD. Intraoperative oxidative damage was associated with increased POCD, and increased cerebral oximeter levels during cardiac surgery can also be a risk factor for POCD.
p53+/-Rb1-ASCL1low Phenotype Predicts Better Prognosis After Surgical Resection in Large Cell Neuroendocrine Carcinoma: a Molecular Characteristic and Clinical-pathological Investigation of Lung Neuroendocrine Tumors
Authors: Dong Yuting , Zhang Qian , Wang Guoping , Duan Yaqi , Huo Zitian
Published: December 2020

Background: Based on morphology, necrosis degree, and proliferation status, lung neuroendocrine tumors (NETs) are commonly divided into four subtypes: typical carcinoid (TC), atypical carcinoid (AC), large cell neuroendocrine carcinoma (LCNEC), and small cell lung carcinoma (SCLC). However, cases difficult to classify still exist in diagnosis. Methods: We immunohistochemically investigated the molecular phenotypes in lung NETs and assessed their prognostic value. Results: After morphological re-analysis of 179 NETs, 19 cases were classified as undefined, which included 3 cases showing carcinoid morphology with high proliferation (Ki67>20% or mitotic count>10/2mm2), and 16 cases showing intermediate differentiated morphology with Ki67 among 20% to 60%. Furthermore, molecular phenotypes were determined by expression of p53, Rb1, ASCL1, STK11, and gene mutation status of KRAS. Interestingly, p53wtRb1+ distinguished an unique subcategory from undefined lung NET cases which differ from SCLC or LCNEC in prognosis, indicating WD-NET G3 existed in lung NETs. Additionally, in LCNEC, high ASCL1 expression was only relevant to lymph node metastasis rather than overall survival. However, in p53+/-Rb1- LCNEC phenotype, low ASCL1 predicted better outcomes, along with less risk of lymph node metastasis. Conclusion: This study provided evidence for existence of WD-NET G3 in NETs and revealed promising prognosis of p53+/-Rb1- ASCL1low subcategory in LCNEC, which could be beneficial to the evaluation of patient status in future clinic practice.
Invasive Pleomorphic Lobular Carcinoma of the Breast With Multiple Metastases: a Case Report
Authors: Chen Xiangrong , Lei Lei , Tian Chunxiang , Ning Ping
Published: December 2020

Background: Invasive pleomorphic lobular carcinoma (IPLC) accounts for less than 1% of breast cancer, and the proportion is lower when systemic metastasis occurred. This paper reports a case of IPLC with multiple metastases and gives review literature. Case presentation: A 42-year-old female with IPLC and multiple metastases. There was nodular enhancement lesion in the liver and liver function showed that transaminase was significantly increased, albumin was low, bilirubin was high, and coagulation function was significantly abnormal. Multiple abnormal signals of the vertebral body, appendages, and sternum of the whole spine; manifestations of compression fractures of C7, T1, and T9 vertebrae.Conclusions: To the best of our knowledge, this is one of the few reported cases in the IPLC with multiple metastases. For patients with IPLC, we should improve the whole body examination to prevent the omission of metastatic lesions.
Low Level of Macrophages M0 in Primary Tumors is a Favorable Factor for Metastasis in Renal Clear Cell Carcinoma
Authors: Wu Yaohai , Yang Tong , Zuo You , Fu Shuai , Zhao Zhongwei , Li Dawei , Xu Zhonghua , Yu Nengwang
Published: December 2020

Background: The relationship between tumor-infiltrating immune cells (TIICs) and different stages or subtypes, especially the M-stage in primary tumors, remains unknown in renal clear cell carcinoma (KIRC). Therefore, the purpose of this study was to determine the relationship between TIICs and distant metastasis and provide new ideas for immunotherapy in KIRC.Methods: Clinical outcomes and transcriptome data were obtained from The Cancer Genome Atlas (TCGA) kidney cohort to characterize the composition of 22 TIICs in KIRC. Propensity score matching (PSM) and CIBERSORT were used to proceed data.Results: A bar plot, heat map, violin plot, bubble plot, box plots, and survival curves were generated. Bar plot and violin plot showed that T cells CD8 (P = 0.032), macrophages M0 (P = 0.033), macrophages M1 (P = 0.035), and mast cells resting (P = 0.001) were correlated to the M-stage. Survival curves showed that only the macrophages M0 group had a P value <0.05 (0.015) that a higher amount of macrophages M0 was associated with a better survival rate, whereas the remaining P values, including those for T cells CD8 (0.915), macrophages M1 (0.88), and mast cells resting (0.347) were >0.05. Conclusions: we got the conclusion that a low level of macrophages M0 in primary tumors was identified as a favorable factor for metastasis in renal clear cell carcinoma, which could provide us new ideas for immunotherapy in KIRC. In order to decrease the distant metastasis, more attention and focus should be paid to increase the level of macrophages M0 in primary tumors.
Epigenetic Silencing of Tumor Suppressor IncRNA NKILA: Implication on NF-κB Signaling in Non-Hodgkin’s Lymphoma
Authors: Zhang Min Yue , Deng Ming Dan , Au-Yeung Rex K.H. , Wang Lu Qian , Chim Chor Sang
Published: December 2020

Background: NKILA, localized to 20q13.31, is a negative regulator of NF-κB signaling implicated in carcinogenesis. As a CpG island is embedded in the promoter region of NKILA, we hypothesized that NKILA is a tumor suppressor lncRNA reversibly silenced by promoter DNA methylation in non-Hodgkin’s lymphoma (NHL). Methods: Methylation-specific PCR (MSP) and quantitative bisulfite pyrosequencing were performed to detect the methylation of NKILA in normal peripheral blood buffy coats, normal tonsils tissue, NHL cell lines and NHL primary samples. SU-DHL-6 cells were treated with 5-Aza-2'-deoxycytidine for reversal of methylation-associated NKILA silencing. Tumor suppressor properties of NKILA were demonstrated by knockdown of NKILA in SU-DHL-1 cells.Results: By pyrosequencing-verified MSP, NKILA was unmethylated in normal healthy controls, including 10 peripheral blood buffy coats and 11 normal tonsils tissue, but completely methylated in one (10%) NHL cell line SU-DHL-6. Among the lymphoma cell lines, by semi-quantitative RT-PCR, methylation of NKILA was inversely correlated with its expression. In the completely methylated SU-DHL-6 cells, hypomethylation treatment with 5-Aza-2'-deoxycytidine resulted in promoter demethylation and re-expression of NKILA transcript. In NHL primary samples (n=102), NKILA methylation was observed none of mantle cell lymphoma (MCL) cases, but in 29 (51.79%) diffuse large-B cell lymphoma (DLBCL) and 4 (20%) peripheral T-cell lymphoma (PTCL) cases, hence preferentially methylated in DLBCL than MCL (P < 0.0001) and PTCL (P = 0.007). Mechanistically, knockdown of NKILA resulted in promoting IkBα phosphorylation, which was associated with nucleus translocation of total p65 and phosphorylated p65 in SU-DHL-1 cells, hence constitutive NF-κB activation. Functionally, knock-down of NKILA in SU-DHL-1 cells led to decreased cell death and increased cellular proliferation, indicating a tumor suppressor role of NKILA in NHL cells. Conclusions: NKILA was a tumour suppressor lncRNA frequently hypermethylated in DLBCL. Promoter DNA methylation-mediated NKILA silencing led to increase of cellular proliferation and decrease of cell death via repression of NF-κB signaling in NHL cells.
Analysis of the Differential Expression and Prognostic Relationship of DEGs in AML based on TCGA Database
Authors: Zhang Hang , Li Qian , Li Lan , Gao Yue , Rong Rong , Sun Kai , Yu Zhengmin , Ji Xinyu , Liu Xiaowen , Han Lei , Zhang Hengdong , Zhu Baoli , Yu Tingting , XU MING
Published: December 2020

Background: Acute myeloid leukemia (AML) is a common and lethal hematological malignant hyperplastic disease originating from hematopoietic stem cells. The purpose of this study is to obtain the key AML survival-related differentially expressed gene. Methods: RNA sequencing (RNA-Seq) data and clinical information of patients were downloaded from the TCGA-LAML database. We focused the intersectional genes of survival-related DEGs, cytogenetics risk related-DEGs, and the top 10 pathways of both up- and down-regulated of Normalization Enrichment Score (NES). Multivariate Cox regression analyses were performed to analyze the independent factors for AML. The Kaplan–Meier and Nomogram analyses were plotted to predict and compare survival of AML patients. The validation of DEGs were performed by a clinical follow-up investigation.Results: 151 RNA-Seq samples for 60,488 genes and 200 clinical samples were selected from the TCGA-database. After filtering with the conditions about survival-related DEGs, cytogenetics-risk associated, and predicted in top 10 pathways, IGHM was the only remaining gene. Cox analysis showed that IGHM expression and age displayed were intendent factors to the patients’ survival (P<0.05). Higher IGHM expression was identified in poor survival group (P<0.05), with 68%, 43%, and 30% in 1, 3, and 5-year survival investigation. GSEA analysis revealed that IGHM were mainly enriched in the immune response. In Chinese population, IGHM displayed its significance not in the childhood AML patients but in adult ones. Conclusion: High expression of IHGM gene is an independent risky factor for the survival of patients with AML, which can be an important molecular marker for AML prognosis.
A Four-Immune Gene Prognostic Risk Model for Colorectal Adenocarcinoma Based on the TCGA and ImmPort Data Sets
Authors: Xu Boyang , Peng Ziqi , An Yue , Yao Xue , Sun Mingjun
Published: December 2020

Background: As one of the hot spots in oncology field, immune research provides new ideas for the diagnosis and treatment of tumors. Different histological types of colorectal cancer are different. Adenocarcinoma, as the type with the highest proportion, has a high research value. This study aims to build an immune gene prognostic risk model for colorectal adenocarcinoma to improve the diagnosis and prognosis prediction of colorectal adenocarcinoma.Methods: The differentially expressed immune genes could be obtained from the gene expression data downloaded from The Cancer Genome Atlas (TCGA) and the immune gene data downloaded from the ImmPort Database. Univariate COX and multivariate COX analyses were used to construct the immune gene prognostic risk model of and the clinical application potential of this model. The correlation between the model and the immune cells infiltration and the influence of each immune cell on the survival were analyzed.Results: 5975 differentially expressed genes were obtained, and 497 differentially expressed immune genes were selected by combining the information of immune genes. Among them, 36 immune genes were associated with prognosis, and 4 immune genes (THRB, IL1RL2, LGR6, LTB4R2) were included in the prognostic risk model of immune genes. Patients with higher Risk Score had shorter survival. Compared with gender, age and pathological stage, the model has better prediction potential. In addition, the model was correlated with Macrophages M0, Macrophages M1, T cells follicular helper and NK cells activated. Among them, T cells follicular helper and Macrophages M0 were related to the survival of patients.Conclusion: We developed a prognostic risk model containing four immune genes, THRB, IL1RL2, LGR6 and LTB4R2, which accurately described the prognosis of the patient, and affected the survival of patients by influencing the infiltration of Macrophages M0 and T cells follicular helper.
Observation of the Long-Period Monotonic Seismic Waves of the November 11, 2018, Mayotte event by the Iranian Broadband Seismic Stations
Authors: Sadeghi Hossein , Suzuki Sadaomi
Published: December 2020

On November 11, 2018, an event generating long-lasting, monotonic long-period surface waves was observed by seismographs around the world. This event occurred at around 09:30 (UTC) east of the Mayotte Island, east Africa. This event is unusual due to the absence of body waves in the seismograms and people’s lack of sense. The purpose of this study is to investigate this unusual event using the waveforms recorded by the Iranian National Broadband Seismic Network. The network consisted of 26 stations in operation on November 11, 2018. The stations are located from 4542 km to 5772 km north-northeast of the event’s epicentre. The arrival of monochromatic long-period signals is visible around 10 UTC in the recordings of all the stations and lasts for more than 30 minutes. Frequency analysis of the seismograms shows a clear peak at 0.064 Hz (15.6 sec/cycle). The maximum amplitude of the transverse components is less than a half of the radial components. This is in agreement with the theoretical radiation pattern of Rayleigh and Love waves at a frequency of 0.06 Hz from a vertical Compensated Linear Vector Dipole (CLVD) source mechanism. The average apparent phase velocities are calculated as 3.31 km/s and 2.97 km/s, in the transverse and radial directions, corresponding respectively to the Love and Rayleigh waves in the range of 0.05 to 0.07 Hz. The surface wave magnitude of Ms 5.07 ± 0.22 was estimated. Just before the monochromatic signal, there is some dispersion in the surface waves. This observation may suggest a regular earthquake that triggered the strange Mayotte event.
The prevalence and distribution of human papillomavirus among 10,910 Chinese Han women
Authors: Guo Chunlei , Du Hui , Belinson Jerome L , Wang Chun , Huang Xia , Qu Xinfeng , Wu Ruifang
Published: December 2020

ObjectiveTo assess the prevalence and distribution of HPV genotypes among Chinese Han women, and to explore the risk of high-grade cervical lesions associated with individual hr-HPV genotypes.MethodsGenotyping and histopathology data from the Chinese Multi-Center Screening Trial (CHIMUST) and its pilot screening trial, from 6 regions across mainland China, were re-analyzed. The data from physician (direct) collected samples from 10910 Chinese Han women (ages 30-69) were used to determine the prevalence and distribution of hr-HPV and to explore the risk association between hr-HPV genotypes and precancerous lesions.Results9.1% of the study population tested hr-HPV positive. The prevalence varied regionally rom the lowest in Guangdong (6.3%) to the highest in Inner Mongolia (12.9%). The most prevalent genotypes found were HPV-52 (21.5%), HPV-16 (19.2%), HPV-58 (15.0%), HPV-39 (8.9%), and HPV-51 (8.2%). The overall odds ratios for CIN2+ and CIN3+ for the presence of HPV-16 was 59.7 (95% CI 39.9-89.3) and, 92.0 (95%CI 54.5- 155.3), respectively and remained the highest odds ratio for CIN3+ in all 6 regions.ConclusionGeographical variation exists in the prevalence and distribution of hr-HPV in mainland China. HPV-16/52/58 were the most prevalent genotypes, and HPV-16 had the highest risk for high-grade cervical lesions.
The DUBs Family in Populus: Identification, Characterization, Evolution and Expression Patterns
Authors: Zheng Wenqing , Du Liang
Published: December 2020

Background: The deubiquitinases (DUB) family are a class of enzymes that regulate the stability or reverse the ubiquitination modification of many proteins in the cell, participating in cell cycle regulation, cell division and differentiation, various physiological activities such as DNA damage repair, growth and development, and response to stress. However, little is known about these genes in the woody plants. Results: In the present study, 88 DUB genes were identified in woody model plant Populus trichocarpa, including 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM with similar domains. According to the phylogenetic analysis, the 44 PtrUBP genes were classified into 14 subfamily, three PtrUCHs were classified into two groups, 23 PtrOTUs had six groups, four PtrMJDs had two groups, and 14 PtrJAMMs had six groups. The structure and motif analysis indicated that the same subfamily had similar genome structure and motif distribution characteristics. Ks/Ka analysis showed that the segmental duplication events played a major role in the expansion of Populus DUB genes. Synteny analysis of Populus DUB genes and four other species provided deep perception into the evolutionary traits of DUB genes. Expression profiles derived from transcriptome data exhibited distinct expression patterns of DUB genes in various tissues. Based on the result of promoter cis-regulatory elements analysis, we selected 16 representative PtrUBP genes to test their response to different hormonal treatments. The results showed that most of PtrUBPs were upregulated in the ABA, SA, and MeJA treatments, implying that their potential roles in abiotic stress response in Populus. Conclusion: The results in this study broaden our understanding of the DUB gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the DUBs provide a solid foundation for exploring their specific functions in Populus as well as indicate potential role of PtrUBP gene in abiotic stress.