bluuebunny/crossref_metadata_2025_split huggingface dataset:
Illuminating the dark side of the human transcriptome with long read transcript sequencing
Authors: Kuo Richard , Cheng Yuanyuan , Zhang Runxuan , Brown John W.S. , Smith Jacqueline , Archibald Alan L. , Burt Dave W. 
Published: April 2020

Abstract
Background The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide stronger evidence for genes that were previously either undetectable or impossible to differentiate from sequencing noise such as rare transcripts, mono-exonic, and non-coding genes.Results We analyzed Sequel II Iso-Seq sequencing data of the Universal Human Reference RNA (UHRR) using the Transcriptome Annotation by Modular Algorithms (TAMA) software. We found that the convention of using mapping identity to measure error correction performance does not reflect actual gain in accuracy of predicted transcript models. In addition, inter-read error correction leads to the thousands of erroneous gene models. Using genome assembly based error correction and gene feature evidence, we identified thousands of potentially functional novel genes.Conclusions The standard of using inter-read error correction for long read RNA sequencing data could be responsible for genome annotations with thousands of biologically inaccurate gene models. More than half of all real genes in the human genome may still be missing in current public annotations. We require better methods for differentiating sequencing noise from real genes in long read RNA sequencing data.
Sperm miRNAs— potential mediators of bull age and early embryo development
Authors: Wu Chongyang , Blondin Patrick , Vigneault Christian , Labrecqu Rémi , Sirard Marc-André 
Published: April 2020

Abstract
Background
Sperm miRNAs were reported to regulate spermatogenesis and early embryonic development in some mammals including bovine. The dairy cattle breeding industry now tends to collect semen from younger bulls under high selection pressure at a time when semen quality may be suboptimal compared to adult bulls. Whether the patterns of spermatic miRNAs are affected by paternal age and/or impact early embryogenesis is not clear. Hence, we generated small non-coding RNA libraries of sperm collected from same bulls at 10, 12, and 16 months of age, using 16 months as control for differential expression and functional analysis.
Results
We firstly excluded all miRNAs present in measurable quantity in oocytes according to the literature. Of the remaining miRNAs, ten sperm-borne miRNAs were significantly differentially expressed in younger bulls (four in the 10 vs 16 months contrast and six in the 12 vs 16 months contrast). Targets of miRNAs were identified and compared to the transcriptomic database of two-cell embryos, to genes related to two-cell competence, and to the transcriptomic database of blastocysts. Ingenuity pathway analysis of the targets of these miRNAs suggested potential influence on the developmental competence of two-cell embryos and on metabolism and protein synthesis in blastocysts.
Conclusions
The results showed that miRNA patterns in sperm are affected by the age of the bull and may mediate the effects of paternal age on early embryonic development.
Prognostic value of serum amyloid A in patients with COVID-19
Authors: Cheng Li 
Published: April 2020

Abstract
Objective: To investigate the prognostic value of serum amyloid A (SAA) in the patients with Corona Virus Disease 2019(COVID-19). Methods The medical data of 89 COVID-19 patients admitted to Renmin Hospital of Wuhan University from January 3, 2020 to February 26, 2020 were collected. 89 cases were divided into survival group (53 cases) and non-survival group (36 cases) according to the results of 28-day follow-up. The SAA levels of all patients were recorded and compared on 1day after admission (before treatment) and 3day, 5day, 7day after treatment. The ROC curve was drawn to analyze the prognosis of patients with COVID-19 by SAA. Results: The difference of comparison of SAA between survival group and non-survival group before treatment was not statistically significant, Z1 = -1.426, P = 0.154. The Z1 values ​​of the two groups of patients at 3d, 5d, 7d after treatment were -5.569, -6.967, and -7.542, respectively. The P values were all less than 0.001, and the difference was statistically significant. The ROC curve results showed that SAA has higher sensitivity to prognostic value for death, the AUC area of 3d, 5d, 7d, which were 80.6%, 97.2%, 86.1%, and 96.1%, respectively. Conclusion: SAA can be used as a death predictor of the prognosis in patients with COVID-19.
LTBP1 plays a potential bridge between depressive disorder and glioblastoma
Authors: Fu Xiaojun , Zhang Pei , Song Hongwang , Wu Chenxing , Li Shengzhen , Li Shouwei , Yan Changxiang 
Published: April 2020

Abstract
Background: Glioblastoma multiforme (GBM) is the most malignant tumor in human brain. Diagnosis and treatment of GBM may lead to psychological disorders such as depressive and anxiety disorders. No researches focusing on the correlation between depressive/anxiety disorder and the outcome of GBM. Thus, the aim of this study was to investigate the possibility of depressive/anxiety disorder on the outcome of GBM patients, as well as the overlapped mechanism bridge which could link depressive/anxiety disorders and GBM.Methods: Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder (GAD-7) were used to investigate the psychological condition of GBM patients in our department. To further explore the potential mechanism, bioinformatic methods were used to screen out genes that could be indicators of outcome in GBM, followed by gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) analysis. Further, cellular experiments were conducted to evaluate the proliferation, migration capacity of primary GBM cells from the patients.Results: It was revealed that patients with higher PHQ-9 and GAD-7 scores had significantly worse prognosis than their lower-scored counterparts. Bioinformatic mining revealed that LTBP1 could be a potential genetic mechanism in both depressive/anxiety disorder and GBM. Primary GBM cells with different expression level of LTBP1 should significantly different proliferation and migration capacity. GO, KEGG analysis confirmed that extracellular matrix (ECM) was the most enriched function of LTBP1. PPI network showed the interaction of proteins altered by LTBP1. Hub genes COL1A2, COL5A1 and COL10A1, as well as mesenchymal marker CD44 and Vimentin were statistically higher expressed in LTBP1 high group; while proneural marker E-cadherin was significantly higher expressed in low LTBP1 group.Conclusion: There is closely correlation between depressive/anxiety disorders and GBM. LTBP1 could be a potential bridge linking the two diseases through the regulation of ECM.
Study on The Change Law of Wave Velocity and Porosity of Triaxial Loaded Coal
Authors: li donghui , liang yanxia , chen shiqiang , zhang kai 
Published: April 2020

Abstract
The mechanical properties of loaded coal time to time, so that the voice wave propagation in coal changes with it. In order to study the relationship between the wave velocity of coal and its mechanical properties.The ultrasonic testing system was used to calculate the wave velocity of loaded coal at different times through laboratory triaxial loading test.The relationship between the wave velocity of loaded coal-body and the confining pressure of different coaxial pressures was analyzed.The results show that the wave velocity is positively correlated with the axial pressure under the same confining pressure. By calculating the variation of wave velocity of different loaded coal bodies. it is concluded that the variation of wave velocity of coal bodies can reflect the mechanical state of coal bodies undergo the compaction stage, the elastic stage and the new stage of crevasse. At the same time, the change of wave velocity in coal is affected by the porosity of the pressure-bearing coal-boby. Porosity was calculated using stress-strain.It was found that porosity and axial pressure presented a good negative correlation under the same confining pressure, and the change in wave velocity is exactly right opposite to the porosity change trend diagram.It can be obtained that the larger the amplitude of wave velocity change is, the smaller the porosity change is, and the smaller the amplitude of wave velocity change is, the larger the porosity change of coal body is, which is consistent with the actual analysis. It verifies the different the pressure-bearing coal-boby change in wave velocity to the feasibility of analyzing the mechanical condition of the loaded coal body. making the analysis more persuasive. It provides basis for coal body bearing and safe mining.
Effectiveness of group counseling with Acceptance and Commitment Therapy (ACT) on sexual Satisfaction of HIV positive women and women with HIV positive husband
Authors: Bokaie mahshid , tahery naieralsadat , Dafeei mariam 
Published: April 2020

Abstract
Background and Aim : AIDS is a progressive, incurable and preventable viral disease that damages the immune system and causes opportunistic infections. The discovery of methods of transmission, prevention and treatment of the disease has prevented researchers from considering the psychological consequences of the disease. The discrimination, adherence to complex treatment regimens, fear of disclosing the disease to the sexual partner exacerbate patients' psychological dissatisfaction and changes their sexual behavior pattern. The present study attempts to investigate the extent of sexual satisfaction of HIV-positive women and their HIV-positive spouses using the Acceptance and Commitment Therapy (ACT). Methods : This double-blind study was performed in 2019 with the aim of investigating the effect of treatment of HIV-positive women and their HIV-positive spouses referred to Behavioral Disease Counseling Center in Yazd and Meybod. 32 eligible women were randomly divided into two groups of 16 and participated in 10 weekly 2-hour sessions. Larsson's demographic and sexual satisfaction questionnaire was used for data collection. Data analysis was done by descriptive statistics and parametric interventions in SPSS software version 16 and significance level 0.05. Findings: There was no significant difference between the two groups in terms of demographic variables. Mean scores of sexual satisfaction before (90.87±13.3) and after intervention (96.31±12.94) and before and one month after the intervention (97.81±12.52) were significantly different in the intervention group. Comparing the mean scores of sexual satisfaction immediately after the intervention and one month later in the intervention group was not significant (P = 0.24). Also, sexual satisfaction was significant between the two groups after the intervention and one month later. Conclusion : The results show that ACT are effective in women with HIV exposure to improve sexual satisfaction. According to the results, it is suggested that this approach be used in order to increase the mental flexibility of patients to accept the disease and the suffering resulting from it, and finally to improve marital relationships and increase sexual satisfaction. In addition, the continuation of sexual health counseling for women is recommended. Trial registration: IRCT20181213041956N1, registered November 2018.
Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes.
Authors: Kenney Toby , Gao Junqiu , Gu Hong 
Published: April 2020

Abstract
Background: The vast majority of Microbiome research so far has focused on the structure of the microbiome at a single time-point. There have been several studies that measure the microbiome from a particular environment over time. However, even in these studies, little has been done to study the temporal dynamics of the microbiome. In this paper, we begin to rectify this situation. We analyse a widely studied microbial data set that contains a time series of the microbiome from four body sites on two healthy individuals. We choose a data set based on healthy individuals because we are interested in the baseline temporal dynamics of the microbiome. Results: For this analysis, we focus on the temporal dynamics of individual genera, ignoring the interactions. We use simple stochastic differential equation models to assess the following three questions. (1) Does the microbiome exhibit temporal continuity? (2) Does the microbiome have a stable state? (3) To better understand the temporal dynamics, how frequently should data be sampled in future studies? We find that a simple Ornstein-Uhlenbeck model which incorporates both temporal continuity and reversion to a stable state fits the data for all genera better than a Brownian motion model that contains only temporal continuity. The Ornstein-Uhlenbeck model also fits the data better than modelling separate time points as independent. Under the Ornstein-Uhlenbeck model, we calculate the variance of the estimated mean reversion rate (the speed with which each genus returns to its stable state). Based on this calculation, we are able to determine the optimal sample schemes for studying temporal dynamics. Conclusions: There is evidence of temporal continuity for at least some genera; there is clear evidence of a stable state; and the optimal sampling frequency for studying temporal dynamics is in the range of one sample every 0.8–3.2 days.
Significance of accurate hilar and intrapulmonary lymph nodes examination in stage IA-IIA non-small cell lung cancer, a retrospective cohort study
Authors: Zhai Wenyu , Duan Fangfang , Zheng Yuzhen , Yan Qihang , Dai Shuqin , Chen Tao , Chen Jianlong , Wang Junye 
Published: April 2020

Abstract
Background The examination of lymph node plays an important part in the nodal staging of non-small cell lung cancer (NSCLC). Till present, on the role of hilar and intrapulmonary (N1) station lymph node (LN) examined is not fully appreciated. In this study, we aimed to confirm the significance of N1 lymph node examined in the long-term survival for stage IA-IIA NSCLC patients and find the minimum number of lymph nodes.Methods The data of patients who underwent radical lobectomy and confirmed as lymph node non-metastatsized from January 2008 to March 2018 were retrospectively screened. Pathology records were reviewed for the number of lymph nodes examined. Kaplan-Meier method and Cox regression model were used to identify survival and prognostic factors.Results The median number of resected N1 LNs was 8. The number of patients with 0-2 N1 LNs, 3-5 N1 LNs, 6-8 N1 LNs, 9-11 N1 LNs and more than 11 N1 LNs examined was 181, 425, 477, 414 and 531, respectively. Gender (P=0.004), age (P<0.001), tumor size (P=0.004), differentiation degree (P=0.001) and the number of N1 LNs examined (P=0.008) were the independent prognostic factors of overall survival. Gender (P=0.006), age (P=0.031), tumor size (P=0.001), differentiation degree (P=0.001), vascular invasion (P=0.034) and the number of N1 LNs examined (P=0.007) were the independent prognostic factors of disease-free survival. Conclusion Increasing the number of N1 LNs examination could improve the long-term survival of T1-2N0 NSCLC patients. At least six LNs should be examined in surgical and pathological management.
Characteristics of high carbon ash as a raw material for spontaneous combustion inhibitor and its field demonstration
Authors: Park Seok Un , Kim Jae Kwan , Shin Dong Ik 
Published: April 2020

Abstract
In this study, we examined the physical chemistry, fuel characteristics and combustion reactivity of high carbon ash as a raw material for spontaneous combustion inhibitor in order to solve the problem of spontaneous combustion which has been often occurring in coal yard of coal-fired power plants in Korea. The high carbon ash has higher activation energy and lower frequency factor than bituminous coal, so combustion began at a relatively higher temperature than bituminous coal. In case of fly ash, the heat transfer characteristics were better than those of bottom ash and pond ash, and in case of coarse particles of fly ash, they were found to be highly applicable as a raw material for spontaneous combustion inhibitor due to their relatively high unburned carbon content. As a result of manufacturing spontaneous combustion inhibitors along with asphalt and PFAD (palm fatty acid distillate), the contact angle to water was more than 90° regardless of the mixing ratio, showing hydrophobic surface characteristics, and it was found that the hardness and viscosity of spontaneous combustion inhibitors increased as the mixing ratio of high carbon ash increased. In addition, when spontaneous combustion inhibitors manufactured were applied to coal stockpiles in coal yard at coal-fired power plants, there was little change in the internal temperature of coal stockpiles and the highest value of instantaneous increasing rate per minute was found to be lowered from 1.60°C/min to 0.061°C/min, indicating that spontaneous combustion inhibitors using high carbon coal ash had a great effect of preventing spontaneous combustion.
Hyperphosphorylation Renders Tau Prone to Aggregate and to Cause Cell Death
Authors: Liu Mengyu , Sui Dexin , Dexheimer Thomas , Hovde Stacy , Deng Xiexiong , Wang Kuang-Wei , Lin Hsin Lian , Chien Hsiao-Tien , Kweon Hye Kyong , Kuo Nora Sheen , Ayoub Christopher A. , Jimenez-Harrison Daniela , Andrews Philip C. , Kwok Roland , Bochar Daniel A , Kuret Jeff , Fortin Jessica , Tsay Yeou-Guang , Kuo Min-Hao 
Published: April 2020

Abstract
BackgroundAlzheimer’s disease (AD) is an irreversible neurodegenerative disease without a cure or prevention to date. The defining features of AD include neurofibrillary tangles (NFTs) of hyperphosphorylated tau fibrils, and the senile plaques of β amyloid (Aβ) aggregates. In addition to AD, aggregation of hyperphosphorylated tau underlies approximately 20 neurodegenerative disorders collectively known as tauopathies, suggesting a pathogenic role of tau fibrils. The majority of AD disease-modifying drug trials targeted Aβ control, which have yet to produce satisfactory outcomes. The interest of developing anti-NFT drugs has been increasing. However, an effective method that produces hyperphosphorylated tau with disease relevant characters to support drug discovery is lacking.MethodsWe previously reported the PIMAX system for the production of recombinant proteins bearing a desired post-translational modification. Here we use PIMAX to express hyperphosphorylated tau (p-tau) in E. coli, and subjected this p-tau to mass spectrometry mapping of phosphorylation, to biochemical and biophysical assays of fibrillogenesis, and to cell culture treatment for the effects of hyperphosphorylation on tau molecular characters.ResultsMass spectrometry mapped p-tau phosphorylation to phosphoepitopes linked to AD pathological progression. In stark contrast to the unmodified tau that required an inducer for efficient aggregation, and which had only mild effects on cell functions, p-tau formed fibrils in an inducer-free and redox-independent manner. Immediately after the purification, a disease-specific conformation recognized by the MC-1 monoclonal antibody was readily detectable, which continued to increase during the fibrillization reaction. When applied to cultured cells, p-tau triggered a spike of mitochondrial superoxide, induced apoptosis, and caused cell death at sub-micromolar concentrations. In both aggregation and cytotoxicity assays, p-tau exhibited seeding activities that converted the unmodified tau into a cytotoxic species with increased propensity for fibrillization, consistent with the emerging view that hyperphosphorylated tau spreads in a prion-like fashion.ConclusionsHyperphosphorylation potentiates tau fibrillization and cytotoxicity. These characters are consistent with the model that abnormally phosphorylated tau plays a direct role in neurodegeneration in tauopathies. We suggest that p-tau produced by PIMAX affords a feasible tool for drug discovery and disease mechanistic studies for Alzheimer's disease and other tauopathies.
Estrogen inhibits the apoptosis of spiral ganglion cells in C57BL/6J mice with presbycusis by downregulating AQP4.
Authors: Chen Long , Yang Yu-qi , Li Xue-rui , Feng Zi-yi , Han Zi-wei , Ma Ke-tao , Li Li , Si Jun-qiang 
Published: April 2020

Abstract
BackgroundEstrogen has a protective effect on age-related hearing loss (ARHL), but the mechanism has not been elucidated. Cochlear spiral ganglion neurons (SGN) are an important link between the cochlear hair cells and the auditory center. This study used C57BL/6J mice as models of elderly individuals to observe the protective effect of estrogen against cochlear spiral ganglion cell apoptosis.MethodsFifty mice were divided into the following five groups (10 mice/group): the young group at 3 months of age (3 m), the elderly group at 12 months of age (12 m), the ovariectomized group at 12 months of age (12 m ovx), the ovariectomized group at 12 months of age + estrogen treatment for 1 month (E2 1 m), and the ovariectomized group at 12 months of age + estrogen treatment for 2 months (E2 2 m). The auditory brain stem response (ABR) was analyzed to detect changes in the hearing threshold, enzyme-linked immunosorbent assays (ELISAs) were used to determine the serum estrogen levels,Hematoxylin eosin (HE) staining and transmission electron microscopy (TEM) were used to observe the morphological changes in the cochlea spiral ganglion neurons (SGN), and TUNEL staining was used to observe the apoptosis of SGN. The expression of AQP4 was observed by immunofluorescence, and the mRNA expression levels of AQP4, Caspase-3, Bax and Bcl-2 in the cochlea spiral ganglion were determined by qRT-PCR. Cell experiments: Primary cultures of spiral ganglion cells were divided into a control group (SGC), DMSO group, D-gal group, D-gal + E2 group, D-gal + TGN020 group and D-gal + E2 + TGN020 group. Immunofluorescence was used to observe the AQP4 expression, qRT-PCR was used to observe the AQP4, Caspase-3, Bax and Bcl-2 mRNA expression levels, and flow cytometry was used to observe the apoptosis rate.ResultsAn increased hearing threshold was observed in the elderly mice (P < 0.001). After removal of the ovaries, the hearing threshold of the mice in the 12 m ovx group was higher than it was in the 12 m control group (P < 0.05), and this increased threshold was accompanied by an increased loss of spiral ganglion cells, increased apoptosis (P < 0.01), and increased AQP4 expression (P < 0.001). Treatment with exogenous estrogen reversed all these changes. Cell experiments: D-gal increased the apoptosis rate (P < 0.001) and AQP4 expression (P < 0.001). Estrogen and the AQP4 inhibitor TGN020 both reduced the apoptosis rate and AQP4 expression.Conclusion﻿Estrogen inhibited apoptosis of cochlear spiral ganglion cells in aged C57BL/6J mice by downregulating AQP4, thus achieving a protective effect on ARHL.