Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.Comment: 14 pages, 8 figures, 10 table

High expression of transcriptional coactivator p300 correlates with aggressive features and poor prognosis of hepatocellular carcinoma

<p>Abstract</p> <p>Background</p> <p>It has been suggested that p300 participates in the regulation of a wide range of cell biological processes and mutation of p300 has been identified in certain types of human cancers. However, the expression dynamics of p300 in hepatocellular carcinoma (HCC) and its clinical/prognostic significance are unclear.</p> <p>Methods</p> <p>In this study, the methods of reverse transcription-polymerase chain reaction (RT-PCR), Western blotting and immunohistochemistry (IHC) were utilized to investigate protein/mRNA expression of p300 in HCCs. Receiver operating characteristic (ROC) curve analysis, spearman's rank correlation, Kaplan-Meier plots and Cox proportional hazards regression model were used to analyze the data.</p> <p>Results</p> <p>Up-regulated expression of p300 mRNA and protein was observed in the majority of HCCs by RT-PCR and Western blotting, when compared with their adjacent non-malignant liver tissues. According to the ROC curves, the cutoff score for p300 high expression was defined when more than 60% of the tumor cells were positively stained. High expression of p300 was examined in 60/123 (48.8%) of HCCs and in 8/123 (6.5%) of adjacent non-malignant liver tissues. High expression of p300 was correlated with higher AFP level, larger tumor size, multiplicity, poorer differentiation and later stage (<it>P </it>< 0.05). In univariate survival analysis, a significant association between overexpression of p300 and shortened patients' survival was found (<it>P </it>= 0.001). In different subsets of HCC patients, p300 expression was also a prognostic indicator in patients with stage II (<it>P </it>= 0.007) and stage III (<it>P </it>= 0.011). Importantly, p300 expression was evaluated as an independent prognostic factor in multivariate analysis (<it>P </it>= 0.021). Consequently, a new clinicopathologic prognostic model with three poor prognostic factors (p300 expression, AFP level and vascular invasion) was constructed. The model could significantly stratify risk (low, intermediate and high) for overall survival (<it>P </it>< 0.0001).</p> <p>Conclusions</p> <p>Our findings provide a basis for the concept that high expression of p300 in HCC may be important in the acquisition of an aggressive phenotype, suggesting that p300 overexpression, as examined by IHC, is an independent biomarker for poor prognosis of patients with HCC. The combined clinicopathologic prognostic model may become a useful tool for identifying HCC patients with different clinical outcomes.</p

Hippocampal Synaptic and Neural Network Deficits in Young Mice Carrying the Human APOE4 Gene

Introduction: Apolipoprotein E4 (APOE4) is a major genetic risk factor for late-onset sporadic Alzheimer disease. Emerging evidence demonstrates a hippocampus-associated learning and memory deficit in aged APOE4 human carriers and also in aged mice carrying human APOE4 gene. This suggests that either exogenous APOE4 or endogenous APOE4 alters the cognitive profile and hippocampal structure and function. However, little is known regarding how Apoe4 modulates hippocampal dendritic morphology, synaptic function, and neural network activity in young mice. Aim: In this study, we compared hippocampal dendritic and spine morphology and synaptic function of young (4 months) mice with transgenic expression of the human APOE4 and APOE3 genes. Methods: Hippocampal dendritic and spine morphology and synaptic function were assessed by neuronal imaging and electrophysiological approaches. Results: Morphology results showed that shortened dendritic length and reduced spine density occurred at hippocampal CA1 neurons in Apoe4 mice compared to Apoe3 mice. Electrophysiological results demonstrated that in the hippocampal CA3-CA1 synapses of young Apoe4 mice, basic synaptic transmission, and paired-pulse facilitation were enhanced but long-term potentiation and carbachol-induced hippocampal theta oscillations were impaired compared to young Apoe3 mice. However, both Apoe genotypes responded similarly to persistent stimulations (4, 10, and 40 Hz for 4 seconds). Conclusion: Our results suggest significant alterations in hippocampal dendritic structure and synaptic function in Apoe4 mice, even at an early age

Epidemiology of birth defects based on a birth defects surveillance system in southwestern China and the associated risk factors

BackgroundBirth defects (BDs) are associated with many potential risk factors, and its causes are complex.ObjectivesThis study aimed to explore the epidemiological characteristics of BDs in Guangxi of China and the associated risk factors of BDs.MethodsBDs data of perinatal infants (PIs) were obtained from the Guangxi birth defects monitoring network between 2016 and 2020. Univariate Poisson regression was used to calculate the prevalence-rate ratios (PRR) to explore the changing trends of BDs prevalence by year and the correlation between the regarding of characteristics of BDs (including infant gender, maternal age, and quarter) and BDs. Clinical characteristics of PIs with BDs and general characteristics of their mothers were documented, and Spearman correlation analysis was used to explore the potential associated risk factors of BDs.ResultsBetween 2016 and 2020, 44,146 PIs with BDs were monitored, with an overall BDs prevalence of 121.71 (95% CI: 120.58–122.84) per 10,000 PIs, showing a significant increase trend (PRR = 1.116, 95% CI: 1.108–1.123), especially the prevalence of congenital heart defects (CHDs) that most significantly increased (PRR = 1.300, 95% CI: 1.283–1.318). The 10 most common BDs were CHDs, polydactyly, congenital talipes equinovarus, other malformation of external ear, syndactyly, hypospadias, cleft lip with cleft palate, cleft lip, hemoglobin Bart's hydrops fetalis syndrome (BHFS), and congenital atresia of the rectum and anus. BDs were positively correlated with pregnant women's age (R = 0.732, P &lt; 0.01) and education level (R = 0.586, P &lt; 0.05) and having pre-gestational diabetes mellitus (PGDM)/gestational diabetes mellitus (GDM) (R = 0.711, P &lt; 0.01), while when the pregnant women had a family history of a dead fetus (R = −0.536, P &lt; 0.05) and a birth of a fetus with BDs (R = −0.528, P &lt; 0.05) were negatively correlated with BDs.ConclusionA significant increase in the prevalence of BDs was detected between 2016 and 2020 in Guangxi, especially the prevalence of CHDs that most significantly increased. Older maternal age, higher maternal education level, and having PGDM before pregnancy or GDM in early pregnancy were the risk factors for BDs

A prospective randomized double-blind study comparing the dose-response curves of epidural ropivacaine for labor analgesia initiation between parturients with and without obesity

Background: Previous studies have explored the median effective concentration (EC50) of ropivacaine for labor epidural analgesia in parturients with obesity. However, the clinical relevance of the 90% effective concentration (EC90) remains unclear. This study aimed to determine and compare the dose–response curve of epidural ropivacaine for labor analgesia between parturients with and without obesity.Methods: Parturients were divided into two groups based on body mass index (BMI): group N, consisting of parturients with BMI &lt;30 kg/m2, and group O, consisting of parturients with BMI &gt;30 kg/m2. Within each group, the patients were randomized to receive one of five concentrations (0.0375%, 0.075%, 0.1125%, 0.15%, or 0.1875%) of epidural ropivacaine for labor analgesia. Analgesia was induced with a loading dose of 15 mL of the assigned concentration. Visual analogue scale (VAS) scores were recorded at baseline and 30 min post-dose to calculate the response (%) using the formula [(baseline VAS pain score—VAS pain score at 30 min)/baseline VAS pain score] ×100%. The EC50 and EC90 values were determined via nonlinear regression analysis.Results: The EC50 and EC90 values of ropivacaine were 0.061% (95% confidence interval [CI], 0.056%–0.066%) and 0.177% (95% CI, 0.152%–0.206%) in group N and 0.056% (95% CI, 0.051%–0.061%) and 0.161% (95% CI, 0.138%–0.187%) in group O, respectively. No significant differences were observed in the EC50 and EC90 values between the two groups (p-values = 0.121 and 0.351, respectively.Conclusion: In conclusion, within the parameters of this study, our findings suggest that obesity, characterized by a mean BMI value of 30.9, does not significantly influence the EC50 and EC90 values of epidural ropivacaine for labor analgesia. Further investigations are warranted to elucidate the dose-response relationship between ropivacaine and obesity with higher BMI values.Clinical trial registration:https://www.chictr.org.cn/showproj.html?proj=190747, Identifier ChiCTR2300073273

Associations between impulsivity, aggression, and suicide in Chinese college students

BACKGROUND: Although there are accumulating data regarding the epidemiology of suicide in China, there are meager data on suicidal ideation and attempts among college students. Interestingly, elevated impulsivity is thought to facilitate the transition from suicidal thoughts to suicidal behavior. Therefore, the objective of this research was to identify the associations between suicide and the personality factors of impulsivity and aggression. METHODS: This study’s sampling method employed stratified random cluster sampling. A multi-stage stratified sampling procedure was used to select participants (n = 5,245). We conducted structured interviews regarding a range of socio-demographic characteristics and suicidal morbidity. The Patient Health Questionnaire depression module (PHQ-9) was used to acquire the information about thoughts of being better off dead or hurting themselves in some ways during the past two weeks. The impulsivity symptoms in this study were assessed with the BIS-11-CH (i.e., the Chinese version of the BIS-11), and the Aggressive symptoms were assessed with the BAQ. The statistical package for social science (SPSS) v.13.0 program (SPSS Inc., Chicago, IL, USA) was used for statistical analysis. Socio-demographic variables such as ethnic and gender were compared between groups, through the use of χ(2) tests. The nonparametric test (k Independent Sample test, Kruskal-Wallis H) was performed to determine differences between the personality factors of impulsivity and aggression and suicide. RESULTS: In total, 9.1% (n = 479) of the 5,245 students reported they have ever thought about committing suicide; and 1% (n = 51) reported a history of attempted suicide (attempters). The analyses detected significant differences in scores on cognitive impulsivity (p < 0.01), when comparing individuals who only had suicidal ideation and individuals who had attempted suicide. Moreover, significant differences were found between ideators only and attempters on scores of self-oriented attack (p < .001). CONCLUSIONS: Suicidal ideation is prevalent among Chinese university students. Students with high aggression scores were more susceptible to committing suicide. Scores on self-oriented attack and cognitive impulsivity may be important factors for differentially predicting suicide ideation and suicide attempts