Visual Query System to Help Users Refine Queries from High-Dimensional Data: A Case Study

Temporal queries are normally issued for cohort selection from the high-dimensional dataset in many contexts, such as medical related research areas. The idea was inspired by the difficulties when interacting with the i2b2 system, an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System, which seldom provides informative feedbacks and interactive exploration about the clinical events of each query or the expecting follow-up cohort. Considering the complexity and time-consuming nature of complicated temporal queries, it would be frustrating when iterative query refining is needed. The paper presents a newly designed web-based visual query system to facilitate refining the initial temporal query to select a satisfactory cohort for a given research. A detailed interface design associated with the query time frame and the implementation of the visual query algorithm that enables advanced arbitrary temporal query logic is included. In addition, a case study with 3 participants in medical related research areas was conducted that shows the system was overall useful to help the users to gain an idea about their follow-up queries.Master of Science in Information Scienc

Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach

Background: The mechanisms through which immunosuppressed patients bear increased risk and worse survival in oral squamous cell carcinoma (OSCC) are unclear. Here, we used deep learning to investigate the genetic mechanisms underlying immunosuppression in the survival of OSCC patients, especially from the aspect of various survival-related subtypes. Materials and methods: OSCC samples data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and OSCCrelated genetic datasets with survival data in the National Center for Biotechnology Information (NCBI). Immunosuppression genes (ISGs) were obtained from the HisgAtlas and DisGeNET databases. Survival analyses were performed to identify the ISGs with significant prognostic values in OSCC. A deep learning (DL)-based model was established for robustly differentiating the survival subpopulations of OSCC samples. In order to understand the characteristics of the different survival-risk subtypes of OSCC samples, differential expression analysis and functional enrichment analysis were performed. Results: A total of 317 OSCC samples were divided into one inferring cohort (TCGA) and four confirmation cohorts (ICGC set, GSE41613, GSE42743, and GSE75538). Eleven ISGs (i.e., BGLAP, CALCA, CTLA4, CXCL8, FGFR3, HPRT1, IL22, ORMDL3, TLR3, SPHK1, and INHBB) showed prognostic value in OSCC. The DL-based model provided two optimal subgroups of TCGA-OSCC samples with significant differences (p = 4.91E-22) and good model fitness [concordance index (C-index) = 0.77]. The DL model was validated by using four external confirmation cohorts: ICGC cohort (n = 40, C-index = 0.39), GSE41613 dataset (n = 97, C-index = 0.86), GSE42743 dataset (n = 71, C-index = 0.87), and GSE75538 dataset (n = 14, C-index = 0.48). Importantly, subtype Sub1 demonstrated a lower probability of survival and thus a more aggressive nature compared with subtype Sub2. ISGs in subtype Sub1 were enriched in the tumorinfiltrating immune cells-related pathways and cancer progression-related pathways, while those in subtype Sub2 were enriched in the metabolism-related pathways. Conclusion: The two survival subtypes of OSCC identified by deep learning can benefit clinical practitioners to divide immunocompromised patients with oral cancer into two subpopulations and give them target drugs and thus might be helpful for improving the survival of these patients and providing novel therapeutic strategies in the precision medicine area

Research on the Relationship between Abnormal Audit Fees of Listed Companies and the Risk of Stock Price Crash

The large-scale stock price fluctuations that occur from time to time in the global stock market highlight the important research significance of stock price crash risk. Existing researches have paid little attention to the impact of abnormal audit fees on stock price crash risk. This article explores its relationship with stock prices from this perspective. The relationship between the crash risk and whether the abnormal audit fee can be used as an early warning signal for the company’s stock price crash risk has enriched the related research on the influencing factors of the stock price crash risk and the early warning mechanism

Understanding Users’ Perceptions of Bicycle-Sharing Systems in Chinese Cities: Evidence from Beijing and Guangzhou

Decades ago, bicycles used to play an important role in urban transportation in Chinese cities, but they have been gradually replaced by private cars, metro, buses, and some other modes, owning to the fast-growing mobility demand as a result of urban expansion and motorization. However, in recent years, with the development of Information and Communication Technologies (ICT) and the initiative of the sharing economy, bike-sharing systems (BSSs) have been implemented extensively in Chinese cities. Their usage patterns can be revealed via system-generated data, yet less is known about users’ attitudes towards and preferences for these systems. In this study, we draw on two surveys conducted in Guangzhou and Beijing on the perceptions of travelers using BSSs to estimate the effect of demographic factors, bicycle ownership, and trip-level factors on the willingness and potential frequency of BSS usage. In addition, a latent class model is built to analyze the different aspects of theses systems concerned with different types of urban travelers. It is found that respondents’ age, occupation, income, mode combination, and the proximity of origin or destination to the docking station, etc., influence the willingness and frequency of using BSSs. In addition, respondents generally value features such as the proximity of docking stations to trip destinations, safety to ride, and appropriate level of fare. However, different latent classes show a different preference for other features of BSSs. According to the model results, proposals are given for the improvement of the existing systems in Chinese cities

Oral Health-Related Quality of Life in Patients With Chronic Respiratory Diseases—Results of a Systematic Review

Background: This systematic review evaluates the oral health-related quality of life (OHRQoL) of patients with chronic respiratory diseases. Methods: A systematic literature search was performed based on the PubMed, Medline, Web of Science, and Scopus, using the search terms: “oral health-related quality of life” and “respiratory disease” or “lung” and “oral health-related quality of life.” Full-text articles published until June 30, 2021 and reporting any OHRQoL measurement in children or adults with a chronic respiratory disease or condition were included and analyzed qualitatively. Results: A total of seven out of 44 studies were included, of which four studies examined adults and three studies investigated children. The respective diseases were chronic obstructive pulmonary disease (COPD) (n = 2), sleep apnea (n = 2), severe asthma (n = 1), cystic fibrosis (n = 1), and lung transplantation (n = 1). Four studies confirmed a worse OHRQoL in the respiratory diseased group compared to healthy controls. The overall OHRQoL was reduced in the included studies. Oral health, healthrelated quality of life, and disease-related parameters were rarely examined with regard to OHRQoL. Conclusion: Patients with chronic respiratory diseases show a reduced OHRQoL. Oral health should be fostered in these individuals to support their OHRQoL

The Effects of Radix Astragali Water Abstract on Energy Metabolism in Rat Yang-Deficiency Cold Syndrome Model through PPAR Signaling Pathway

Radix Astragali (RA) herb with warm property and significant “tonifying qi” effects is indicated for the syndrome of internal cold due to Yang deficiency. The purpose of this research was to explore effects of Radix Astragali (RA) through PPAR signaling pathway on gene expression profiles related to energy metabolism in rats with the Yang-deficiency cold (YDC) syndrome, for identifying the pathological mechanism of Yang-deficiency cold (YDC) syndrome and the effects mechanism of RA. The results indicated that RA could significantly increase body weight (BM), cold and heat tendency (CT), overall temperature (OT), rectum temperature (RT), toe temperature (TT), energy intake (EI), and V(O2)/V(CO2) ratio (which indicates basal metabolism, BM) (P<0.05), enhancing the depressed metabolic function in YDC syndrome model rat. Our data also indicated differentially expressed genes (DEGs) related to energy metabolism involving lipids, carbohydrates, and amino acids metabolic process; the expression of CPT-1 and FABP4 (ap2) was improved; PPAR, Glycolysis, Wnt, cAMP, MAPK, AMPK, and fatty acid degradation signaling pathway may be related to energy metabolism. However, the Chinese herbal medicine RA plays a certain role in promoting the metabolism of substances and energy in rats by its warming and beneficial effect. Our results suggest that the mechanism underlying the function of RA may take effect through the regulation of PPAR signaling pathway and related gene expression. Lipids, carbohydrates, and amino acids metabolic process may be affected to adjust the reduced metabolic function in the model animals. In general, results indicate that RA could promote energy metabolism in rats with the YDC syndrome via PPAR signaling pathway regulating the expression of CPT-1 and FABP4 (ap2), which reflected the warm and qi tonifying properties of RA

Maize ZmBES1/BZR1-3 and -9 Transcription Factors Negatively Regulate Drought Tolerance in Transgenic <i>Arabidopsis</i>

The BRI1-EMS suppressor 1 (BES1)/brassinazole-resistant 1(BZR1) transcription factors play crucial roles in plant growth, development, and stress response. However, little is known about the function of maize’s BES1/BZR1s. In this study, the ZmBES1/BZR1-3 and ZmBES1/BZR1-9 genes were cloned from maize’s inbred line, B73, and they were functionally evaluated by analyzing their expression pattern, subcellular localization, transcriptional activation activity, as well as their heterologous expression in Arabidopsis, respectively. The results of the qRT-PCR showed that the ZmBES1/BZR1-3 and ZmBES1/BZR1-9 genes were predominantly expressed in the root, and their expression was significantly down-regulated by drought stress. The ZmBES1/BZR1-3 and ZmBES1/BZR1-9 proteins localized in the nucleus but showed no transcriptional activation activity as a monomer. Subsequently, it was found that the heterologous expression of the ZmBES1/BZR1-3 and ZmBES1/BZR1-9 genes in Arabidopsis decreased drought tolerance, respectively. The transgenic lines showed a more serious wilting phenotype, shorter root length, lower fresh weight, and higher relative electrolyte leakage (REL) and malondialdehyde (MDA) content compared to the control under drought stress. The RNA-sequencing data showed that the 70.67% and 93.27% differentially expressed genes (DEGs) were significantly down-regulated in ZmBES1/BZR1-3 and ZmBES1/BZR1-9 transgenic Arabidopsis, respectively. The DEGs of ZmBES1/BZR1-3 gene’s expressing lines were mainly associated with oxidative stress response and amino acid metabolic process and enriched in phenylpropanoid biosynthesis and protein processing in the endoplasmic reticulum. But the DEGs of the ZmBES1/BZR1-9 gene’s expressing lines were predominantly annotated with water deprivation, extracellular stimuli, and jasmonic acid and enriched in phenylpropanoid biosynthesis and plant hormone signal transduction. Moreover, ZmBES1/BZR1-9 increased stomatal aperture in transgenic Arabidopsis under drought stress. This study indicates that ZmBES1/BZR1-3 and ZmBES1/BZR1-9 negatively regulate drought tolerance via different pathways in transgenic Arabidopsis, and it provides insights into the underlying the function of BES1/BZR1s in crops