ChimerDB—a knowledgebase for fusion sequences

Chromosome translocation and gene fusion are frequent events in the human genome and are often the cause of many types of tumor. ChimerDB is the database of fusion sequences encompassing bioinformatics analysis of mRNA and expressed sequence tag (EST) sequences in the GenBank, manual collection of literature data and integration with other known database such as OMIM. Our bioinformatics analysis identifies the fusion transcripts that have non-overlapping alignments at multiple genomic loci. Fusion events at exon–exon borders are selected to filter out the cloning artifacts in cDNA library preparation. The result is classified into two groups—genuine chromosome translocation and fusion between neighboring genes owing to intergenic splicing. We also integrated manually collected literature and OMIM data for chromosome translocation as an aid to assess the validity of each fusion event. The database is available at for human, mouse and rat genomes

ECgene: genome annotation for alternative splicing

ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration. The gene-modeling algorithm combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. The website provides several viewers and applications that have many unique features useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. We also provide two unique ways of analyzing gene expression. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publically. Furthermore, the cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. It should be noted that the ECgene website provides annotation for the whole transcriptome, not just the alternatively spliced genes. Currently, ECgene supports the human, mouse and rat genomes. The ECgene suite of tools and programs is available at http://genome.ewha.ac.kr/ECgene/

ECgene: an alternative splicing database update

ECgene () was developed to provide functional annotation for alternatively spliced genes. The applications encompass the genome-based transcript modeling for alternative splicing (AS), domain analysis with Gene Ontology (GO) annotation and expression analysis based on the EST and SAGE data. We have expanded the ECgene's AS modeling and EST clustering to nine organisms for which sufficient EST data are available in the GenBank. As for the human genome, we have also introduced several new applications to analyze differential expression. ECprofiler is an ontology-based candidate gene search system that allows users to select an arbitrary combination of gene expression pattern and GO functional categories. DEGEST is a database of differentially expressed genes and isoforms based on the EST information. Importantly, gene expression is analyzed at three distinctive levels—gene, isoform and exon levels. The user interfaces for functional and expression analyses have been substantially improved. ASviewer is a dedicated java application that visualizes the transcript structure and functional features of alternatively spliced variants. The SAGE part of the expression module provides many additional features including SNP, differential expression and alternative tag positions

Imidazole-Based Excited-State Intramolecular Proton-Transfer (ESIPT) Materials: Observation of Thermally Activated Delayed Fluorescence (TDF)

We report the first observation of thermally activated delayed fluorescence (TDF) from an excited-state intramolecular proton-transfer (ESIPT) molecule, a hydroxyl-substituted tetraphenyl imidazole derivative (HPI−Ac), in degassed solutions as well as in low-temperature organic matrixes. In the absence of oxygen, the blue emission of an identical spectral feature was observed in the nanosecond (∼4.4 ns) and microsecond (∼25 μs) time domains, and the fluorescence intensity increased with temperature. From the temperature dependence of the time-resolved spectra of HPI−Ac, the energy gap between the first-excited singlet state and the lowest triplet state was determined to be 7.6 ± 0.3 kJ/mol (630 ± 25 cm^(-1)), and the limiting rate constant of intrinsic reverse intersystem crossing was estimated to be 1.3 (±0.5) × 10^7 s^(-1)

Collision of Three Pandemics: The Coexistence of Cervical Cancer, HIV Infection, and Prior Tuberculosis in the Sub-Saharan Country of Botswana.

Cervical cancer is the leading cause of cancer-related mortality in the developing world, where HIV and Mycobacterium tuberculosis (TB) infection are also endemic. HIV infection is independently associated with increased morbidity and mortality among women with cervical cancer. TB is believed to increase the risk of malignancies and could cause chronic inflammation in the gynecologic tract. However, the relationship between cervical cancer and TB in settings hyperendemic for HIV is unknown. We found that 18 (10%) of a cohort of 180 women with cervical cancer in Botswana had a history of TB disease. Age and HIV infection were also associated with a history of TB disease. Our data show that prior TB disease is highly prevalent among patients with cervical cancer infected with HIV. The coexistence of cervical cancer, HIV infection, and prior TB infection might be higher than expected in the general population. Prospective studies are needed to better determine the impact of the collision of these three world health epidemics

The cascade of care for latent tuberculosis infection in congregate settings:a national cohort 1 analysis, Korea, 2017-18

BACKGROUND: In 2017, Korea implemented a nationwide project to screen and treat latent tuberculosis infection (LTBI) in high-risk for transmission public congregate settings. We aimed to assess programme success using a cascade of care framework. MATERIALS AND METHODS: We undertook a cohort study of people from three congregate settings screened between March 2017 and December 2018: (1) first-grade high school students, (2) employees of educational institutions, (3) employees of social welfare facilities. We report percentages of participants with LTBI completing each step in the cascade of care model. Poisson regression models were used to determine factors associated with not visiting clinics, not initiating treatment, and not completing treatment. RESULTS: Among the 96,439 participants who had a positive interferon-gamma release assay result, the percentage visiting clinics for further assessment, to initiate treatment, and who then completed treatment were 50.7, 34.7, and 28.9%, respectively. Compared to those aged 20-34 years, individuals aged < 20 years and aged ≥ 65 years were less likely to visit clinics, though more likely to complete treatment once initiated. Using public health centres rather than private hospitals was associated with people "not initiating treatment" (adjusted risk ratio [aRR], 3.72; 95% confidence interval [CI], 3.95-3.86). Nine-month isoniazid monotherapy therapy was associated with "not completing treatment," compared to 3-month isoniazid and rifampin therapy (aRR, 1.28; 95% CI, 1.16-1.41). CONCLUSION: Among participants with LTBI from three congregate settings, less than one third completed treatment. Age, treatment centre, and initial regimen were important determinants of losses to care through the cascade

Smoking among Young Rural to Urban Migrant Women in China: A Cross-Sectional Survey

Rural-to-urban migrant women may be vulnerable to smoking initiation as they are newly exposed to risk factors in the urban environment. We sought to identify correlates of smoking among rural-to-urban migrant women in China.A cross-sectional survey of rural-to-urban migrant women working in restaurants and hotels (RHW) and those working as commercial sex workers (CSW) was conducted in ten provincial capital cities in China. Multiple logistic regression was conducted to identify correlates of smoking. We enrolled 2229 rural-to-urban migrant women (1697 RHWs aged 18–24 years and 532 CSWs aged 18–30 years). Of these, 18.4% RHWs and 58.3% CSWs reported ever tried smoking and 3.2% RHWs and 41.9% CSWs reported current smoking. Participants who first tried smoking after moving to the city were more likely to be current smokers compared to participants who first tried smoking before moving to the city (25.3% vs. 13.8% among RHWs, p = 0.02; 83.6% vs. 58.6% among CSWs, p = <0.01). Adjusting for other factors, “tried female cigarette brands” had the strongest association with current smoking (OR 5.69, 95%CI 3.44 to 9.41) among participants who had ever tried smoking.Exposure to female cigarette brands may increase the susceptibility to smoking among rural-to-urban migrant women. Smoke-free policies and increased taxes may be effective in preventing rural-to-urban migrant women from smoking initiation

Border Crossing to Inject Drugs in Mexico Among Injection Drug Users in San Diego, California

We examined correlates of ever injecting drugs in Mexico among residents of San Diego, California. From 2007 to 2010, injecting drug users (IDUs) in San Diego underwent an interviewer-administered survey. Logistic regression identified correlates of injection drug use in Mexico. Of 302 IDUs, 38% were Hispanic, 72% male and median age was 37; 27% ever injected in Mexico; 43% reported distributive syringe sharing there. Factors independently associated with ever injecting drugs in Mexico included being younger at first injection, injecting heroin, distributive syringe sharing at least half of the time, and transporting drugs over the last 6 months. One-quarter of IDUs reported ever injecting drugs in Mexico, among whom syringe sharing was common, suggesting possible mixing between IDUs in the Mexico-US border region. Prospective studies should monitor trends in cross-border drug use in light of recent Mexican drug policy reforms partially decriminalizing drug possession