ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data

ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing information in the database can help users investigate the alternative splicing and tissue-specific expression of genes

Synthesis and Annealing Study of Silicon- and Fluorine-containing Low Bandgap Conjugated Polymers for Solar Cell Applications

Two donor-acceptor alternating conjugated copolymers were synthesized as the donor materials of the active layer in polymer solar cells via Stille coupling reaction. Both copolymers consisted of dithienosilole as the donor unit and nonfluorinated 2,1,3-benzooxadiazole or fluorinated 2,1,3-benzooxadiazole as the acceptor unit. The nonfluorinated polymer and fluorinated polymer were designated as P1 and P2, respectively. The structures of copolymers were confirmed by FT-IR, 1H NMR, and 13C NMR. Optoelectronic properties of the polymer were investigated and observed by UV-vis spectrum, photoluminescence spectrum, and cyclic voltammetry. Both polymers exhibited a panchromatic absorption ranging from 300 nm to 1100 nm and displayed low band gaps of 1.46 eV and 1.42 eV, respectively. Both of the synthesized materials were used as the donor material in the bulk heterojunction (BHJ) solar cells and then power conversion efficiency (PCE) measurements were conducted in different weight ratios of the polymer:PC61BM blends. Compared to the nonfluorinated one, the fluorinated polymer exhibited a higher PCE of 2.67% at room temperature under the illumination of AM 1.5 (100 mW/cm2). Study of the effect of annealing on the performance of the P1/PC61BM devices using a 1:2 blend ratio of P1:PC61BM exhibited the highest short-circuit current density of 5.88 mA/cm2 and a power conversion efficiency of 2.76% at annealing temperature of 125℃. The bulk heterojunction polymer solar cell employing P2 and PC61BM at a blend ratio of 1:2 exhibited the highest short-circuit current density of 6.44 mA/cm2 and a power conversion efficiency of 3.54% at annealing temperature of 150℃

Rapid Detection of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight: Using a Machine Learning Approach and Unbiased Validation

Heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) is an emerging superbug with implicit drug resistance to vancomycin. Detecting hVISA can guide the correct administration of antibiotics. However, hVISA cannot be detected in most clinical microbiology laboratories because the required diagnostic tools are either expensive, time consuming, or labor intensive. By contrast, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) is a cost-effective and rapid tool that has potential for providing antibiotics resistance information. To analyze complex MALDI-TOF mass spectra, machine learning (ML) algorithms can be used to generate robust hVISA detection models. In this study, MALDI-TOF mass spectra were obtained from 35 hVISA/vancomycin-intermediate S. aureus (VISA) and 90 vancomycin-susceptible S. aureus isolates. The vancomycin susceptibility of the isolates was determined using an Etest and modified population analysis profile–area under the curve. ML algorithms, namely a decision tree, k-nearest neighbors, random forest, and a support vector machine (SVM), were trained and validated using nested cross-validation to provide unbiased validation results. The area under the curve of the models ranged from 0.67 to 0.79, and the SVM-derived model outperformed those of the other algorithms. The peaks at m/z 1132, 2895, 3176, and 6591 were noted as informative peaks for detecting hVISA/VISA. We demonstrated that hVISA/VISA could be detected by analyzing MALDI-TOF mass spectra using ML. Moreover, the results are particularly robust due to a strict validation method. The ML models in this study can provide rapid and accurate reports regarding hVISA/VISA and thus guide the correct administration of antibiotics in treatment of S. aureus infection

Rapid Detection of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight: Using a Machine Learning Approach and Unbiased Validation

<p>Heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) is an emerging superbug with implicit drug resistance to vancomycin. Detecting hVISA can guide the correct administration of antibiotics. However, hVISA cannot be detected in most clinical microbiology laboratories because the required diagnostic tools are either expensive, time consuming, or labor intensive. By contrast, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) is a cost-effective and rapid tool that has potential for providing antibiotics resistance information. To analyze complex MALDI-TOF mass spectra, machine learning (ML) algorithms can be used to generate robust hVISA detection models. In this study, MALDI-TOF mass spectra were obtained from 35 hVISA/vancomycin-intermediate S. aureus (VISA) and 90 vancomycin-susceptible S. aureus isolates. The vancomycin susceptibility of the isolates was determined using an Etest and modified population analysis profile–area under the curve. ML algorithms, namely a decision tree, k-nearest neighbors, random forest, and a support vector machine (SVM), were trained and validated using nested cross-validation to provide unbiased validation results. The area under the curve of the models ranged from 0.67 to 0.79, and the SVM-derived model outperformed those of the other algorithms. The peaks at m/z 1132, 2895, 3176, and 6591 were noted as informative peaks for detecting hVISA/VISA. We demonstrated that hVISA/VISA could be detected by analyzing MALDI-TOF mass spectra using ML. Moreover, the results are particularly robust due to a strict validation method. The ML models in this study can provide rapid and accurate reports regarding hVISA/VISA and thus guide the correct administration of antibiotics in treatment of S. aureus infection.</p

Childhood invasive pneumococcal disease caused by non-7-valent pneumococcal vaccine (PCV7) serotypes under partial immunization in Taiwan

Emerging non-7-valent pneumococcal conjugate vaccine (PCV7) serotypes have replaced PCV7 serotypes in childhood invasive pneumococcal disease (IPD). This study was designed to describe the IPD caused by non-PCV7 serotypes under partial PCV7 immunization in Taiwan. Methods: All children <18 years of age diagnosed with IPD at National Cheng Kung University Hospital from 1998 to 2010 were enrolled. Clinical and laboratory information was collected. Pneumococcal isolates were tested for antimicrobial susceptibility and interpreted using Clinical Laboratory Standard Institute guidelines (2008). Serotypes were determined using the capsular swelling method. Results: One hundred and five patients with IPD were identified, including 75 PCV7 and 30 non-PCV7 isolates. Pneumonia (63.3%) was the leading clinical manifestation of non-PCV7 IPDs and 78.9% of pneumonia cases were associated with necrotizing pneumonia or empyema. Children with non-PCV7 IPDs had longer febrile days, required longer intensive care unit stays, and had a higher C-reactive protein level than those with PCV7 IPDs (p < 0.05). Serotype 3 is the most common non-PCV7 serotype (46.7%) and possesses the highest potential for pulmonary complications (p < 0.05, odds ratio: 0.114; 95% confidence interval, 0.013 – 0.973). Conclusion: The changing epidemiology of IPDs following the introduction of PCV7 has been noted. Expanded serotype coverage of the vaccine is warranted

Clinical perspectives of childhood tuberculosis in Taiwan

Tuberculosis (TB) is an important public health issue in Taiwan and worldwide. Taiwan has made major progress in combating TB in the past 40 years. However, childhood TB still constitutes a significant challenge in disease control. From January to mid December 2011, 369 new cases of pediatric TB were confirmed. The relatively low case number and variable clinical presentations made it difficult for early detection. Latent TB infections in children also pose further complexity in clinical management. Knowledge of the clinical features of active and latent TB infection is crucial for efficient TB control

The Low Proportion and Associated Factors of Involuntary Admission in the Psychiatric Emergency Service in Taiwan.

The involuntary admission regulated under the Mental Health Act has become an increasingly important issue in the developed countries in recent years. Most studies about the distribution and associated factors of involuntary admission were carried out in the western countries; however, the results may vary in different areas with different legal and socio-cultural backgrounds.The aim of this study was to investigate the proportion and associated factors of involuntary admission in a psychiatric emergency service in Taiwan.The study cohort included patients admitted from a psychiatric emergency service over a two-year period. Demographic, psychiatric emergency service utilization, and clinical variables were compared between those who were voluntarily and involuntarily admitted to explore the associated factors of involuntary admission.Among 2,777 admitted patients, 110 (4.0%) were involuntarily admitted. Police referrals and presenting problems as violence assessed by psychiatric nurses were found to be associated with involuntary admission. These patients were more likely to be involuntarily admitted during the night shift and stayed longer in the psychiatric emergency service.The proportion of involuntary admissions in Taiwan was in the lower range when compared to Western countries. Dangerous conditions evaluated by the psychiatric nurses and police rather than diagnosis made by the psychiatrists were related factors of involuntary admission. As it spent more time to admit involuntary patients, it was suggested that multidisciplinary professionals should be included in and educated for during the process of involuntary admission

A Computational Approach to Discover Differential Cooperation of Regulatory Sites in Functionally Related Genes in Yeast Genome

The availability of genome-wide gene expression data provides a unique set of genes from which to decipher the mechanisms underlying the common transcriptional response. A set of transcription factors which bind to target sites regulate the gene transcription cooperatively. This motivates us to discover the site associations of known transcription factor binding sites and certain repetitive elements. Those over-represented repetitive elements in the promoter regions of functionally related genes are predicted as putative regulatory elements. The study is to analyze how the differential site associations of the known regulatory sites and putative regulatory elements are distributed in the promoter regions of groups of functionally related genes. The functional-specific site associations are discovered by a statistical approach and the over-represented repetitive elements involving in the site associations are possible to be transcription factor binding sites. The site associations facilitate to predict functional-specific putative regulatory elements and to identify genes potentially co-regulated by the putative regulatory elements. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of yeast ORFs