Using a kernel density estimation based classifier to predict species-specific microRNA precursors

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are short non-coding RNA molecules participating in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs) over the years. Recently, <it>ab initio </it>approaches obtain more attention because that they can discover species-specific pre-miRNAs. Most <it>ab initio </it>approaches proposed novel features to characterize RNA molecules. However, there were fewer discussions on the associated classification mechanism in a miRNA predictor.</p> <p>Results</p> <p>This study focuses on the classification algorithm for miRNA prediction. We develop a novel <it>ab initio </it>method, miR-KDE, in which most of the features are collected from previous works. The classification mechanism in miR-KDE is the relaxed variable kernel density estimator (RVKDE) that we have recently proposed. When compared to the famous support vector machine (SVM), RVKDE exploits more local information of the training dataset. MiR-KDE is evaluated using a training set consisted of only human pre-miRNAs to predict a benchmark collected from 40 species. The experimental results show that miR-KDE delivers favorable performance in predicting human pre-miRNAs and has advantages for pre-miRNAs from the genera taxonomically distant to humans.</p> <p>Conclusion</p> <p>We use a novel classifier of which the characteristic of exploiting local information is particularly suitable to predict species-specific pre-miRNAs. This study also provides a comprehensive analysis from the view of classification mechanism. The good performance of miR-KDE encourages more efforts on the classification methodology as well as the feature extraction in miRNA prediction.</p

To Enhance the Fire Resistance Performance of High-Speed Steel Roller Door with Water Film System

The structure of high-speed roller door with water film has improved in this study. The flameproof water film system is equipped with a water circulating device to reduce the water consumption of water film system. The water film is generated at the roller box of the high-speed roller door in this study. The heating test is done with the full-scale heating furnace. Both cases of the water film on unexposed surface and water film on exposed surface passed the fire resistance test based on ISO 834, proving that the high-speed roller door with water film system has 120A fire resistance period. The main findings indicate that the water film on exposed surface shows that as the amount of water film evaporated by high temperature inside the furnace must be greater than the evaporation capacity of water film on unexposed surface, the required water supply is 660 L more than the water film on unexposed surface

Yang-Dan-Tang, Identified from 15 Chinese Herbal Formulae, Inhibits Human Lung Cancer Cell Proliferation via Cell Cycle Arrest

Lung cancer has long been one of the most deadly forms of cancer. The majority of lung cancers are of the non-small-cell lung cancer (NSCLC) type. Here we used the non-small-cell lung carcinoma cell line A549 to screen 15 different traditional Chinese herbal medicine (CHM) formulae to explore the possible mechanisms of alternative medicine in lung cancer therapy. We identified three formulae (Formulae 3, 5, and 14) that substantially decreased the survival of A549 cells but did not affect MRC5 normal lung tissue cells. Formula 14, Yang-Dan-Tang, a modified decoction of Ramulus Cinnamomi Cassiae, was chosen for further characterization. Flow cytometry analysis showed that treatment of Formula 14 induced cell cycle arrest in G1 and G2 phase without causing significant cell death. These results were also confirmed by Western blot analysis, with decreased expression of G1/S and G2/M promoting cell cycle machinery including cyclin D3, cyclin B1, CDK4, and CDK6. This study provides further insight into the possible working mechanism of Yang-Dan-Tang in patients

Associations between blood glucose level and outcomes of adult in-hospital cardiac arrest: a retrospective cohort study

Additional file 3: Table S3. Features, interventions, and outcomes of cardiac arrest events stratified by the presence of measurement of blood glucose level after sustained return of spontaneous circulation

Neuron Regeneration and Proliferation Effects of Danshen and Tanshinone IIA

This study evaluates the proliferative effects of danshen and its monomer extract, tanshinone IIA, on Schwann cell proliferation. A piece of silicone rubber was guided across a 15-mm gap in the sciatic nerve of a rat. This nerve gap was then filled with different concentrations of danshen (0–100 mg/mL). The results showed that danshen increased the expressions of uPA, cyclin D1, E and ERK, JNK, and P38 MAP kinases via the FGF-2 signaling pathway in a dose-dependent manner. RSC96, Schwann cells were also administered with danshen (0, 20, 40, 60, 80, and 100 μg/mL) and tanshinone IIA (0, 2, 4, 6, 8, and 10 μg/mL). In lower concentrations, danshen and tanshinone IIA exhibited an apparent effect on Schwann cells. Similar effects were also demonstrated in the FGF-2-uPA regulating cascade and cell cycle proliferative protein results. Schwann cell migration was elevated as well. We used MAPK-signaling chemical inhibitors and identified the proliferative effects of danshen and tanshinone IIA as MAPK-signaling dependent. The results from the in vitro systems indicate that danshen and tanshinone IIA can be used to induce Schwann cell proliferation, and in vivo results potentially suggest that danshen and tanshinone IIA might enhance neuron regeneration

Correlation of virulence genes to clinical manifestations and outcome in patients with Streptococcus dysgalactiae subspecies equisimilis bacteremia

Background/PurposeStreptococcus dysgalactiae subsp. equisimilis (SDSE) is increasingly recognized as a human pathogen responsible for invasive infection and streptococcal toxic shock syndrome (STSS). The pathogen possesses virulence genes that resemble those found in Streptococcus pyogenes (GAS). We analyzed the association between these specific toxic genes, clinical presentations, and outcome in patients with SDSE infections.MethodsPatients (older than 18 years) with community-acquired invasive bacteremia caused by SDSE bacteremia who were undergoing treatment at China Medical University Hospital from June 2007 to December 2010 were included in this study. Multiplex polymerase chain reaction was performed to identify virulence genes of the SDSE isolates. Demographic data, clinical presentations, and outcome in patients with SDSE infections were reviewed and analyzed.ResultsForty patients with 41 episodes of SDSE bacteremia were reviewed. The median age of the patients with SDSE infection was 69.7 years; 55% were female and 78% had underlying diseases. Malignancy (13, 33%) and diabetes mellitus (13, 33%) were the most common comorbidities. The 30-day mortality rate was 12%. Compared with the survivors, the non-survivors had a higher rate of diabetes mellitus (80% vs. 26%), liver cirrhosis (60% vs.11%), shock (60% vs.17%), STSS (60% vs. 8%), and a high Pittsburgh bacteremia score >4 (40% vs. 6%). Most isolates had scpA, ska, saga, and slo genes, whereas speC, speG, speH, speI, speK, smez, and ssa genes were not detected. speA gene was identified only in one patient with STSS (1/6, 17%). All isolates were susceptible to penicillin, cefotaxime, levofloxacin, moxifloxacin, vancomycin, and linezolid.ConclusionIn invasive SDSE infections, most isolates carry putative virulence genes, such as scpA, ska, saga, and slo. Clinical SDSE isolates in Taiwan remain susceptible to penicillin cefotaxime, and levofloxacin

Increased requirement for minute ventilation and negative arterial to end-tidal carbon dioxide gradient may indicate malignant hyperthermia

Abstract Characteristic signs of malignant hyperthermia (MH) include unexplained tachycardia, increased end-tidal carbon dioxide (EtCO 2 ) concentration, metabolic and respiratory acidosis, and an increase in body temperature above 38.8 C. We present the case of a patient with highly probable MH. In addition to sinus tachycardia and metabolic and respiratory acidosis, this patient also had a negative arterial to EtCO 2 gradient and an increased requirement for minute ventilation to maintain a normal EtCO 2 concentration, with signs of increased CO 2 production. Despite these signs of MH, the patient&apos;s rectal temperature monitoring equipment did not show an increase in temperature, although the temperature measured in the mouth was increased. This case illustrates the unreliability of measuring rectal temperature as a means of reflecting body temperature during MH and the usefulness of increased CO 2 production signs in helping to diagnose MH