iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power

Prediction of Protein Domain with mRMR Feature Selection and Analysis

The domains are the structural and functional units of proteins. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop effective methods for predicting the protein domains according to the sequences information alone, so as to facilitate the structure prediction of proteins and speed up their functional annotation. However, although many efforts have been made in this regard, prediction of protein domains from the sequence information still remains a challenging and elusive problem. Here, a new method was developed by combing the techniques of RF (random forest), mRMR (maximum relevance minimum redundancy), and IFS (incremental feature selection), as well as by incorporating the features of physicochemical and biochemical properties, sequence conservation, residual disorder, secondary structure, and solvent accessibility. The overall success rate achieved by the new method on an independent dataset was around 73%, which was about 28–40% higher than those by the existing method on the same benchmark dataset. Furthermore, it was revealed by an in-depth analysis that the features of evolution, codon diversity, electrostatic charge, and disorder played more important roles than the others in predicting protein domains, quite consistent with experimental observations. It is anticipated that the new method may become a high-throughput tool in annotating protein domains, or may, at the very least, play a complementary role to the existing domain prediction methods, and that the findings about the key features with high impacts to the domain prediction might provide useful insights or clues for further experimental investigations in this area. Finally, it has not escaped our notice that the current approach can also be utilized to study protein signal peptides, B-cell epitopes, HIV protease cleavage sites, among many other important topics in protein science and biomedicine

MemBrain: Improving the Accuracy of Predicting Transmembrane Helices

Prediction of transmembrane helices (TMH) in α helical membrane proteins provides valuable information about the protein topology when the high resolution structures are not available. Many predictors have been developed based on either amino acid hydrophobicity scale or pure statistical approaches. While these predictors perform reasonably well in identifying the number of TMHs in a protein, they are generally inaccurate in predicting the ends of TMHs, or TMHs of unusual length. To improve the accuracy of TMH detection, we developed a machine-learning based predictor, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold. MemBrain demonstrates an overall improvement of about 20% in prediction accuracy, particularly, in predicting the ends of TMHs and TMHs that are shorter than 15 residues. It also has the capability to detect N-terminal signal peptides. The MemBrain predictor is a useful sequence-based analysis tool for functional and structural characterization of helical membrane proteins; it is freely available at http://chou.med.harvard.edu/bioinf/MemBrain/

SPH Simulations of Negative (Nodal) Superhumps: A Parametric Study

Negative superhumps in cataclysmic variable systems result when the accretion disc is tilted with respect to the orbital plane. The line of nodes of the tilted disc precesses slowly in the retrograde direction, resulting in a photometric signal with a period slightly less than the orbital period. We use the method of smoothed particle hydrodynamics to simulate a series of models of differing mass ratio and effective viscosity to determine the retrograde precession period and superhump period deficit $\varepsilon_-$ as a function of system mass ratio $q$. We tabulate our results and present fits to both $\varepsilon_-$ and $\varepsilon_+$ versus $q$, as well as compare the numerical results with those compiled from the literature of negative superhump observations. One surprising is that while we find negative superhumps most clearly in simulations with an accretion stream present, we also find evidence for negative superhumps in simulations in which we shut off the mass transfer stream completely, indicating that the origin of the photometric signal is more complicated than previously believed.Comment: 14 pages, 15 figures. Accepted for publication in MNRA

Impedance of nanometer thickness ferromagnetic Co40Fe40B20 films

Nanocrystalline Co40Fe40B20 films, with film thickness tf = 100 nm, were deposited on glass substrates by the magnetron sputtering method at room temperature. During the film deposition period, a dc magnetic field, h = 40 Oe, was applied to introduce an easy axis for each film sample: one with h||L and the other with h||w, where L and w are the length and width of the film. Ferromagnetic resonance (FMR), ultrahigh frequency impedance (IM), dc electrical resistivity (ρ), and magnetic hysteresis loops (MHL) of these films were studied. From the MHL and r measurements, we obtain saturation magnetization 4πMs = 15.5 kG, anisotropy field Hk = 0.031 kG, and r = 168 mW.cm. From FMR, we can determine the Kittel mode ferromagnetic resonance (FMR-K) frequency fFMRK = 1,963 MHz. In the h||L case, IM spectra show the quasi-Kittel-mode ferromagnetic resonance (QFMR-K) at f0 and the Walker-mode ferromagnetic resonance (FMR-W) at fn, where n = 1, 2, 3, and 4. In the h||w case, IM spectra show QFMR-K at F0 and FMR-W at Fn. We find that f0 and F0 are shifted from fFMRK, respectively, and fn = Fn. The in-plane spin-wave resonances are responsible for those relative shifts

Gene expression changes induced by the tumorigenic pyrrolizidine alkaloid riddelliine in liver of Big Blue rats

<p>Abstract</p> <p>Background</p> <p>Pyrrolizidine alkaloids (PAs) are probably the most common plant constituents that poison livestock, wildlife, and humans worldwide. Riddelliine is isolated from plants grown in the western United States and is a prototype of genotoxic PAs. Riddelliine was used to investigate the genotoxic effects of PAs via analysis of gene expression in the target tissue of rats in this study. Previously we observed that the mutant frequency in the liver of rats gavaged with riddelliine was 3-fold higher than that in the control group. Molecular analysis of the mutants indicated that there was a statistically significant difference between the mutational spectra from riddelliine-treated and control rats.</p> <p>Results</p> <p>Riddelliine-induced gene expression profiles in livers of Big Blue transgenic rats were determined. The female rats were gavaged with riddelliine at a dose of 1 mg/kg body weight 5 days a week for 12 weeks. Rat whole genome microarray was used to perform genome-wide gene expression studies. When a cutoff value of a two-fold change and a <it>P</it>-value less than 0.01 were used as gene selection criteria, 919 genes were identified as differentially expressed in riddelliine-treated rats compared to the control animals. By analysis with the Ingenuity Pathway Analysis Network, we found that these significantly changed genes were mainly involved in cancer, cell death, tissue development, cellular movement, tissue morphology, cell-to-cell signaling and interaction, and cellular growth and proliferation. We further analyzed the genes involved in metabolism, injury of endothelial cells, liver abnormalities, and cancer development in detail.</p> <p>Conclusion</p> <p>The alterations in gene expression were directly related to the pathological outcomes reported previously. These results provided further insight into the mechanisms involved in toxicity and carcinogenesis after exposure to riddelliine, and permitted us to investigate the interaction of gene products inside the signaling networks.</p

Snap-through instability of graphene on substrates

We determine the graphene morphology regulated by substrates with herringbone and checkerboard surface corrugations. As the graphene/substrate interfacial bonding energy and the substrate surface roughness vary, the graphene morphology snaps between two distinct states: 1) closely conforming to the substrate and 2) remaining nearly flat on the substrate. Such a snapthrough instability of graphene can potentially lead to desirable electronic properties to enable graphene-based devices.Comment: 13 pages, 4 figures; Nanoscale Research Letters, in press, 200

Price regulation, new entry, and information shock on pharmaceutical market in Taiwan: a nationwide data-based study from 2001 to 2004

<p>Abstract</p> <p>Background</p> <p>Using non-steroidal anti-inflammatory drugs (NSAIDs) as a case, we used Taiwan's National Health Insurance (NHI) database, to empirically explore the association between policy interventions (price regulation, new drug entry, and an information shock) and drug expenditures, utilization, and market structure between 2001 and 2004.</p> <p>Methods</p> <p>All NSAIDs prescribed in ambulatory visits in the NHI system during our study period were included and aggregated quarterly. Segmented regression analysis for interrupted time series was used to examine the associations between two price regulations, two new drug entries (cyclooxygennase-2 inhibitors) and the rofecoxib safety signal and expenditures and utilization of all NSAIDs. Herfindahl index (HHI) was applied to further examine the association between these interventions and market structure of NSAIDs.</p> <p>Results</p> <p>New entry was the only variable that was significantly correlated with changes of expenditures (positive change, p = 0.02) and market structure of the NSAIDs market in the NHI system. The correlation between price regulation (first price regulation, p = 0.62; second price regulation, p = 0.26) and information shock (p = 0.31) and drug expenditure were not statistically significant. There was no significant change in the prescribing volume of NSAIDs per rheumatoid arthritis (RA) or osteoarthritis (OA) ambulatory visit during the observational period. The market share of NSAIDs had also been largely substituted by these new drugs up to 50%, in a three-year period and resulted in a more concentrated market structure (HHI 0.17).</p> <p>Conclusions</p> <p>Our empirical study found that new drug entry was the main driving force behind escalating drug spending, especially by altering the market share.</p

Acinic cell carcinoma in pregnancy: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>We report an observational study on the etiology and recurrence of acinic cell carcinoma of the parotid gland that seemed to be related to pregnancy. The medical literature has never reported such an association; therefore, our case report is probably the first to mention this observation.</p> <p>Case presentation</p> <p>This report is of a 25-year-old Arabic female patient from the United Arab Emirates, who, during her first pregnancy, developed acinic cell carcinoma of the right parotid gland that was managed with surgical excision in the form of superficial parotidectomy. During her second pregnancy, which occurred four years later, she had a recurrence of the same malignant neoplasm associated with ipsilateral malignant cervical lymphadenopathy. The patient was managed with total parotidectomy and neck dissection, as well as postoperative adjuvant radiotherapy. Our observation on this particular case of acinic cell carcinoma is that the initial onset of her neoplasm was during her first pregnancy, and the recurrence of the same malignant disease was during a subsequent pregnancy. This chronologic association raised our suspicion that there might be a possible etiologic effect of pregnancy or its associated hormonal or physiologic changes or both on the pathogenesis or etiology of acinic cell carcinoma.</p> <p>Conclusion</p> <p>Some association might exist between pregnancy and the pathogenesis or etiology of acinic cell carcinoma.</p