PPI-IRO: A two-stage method for protein-protein interaction extraction based on interaction relation ontology

Mining Protein-Protein Interactions (PPIs) from the fast-growing biomedical literature resources has been proven as an effective approach for the identifi cation of biological regulatory networks. This paper presents a novel method based on the idea of Interaction Relation Ontology (IRO), which specifi es and organises words of various proteins interaction relationships. Our method is a two-stage PPI extraction method. At fi rst, IRO is applied in a binary classifi er to determine whether sentences contain a relation or not. Then, IRO is taken to guide PPI extraction by building sentence dependency parse tree. Comprehensive and quantitative evaluations and detailed analyses are used to demonstrate the signifi cant performance of IRO on relation sentences classifi cation and PPI extraction. Our PPI extraction method yielded a recall of around 80% and 90% and an F1 of around 54% and 66% on corpora of AIMed and Bioinfer, respectively, which are superior to most existing extraction methods. Copyright © 2014 Inderscience Enterprises Ltd

Long-term Variability Properties and Periodicity Analysis for Blazars

In this paper, the compiled long-term optical and infrared measurements of some blazars are used to analyze the variation properties and the optical data are used to search for periodicity evidence in the lightcurve by means of the Jurkevich technique and the discrete correlation function (DCF) method. Following periods are found: 4.52-year for 3C 66A; 1.56 and 2.95 years for AO 0235+164; 14.4, 18.6 years for PKS 0735+178; 17.85 and 24.7 years for PKS 0754+100; 5.53 and 11.75 for OJ 287. 4.45, and 6.89 years for PKS 1215; 9 and 14.84 years for PKS 1219+285; 2.0, 13.5 and 22.5 for 3C273; 7.1 year for 3C279; 6.07 for PKS 1308+326; 3.0 and 16.5 years for PKS 1418+546; 2.0 and 9.35 years for PKS 1514-241; 18.18 for PKS 1807+698; 4.16 and 7.0 for 2155-304; 14 and 20 years for BL Lacertae. Some explanations have been discussed.Comment: 10 pages, 2 table, no figure, a proceeding paper for Pacific Rim Conference on Stellar Astrophysics, Aug. 1999, HongKong, Chin

Cutting tool tracking and recognition based on infrared and visual imaging systems using principal component analysis (PCA) and discrete wavelet transform (DWT) combined with neural networks

The implementation of computerised condition monitoring systems for the detection cutting tools’ correct installation and fault diagnosis is of a high importance in modern manufacturing industries. The primary function of a condition monitoring system is to check the existence of the tool before starting any machining process and ensure its health during operation. The aim of this study is to assess the detection of the existence of the tool in the spindle and its health (i.e. normal or broken) using infrared and vision systems as a non-contact methodology. The application of Principal Component Analysis (PCA) and Discrete Wavelet Transform (DWT) combined with neural networks are investigated using both types of data in order to establish an effective and reliable novel software program for tool tracking and health recognition. Infrared and visual cameras are used to locate and track the cutting tool during the machining process using a suitable analysis and image processing algorithms. The capabilities of PCA and Discrete Wavelet Transform (DWT) combined with neural networks are investigated in recognising the tool’s condition by comparing the characteristics of the tool to those of known conditions in the training set. The experimental results have shown high performance when using the infrared data in comparison to visual images for the selected image and signal processing algorithms

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

Background:Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Results:Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ~20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. Conclusions:We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents

Metabonomics and Intensive Care

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency medicine 2016. Other selected articles can be found online at http://www.biomedcentral.com/collections/annualupdate2016. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901

Differential expression analysis with global network adjustment

<p>Background: Large-scale chromosomal deletions or other non-specific perturbations of the transcriptome can alter the expression of hundreds or thousands of genes, and it is of biological interest to understand which genes are most profoundly affected. We present a method for predicting a gene’s expression as a function of other genes thereby accounting for the effect of transcriptional regulation that confounds the identification of genes differentially expressed relative to a regulatory network. The challenge in constructing such models is that the number of possible regulator transcripts within a global network is on the order of thousands, and the number of biological samples is typically on the order of 10. Nevertheless, there are large gene expression databases that can be used to construct networks that could be helpful in modeling transcriptional regulation in smaller experiments.</p> <p>Results: We demonstrate a type of penalized regression model that can be estimated from large gene expression databases, and then applied to smaller experiments. The ridge parameter is selected by minimizing the cross-validation error of the predictions in the independent out-sample. This tends to increase the model stability and leads to a much greater degree of parameter shrinkage, but the resulting biased estimation is mitigated by a second round of regression. Nevertheless, the proposed computationally efficient “over-shrinkage” method outperforms previously used LASSO-based techniques. In two independent datasets, we find that the median proportion of explained variability in expression is approximately 25%, and this results in a substantial increase in the signal-to-noise ratio allowing more powerful inferences on differential gene expression leading to biologically intuitive findings. We also show that a large proportion of gene dependencies are conditional on the biological state, which would be impossible with standard differential expression methods.</p> <p>Conclusions: By adjusting for the effects of the global network on individual genes, both the sensitivity and reliability of differential expression measures are greatly improved.</p&gt

Vitamins A & D Inhibit the Growth of Mycobacteria in Radiometric Culture

The role of vitamins in the combat of disease is usually conceptualized as acting by modulating the immune response of an infected, eukaryotic host. We hypothesized that some vitamins may directly influence the growth of prokaryotes, particularly mycobacteria. complex).Vitamins A and D cause dose-dependent inhibition of all three mycobacterial species studied. Vitamin A is consistently more inhibitory than vitamin D. The vitamin A precursor, β-carotene, is not inhibitory, whereas three vitamin A metabolites cause inhibition. Vitamin K has no effect. Vitamin E causes negligible inhibition in a single strain.We show that vitamin A, its metabolites Retinyl acetate, Retinoic acid and 13-cis Retinoic acid and vitamin D directly inhibit mycobacterial growth in culture. These data are compatible with the hypothesis that complementing the immune response of multicellular organisms, vitamins A and D may have heretofore unproven, unrecognized, independent and probable synergistic, direct antimycobacterial inhibitory activity

Observation of a red-blue detuning asymmetry in matter-wave superradiance

We report the first experimental observations of strong suppression of matter-wave superradiance using blue-detuned pump light and demonstrate a pump-laser detuning asymmetry in the collective atomic recoil motion. In contrast to all previous theoretical frameworks, which predict that the process should be symmetric with respect to the sign of the pump-laser detuning, we find that for condensates the symmetry is broken. With high condensate densities and red-detuned light, the familiar distinctive multi-order, matter-wave scattering pattern is clearly visible, whereas with blue-detuned light superradiance is strongly suppressed. In the limit of a dilute atomic gas, however, symmetry is restored.Comment: Accepted by Phys. Rev. Let

Successful Closed Reduction of a Dislocated Constrained Total Hip Arthroplasty: A Case Report and Literature Review

Many surgeons use acetabular components with constrained polyethylene liners to improve stability after total hip arthroplasty in patients with a history of hip dislocation. Surgical treatment is generally thought to be the only available option for the dislocated constrained liner. The success rate and clinical results of closed reduction for such patients is unclear. This report presents a case of a successful closed reduction of a dislocated constrained liner. Few papers have so far addressed closed reduction of a dislocated constrained liner. Furthermore, previous studies reported a variety of components. Publication of additional successful and unsuccessful case reports is therefore needed to help establish the optimal treatment protocol for a dislocated constrained liner

The filamentary structures in the CO emission toward the Milky Way disk

We present a statistical study of the filamentary structure orientation in the CO emission observations obtained in the Milky Way Imaging Scroll Painting survey in the range 25 (.)degrees . degrees 8 < l < 49 (.)degrees . degrees 7, |b| <= 1 (.)degrees degrees 25, and -100 < v(LSR) < 135 km s(-1). We found that most of the filamentary structures in the (CO)-C-12 and (CO)-C-13 emission do not show a global preferential orientation either parallel or perpendicular to the Galactic plane. However, we found ranges in Galactic longitude and radial velocity where the (CO)-C-12 and (CO)-C-13 filamentary structures are parallel to the Galactic plane. These preferential orientations are different from those found for the HI emission. We consider this an indication that the molecular structures do not simply inherit these properties from parental atomic clouds. Instead, they are shaped by local physical conditions, such as stellar feedback, magnetic fields, and Galactic spiral shocks