A Consistency-Based Feature Selection Method Allied with Linear SVMs for HIV-1 Protease Cleavage Site Prediction

Background

Predicting type-1 Human Immunodeficiency Virus (HIV-1) protease cleavage site in protein molecules and determining its specificity is an important task which has attracted considerable attention in the research community. Achievements in this area are expected to result in effective drug design (especially for HIV-1 protease inhibitors) against this life-threatening virus. However, some drawbacks (like the shortage of the available training data and the high dimensionality of the feature space) turn this task into a difficult classification problem. Thus, various machine learning techniques, and specifically several classification methods have been proposed in order to increase the accuracy of the classification model. In addition, for several classification problems, which are characterized by having few samples and many features, selecting the most relevant features is a major factor for increasing classification accuracy.

Results

We propose for HIV-1 data a consistency-based feature selection approach in conjunction with recursive feature elimination of support vector machines (SVMs). We used various classifiers for evaluating the results obtained from the feature selection process. We further demonstrated the effectiveness of our proposed method by comparing it with a state-of-the-art feature selection method applied on HIV-1 data, and we evaluated the reported results based on attributes which have been selected from different combinations.

Conclusion

Applying feature selection on training data before realizing the classification task seems to be a reasonable data-mining process when working with types of data similar to HIV-1. On HIV-1 data, some feature selection or extraction operations in conjunction with different classifiers have been tested and noteworthy outcomes have been reported. These facts motivate for the work presented in this paper.

Software availability

The software is available at http://ozyer.etu.edu.tr/c-fs-svm.rar.The software can be downloaded at esnag.etu.edu.tr/software/hiv_cleavage_site_prediction.rar; you will find a readme file which explains how to set the software in order to work.     

Identification of a novel function for the FtsL cell division protein from Escherichia coli K12

Analysis of the essential cell division protein FtsL demonstrates the partial conservation of a cysteine-pair within the trans-membrane region which itself is flanked by histidine-pairs in the cytosol and periplasm. Similar arrangements of such amino acids are seen in proteins known to transport/bind metal ions in biological systems. Heterologous expression of ftsL in Escherichia coli K12 confers a Zn(II)-sensitive phenotype and alteration of the candidate metal-ion binding residues cysteine or histidine substantially alters this phenotype. Whilst the cysteine/histidine replacement derivatives of ftsL were able to complement an otherwise ftsL-null strain, the derivative carrying ftsL lacking the cysteine pair was sensitive to raised metal-ion concentrations in the media. We show that ftsL can confer a metal-ion sensitive phenotype and that trans-membrane cysteine residues play a role in FtsL function in elevated metal-ion concentrations.     

One-Stage vs. Two-Stage Brachio-Basilic Arteriovenous Fistula for Dialysis Access: A Systematic Review and a Meta-Analysis

Introduction

A brachiobasilic arteriovenous fistula (BB-AVF) can provide access for haemodialysis in patients who are not eligible for a more superficial fistula. However, it is unclear whether one- or two-stage BB-AVF is the best option for patients.

Aim

To systematically assess the difference between both procedures in terms of access maturation, patency and postoperative complications.

Methods

Online search for randomised controlled trials (RCTs) and observational studies that compared the one-stage versus the two-stage technique for creating a BB-AVF.

Results

Eight studies were included (849 patients with 859 fistulas), 366 created using a one-stage technique, while 493 in a two-stage approach. There was no statistically significant difference between the two groups in the rate of successful maturation (Pooled risk ratio = 0.95 [0.82, 1.11], P = 0.53). Similarly, the incidence of postoperative haematoma (Pooled risk ratio = 0.73 [0.34, 1.58], P = 0.43), wound infection (Pooled risk ratio = 0.77 [0.35, 1.68], P = 0.51) and steal syndrome (Pooled risk ratio = 0.65 [0.27, 1.53], P = 0.32) were statistically comparable.

Conclusion

Although more studies seem to favour the two-stage BVT approach, evidence in the literature is not sufficient to draw a final conclusion as the difference between the one-stage and the two-stage approaches for creation of a BB-AVF is not statistically significant in terms of the overall maturation rate and postoperative complications. Patency rates (primary, assisted primary and secondary) were comparable in the majority of studies. Large randomised properly conducted trials with superior methodology and adequate sub-group analysis are needed before making a final recommendation.     

Effect of Misalignment between Successive Corneal Videokeratography Maps on the Repeatability of Topography Data

Purpose

To improve the reliability of corneal topographic data through the development of a method to estimate the magnitude of misalignment between successive corneal videokeratography (VK) maps and eliminate the effect of misalignment on the repeatability of topography data.

Methods

Anterior and posterior topography maps were recorded twice for 124 healthy eyes of 124 participants using a Pentacam, and the repeatability of measurements was assessed by calculating the differences in elevation between each two sets of data. The repeatability of measurements was re-assessed following the determination of the magnitude of misalignment components (translational displacements: x₀, y₀ and z₀, and rotational displacements: α, β and γ) between each two data sets and using them to modify the second data set within each pair based on an Iterative Closest Point (ICP) algorithm. The method simultaneously considered the anterior and posterior maps taken for the same eye since they were assumed to have the same set of misalignment components. A new parameter, named Combined Misalignment parameter (CM), has been developed to combine the effect of all six misalignment components on topography data and so enable study of the association between misalignment and the data repeatability test results.

Results

The repeatability tests resulted in average root mean square (RMS) differences in elevation data of 8.46±2.75 μm before ICP map matching when simultaneously considering anterior and posterior surfaces. With map matching and misalignment correction, the differences decreased to 7.28±2.58 μm (P = 0.00). When applied to only the anterior maps, misalignment correction led to a more pronounced reduction in elevation data differences from 4.58±1.84 μm to 2.97±1.29 μm (P = 0.00). CM was found to be associated with the repeatability error (P = 0.00), with posterior maps being responsible for most of the error due to their relatively lower accuracy compared to anterior maps.

Conclusions

The ICP algorithm can be used to estimate, and effectively correct for, the potential misalignment between successive corneal videokeratography maps.     

NPY, ET-1, and Ang II nuclear receptors in human endocardial endothelial cells

Neuropeptide Y (NPY), endothelin-1 (ET-1), and angiotensin II (Ang II) are peptides that are known to play many important roles in cardiovascular homeostasis. The physiological actions of these peptides are thought to be primarily mediated by plasma membrane receptors that belong to the G-protein-coupled receptor superfamily. However, there is increasing evidence that suggests the existence of functional G-protein-coupled receptors at the level of the nucleus and that the nucleus could be a cell within a cell. Here, we review our work showing the presence in the nucleus of the NPY Y(1) receptor, the ET(A) and ET(B) receptors, as well as the AT(1) and AT(2) receptors and their respective ligands. This work was carried out in 20-week-old fetal human endocardial endothelial cells. Our results demonstrate that nuclear Y1, AT(1), and ET(A) receptors modulate nuclear calcium in these cells.     

Continuous measurement of galactolipid hydrolysis by pancreatic lipolytic enzymes using the pH-stat technique and a medium chain monogalactosyl diglyceride as substrate

Galactolipids are the main lipids from plants and galactolipases play a major role in their metabolism. These enzymes were however poorly studied so far and only few assays have been developed. A specific and continuous galactolipase assay using synthetic medium chain monogalactosyl diacylglycerol (MGDG) as substrate was developed using the pH-stat technique and recombinant human (rHPLRP2) and guinea pig (rGPLRP2) pancreatic lipase-related protein 2 as model enzymes. PLRP2s are the main enzymes involved in the digestion of galactolipids in the gastrointestinal tract. Monogalactosyl di-octanoylglycerol was mixed with bile salt solutions by sonication to form a micellar substrate before launching the assay. The nature of the bile salt and the bile salt to MGDG ratio were found to significantly affect the rate of MGDG hydrolysis by rHPLRP2 and rGPLRP2. The maximum galactolipase activity of both enzymes was recorded with sodium deoxycholate (NaDC) and at a NaDC to MGDG ratio of 1.33 and at basic pH values (8.0–9.0). The maximum rates of hydrolysis were obtained using a MGDG concentration of 10^− 2 M and calcium chloride was found to be not necessary to obtain the maximum of activity. Under these conditions, the maximum turnovers of rGPLRP2 and rHPLRP2 on mixed NaDC/MGDG micelles were found to be 8000 ± 500 and 2800 ± 60 μmol/min/mg (U/mg), respectively. These activities are in the same order of magnitude as the activities on triglycerides of lipases and they are the highest specific activities ever reported for galactolipases. For the sake of comparison, the hydrolysis of mixed bile salt/MGDG micelles was also tested using other pancreatic lipolytic enzymes and only native and recombinant human carboxyl ester hydrolase were found to display significant but lower activities (240 ± 17 and 432 ± 62 U/mg, respectively) on MGDG.     

Linalool decreases HepG2 viability by inhibiting mitochondrial complexes I and II, increasing reactive oxygen species and decreasing ATP and GSH levels

Coriander is used as an appetizer, a common food seasoning in Mediterranean dishes, and a remedy for many ailments. In this study we tested the biochemical effect of its essential oil components, in particular linalool, its main component. The oil extract was prepared by hydro-distillation of coriander seeds. The various components were identified by gas chromatography coupled to mass spectroscopy. The effect of the various oil components on the viability of different cell lines (HepG2, Caco2, NIH3t3, MCF7 and Hek293) was examined using MTT assay. Linalool was the most potent and HepG2 cells the most sensitive. A 50% and 100% decrease in the viability of HepG2 was obtained at 0.4 μM and 2 μM linalool, respectively. Whereas none of the other components exerted a significant effect at concentrations lower than 50 μM, myrcene and nerolidol, the structural analogues of linalool, were more potent at 100 μM than the other components decreasing HepG2 viability to 26%. The biochemical effect of linalool on mitochondria isolated from HepG2 showed a concentration-dependent inhibition in complexes I and II activities of the respiratory chain, and a time-dependent decrease in ATP level. In addition, a time-dependent decrease in glutathione (GSH) level and in the reduction of nitroblue tetrazolium was obtained, indicating increase in reactive oxygen species (ROS) generation. Pretreatment with the antioxidants: N-acetyl cysteine (2 mM), Trolox (100 μM) and different flavonoids (50 μM) was partially protective against the linalool-induced cell death; the most effective response was that of rutin and apigenin which restored 91% of HepG2 viability. We hereby report a decrease in cell viability of HepG2 cells by linalool and identify the mitochondria as one possible target for its site of action, inhibiting complexes I and II and decreasing ATP. In addition linalool increased ROS generation and decreased GSH level.     

Tumor necrosis factor alpha down-regulates the Na+-K+ ATPase and the Na+-K+2Cl- cotransporter in the kidney cortex and medulla

The effect of TNF-alpha on the renal Na+-K+ pump and the Na+-K+2Cl- cotransporter was investigated in the rat. Animals were injected with the cytokine, and 4h later, a homogenate from the cortical and medullary tissues was prepared and used to assay the activity of the Na+-K+ ATPase and the protein expression of the pump and symporter. TNF-alpha reduced the activity and expression of the pump in both cortex and medulla, and its effect disappeared when animals were pre-treated with indomethacin, suggesting that TNF-alpha acts via PGE2. Higher levels of PGE2 were detected by enzyme immunoassay, in kidney tissues isolated from rats treated with PGE2, thus confirming this hypothesis. The cytokine also down-regulated the Na+-K+2Cl- cotransporter but this effect was not abrogated by indomethacin. PGE2, injected into animals, exerted a dose-dependent effect. Low doses did not have any effect on the two transporters in the cortex while high doses inhibited and down-regulated the pump and up-regulated the cotransporter. In the medulla low doses increased the activity and expression of the pump but down-regulated the cotransporter while high doses exerted an exactly opposite effect on the two transporters. It was concluded that the effect of TNF-alpha on the pump is mediated via PGE2 which is released at relatively high doses. The effect of the cytokine on the cotransporter is, however, independent of PGE2.