Prediction of MHC class I binding peptides with a new feature encoding technique

The recognition of specific peptides, bound to major histocompatibility complex (MHC) class I molecules, is of particular importance to the robust identification of T-cell epitopes and thus the successful design of protein-based vaccines. Here, we present a new feature amino acid encoding technique termed OEDICHO to predict MHC class I/peptide complexes. In the proposed method, we have combined orthonormal encoding (OE) and the binary representation of selected 10 best physicochemical properties of amino acids derived from Amino Acid Index Database (AAindex). We also have compared our method to current feature encoding techniques. The tests have been carried out on comparatively large Human Leukocyte Antigen (HLA)-A and HLA-B allele peptide binding datasets. Empirical results show that our amino acid encoding scheme leads to better classification performance on a standalone classifier.     

Cytogenetic effects of nine <Emphasis Type="Italic">Helichrysum</Emphasis> taxa in human lymphocytes culture

Helichrysum Mill. (Asteraceae) species have been used in folk medicine for thousands of years in the world. The in vitro cytogenetic effects in human lymphocytes of nine Helichrysum taxa used in Turkey folk medicine were investigated. Blood samples were obtained from healthy donors, non-smoking volunteers, which were incubated and exposed to increasing concentrations of methanol extracts of Helichrysum taxa (0.01, 0.05, 0.1, 0.5 and 1 mg/mL). The inhibitory effects of H. stoechas (L.) Moench subsp. barrelieri (Ten.) Nyman, H. armenium DC. subsp. armenium, H. armenium DC. subsp. araxinum (Kirp.) Takht., H. plicatum DC. subsp. plicatum, H. compactum Boiss. and H. artvinense P.H.Davis & Kupicha on the mitotic index and replication index indicate that these taxa can have genotoxic and mutagenic effects. They should therefore not be used freely in alternative medicine although their antiproliferative activity may suggest anticarcinogenic properties. Increase effects of H. stoechas subsp. barrelieri, H. armenium subsp. armenium, H. armenium subsp. araxinum, H. chasmolycicum P.H.Davis, H. plicatum subsp. plicatum, H. compactum and H. artvinense on the micronucleus rates showed that these taxa can have genotoxic and carcinogenic effects.     

Association between Gene Polymorphism of Manganese Superoxide Dismutase and Prostate Cancer Risk

Manganese superoxide dismutase (MnSOD) is the most effective antioxidant enzyme in mitochondria and protects cells from reactive oxygen species‐induced oxidative damage. The aim of this study was to investigate the association between MnSOD Ala‐9Val gene polymorphism and prostate cancer (PCa) risk in Turkish men with prostate cancer. 33 patients with PCa and 81 control individuals were included in the study. We observed an association between MnSOD Ala/Ala frequency and a higher PCa risk. In addition, we found that the increased risk of early‐onset PCa (under age of 65) in the men homozygous for Ala allele was higher than the men homozygous for Val allele. However, we determined that MnSOD Ala‐9Val genotype was not associated with the aggressiveness of the disease. The results of our study suggest that MnSOD Ala/Ala genotype may influence on early‐onset of PCa patients, but no effect on subsequent development of the disease in Turkish men. However, our study has a limitation that is small numbers of individuals for cases and controls. Therefore, the presented study limited our statistical power to fully investigate the gene polymorphism on cancer risk. © 2013 Wiley Periodicals, Inc. J BiochemMol Toxicol 27:213‐218, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.21472     

Identifying Topics in Microblogs Using Wikipedia

Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail.     

Studies of short-wavelength collective molecular motions in lipid bilayers using high resolution inelastic X-ray scattering

We summarize a series of experimental results made with the newly developed high resolution X-ray scattering (IXS) instrument on two pure lipid bilayers, including dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) in both gel and liquid crystal phases, and lipid bilayers containing cholesterol. By analyzing the IXS data based on the generalized three effective eigenmode model (GTEE), we obtain dispersion relations of the high frequency density oscillations (phonons) of lipid molecules in these bilayers. We then compare the dispersion relations of pure lipid bilayers of different chain lengths among themselves and the dispersion relations of pure lipid bilayers with those of the cholesterol containing bilayers. We also compare our experimental results with collective dynamics data generated by computer molecular dynamics (MD) simulations for dipalmitoylphosphatidylcholine (DPPC) in gel phase and DMPC in liquid crystal phase.     

Distributions of western flower thrips (Thysanoptera: Thripidae) and its predatory bug Orius niger (Hemiptera: Anthocoridae) assessed by coloured sticky traps and plant samplings in cotton

The capturing efficiency of four coloured (yellow, green, white and blue) sticky traps, placed at the top, middle and bottom strata of cotton plants, was tested for the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), and its predatory bug, Orius niger (Wolff) (Hemiptera: Anthocoridae), as well as spatial distributions of both insects on the plant in years 2006 and 2007. The white coloured trap was the most attractive to F. occidentalis and O. niger in the 2-year study. The blue coloured trap was the least attractive for Orius. The mean numbers of F. occidentalis and O. niger on the top plant parts (flowers and leaves) and in all coloured traps positioned on the upper parts of the plants were greater than those found in the lower two strata. Taylor's power law analysis showed that F. occidentalis and O. niger adults aggregated in the flowers or on the leaves. This study suggests that top flowers could be preferentially sampled to determine population densities of Frankliniella flower thrips and Orius species in cotton, and thus, sticky traps should be placed on the top level of plants. F. occidentalis: O. niger ratios in the flowers varied from 4 to 60 thrips per Orius adult in the three plant strata. This result may indicate that F. occidentalis experiences more predation from Orius.     

Phytoplankton distribution in the Caspian Sea during March 2001

Phytoplankton abundance, biomass and species composition of the Caspian Sea were evaluated by using samples collected from the Iranian (southern Caspian Sea) and southern Kazakhstan (eastern Caspian Sea) surface waters in March 2001. A total of 45 taxa were found in the samples (20 diatoms, 17 dinoflagellates and 8 others). Abundance and biomass of diatoms were high at the eastern stations, while dinoflagellates were dominant in terms of both biomass and abundance in the southern region. Average abundance and biomass were 40 000 ± 35 000 cell l⁻¹ and 580 ± 690 μg l⁻¹. The mean biomass value found here for the Middle and southern Caspian Sea in March are difficult to compare with the past due to limited information, but seems higher than previously registered values. Higher chlorophyll values were also apparent from the SeaWIFS images in 2001 compared to those in 1998. This is suggested to be due to decreased grazing of phytoplankton by zooplankton which is voraciously preyed by the recent invasive ctenophore Mnemiopsis leidyi.     

Material heterogeneity,microstructure, and microcracks demonstrate differential influence on crack initiation and propagation in cortical bone

The recent studies have shown that long-term bisphosphonate use may result in a number of mechanical alterations in the bone tissue including a reduction in compositional heterogeneity and an increase in microcrack density. There are limited number of experimental and computational studies in the literature that evaluated how these modifications affect crack initiation and propagation in cortical bone. Therefore, in this study, the entire crack growth process including initiation and propagation was simulated at the microscale by using the cohesive extended finite element method. Models with homogeneous and heterogeneous material properties (represented at the microscale capturing the variability in material property values and their distribution) as well as different microcrack density and microstructure were compared. The results showed that initiation fracture resistance was higher in models with homogeneous material properties compared to heterogeneous ones, whereas an opposite trend was observed in propagation fracture resistance. The increase in material heterogeneity level up to 10 different material property sets increased the propagation fracture resistance beyond which a decrease was observed while still remaining higher than the homogeneous material distribution. The simulation results also showed that the total osteonal area influenced crack propagation and the local osteonal area near the initial crack affected the crack initiation behavior. In addition, the initiation fracture resistance was higher in models representing bisphosphonate treated bone (low material heterogeneity, high microcrack density) compared to untreated bone models (high material heterogeneity, low microcrack density), whereas an opposite trend was observed at later stages of crack growth. In summary, the results demonstrated that tissue material heterogeneity, microstructure, and microcrack density influenced crack initiation and propagation differently. The findings also elucidate how possible modifications in material heterogeneity and microcrack density due to bisphosphonate treatment may influence the initiation and propagation fracture resistance of cortical bone.