Showing papers by "Kyungpook National University published in 2013"

Protein Analysis by Shotgun/Bottom-up Proteomics

Abstract: According to Genome Sequencing Project statistics (http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html), as of Feb 16, 2012, complete gene sequences have become available for 2816 viruses, 1117 prokaryotes, and 36 eukaryotes.1–2 The availability of full genome sequences has greatly facilitated biological research in many fields, and has greatly contributed to the growth of proteomics. Proteins are important because they are the direct bio-functional molecules in the living organisms. The term “proteomics” was coined from merging “protein” and “genomics” in the 1990s.3–4 As a post-genomic discipline, proteomics encompasses efforts to identify and quantify all the proteins of a proteome, including expression, cellular localization, interactions, post-translational modifications (PTMs), and turnover as a function of time, space and cell type, thus making the full investigation of a proteome more challenging than sequencing a genome. There are possibly 100,000 protein forms encoded by the approximate 20,235 genes of the human genome,5 and determining the explicit function of each form will be a challenge. The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis. Mass spectrometry has emerged as a core tool for large-scale protein analysis. In the past decade, there has been a rapid advance in the resolution, mass accuracy, sensitivity and scan rate of mass spectrometers used to analyze proteins. In addition, hybrid mass analyzers have been introduced recently (e.g. Linear Ion Trap-Orbitrap series6–7) which have significantly improved proteomic analysis. “Bottom-up” protein analysis refers to the characterization of proteins by analysis of peptides released from the protein through proteolysis. When bottom-up is performed on a mixture of proteins it is called shotgun proteomics,8–10 a name coined by the Yates lab because of its analogy to shotgun genomic sequencing.11 Shotgun proteomics provides an indirect measurement of proteins through peptides derived from proteolytic digestion of intact proteins. In a typical shotgun proteomics experiment, the peptide mixture is fractionated and subjected to LC-MS/MS analysis. Peptide identification is achieved by comparing the tandem mass spectra derived from peptide fragmentation with theoretical tandem mass spectra generated from in silico digestion of a protein database. Protein inference is accomplished by assigning peptide sequences to proteins. Because peptides can be either uniquely assigned to a single protein or shared by more than one protein, the identified proteins may be further scored and grouped based on their peptides. In contrast, another strategy, termed ‘top-down’ proteomics, is used to characterize intact proteins (Figure 1). The top-down approach has some potential advantages for PTM and protein isoform determination and has achieved notable success. Intact proteins have been measured up to 200 kDa,12 and a large scale study has identified more than 1,000 proteins by multi-dimensional separations from complex samples.13 However, the top-down method has significant limitations compared with shotgun proteomics due to difficulties with protein fractionation, protein ionization and fragmentation in the gas phase. By relying on the analysis of peptides, which are more easily fractionated, ionized and fragmented, shotgun proteomics can be more universally adopted for protein analysis. In fact, a hybrid of bottom-up and top-down methodologies and instrumentation has been introduced as middle-down proteomics.14 Essentially, middle-down proteomics analyzes larger peptide fragments than bottom-up proteomics, minimizing peptide redundancy between proteins. Additionally the large peptide fragments yield similar advantages as top-down proteomics, such as gaining further insight into post-translational modifications, without the analytical challenges of analyzing intact proteins. Shotgun proteomics has become a workhorse for the analysis of proteins and their modifications and will be increasingly combined with top-down methods in the future. Figure 1 Proteomic strategies: bottom-up vs. top-down vs. middle-down. The bottom-up approach analyzes proteolytic peptides. The top-down method measures the intact proteins. The middle-down strategy analyzes larger peptides resulted from limited digestion or ... In the past decade shotgun proteomics has been widely used by biologists for many different research experiments, advancing biological discoveries. Some applications include, but are not limited to, proteome profiling, protein quantification, protein modification, and protein-protein interaction. There have been several reviews nicely summarizing mass spectrometry history,15 protein quantification with mass spectrometry,16 its biological applications,5,17–26 and many recent advances in methodology.27–32 In this review, we try to provide a full and updated survey of shotgun proteomics, including the fundamental techniques and applications that laid the foundation along with those developed and greatly improved in the past several years.

First result from the Alpha Magnetic Spectrometer on the International Space Station: precision measurement of the positron fraction in primary cosmic rays of 0.5-350 GeV.

Abstract: A precision measurement by the Alpha Magnetic Spectrometer on the International Space Station of the positron fraction in primary cosmic rays in the energy range from 0.5 to 350 GeV based on 6.8 × 10(6) positron and electron events is presented. The very accurate data show that the positron fraction is steadily increasing from 10 to ∼ 250 GeV, but, from 20 to 250 GeV, the slope decreases by an order of magnitude. The positron fraction spectrum shows no fine structure, and the positron to electron ratio shows no observable anisotropy. Together, these features show the existence of new physical phenomena.

Surface modification of TiO2 photocatalyst for environmental applications

Abstract: This paper reviews recent studies on the semiconductor photocatalysis based on surface-modified TiO2 of which application is mainly focused on environmental remediation. TiO2 photocatalysis that is based on the photoinduced interfacial charge transfer has been extensively studied over the past four decades. A great number of modification methods of semiconductor photocatalysts have been developed and investigated to accelerate the photoconversion, to enable the absorption of visible light, or to alter the reaction mechanism to control the products and intermediates. In this regard, various modification methods of TiO2 are classified according to the kind of surface modifiers (metal-loading, impurity doping, inorganic adsorbates, polymer coating, dye-sensitization, charge transfer complexation) and their effects on photocatalytic reaction mechanism and kinetics are discussed in detail. Modifying TiO2 in various ways not only changes the mechanism and kinetics under UV irradiation but also introduces visible light activity that is absent with pure TiO2. Each modification method influences the photocatalytic activity and mechanism in a way different from others and the observed modification effects are often different depending on the test substrates and conditions even for the same modification method. Better understanding of the modification effects on TiO2 photocatalysis is necessary to obtain reliable results, to assess the photoconversion efficiency more quantitatively, and to further improve the modification methods.

LipidBlast in silico tandem mass spectrometry database for lipid identification

Abstract: Current tandem mass spectral libraries for lipid annotations in metabolomics are limited in size and diversity. We provide a freely available computer-generated tandem mass spectral library of 212,516 spectra covering 119,200 compounds from 26 lipid compound classes, including phospholipids, glycerolipids, bacterial lipoglycans and plant glycolipids. We show platform independence by using tandem mass spectra from 40 different mass spectrometer types including low-resolution and high-resolution instruments.

Brivanib Versus Sorafenib As First-Line Therapy in Patients With Unresectable, Advanced Hepatocellular Carcinoma: Results From the Randomized Phase III BRISK-FL Study

Abstract: Purpose Brivanib is a dual inhibitor of vascular-endothelial growth factor and fibroblast growth factor receptors that are implicated in the pathogenesis of hepatocellular carcinoma (HCC). Our multinational, randomized, double-blind, phase III trial compared brivanib with sorafenib as first-line treatment for HCC. Patients and Methods Advanced HCC patients who had no prior systemic therapy were randomly assigned (ratio, 1:1) to receive sorafenib 400 mg twice daily orally (n = 578) or brivanib 800 mg once daily orally (n = 577). Primary end point was overall survival (OS). Secondary end points included time to progression (TTP), objective response rate (ORR), disease control rate (DCR) based on modified Response Evaluation Criteria in Solid Tumors (mRECIST), and safety. Results The primary end point of OS noninferiority for brivanib versus sorafenib in the per-protocol population (n = 1,150) was not met (hazard ratio [HR], 1.06; 95.8% CI, 0.93 to 1.22), based on the prespecified margin (upper CI limit for ...

Observation of a new boson with mass near 125 GeV in pp collisions at $ \sqrt{s}=7 $ and 8 TeV

Abstract: A detailed description is reported of the analysis used by the CMS Collaboration in the search for the standard model Higgs boson in pp collisions at the LHC, which led to the observation of a new boson. The data sample corresponds to integrated luminosities up to 5.1 inverse femtobarns at sqrt(s) = 7 TeV, and up to 5.3 inverse femtobarns at sqrt(s) = 8 TeV. The results for five Higgs boson decay modes gamma gamma, ZZ, WW, tau tau, and bb, which show a combined local significance of 5 standard deviations near 125 GeV, are reviewed. A fit to the invariant mass of the two high resolution channels, gamma gamma and ZZ to 4 ell, gives a mass estimate of 125.3 +/- 0.4 (stat) +/- 0.5 (syst) GeV. The measurements are interpreted in the context of the standard model Lagrangian for the scalar Higgs field interacting with fermions and vector bosons. The measured values of the corresponding couplings are compared to the standard model predictions. The hypothesis of custodial symmetry is tested through the measurement of the ratio of the couplings to the W and Z bosons. All the results are consistent, within their uncertainties, with the expectations for a standard model Higgs boson.

Study of e + e - →π + π - J/ψ and Observation of a Charged Charmoniumlike State at Belle

Abstract: The cross section for ee+ e- → π+ π- J/ψ between 3.8 and 5.5 GeV is measured with a 967 fb(-1) data sample collected by the Belle detector at or near the Υ(nS) (n = 1,2,…,5) resonances. The Y(4260) state is observed, and its resonance parameters are determined. In addition, an excess of π+ π- J/ψ production around 4 GeV is observed. This feature can be described by a Breit-Wigner parametrization with properties that are consistent with the Y(4008) state that was previously reported by Belle. In a study of Y(4260) → π+ π- J/ψ decays, a structure is observed in the M(π(±)J/ψ) mass spectrum with 5.2σ significance, with mass M = (3894.5 ± 6.6 ± 4.5) MeV/c2 and width Γ = (63 ± 24 ± 26) MeV/c2, where the errors are statistical and systematic, respectively. This structure can be interpreted as a new charged charmoniumlike state.

Landslide susceptibility mapping using certainty factor, index of entropy and logistic regression models in GIS and their comparison at Mugling–Narayanghat road section in Nepal Himalaya

Abstract: Landslide susceptibility maps are vital for disaster management and for planning development activities in the mountainous country like Nepal. In the present study, landslide susceptibility assessment of Mugling–Narayanghat road and its surrounding area is made using bivariate (certainty factor and index of entropy) and multivariate (logistic regression) models. At first, a landslide inventory map was prepared using earlier reports and aerial photographs as well as by carrying out field survey. As a result, 321 landslides were mapped and out of which 241 (75 %) were randomly selected for building landslide susceptibility models, while the remaining 80 (25 %) were used for validating the models. The effectiveness of landslide susceptibility assessment using GIS and statistics is based on appropriate selection of the factors which play a dominant role in slope stability. In this case study, the following landslide conditioning factors were evaluated: slope gradient; slope aspect; altitude; plan curvature; lithology; land use; distance from faults, rivers and roads; topographic wetness index; stream power index; and sediment transport index. These factors were prepared from topographic map, drainage map, road map, and the geological map. Finally, the validation of landslide susceptibility map was carried out using receiver operating characteristic (ROC) curves. The ROC plot estimation results showed that the susceptibility map using index of entropy model with AUC value of 0.9016 has highest prediction accuracy of 90.16 %. Similarly, the susceptibility maps produced using logistic regression model and certainty factor model showed 86.29 and 83.57 % of prediction accuracy, respectively. Furthermore, the ROC plot showed that the success rate of all the three models performed more than 80 % accuracy (i.e. 89.15 % for IOE model, 89.10 % for LR model and 87.21 % for CF model). Hence, it is concluded that all the models employed in this study showed reasonably good accuracy in predicting the landslide susceptibility of Mugling–Narayanghat road section. These landslide susceptibility maps can be used for preliminary land use planning and hazard mitigation purpose.

Study of the Mass and Spin-Parity of the Higgs Boson Candidate via Its Decays to Z Boson Pairs

Abstract: A study is presented of the mass and spin-parity of the new boson recently observed at the LHC at a mass near 125 GeV. An integrated luminosity of 17.3 fb^(-1), collected by the CMS experiment in proton-proton collisions at center-of-mass energies of 7 and 8 TeV, is used. The measured mass in the ZZ channel, where both Z bosons decay to e or μ pairs, is 126.2±0.6(stat)±0.2(syst) GeV. The angular distributions of the lepton pairs in this channel are sensitive to the spin-parity of the boson. Under the assumption of spin 0, the present data are consistent with the pure scalar hypothesis, while disfavoring the pure pseudoscalar hypothesis.

Multicenter Analysis of Risk Factors for Anastomotic Leakage After Laparoscopic Rectal Cancer Excision The Korean Laparoscopic Colorectal Surgery Study Group

Abstract: Objective:To assess the risk factors for clinical anastomotic leakage (AL) in patients undergoing laparoscopic surgery for rectal cancer.Background:Little data are available about risk factors for AL after laparoscopic rectal cancer resection.Methods:This was a retrospective analysis of 1609 patient

Turboiso: towards ultrafast and robust subgraph isomorphism search in large graph databases

Abstract: Given a query graph q and a data graph g, the subgraph isomorphism search finds all occurrences of q in g and is considered one of the most fundamental query types for many real applications While this problem belongs to NP-hard, many algorithms have been proposed to solve it in a reasonable time for real datasets However, a recent study has shown, through an extensive benchmark with various real datasets, that all existing algorithms have serious problems in their matching order selection Furthermore, all algorithms blindly permutate all possible mappings for query vertices, often leading to useless computations In this paper, we present an efficient and robust subgraph search solution, called TurboISO, which is turbo-charged with two novel concepts, candidate region exploration and the combine and permute strategy (in short, Comb/Perm) The candidate region exploration identifies on-the-fly candidate subgraphs (ie, candidate regions), which contain embeddings, and computes a robust matching order for each candidate region explored The Comb/Perm strategy exploits the novel concept of the neighborhood equivalence class (NEC) Each query vertex in the same NEC has identically matching data vertices During subgraph isomorphism search, Comb/Perm generates only combinations for each NEC instead of permutating all possible enumerations Thus, if a chosen combination is determined to not contribute to a complete solution, all possible permutations for that combination will be safely pruned Extensive experiments with many real datasets show that TurboISO consistently and significantly outperforms all competitors by up to several orders of magnitude

Lifelong Bilingualism Maintains Neural Efficiency for Cognitive Control in Aging

Abstract: Recent behavioral data have shown that lifelong bilingualism can maintain youthful cognitive control abilities in aging Here, we provide the first direct evidence of a neural basis for the bilingual cognitive control boost in aging Two experiments were conducted, using a perceptual task-switching paradigm, including a total of 110 participants In Experiment 1, older adult bilinguals showed better perceptual switching performance than their monolingual peers In Experiment 2, younger and older adult monolinguals and bilinguals completed the same perceptual task-switching experiment while functional magnetic resonance imaging (fMRI) was performed Typical age-related performance reductions and fMRI activation increases were observed However, like younger adults, bilingual older adults outperformed their monolingual peers while displaying decreased activation in left lateral frontal cortex and cingulate cortex Critically, this attenuation of age-related over-recruitment associated with bilingualism was directly correlated with better task-switching performance In addition, the lower blood oxygenation level-dependent response in frontal regions accounted for 82% of the variance in the bilingual task-switching reaction time advantage These results suggest that lifelong bilingualism offsets age-related declines in the neural efficiency for cognitive control processes

Measurement of the Bs0→μ+μ- branching fraction and search for B0→μ+μ- with the CMS experiment

Abstract: Results are presented from a search for the rare decays B0s→μ+μ− and B0→μ+μ− in pp collisions at s√=7 and 8 TeV, with data samples corresponding to integrated luminosities of 5 and 20 fb−1, respectively, collected by the CMS experiment at the LHC. An unbinned maximum-likelihood fit to the dimuon invariant mass distribution gives a branching fraction B(B0s→μ+μ−)=(3.0+1.0−0.9)×10−9, where the uncertainty includes both statistical and systematic contributions. An excess of B0s→μ+μ− events with respect to background is observed with a significance of 4.3 standard deviations. For the decay B0→μ+μ− an upper limit of B(B0→μ+μ−)<1.1×10−9 at the 95% confidence level is determined. Both results are in agreement with the expectations from the standard model.

Search for top-squark pair production in the single-lepton final state in pp collisions at √s=8 TeV

Abstract: This paper presents a search for the pair production of top squarks in events with a single isolated electron or muon, jets, large missing transverse momentum, and large transverse mass. The data sample corresponds to an integrated luminosity of 19.5 inverse femtobarns of pp collisions collected in 2012 by the CMS experiment at the LHC at a center-of-mass energy of sqrt(s) = 8 TeV. No significant excess in data is observed above the expectation from standard model processes. The results are interpreted in the context of supersymmetric models with pair production of top squarks that decay either to a top quark and a neutralino or to a bottom quark and a chargino. For small mass values of the lightest supersymmetric particle, top-squark mass values up to around 650 GeV are excluded.

Evaluation of the Association between Persistent Organic Pollutants (POPs) and Diabetes in Epidemiological Studies: A National Toxicology Program Workshop Review

Abstract: BACKGROUND: Diabetes is a major threat to public health in the United States and worldwide. Understanding the role of environmental chemicals in the development or progression of diabetes is an emerging issue in environmental health. OBJECTIVE: We assessed the epidemiologic literature for evidence of associations between persistent organic pollutants (POPs) and type 2 diabetes. METHODS: Using a PubMed search and reference lists from relevant studies or review articles, we identified 72 epidemiological studies that investigated associations of persistent organic pollutants (POPs) with diabetes. We evaluated these studies for consistency, strengths and weaknesses of study design (including power and statistical methods), clinical diagnosis, exposure assessment, study population characteristics, and identification of data gaps and areas for future research. CONCLUSIONS: Heterogeneity of the studies precluded conducting a meta-analysis, but the overall evidence is sufficient for a positive association of some organochlorine POPs with type 2 diabetes. Collectively, these data are not sufficient to establish causality. Initial data mining revealed that the strongest positive correlation of diabetes with POPs occurred with organochlorine compounds, such as trans-nonachlor, dichlorodiphenyldichloroethylene (DDE), polychlorinated biphenyls (PCBs), and dioxins and dioxin-like chemicals. There is less indication of an association between other nonorganochlorine POPs, such as perfluoroalkyl acids and brominated compounds, and type 2 diabetes. Experimental data are needed to confirm the causality of these POPs, which will shed new light on the pathogenesis of diabetes. This new information should be considered by governmental bodies involved in the regulation of environmental contaminants.

Surface electronic structure of the topological Kondo-insulator candidate correlated electron system SmB6.

Abstract: The Kondo insulator SmB6 has long been known to exhibit low-temperature transport anomalies whose origin is of great interest. Here we uniquely access the surface electronic structure of the anomalous transport regime by combining state-of-the-art laser and synchrotron-based angle-resolved photoemission techniques. We observe clear in-gap states (up to ~4 meV), whose temperature dependence is contingent on the Kondo gap formation. In addition, our observed in-gap Fermi surface oddness tied with the Kramers' point topology, their coexistence with the two-dimensional transport anomaly in the Kondo hybridization regime, as well as their robustness against thermal recycling, taken together, collectively provide strong evidence for protected surface metallicity with a Fermi surface whose topology is consistent with the theoretically predicted topological Fermi surface. Our observations of systematic surface electronic structure provide the fundamental electronic parameters for the anomalous Kondo ground state of correlated electron material SmB6.

Induction of Drought Stress Resistance by Multi-Functional PGPR Bacillus licheniformis K11 in Pepper.

Abstract: Drought stress is one of the major yield affecting factor for pepper plant. The effects of PGPRs were analyzed in relation with drought resistance. The PGPRs inoculated pepper plants tolerate the drought stress and survived as compared to non-inoculated pepper plants that died after 15 days of drought stress. Variations in protein and RNA accumulation patterns of inoculated and non-inoculated pepper plants subjected to drought conditions for 10 days were confirmed by two dimensional polyacrylamide gel electrophoresis (2D-PAGE) and differential display PCR (DD-PCR), respectively. A total of six differentially expressed stress proteins were identified in the treated pepper plants by 2D-PAGE. Among the stress proteins, specific genes of Cadhn, VA, sHSP and CaPR-10 showed more than a 1.5-fold expressed in amount in B. licheniformis K11-treated drought pepper compared to untreated drought pepper. The changes in proteins and gene expression patterns were attributed to the B. licheniformis K11. Accordingly, auxin and ACC deaminase producing PGPR B. licheniformis K11 could reduce drought stress in drought affected regions without the need for overusing agrochemicals and chemical fertilizer. These results will contribute to the development of a microbial agent for organic farming by PGPR.

Searches for long-lived charged particles in pp collisions at sqrt(s) = 7 and 8 TeV

Abstract: Results of searches for heavy stable charged particles produced in pp collisions at sqrt(s) = 7 and 8 TeV are presented corresponding to an integrated luminosity of 5.0 inverse femtobarns and 18.8 inverse femtobarns, respectively. Data collected with the CMS detector are used to study the momentum, energy deposition, and time-of-flight of signal candidates. Leptons with an electric charge between e/3 and 8e, as well as bound states that can undergo charge exchange with the detector material, are studied. Analysis results are presented for various combinations of signatures in the inner tracker only, inner tracker and muon detector, and muon detector only. Detector signatures utilized are long time-of-flight to the outer muon system and anomalously high (or low) energy deposition in the inner tracker. The data are consistent with the expected background, and upper limits are set on the production cross section of long-lived gluinos, scalar top quarks, and scalar tau leptons, as well as pair produced long-lived leptons. Corresponding lower mass limits, ranging up to 1322 GeV for gluinos, are the most stringent to date.

Supplementation of Lactobacillus Curvatus HY7601 and Lactobacillus Plantarum KY1032 in Diet-Induced Obese Mice Is Associated With Gut Microbial Changes and Reduction in Obesity

Abstract: Objective To investigate the functional effects of probiotic treatment on the gut microbiota, as well as liver and adipose gene expression in diet-induced obese mice

Tumour-infiltrating CD8+ lymphocytes as an independent predictive factor for pathological complete response to primary systemic therapy in breast cancer

Abstract: Tumour-infiltrating lymphocytes (TILs) are known to be associated with response to primary systemic therapy (PST) in breast cancer. This study was conducted to assess the association of TIL subsets with pathological complete response (pCR) after PST in breast cancer in relation to breast cancer subtype, breast cancer stem cell (BCSC) phenotype and epithelial–mesenchymal transition (EMT). The pre-chemotherapeutic biopsy specimens of 153 breast cancer patients who underwent surgical resection after anthracycline- or anthracycline/taxane-based PST were analysed. TIL subsets (CD4+, CD8+, and FOXP3+ TILs), BCSC phenotype, and the expression of EMT markers were evaluated by immunohistochemistry and were correlated with pCR after PST. Infiltration of CD4+ and CD8+ T lymphocytes was closely correlated with BCSC phenotype and EMT. High levels of CD4+, CD8+, and FOXP3+ TILs were associated with pCR, and CD8+ TILs were found to be an independent predictive factor for pCR. In addition, CD8+ TILs were associated with pCR irrespective of breast cancer subtype, CD44+/CD24− phenotype, EMT, and chemotherapeutic regimen in subgroup analyses. These findings indicate that CD8+ cytotoxic T lymphocytes are a key component of TILs associated with chemo-response and can be used as a reliable predictor of response to anthracycline- or anthracycline/taxane-based PST in breast cancer.