bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of HLA‐A2‐restricted immunogenic peptides derived from a xenogenic porcine major histocompatibility complex
Authors: Park Chan‐Su , Im Sun‐A , Song Sukgil , Kim Kyungjae , Lee Chong‐Kil 
Published: July 2014

AbstractBackgroundLittle information is available regarding the precise swine leukocyte antigen (SLA)‐derived immunogenic peptides that are presented in the context of human HLA molecules. Here, we identified SLA‐derived immunogenic peptides that are presented in association with human HLA‐A2 molecule.MethodsThe SLA‐derived peptides that bind to HLA‐A*0201, a representative of the A2 supertype, were predicted using a computer‐assisted algorithm. The candidate peptides were synthesized, and the stabilities of complexes formed between peptides and HLA‐A*0201 were compared using major histocompatibility complex (MHC) stabilization assays. The cytotoxic T lymphocyte (CTL)‐inducing activity of the selected peptides was examined in HLA‐A*0201‐transgenic mice.ResultsAmong 15 candidate peptides synthesized, two peptides, peptide‐35 (YLGPDGLLL) and peptide‐43 (TLICHVDSI), were selected to have high affinity and stability with HLA‐A*0201. Examination of the CTL‐inducing activity of the two peptides in HLA‐A*0201‐transgenic mice showed that immunization with peptide‐35, but not peptide‐43, elicited potent CD8‐specific CTL responses. The Peptide‐35 is present in non‐polymorphic α2 domains of 34 SLA‐1 alleles, 18 SLA‐2 alleles, and 1 SLA‐3 allele.ConclusionThis study identifies an immunogenic HLA‐A*0201‐restricted epitope derived from the SLA, which may be valuable for the development of epitope‐specific immunoregulation strategies.
Virtual Data Mart for Measuring Organizational Achievement Using Data Virtualization Technique (KPIVDM)
Authors: Hameed Mousa Ayad , Shiratuddin Norshuhada , Abu Bakar Muhamad Shahbani 
Published: July 2014

Currently in the dynamic environment, organizations are confronted with new and growingly vital decisions which can impact their very survival. In fact, these demands are increasing the pressure on Information Technology in order to ensure that data will be delivered properly at the right time and faster rate. In this paper, we propose to build a virtual data mart, especially for Organizational KPIs by using data virtualization technology, which can be used to help KPI developers to build and update performance management system quickly and make these systems work in real time. In this paper, we present a way of identifying and building virtual data marts for Organizational KPIs. The basic principle underlying the proposed approach is that the design of virtual data marts should be driven by the business needs and organizational requirements that each virtual data mart is expected to address. As a consequence, the virtual data mart design process must be based on a deep understanding of the top management’s need and users' expectations. A prototype is recommended to validate the use of the proposed method.
Designing a Prototype of Digital Museum to Promote Woven Songket, A Local Product of Sumatera, Indonesia
Authors: Bertalya Bertalya , Prihandoko Prihandoko , Oktavina Rakhma , Ramadhan Danu Satria 
Published: July 2014

One of Indonesia's cultural heritage is woven songket. Songket is not just a piece of cloth but with a diversity of functions and motifs contained profound philosophy about human life. Hence, the songket fabric must be preserved so as not to disappear due to the influx of modern cloth products from outside.This study aims to create a digital museum that displays digital images of woven songket and provide information relating to the various motifs representing the cultural distinctiveness of local centers in Sumatra. In addition, a digital gallery is developed to display a wide range of products derived from the local creative industries of songket cloth. The methods used for data collection are observation and interview. The development of digital museum consists of the process of formulation, planning, analysis, design, manufacture and testing of web pages, as well as evaluation.
Comparison of Physical Capacities Between Nonselected and Selected Elite Male Competitive Surfers for the National Junior Team
Authors: Tran Tai T. , Lundgren Lina , Secomb Josh , Farley Oliver R.L. , Haff G. Gregory , Seitz Laurent B. , Newton Robert U. , Nimphius Sophia , Sheppard Jeremy M. 
Published: July 2014

Purpose:To determine whether a previously validated performance-testing protocol for competitive surfers is able to differentiate between Australian elite junior surfers selected (S) to the national team and those not selected (NS).Methods:Thirty-two elite male competitive junior surfers were divided into 2 groups (S = 16, NS = 16). Their age, height, body mass, sum of 7 skinfolds, and lean-body-mass ratio (mean ± SD) were 16.17 ± 1.26 y, 173.40 ± 5.30 cm, 62.35 ± 7.40 kg, 41.74 ± 10.82 mm, 1.54 ± 0.35 for the S athletes and 16.13 ± 1.02 y, 170.56 ± 6.6 cm, 61.46 ± 10.10 kg, 49.25 ± 13.04 mm, 1.31 ± 0.30 for the NS athletes. Power (countermovement jump [CMJ]), strength (isometric midthigh pull), 15-m sprint paddling, and 400-m endurance paddling were measured.Results:There were significant (P ≤ .05) differences between the S and NS athletes for relative vertical-jump peak force (P = .01, d = 0.9); CMJ height (P = .01, d = 0.9); time to 5-, 10-, and 15-m sprint paddle; sprint paddle peak velocity (P = .03, d = 0.8; PV); time to 400 m (P = .04, d = 0.7); and endurance paddling velocity (P = .05, d = 0.7).Conclusions:All performance variables, particularly CMJ height; time to 5-, 10-, and 15-m sprint paddle; sprint paddle PV; time to 400 m; and endurance paddling velocity, can effectively discriminate between S and NS competitive surfers, and this may be important for athlete profiling and training-program design.
Knowledge boosting: a graph-based integration approach with multi-omics data and genomic knowledge for cancer clinical outcome prediction
Authors: Kim Dokyoon , Joung Je-Gun , Sohn Kyung-Ah , Shin Hyunjung , Park Yu Rang , Ritchie Marylyn D , Kim Ju Han 
Published: July 2014

AbstractObjective Cancer can involve gene dysregulation via multiple mechanisms, so no single level of genomic data fully elucidates tumor behavior due to the presence of numerous genomic variations within or between levels in a biological system. We have previously proposed a graph-based integration approach that combines multi-omics data including copy number alteration, methylation, miRNA, and gene expression data for predicting clinical outcome in cancer. However, genomic features likely interact with other genomic features in complex signaling or regulatory networks, since cancer is caused by alterations in pathways or complete processes.Methods Here we propose a new graph-based framework for integrating multi-omics data and genomic knowledge to improve power in predicting clinical outcomes and elucidate interplay between different levels. To highlight the validity of our proposed framework, we used an ovarian cancer dataset from The Cancer Genome Atlas for predicting stage, grade, and survival outcomes.Results Integrating multi-omics data with genomic knowledge to construct pre-defined features resulted in higher performance in clinical outcome prediction and higher stability. For the grade outcome, the model with gene expression data produced an area under the receiver operating characteristic curve (AUC) of 0.7866. However, models of the integration with pathway, Gene Ontology, chromosomal gene set, and motif gene set consistently outperformed the model with genomic data only, attaining AUCs of 0.7873, 0.8433, 0.8254, and 0.8179, respectively.Conclusions Integrating multi-omics data and genomic knowledge to improve understanding of molecular pathogenesis and underlying biology in cancer should improve diagnostic and prognostic indicators and the effectiveness of therapies.
Approximate Stokes Drift Profiles in Deep Water
Authors: Breivik Øyvind , Janssen Peter A. E. M. , Bidlot Jean-Raymond 
Published: July 2014

AbstractA deep-water approximation of the Stokes drift velocity profile is explored as an alternative to the monochromatic profile. The alternative profile investigated relies on the same two quantities required for the monochromatic profile, namely, the Stokes transport and the surface Stokes drift velocity. Comparisons with parametric spectra and profiles under wave spectra from the Interim ECMWF Re-Analysis (ERA-Interim) and buoy observations reveal much better agreement than the monochromatic profile even for complex sea states. That the profile gives a closer match and a more correct shear has implications for ocean circulation models since the Coriolis–Stokes force depends on the magnitude and direction of the Stokes drift profile, and Langmuir turbulence parameterizations depend sensitively on the shear of the profile. The alternative profile comes at no added numerical cost compared to the monochromatic profile.
Coexistence of halloysite and iron-bearing clays in an altered ignimbrite, Patagonia, Argentina
Authors: Cravero F. , Marfil S. A. , Ramos C. P. , Maiza P. 
Published: July 2014

AbstractThe Mamil Choique halloysite deposits of Patagonia, Argentina, contain randomly distributed green clay inclusions and patches within the halloysite mass. Halloysite has been formed from the thorough alteration of rhyolitic to dacitic ash fall tuffs and ignimbrites of the Huitrera Formation, Eocene age, under ambient conditions. The smectites present in the clay inclusions have been determined as ferruginous beidellites with variables amounts of Fe3+in octahedral sites. The weathering activity that caused the formation of halloysite was also responsible for the genesis of the iron-bearing clay minerals, the formation of which was controlled mainly by permeability. Textural variations within the rock indicate favourable local geochemical environments for the formation of the green clay minerals.
A collection of aspect ratios of common clay minerals determined from conductometric titrations
Authors: Weber C. , Heuser M. , Stanjek H. 
Published: July 2014

AbstractThe aspect ratios of common clay minerals have been determined from conductometric titrations. The sample set comprises 11 Na-saturated bentonites, 16 smectites with different interlayer cations, three illites/muscovites and two talc dominated specimens. It is shown that the aspect ratios of smectites saturated with divalent cations are lower than those of the same smectite saturated with a monovalent cation. This observation is discussed in terms of the number of smectite layers making up a particle.
Higher Serum S100B and BDNF Levels are Correlated with a Lower Pressure-Pain Threshold in Fibromyalgia
Authors: Zanette Simone Azevedo , Dussan-Sania Jairo Alberto , Souza Andressa , Deitos Alicia , Torres Iraci Lucena Silva , Caumo Wolnei 
Published: July 2014

Background: Fibromyalgia (FM) is conceptualized as a central sensitization (CS) condition, that presents high serum brain-derived neurotrophic factor (BDNF) and neuroglia activation. Although the S100B protein regulates neuroglia functions, it has been traditionally used as a proxy of central nervous system damage. However, neither BDNF nor S100B association with the clinical picture of FM has been elucidated. To explore their association with the pressure-pain threshold (PPT) in FM, we performed a cross-sectional study, including 56 females with confirmed FM aged 18–65 years. Linear regression models were used to adjust for potential confounding factors between serum BDNF, S100B and PPT. Results: Serum BDNF and S100B were correlated (Spearman's Rho = 0.29). Serum BDNF ( log) and S100B ( log) were correlated with the PPT ( log) (Partial η2 = 0.129, P = 0.012 for the BDNF ( log), and Partial η2 = 0.105, P = 0.025 for the S100B ( log)). Serum BDNF ( log) was inversely associated with PPT ( log) (β = −1.01, SE = 0.41), age (β = −0.02, SE = 0.15) and obsessive compulsive disorder (β = −0.36, SE = 0.15), while serum S100B ( log) was inversely associated with PPT ( log) (β = −1.38, SE = 0.50), only. Conclusions: Both neuroglia key mediators in the CS process were inversely correlated with the PPT. Serum assessment of BDNF and S100B deserve further study to determine its potential as a proxy for the CS spectrum in FM.
Evaluating the predictive value of biomarkers for efficacy outcomes in response to pertuzumab- and trastuzumab-based therapy: an exploratory analysis of the TRYPHAENA study
Authors: Schneeweiss Andreas , Chia Stephen , Hegg Roberto , Tausch Christoph , Deb Rahul , Ratnayake Jayantha , McNally Virginia , Ross Graham , Kiermaier Astrid , Cortés Javier 
Published: July 2014

Abstract
Introduction
Molecular markers that predict responses to particular therapies are invaluable for optimization of patient treatment. The TRYPHAENA study showed that pertuzumab and trastuzumab with chemotherapy was an efficacious and tolerable combination for patients with human epidermal growth factor receptor 2 (HER2)-positive breast cancer in the neoadjuvant setting. We analyzed whether particular biomarkers correlated with the responses observed and therefore may predict outcomes in patients given pertuzumab plus trastuzumab.

Methods
We describe the analysis of a panel of biomarkers including HER2, human epidermal growth factor receptor 3 (HER3), epidermal growth factor receptor (EGFR), phosphatase and tensin homolog (PTEN), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) by qRT-PCR, immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), enzyme-linked immunosorbent assay (ELISA), and PCR-based mutational analyses as appropriate. For each marker analyzed, patients were categorized into ‘low’ (generally below median) or ‘high’ (generally above median) subgroups at baseline and post-treatment.

Results
Correlation of marker subgroups with the achievement of a pathological complete response (pCR) (ypT0/is) was analyzed. HER2 protein and mRNA expression levels were associated with pCR rate in two of the three study arms and the pooled analyses. Correlations of biomarker status with pCR occurred in one individual arm only and the pooled analyses with EGFR and PTEN; however, interpretation of these results is limited by a strong imbalance in patient numbers between the high and low subgroups and inconsistency between arms. We also found no association between expression levels of TOP2A and pCR rate in either the anthracycline-containing or free arms of TRYPHAENA.

Conclusions
According to these analyses, and in line with other analyses of pertuzumab and trastuzumab in the neoadjuvant setting, we conclude that HER2 expression remains the only marker suitable for patient selection for this regimen at present.

Trial registration
The TRYPHAENA study was registered with ClinicalTrials.gov, NCT00976989, on September 14 2009.
Research roundup: July 2014
Authors: Greener Mark 
Published: July 2014

In brief ▪ Correcting anaemia in women with heavy menstrual bleeding improves health-related quality of life scores ▪ Statins appear to slightly reduce physical activity in older males ▪ E-cigarettes are more effective than nicotine replacement therapy or no cessation aid in people who attempt to quit smoking without help from a health professional ▪ Women with diabetes are more likely to develop coronary heart disease than men with diabetes
Generic tools for conditionally altering protein abundance and phenotypes on demand
Authors: Faden Frederik , Mielke Stefan , Lange Dieter , Dissmeyer Nico 
Published: July 2014

Abstract
Conditional gene expression and modulating protein stability under physiological conditions are important tools in biomedical research. They led to a thorough understanding of the roles of many proteins in living organisms. Current protocols allow for manipulating levels of DNA, mRNA, and of functional proteins. Modulating concentrations of proteins of interest, their post-translational processing, and their targeted depletion or accumulation are based on a variety of underlying molecular modes of action. Several available tools allow a direct as well as rapid and reversible variation right on the spot, i.e., on the level of the active form of a gene product. The methods and protocols discussed here include inducible and tissue-specific promoter systems as well as portable degrons derived from instable donor sequences. These are either constitutively active or dormant so that they can be triggered by exogenous or developmental cues. Many of the described techniques here directly influencing the protein stability are established in yeast, cell culture and in vitro systems only, whereas the indirectly working promoter-based tools are also commonly used in higher eukaryotes. Our major goal is to link current concepts of conditionally modulating a protein of interest’s activity and/or abundance and approaches for generating cell and tissue types on demand in living, multicellular organisms with special emphasis on plants.
Outcomes of the Extracardiac Fontan Procedure Using Cardiopulmonary Bypass: Early Results
Authors: Ugurlucan Murat , Tuncer Eylem Yayla , Guzelmeric Fusun , Kafali Eylul , Sayin Omer Ali , Cine Nihat , Oner Naci , Yildirim Ayse , Ceyran Hakan , Basaran Murat 
Published: July 2014

<p><strong>Background</strong>: Although the avoidance of cardiopulmonary bypass during the Fontan procedure has potential advantages, using cardiopulmonary bypass during this procedure has no adverse effects in terms of morbidity and mortality rates. In this study, we assessed the postoperative outcomes of our first 9 patients who have undergone extracardiac Fontan operation by the same surgeon using cardiopulmonary bypass.</p><p><strong>Methods</strong>: Between September 2011 and April 2013, 9 consecutive patients (3 males and 6 females) underwent extra-cardiac Fontan operation. All operations were performed under cardiopulmonary bypass at normothermia by the same surgeon. The age of patients ranged between 4 and 17 (9.8 ± 4.2) years. Previous operations performed on these patients were modified Blalock-Taussig shunt procedure in 2 patients, bidirectional cavopulmonary shunt operation in 6 patients, and pulmonary arterial banding in 1 patient. Except 2 patients who required intracardiac intervention, cross-clamping was not applied. In all patients, the extracardiac Fontan procedure was carried out by interposing an appropriately sized tube graft between the infe-rior vena cava and right pulmonary artery.</p><p><strong>Results</strong>: The mean intraoperative Fontan pressure and transpulmonary gradient were 12.3 ± 2.5 and 6.9 ± 2.2 mm Hg, respectively. Intraoperative fenestration was not required. There was no mortality and 7 patients were discharged with-out complications. Complications included persistent pleural effusion in 1 patient and a transient neurological event in 1 patient. All patients were weaned off mechanical ventila-tion within 24 hours. The mean arterial oxygen saturation increased from 76.1% ± 5.3% to 93.5% ± 2.2%. All patients were in sinus rhythm postoperatively. Five patients required blood and blood-product transfusions. The mean intensive care unit and hospital stay periods were 2.9 ± 1.7 and 8.2 ± 1.9 days, respectively.</p><p><strong>Conclusions</strong>: The extracardiac Fontan operation per-formed using cardiopulmonary bypass provides satisfactory results in short-term follow-up and is associated with favor-able postoperative hemodynamics and morbidity rates.</p>
On some flat connection associated with locally symmetric surface
Authors: Robaszewska Maria 
Published: July 2014

Abstract
For every two-dimensional manifold M with locally symmetric linear connection ∇, endowed also with ∇-parallel volume element, we construct a flat connection on some principal fibre bundle P(M,G). Associated with - satisfying some particular conditions - local basis of TM local connection form of such a connection is an R(G)-valued 1-form build from the dual basis ω1, ω2 and from the local connection form ω of ▽. The structural equations of (M,∇) are equivalent to the condition dΩ-Ω∧Ω=0.
This work was intended as an attempt to describe in a unified way the construction of similar 1-forms known for constant Gauss curvature surfaces, in particular of that given by R. Sasaki for pseudospherical surfaces.
Comparison of Phytotoxicity of Selected Phosphonium Ionic Liquid
Authors: Biczak Robert , Bałczewski Piotr , Pawłowska Barbara , Bachowska Barbara , Rychter Piotr 
Published: July 2014

Abstract
Ionic liquids have attracted considerable interest in various areas as new, non-volatile and non-flammable organic solvents, catalysts, reaction additives, ligands, drugs and other dedicated materials etc. Their general use, sometimes in bulky quantities, requires determination of their potential ecotoxicity on selected organisms. In the present work, influence of triphenylmethylphosphonium iodide (1) and triphenylhexadecylphosphonium iodide (2), introduced to soil, on germination and early stages of growth and development of superior plants was investigated using the plant growth test based on the OECD/OCDE 208/2006. In this test, the seeds of selected species, i.e. land superior plants - spring barley (Hordeum vulgare) and common radish (Raphanus sativus L. subvar. radicula Pers.) were planted in pots containing soil to which a test chemical compound had been added and in pots with control soil. To evaluate the phytotoxicity of ionic liquids 1 and 2 germination and weight (dry and fresh) of control plant seedlings were determined and compared with the germination and weight (dry and fresh) of the seedlings of plants grown in the soil watered with appropriate amounts of the test chemicals. The visual assessment of any types of damage to the test species, such as growth inhibition, chlorosis and necrosis, was also carried out and documented by digital photographs. Based on the obtained results, magnitudes of the LOEC - the lowest concentration causing observable effects in the form of reduction in growth and germination compared with the control and the NOEC - the highest concentration not causing observable, toxic effects - were also determined.
Influence of Feature Selection Methods on Classification Sensitivity Based on the Example of A Study of Polish Voivodship Tourist Attractiveness
Authors: Bąk Iwona 
Published: July 2014

Abstract
The purpose of this article is to determine the influence of various methods of selection of diagnostic features on the sensitivity of classification. Three options of feature selection are presented: a parametric feature selection method with a sum (option I), a median of the correlation coefficients matrix column elements (option II) and the method of a reversed matrix (option III). Efficiency of the groupings was verified by the indicators of homogeneity, heterogeneity and the correctness of grouping. In the assessment of group efficiency the approach with the Weber median was used. The undertaken problem was illustrated with a research into the tourist attractiveness of voivodships in Poland in 2011.