Application of support vector machines for T-cell epitopes prediction

Motivation: The T-cell receptor, a major histocompatibility complex (MHC) molecule, and a bound antigenic peptide, play major roles in the process of antigen-specific T-cell activation. T-cell recognition was long considered exquisitely specific. Recent data also indicate that it is highly flexible, and one receptor may recognize thousands of different peptides. Deciphering the patterns of peptides that elicit a MHC restricted T-cell response is critical for vaccine development. Results: For the first time we develop a support vector machine (SVM) for T-cell epitope prediction with an MHC type I restricted T-cell clone. Using cross-validation, we demonstrate that SVMs can be trained on relatively small data sets to provide prediction more accurate than those based on previously published methods or on MHC binding. Supplementary information: Data for 203 synthesized peptides is available at http://linus.nci.nih.gov/Data/LAU203_Peptide.pd

Knowledge and attitudes associated with the onset of smoking during college life

Introducción: Se determinó la asociación entre conocimientos y actitudes frente al inicio del hábito de fumar en estudiantes universitarios. Materiales y métodos: Estudio de corte transversal realizado mediante una  encuesta auto-diligenciada por 433 estudiantes seleccionados aleatoriamente entre abril y mayo de 2010. Se  realizaron análisis de regresión de Poisson simple y múltiple y se calcularon las razones de prevalencia (RP)  crudas y ajustadas. Resultados: Se encontró que ser hombre (RP = 1,62; IC95%: 1,21-2,18) y conocer la  legislación colombiana sobre tabaco (RP = 1,75; IC95%: 1,25-2,45) aumenta la probabilidad de inicio del hábito tabáquico durante la carrera. En contraste, conocer que generalmente los fumadores mueren más jóvenes  (RP = 0,72; IC95%: 0,53-0,98), que la mayoría de pacientes con cáncer de pulmón son o han sido fumadores  (RP = 0,64; IC95%: 0,46-0,89) y considerar el fumar un vicio (RP = 0,58; IC95%: 0,42-0,80) o una  drogodependencia (RP = 0,48; IC95%: 0,27- 0,82) están asociados con menor probabilidad de inicio del hábito  de fumar durante la vida universitaria. Conclusión: El conocimiento sobre los efectos de fumar disminuye el  inicio de este hábito durante la carrera.Introduction: The association between knowledge and attitudes before the onset of smoking during college  life in college students was determined. Materials and Methods: Cross-sectional study carried out through  self-report survey in a sample of 433 students randomly selected between April and May 2010. Simple and  multiple Poisson regression analysis were carried put and, crude and adjusted prevalence reasons (PR) were  calculated. Results: We found that being male (PR = 1.62; 95%CI: 1.21- 2.18) and knowing Colombian  legislation about tobacco use (PR = 1.75; 95%CI: 1.25-2.45) increases the likelihood of smoking onset during  college. In contrast, knowing that smokers generally die younger than nonsmokers (PR = 0.72; 95%CI: 0.53- 0.98), that most patients with lung cancer are or have been smokers (PR = 0.64; 95%CI: 0.46-0.89), and  considering smoking is a bad habit (PR = 0.58; 95%CI: 0.42-0.80) or a drug dependence (PR = 0.48; 95%CI:  0.27-0.82) are associated with lower likelihood of smoking onset during college. Conclusion: Knowledge  about the effects of smoking decreases the onset of smoking during college life

Registros y allanamientos en Colombia : Estudio constitucional sobre la figura del registro y allanamiento en el nuevo contexto jurídico penal colombiano en la ciudad de Manizales durante los años 2012 al 2014

CD-T 342.041 8 M268;68 p.El presente trabajo abordará el contenido de la figura jurídica de los Registros y Allanamientos en el Código de Procedimiento Penal Colombiano y la colisión que existe frente al principio fundamental de la “inviolabilidad de domicilio” y desde el análisis del Bloque de Constitucionalidad, arribando a la conclusión de como efectivamente con la materialización de dicha norma no se desconocen Derechos Fundamentales como la Intimidad, temas que la Corte Constitucional en su diferentes pronunciamientos que estudiaremos determina el fundamento legal de la figura de Registro.Universidad Libre Seccional Pereir

The Mathematics of a Successful Deconvolution: A Quantitative Assessment of Mixture-Based Combinatorial Libraries Screened Against Two Formylpeptide Receptors

In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds and active ligands. Here we present a quantitative assessment of the screening of 32 positional scanning libraries in the identification of highly specific and selective ligands for two formylpeptide receptors. We also compare and contrast two mixture-based library approaches using a mathematical model to facilitate the selection of active scaffolds and libraries to be pursued for further evaluation. The flexibility demonstrated in the differently formatted mixture-based libraries allows for their screening in a wide range of assays

Improvement of IFNg ELISPOT Performance Following Overnight Resting of Frozen PBMC Samples Confirmed Through Rigorous Statistical Analysis

Immune monitoring of functional responses is a fundamental parameter to establish correlates of protection in clinical trials evaluating vaccines and therapies to boost antigen-specific responses. The IFNg ELISPOT assay is a well-standardized and validated method for the determination of functional IFNg-producing T-cells in peripheral blood mononuclear cells (PBMC); however, its performance greatly depends on the quality and integrity of the cryopreserved PBMC. Here, we investigate the effect of overnight (ON) resting of the PBMC on the detection of CD8-restricted peptide-specific responses by IFNg ELISPOT. The study used PBMC from healthy donors to evaluate the CD8 T-cell response to five pooled or individual HLA-A2 viral peptides. The results were analyzed using a modification of the existing distribution free resampling (DFR) recommended for the analysis of ELISPOT data to ensure the most rigorous possible standard of significance. The results of the study demonstrate that ON resting of PBMC samples prior to IFNg ELISPOT increases both the magnitude and the statistical significance of the responses. In addition, a comparison of the results with a 13-day preculture of PBMC with the peptides before testing demonstrates that ON resting is sufficient for the efficient evaluation of immune functioning

contribution of individual amino acids within mhc molecule or antigenic peptide to tcr ligand potency

The TCR recognition of peptides bound to MHC class II molecules is highly flexible in some T cells. Although progress has been made in understanding the interactions within the trimolecular complex, to what extent the individual components and their amino acid composition contribute to ligand recognition by individual T cells is not completely understood. We investigated how single amino acid residues influence Ag recognition of T cells by combining several experimental approaches. We defined TCR motifs for CD4+ T cells using peptide synthetic combinatorial libraries in the positional scanning format (PS-SCL) and single amino acid-modified peptide analogues. The similarity of the TCR motifs defined by both methods and the identification of stimulatory antigenic peptides by the PS-SCL approach argue for a contribution of each amino acid residue to the overall potency of the antigenic peptide ligand. In some instances, however, motifs are formed by adjacent amino acids, and their combined influence is superimposed on the overall contribution of each amino acid within the peptide epitope. In contrast to the flexibility of the TCR to interact with different peptides, recognition was very sensitive toward modifications of the MHC-restriction element. Exchanges of just one amino acid of the MHC molecule drastically reduced the number of peptides recognized. The results indicate that a specific MHC molecule not only selects certain peptides, but also is crucial for setting an affinity threshold for TCR recognition, which determines the flexibility in peptide recognition for a given TCR

Antigen Discovery for the Identification of Vaccine Candidates and Biomarkers Using a T Cell Driven Approach in Combination with Positional Scanning Peptide Libraries

The prevention and treatment of infectious diseases is highly dependent on the availability of reliable diagnostic tests and protective or therapeutic vaccines. There also exists an urgent need to develop reliable biomarkers to monitor treatment success and to predict disease progression from asymptomatic to symptomatic disease in several disease scenarios. The elucidation of the disease-relevant antigens that elicit the protective immune responses is critical and required for the development of biomarkers, diagnostics, and vaccines. However; one of the main obstacles to the study of antigen specificity in human T cells is their low frequency in PBMC samples. To overcome this problem we have implemented strategies to generate memory T cell libraries and clones specific to the pathogen of interest. Due to the fact that memory T cells represent a repository of the human T cell response to infection, examination of their antigen specificity can efficiently reveal immunogenic and relevant antigens involved in the in vivo response to infection or vaccines. To examine the specificity of the memory T cells we use an unbiased collection of antigens together with an in silico analysis, namely positional scanning based biometrical analysis. Here we present a summary of our approach and ongoing work on the development of strategies for the culture of memory T cells from patients with Chagas disease. While most studies focus on the identification of vaccine candidates using preselected immunogenic proteins derived from animal models or by or bioinformatics prediction, here we present an innovative approach that directly examines the specificity of the memory response following infection or immunization in humans

Variability of Staphylococcus Aureus Carriers on a Medicine Student’s Population

Para evaluar en estudiantes de medicina la variación del estado de portador de Staphylococcus aureus y su resistencia antimicrobiana, antes y después de la práctica clínica, se realizó un estudio longitudinal en una cohorte de 159 estudiantes de cuarto y noveno semestre universitario. Se tomaron muestras de las zonas periamigdalianas y/o pared posterior de orofaringe, de las fosas nasales y las manos, se cultivaron en agar sangre de cordero al 5% y se incubaron en aerobiosis a 37°C, durante 48 horas. La identificación de Staphylococcus aureus se realizó según las características macroscópicas y pruebas bioquímicas. La susceptibilidad a los antimicrobianos se evaluó mediante el método de difusión de disco, por la técnica de Kirby-Bauer, siguiendo las normas internacionales del Clinical and Laboratory Standards Institute (CLSI), con los siguientes antimicrobianos: ciprofloxacina, vancomicina, oxacilina, cefalotina,clindamicina y rifampicina. La edad promedio de los alumnos de cuarto semestre fue 19,1±1,2 años y el género femenino fue 2/1 más frecuente que el masculino. Se analizaron la presencia de antecedentes como: infecciones, alergias, estado de fumador, otras patologías no infecciosas, uso de antibióticos en los últimos tres meses y procedimientos quirúrgicos u hospitalizaciones seis meses previos a la toma de las muestras. No hubo relación significativa entre la incidencia del estado de portador y los antecedentes estudiados. Se observó un aumento significativo del 15,1%, con respecto al grupo de estudiantes de cuarto semestre, en el estado de portador de S. aureus en el grupo de estudiantes de noveno semestre, después de haber estado expuestos durante tres años al ambiente hospitalario, (p=0,001 Test exacto de Mc Nemar). De los portadores, el 16,4% presentó la bacteria en manos (p<0,001), el 13,8% en fosas nasales (p=0,0015) y el 3,2% en faringe. Por otra parte,el 35,8% de los portadores presentó persistencia, de los cuales el 25,2% fue en fosas nasales; el 4,4%, en faringe y el 3,8% en manos. En cuanto a la resistencia a los antimicrobianos, el 1,9% de las cepas aisladas de los estudiantes de cuarto semestre presentó resistencia: una a ciprofloxacina y dos a clindamicina (tres estudiantes). Por su parte, el 2,5% de las cepas aisladas de estudiantes de noveno semestre fue resistente: una a cefalotina, ciprofloxacina, oxacilina y clindamicina, una a cefalotina y oxacilina y dos a clindamicina (cuatro estudiantes). En el 1,3% del grupo estudiado se aislaron cepas de Staphylococcus aureus Resistentes a la Meticilina (MRSA, por sus siglas en inglés). Estos resultados no muestran diferencias significativas (p=1.000). This is a longitudinal study performed in a 159 medicine student’s cohort, of fourth and ninth study semester, in order to evaluate the variation of Staphylococcus aureus carriers and its antimicrobial susceptibility on students, before and after clinical practice. Clinical samples were taken with a swab from the tonsils, pharynx posterior wall, nasal fosses and hands and were cultured in 5% sheep blood and incubated at 37oC in aerobic conditions during 48 hours. The identification of Sthaphylococcus aureus was performed according to the phenotypic and biochemical test. The antimicrobial susceptibility was evaluated by the diffusion disc method using the Kirby-Bauer technique, according to Clinical and Laboratory Standards Institute (CLSI), with the following antibiotics: Ciprofloxacyn, Vancomycin, Oxacyclin, Cephalotine, Clyndamycin, and Ryphampycin. The average age of the fourth semester students was 19.1± 1,2 years and the female gender was 2/1 more frequent than the male. The history of infections, allergy, smoke habit, non infectious diseases, surgeries, antibiotic use during the last three months and hospitalizations six months before sampling was analyzed. There was no significant relationship between previous history analysis and the carrier state incidence (p=0.001 Mc Nemar exact Test). A significant increase of 15,1% for S. aureus carrier state was observed after three years of exposure to hospital environment on ninth semester students, compared to fourth semester students (p=0.001 Test Mc Nemar); from which 16.4% (p<0.001) was founded in hands, 13.8% in nasal fosses (p=0.0015) and 3.2% in pharynx. 35.8% of S. aureus carrier was persistent: 25.2% in nasal fosses, 4.4% in pharynx and 3.8% in hands. Antimicrobial resistance was observed in 1.9% of the bacterial strains isolated from fourth semester students: One to Ciprofloxacyn and two to Clyndamycin. Besides was observed 2.5% of bacterial strains isolated from ninth semester students: one to Ciprofloxacyn, Oxacyclin, Cephalotine and Clyndamycin, one to Cephalotine and Oxacyclin and two to Clyndamycin. Finally, Methycylin Resistant Sthaphylococcus Aureus (MRSA) strains were isolated from 1.3% of the studied group. This results didn’t show significant differences b(p=1.000)

Recognition of Conserved Amino Acid Motifs of Common Viruses and Its Role in Autoimmunity

The triggers of autoimmune diseases such as multiple sclerosis (MS) remain elusive. Epidemiological studies suggest that common pathogens can exacerbate and also induce MS, but it has been difficult to pinpoint individual organisms. Here we demonstrate that in vivo clonally expanded CD4(+) T cells isolated from the cerebrospinal fluid of a MS patient during disease exacerbation respond to a poly-arginine motif of the nonpathogenic and ubiquitous Torque Teno virus. These T cell clones also can be stimulated by arginine-enriched protein domains from other common viruses and recognize multiple autoantigens. Our data suggest that repeated infections with common pathogenic and even nonpathogenic viruses could expand T cells specific for conserved protein domains that are able to cross-react with tissue-derived and ubiquitous autoantigens