Jose Garzon

Cabbage, Brassica olerecea var. Capitata, is a significant vegetable crop in North Carolina with approximately 5000 acres harvested annually and an estimated market value of 15 million dollars. This is partly driven by increased interest by consumers in the health and phytonutrient quality of this crop. Members of the Brassicaceae family produce glucosinolates, which have been shown to have anti-cancer properties. These compounds play a role in both flavor development and influence the crops insect susceptibility. The purpose of this study was to evaluate established varieties and elite breeding germplasm in the field, with an emphasis on the impact of nitrogen fertilization and growing season influence on both production and the concentration of glucosinolates present. Eleven commercially available cultivars and 17 elite selections from the North Carolina State University Plants for Human Health germplasm collection were planted at the Piedmont Research Station in Salisbury, NC, in...

DIRECCION: Thamer Arana Grajales, ACTORES: Alejandro Alvarez, Leidy Jhoana Osorio, Mayra Alejandra Vargas, Gloria Maria Rodriguez, Jhonny Restrepo, Karen Melissa Gomez, Jairo Arturo Ramirez, Astrid Jhoana Parra, Miguel Angel Zuleta , DISENO GRAFICO Y ESCENOGRAFICO: Mauricio Celis, DISENO DE LUCES: Fernando Henao, MAQUILLAJE: Carlos Dario Caicedo

Author Index Alonso, Antonio A. 197 Alonso, Jesus B. 243 Alves, Alexssander 175 Antunes, Mario 60 Arrais, Joel P. 74 Bajo, Javier 102 Banga, Julio R. 197, 233 Bello, Rafael 223 Blanco, JA Munoz 21 Bosnians, Frank 223 Braga, Ana Cristina 217 Brito, Rui MM 175, 180 Camacho, Rui 175 Carneiro, Soma 92 Carrera, Cristina 55 Carrera, Pablo Vicente 128 Carvalho, Paulo MM 206 Castellanos-Garzon, Jose A. 118 Chagoyen, Monica 147 Corchado, Juan M. 102 Correia, Manuel 60 Costa, Lino 217 De Paz, Juan F. 102 Deris, ...

We present a database, PrePPI (Predicting Protein-Protein Interactions), of more than 1.35 million predicted protein-protein interactions (PPIs). Of these at least 127,000 are expected to constitute direct physical interactions although the actual number may be much larger (~500,000). The current PrePPI, which contains predicted interactions for about 85% of the human proteome is related to an earlier version but is based on additional sources of interaction evidence and is far larger in scope. The use of structural relationships allows PrePPI to infer numerous previously unreported interactions. PrePPI has been subjected to a series of validation tests including reproducing known interactions, recapitulating multi-protein complexes, analysis of disease associated SNPs, and identifying functional relationships between interacting proteins. We show, using Gene Set Enrichment Analysis (GSEA), that predicted interaction partners can be used to annotate a protein's function. We prov...

Summary: Hidden Markov models are widely applied within computational biology. The large data sets and complex models involved demand optimized implementations, while efficient exploration of model space requires rapid prototyping. These requirements are not met by existing ...

Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage. http://sbg.cib.csic.es/Software/ADP_EM. Supplementary data are available at Bioinformatics online.

Protein-protein interfaces have been evolutionarily-designed to enable transduction between the interacting proteins. Thus, we hypothesize that analysis of the dynamics of the complex can reveal details about the nature of the interaction, and in particular whether it is obligatory, i.e., persists throughout the entire lifetime of the proteins, or not. Indeed, normal mode analysis, using the Gaussian network model, shows that for the most part obligatory and non-obligatory complexes differ in their decomposition into dynamic domains, i.e., the mobile elements of the protein complex. The dynamic domains of obligatory complexes often mix segments from the interacting chains, and the hinges between them do not overlap with the interface between the chains. In contrast, in non-obligatory complexes the interface often hinges between dynamic domains, held together through few anchor residues on one side of the interface that interact with their counterpart grooves in the other end. In aut...

La tesis doctoral presentada se ha enfocado a la obtención de aplicaciones que implementen eficientemente operaciones de ajuste (también denominado docking) en el campo de la biología estructural. Para ello, se han establecido dos objetivos principales: - Diseño de aplicaciones de ajuste mediante una nueva metodología que proporciona una búsqueda más rápida. - Adaptación óptima de las aplicaciones para su ejecución sobre un entorno de computación Grid. Estas adaptaciones han requerido la creación de un nuevo sistema cache sobre sistemas Grid que permita un óptimo uso de las transferencias de datos realizadas. El diseño de nuevas aplicaciones para acelerar la búsqueda del mejor ajuste ha sido desarrollado empleando una novedosa metodología denominada Fast Rotational Matching (FRM). La búsqueda del mejor ajuste entre dos elementos conlleva explorar un amplio espacio de búsqueda, resultando ineficiente su exploración sistemática. FRM permite acelerar esta exploración en el espacio rota...

We describe a method to predict protein-protein interactions (PPIs) formed between structured domains and short peptide motifs. We take an integrative approach based on consensus patterns of known motifs in databases, structures of domain-motif complexes from the PDB and various sources of non-structural evidence. We combine this set of clues using a Bayesian classifier that reports the likelihood of an interaction and obtain significantly improved prediction performance when compared to individual sources of evidence and to previously reported algorithms. Our Bayesian approach was integrated into PrePPI, a structure-based PPI prediction method that, so far, has been limited to interactions formed between two structured domains. Around 80,000 new domain-motif mediated interactions were predicted, thus enhancing PrePPI's coverage of the human protein interactome.

We discuss recent approaches for structure-based protein function annotation. We focus on template-based methods where the function of a query protein is deduced from that of a template for which both the structure and function are known. We describe the different ways of identifying a template. These are typically based on sequence analysis but new methods based on purely structural similarity are also being developed that allow function annotation based on structural relationships that cannot be recognized by sequence. The growing number of available structures of known function, improved homology modeling techniques and new developments in the use of structure allow template-based methods to be applied on a proteome-wide scale and in many different biological contexts. This progress significantly expands the range of applicability of structural information in function annotation to a level that previously was only achievable by sequence comparison.

The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking "unbound perturbation" ("unbound docking") decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScore(PPI)/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼ 2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScore(PPI) balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScore(PPI)/FRODOCK will be successful.

Cache techniques are an efficient tool to reduce latency times in transfer operations through Grid systems. Although different approximations to introduce cache facilities into Grid computing have already been studied, they require intrusive modifications of Grid software and hardware. Here, we propose an end-to-end cache system that is implemented over scheduling services. This cache system requires neither changes in the

The use of supraglottic devices as a means of rescue in patients difficult to intubate or ventilate has increased in the field of anaesthetics and in emergency medicine. This study is designed to evaluate the success rate of blind intubations using two supraglottic devices, the Fastrach ILMA and the i-gel mask. A total of 80 patients (40 per group) were included. After positioning them a leak test was performed, the glottis view was checked with a fibrobronchoscope, and an attempt was made to introduce an endotracheal tube through the device, and the procedure was repeated. Adequate ventilation was evaluated, as well as the grade of fibrobronchoscope view, the success of the intubation, and the complications observed after their use. There were no differences in the incidence of adequate ventilation with either device. The glottis view (Brimacombe scale) was better with i-gel (77.78% versus 68.42%) at the second attempt, but not on the first. A higher percentage of intubations were ...

To study the effect of the trauma of anesthesia and surgery, and their duration, on immune status. Fifty patients undergoing cholecystectomy were studied in 2 groups. In group A surgery was of short duration ( < 60 min) and in group B surgery was longer ( > 60 min). Immunological analysis were performed at 5 times: t0 (before surgery), t1 (1 h), t2 (24 h), t3 (4 days) and t4 (7 days). Group A patients experienced a non significant decrease in T lymphocytes, activated T lymphocytes and B lymphocytes, with levels returning to normal after 7 days. T-suppression, on the other hand, decreased significantly in the first 24 h, but gradually returned to normal after 7 days. T lymphocytes, activated T lymphocytes and B lymphocytes decreased in group B and regressed after 7 days. The population of B lymphocytes decreased significantly and had not fully recovered 7 days after surgery. The act of anesthesia/surgery depresses immune response in function of duration, with the effect being g...

ABSTRACT ResumenIntroducción y objetivos: El uso de los dispositivos supraglóticos en pacientes con dificultadespara la intubación y/o ventilación se ha incrementado de manera progresiva tanto en el ámbitode la anestesia como en la medicina de urgencias. Este estudio se dise˜nó para evaluar la tasa deéxito de intubación «a ciegas» en pacientes sin criterios de vía aérea difícil con la mascarilla air-Q®, comparándola con el dispositivo supraglótico patrón: la mascarilla laríngea de intubaciónILMA-FastrachTM.Pacientes y métodos:Se incluyeron 80 pacientes (40 por grupo). La inserción de los dispositivosse realizó de acuerdo con las instrucciones de los fabricantes. Tras la colocación, se realizó untest de fugas (aplicando una presión inspiratoria de 20 cmH2O por el ventilador). Se comprobóposteriormente la visión glótica usando un fibrobroncoscopio pediátrico, y se realizó la inserciónde un tubo endotraqueal a través del dispositivo. En aquellos casos en que el intento resultófallido, se retiró el dispositivo y se repitió nuevamente la secuencia. Se evaluaron, como obje-tivo primario, el éxito en la intubación, y como objetivos secundarios, la ventilación adecuada,el grado de visión fibrobroncoscópica y las complicaciones observadas tras su uso.Resultados: La ventilación adecuada en el primer intento de colocación fue mayor con ILMA-FastrachTMque con air-Q®(90 frente a 60%, p = 0,0019), y el éxito global en la ventilación (primery segundo intentos incluidos) fue mejor con ILMA-FastrachTM(95 frente a 80%, p = 0,04). El gradode visión glótica de acuerdo con la escala de Brimacombe fue mejor con air-Q®(84,62 frentea 37,50%, p = 0,0017) en el segundo intento, pero no en el primero. No hubo diferencias en elporcentaje de intubación con ambos dispositivos. La incidencia de dolor de garganta fue similarcon los 2 dispositivos empleados. Dos pacientes en el grupo de air-Q®presentaron ronquera ydesaturación arterial.

Postdural puncture headache (PDPH; or "spinal headache) is the most common significant complication from regional anesthesia or analgesia in obstetrics. Recent advances in spinal needle design have dramatically decreased the incidence of headache after spinal anesthesia, and now the most common cause of PDPH is inadvertent puncture of the dura with an epidural needle. The diagnosis and treatment of a PDPH should usually be the responsibility of the anesthesiologist, but it is important for the obstetrician to be familiar with the clinical course and options for therapy, and the usual treatment strategies. This article discusses the differential diagnosis of postdelivery headache, the current understanding of the pathophysiology of PDPH, options for medical treatment, and the controversial issue of whether and when to treat the headache with an epidural blood patch.