MODBASE, a database of annotated comparative protein structure models and associated resources.

MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)

An Alternative Model of Amino Acid Replacement

The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment. We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment.Comment: Minor improvements. Added figure and reference

Experimental study of excited states of 62{}^{62}Ni via one-neutron (d,p)(d,p) transfer up to the neutron-separation threshold and characteristics of the pygmy dipole resonance states

The degree of collectivity of the Pygmy Dipole Resonance (PDR) is an open question. Recently, Ries {\it et al.} have suggested the onset of the PDR beyond $N=28$ based on the observation of a significant $E1$ strength increase in the Cr isotopes and proposed that the PDR has its origin in a few-nucleon effect. Earlier, Inakura {\it et al.} had predicted by performing systematic calculations using the random-phase approximation (RPA) with the Skyrme functional SkM* that the $E1$ strength of the PDR strongly depends on the position of the Fermi level and that it displays a clear correlation with the occupation of orbits with orbital angular momenta less than $3\hbar$ $(l \leq 2)$. To further investigate the microscopic structures causing the possible formation of a PDR beyond the $N=28$ neutron shell closure, we performed a $^{61}$Ni$(d,p){}^{62}$Ni experiment at the John D. Fox Superconducting Linear Accelerator Laboratory of Florida State University. To determine the angular momentum transfer populating possible $J^{\pi} = 1^-$ states and other excited states of ${}^{62}$Ni, angular distributions and associated single-neutron transfer cross sections were measured with the Super-Enge Split-Pole Spectrograph. A number of $J^{\pi} = 1^-$ states were observed below the neutron-separation threshold after being populated through $l=2$ angular momentum transfers. A comparison to available $(\gamma,\gamma')$ data for ${}^{58,60}$Ni provides evidence that the $B(E1)$ strength shifts further down in energy. The $(d,p)$ data clearly prove that $l=0$ strength, i.e., the neutron $(2p_{3/2})^{-1}(3s_{1/2})^{+1}$ one-particle-one-hole configuration plays only a minor role for $1^-$ states below the neutron-separation threshold in ${}^{62}$Ni.Comment: 15 pages, 8 figures, accepted for publication in Physical Review

Efectos de los patrones atípicos de respuesta sobre la influencia del contexto socioeconómico en el rendimiento académico

Amb el suport del Consell Superior d'Avaluació de CatalunyaSobre el rendimiento académico influyen múltiples factores. Es sabido que uno de ellos es el contexto socio-cultural (CSC) del estudiante, de manera que la probabilidad de éxito académico de un estudiante con un CSC alto es mayor que el de uno con CSC bajo. Las diferencias en el rendimiento pueden verse alteradas por la presencia de otros factores. Así, aspectos personales como la procedencia de los estudiantes, o del entorno, como la tipología del centro educativo, son algunos de estos factores ampliamente estudiados. En el presente trabajo analizamos el papel que tienen los patrones atípicos de respuesta (PAR) en la relación entre el CSC y el rendimiento académico. En pruebas estandarizadas con preguntas de elección múltiple, los PAR hacen referencia a perfiles inesperados de respuestas a las preguntas de la prueba de evaluación. La presencia o ausencia de PAR puede identificarse mediante índices estadísticos. Se analizan las respuestas a dos pruebas de elección múltiple que evalúan competencias básica, y que el Consell Superior d'Avaluació de Catalunya ha administrado a alumnos que cursan el último año de la etapa de Educación Secundaria Obligatoria (ESO). Los resultados del estudio nos permiten concluir que los PAR interactúan con el CSC en su efecto sobre el rendimiento académico, de manera que la presencia de patrones atípicos en las respuestas de los estudiantes tiene un efecto modificador sobre la brecha que el CSC muestra sobre el rendimiento escolar. Estos resultados apuntan a la necesidad de incluir el análisis de los PAR en los estudios de equidad educativa

DBAli tools: mining the protein structure space

The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions

Effectiveness of community-based integrated care in frail COPD patients: a randomised controlled trial

Background: Chronic obstructive pulmonary disease (COPD) generates a high burden on health care, and hospital admissions represent a substantial proportion of the overall costs of the disease. Integrated care (IC) has shown efficacy to reduce hospitalisations in COPD patients at a pilot level. Deployment strategies for IC services require assessment of effectiveness at the health care system level. Aims: The aim of this study was to explore the effectiveness of a community-based IC service in preventing hospitalisations and emergency department (ED) visits in stable frail COPD patients. Methods: From April to December 2005, 155 frail community-dwelling COPD patients were randomly allocated either to IC (n=76, age 73 (8) years, forced expiratory volume during the first second, FEV1 41(19) % predicted) or usual care (n=84, age 75(9) years, FEV1 44 (20) % predicted) and followed up for 12 months. The IC intervention consisted of the following: (a) patient's empowerment for self-management; (b) an individualised care plan; (c) access to a call centre; and (d) coordination between the levels of care. Thereafter, hospital admissions, ED visits and mortality were monitored for 6 years. Results: IC enhanced self-management (P=0.02), reduced anxiety-depression (P=0.001) and improved health-related quality of life (P=0.02). IC reduced both ED visits (P=0.02) and mortality (P=0.03) but not hospital admission. No differences between the two groups were seen after 6 years. Conclusion: The intervention improved clinical outcomes including survival and decreased the ED visits, but it did not reduce hospital admissions. The study facilitated the identification of two key requirements for adoption of IC services in the community: appropriate risk stratification of patients, and preparation of the community-based work force

Selecting subpopulations of high-quality protein conformers among conformational mixtures of recombinant bovine MMP-9 solubilized from inclusion bodies

Altres ajuts: CERCA Programme/Generalitat de CatalunyaA detailed workflow to analyze the physicochemical characteristics of mammalian matrix metalloproteinase (MMP-9) protein species obtained from protein aggregates (inclusion bodies-IBs) was followed. MMP-9 was recombinantly produced in the prokaryotic microbial cell factories Clearcoli (an engineered form of Escherichia coli) and Lactococcus lactis, mainly forming part of IBs and partially recovered under non-denaturing conditions. After the purification by affinity chromatography of solubilized MMP-9, four protein peaks were obtained. However, so far, the different conformational protein species forming part of IBs have not been isolated and characterized. Therefore, with the aim to link the physicochemical characteristics of the isolated peaks with their biological activity, we set up a methodological approach that included dynamic light scattering (DLS), circular dichroism (CD), and spectrofluorometric analysis confirming the separation of subpopulations of conformers with specific characteristics. In protein purification procedures, the detailed analysis of the individual physicochemical properties and the biological activity of protein peaks separated by chromatographic techniques is a reliable source of information to select the best-fitted protein populations

Consistencia en las respuestas inconsistentes a preguntas tipo test

Amb el suport del Consell Superior d'Avaluació de CatalunyaEn las evaluaciones realizadas mediante pruebas tipo test suele utilizarse como un indicador del nivel de conocimientos o competencias la puntuación obtenida a partir de la cantidad de respuestas contestadas correctamente. Esta puntuación, sin embargo, puede obtenerse a partir de respuestas muy variadas, algunas de ellas configurando un patrón atípico de respuesta (PAR), como cuando se contesta correctamente a preguntas muy difíciles y sin embargo se fallan preguntas muy fáciles. En el presente trabajo pretendemos aportar evidencia acerca de si la presencia de PAR en pruebas de evaluación tipo test corresponde a características aisladas, propias de la prueba, o por el contrario puede considerarse un estilo consistente de la persona evaluada. Se analizan las respuestas a unas pruebas de evaluación de competencias básicas de lengua castellana y catalana aplicadas durante el curso 2012-13 a los alumnos de cuatro de ESO de Cataluña. En total 56158 alumnos completaron la prueba de castellano y 56450 la de catalán. La proporción de respuestas correctas promedio en las pruebas fue de 0,83 y 0,81 respectivamente, con desviaciones estándar de 0,09 y 0,14. El porcentaje de alumnos que tenían una puntuación asociada a PAR fue del 29,3% en castellano y del 24,5% en catalán. El 8,5% de los alumnos evaluados contestaron a las dos pruebas siguiendo un patrón atípico. Las respuestas atípicas a una prueba hacen dudar de la validez de las puntuaciones resultantes. El hecho de que esta forma de contestar se mantenga en diferentes pruebas puede, además, señalar la presencia de algún problema estructural en el proceso de enseñanza-aprendizaje. Algunos de estos problemas pueden estar relacionados con déficits en el trabajo en el aula, con malas pautas de estudio, con ansiedad ante las evaluaciones o simplemente con la presencia de copia durante la evaluación