Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors.

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.

Grimm

Durant molts anys els infants d'arreu del món varen adquirir gran part deis seus coneixements mitjançant els contes transmesos oralment. Els germans Grimm varen col-laborar de manera rellevant a passar aquesta informació del suport oral al paper, a la tradició escrita. El projecte Grimm pretén introduir a les aules d'educació infantil un canvi: del paper al multimedia, la qual cosa su posa una nova manera d'aprendre.

Protocol per a la implantació de noves eines didàctiques: competències i habilitats adquirides pels estudiants

L'adaptació al nou espai europeu d'educació superior (EEES) ha plantejat alguns canvis en l'enfocament de la formació universitària al nostre país. On abans era el docent el protagonista, ara és l'estudiant el que pren el rol d'actor principal de la seva formació, i l'aprenentatge s¿orienta cap a una autonomia i reflexió més grans. En aquest escenari, les noves tecnologies ofereixen un ampli ventall d'opcions per millorar els processos formatius. En aquests sentit, el Grup d'Innovació Docent G¿IDEA ha participat activament en aquest procés d'adaptació des de ja fa uns quants anys, i ha creat una sèrie de recursos docents digitals que han estat àmpliament provats en diversos ensenyaments de la Facultat d'Economia i Empresa de la Universitat de Barcelona. L'objectiu d¿aquest article és presentar el protocol dissenyat per l'equip d'investigadors del G¿IDEA per implantar aquestes eines didàctiques (webquestes i exercicis tutoritzats), i també els resultats d'una enquesta de satisfacció sobre les competències i habilitats adquirides pels nostres estudiants en la utilització dels recursos. Els resultats mostren, d'una banda, que no ha estat possible crear un mateix protocol aplicable a tots els recursos, a causa de les diferències en els objectius didàctics de les distintes eines docents implantades. D'altra banda, la valoració que els estudiants fan de la utilització de les eines és molt positiva, tot i que hi ha algunes diferències entre els recursos analitzats. Conèixer la valoració que l'alumnat fa d'aquests recursos permet al grup d'investigadors poder-los millorar i adequar al perfil dels estudiants perquè aquests en puguin treure el màxim profit possible.

La incidencia de las tecnologías de la información y comunicación en los programas de formación continuada de jueces y magistrados

[spa] Los programas de formación continuada a distancia para jueces presentan problemas de ejecución debido de un lado a la dispersión geográfica de los destinatarios y de otra, a la necesidad de alcanzar cierto nivel de competencias tanto para su uso como para su diseño. En este contexto cobran especial significación la determinación de los objetivos así como el diseño curricular del programa que se pretende ejecutar.

Autorregulación de aprendizajes en educación superior mediante la escritura de blogs

La importancia de mecanismos de regulación de los propios aprendizajes por parte de los estudiantes, así como de la calidad de la retroalimentación y de la evaluación formativa por parte de los profesores está en las agendas internacionales de la calidad de la enseñanza superior. El uso de herramientas de lectura, escritura e interacción web 2.0 se enmarca claramente en ese propósito general. El artículo ofrece resultados de una investigación-acción interuniversitaria sobre la evaluación de competencias con blogs. Más concretamente, presenta tres escenarios formativos en los que el blog se utiliza como herramienta de evaluación reflexiva; indaga el grado en que el alumnado se hace consciente de su proceso de aprendizaje, cómo lo evidencia y cómo lo autorregula; y, finalmente, analiza el tipo de feed-back utilizado por el profesorado. Se presentan resultados del análisis documental tanto de las producciones llevadas a cabo en los blogs como del feed-back facilitado por el profesorado. Los resultados muestran el peso que tiene la calidad del feed-back que facilita el profesorado en el proceso de acompañamiento de construcción de competencias.

Investigation of high-resolution functional magnetic resonance imaging by means of surface and array radiofrequency coils at 7 T.

In this investigation, high-resolution, 1x1x1-mm(3) functional magnetic resonance imaging (fMRI) at 7 T is performed using a multichannel array head coil and a surface coil approach. Scan geometry was optimized for each coil separately to exploit the strengths of both coils. Acquisitions with the surface coil focused on partial brain coverage, while whole-brain coverage fMRI experiments were performed with the array head coil. BOLD sensitivity in the occipital lobe was found to be higher with the surface coil than with the head array, suggesting that restriction of signal detection to the area of interest may be beneficial for localized activation studies. Performing independent component analysis (ICA) decomposition of the fMRI data, we consistently detected BOLD signal changes and resting state networks. In the surface coil data, a small negative BOLD response could be detected in these resting state network areas. Also in the data acquired with the surface coil, two distinct components of the positive BOLD signal were consistently observed. These two components were tentatively assigned to tissue and venous signal changes.

Shielding requirements in helical tomotherapy.

Helical tomotherapy is a relatively new intensity-modulated radiation therapy (IMRT) treatment for which room shielding has to be reassessed for the following reasons. The beam-on-time needed to deliver a given target dose is increased and leads to a weekly workload of typically one order of magnitude higher than that for conventional radiation therapy. The special configuration of tomotherapy units does not allow the use of standard shielding calculation methods. A conventional linear accelerator must be shielded for primary, leakage and scatter photon radiations. For tomotherapy, primary radiation is no longer the main shielding issue since a beam stop is mounted on the gantry directly opposite the source. On the other hand, due to the longer irradiation time, the accelerator head leakage becomes a major concern. An analytical model based on geometric considerations has been developed to determine leakage radiation levels throughout the room for continuous gantry rotation. Compared to leakage radiation, scatter radiation is a minor contribution. Since tomotherapy units operate at a nominal energy of 6 MV, neutron production is negligible. This work proposes a synthetic and conservative model for calculating shielding requirements for the Hi-Art II TomoTherapy unit. Finally, the required concrete shielding thickness is given for different positions of interest.

Desenvolupament d’una eina per a l’escriptura de nous exercicis de l’ACME

L'ACME és una plataforma d'e-learning utilitzada a la Universitat de Girona que permet la correcció automètica d'un gran nombre d'exercicis de tipologies variades via web. Actualments'utilitza com a eina de seguiment del treball diari dels alumnes en moltes carreresi facultats de la Universitat de Girona, que els permet consolidar la matèria explicada aclasse.Actualment tots els fitxers que contenen la implementació dels exercicis definits a l'ACMEestan en format LATEXi segueixen uns formats d'escriptura concrets, no estàndards i moltsdefiits per a la seva posterior lectura i interpretació. Aquesta alta especificitat i mancad'estandardització fa difícil l'aprenentatge de l'escriptura per part dels professors que volenfer servir l'ACME. La majoria d'ells es limiten a escriure exercicis nous a partir d'exercicisantics, desconeixen per complet si amb la tipologia d'exercici que utilitzen estan fent servirtot el potencial, o no, que permet l'eina. És en aquest punt que neix aquest ProjecteFinal de Carrera amb la intenció de desenvolupar una eina que permeti facilitar, millorar iampliar la metodologia d'escriptura de nous exercicis a l'ACME.L'objectiu d'aquest Projecte Final de Carrera era desenvolupar una metodologia d'escripturad'exercicis diferent, innovadora i a l'abast de qualsevol professor per poder crear noustipus d'exercicis amb facilitat i sense haver de necessitar coneixements sobre programació

Development of Object-Oriented Design and Specifications for Iowa DOT and Urban Standards: Phase I, TR-487, 2004

Currently, individuals including designers, contractors, and owners learn about the project requirements by studying a combination of paper and electronic copies of the construction documents including the drawings, specifications (standard and supplemental), road and bridge standard drawings, design criteria, contracts, addenda, and change orders. This can be a tedious process since one needs to go back and forth between the various documents (paper or electronic) to obtain information about the entire project. Object-oriented computer-aided design (OO-CAD) is an innovative technology that can bring a change to this process by graphical portrayal of information. OO-CAD allows users to point and click on portions of an object-oriented drawing that are then linked to relevant databases of information (e.g., specifications, procurement status, and shop drawings). The vision of this study is to turn paper-based design standards and construction specifications into an object-oriented design and specification (OODAS) system or a visual electronic reference library (ERL). Individuals can use the system through a handheld wireless book-size laptop that includes all of the necessary software for operating in a 3D environment. All parties involved in transportation projects can access all of the standards and requirements simultaneously using a 3D graphical interface. By using this system, users will have all of the design elements and all of the specifications readily available without concerns of omissions. A prototype object-oriented model was created and demonstrated to potential users representing counties, cities, and the state. Findings suggest that a system like this could improve productivity to find information by as much as 75% and provide a greater sense of confidence that all relevant information had been identified. It was also apparent that this system would be used by more people in construction than in design. There was also concern related to the cost to develop and maintain the complete system. The future direction should focus on a project-based system that can help the contractors and DOT inspectors find information (e.g., road standards, specifications, instructional memorandums) more rapidly as it pertains to a specific project.

Automatic quality assessment in structural brain magnetic resonance imaging

MRI has evolved into an important diagnostic technique in medical imaging. However, reliability of the derived diagnosis can be degraded by artifacts, which challenge both radiologists and automatic computer-aided diagnosis. This work proposes a fully-automatic method for measuring image quality of three-dimensional (3D) structural MRI. Quality measures are derived by analyzing the air background of magnitude images and are capable of detecting image degradation from several sources, including bulk motion, residual magnetization from incomplete spoiling, blurring, and ghosting. The method has been validated on 749 3D T(1)-weighted 1.5T and 3T head scans acquired at 36 Alzheimer's Disease Neuroimaging Initiative (ADNI) study sites operating with various software and hardware combinations. Results are compared against qualitative grades assigned by the ADNI quality control center (taken as the reference standard). The derived quality indices are independent of the MRI system used and agree with the reference standard quality ratings with high sensitivity and specificity (>85%). The proposed procedures for quality assessment could be of great value for both research and routine clinical imaging. It could greatly improve workflow through its ability to rule out the need for a repeat scan while the patient is still in the magnet bore.

A Classification of Tools for Learning Logic

A table showing a comparison and classification of tools (intelligent tutoring systems) for e-learning of Logic at a college level.

Spatial visualization of DNA in solution.

An image analysis method is presented which allows for the reconstruction of the three-dimensional path of filamentous objects from two of their projections. Starting with stereo pairs, this method is used to trace the trajectory of DNA molecules embedded in vitreous ice and leads to a faithful representation of their three-dimensional shape in solution. This computer-aided reconstruction is superior to the subjective three-dimensional impression generated by observation of stereo pairs of micrographs because it enables one to look at the reconstructed molecules from any chosen direction and distance and allows quantitative analysis such as determination of distances, curvature, persistence length, and writhe of DNA molecules in solution.

Improving breast cancer education: the case of an evolving multidisciplinary module for undergraduate medical students (lausanne medical school, 1993-2008).

Breast cancer is a public health issue in numerous countries. Multidisciplinary collaboration is required for patient care, research, and also education of future physicians. This paper uses Kern's framework for curriculum design to demonstrate how a breast diseases module for undergraduate medical students created in 1993 evolved over 15 years. The main outcomes of program refinements were better integrated course content, the development of electronic course documents, and implementation of computer-aided small group learning. A main future challenge is to further develop efficient instructional strategies in line with well-defined learning needs for undergraduate students.

The organizational structure of online academic advising

Academic advising is a key element for learning success in virtual environments that has received little attention from researchers. This paper focuses on the organizational arrangements needed for the delivery of academic advising in online higher education. We present the general dimensions of organizational structures (division of labor, hierarchy of authority and formalization) and their possible forms when applied to academic advising. The specific solution adopted at the Open University of Catalonia is described and assessed in order to draw general conclusions of interest for other institutions.