Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

LCD-OpenPACS: sistema integrado de telerradiologia com auxílio ao diagnóstico de nódulos pulmonares em exames de tomografia computadorizada

Lung cancer is one of the most common types of cancer and has the highest mortality rate. Patient survival is highly correlated with early detection. Computed Tomography technology services the early detection of lung cancer tremendously by offering aminimally invasive medical diagnostic tool. However, the large amount of data per examination makes the interpretation difficult. This leads to omission of nodules by human radiologist. This thesis presents a development of a computer-aided diagnosis system (CADe) tool for the detection of lung nodules in Computed Tomography study. The system, called LCD-OpenPACS (Lung Cancer Detection - OpenPACS) should be integrated into the OpenPACS system and have all the requirements for use in the workflow of health facilities belonging to the SUS (Brazilian health system). The LCD-OpenPACS made use of image processing techniques (Region Growing and Watershed), feature extraction (Histogram of Gradient Oriented), dimensionality reduction (Principal Component Analysis) and classifier (Support Vector Machine). System was tested on 220 cases, totaling 296 pulmonary nodules, with sensitivity of 94.4% and 7.04 false positives per case. The total time for processing was approximately 10 minutes per case. The system has detected pulmonary nodules (solitary, juxtavascular, ground-glass opacity and juxtapleural) between 3 mm and 30 mm.

Classificação de nódulos pulmonares em imagens tomográficas utilizando redes neurais artificiais em cascata

Lung cancer is the most common of malignant tumors, with 1.59 million new cases worldwide in 2012. Early detection is the main factor to determine the survival of patients affected by this disease. Furthermore, the correct classification is important to define the most appropriate therapeutic approach as well as suggest the prognosis and the clinical disease evolution. Among the exams used to detect lung cancer, computed tomography have been the most indicated. However, CT images are naturally complex and even experts medical are subject to fault detection or classification. In order to assist the detection of malignant tumors, computer-aided diagnosis systems have been developed to aid reduce the amount of false positives biopsies. In this work it was developed an automatic classification system of pulmonary nodules on CT images by using Artificial Neural Networks. Morphological, texture and intensity attributes were extracted from lung nodules cut tomographic images using elliptical regions of interest that they were subsequently segmented by Otsu method. These features were selected through statistical tests that compare populations (T test of Student and U test of Mann-Whitney); from which it originated a ranking. The features after selected, were inserted in Artificial Neural Networks (backpropagation) to compose two types of classification; one to classify nodules in malignant and benign (network 1); and another to classify two types of malignancies (network 2); featuring a cascade classifier. The best networks were associated and its performance was measured by the area under the ROC curve, where the network 1 and network 2 achieved performance equal to 0.901 and 0.892 respectively.

BDI reasoning with normative considerations

F. Meneguzzi thanks Fundaç ao de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS, Brazil) for the financial support through the ACI program (Grant ref. 3541-2551/12-0) and the ARD program (Grant ref. 12/0808-5), as well as Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) through the Universal Call (Grant ref. 482156/2013-9) and PQ fellowship (Grant ref. 306864/2013-4). N. Oren and W.W. Vasconcelos acknowledge the support of the Engineering and Physical Sciences Research Council (EPSRC, UK) within the research project “Scrutable Autonomous Systems” (SAsSY11, Grant ref. EP/J012084/1).

Designing Emotional Support Messages Tailored to Stressors

This work was funded by the RCUK Digital Economy award to the dot.rural Digital Economy Hub, University of Aberdeen; award reference: EP/G066051/1. The dataset used by this paper can be acquired by emailing the first author. We thank Matt Dennis, Kirsten A. Smith and Michael Gibson for their contributions to the research.

Personal Storytelling : Using Natural Language Generation for Children with Complex Communication Needs, in the Wild...

Acknowledgements The authors thank the children, their parents and school staff, who participated in this research, and who so willingly gave us their time, help and support. They also thank Steven Knox and Alan Clelland for their work on programming the mobile phone application. Additional thanks to DynaVox Inc. for supplying the Vmax communication devices to run our system on and Sensory Software Ltd for supplying us with their AAC software. This research was supported by the Research Council UKs Digittal Economy Programme and EPSRC (Grant numbers EP/F067151/1, EP/F066880/1, EP/E011764/1, EP/H022376/1, and EP/H022570 /1).

Modelling Provenance of Sensor Data for Food Safety Compliance Checking

Postprint

Spacetime foam induced collective bundling of intense fields

This research is supported by the Carnegie Trust for the Universities of Scotland (TO) and by the EPSRC GG-Top Project and the Cruickshank Trust (CW).

Modeling and simulation of bulk gallium nitride power semiconductor devices

Bulk gallium nitride (GaN) power semiconductor devices are gaining significant interest in recent years, creating the need for technology computer aided design (TCAD) simulation to accurately model and optimize these devices. This paper comprehensively reviews and compares different GaN physical models and model parameters in the literature, and discusses the appropriate selection of these models and parameters for TCAD simulation. 2-D drift-diffusion semi-classical simulation is carried out for 2.6 kV and 3.7 kV bulk GaN vertical PN diodes. The simulated forward current-voltage and reverse breakdown characteristics are in good agreement with the measurement data even over a wide temperature range.

Informelles Lernen Studierender mit Social Software unterstützen

E-Learning-Aktivitäten von Hochschulen haben häufig eine einseitige Ausrichtung auf die Unterstützung von Lehrveranstaltungen durch Technologien, insbesondere Lernmanagementsysteme. Dabei geraten die Studierenden als Zielgruppe nur mittelbar in den Blick. Diese Beobachtung nehmen die Autorinnen und Autoren des Bandes zum Anlass, das Lern-Erleben und die unterschiedlichen Phasen des Studiums aus Perspektive der Studierenden zu betrachten. Untersucht wird zudem, welche Unterstützungsangebote Hochschulen in welchen Phasen idealerweise bereitstellen. Die Autorinnen und Autoren formulieren detailliert, wie Hochschulen das studentische Lernen mit Hilfe von Social Software unterstützen können. Diese Empfehlungen basieren auf den Ergebnissen empirischer Untersuchungen sowie auf Fallstudien nationaler und internationaler Beispiele guter Praxis, die ausführlich präsentiert werden. Mit diesem Band möchten die Autorinnen und Autoren denjenigen, die in Bildungseinrichtungen des tertiären Sektors (aber auch in anderen Sektoren) tätig sind, konkrete Anregungen liefern, Unterstützungsangebote für das informelle Lernen von Studierenden mit Social Software stärker in den Blick zu nehmen und geeignete Angebote zu entwickeln. Die Publikation basiert auf Ergebnissen des Projekts „Learner Communities of Practice“, das zwischen 2009 und 2012 als Verbundprojekt sächsischer Hochschulen mit Förderung durch das SMWK unter Leitung des Medienzentrums der TU Dresden bearbeitet wurde.

Pilot Study on Improving the Efficiency of Transportation Projects Using Laser Scanning, 2003

Laser scanning is a terrestrial laser-imaging system that creates highly accurate three-dimensional images of objects for use in standard computer-aided design software packages. This report describes results of a pilot study to investigate the use of laser scanning for transportation applications in Iowa. After an initial training period on the use of the scanner and Cyclone software, pilot tests were performed on the following projects: intersection and railroad bridge for training purposes; section of highway to determine elevation accuracy and pair of bridges to determine level of detail that can be captured; new concrete pavement to determine smoothness; bridge beams to determine camber for deck-loading calculations; stockpile to determine volume; and borrow pit to determine volume. Results show that it is possible to obtain 2-6 mm precision with the laser scanner as claimed by the manufacturer compared to approximately one-inch precision with aerial photogrammetry using a helicopter. A cost comparison between helicopter photogrammetry and laser scanning showed that laser scanning was approximately 30 percent higher in cost depending on assumptions. Laser scanning can become more competitive to helicopter photogrammetry by elevating the scanner on a boom truck and capturing both sides of a divided roadway at the same time. Two- and three-dimensional drawings were created in MicroStation for one of the scanned highway bridges. It was demonstrated that it is possible to create such drawings within the accuracy of this technology. It was discovered that a significant amount of time is necessary to convert point cloud images into drawings. As this technology matures, this task should become less time consuming. It appears that laser scanning technology does indeed have a place in the Iowa Department of Transportation design and construction toolbox. Based on results from this study, laser scanning can be used cost effectively for preliminary surveys to develop TIN meshes of roadway surfaces. It also appears that this technique can be used quite effectively to measure bridge beam camber in a safer and quicker fashion compared to conventional approaches. Volume calculations are also possible using laser scanning. It seems that measuring quantities of rock could be an area where this technology would be quite beneficial since accuracy is more important with this material compared to soil. Other applications for laser scanning could include developing as-built drawings of historical structures such as the bridges of Madison County. This technology could also be useful where safety is a concern such as accurately measuring the surface of a highway active with traffic or scanning the underside of a bridge damaged by a truck. It is recommended that the Iowa Department of Transportation initially rent the scanner when it is needed and purchase the software. With time, it may be cost justifiable to purchase the scanner as well. Laser scanning consultants can be hired as well but at a higher cost.

Modelo organizacional de ensino a distancia para instituicoes tecnologicas

Tese (Doutoramento)

A generic strategy for dynamic load balancing of distributed memory parallel computational mechanics using unstructured meshes

A large class of computational problems are characterised by frequent synchronisation, and computational requirements which change as a function of time. When such a problem is solved on a message passing multiprocessor machine [5], the combination of these characteristics leads to system performance which deteriorate in time. As the communication performance of parallel hardware steadily improves so load balance becomes a dominant factor in obtaining high parallel efficiency. Performance can be improved with periodic redistribution of computational load; however, redistribution can sometimes be very costly. We study the issue of deciding when to invoke a global load re-balancing mechanism. Such a decision policy must actively weigh the costs of remapping against the performance benefits, and should be general enough to apply automatically to a wide range of computations. This paper discusses a generic strategy for Dynamic Load Balancing (DLB) in unstructured mesh computational mechanics applications. The strategy is intended to handle varying levels of load changes throughout the run. The major issues involved in a generic dynamic load balancing scheme will be investigated together with techniques to automate the implementation of a dynamic load balancing mechanism within the Computer Aided Parallelisation Tools (CAPTools) environment, which is a semi-automatic tool for parallelisation of mesh based FORTRAN codes.

Semi-automatic parallelisation of unstructured mesh codes

The availability of CFD software that can easily be used and produce high efficiency on a wide range of parallel computers is extremely limited. The investment and expertise required to parallelise a code can be enormous. In addition, the cost of supercomputers forces high utilisation to justify their purchase, requiring a wide range of software. To break this impasse, tools are urgently required to assist in the parallelisation process that dramatically reduce the parallelisation time but do not degrade the performance of the resulting parallel software. In this paper we discuss enhancements to the Computer Aided Parallelisation Tools (CAPTools) to assist in the parallelisation of complex unstructured mesh-based computational mechanics codes.