The QUASAR reproducibility study, Part II: Results from a multi-center Arterial Spin Labeling test-retest study.

Arterial Spin Labeling (ASL) is a method to measure perfusion using magnetically labeled blood water as an endogenous tracer. Being fully non-invasive, this technique is attractive for longitudinal studies of cerebral blood flow in healthy and diseased individuals, or as a surrogate marker of metabolism. So far, ASL has been restricted mostly to specialist centers due to a generally low SNR of the method and potential issues with user-dependent analysis needed to obtain quantitative measurement of cerebral blood flow (CBF). Here, we evaluated a particular implementation of ASL (called Quantitative STAR labeling of Arterial Regions or QUASAR), a method providing user independent quantification of CBF in a large test-retest study across sites from around the world, dubbed "The QUASAR reproducibility study". Altogether, 28 sites located in Asia, Europe and North America participated and a total of 284 healthy volunteers were scanned. Minimal operator dependence was assured by using an automatic planning tool and its accuracy and potential usefulness in multi-center trials was evaluated as well. Accurate repositioning between sessions was achieved with the automatic planning tool showing mean displacements of 1.87+/-0.95 mm and rotations of 1.56+/-0.66 degrees . Mean gray matter CBF was 47.4+/-7.5 [ml/100 g/min] with a between-subject standard variation SD(b)=5.5 [ml/100 g/min] and a within-subject standard deviation SD(w)=4.7 [ml/100 g/min]. The corresponding repeatability was 13.0 [ml/100 g/min] and was found to be within the range of previous studies.

Optimization of Snow Drifting Mitigation and Control Methods for Iowa Conditions Part II, TR-626, 2015

Blowing and drifting of snow is a major concern for transportation efficiency and road safety in regions where their development is common. One common way to mitigate snow drift on roadways is to install plastic snow fences. Correct design of snow fences is critical for road safety and maintaining the roads open during winter in the US Midwest and other states affected by large snow events during the winter season and to maintain costs related to accumulation of snow on the roads and repair of roads to minimum levels. Of critical importance for road safety is the protection against snow drifting in regions with narrow rights of way, where standard fences cannot be deployed at the recommended distance from the road. Designing snow fences requires sound engineering judgment and a thorough evaluation of the potential for snow blowing and drifting at the construction site. The evaluation includes site-specific design parameters typically obtained with semi-empirical relations characterizing the local transport conditions. Among the critical parameters involved in fence design and assessment of their post-construction efficiency is the quantification of the snow accumulation at fence sites. The present study proposes a joint experimental and numerical approach to monitor snow deposits around snow fences, quantitatively estimate snow deposits in the field, asses the efficiency and improve the design of snow fences. Snow deposit profiles were mapped using GPS based real-time kinematic surveys (RTK) conducted at the monitored field site during and after snow storms. The monitored site allowed testing different snow fence designs under close to identical conditions over four winter seasons. The study also discusses the detailed monitoring system and analysis of weather forecast and meteorological conditions at the monitored sites. A main goal of the present study was to assess the performance of lightweight plastic snow fences with a lower porosity than the typical 50% porosity used in standard designs of such fences. The field data collected during the first winter was used to identify the best design for snow fences with a porosity of 50%. Flow fields obtained from numerical simulations showed that the fence design that worked the best during the first winter induced the formation of an elongated area of small velocity magnitude close to the ground. This information was used to identify other candidates for optimum design of fences with a lower porosity. Two of the designs with a fence porosity of 30% that were found to perform well based on results of numerical simulations were tested in the field during the second winter along with the best performing design for fences with a porosity of 50%. Field data showed that the length of the snow deposit away from the fence was reduced by about 30% for the two proposed lower-porosity (30%) fence designs compared to the best design identified for fences with a porosity of 50%. Moreover, one of the lower-porosity designs tested in the field showed no significant snow deposition within the bottom gap region beneath the fence. Thus, a major outcome of this study is to recommend using plastic snow fences with a porosity of 30%. It is expected that this lower-porosity design will continue to work well for even more severe snow events or for successive snow events occurring during the same winter. The approach advocated in the present study allowed making general recommendations for optimizing the design of lower-porosity plastic snow fences. This approach can be extended to improve the design of other types of snow fences. Some preliminary work for living snow fences is also discussed. Another major contribution of this study is to propose, develop protocols and test a novel technique based on close range photogrammetry (CRP) to quantify the snow deposits trapped snow fences. As image data can be acquired continuously, the time evolution of the volume of snow retained by a snow fence during a storm or during a whole winter season can, in principle, be obtained. Moreover, CRP is a non-intrusive method that eliminates the need to perform man-made measurements during the storms, which are difficult and sometimes dangerous to perform. Presently, there is lots of empiricism in the design of snow fences due to lack of data on fence storage capacity on how snow deposits change with the fence design and snow storm characteristics and in the estimation of the main parameters used by the state DOTs to design snow fences at a given site. The availability of such information from CRP measurements should provide critical data for the evaluation of the performance of a certain snow fence design that is tested by the IDOT. As part of the present study, the novel CRP method is tested at several sites. The present study also discusses some attempts and preliminary work to determine the snow relocation coefficient which is one of the main variables that has to be estimated by IDOT engineers when using the standard snow fence design software (Snow Drift Profiler, Tabler, 2006). Our analysis showed that standard empirical formulas did not produce reasonable values when applied at the Iowa test sites monitored as part of the present study and that simple methods to estimate this variable are not reliable. The present study makes recommendations for the development of a new methodology based on Large Scale Particle Image Velocimetry that can directly measure the snow drift fluxes and the amount of snow relocated by the fence.

Rehabilitation of Concrete Pavements Utilizing Rubblization and Crack and Seat Methods (Phase II): Performance Evaluation of Rubblized Pavements in Iowa, TR-550, 2008

This Phase II follow-up study of IHRB Project TR-473 focused on the performance evaluation of rubblized pavements in Iowa. The primary objective of this study was to evaluate the structural condition of existing rubblized concrete pavements across Iowa through Falling Weight Deflectometer (FWD) tests, Dynamic Cone Penetrometer (DCP) tests, visual pavement distress surveys, etc. Through backcalculation of FWD deflection data using the Iowa State University's advanced layer moduli backcalculation program, the rubblized layer moduli were determined for various projects and compared with each other for correlating with the long-term pavement performance. The AASHTO structural layer coefficient for rubblized layer was also calculated using the rubblized layer moduli. To validate the mechanistic-empirical (M-E) hot mix asphalt (HMA) overlay thickness design procedure developed during the Phase I study, the actual HMA overlay thicknesses from the rubblization projects were compared with the predicted thicknesses obtained from the design software. The results of this study show that rubblization is a valid option to use in Iowa in the rehabilitation of portland cement concrete pavements provided the foundation is strong enough to support construction operations during the rubblization process. The M-E structural design methodology developed during Phase I can estimate the HMA overlay thickness reasonably well to achieve long-lasting performance of HMA pavements. The rehabilitation strategy is recommended for continued use in Iowa under those conditions conducive for rubblization.

Iowa Mass Concrete for Bridge Foundation Study - Phase II, Final Report, 2014

The early-age thermal development of structural mass concrete elements has a significant impact on the future durability and longevity of the elements. If the heat of hydration is not controlled, the elements may be susceptible to thermal cracking and damage from delayed ettringite formation. In the Phase I study, the research team reviewed published literature and current specifications on mass concrete. In addition, the team observed construction and reviewed thermal data from the westbound (WB) I-80 Missouri River Bridge. Finally, the researchers conducted an initial investigation of the thermal analysis software programs ConcreteWorks and 4C-Temp&Stress. The Phase II study is aimed at developing guidelines for the design and construction of mass concrete placements associated with large bridge foundations. This phase included an additional review of published literature and a more in-depth investigation of current mass concrete specifications. In addition, the mass concrete construction of two bridges, the WB I-80 Missouri River Bridge and the US 34 Missouri River Bridge, was documented. An investigation was conducted of the theory and application of 4C-Temp&Stress. ConcreteWorks and 4C-Temp&Stress were calibrated with thermal data recorded for the WB I-80 Missouri River Bridge and the US 34 Missouri River Bridge. ConcreteWorks and 4C-Temp&Stress were further verified by means of a sensitivity study. Finally, conclusions and recommendations were developed, as included in this report.

DnaSP v5: A software for comprehensive analysis of DNA polymorphism data

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

High c-Met expression in stage I-II pancreatic adenocarcinoma: proposal for an immunostaining scoring method and correlation with poor prognosis.

AIMS: c-Met is an emerging biomarker in pancreatic ductal adenocarcinoma (PDAC); there is no consensus regarding the immunostaining scoring method for this marker. We aimed to assess the prognostic value of c-Met overexpression in resected PDAC, and to elaborate a robust and reproducible scoring method for c-Met immunostaining in this setting. METHODS AND RESULTS: c-Met immunostaining was graded according to the validated MetMab score, a classic visual scale combining surface and intensity (SI score), or a simplified score (high c-Met: ≥20% of tumour cells with strong membranous staining), in stage I-II PDAC. A computer-assisted classification method (Aperio software) was developed. Clinicopathological parameters were correlated with disease-free survival (DFS) and overall survival(OS). One hundred and forty-nine patients were analysed retrospectively in a two-step process. Thirty-seven samples (whole slides) were analysed as a pre-run test. Reproducibility values were optimal with the simplified score (kappa = 0.773); high c-Met expression (7/37) was associated with shorter DFS [hazard ratio (HR) 3.456, P = 0.0036] and OS (HR 4.257, P = 0.0004). c-Met expression was concordant on whole slides and tissue microarrays in 87.9% of samples, and quantifiable with a specific computer-assisted algorithm. In the whole cohort (n = 131), patients with c-Met(high) tumours (36/131) had significantly shorter DFS (9.3 versus 20.0 months, HR 2.165, P = 0.0005) and OS (18.2 versus 35.0 months, HR 1.832, P = 0.0098) in univariate and multivariate analysis. CONCLUSIONS: Simplified c-Met expression is an independent prognostic marker in stage I-II PDAC that may help to identify patients with a high risk of tumour relapse and poor survival.

Metodologia para obtenção do hidrograma de escoamento superficial em encostas e canais. Parte II: modelo computacional e análise de sensibilidade

Estimativas de vazão máxima de escoamento superficial são necessárias para o projeto de obras hidráulicas em bacias urbanas e rurais. A dificuldade em aplicar os procedimentos disponíveis para calcular a variação do escoamento superficial com o tempo e de seu valor máximo deve-se à inexatidão dos métodos usados para esse objetivo e à variabilidade nos resultados que podem ser obtidos por profissionais que usem o mesmo procedimento. Dessa forma, a investigação de um método que produza estimativas confiáveis da vazão máxima e do hidrograma de escoamento superficial é de grande interesse. Neste trabalho, desenvolveu-se e avaliou-se a sensibilidade de um software (HIDROGRAMA 2.1) que permite a obtenção do hidrograma de escoamento superficial, da vazão máxima e seu tempo de ocorrência, da altura e da velocidade máximas do escoamento, do volume e da lâmina de escoamento superficial em encosta e em canais. O modelo apresentou grande sensibilidade ao período de retorno, à taxa de infiltração estável e ao comprimento da encosta e do canal.

Using Moodle to provide added value in the teaching of a software development course

The rate of adoption and use of learning management systems to support teaching and learning processes in academic institutions is growing rapidly. Universities are acquiring systems with functionalities that can match with their specific needs and requirements. Moodle is one of the most popular and widely deployed learning management systems in academic institutions today. However, apart from the system, universities tend to maintain other applications for the purpose of supplementing their teaching and learning processes. This situation is similar to Lappeenranta University of Technology (LUT), which is our case study in this project. Apart from Moodle, the university also maintains other systems such as Oodi, Noppa and Uni portal for the purpose of supporting its educational activities. This thesis has two main goals. The first goal is to understand the specific role of Moodle at LUT. This information is fundamental in assessing whether Moodle is needed in the university’s current teaching and learning environment. The second aim is to provide insights to teachers and other departmental stakeholders on how Moodle can provide added value in the teaching of a software development course. In response to this, a Moodle module for a software development course is created and the underlying features are tested. Results of the constructive work proposed some improvements through (i) the use of Moodle for in-class surveys, (ii) transfer of grades from Moodle to Oodi, (iii) use of Moodle in self-study courses and MOOCs, (iv) online examinations, and (v) Moodle integrations with third party applications. The proposed items were then evaluated for their utility through interviews of five expert interviews. The final results of this work are considered useful to LUT administration and management specifically on ways that Moodle can bring changes to the university at managerial, economical and technical level. It also poses some challenges on platform innovations and research.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

Arquitectura SIG corporativa apoyada en software libre y estándares

Presentación de SIG corporativos, software libre, estandáres y casos prácticos

Panorama actual del ecosistema de software libre para SIG

Los proyectos y productos comúnmente llamados Free and Open Source Software1 relacionados con la geomática están experimentando una evolución y actualización vertiginosa. A los “tradicionales” proyectos de servicios de mapas, bases de datos espaciales o clientes pesados, se les están uniendo un amplio conjunto de componentes como servicios de publicación, clientes ligeros, servicios de geoprocesamiento, movilidad, frameworks, …o nuevos estándares como GeoRSS, WMS Tiled, WPS,… Este artículo pretende efectuar una breve pausa para analizar el panorama actual del mundo del software libre, categorizando los proyectos y productos existentes en la actualidad, para valorar cada uno de ellos, analizando su situación actual, su trayectoria, su evolución futura y las interrelaciones existentes en el ecosistema de software libre SIG. Se analizará la situación y el catálogo disponible de proyectos/productos de servidores de datos espaciales, servidores OGC , publicación/clientes de mapas ligeros, aplicaciones de escritorio, clientes IDE, bibliotecas de desarrollo, herramientas de catálogo cliente y servidor, etc.. Se mostrará el ecosistema de proyectos, organizaciones y personas que colaboran con los principales productos, con sus interrelaciones entre sí, y los planes de futuro conocidos. El resultado esperado es mostrar al lector una imagen general (“big-picture”) que le permita posicionar sus necesidades con criterio dentro del panorama actual de las soluciones SIG basadas en software libre

El Sistema defensivo de Villasviejas de Tamuja (Botija, Cáceres): una aplicación de software libre en el análisis de paisajes arqueológicos

El análisis de cuencas visuales es una de las aplicaciones de los SIG que más repercusión han tenido en Arqueología. El éxito de su uso está condicionado también por la elección del método de elaboración de los modelos digitales del terreno, bien sea a partir de modelos obtenidos por triangulación o por interpolación (splines, etc). Es ésta una consideración de partida que pretendemos incluir en esta comunicación. En este trabajo se ha empleado el software GRASS para tratar de comprender diversos aspectos sobre la función del sistema defensivo de un poblado amurallado de la II Edad del Hierro, especialmente módulos adicionales específicamente desarrollados para Arqueología. Nuestro trabajo se ha centrado esencialmente en las cuencas visuales y en el análisis de prominencia, aunque no hemos querido obviar otras posibilidades como el cálculo de caminos óptimos para comprender los accesos al castro. Con esta aplicación práctica puede ponerse de relieve la versatilidad de este paquete de software libre frente a otras soluciones que se emplean en el mercado

Migración a software libre del SIG de la Diputación de A Coruña

En el año 2006, la Diputación de A Coruña junto con el Laboratorio de Bases de Datos de la Universidad de A Coruña emprendieron un proyecto para la migración a software libre de webEIEL, la aplicación de publicación en web y descarga de la información cartográfica y alfanumérica contenida en la base de datos territoriales de la Encuesta sobre Infraestructura y Equipamiento Local (EIEL) de la provincia de A Coruña. Un objetivo adicional en este proyecto era la construcción de un nodo de la infraestructura de datos espaciales de España (IDEE) que actuara como proveedor para la red de IDEs de los datos georreferenciados de la EIEL de A Coruña y de la red provincial de carreteras recogidos a escalas mayores que 1/10.000, con generalizaciones a escalas menores de estos mismos datos, y con servicios interoperables relacionados con los mismos. Este nodo incluye los siguientes servicios de acceso a datos: • Servidor de mapas (WMS) • Servidor de entidades (WFS) • Servicio de catálogo de metadatos, y • Servicio de nomenclátor. El objetivo de este artículo es describir el nodo ideAC de la Diputación de A Coruña tanto en términos de funcionalidad como en términos técnicos

Migración a software libre de la Plataforma Geomática de CVG Edelca

CVG Electrificación del Caroní, C.A (CVG EDELCA), es la empresa hidroeléctrica más importante de Venezuela, y se encarga de las operaciones de las centrales hidroeléctricas “Simón Bolívar” en Guri con una capacidad instalada de 10.000 MW, considerada la segunda en importancia en el mundo, la Central Hidroeléctrica “Antonio José de Sucre” en Macagua con una capacidad instalada de 3.140 MW y “Francisco de Miranda” en Caruachi, con una capacidad instalada de 2.280 MW. (...)

Elaboración de software para la supervisión in situ de ejercicios prácticos de análisis de estructuras con enunciado personalizado

Se expone la experiencia de los autores en el desarrollo de las clases prácticas de análisis de estructuras, en la asignatura ESTRUCTURAS II de la ETS de Arquitectura de la Universidad de Granada, consistente en el desarrollo de ejercicios prácticos semanales con enunciados personalizados para cada alumno, previa elaboración de software que permite la supervisión y corrección in situ de los mismos. El objetivo de la metodología docente que se presenta, es la mejora de los tradicionalmente muy bajos índices de rendimiento académico, en las asignaturas de Análisis de Estructuras, en las escuelas de ingeniería y arquitectura, propiciando la participación activa del alumnado en el desarrollo de las clases mediante el planteamiento y resolución de ejercicios prácticos semanales de enunciado personalizado