Feasibility assessment of the interactive use of a Monte Carlo algorithm in treatment planning for intraoperative electron radiation therapy

This work analysed the feasibility of using a fast, customized Monte Carlo (MC) method to perform accurate computation of dose distributions during pre- and intraplanning of intraoperative electron radiation therapy (IOERT) procedures. The MC method that was implemented, which has been integrated into a specific innovative simulation and planning tool, is able to simulate the fate of thousands of particles per second, and it was the aim of this work to determine the level of interactivity that could be achieved. The planning workflow enabled calibration of the imaging and treatment equipment, as well as manipulation of the surgical frame and insertion of the protection shields around the organs at risk and other beam modifiers. In this way, the multidisciplinary team involved in IOERT has all the tools necessary to perform complex MC dosage simulations adapted to their equipment in an efficient and transparent way. To assess the accuracy and reliability of this MC technique, dose distributions for a monoenergetic source were compared with those obtained using a general-purpose software package used widely in medical physics applications. Once accuracy of the underlying simulator was confirmed, a clinical accelerator was modelled and experimental measurements in water were conducted. A comparison was made with the output from the simulator to identify the conditions under which accurate dose estimations could be obtained in less than 3 min, which is the threshold imposed to allow for interactive use of the tool in treatment planning. Finally, a clinically relevant scenario, namely early-stage breast cancer treatment, was simulated with pre- and intraoperative volumes to verify that it was feasible to use the MC tool intraoperatively and to adjust dose delivery based on the simulation output, without compromising accuracy. The workflow provided a satisfactory model of the treatment head and the imaging system, enabling proper configuration of the treatment planning system and providing good accuracy in the dosage simulation.

TITIM GIS-tool: A GIS-based decision support system for measuring the territorial impact of transport infrastructures

To achieve sustainability in the area of transport we need to view the decision-making process as a whole and consider all the most important socio-economic and environmental aspects involved. Improvements in transport infrastructures have a positive impact on regional development and significant repercussions on the economy, as well as affecting a large number of ecological processes. This article presents a DSS to assess the territorial effects of new linear transport infrastructures based on the use of GIS. The TITIM ? Transport Infrastructure Territorial Impact Measurement ? GIS tool allows these effects to be calculated by evaluating the improvement in accessibility, loss of landscape connectivity, and the impact on other local territorial variables such as landscape quality, biodiversity and land-use quality. The TITIM GIS tool assesses these variables automatically, simply by entering the required inputs, and thus avoiding the manual reiteration and execution of these multiple processes. TITIM allows researchers to use their own GIS databases as inputs, in contrast with other tools that use official or predefined maps. The TITIM GIS-tool is tested by application to six HSR projects in the Spanish Strategic Transport and Infrastructure Plan 2005?2020 (PEIT). The tool creates all 65 possible combinations of these projects, which will be the real test scenarios. For each one, the tool calculates the accessibility improvement, the landscape connectivity loss, and the impact on the landscape, biodiversity and land-use quality. The results reveal which of the HSR projects causes the greatest benefit to the transport system, any potential synergies that exist, and help define a priority for implementing the infrastructures in the plan

Enhancing web-based learning resources with quizzes through an Authoring Tool and an Audience Response System

Quizzes are among the most widely used resources in web-based education due to their many benefits. However, educators need suitable authoring tools that can be used to create reusable quizzes and to enhance existing materials with them. On the other hand, if teachers use Audience Response Systems (ARSs) they can get instant feedback from their students and thereby enhance their instruction. This paper presents an online authoring tool for creating reusable quizzes and enhancing existing learning resources with them, and a web-based ARS that enables teachers to launch the created quizzes and get instant feedback from the class. Both the authoring tool and the ARS were evaluated. The evaluation of the authoring tool showed that educators can effectively enhance existing learning resources in an easy way by creating and adding quizzes using that tool. Besides, the different factors that assure the reusability of the created quizzes are also exposed. Finally, the evaluation of the developed ARS showed an excellent acceptance of the system by teachers and students, and also it indicated that teachers found the system easy to set up and use in their classrooms.

A tool assisting teachers in automating the assessment of programming assignments

Automating the assessment of programming assignments brings benefits for both students and teachers, since it helps the formers to gain a timely feedback and releases the latter from tedious tasks. The related literature in the domain has usually focused on the assessment process and the tools required for it, proposing libraries and systems that teachers can use in this process. However, few of them have work rowards reducing the effort and time teacher require to properly set up new assessente processes. This paper describes our experience with the analysis and design of a new tool to support teachers in visually developing automatic grades of programming assignments, introducing the underlying concepts and technologies and presenting the system architecture.

Design of a generalized tool for the performance assessment under sail based on analytical, numerical and empirical results : a global sailing yacht meta-model

La evaluación de las prestaciones de las embarcaciones a vela ha constituido un objetivo para ingenieros navales y marinos desde los principios de la historia de la navegación. El conocimiento acerca de estas prestaciones, ha crecido desde la identificación de los factores clave relacionados con ellas(eslora, estabilidad, desplazamiento y superficie vélica), a una comprensión más completa de las complejas fuerzas y acoplamientos involucrados en el equilibrio. Junto con este conocimiento, la aparición de los ordenadores ha hecho posible llevar a cabo estas tareas de una forma sistemática. Esto incluye el cálculo detallado de fuerzas, pero también, el uso de estas fuerzas junto con la descripción de una embarcación a vela para la predicción de su comportamiento y, finalmente, sus prestaciones. Esta investigación tiene como objetivo proporcionar una definición global y abierta de un conjunto de modelos y reglas para describir y analizar este comportamiento. Esto se lleva a cabo sin aplicar restricciones en cuanto al tipo de barco o cálculo, sino de una forma generalizada, de modo que sea posible resolver cualquier situación, tanto estacionaria como en el dominio del tiempo. Para ello se comienza con una definición básica de los factores que condicionan el comportamiento de una embarcación a vela. A continuación se proporciona una metodología para gestionar el uso de datos de diferentes orígenes para el cálculo de fuerzas, siempre con el la solución del problema como objetivo. Esta última parte se plasma en un programa de ordenador, PASim, cuyo propósito es evaluar las prestaciones de diferentes ti pos de embarcaciones a vela en un amplio rango de condiciones. Varios ejemplos presentan diferentes usos de PASim con el objetivo de ilustrar algunos de los aspectos discutidos a lo largo de la definición del problema y su solución . Finalmente, se presenta una estructura global de cara a proporcionar una representación virtual de la embarcación real, en la cual, no solo e l comportamiento sino también su manejo, son cercanos a la experiencia de los navegantes en el mundo real. Esta estructura global se propone como el núcleo (un motor de software) de un simulador físico para el que se proporciona una especificación básica. ABSTRACT The assessment of the performance of sailing yachts, and ships in general, has been an objective for naval architects and sailors since the beginning of the history of navigation. The knowledge has grown from identifying the key factors that influence performance(length, stability, displacement and sail area), to a much more complete understanding of the complex forces and couplings involved in the equilibrium. Along with this knowledge, the advent of computers has made it possible to perform the associated tasks in a systematic way. This includes the detailed calculation of forces, but also the use of those forces, along with the description of a sailing yacht, to predict its behavior, and ultimately, its performance. The aim of this investigation is to provide a global and open definition of a set of models and rules to describe and analyze the behavior of a sailing yacht. This is done without applying any restriction to the type of yacht or calculation, but rather in a generalized way, capable of solving any possible situation, whether it is in a steady state or in the time domain. First, the basic definition of the factors that condition the behavior of a sailing yacht is given. Then, a methodology is provided to assist with the use of data from different origins for the calculation of forces, always aiming towards the solution of the problem. This last part is implemented as a computational tool, PASim, intended to assess the performance of different types of sailing yachts in a wide range of conditions. Several examples then present different uses of PASim, as a way to illustrate some of the aspects discussed throughout the definition of the problem and its solution. Finally, a global structure is presented to provide a general virtual representation of the real yacht, in which not only the behavior, but also its handling is close to the experience of the sailors in the real world. This global structure is proposed as the core (a software engine) of a physical yacht simulator, for which a basic specification is provided.

Bacteria lacking a multidrug pump: A sensitive tool for drug discovery

Microorganisms express multidrug resistance pumps (MDRs) that can confound antibiotic discovery. We propose the use of mutants deficient in MDRs to overcome this problem. Sensitivity to quinolones and to amphipathic cations (norfloxacin, benzalkonium chloride, cetrimide, pentamidine, etc.) was increased 5- to 30-fold in a Staphylococcus aureus mutant with a disrupted chromosomal copy of the NorA MDR. NorA was required both for increased sensitivity to drugs in the presence of an MDR inhibitor and for increased rate of cation efflux. This requirement suggests that NorA is the major MDR protecting S. aureus from the antimicrobials studied. A 15- to 60-fold increase in sensitivity to antimicrobials also was observed in wild-type cells at an alkaline pH that favors accumulation of cations and weak bases. This effect was synergistic with a norA mutation, resulting in an increase up to 1,000-fold in sensitivity to antimicrobials. The usefulness of applying MDR mutants for natural product screening was demonstrated further by increased sensitivity of the norA− strain to plant alkaloid antimicrobials, which might be natural MDR substrates.

Development of a Digital Tool to Overcome the Challenges of Rural Food SMEs

Peer reviewed

On roads not taken in the evolution of protein catalysts: Antibody steroid isomerases that use an enamine mechanism

Reactive immunization has emerged as a new tool for the study of biological catalysis. A powerful application resulted in catalytic antibodies that use an enamine mechanism akin to that used by the class I aldolases. With regard to the evolution of enzyme mechanisms, we investigated the utility of an enamine pathway for the allylic rearrangement exemplified by Δ5-3-ketosteroid isomerase (KSI; EC 5.3.3.1). Our aldolase antibodies were found to catalyze the isomerization of both steroid model compounds and steroids. The kinetic and chemical studies showed that the antibodies afforded rate accelerations up to a factor of 104 by means of an enamine mechanism in which imine formation was the rate-determining step. In light of our observations and the enzyme studies by other workers, we suggest that an enamine pathway could have been an early, viable KSI mechanism. Although this pathway is amenable to optimization for increased catalytic power, it appears that certain factors precluded its evolution in known KSI enzymes.

Mössbauer spectroscopy as a tool for the study of activation/inactivation of the transcription regulator FNR in whole cells of Escherichia coli

The global regulator FNR (for fumarate nitrate reduction) controls the transcription of >100 genes whose products facilitate adaptation of Escherichia coli to growth under O2-limiting conditions. Previous Mössbauer studies have shown that anaerobically purified FNR contains a [4Fe-4S]2+ cluster that, on exposure to oxygen, is converted into a [2Fe-2S]2+ cluster, a process that decreases DNA binding by FNR. Using 57Fe Mössbauer spectroscopy of E. coli cells containing overexpressed FNR, we show here that the same cluster conversion also occurs in vivo on exposure to O2. Furthermore, the data show that a significant amount of the [4Fe-4S]2+ cluster is regenerated when the cells are shifted back to an anaerobic environment. The present study also demonstrates that 57Fe Mössbauer spectroscopy can be employed to study the in vivo behavior of (overexpressed) proteins. The use of this technique to study other iron-containing cell components is discussed.

Development of a K(+)-channel probe and its use for identification of an intracellular plant membrane K+ channel.

Polyclonal antibodies were generated against a 9-amino acid, synthetic peptide corresponding to the selectivity filter in the pore region of K(+)-channel proteins. The sequence of amino acids in the ion-conducting pore region of K+ channels is the only highly conserved region of members of this protein family. The objectives of the present work were (i) to determine whether the anti-channel pore peptide antibody was immunoreactive with known K(+)-channel proteins and (ii) to demonstrate the usefulness of the antibody by employing it to identify a newly discovered K(+)-channel protein. Anti-channel pore peptide was immunoreactive with various K(+)-channel subtypes native to a number of different species. Immunoblot analysis demonstrated affinity of the antibody for the drk1, maxi-K, and KAT1 K(+)-channel proteins. Studies also suggested that the anti-channel pore peptide antibody did not immunoreact with membrane proteins other than K+ channels. The anti-channel pore peptide antibody was used to establish the identity of a 62-kDa chloroplast inner envelope polypeptide as a putative component of a K(+)-channel protein. It was concluded that an antibody generated against the conserved pore region/selectivity filter of K+ channels has broad but selective affinity for this class of proteins. This K(+)-channel probe may be a useful tool for identification of K(+)-channel proteins in native membranes.

bioNMF: a versatile tool for non-negative matrix factorization in biology

Medical imaging has become an absolutely essential diagnostic tool for clinical practices; at present, pathologies can be detected with an earliness never before known. Its use has not only been relegated to the field of radiology but also, increasingly, to computer-based imaging processes prior to surgery. Motion analysis, in particular, plays an important role in analyzing activities or behaviors of live objects in medicine. This short paper presents several low-cost hardware implementation approaches for the new generation of tablets and/or smartphones for estimating motion compensation and segmentation in medical images. These systems have been optimized for breast cancer diagnosis using magnetic resonance imaging technology with several advantages over traditional X-ray mammography, for example, obtaining patient information during a short period. This paper also addresses the challenge of offering a medical tool that runs on widespread portable devices, both on tablets and/or smartphones to aid in patient diagnostics.

The Development of an Intervention Tool to Address Challenges in the Medical Treatment of Children with Autism .

Challenges in treating children with an autism spectrum disorder (ASD) in medical settings are identified and discussed. Although research supports interventions for children with ASD including positive reinforcement, environmental modification, and visual supports and systems, limited research on the efficacy of these interventions in medical environments and with specific procedures exists. Based on the available intervention literature, this project proposes a picture schedule reinforcement system for use during blood draw procedures for ASD children with diabetes. Future efforts should include increased education for medical providers and health professionals as psychological interventions continue to inform best practices in care for children with ASD in medical settings.

JRNL: Journal Retention and Needs Listing — A Software Tool for Managing Print Journal Archives

The Journal Retention and Needs Listing (JRNL) program: 1) allows libraries to expose lists of print journals for which they have made retention commitments; 2) express needs (or gaps) in their holdings; and 3) communicate offers to fill the gaps in other participating libraries’ holdings. Multiple library consortia and their member libraries use JRNL to facilitate communication between library staff to identify holding commitments, fill gaps, and guide deselection decisions. JRNL is commonly developed and governed by the participating consortia. Currently, those consortia are the Florida Academic Repository (FLARE), the Association of Southeastern Research Libraries (ASERL)/Washington Research Library Consortium (WRLC), and the Western Regional Storage Trust (WEST).

Dragon Tears: Highlighting the Christian Salvation Message Through the Use of Allegorical Fantasy Fiction

The recent movie versions of the Chronicles of Narnia and the Lord of the Rings Trilogy have raised in the publishing world a public demand for good quality fantasy fiction that can be used as a teaching tool for spreading the Christian salvation message. Dragon Tears was written to fulfill this need, providing young adult readers with both an engaging fantasy story and at the same time, an allegorical format through which to receive the Christian salvation story. Dragon Tears draws its foundational material from two educational backgrounds in religion and creative writing.