Programa com abordagem probabilística do sistema de avaliação de qualidade de taludes Slope Quality Index (SQI)

Dissertação de mestrado integrado em Engenharia Civil

Utilización de biomarcadores para la evaluación integrada de la calidad del agua de la cuenca del río Suquía.Utilization of biomarkers for the integrated evaluation of water quality of the Suquía River Basin.

En los últimos años el grupo de investigación ha caracterizado la calidad de los cuerpos de agua, detectando gradientes de calidad ambiental que se manifiestan por la aparición de tóxicos que generan cambios en la calidad del agua, sedimento y especialmente en la biota. El presente proyecto propone una evaluación integrada de la contaminación de los recursos hídricos abarcando el estudio de las causas de la contaminación y las respuestas biológicas que se producen ante dichas alteraciones. Por ello nuestro objetivo principal es evaluar la contaminación de los recursos acuáticos a través del desarrollo y aplicación de diversas herramientas. El enfoque multidisciplinario del mismo permitirá integrar los análisis de las diferentes áreas de estudio, con el fin de brindarán soluciones al problema generalizado de la contaminación acuática. El fin último es alcanzar una mejor valoración de los cambios temporales y espaciales en la calidad de las cuencas hídricas. Se propone analizar la presencia y concentración de tóxicos en agua, suelo, sedimento y biota conjuntamente con la evaluación de los efectos sobre los organismos a diferentes niveles de organización, lo que permitirá determinar y seleccionar los indicadores más eficientes de la contaminación ambiental. Se desarrollarán biomarcadores moleculares basados en expresión genética en la biota acuática y biomarcadores morfológicos, histológicos y bioquímicos. Además se evaluará el efecto del estrés tóxico sobre los hábitos natatorios de peces utilizando un software recientemente desarrollado por el grupo. También se intensificará la búsqueda de biomarcadores específicos de disrupción endocrina en peces tales como aromatasa, vitelogenina, parámetros estáticos y dinámicos de espermatozoides y comportamiento de cortejo y cópula. Así, el plan propuesto brindará un conjunto de herramientas, con diverso grado de complejidad, para ser usadas en la correcta evaluación del impacto ambiental de las actividades humanas. El grupo de trabajo pretende realizar una fuerte contribución a los conocimientos de base para crear conciencia sobre el problema de las diferentes cuencas en estudio, a fin de llevar a cabo un control sostenido de la calidad de los recursos acuáticos.

Quality control and conduct of genome-wide association meta-analyses.

Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.

MSight: an image analysis software for liquid chromatography-mass spectrometry.

Images obtained from high-throughput mass spectrometry (MS) contain information that remains hidden when looking at a single spectrum at a time. Image processing of liquid chromatography-MS datasets can be extremely useful for quality control, experimental monitoring and knowledge extraction. The importance of imaging in differential analysis of proteomic experiments has already been established through two-dimensional gels and can now be foreseen with MS images. We present MSight, a new software designed to construct and manipulate MS images, as well as to facilitate their analysis and comparison.

Copper filtration in pediatric digital X-ray imaging: its impact on image quality and dose.

The effect of copper (Cu) filtration on image quality and dose in different digital X-ray systems was investigated. Two computed radiography systems and one digital radiography detector were used. Three different polymethylmethacrylate blocks simulated the pediatric body. The effect of Cu filters of 0.1, 0.2, and 0.3 mm thickness on the entrance surface dose (ESD) and the corresponding effective doses (EDs) were measured at tube voltages of 60, 66, and 73 kV. Image quality was evaluated in a contrast-detail phantom with an automated analyzer software. Cu filters of 0.1, 0.2, and 0.3 mm thickness decreased the ESD by 25-32%, 32-39%, and 40-44%, respectively, the ranges depending on the respective tube voltages. There was no consistent decline in image quality due to increasing Cu filtration. The estimated ED of anterior-posterior (AP) chest projections was reduced by up to 23%. No relevant reduction in the ED was noted in AP radiographs of the abdomen and pelvis or in posterior-anterior radiographs of the chest. Cu filtration reduces the ESD, but generally does not reduce the effective dose. Cu filters can help protect radiosensitive superficial organs, such as the mammary glands in AP chest projections.

EORTC Radiation Oncology Group quality assurance platform: establishment of a digital central review facility.

OBJECTIVE: Quality assurance (QA) in clinical trials is essential to ensure treatment is safely and effectively delivered. As QA requirements have increased in complexity in parallel with evolution of radiation therapy (RT) delivery, a need to facilitate digital data exchange emerged. Our objective is to present the platform developed for the integration and standardization of QART activities across all EORTC trials involving RT. METHODS: The following essential requirements were identified: secure and easy access without on-site software installation; integration within the existing EORTC clinical remote data capture system; and the ability to both customize the platform to specific studies and adapt to future needs. After retrospective testing within several clinical trials, the platform was introduced in phases to participating sites and QART study reviewers. RESULTS: The resulting QA platform, integrating RT analysis software installed at EORTC Headquarters, permits timely, secure, and fully digital central DICOM-RT based data review. Participating sites submit data through a standard secure upload webpage. Supplemental information is submitted in parallel through web-based forms. An internal quality check by the QART office verifies data consistency, formatting, and anonymization. QART reviewers have remote access through a terminal server. Reviewers evaluate submissions for protocol compliance through an online evaluation matrix. Comments are collected by the coordinating centre and institutions are informed of the results. CONCLUSIONS: This web-based central review platform facilitates rapid, extensive, and prospective QART review. This reduces the risk that trial outcomes are compromised through inadequate radiotherapy and facilitates correlation of results with clinical outcomes.

Andalusian Health Repository: Promoting the scientific health output among professionals and providing citizens with quality health information

The Andalusian Public Health System (Sistema Sanitario Público de Andalucía -SSPA) Repository is the open environment where all the scientific output generated by the SSPA professionals, resulting from their medical care, research and administrative activities, is comprehensively collected and managed. This repository possesses special features which determined its development: the SSPA organization and its purpose as a health institution, the specific sets of documents that it generates and the stakeholders involved in it. The repository uses DSpace 1.6.2, to which several changes were implemented in order to achieve the SSPA initial goals and requirements. The main changes were: the addition of specific qualifiers to the Metadata Dublin Core scheme, the modification of the submission form, the integration of the MeSH Thesaurus as controlled vocabulary and the optimization of the advanced search tool. Another key point during the setting up of the repository was the initial batch ingest of the documents.

Basic life support teaching in the second year pregraduate medical curriculum: quality of acquisition after 6 months

Purpose of the study: Basic life support (BLS) and automated externaldefibrillation (AED) represent important skills to be acquired duringpregraduate medical training. Since 3 years, our medical school hasintroduced a BLS-AED course (with certification) for all second yearmedical students. Few reports about quality and persistence over timeof BLS-AED learning are available to date in the medical literature.Comprehensive evaluation of students' acquired skills was performedat the end of the 2008 academic year, 6 month after certification.Materials and methods: The students (N = 142) were evaluated duringa 9 minutes «objective structured clinical examination» (OSCE) station.Out of a standardized scenario, they had to recognize a cardiac arrestsituation and start a resuscitation process. Their performance wererecorded on a PC using an Ambuman(TM) mannequin and the AmbuCPR software kit(TM) during a minimum of 8 cycles (30 compressions:2 ventilations each). BLS parameters were systematically checked. Nostudent-rater interactions were allowed during the whole evaluation.Results: Response of the victim was checked by 99% of the students(N = 140), 96% (N = 136) called for an ambulance and/or an AED. Openthe airway and check breathing were done by 96% (N = 137), 92% (N =132) gave 2 rescue breaths. Pulse was checked by 95% (N=135), 100%(N = 142) begun chest compression, 96% (N = 136) within 1 minute.Chest compression rate was 101 ± 18 per minute (mean ± SD), depthcompression 43 ± 8 mm, 97% (N = 138) respected a compressionventilationratio of 30:2.Conclusions: Quality of BLS skills acquisition is maintained during a6-month period after a BLS-AED certification. Main targets of 2005 AHAguidelines were well respected. This analysis represents one of thelargest evaluations of specific BLS teaching efficiency reported. Furtherfollow-up is needed to control the persistence of these skills during alonger time period and noteworthy at the end of the pregraduatemedical curriculum.

Binary proposal for assessing quality of Open Access Institutional Repositories : the case of Spanish repositories

The reason for this study is to propose a new quantitative approach on how to assess the quality of Open Access University Institutional Repositories. The results of this new approach are tested in the Spanish University Repositories. The assessment method is based in a binary codification of a proposal of features that objectively describes the repositories. The purposes of this method are assessing the quality and an almost automatically system for updating the data of the characteristics. First of all a database was created with the 38 Spanish institutional repositories. The variables of analysis are presented and explained either if they are coming from bibliography or are a set of new variables. Among the characteristics analyzed are the features of the software, the services of the repository, the features of the information system, the Internet visibility and the licenses of use. Results from Spanish universities ARE provided as a practical example of the assessment and for having a picture of the state of the development of the open access movement in Spain.

The appropriateness of renal angioplasty: the ANPARIA software: a multidisciplinary expert panel approach

Percutaneous transluminal renal angioplasty (PTRA) is an invasive technique that is costly and involves the risk of complications and renal failure. The ability of PTRA to reduce the administration of antihypertensive drugs has been demonstrated. A potentially greater benefit, which nevertheless remains to be proven, is the deferral of the need for chronic dialysis. The aim of the study (ANPARIA) was to assess the appropriateness of PTRA to impact on the evolution of renal function. A standardized expert panel method was used to assess the appropriateness of medical treatment alone or medical treatment with revascularization in various clinical situations. The choice of revascularization by either PTRA or surgery was examined for each clinical situation. Analysis was based on a detailed literature review and on systematically elicited expert opinion, which were obtained during a two-round modified Delphi process. The study provides detailed responses on the appropriateness of PTRA for 1848 distinct clinical scenarios. Depending on the major clinical presentation, appropriateness of revascularization varied from 32% to 75% for individual scenarios (overal 48%). Uncertainty as to revascularization was 41% overall. When revascularization was appropriate, PTRA was favored over surgery in 94% of the scenarios, except in certain cases of aortic atheroma where sugery was the preferred choice. Kidney size [7 cm, absence of coexisting disease, acute renal failure, a high degree of stenosis (C70%), and absence of multiple arteries were identified as predictive variables of favorable appropriateness ratings. Situations such as cardiac failure with pulmonary edema or acute thrombosis of the renal artery were defined as indications for PTRA. This study identified clinical situations in which PTRA or surgery are appropriate for renal artery disease. We built a decision tree which can be used via Internet: the ANPARIA software (http://www.chu-clermontferrand.fr/anparia/). In numerous clinical situations uncertainty remains as to whether PTRA prevents deterioration of renal function.

A New Imaging Software To Evaluate The Centration Of Capsulorhexis And Intraocular Lens (IOL) After Cataract Surgery

Purpose: IOL centration and stability after cataract surgery is of high interest for cataract surgeons and IOL-producing companies. We present a new imaging software to evaluate the centration of the rhexis and the centration of the IOL after cataract surgery.Methods: We developed, in collaboration with the Biomedical Imaging Group (BIG), EPFL, Lausanne, a new working tool in order to assess precisely outcomes after IOL-implantation, such as ideal capsulorhexis and IOL-centration. The software is a plug-in of ImageJ, a general-purpose image processing and image-analysis package. The specifications of this software are: evaluation of the rhexis-centration and evaluation the position of the IOL in the posterior chamber. The end points are to analyze the quality of the centration of a rhexis after cataract surgery, the deformation of the rhexis with capsular bag retraction and the centration of the IOL after implantation.Results: This software delivers tools to interactively measure the distances between limbus, IOL and capsulorhexis and its changes over time. The user is invited to adjust nodes of three radial curves for the limbus, rhexis and the optic of the IOL. The radial distances of the curves are computed to evaluate the IOL implantation. The user is also able to define patterns for ideal capsulorhexis and optimal IOL-centration. We are going to present examples of calculations after cataract surgery.Conclusions: Evaluation of the centration of the rhexis and of the IOL after cataract surgery is an important end point for optimal IOL implantation after cataract surgery. Especially multifocal or accommodative lenses need a precise position in the bag with a good stability over time. This software is able to evaluate these parameters just after the surgery but also its changes over time. The results of these evaluations can lead to an optimizing of surgical procedures and materials.

Propuesta para incorporar evaluación y pruebas de usabilidad dentro de un proceso de desarrollo de software

Usability is critical to consider an interactive software system successful. Usability testing and evaluation during product development have gained wide acceptance as a strategy to improve product quality. Early introduction of usability perspectives in a product is very important in order to provide a clear visibility of the quality aspects not only for the developers, but also for the testing users as well. However, usability evaluation and testing are not commonly taken into consideration as an essential element of the software development process. Then, this paper exposes a proposal to introduce usability evaluation and testing within a software development through reuse of software artifacts. Additionally, it suggests the introduction of an auditor within the classification of actors for usability tests. It also proposes an improvement of checklists used for heuristics evaluation, adding quantitative and qualitative aspects to them

Quality assurance of the EORTC 22043-30041 trial in post-operative radiotherapy in prostate cancer: Results of the Dummy Run procedure.

BACKGROUND AND PURPOSE: The EORTC 22043-30041 trial investigates the role of the addition of androgen suppression to post-operative radiotherapy in patients who have undergone radical prostatectomy. As part of the quality assurance of radiotherapy (QART) a Dummy Run (DR) procedure was performed. MATERIALS AND METHOD: The protocol included detailed and published delineation guidelines. Participating institutions digitally submitted radiotherapy treatment volumes and a treatment plan for a standard clinical case. Submissions were centrally reviewed using the VODCA software platform. RESULTS: Thirty-eight submissions from thirty-one institutions were reviewed. Six were accepted without comments. Twenty-three were accepted with comments on one or more items: target volume delineation (22), OAR delineation (23), planning and dosimetry (3) or treatment verification (1). Nine submissions were rejected requiring resubmission, seven for target volume delineation reasons alone. Intervention to highlight the importance of delineation guidelines was made prior to the entry of the first patient in the trial. After this, a lower percentage of resubmissions was required. CONCLUSIONS: The EORTC 22043-30041 Dummy Run highlights the need for timely and effective QART in clinical trials. The variation in target volume and OAR definition demonstrates that clinical guidelines and radiotherapy protocols are not a substitute for QART procedures. Early intervention in response to the Dummy Run improved protocol understanding.

Visualization and quality assessment of de novo genome assemblies.

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds.Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.

Estudi de software lliure en diferents entorns

El software lliure està tenint últimament un pes cada cop més important en les empreses, però encara és el gran desconegut per a molta gent. Des de la seva creació als anys 80 fins ara, hi ha hagut un creixement exponencial de software lliure de gran qualitat, oferint eines per a tot tipus de necessitats, eines ofimàtiques, gestors de correu, sistemes de fitxer, sistemes operatius…. Tot aquest moviment no ha passat desapercebut per a molts usuaris i empreses, que s’han aprofitat d’ell per cobrir les seves necessitats. Pel que fa a les empreses, cada cop n’hi ha més que en petita o gran mesura, utilitzen el software lliure, ja sigui per el seu menor cost d’adquisició, o bé per la seva gran fiabilitat o per que és fàcilment adaptable o per no establir cap lligam tecnològic, en definitiva per tenir més llibertat. En el moment de la creació d’una nova empresa, on es parteix de zero en tota la tecnologia informàtica, és el moment menys costòs d’implementar l’arquitectura informàtica amb software lliure, és quan l’impacte que té sobre l’empresa, usuaris i clients és menor. En les empreses que ja tenen un sistema informàtic, caldrà establir un pla de migració, ja sigui total o parcial. La finalitat d’aquest projecte no és la de dir quin software és millor que l’altre o de dir quin s’ha d’instal•lar, sinó el de donar a conèixer el món del software lliure, mostrar part d’aquest software, fer alguna comparativa de software lliure amb software propietari, donant idees i un conjunt de solucions per a empreses, per què una empresa pugui agafar idees d’implementació d’algunes de les solucions informàtiques exposades o seguir algun dels consells proposats. Actualment ja hi ha moltes empreses que utilitzen software lliure. Algunes només n’utilitzen una petita part en les seves instal•lacions, ja que el fet de que una empresa funcioni al 100% amb software lliure, tot i que n’hi comença ha haver, de moment ho considero una mica arriscat, però que en poc temps, aquest fet serà cada cop més habitual.