Developing an aquaponics system to learn sustainability and social compromise skills

The goal of this project, one of the proposals of the EPS@ISEP Spring 2014, was to develop an Aquaponics System. Over recent years Aquaponics systems have received increased attention since they contribute to reduce the strain on resources within 1st and 3rd world countries. Aquaponics is the combination of Hydroponics and Aquaculture, mimicking a natural environment in order to successfully apply and enhance the understanding of natural cycles within an indoor process. Using this knowledge of natural cycles, it was possible to create a system with capabilities similar to that of a natural environment with the support of electronics, enhancing the overall efficiency of the system. The multinational team involved in the development of this system was composed of five students from five countries and fields of study. This paper describes their solution, including the overall design, the technology involved and the benefits it can bring to the current market. The team was able to design and render the Computer Aided Design (CAD) drawings of the prototype, assemble all components, successfully test the electronics and comply with the budget. Furthermore, the designed solution was supported by a product sustainability study and included a specific marketing plan. Last but not least, the students enrolled in this project obtained new multidisciplinary knowledge and increased their team work and cross-cultural communication skills.

Development of procedures for the design, optimization and manufacturing of customized orthopaedic and trauma implants: Geometrical/anatomical modelling from 3D medical imaging

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

Gestió d'un magatzem de fruits secs

Estudi i disseny de la implantació d'un ERP (Enterprise Resource Planning) en una fàbrica de fruits secs.

Planificació, anàlisi i disseny d'un programari de gestió d'un magatzem d'olives i conserves

Disseny d'un programari de gestió de magatzems on quedin reflectides les seves entrades, sortides i altres operacions pròpies dels magatzems. El programari ha de ser escalable i perdurar en el temps a més a més de permetre operacions d¿actualització, esborrat, addicció de dades i les operacionsfonamentals de consulta.

Variability of ascending aorta diameter measurements as assessed with electrocardiography-gated multidetector computerized tomography and computer assisted diagnosis software.

Recently, morphometric measurements of the ascending aorta have been done with ECG-gated multidector computerized tomography (MDCT) to help the development of future novel transcatheter therapies (TCT); nevertheless, the variability of such measurements remains unknown. Thirty patients referred for ECG-gated CT thoracic angiography were evaluated. Continuous reformations of the ascending aorta, perpendicular to the centerline, were obtained automatically with a commercially available computer aided diagnosis (CAD). Then measurements of the maximal diameter were done with the CAD and manually by two observers (separately). Measurements were repeated one month later. The Bland-Altman method, Spearman coefficients, and a Wilcoxon signed-rank test were used to evaluate the variability, the correlation, and the differences between observers. The interobserver variability for maximal diameter between the two observers was up to 1.2 mm with limits of agreement [-1.5, +0.9] mm; whereas the intraobserver limits were [-1.2, +1.0] mm for the first observer and [-0.8, +0.8] mm for the second observer. The intraobserver CAD variability was 0.8 mm. The correlation was good between observers and the CAD (0.980-0.986); however, significant differences do exist (P<0.001). The maximum variability observed was 1.2 mm and should be considered in reports of measurements of the ascending aorta. The CAD is as reproducible as an experienced reader.

Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors

Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors (NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the highly active antiretroviral therapy in combination with other anti-HIV drugs. However, the rapid emergence of drug-resistant viral strains has limited the successful rate of the anti-HIV agents. Computational methods are a significant part of the drug design process and indispensable to study drug resistance. In this review, recent advances in computer-aided drug design for the rational design of new compounds against HIV-1 RT using methods such as molecular docking, molecular dynamics, free energy calculations, quantitative structure-activity relationships, pharmacophore modelling and absorption, distribution, metabolism, excretion and toxicity prediction are discussed. Successful applications of these methodologies are also highlighted.

To Monty Kier, a friendly tribute.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Exploring unfrequent events with accelerated molecular dynamics simulations: from photochemistry to drug design

La meva incorporació al grup de recerca del Prof. McCammon (University of California San Diego) en qualitat d’investigador post doctoral amb una beca Beatriu de Pinós, va tenir lloc el passat 1 de desembre de 2010; on vaig dur a terme les meves tasques de recerca fins al darrer 1 d’abril de 2012. El Prof. McCammon és un referent mundial en l’aplicació de simulacions de dinàmica molecular (MD) en sistemes biològics d’interès humà. La contribució més important del Prof. McCammon en la simulació de sistemes biològics és el desenvolupament del mètode de dinàmiques moleculars accelerades (AMD). Les simulacions MD convencionals, les quals estan limitades a l’escala de temps del nanosegon (~10-9s), no son adients per l’estudi de sistemes biològics rellevants a escales de temps mes llargues (μs, ms...). AMD permet explorar fenòmens moleculars poc freqüents però que son clau per l’enteniment de molts sistemes biològics; fenòmens que no podrien ser observats d’un altre manera. Durant la meva estada a la “University of California San Diego”, vaig treballar en diferent aplicacions de les simulacions AMD, incloent fotoquímica i disseny de fàrmacs per ordinador. Concretament, primer vaig desenvolupar amb èxit una combinació dels mètodes AMD i simulacions Car-Parrinello per millorar l’exploració de camins de desactivació (interseccions còniques) en reaccions químiques fotoactivades. En segon lloc, vaig aplicar tècniques estadístiques (Replica Exchange) amb AMD en la descripció d’interaccions proteïna-lligand. Finalment, vaig dur a terme un estudi de disseny de fàrmacs per ordinador en la proteïna-G Rho (involucrada en el desenvolupament de càncer humà) combinant anàlisis estructurals i simulacions AMD. Els projectes en els quals he participat han estat publicats (o estan encara en procés de revisió) en diferents revistes científiques, i han estat presentats en diferents congressos internacionals. La memòria inclosa a continuació conté més detalls de cada projecte esmentat.

SwissParam: a fast force field generation tool for small organic molecules.

The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch.

Maintenance Asset Management Project -- Phase II, July 31, 2013

Expanded abstract: Iowa Department of Transportation (IA DOT) is finalizing research to streamline field inventory/inspection of culverts by Maintenance and Construction staff while maximizing the use of tablet technologies. The project began in 2011 to develop some new best practices for field staff to assist in the inventory, inspection and maintenance of assets along the roadway. The team has spent the past year working through the complexities of identifying the most appropriate tablet hardware for field data collection. A small scale deployment of tablets occurred in spring of 2013 to collect several safety related assets (culverts, signs, guardrail, and incidents). Data can be collected in disconnected or connected modes and there is an associated desktop environment where data can be viewed and queried after being synced into the master database. The development of a deployment plan and related workflow processes are underway; which will eventually feed information into IA DOTs larger asset management system and make the information available for decision making. The team is also working with the IA DOT Design Office on Computer Aided Drafting (CAD) data processing and the IA DOT Construction office with a new digital As-Built plan process to leverage the complete data life-cycle so information can be developed once and leveraged by the Maintenance staff farther along in the process.

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.

Tuning the design procedures for laser processed microwave mechanics

This research has been focused at the development of a tuned systematic design methodology, which gives the best performance in a computer aided environment and utilises a cross-technological approach, specially tested with and for laser processed microwave mechanics. A tuned design process scheme is also presented. Because of the currently large production volumes of microwave and radio frequency mechanics even slight improvements of design methodologies or manufacturing technologies would give reasonable possibilities for cost reduction. The typical number of required iteration cycles could be reduced to one fifth of normal. The research area dealing with the methodologies is divided firstly into a function-oriented, a performance-oriented or a manufacturability-oriented product design. Alternatively various approaches can be developed for a customer-oriented, a quality-oriented, a cost-oriented or an organisation-oriented design. However, the real need for improvements is between these two extremes. This means that the effective methodology for the designers should not be too limited (like in the performance-oriented design) or too general (like in the organisation-oriented design), but it should, include the context of the design environment. This is the area where the current research is focused. To test the developed tuned design methodology for laser processing (TDMLP) and the tuned optimising algorithm for laser processing (TOLP), seven different industrial product applications for microwave mechanics have been designed, CAD-modelled and manufactured by using laser in small production series. To verify that the performance of these products meets the required level and to ensure the objectiveness ofthe results extensive laboratory tests were used for all designed prototypes. As an example a Ku-band horn antenna can be laser processed from steel in 2 minutes at the same time obtaining a comparable electrical performance of classical aluminium units or the residual resistance of a laser joint in steel could be limited to 72 milliohmia.

Evolutionary computing in search-based software engineering

This master’s thesis aims to study and represent from literature how evolutionary algorithms are used to solve different search and optimisation problems in the area of software engineering. Evolutionary algorithms are methods, which imitate the natural evolution process. An artificial evolution process evaluates fitness of each individual, which are solution candidates. The next population of candidate solutions is formed by using the good properties of the current population by applying different mutation and crossover operations. Different kinds of evolutionary algorithm applications related to software engineering were searched in the literature. Applications were classified and represented. Also the necessary basics about evolutionary algorithms were presented. It was concluded, that majority of evolutionary algorithm applications related to software engineering were about software design or testing. For example, there were applications about classifying software production data, project scheduling, static task scheduling related to parallel computing, allocating modules to subsystems, N-version programming, test data generation and generating an integration test order. Many applications were experimental testing rather than ready for real production use. There were also some Computer Aided Software Engineering tools based on evolutionary algorithms.

Monikappalesysteemin esikäsittelijä kaupallisessa ympäristössä

Työn tavoitteena oli tehdä monikappalesysteemin esikäsittelijä, joka toimii CAD-ohjelmiston yhteydessä. CAD-ohjelmistoksi valittiin SolidWorks-ohjelmisto. Esikäsittelijästä tehtiin yhteensopiva monikappaledynamiikan simulointi ohjelmiston kanssa, joka on kehitetty Lappeenrannan teknillisessä yliopistossa. Aikaansaadun esikäsittelijän avulla pystytään tuottamaan monikappaledynamiikan simuloinnissa tarvittavat lähtötiedot. Lähtötiedot esikäsittelijä laskee käyttäjän tekemästä kokoonpanokuvasta ja käyttäjän antamista tiedoista. Esikäsittelijän toiminta verifioitiin kaupallisin simulointiohjelmisto ADAMS:n avulla. Esikäsittelijän todettiin toimivan luotettavasti ja täyttävän sille asetetut vaatimukset. Lisäksi esikäsittelijän todettiin nopeuttavan huomattavasti simulointimallien tekoa.

Protein pocket and ligand shape comparison and its application in virtual screening.

Understanding molecular recognition is one major requirement for drug discovery and design. Physicochemical and shape complementarity between two binding partners is the driving force during complex formation. In this study, the impact of shape within this process is analyzed. Protein binding pockets and co-crystallized ligands are represented by normalized principal moments of inertia ratios (NPRs). The corresponding descriptor space is triangular, with its corners occupied by spherical, discoid, and elongated shapes. An analysis of a selected set of sc-PDB complexes suggests that pockets and bound ligands avoid spherical shapes, which are, however, prevalent in small unoccupied pockets. Furthermore, a direct shape comparison confirms previous studies that on average only one third of a pocket is filled by its bound ligand, supplemented by a 50 % subpocket coverage. In this study, we found that shape complementary is expressed by low pairwise shape distances in NPR space, short distances between the centers-of-mass, and small deviations in the angle between the first principal ellipsoid axes. Furthermore, it is assessed how different binding pocket parameters are related to bioactivity and binding efficiency of the co-crystallized ligand. In addition, the performance of different shape and size parameters of pockets and ligands is evaluated in a virtual screening scenario performed on four representative targets.