Identification of motifs in biological sequences using genetic programming

Current tools for motif discovery search patterns that are over-represented in DNA sequences but do not use DNA curvature or cofactors associated with the protein bind. We developed a tool that searches for motifs with a variable gap between patterns. The search is done using a genetic programming algorithm that searches for possible models that could be the motif and tries to fit them in a set of positive sequences with the motif against a control dataset. To evaluate the fitness of the organisms we have created an energy model for each component of the regulated bacterial promoters. The final genetic algorithm is able to find hidden motifs in synthetic sequences and real biological sequences.Les eines actuals per al descobriment de motius busquen patrons que estan sobre-representats a les seqüències d'ADN, però no utilitzen la curvatura de l'ADN o cofactors associats a la unió de la proteïna. Hem desenvolupat una eina que busca motius amb un espaiador variable entre patrons. La cerca es fa mitjançant un algorisme de programació genètica que busca possibles models que podrien ser el motiu i intenta encaixar-los en un conjunt de seqüències positives que inclouen el motiu envers un conjunt de seqüències de control. Per avaluar l'encaix dels organismes hem creat un model d'energia per a cada component dels promotors reguladors bacterians. L'algorisme genètic final és capaç de trobar motius ocults a seqüències sintètiques i seqüències reals.Las herramientas actuales para el descubrimiento de motivos buscan patrones que están sobrerepresentados en las secuencias de ADN, pero no usan la curvatura del ADN o cofactores asociados a la unión de la proteína. Hemos desarrollado una herramienta que busca motivos con un espaciado variable entre patrones. La búsqueda se hace mediante un algoritmo de programación genética que busca posibles modelos que podrían ser el motivo y los intenta encajar en un conjunto de secuencias positivas que incluyen el motivo contra un conjunto de secuencias de control. Para evaluar el encaje de los organismos, hemos creado un modelo de energía para cada componente de los promotores reguladores bacterianos. El algoritmo genético final es capaz de encontrar motivos ocultos en secuencias sintéticas y secuencias reales

Geometric-based Optimization Algorithms for Cable Routing and Branching in Cluttered Environments

The need for designing lighter and more compact systems often leaves limited space for planning routes for the connectors that enable interactions among the system’s components. Finding optimal routes for these connectors in a densely populated environment left behind at the detail design stage has been a challenging problem for decades. A variety of deterministic as well as heuristic methods has been developed to address different instances of this problem. While the focus of the deterministic methods is primarily on the optimality of the final solution, the heuristics offer acceptable solutions, especially for such problems, in a reasonable amount of time without guaranteeing to find optimal solutions. This study is an attempt to furthering the efforts in deterministic optimization methods to tackle the routing problem in two and three dimensions by focusing on the optimality of final solutions. The objective of this research is twofold. First, a mathematical framework is proposed for the optimization of the layout of wiring connectors in planar cluttered environments. The problem looks at finding the optimal tree network that spans multiple components to be connected with the aim of minimizing the overall length of the connectors while maximizing their common length (for maintainability and traceability of connectors). The optimization problem is formulated as a bi-objective problem and two solution methods are proposed: (1) to solve for the optimal locations of a known number of breakouts (where the connectors branch out) using mixed-binary optimization and visibility notion and (2) to find the minimum length tree that spans multiple components of the system and generates the optimal layout using the previously-developed convex hull based routing. The computational performance of these methods in solving a variety of problems is further evaluated. Second, the problem of finding the shortest route connecting two given nodes in a 3D cluttered environment is considered and addressed through deterministically generating a graphical representation of the collision-free space and searching for the shortest path on the found graph. The method is tested on sample workspaces with scattered convex polyhedra and its computational performance is evaluated. The work demonstrates the NP-hardness aspect of the problem which becomes quickly intractable as added components or increase in facets are considered

Applications of aerospace technology in biology and medicine

Utilization of National Aeronautics and Space Administration (NASA) technology in medicine is discussed. The objective is best obtained by stimulation of the introduction of new or improved commercially available medical products incorporating aerospace technology. A bipolar donor/recipient model of medical technology transfer is presented to provide a basis for the team's methodology. That methodology is designed to: (1) identify medical problems and NASA technology that, in combination, constitute opportunities for successful medical products; (2) obtain the early participation of industry in the transfer process; and (3) obtain acceptance by the medical community of new medical products based on NASA technology. Two commercial transfers were completed: the Stowaway, a lightweight wheelchair that provides mobility for the disabled and elderly in the cabin of commercial aircraft, and Micromed, a portable medication infusion pump for the reliable, continuous infusion of medications such as heparin or insulin. The marketing and manufacturing factors critical to the commercialization of the lightweight walker incorporating composite materials were studied. Progress was made in the development and commercialization of each of the 18 currently active projects

Computational design of steady 3D dissection puzzles

Dissection puzzles require assembling a common set of pieces into multiple distinct forms. Existing works focus on creating 2D dissection puzzles that form primitive or naturalistic shapes. Unlike 2D dissection puzzles that could be supported on a tabletop surface, 3D dissection puzzles are preferable to be steady by themselves for each assembly form. In this work, we aim at computationally designing steady 3D dissection puzzles. We address this challenging problem with three key contributions. First, we take two voxelized shapes as inputs and dissect them into a common set of puzzle pieces, during which we allow slightly modifying the input shapes, preferably on their internal volume, to preserve the external appearance. Second, we formulate a formal model of generalized interlocking for connecting pieces into a steady assembly using both their geometric arrangements and friction. Third, we modify the geometry of each dissected puzzle piece based on the formal model such that each assembly form is steady accordingly. We demonstrate the effectiveness of our approach on a wide variety of shapes, compare it with the state-of-the-art on 2D and 3D examples, and fabricate some of our designed puzzles to validate their steadiness

EVALUATION OF CORROSION PROPERTIES FOR USE OF AZ31B IN BIOABSORBABLE STENTS AND IN VIVO CORROSION RATE PREDICTION USING FEA

AZ31B was heat treated to evoke more controlled and uniform corrosion. 1/16” diameter AZ31B wire was cut into six samples each 1” long. The samples underwent heat treatments following ASTM B661-06. Samples were weighed and placed into three different in vitro environments. In the first scenario two samples of each heat treatment were individually placed in 50 ml of saline solution at 0.9% sodium, in a static test tube at 37°C temperature. Two samples were placed in 100 ml of 0.9% saline solution in a 250 ml stirring beaker with an average whirlpool depth of 1”. Two of each sample was placed into 50 ml of saline solution at 0.9% sodium at room temperature. The final experiment placed an air cooled sample in 0.9% saline solution in a 6mm tube with a flow rate of 325ml/min at 37°C. All samples were removed at a 3 day, dried, and weighed. Mass loss was recorded, and samples were returned to solution. Samples ranged from 32% mass loss in quenched samples to 17% mass loss in the control samples (as manufactured) over fifteen days. All samples failed as possible stent candidate materials do to the unpredictability of their corrosion in both rate and uniformity. Experimental data was used to create a theoretical mathematic model and COMSOL FEA model that synthesized experimental data and physiological effects such as wall shear stress to predict the corrosion rate for future testing as well as stent geometry optimization to promote vascular health and limit the restenosis event

Reducing Thermal Bridging and Understanding Second-Order Effects in Concrete Sandwich Wall Panels

Structural engineers have traditionally detailed structures with structural and fabrication efficiency in mind, but often based on a limited understanding of thermal efficiency. Some connection designs can create significant thermal bridging, leading to unnecessary heat transfer and even premature degradation through condensation. Thermal bridging occurs when heat transfer is given a path through a more conductive material like concrete or steel rather than insulation. Concrete sandwich wall panels (SWP) tend to be highly efficient at preventing heat transfer in the middle of panels, with greatest heat transfer occurring at connections. This project identified thermally efficient details for future SWP construction to reduce heat transfer, lessen environmental impact, and increase sustainability of SWP structures. It can be particularly difficult to avoid thermal bridging at corbel connections, so 12 corbel specimens were created and tested to provide alternative corbel design options for engineers. Nine details were successfully created and are presented. Corbel specimens were modeled using the Beam-Spring Method with good agreement. After validating the Beam-Spring Model, a parametric study investigated effectiveness of the PCI Second Order Analysis and the effect of length, panel stiffness, and wythe configuration on SWP behavior under axial and flexural loads

Field Testing of a Stochastic Planner for ASV Navigation Using Satellite Images

We introduce a multi-sensor navigation system for autonomous surface vessels (ASV) intended for water-quality monitoring in freshwater lakes. Our mission planner uses satellite imagery as a prior map, formulating offline a mission-level policy for global navigation of the ASV and enabling autonomous online execution via local perception and local planning modules. A significant challenge is posed by the inconsistencies in traversability estimation between satellite images and real lakes, due to environmental effects such as wind, aquatic vegetation, shallow waters, and fluctuating water levels. Hence, we specifically modelled these traversability uncertainties as stochastic edges in a graph and optimized for a mission-level policy that minimizes the expected total travel distance. To execute the policy, we propose a modern local planner architecture that processes sensor inputs and plans paths to execute the high-level policy under uncertain traversability conditions. Our system was tested on three km-scale missions on a Northern Ontario lake, demonstrating that our GPS-, vision-, and sonar-enabled ASV system can effectively execute the mission-level policy and disambiguate the traversability of stochastic edges. Finally, we provide insights gained from practical field experience and offer several future directions to enhance the overall reliability of ASV navigation systems.Comment: 33 pages, 20 figures. Project website https://pcctp.github.io. arXiv admin note: text overlap with arXiv:2209.1186

Enhancing Variability Modeling in Process-Aware Information Systems through Change Patterns

[EN] The increasing adoption of process-aware information systems (PAISs) together with the high variability in business processes has resulted in collections of process families. These families correspond to a business process model and its variants, which can comprise hundreds or thousands of different ways of realizing this process. Modeling and managing process variability in this context can be very challenging due to the size of these families. Motivated by this challenge, several approaches enabling process variability have been developed. However, with these approaches PAIS engineers usually are required to model and manage one by one all the elements of a process family and ensure its correctness by their own. This can be tedious and error-prone especially when a process family comprises hundreds or thousands of process variants. For example, variability may not be properly reflected since PAIS engineers need to be aware of each variation of each process variant. Thus, there is a need of methods that allow PAIS engineers to model process variability more explicitly, especially at a level of abstraction higher than the one provided by the existing process variability approaches. However, how process variability is represented in existing approaches becomes critical for these methods (e.g., what language constructs are used to model process variability). In this context, the use of modeling patterns (reusable solutions to a commonly occurring problem) is a promising way to address these issues. For example, patterns have been proved as an efficient solution to model individual business processes. The objective of this thesis is to enhance the modeling of variability in process families through change patterns. First, we conduct a systematic study to analyze existing process variability approaches regarding their expressiveness with respect to process variability modeling as well as their process support. Thus, we can identify how process variability is actually modeled by existing approaches (i.e., a core set of variability-specific language constructs). In addition, based on the obtained empirical evidence, we derive the VIVACE framework, a complete characterization of process variability which comprises also a core set of features fostering process variability. VIVACE enables PAIS engineers to evaluate existing process variability approaches as well as to select that variability approach meeting their requirements best. In addition, it helps process engineers in dealing with PAISs supporting process variability. Second, to facilitate variability modeling in process families, based on the identified language constructs, we present a set of 10 change patterns and show how they can be implemented in a process variability approach. In particular, these patterns support process family modeling and evolution and are able to ensure process family correctness. In order to prove their effectiveness and analyze their suitability, we applied these change patterns in a real scenario. More concretely, we conduct a case study with a safety standard with a high degree of variability. The case study results show that the application of the change patterns can reduce the effort for process family modeling in a 34% and for evolution in a 40%. In addition, we have analyzed how PAIS engineers apply the patterns and their perceptions of this application. Most of them expressed some benefit when applying the change patterns, did not perceived an increase of mental effort for applying the patterns, and agreed upon the usefulness and ease of use of the patterns.[ES] La creciente adopción de sistemas de información dirigidos por procesos de negocio (PAIS) junto con la alta variabilidad en dichos procesos, han dado lugar a la aparición de colecciones de familias de procesos. Estas familias están constituidas por un modelo de proceso de negocio y sus variantes, las cuales pueden comprender entre cientos y miles de diferentes formas de llevar a cabo ese proceso. Gestionar la variabilidad en este contexto puede resultar muy difícil dado el tamaño que estas familias pueden alcanzar. Motivados por este desafío, se han desarrollado varias soluciones que permiten la gestión de la variabilidad en los procesos de negocio. Sin embargo, con estas soluciones los ingenieros deben crear y gestionar uno por uno todos los elementos de las familias de procesos y asegurar ellos mismos su corrección. Esto puede resultar tedioso y propenso a errores especialmente cuando las familias están compuestas de miles de variantes. Por ejemplo, la variabilidad puede no quedar adecuadamente representada ya que los ingenieros deben ser conscientes de todas y cada una de las variaciones de todas las variantes. Así, son necesarios nuevos métodos que permitan modelar la variabilidad de los procesos de una manera más explícita, a un nivel de abstracción más alto del proporcionado por las soluciones actuales. Sin embargo, cómo se representa la variabilidad en estos métodos resulta crítico (ej.: qué primitivas se utilizan). En este contexto, el uso de patrones de modelado (soluciones reutilizables a un problema recurrente) resultan un camino prometedor. Por ejemplo, los patrones han sido probados como una solución eficaz para gestionar procesos de negocio individuales. El objetivo de esta tesis es mejorar el modelado de la variabilidad en las familias de procesos a través del uso de patrones de cambio. En primer lugar, hemos llevado a cabo un estudio sistemático con el fin de analizar las soluciones existentes que permiten gestionar la variabilidad en los procesos, así como el soporte que estas proporcionan. Así, hemos sido capaces de identificar y analizar cuál es el conjunto básico de primitivas específicas para representar la variabilidad. Además, basándonos en la evidencia empírica obtenida, hemos derivado el marco de evaluación VIVACE, el cual recoge las primitivas de variabilidad y un conjunto básico de características que favorecen la variabilidad en los procesos. El principal objetivo de VIVACE es conformar una completa caracterización de la variabilidad en los procesos de negocio. Asimismo, VIVACE permite evaluar las soluciones que gestionan la variabilidad en los procesos, así como seleccionar la solución que se ajuste mejor a sus necesidades. Finalmente, VIVACE puede ayudar a los ingenieros a gestionar PAISs con variabilidad. En segundo lugar, para facilitar el modelado de la variabilidad en las familias de procesos, basándonos en las primitivas identificadas, hemos definido un conjunto de 10 patrones de cambio y hemos mostrado cómo estos patrones pueden ser implementados. En particular, estos patrones ayudan al modelado y la evolución de familias de procesos y son capaces de garantizar la corrección de la propia familia. Para probar su efectividad y analizar su idoneidad, hemos aplicado estos patrones de cambio en un escenario real. En concreto, hemos llevado a cabo un caso de estudio con un estándar de seguridad con un alto nivel de variabilidad. Los resultados de este caso demuestran que la aplicación de nuestros patrones de cambio puede reducir el esfuerzo para el modelado de familias de procesos en un 34% y para la evolución de esos modelos en un 40%. Además, hemos analizado cómo los ingenieros aplican los patrones y cuáles son sus percepciones de esta aplicación. Como resultado, la mayoría de ellos encontró beneficios al aplicar los patrones. Además, no percibieron un aumento en el esfuerzo mental necesario para aplicarlos y estuvieron de acuerdo en la utilid[CA] La creixent adopció de sistemes d'informació dirigits per processos de negoci (PAIS) junt amb l'alta variabilitat en eixos processos, han donat lloc a la aparició de col·leccions de famílies de processos. Estes famílies es formen de un model de procés de negoci i les seues variants, les quals poden comprendre entre cents i milers de diferents formes de dur a terme eixe procés. Modelar la variabilitat dels processos en este context pot resultar molt difícil donat la grandària que aquestes famílies poden aconseguir. Motivats per este desafiament, s'han desenvolupat diverses solucions que permeten la gestió de la variabilitat en els processos de negoci. No obstant, amb aquestes solucions els enginyers que treballen amb PAIS han de crear i gestionar un a un tots els elements de les famílies de processos i assegurar ells mateixos la seua correcció. Això pot resultar tediós i propens a errors especialment quan les famílies es componen de cents o milers de variants. Per exemple, la variabilitat pot no quedar adequadament representada ja que els enginyers han de ser conscients de totes i cadascuna una de les variacions de totes les variants. Per quest motiu, son necessaris nous mètodes que permeten als enginyers de PAIS modelar la variabilitat dels processos de manera més explícita, sobretot a un nivell d'abstracció més alt del proporcionat per les solucions actuals. No obstant, com es representa la variabilitat en aquestos mètodes resulta crític (ex.: quines primitives s'utilitzen per a modelar la variabilitat en els processos). En aquest context, l'ús de patrons de modelatge (solucions reutilitzables a un problema recurrent) resulten un camí prometedor. Per exemple, els patrons han sigut provats com una solució eficaç per modelar i gestionar processos de negoci individuals. L'objectiu d'aquesta tesi 'es millorar el modelatge de la variabilitat en les famílies de processos a través de l'ús de patrons de canvi. En primer lloc, hem dut a terme un estudi sistemàtic per a analitzar les solucions existents per a gestionar la variabilitat en els processos, així com el suport que aquestes proporcionen. D'aquesta manera, som capaços d'identificar i analitzar quin 'es el conjunt bàsic de primitives específiques per a representar la variabilitat. A més, basant-nos en l'evidència empírica obtinguda, hem derivat el marc d'evacuació VIVACE, el qual arreplega les primitives de variabilitat i un conjunt bàsic de característiques que afavoreixen la variabilitat en els processos. Així mateix, VIVACE permet als enginyers de PAIS avaluar les solucions per a gestionar la variabilitat en els processos, així com seleccionar la solució que s'ajusta millor a les seues necessitats. Finalment, VIVACE també pot ajudar als enginyers a gestionar PAISs que donen suport a aquesta variabilitat. En segon lloc, per a facilitar el modelatge de la variabilitat en les famílies de processos, basant-nos en les primitives identificades, hem definit un conjunt de 10 patrons de canvi i hem mostrat com aquestos poden ser implementats. En particular, estos patrons ajuden al modelatge i l'evolució de famílies de processos i garanteixen la correcció de la pròpia família. Per a provar la seua efectivitat i analitzar la seua idoneïtat, hem aplicat els patrons de canvi en un escenari real. En particular, hem dut a terme un cas d'estudi amb un estàndard de seguretat amb un alt nivell de variabilitat. Els resultats de aquest cas demostren que l'aplicació dels nostres patrons de canvi poden reduir l'esforç per al modelatge de famílies de processos en un 34% i per a l'evolució de eixos models en un 40%. A més, hem analitzat com els enginyers de PAIS apliquen els patrons i quines son les seues percepcions d'esta aplicació. Com a resultat, la majoria d'ells va trobar beneficis al aplicar els patrons de canvi. A més, no van percebre un augment en l'esforç mental necessari per a aplicar-los i van estar d'acord en la utilitat i fAyora Esteras, C. (2015). Enhancing Variability Modeling in Process-Aware Information Systems through Change Patterns [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/58426TESI

Improving Loss Estimation for Woodframe Buildings. Volume 2: Appendices

This report documents Tasks 4.1 and 4.5 of the CUREE-Caltech Woodframe Project. It presents a theoretical and empirical methodology for creating probabilistic relationships between seismic shaking severity and physical damage and loss for buildings in general, and for woodframe buildings in particular. The methodology, called assembly-based vulnerability (ABV), is illustrated for 19 specific woodframe buildings of varying ages, sizes, configuration, quality of construction, and retrofit and redesign conditions. The study employs variations on four basic floorplans, called index buildings. These include a small house and a large house, a townhouse and an apartment building. The resulting seismic vulnerability functions give the probability distribution of repair cost as a function of instrumental ground-motion severity. These vulnerability functions are useful by themselves, and are also transformed to seismic fragility functions compatible with the HAZUS software. The methods and data employed here use well-accepted structural engineering techniques, laboratory test data and computer programs produced by Element 1 of the CUREE-Caltech Woodframe Project, other recently published research, and standard construction cost-estimating methods. While based on such well established principles, this report represents a substantially new contribution to the field of earthquake loss estimation. Its methodology is notable in that it calculates detailed structural response using nonlinear time-history structural analysis as opposed to the simplifying assumptions required by nonlinear pushover methods. It models physical damage at the level of individual building assemblies such as individual windows, segments of wall, etc., for which detailed laboratory testing is available, as opposed to two or three broad component categories that cannot be directly tested. And it explicitly models uncertainty in ground motion, structural response, component damageability, and contractor costs. Consequently, a very detailed, verifiable, probabilistic picture of physical performance and repair cost is produced, capable of informing a variety of decisions regarding seismic retrofit, code development, code enforcement, performance-based design for above-code applications, and insurance practices