PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models

[Abstract] Background Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area under active research because it could be the cause of many complex traits. The most common way to specify an epistasis interaction is through a penetrance table. Results This paper presents PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. Unlike other tools available in the bibliography, PyToxo is able to work with high-order models and realistic penetrance and heritability values, achieving high-precision results in a short time. In addition, PyToxo is distributed as open-source software and includes several interfaces to ease its use. Conclusions PyToxo provides the scientific community with a useful tool to evaluate algorithms and methods that can detect high-order epistasis to continue advancing in the discovery of the causes behind complex diseases.This study and publication costs were funded by the Ministry of Science and Innovation of Spain (grant PID2019-104184RB-I00/AEI/10.13039/501100011033) and by Xunta de Galicia and FEDER funds of the EU (CITIC-Centro de Investigación de Galicia accreditation, grant ED431G 2019/01; Consolidation Program of Competitive Reference Groups, grant ED431C 2021/30). CP was funded by the Ministry of Education of Spain (grant FPU16/01333). The funders did not play any role in the design of the study, the collection, analysis, and interpretation of data, or in writing of the manuscriptXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431C 2021/3

Segmentación de la Luz Aórtica en Imágenes de Resonancia Magnética para Guiado de Catéteres Aórticos

Los procedimientos de cateterismo se han convertido en una herramienta fundamental para las intervenciones cardiovasculares. El proyecto SCATh pretende facilitar el guiado del catéter a partir de un modelo preoperatorio del paciente basado en imágenes 3D, para lo que se requiere la segmentación de la luz y la pared aórtica. Aunque la mayoría de los centros hacen uso de CTA, está estudiándose el uso de imágenes de RM para este fin, puesto que puede permitir la segmentación de la luz y la pared aórtica sin el uso de agentes de contraste nefrotóxicos. Se ha implementado un método de segmentación de la luz de la aorta en imágenes de RM sin agentes de contraste basado en el uso de un algoritmo de realzado de estructuras vasculare

Extracción Automática de la Línea Central de Estructuras Tubulares: Implementación Matricial

Se propone una nueva implementación matricial de un algoritmo para la extracción automática de la línea central de estructuras tubulares. El algoritmo seleccionado calcula la línea central de estructuras complejas sin la necesidad de interacción con el usuario. En el trabajo se explica detalladamente cómo llevar a cabo la implementación matricial utilizando el lenguaje de computación de Matlab. La implementación matricial permite el cálculo de la línea central en pocos segundos, mejorando en varios grados de magnitud la implementación disponible en ITK

A comparative study between wmms and tls for the stability analysis of the San Pedro church barrel vault by means of the finite element method

Stability of masonry constructions is highly conditioned by the geometric disposition of its elements due to its low tensile strength and great compressive mechanical properties. Under this framework, this paper attempts to evaluate the suitability of a wearable mobile mapping solution, equipped in a backpack and based on the well-known simultaneous location and mapping paradigm, for the structural diagnosis of historical constructions. To evaluate the suitability of this device, the structural analysis obtained is compared with a high precision terrestrial laser scanner, which is considered as ground truth. The Romanesque church of San Pedro (Becerril del Carpio, Spain) was selected as a study case. This construction, initially conceived in the XIIIth century, has experimented in the past a soil settlement promoting the leaning of the north wall, several plastic hinges in its barrel vault and a visible geometrical deformation. The comparison of both techniques was carried out at different levels: i) an evaluation of the time needed to obtain the point cloud of the church; ii) an accuracy assessment based on the comparison of a terrestrial network using artificial spheres as checkpoints and; iii) an evaluation of the discrepancies, in terms of safety factor and collapse topology, found during the advance numerical evaluation of the barrel vault by means of the finite element method. This comparison places this wearable mobile mapping solution as an interesting tool for the creation of advanced numerical simulations to evaluate the structural stability of historical constructionsJunta de Castilla y León | Ref. SA075P17FEDER | Ref. SOE1/P5/P025

SkyCDS: A resilient content delivery service based on diversified cloud storage

Cloud-based storage is a popular outsourcing solution for organizations to deliver contents to end-users. However, there is a need for contingency plans to ensure service provision when the provider either suffers outages or is going out of business. This paper presents SkyCDS: a resilient content delivery service based on a publish/subscribe overlay over diversified cloud storage. SkyCDS splits the content delivery into metadata and content storage flow layers. The metadata flow layer is based on publish-subscribe patterns for insourcing the metadata control back to content owner. The storage layer is based on dispersal information over multiple cloud locations with which organizations outsource content storage in a controlled manner. In SkyCDS, the content dispersion is performed on the publisher side and the content retrieving process on the end-user side (the subscriber), which reduces the load on the organization side only to metadata management. SkyCDS also lowers the overhead of the content dispersion and retrieving processes by taking advantage of multi-core technology. A new allocation strategy based on cloud storage diversification and failure masking mechanisms minimize side effects of temporary, permanent cloud-based service outages and vendor lock-in. We developed a SkyCDS prototype that was evaluated by using synthetic workloads and a study case with real traces. Publish/subscribe queuing patterns were evaluated by using a simulation tool based on characterized metrics taken from experimental evaluation. The evaluation revealed the feasibility of SkyCDS in terms of performance, reliability and storage space profitability. It also shows a novel way to compare the storage/delivery options through risk assessment. (C) 2015 Elsevier B.V. All rights reserved.The work presented in this paper has been partially supported by EU under the COST programme Action IC1305, Network for Sustainable Ultrascale Computing (NESUS)

Energy-based monitoring and correction to enhance the accuracy and stability of explicit co-simulation

[Abstract] The simulation of complex engineering applications often requires the consideration of component-level dynamics whose nature and time-scale differ across the elements of which the system is composed. Co-simulation offers an effective approach to deal with the modelling and numerical integration of such assemblies by assigning adequate description and solution methods to each component. Explicit co-simulation, in particular, is frequently used when efficient code execution is a requirement, for instance in real-time setups. Using explicit schemes, however, can lead to the introduction of energy artifacts at the discrete-time interface between subsystems. The resulting energy errors deteriorate the accuracy of the co-simulation results and may in some cases develop into the instability of the numerical integration process. This paper discusses the factors that influence the severity of the energy errors generated at the interface in explicit co-simulation applications, and presents a monitoring and correction methodology to detect and remove them. The method uses only the information carried by the variables exchanged between the subsystems and the co-simulation manager. The performance of this energy-correction technique was evaluated in multi-rate co-simulation of mechanical and multiphysics benchmark examples.Xunta de Galicia; ED431B2016/031Xunta de Galicia; ED431F2021/04Ministerio de Economía, Industria y Competitividad; RYC-2016-20222Ministerio de Economía, Industria y Competitividad; TRA2017-86488-

Estudio cinegético de la digestión anaerobia de alpechín, procedente de la extracción de aceite utilizando olivex, previamente biotratado con Geotrichum Candidum

A kinetic study of the anaerobic digestion of olive mill wastewater (OMW) which was obtained with the technological helper "Olivex", was carried out. An identical wastewater, obtained without this enzyme was also used. Both OMW were pre-treated aerobically with Geotrichum Candidum to eliminate the greater part of the phenolic compounds responsible for inhibition. The anaerobic process was carried out in bioreactors with microorganisms immobilized on two micronized clay supports, Sepiolite and Bentonite. Assuming that the overall anaerobic digestion process conforms to a first-order kinetic, specific rate constants, Ko, were obtained by using the Roediger's equation in each case. In contrast to what takes place with both OMW without pretreatment, kinetic constant was observed virtually constant when the substrate concentration was increased, in the range of COD (chemical oxygen demand) studied. The mean value of this kinetic parameter was a 40% larger for the OMW obtained with Olivex compared to the reference OMW, in the two digesters used. Sepiolite favoured the kinetic and increased the yield coefficient compared to Bentonite.Se ha efectuado un estudio cinético del proceso de digestión anaerobia de un alpechín obtenido con el coadyuvante tecnológico "Olivex" en comparación con un testigo obtenido sin este enzima, que previamente han sido tratados de forma aerobia con Geotrichum Candidum para eliminar la mayor parte de los compuestos fenólicos responsables de su poder inhibidor. El proceso anaerobio se ha realizado en biorreactores con microorganismos inmovilizados en dos soportes micronizados arcillosos, Sepiolita y Bentonita. Admitiendo que globalmente el proceso de digestión anaerobia sigue una cinética de primer orden, se obtienen las constantes específicas de velocidad, Ko, para cada caso estudiado usando la ecuación de Roediger. A diferencia de lo que ocurre con ambos alpechines sin pretratar, la constante cinética se mantiene prácticamente constante al aumentar la concentración de sustrato, dentro del intervalo DQO (demanda química de oxígeno) estudiado, no apreciándose fenómenos de inhibición. El valor medio de este parámetro cinético para el alpechín obtenido con Olivex es más del 40% superior que el correspondiente al alpechín testigo en los dos digestores utilizados. El soporte Sepiolita favorece la cinética y aumenta el coeficiente de rendimiento respecto a la Bentonita

Gene expression profiling in human neutrophils after infection with Acinetobacter baumannii in vitro

Acinetobacter baumannii is a Gram negative nosocomial pathogen that has acquired increasing worldwide notoriety due to its high antibiotic resistance range and mortality rates in hospitalized patients. Therefore, it is necessary to better understand key aspects of A. baumannii pathogenesis such as host-pathogen interactions. In this report, we analyzed both gene expression and cytokine production by human neutrophils infected with A. baumannii. Our assays reveal a proinflammatory response of neutrophils after A. baumannii infection, since intracellular transcription of effector proteins such as COX-2, transcription factors, and proinflammatory cytokines resulted significantly upregulated in neutrophils infected by A. baumannii, compared with unstimulated human neutrophils. Translation and release of CXCL-8, IL-1? and TNF-? by neutrophils was confirmed by protein quantification in culture supernatants. Results obtained in this report reinforce the importance of human neutrophils in controlling A. baumannii infections but also emphasize the proinflammatory nature of these host-pathogen interactions as a target for future immunomodulatory therapies

Virtual reality training platform for flexible ureterorenoscopy interventions with a minimally invasive surgical robot

The total number of ureteroscopy (URS) interventions during the past years has dramatically increased due to the ongoing technological advances and the benefits associated with these techniques. However, the current URS procedure presents some drawbacks to urologic surgeons. The LITHOS project was created with the main objective of developing a surgical robotic system for flexible ureterorenoscopic lithotripsy interventions, offering a technological solution that meets the real needs of both patients and surgeons in this type of procedures. In this paper, a virtual reality environment for flexible ureterorenoscopy interventions is presented. The proposed environment provides a suitable training platform for surgeons manipulating the surgical robotic system

Entorno didáctico de bajo coste para formación en tecnologías de cirugía guiada por imagen y robótica

Este trabajo de investigación presenta un nuevo entorno didáctico de bajo coste para la formación ingenieril de temáticas de cirugía guiada por imagen y robótica. Con este entorno se pretende mejorar la motivación y autonomía del alumnado, que hasta el momento se hallaba acotada debido al alto componente teórico de las sesiones impartidas. El entorno está formado por un phantom, una herramienta software, un sistema robótico y un manipulador que permite obtener una realimentación háptica. Se ha llevado a cabo una experiencia piloto en la asignatura de cuarto curso "Simulación y planificación quirúrgica" del Grado de Ingeniería Biomédica de la Universidad Politécnica de Madrid. Los resultados de las encuestas llevadas a cabo muestran que la nueva metodología mejora en todos los casos los valores obtenidos usando la metodología clásica basada en la clase magistral y prácticas