Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Time Discretization of the SST-generalized Navier-Stokes Equations: Positive and Negative Results

In the theory of the Navier-Stokes equations, the proofs of some basic known results, like for example the uniqueness of solutions to the stationary Navier-Stokes equations under smallness assumptions on the data or the stability of certain time discretization schemes, actually only use a small range of properties and are therefore valid in a more general context. This observation leads us to introduce the concept of SST spaces, a generalization of the functional setting for the Navier-Stokes equations. It allows us to prove (by means of counterexamples) that several uniqueness and stability conjectures that are still open in the case of the Navier-Stokes equations have a negative answer in the larger class of SST spaces, thereby showing that proof strategies used for a number of classical results are not sufficient to affirmatively answer these open questions. More precisely, in the larger class of SST spaces, non-uniqueness phenomena can be observed for the implicit Euler scheme, for two nonlinear versions of the Crank-Nicolson scheme, for the fractional step theta scheme, and for the SST-generalized stationary Navier-Stokes equations. As far as stability is concerned, a linear version of the Euler scheme, a nonlinear version of the Crank-Nicolson scheme, and the fractional step theta scheme turn out to be non-stable in the class of SST spaces. The positive results established in this thesis include the generalization of classical uniqueness and stability results to SST spaces, the uniqueness of solutions (under smallness assumptions) to two nonlinear versions of the Euler scheme, two nonlinear versions of the Crank-Nicolson scheme, and the fractional step theta scheme for general SST spaces, the second order convergence of a version of the Crank-Nicolson scheme, and a new proof of the first order convergence of the implicit Euler scheme for the Navier-Stokes equations. For each convergence result, we provide conditions on the data that guarantee the existence of nonstationary solutions satisfying the regularity assumptions needed for the corresponding convergence theorem. In the case of the Crank-Nicolson scheme, this involves a compatibility condition at the corner of the space-time cylinder, which can be satisfied via a suitable prescription of the initial acceleration.

Parallel Methods for Synthesizing Whole-Hand Grasps from Generalized Prototypes

This report addresses the problem of acquiring objects using articulated robotic hands. Standard grasps are used to make the problem tractable, and a technique is developed for generalizing these standard grasps to increase their flexibility to variations in the problem geometry. A generalized grasp description is applied to a new problem situation using a parallel search through hand configuration space, and the result of this operation is a global overview of the space of good solutions. The techniques presented in this report have been implemented, and the results are verified using the Salisbury three-finger robotic hand.

Virtual Model Control of a Biped Walking Robot

The transformation from high level task specification to low level motion control is a fundamental issue in sensorimotor control in animals and robots. This thesis develops a control scheme called virtual model control which addresses this issue. Virtual model control is a motion control language which uses simulations of imagined mechanical components to create forces, which are applied through joint torques, thereby creating the illusion that the components are connected to the robot. Due to the intuitive nature of this technique, designing a virtual model controller requires the same skills as designing the mechanism itself. A high level control system can be cascaded with the low level virtual model controller to modulate the parameters of the virtual mechanisms. Discrete commands from the high level controller would then result in fluid motion. An extension of Gardner's Partitioned Actuator Set Control method is developed. This method allows for the specification of constraints on the generalized forces which each serial path of a parallel mechanism can apply. Virtual model control has been applied to a bipedal walking robot. A simple algorithm utilizing a simple set of virtual components has successfully compelled the robot to walk eight consecutive steps.

Retargeting of pre-set regions on chromosome for high gene expression in mammalian cells

We have developed a system to hunt and reuse special gene integration sites that allow for high and stable gene expression. A vector, named pRGFP8, was constructed. The plasmid pRGFP8 contains a reporter gene, gfp2 and two extraneous DNA fragments. The gene gfp2 makes it possible to screen the high expression regions on the chromosome. The extraneous DNA fragments can help to create the unique loci on the chromosome and increase the gene targeting frequency by increasing the homology. After transfection into Chinese hamster ovary cells (CHO) cells, the linearized pRGFP8 can integrate into the chromosome of the host cells and form the unique sites. With FACS, 90 millions transfected cells were sorted and the cells with strongest GFP expression were isolated, and then 8 stable high expression GFP CHO cell lines were selected as candidates for the new host cell. Taking the unique site created by pRGFP8 on the chromosome in the new host cells as a targeting locus, the gfp2 gene was replaced with the gene of interest, human ifngamma, by transfecting the targeting plasmid pRIH-IFN. Then using FACS, the cells with the dimmest GFP fluorescence were selected. These cells showed they had strong abilities to produce the protein of interest, IFN-gamma. During the gene targeting experiment, we found there is positive correlation between the fluorescence density of the GFP CHO host cells and the specific production rate of IFN-gamma. This result shows that the strategy in our expression system is correct: the production of the interesting protein increases with the increase fluorescence of the GFP host cells. This system, the new host cell lines and the targeting vector, can be utilized for highly expressing the gene of interest. More importantly, by using FACS, we can fully screen all the transfected cells, which can reduce the chances of losing the best cells.

Hilbert space on probability density functions with Aitchison geometry

Compositional data analysis motivated the introduction of a complete Euclidean structure in the simplex of D parts. This was based on the early work of J. Aitchison (1986) and completed recently when Aitchinson distance in the simplex was associated with an inner product and orthonormal bases were identified (Aitchison and others, 2002; Egozcue and others, 2003). A partition of the support of a random variable generates a composition by assigning the probability of each interval to a part of the composition. One can imagine that the partition can be refined and the probability density would represent a kind of continuous composition of probabilities in a simplex of infinitely many parts. This intuitive idea would lead to a Hilbert-space of probability densities by generalizing the Aitchison geometry for compositions in the simplex into the set probability densities

When a data set can be considered compositional?

Traditionally, compositional data has been identified with closed data, and the simplex has been considered as the natural sample space of this kind of data. In our opinion, the emphasis on the constrained nature of compositional data has contributed to mask its real nature. More crucial than the constraining property of compositional data is the scale-invariant property of this kind of data. Indeed, when we are considering only few parts of a full composition we are not working with constrained data but our data are still compositional. We believe that it is necessary to give a more precise definition of composition. This is the aim of this oral contribution

An Interval Intelligent-based Approach for Fault Detection and Modelling

Not considered in the analytical model of the plant, uncertainties always dramatically decrease the performance of the fault detection task in the practice. To cope better with this prevalent problem, in this paper we develop a methodology using Modal Interval Analysis which takes into account those uncertainties in the plant model. A fault detection method is developed based on this model which is quite robust to uncertainty and results in no false alarm. As soon as a fault is detected, an ANFIS model is trained in online to capture the major behavior of the occurred fault which can be used for fault accommodation. The simulation results understandably demonstrate the capability of the proposed method for accomplishing both tasks appropriately

Factores comportamentales hacia la fotoprotección

Introducción: la fotoprotección constituye las actividades preventivas que minimizan los efectos deletéreos de la exposición solar; estos comportamientos de salud pueden estar relacionados con actitudes y conocimientos adquiridos. Objetivo: Identificar estas asociaciones en Estudiantes de Medicina de la Escuela de Medicina y Ciencias de la Salud de la Universidad del Rosario, quienes se encargarán de transmitir educación y ejemplo de comportamiento en su contexto personal y profesional. Metodología: estudio de corte transversal. Se implementó una encuesta voluntaria por correo institucional y físicamente entre estudiantes de 1-8 semestre matriculados en el segundo semestre de 2009; n= 122 estudiantes, la mayoría menores de 20 años y de género femenino; factores de estudio analizados: biológico – demográficos, informador, actitudes, conocimientos, personas modelo y comportamiento, expresados en frecuencias, analizados con pruebas y fuerzas de asociación con intervalo de confianza del 95%. Resultados: factores asociados a fotoprotección: ser de 1-4 semestre (p=0,008), ser =19 años (p=0,028), reconocer como consecuencias las alteraciones en los ojos y la visión (p=0,043) y las alteraciones producidas en el sistema inmune (p=0,021), uso de la pareja de ropa protectora (p=0,019), permanencia de un amigo a la sombra (p=0,055), conocimiento de la posibilidad de quemadura independiente al clima (p=0,001) y conocimiento de la posibilidad de quemadura sin sentir los rayos calientes del sol (p=0,049). Conclusiones: es posible reforzar comportamientos preventivos, favorecer el seguimiento de modelos positivos afines a los jóvenes, incrementar el conocimiento en salud y afirmar la educación primaria en salud desde la Medicina General y mejorar así la fotoprotección.

Point Set Topology

Lecture notes about point set toplogy

Team Quintinlessness: Open source software resource set

INFO2009 Assignment 2 reference list for team "Quintinlessness" - Subject: Open source software

Green ICT Resource Set - INFO2009 Coursework, Bobs' Finest Group

Online resource set which details in full the Green ICT topic and associated areas. Online multiple choice quiz also included to test readers knowledge of topic once the tutorial has been read.

Aplicación de colas de Poisson en procesos de ‘toma de decisiones’ en la gestión de servicios médicos

En este documento se revisa teóricamente la distribución de probabilidad de Poisson como función que asigna a cada suceso definido, sobre una variable aleatoria discreta, la probabilidad de ocurrencia en un intervalo de tiempo o región del espacio disjunto. Adicionalmente se revisa la distribución exponencial negativa empleada para modelar el intervalo de tiempo entre eventos consecutivos de Poisson que ocurren de manera independiente; es decir, en los cuales la probabilidad de ocurrencia de los eventos sucedidos en un intervalo de tiempo no depende de los ocurridos en otros intervalos de tiempo, por esta razón se afirma que es una distribución que no tiene memoria. El proceso de Poisson relaciona la función de Poisson, que representa un conjunto de eventos independientes sucedidos en un intervalo de tiempo o región del espacio con los tiempos dados entre la ocurrencia de los eventos según la distribución exponencial negativa. Los anteriores conceptos se usan en la teoría de colas, rama de la investigación de operaciones que describe y brinda soluciones a situaciones en las que un conjunto de individuos o elementos forman colas en espera de que se les preste un servicio, por lo cual se presentan ejemplos de aplicación en el ámbito médico.

INFO2009 Academic Year 09-10: Luc Moreau's Tutor Group's Accessibility Resource Set

Our resource set

Annotated Bibliographies Notes Set

Slides, handouts and links covering relevant topics including how to create an annotated bibliography, exemplar bibliography, reference managers etc. The coursework specification with assessment criteria is available as a single item from http://www.edshare.soton.ac.uk/6044/