Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

Are state–local government expenditures converging? New evidence based on sequential unit root tests

Large and persistent gaps in subnational public expenditure have important implications regarding growth, equity, and migration. In this context, we revisit the question of expenditure convergence across the American states to provide more nuanced evidence than found by a small number of previous studies. We employ a methodology due to Smeekes (Bootstrap sequential tests to determine the stationary units in a panel, 2011) that sequentially tests for unit roots in pairwise (real per capita) expenditure gaps based on user specified fractions. In a panel of 48 combined state–local government units (1957–2008), we found that expenditures on highways, sanitation, utility, and education were far more convergent than expenditures on health and hospitals, police and fire protection, and public welfare. There was little evidence of “club convergence” based on the proportion of intraregional convergent pairs. Several historically high-grant receiving states showed relatively strong evidence of convergence. Our results bode well for future output convergence and opportunities for Tiebout-type migration across jurisdictions. They also imply a diminished role for public infrastructure and education spending in business location choices over time and a mixed role for federal grants in inducing convergence.

Establishing precise estimates of abundance in patchy habitats of the marine nearshore

Exploratory investigations of optimal sampling designs are a critical component of the decision-making process in ecology where inherent natural variation can lead to erroneous conclusions if left unexamined. Pilot studies and exploratory analyses that investigate the precision of sampling regimes may reduce the chances of erroneous results and can be used to optimise processing time in larger ecological research programs. In our study, we calculated optimal precision estimates for sampling macroinvertebrates and ichthyofauna in surf-zone wrack accumulations by investigating the precision of the mean for sub-samples of seine nets and also for the number of replicate seine nets to guide future sampling regimes. We discovered that the processing time for individual seine net samples could be reduced by 50% using sub-sampling and that time to process replicate seine net samples could be reduced by 25% while maintaining acceptable precision. In future, we suggest that the use of pilot studies with similar exploratory approaches should be less of an exception and more a critical component of ecological investigations, particularly in under-studied or newly-developing areas of research. Further, these types of exploratory approaches are crucially important in a variety of extremely patchy environments where variability is likely to be high.

POSE ESTIMATION AND 3D RECONSTRUCTION USING SENSOR FUSION

A camera maps 3-dimensional (3D) world space to a 2-dimensional (2D) image space. In the process it loses the depth information, i.e., the distance from the camera focal point to the imaged objects. It is impossible to recover this information from a single image. However, by using two or more images from different viewing angles this information can be recovered, which in turn can be used to obtain the pose (position and orientation) of the camera. Using this pose, a 3D reconstruction of imaged objects in the world can be computed. Numerous algorithms have been proposed and implemented to solve the above problem; these algorithms are commonly called Structure from Motion (SfM). State-of-the-art SfM techniques have been shown to give promising results. However, unlike a Global Positioning System (GPS) or an Inertial Measurement Unit (IMU) which directly give the position and orientation respectively, the camera system estimates it after implementing SfM as mentioned above. This makes the pose obtained from a camera highly sensitive to the images captured and other effects, such as low lighting conditions, poor focus or improper viewing angles. In some applications, for example, an Unmanned Aerial Vehicle (UAV) inspecting a bridge or a robot mapping an environment using Simultaneous Localization and Mapping (SLAM), it is often difficult to capture images with ideal conditions. This report examines the use of SfM methods in such applications and the role of combining multiple sensors, viz., sensor fusion, to achieve more accurate and usable position and reconstruction information. This project investigates the role of sensor fusion in accurately estimating the pose of a camera for the application of 3D reconstruction of a scene. The first set of experiments is conducted in a motion capture room. These results are assumed as ground truth in order to evaluate the strengths and weaknesses of each sensor and to map their coordinate systems. Then a number of scenarios are targeted where SfM fails. The pose estimates obtained from SfM are replaced by those obtained from other sensors and the 3D reconstruction is completed. Quantitative and qualitative comparisons are made between the 3D reconstruction obtained by using only a camera versus that obtained by using the camera along with a LIDAR and/or an IMU. Additionally, the project also works towards the performance issue faced while handling large data sets of high-resolution images by implementing the system on the Superior high performance computing cluster at Michigan Technological University.

Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group

Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovis isolates that are representative of the most frequent spoligotype in the Iberian Peninsula, SB0121. VNTR typing targeted nine loci: ETR-A (alias VNTR2165), ETR-B (VNTR2461), ETR-D (MIRU4, VNTR580), ETR-E (MIRU31, VNTR3192), MIRU26 (VNTR2996), QUB11a (VNTR2163a), QUB11b (VNTR2163b), QUB26 (VNTR4052), and QUB3232 (VNTR3232). We found a high degree of diversity among the studied isolates (discriminatory index [D] = 0.9856), which were split into 65 different MIRU-VNTR types. An alternative short-format MIRU-VNTR typing targeting only the four loci with the highest variability values was found to offer an equivalent discriminatory index. Minimum spanning trees using the MIRU-VNTR data showed the hypothetical evolution of an apparent clonal group. MIRU-VNTR analysis was also applied to the isolates of 176 animals from 15 farms infected by M. bovis SB0121; in 10 farms, the analysis revealed the coexistence of two to five different MIRU types differing in one to six loci, which highlights the frequency of undetected heterogeneity.

Occurrence of Mycobacterium avium subspecies paratuberculosis across host species and European countries with evidence for transmission between wildlife and domestic ruminants

BACKGROUND Mycobacterium avium subspecies paratuberculosis (Map) causes an infectious chronic enteritis (paratuberculosis or Johne's disease) principally of ruminants. The epidemiology of Map is poorly understood, particularly with respect to the role of wildlife reservoirs and the controversial issue of zoonotic potential (Crohn's disease). Genotypic discrimination of Map isolates is pivotal to descriptive epidemiology and resolving these issues. This study was undertaken to determine the genetic diversity of Map, enhance our understanding of the host range and distribution and assess the potential for interspecies transmission. RESULTS 164 Map isolates from seven European countries representing 19 different host species were genotyped by standardized IS900--restriction fragment length polymorphism (IS900-RFLP), pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphisms (AFLP) and mycobacterial interspersed repeat unit-variable number tandem repeat (MIRU-VNTR) analyses. Six PstI and 17 BstEII IS900-RFLP, 31 multiplex [SnaBI-SpeI] PFGE profiles and 23 MIRU-VNTR profiles were detected. AFLP gave insufficient discrimination of isolates for meaningful genetic analysis. Point estimates for Simpson's index of diversity calculated for the individual typing techniques were in the range of 0.636 to 0.664 but a combination of all three methods increased the discriminating power to 0.879, sufficient for investigating transmission dynamics. Two predominant strain types were detected across Europe with all three typing techniques. Evidence for interspecies transmission between wildlife and domestic ruminants on the same property was demonstrated in four cases, between wildlife species on the same property in two cases and between different species of domestic livestock on one property. CONCLUSION The results of this study showed that it is necessary to use multiple genotyping techniques targeting different sources of genetic variation to obtain the level of discrimination necessary to investigate transmission dynamics and trace the source of Map infections. Furthermore, the combination of genotyping techniques may depend on the geographical location of the population to be tested. Identical genotypes were obtained from Map isolated from different host species co-habiting on the same property strongly suggesting that interspecies transmission occurs. Interspecies transmission of Map between wildlife species and domestic livestock on the same property provides further evidence to support a role for wildlife reservoirs of infection.

Validation of thigh-based accelerometer estimates of postural allocation in 5-12 year-olds

OBJECTIVES: To validate activPAL3™ (AP3) for classifying postural allocation, estimating time spent in postures and examining the number of breaks in sedentary behaviour (SB) in 5-12 year-olds. DESIGN: Laboratory-based validation study. METHODS: Fifty-seven children completed 15 sedentary, light- and moderate-to-vigorous intensity activities. Direct observation (DO) was used as the criterion measure. The accuracy of AP3 was examined using a confusion matrix, equivalence testing, Bland-Altman procedures and a paired t-test for 5-8y and 9-12y. RESULTS: Sensitivity of AP3 was 86.8%, 82.5% and 85.3% for sitting/lying, standing, and stepping, respectively, in 5-8y and 95.3%, 81.5% and 85.1%, respectively, in 9-12y. Time estimates of AP3 were equivalent to DO for sitting/lying in 9-12y and stepping in all ages, but not for sitting/lying in 5-12y and standing in all ages. Underestimation of sitting/lying time was smaller in 9-12y (1.4%, limits of agreement [LoA]: -13.8 to 11.1%) compared to 5-8y (12.6%, LoA: -39.8 to 14.7%). Underestimation for stepping time was small (5-8y: 6.5%, LoA: -18.3 to 5.3%; 9-12y: 7.6%, LoA: -16.8 to 1.6%). Considerable overestimation was found for standing (5-8y: 36.8%, LoA: -16.3 to 89.8%; 9-12y: 19.3%, LoA: -1.6 to 36.9%). SB breaks were significantly overestimated (5-8y: 53.2%, 9-12y: 28.3%, p<0.001). CONCLUSIONS: AP3 showed acceptable accuracy for classifying postures, however estimates of time spent standing were consistently overestimated and individual error was considerable. Estimates of sitting/lying were more accurate for 9-12y. Stepping time was accurately estimated for all ages. SB breaks were significantly overestimated, although the absolute difference was larger in 5-8y. Surveillance applications of AP3 would be acceptable, however, individual level applications might be less accurate.

Detectability of migrating raptors and its effect on bias and precision of trend estimates

Annual counts of migrating raptors at fixed observation points are a widespread practice, and changes in numbers counted over time, adjusted for survey effort, are commonly used as indices of trends in population size. Unmodeled year-to-year variation in detectability may introduce bias, reduce precision of trend estimates, and reduce power to detect trends. We conducted dependent double-observer surveys at the annual fall raptor migration count at Lucky Peak, Idaho, in 2009 and 2010 and applied Huggins closed-capture removal models and information-theoretic model selection to determine the relative importance of factors affecting detectability. The most parsimonious model included effects of observer team identity, distance, species, and day of the season. We then simulated 30 years of counts with heterogeneous individual detectability, a population decline (λ = 0.964), and unexplained random variation in the number of available birds. Imperfect detectability did not bias trend estimation, and increased the time required to achieve 80% power by less than 11%. Results suggested that availability is a greater source of variance in annual counts than detectability; thus, efforts to account for availability would improve the monitoring value of migration counts. According to our models, long-term trends in observer efficiency or migratory flight distance may introduce substantial bias to trend estimates. Estimating detectability with a novel count protocol like our double-observer method is just one potential means of controlling such effects. The traditional approach of modeling the effects of covariates and adjusting the index may also be effective if ancillary data is collected consistently.

Use of bird carcass removals by urban scavengers to adjust bird-window collision estimates

Carcass removal by scavengers has been identified as one of the largest biases in estimating bird mortality from anthropogenic sources. Only two studies have examined carcass removal by scavengers in an urban environment, and previous estimates of bird-window collision mortality at houses have relied on carcass removal rates from wind turbine studies. We placed a bird carcass and time-lapse camera at 44 houses in Edmonton, Alberta. In total, 166 7-day trials were conducted throughout 2015. Time-to-event (survival) analysis was used to identify covariates that affected removal. The carcass removal rate was determined for use in estimating the number of birds killed from bird-window collisions at houses in Alberta. In total, 67.5% of carcasses were removed. The date the carcass was placed, the year the house was built, and the level of development within 50 m of the house were the covariates that had the largest effect on carcass removal. In calculating our removal rate, the number of detected carcasses in the first 24 hours was adjusted by 1.47 to account for removal by scavengers. Previously collected citizen science data were used to create an estimate of 957,440 bird deaths each year in Alberta as a result of bird-window collisions with houses. This number is based on the most detailed bird-window collision study at houses to date and a carcass removal study conducted in the same area. Similar localized studies across Canada will need to be completed to reduce the biases that exist with the previous bird-window collision mortality estimate for houses in Canada.

Ordonnancement des opérations dans une unité d’extrusion

Les travaux de ce mémoire traitent du problème d’ordonnancement et d’optimisation de la production dans un environnement de plusieurs machines en présence de contraintes sur les ressources matérielles dans une usine d’extrusion plastique. La minimisation de la somme pondérée des retards est le critère économique autour duquel s’articule cette étude car il représente un critère très important pour le respect des délais. Dans ce mémoire, nous proposons une approche exacte via une formulation mathématique capable des donner des solutions optimales et une approche heuristique qui repose sur deux méthodes de construction de solution sérielle et parallèle et un ensemble de méthodes de recherche dans le voisinage (recuit-simulé, recherche avec tabous, GRASP et algorithme génétique) avec cinq variantes de voisinages. Pour être en totale conformité avec la réalité de l’industrie du plastique, nous avons pris en considération certaines caractéristiques très fréquentes telles que les temps de changement d’outils sur les machines lorsqu’un ordre de fabrication succède à un autre sur une machine donnée. La disponibilité des extrudeuses et des matrices d’extrusion représente le goulot d’étranglement dans ce problème d’ordonnancement. Des séries d’expérimentations basées sur des problèmes tests ont été effectuées pour évaluer la qualité de la solution obtenue avec les différents algorithmes proposés. L’analyse des résultats a démontré que les méthodes de construction de solution ne sont pas suffisantes pour assurer de bons résultats et que les méthodes de recherche dans le voisinage donnent des solutions de très bonne qualité. Le choix du voisinage est important pour raffiner la qualité de la solution obtenue. Mots-clés : ordonnancement, optimisation, extrusion, formulation mathématique, heuristique, recuit-simulé, recherche avec tabous, GRASP, algorithme génétique

Registro de pacientes con distrofinopatías en Colombia

INTRODUCCIÓN. La distrofia muscular de Duchenne es una enfermedad neuromuscular con una herencia recesiva ligada al X que afecta a 1 de cada 3500 niños nacidos vivos. Se produce por mutaciones en el gen DMD que codifica para la distrofina. Se caracteriza por manifestaciones clínicas variables típicas de una distrofia muscular proximal progresiva. OBJETIVO. Realizar el primer registro en Colombia de los pacientes identificados con distrofinopatías, teniendo en cuenta características clínicas y paraclínicas, así como las mutaciones causales de esta patología. METODOLOGÍA Es un estudio descriptivo, transversal, de la revisión de historias clínicas de los pacientes con diagnóstico de DMD atendidos en la consulta de Genética de la Universidad del Rosario durante los años 2006 a 2015. RESULTADOS Se identificaron 99 pacientes, de los cuales 56 (56,56%) corresponden al fenotipo Duchenne y 12 (12,12%) al Becker. No fue posible clasificar a 31 pacientes (31,3%) por falta de datos clínicos. La edad de inicio de los síntomas fue en promedio de 4,41 años. Las mutaciones más frecuentes fueron las deleciones (69%), seguidas por las mutaciones puntuales(14%), las duplicaciones (11%) y por otras mutaciones (4%). CONCLUSIONES Este registro de distrofinopatías es el primero reportado en Colombia y el punto de partida para conocer la incidencia de la enfermedad, caracterización clínica y molecular de los pacientes, garantizando así el acceso oportuno a los nuevos tratamientos de medicina de precisión que permitan mejorar la calidad de vida de los pacientes y sus familias.