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.

En busca de la profesión: cambios y realidades en la condición social de los artistas en Bogotá entre 1910 y 1930

En las primeras décadas del siglo XX en Bogotá se desarrolló un proceso de profesionalización de los artistas que permitió que estos mejoraran el estatus que tenían en la sociedad y se consolidaran una serie de roles que los identificarían como representantes de su ocupación. Este cambio se evidencia al notar que hasta finales del siglo XIX no existía una clara diferenciación entre las categorías de artista y artesano, mientras que para la década de 1930 comenzaron a aparecer propuestas estéticas que rompieron con los cánones tradicionales del arte académico. De este modo, a partir de la aplicación de un marco teórico basado en la sociología e historia de las profesiones y basándose en la socióloga e historia social del arte y los artistas se analizan las distintas etapas que atravesaron los integrantes de esta ocupación para poder ser reconocidos como “profesionales”. Se logró evidenciar que este tipo de procesos sociales se caracterizan por ser muy complejos, ya que para entender las dinámicas que se presentan dentro de los grupos profesionales se debe tener en cuenta que los distintos integrantes poseen identidades de género, clase o región, entre otras, que generan relaciones de amistad, enemistad y rivalidad, las cuales no siempre son visibilizadas en las investigaciones que han abordado este periodo.

De la literatura y la estadística a la apropiación territorial: análisis de la narración geográfica sobre las provincias del norte neogranadinas en la segunda mitad del siglo XIX

Las obras geográficas de Manuel Ancízar y Felipe Pérez dan cuenta de la manera en la que la élite intelectual neogranadina se apropió y representó el aspecto físico y humano de la nación al inicio y final de la Comisión Corográfica (1850-1859). Un análisis comparativo de las obras mostrará la manera en la que la narración literaria y la geográfica influyen en la elaboración de imaginarios territoriales para unificar la nación y consolidar la identidad nacional a partir de la apropiación territorial en la segunda mitad del siglo XIX

Eficacia de la estimulación magnética transcraneal en la disminución de severidad en el trastorno depresivo mayor en monoterapia y coadyuvante comparado con tratamientos farmacológicos. Revisión sistemática y meta-análisis

Resumen Introducción Una posible opción de tratamiento para el manejo del trastorno depresivo mayor (TDM) es la estimulación magnética transcraneal (EMT) que ha mostrado propiedades antidepresivas superiores al placebo con un buen perfil de seguridad. El objetivo del presente trabajo es determinar la reducción en la severidad del TDM y la proporción de eventos adversos (EA) en pacientes con TDM refractario y no refractario, posterior al uso de EMT administrada en monoterapia o tratamiento coadyuvante comparado con terapia farmacológica. Metodología Se planteó una pregunta PICOT de la cual se realizó una búsqueda sistemática de estudios clínicos en las bases de datos Medline, EMBASE y Cochrane. Dos investigadores en forma independiente realizaron la selección de artículos, evaluación de calidad con la herramienta de la colaboración Cochrane y extracción de datos. Se extrajeron datos de eficacia como tasa de respuesta, porcentaje de remisión, calidad de vida, diminución sintomática del trastorno depresivo mayor en la escala de Hamilton y capacidad funcional. Igualmente, proporción de pacientes con EA. Se realizó un meta-análisis de estas variables teniendo en cuenta la heterogeneidad. Resultados La presente revisión sistemática incluyó 26 estudios clínicos aleatorizados de baja calidad metodológica mostrando que la EMT presentó una eficacia superior cuando es usada como coadyuvante a las terapias con que venían siendo tratados los pacientes con TDM refractario y no refractario en los desenlaces de tasa de respuesta y porcentaje de remisión. En el caso de intervenciones farmacológicas específicas, la EMT presento eficacia similar, tanto en terapia coadyuvante como en monoterapia comparado con las intervenciones farmacológicas. En cuanto a seguridad, la EMT presenta un buen perfil de seguridad debido a que en todos los escenarios estudiados los EA fueron no serios y baja frecuencia Conclusiones La evidencia disponible sugiere que la EMT mostró ser efectivo y seguro para el manejo del TDM refractario y no refractario. Sin embargo, la evidencia es débil por lo tanto se necesita mayor investigación clínica que soporte su uso.

Santa Bárbara, el barrio que no soportó las tempestades: el olvido y la demolición del patrimonio arquitectónico en la construcción del relato histórico de Bogotá entre 1980 y 1983

Esta investigación analiza la construcción del límite sur de la zona patrimonial de Bogotá de los años 80, a partir de dos procesos simultáneos: la demolición de un sector del barrio Santa Bárbara y la patrimonialización de La Candelaria. A pesar de que estos dos sectores de la ciudad hicieron parte de la ciudad antigua y compartieron un origen común, solo La Candelaria logró hacer parte de la zona considerada de valor histórico. Por lo tanto, este proyecto de grado se interesa, principalmente, por conocer por qué el barrio Santa Bárbara fue excluido del relato histórico de la ciudad, a partir del estudio de la discusión sobre su valor histórico que dio paso al uso público del pasado y a una “lucha por la memoria”, en palabras de Elizabeth Jelin.

Instrumentos del crecimiento económico.

Se transcribe la conferencia pronunciada en Madrid por el Director General de Asuntos Científicos de la OCDE, en los Seminarios de Información de dicho organismo, bajo el título 'Instrumentos del crecimiento económico', donde habló del desafío planteado a la educación, de la política científica, de las Conferencias de los Ministros de la Ciencia, de la evolución de las ideas sobre la política científica y sobre los problemas que acontecían a la sociedad contemporánea.

Public libraries in the cities of the Roman Empire

A chapter based on a paper given at major conference, arguing that the civic and architectural contexts of many public libraries in the Roman world contributed strongly to their status as conspicuous 'public' buildings, and should inform the way we think of library functions in the Roman world

The SAFE FOODS framework for improved risk analysis of foods

Three main changes to current risk analysis processes are proposed to improve their transparency, openness, and accountability. First, the addition of a formal framing stage would allow interested parties, experts and officials to work together as needed to gain an initial shared understanding of the issue, the objectives of regulatory action, and alternative risk management measures. Second, the scope of the risk assessment is expanded to include the assessment of health and environmental benefits as well as risks, and the explicit consideration of economic- and social-impacts of risk management action and their distribution. Moreover approaches were developed for deriving improved information from genomic, proteomic and metabolomic profiling methods and for probabilistic modelling of health impacts for risk assessment purposes. Third, in an added evaluation stage, interested parties, experts, and officials may compare and weigh the risks, costs, and benefits and their distribution. As part of a set of recommendations on risk communication, we propose that reports on each stage should be made public.

High resolution simulation of recent Arctic and Antarctic stratospheric chemical ozone loss compared to observations

Simulations of polar ozone losses were performed using the three-dimensional high-resolution (1∘ × 1∘) chemical transport model MIMOSA-CHIM. Three Arctic winters 1999–2000, 2001–2002, 2002–2003 and three Antarctic winters 2001, 2002, and 2003 were considered for the study. The cumulative ozone loss in the Arctic winter 2002–2003 reached around 35% at 475 K inside the vortex, as compared to more than 60% in 1999–2000. During 1999–2000, denitrification induces a maximum of about 23% extra ozone loss at 475 K as compared to 17% in 2002–2003. Unlike these two colder Arctic winters, the 2001–2002 Arctic was warmer and did not experience much ozone loss. Sensitivity tests showed that the chosen resolution of 1∘ × 1∘ provides a better evaluation of ozone loss at the edge of the polar vortex in high solar zenith angle conditions. The simulation results for ozone, ClO, HNO3, N2O, and NO y for winters 1999–2000 and 2002–2003 were compared with measurements on board ER-2 and Geophysica aircraft respectively. Sensitivity tests showed that increasing heating rates calculated by the model by 50% and doubling the PSC (Polar Stratospheric Clouds) particle density (from 5 × 10−3 to 10−2 cm−3) refines the agreement with in situ ozone, N2O and NO y levels. In this configuration, simulated ClO levels are increased and are in better agreement with observations in January but are overestimated by about 20% in March. The use of the Burkholder et al. (1990) Cl2O2 absorption cross-sections slightly increases further ClO levels especially in high solar zenith angle conditions. Comparisons of the modelled ozone values with ozonesonde measurement in the Antarctic winter 2003 and with Polar Ozone and Aerosol Measurement III (POAM III) measurements in the Antarctic winters 2001 and 2002, shows that the simulations underestimate the ozone loss rate at the end of the ozone destruction period. A slightly better agreement is obtained with the use of Burkholder et al. (1990) Cl2O2 absorption cross-sections.

Comparative structural analysis of neuromuscular junctions in mice at different ages

The authors studied the histochemical and ultrastructural modifications that occur in the neuromuscular junctions (NMJ) of fibularis longus muscles of mice with an age range of 3 to 21 months. Twenty-four male and female animals were killed at 3, 5, 14 and 21 months of age: 7 of them at 3 months, 4 of them at 5 month, 9 at 14 months and 4 at 21 months. The fibularis longus muscles were processed and their NMJ examined with the transmission electron microscope. The most relevant changes were associated with the degeneration and retraction of terminal axons, i.e., axons poor in synaptic vesicles with degenerated mitochondria, and exhibiting multivesicular bodies and vacuoles; exposed and widened junctional folds and cytoplasmic processes of Schwann cells located in the synaptic gutter. The presence of lysosomes or lipofuchsin in the juxtajunctional sarcoplasm was also noted. These observations suggest that the phenomena of retraction and budding occur in the NMJ with advancing age, with a predominance of events associated with degeneration, leading to profound changes in NMJ shape.

A study of different calcification areas in newly formed bone 8 weeks after insertion of dental implants in rabbit tibias

In orofacial implantology there are many types of implants for the different systems. Among these is the implant surface type, e.g., a screw type, cylindrical and laminar. Furthermore, the implants are different in their dimensions, their metal composition, their surface condition, such as smooth, grit or layered surfaces and in their methods of application. Two different self-tapping implants, one smooth and the other grit-blasted, are screwed into the bone, and another one with a plasma of titanium coating, which is also in a screw form but with greater spaces between the screw threads are compared. The greatest amount of bone deposition in the bone/implant interface was encountered in the latter one, the smooth surfaced implant being in second place. All of these systems can alter the implant healing process and to demonstrate this, we injected bone markers in the rabbits over different periods of time so as to observe the different areas of bone deposition in the tibias where the implants had been inserted. The bone tracers used were Alizarin, Calcein and Xylenol-orange. The amount of deposition was calculated by using the method of surface morphometry.

Electromyographic analysis of superior belly of the omohyoid muscle and anterior belly of the digastric muscle in mandibular movements

The superior belly of the omohyoid muscle and the anterior belly of the digastric muscle, were studied electromyographically in 20 young volunteers. For each muscle, 1 pair of monopolar electrodes was employed. One was a surface electrode and the other a needle electrode, which was inserted in the belly of the muscle. The surface electrode was placed 1 cm apart from the needle electrode. The most marked action of both muscles was on the movement of lowering the mandible. They also act in those movements for the performance of which they have associated a component of lowering the jaw, propulsion, laterality to the right and the left and retrusion. They are not active in the resting position and during jaw movements of elevation, extrusion and protrusion. Both muscles are active most of the time, simultaneously, but it is not possible to demonstrate that there is a synchronism between their actions.

Measurement of the charge ratio of atmospheric muons with the CMS detector

We present a measurement of the ratio of positive to negative muon fluxes from cosmic ray interactions in the atmosphere, using data collected by the CMS detector both at ground level and in the underground experimental cavern at the CERN LHC. Muons were detected in the momentum range from 5 GeV/. c to 1 TeV/. c. The surface flux ratio is measured to be 1.2766±0.0032(stat.)±0.0032(syst.), independent of the muon momentum, below 100 GeV/. c. This is the most precise measurement to date. At higher momenta the data are consistent with an increase of the charge ratio, in agreement with cosmic ray shower models and compatible with previous measurements by deep-underground experiments. © 2010.