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.

Interrelatedness of grazing livestock with vegetation parameters and farmers’ livelihoods in the Mahafaly region, southwestern Madagascar

The study aims to get deeper insight into the highly extensive system of animal husbandry in the Mahafaly region of southwestern Madagascar. It tries to understand the major drivers for pastoral dynamics, land and resource use along a gradient in altitude and vegetation to consider the area’s high spatial and temporal heterogeneity. The study also analyzes the reproductive performance of local livestock as well as the owners’ culling strategies to determine herd dynamics, opportunities for economic growth, and future potential for rural development. Across seasons, plateau herds from both livestock species covered longer distances (cattle 13.6±3.02 km, goats 12.3±3.48 km) and were found further away from the settlements (cattle 3.1±0.96 km, goats 2.8±0.98 km) than those from the coastal plain (walking_dist: cattle 9.5±3.25 km, goats 9.2±2.57 km; max_dist: cattle 2.6±1.28 km, goats 1.8±0.61 km). Transhumant cattle were detected more vulnerable through limited access to pasture land and water resources compared to local herds. Seasonal water shortage has been confirmed as a key constraint on the plateau while livestock keeping along the coast is more limited by dry season forage availability. However, recent security issues and land use conflicts with local crop farmers are gaining importance and force livestock owners to adapt their traditional grazing management, resulting in spatio-temporal variation of livestock numbers and in the impending risk of local overgrazing and degradation of rangelands. Among the 133 plant species consumed by livestock, 13 were determined of major importance for the animals’ nutrition. The nutritive value and digestibility of the natural forage, as well as its abundance in the coastal zone, substantially decreased over the course of the dry season and emphasized the importance of supplementary forage plants, in particular Euphorbia stenoclada. At the same time, an unsustainable utilization and overexploitation of its wild stocks may raise the pressure on the vegetation and pasture resources within the nearby Tsimanampetsotsa National Park. Age at first parturition was 40.5±0.59 months for cattle and 21.3±0.63 months for goats. Both species showed long parturition intervals (cattle 24.2±0.48 months, goats 12.4±0.30 months), mostly due to the maintenance of poorly performing breeding females within the herds. Reported offspring mortality, however, was low with 2.5% of cattle and 18.8% of goats dying before reaching maturity. The analysis of economic information revealed higher than expected market dynamics, especially for zebus, resulting in annual contribution margins of 33 € per cattle unit and 11 € per goat unit. The application of the PRY Herd Life model to simulate herd development for present management and two alternate scenarios confirmed the economic profitability of the current livestock system and showed potential for further productive and economic development. However, this might be clearly limited by the region’s restricted carrying capacity. Summarizing, this study illustrates the highly extensive and resources-driven character of the livestock system in the Mahafaly region, with herd mobility being a central element to cope with seasonal shortages in forage and water. But additional key drivers and external factors are gaining importance and increasingly affect migration decisions and grazing management. This leads to an increased risk of local overgrazing and overexploitation of natural pasture resources and intensifies the tension between pastoral and conservation interests. At the same time, it hampers the region’s agronomic development, which has not yet been fully exploited. The situation therefore demonstrates the need for practical improvement suggestions and implication measures, such as the systematic forestation of supplemental forage plant species in the coastal zone or a stronger integration of animal husbandry and crop production, to sustain the traditional livestock system without compromising peoples’ livelihoods while at the same time minimizing the pastoral impact on the area’s unique nature and environment.

Values and their influence on the life satisfaction of adolescents aged 12 to 16: a study of some correlates

In this research we explore several aspects of quality of life in young people, working with factors such as self-esteem, locus of control, perceived social support, values, and so on. We examine the correlations among factors that influence the values and life satisfaction of adolescents aged 12-16. Furthermore, we analyze the data obtained from the children, on the one hand, and their parents, on the other, we explore the relationships between the factors and we consider the agreements and discrepancies between the responses of parents and their offspring

Noción de vínculo en la mediación del modelo relacional simbólico en una pareja de separados

Este es un estudio de caso realizado con una pareja de separados con quien se realizó un proceso de mediación familiar en el Consultorio Jurídico de la Universidad del Rosario. El propósito del mismo fue identificar la noción de vínculo que emergiera durante el proceso de intervención, base fundamental del Modelo Relacional Simbólico (MRS) desarrollado por la Escuela de Altos Estudios de la Familia de la Universidad Cattolica del Sacre Cuore de Milán, para la mediación de conflictos en familia y en comunidad. La identificación se hizo con base en las siguientes categorías explicativas del concepto de vínculo planteadas en el MRS: (1) lo afectivo (que incluye la confianza y la esperanza), (2) lo ético (que incluye la justicia y la lealtad), (3) el género (se refiere a la relación de la pareja conyugal) y (4) la generación (entendida como la relación entre los padres y los hijos). Los instrumentos utilizados para la recolección de la información, se diseñaron con base en el MRS y la pragmática formal del lenguaje de Jurgen Habermas y son unos de los productos de esta investigación. Adicionalmente, esta última se utilizó también para analizar la acción comunicativa a partir de la identificación de los actos de habla de los enunciados textuales de los miembros de la pareja en las diferentes fases del proceso de mediación lo que además, permitió visibilizar algunos efectos de la mediación. Este estudio posibilitó el análisis de la noción de vínculo a través de las categorías del MRS y de la teoría de la acción comunicativa a través de la pragmática formal del lenguaje. Los instrumentos desarrollados con este fin y los resultados arrojados en su aplicación, permiten enunciar que la pragmática formal del lenguaje puede ser una herramienta para articular la conceptualización teórica del modelo MRS con la investigación empírica, de tal manera que se pueda proponer como metodología de investigación aplicada para promover el desarrollo del MRS.

Seguridad de los antipsicoticos en embarazo en pacientes con psicosis. Revisión sistemática

Enfermedades mentales de tipo psicótico en gestantes se han asociado con mayor número de resultados negativos. Los síntomas psicóticos durante el embarazo se presentan aproximadamente 7.1 por 100.000 casos. Dentro de las consecuencias se incluye mayor riesgo de parto pretérmino, bajo peso al nacer, alteraciones placentarias, malformaciones congénitas de predominio cardiovascular y mayor tasa de muertes perinatales. Como abordaje terapéutico son frecuentes los antipsicóticos de primera generación, aceptados como seguros pero en menor grado se han considerados los antipsicóticos de segunda generación pues ha sido escasamente evaluada su seguridad durante la gestación. Aún existe controversia sobre los potenciales efectos secundarios de algunos antipsicóticos dado los resultados contradictorios. Métodos: Revisión sistemática de la literatura de artículos que proporcionaron mejor evidencia para determinar cuáles antipsicóticos de elección durante la gestación en pacientes con esquizofrenia de acuerdo a su perfil de seguridad. Se evaluó calidad metodológica reconociendo particularidades y resultados de los estudios incluidos. Resultados: De 39 estudios seleccionados, cinco fueron incluidos en esta revisión, clasificándose como nivel de evidencia IIa y evaluados según su calidad metodológica con escala NOS. Se evaluó paso placentario de antipsicóticos, malformaciones fetales, complicaciones obstétricas como parto pretérmino, bajo y alto peso fetal, complicaciones respiratorias, diabetes gestacional, aborto espontáneo, entre otros. Discusión: Se debe sopesar el riesgo-beneficio, la significancia estadística, la significancia clínica y las particularidades de las pacientes a tratar. Conclusión: Los estudios analizados evaluaron diferentes medicamentos antipsicóticos, dificultando consolidación de información en especial en conclusiones solidas ante algunas premisas como fármacos de elección.

Diseño de un modelo de intervención del suicidio en niños y adolescentes

Resumen El objetivo de este estudio fue el de diseñar un modelo de intervención para la prevención del suicidio en la población escolar de niños y adolescentes, con 72 participantes de un colegio público y un colegio privado de la ciudad de Bogotá. Se caracterizó el suicidio en la ciudad de Bogotá en los últimos nueve años, los aspectos legales, se analizaron algunos modelos de prevención, se identificaron los principales factores de riesgo y factores protectores y se propusieron estrategias para su prevención. Este modelo está basado en la administración social del riesgo y los factores protectores y de riesgo, susceptibles de modificación. Se realizó una prueba de tamizaje y fueron utilizados: el Inventario de depresión infantil (CDI de Kovacs), la escala de desesperanza de Beck y la escala de ansiedad para niños y adolescentes de Spence, validadas a nivel internacional. Se observó una correlación positiva (0.490) mediante el coeficiente de rangos de Spearman, con una significación de 0,01 (bilateral) para los tres factores de riesgo. Se hace entrega de un manual de instrucción para la intervención temprana del suicidio en esta población y un folleto informativo dirigido a padres de familia sobre los factores de riesgo y factores protectores. A partir de esto se plantean implicaciones futuras.

Epigenética: definición, bases moleculares e implicaciones en la salud y en la evolución humana

La Epigenética se refiere a los cambios heredables en el ADN e histonas que no implican alteraciones en la secuencia de nucleótidos y modifican la estructura y condensación de la cromatina, por lo que afectan la expresión génica y el fenotipo. Las modificaciones epigenéticas son metilación del ADN y modificaciones de histonas. Objetivo: hacer una revisión de la literatura sobre el concepto de epigenética y su impacto en la salud. Materiales y métodos: se realizó una revisión de la bibliografía sobre el concepto de epigenética, sus bases biológicas, el impacto sobre la salud y la enfermedad y su relación con la evolución. Resultados: los mecanismos epigenéticos han cobrado cada vez más importancia debido a la creciente asociación con enfermedades complejas y comunes, así como por su impacto en la salud de generaciones futuras y en la evolución humana. Conclusiones: la Epigenética tiene un claro impacto en la salud del individuo, en la de su descendencia y en la evolución de la especie humana.

El abismo lógico (Borges y los filósofos de las ideas)

Este libro explora un fenómeno que se repite en algunos textos del escritor argentino Jorge Luis Borges (1899-1986). Está compuesto por nueve capítulos, que corresponden al análisis de la reescritura de nueve distintas propuestas filosóficas. Las propuestas están cobijadas bajo la misma doctrina: el idealismo. Es un libro que se escribe para validar la propuesta de un método de lectura que cuenta a la vez con una dosis de ingenio y con planteamientos rigurosos, permitiendo así un tipo de análisis que, siendo sistemático, es también lúdico, conservando de este modo las funciones fundamentales de la literatura. No pocas conjeturas ha habido acerca de las intenciones de Borges o de sus creencias.El texto propone análisis novedosos de los cuentos de Borges y reevalúa y critica algunos análisis existentes elaborados por diferentes comentaristas. El tipo de análisis propuesto se haría extensivo a otros cuentos de Borges y a otros autores. Es un texto que se esfuerza por tomar distancia de las interpretaciones existentes que hay sobre la obra de Borges y de proponer nuevas lecturas siguiendo un cierto rigor interpretativo. Las conclusiones finales sitúan la propuesta del libro en el centro de debates contemporáneos de la literatura como la muerte del autor, los límites de la interpretación y la intertextualidad. La misma propuesta se encarga de establecer su relación y su distancia con los comentaristas reconocidos y se aparta de propuestas interpretativas pasadas de moda. La aproximación al tema, además, vincula el análisis literario con la historia de la filosofía, haciéndolo interesante para un público más amplio.El texto propone análisis novedosos de los cuentos de Borges y reevalúa y critica algunos análisis existentes elaborados por diferentes comentaristas. El tipo de análisis propuesto se haría extensivo a otros cuentos de Borges y a otros autores. Es un texto que se esfuerza por tomar distancia de las interpretaciones existentes que hay sobre la obra de Borges y de proponer nuevas lecturas siguiendo un cierto rigor interpretativo. Las conclusiones finales sitúan la propuesta del libro en el centro de debates contemporáneos de la literatura como la muerte del autor, los límites de la interpretación y la intertextualidad. La misma propuesta se encarga de establecer su relación y su distancia con los comentaristas reconocidos y se aparta de propuestas interpretativas pasadas de moda. La aproximación al tema, además, vincula el análisis literario con la historia de la filosofía, haciéndolo interesante para un público más amplio.

Estado situacional de los algoritmos genéticos en los negocios internacionales

La computación evolutiva y muy especialmente los algoritmos genéticos son cada vez más empleados en las organizaciones para resolver sus problemas de gestión y toma de decisiones (Apoteker & Barthelemy, 2000). La literatura al respecto es creciente y algunos estados del arte han sido publicados. A pesar de esto, no hay un trabajo explícito que evalúe de forma sistemática el uso de los algoritmos genéticos en problemas específicos de los negocios internacionales (ejemplos de ello son la logística internacional, el comercio internacional, el mercadeo internacional, las finanzas internacionales o estrategia internacional). El propósito de este trabajo de grado es, por lo tanto, realizar un estado situacional de las aplicaciones de los algoritmos genéticos en los negocios internacionales.

The dialectic of silence and remembrance in Lily Brett’s ''Things could be worse''

The dynamics of silence and remembrance in Australian writer Lily Brett’s autobiographic fiction Things Could Be Worse reflects the crisis of memory and understanding experienced by both first and second-generation Holocaust survivors within the diasporic space of contemporary Australia. It leads to issues of handling traumatic and transgenerational memory, the latter also known as postmemory (M. Hirsch), in the long aftermath of atrocities, and problematises the role of forgetting in shielding displaced identities against total dissolution of the self. This paper explores the mechanisms of remembrance and forgetting in L. Brett’s narrative by mainly focusing on two female characters, mother and daughter, whose coming to terms with (the necessary) silence, on the one hand, and articulated memories, on the other, reflects different modes of comprehending and eventually coping with individual trauma. By differentiating between several types of silence encountered in Brett’s prose (that of the voiceless victims, of survivors and their offspring, respectively), I argue that silence can equally voice and hush traumatic experience, that it is never empty, but invested with individual and collective meaning. Essentially, I contend that beside the (self-)damaging effects of silence, there are also beneficial consequences of it, in that it plays a crucial role in emplacing the displaced, rebuilding their shattered self, and contributing to their reintegration, survival and even partial healing.

Costs of Reproduction in Breeding Female Mallards: Predation Risk during Incubation Drives Annual Mortality

The effort expended on reproduction may entail future costs, such as reduced survival or fecundity, and these costs can have an important influence on life-history optimization. For birds with precocial offspring, hypothesized costs of reproduction have typically emphasized nutritional and energetic investments in egg formation and incubation. We measured seasonal survival of 3856 radio-marked female Mallards (Anas platyrhynchos) from arrival on the breeding grounds through brood-rearing or cessation of breeding. There was a 2.5-fold direct increase in mortality risk associated with incubating nests in terrestrial habitats, whereas during brood-rearing when breeding females occupy aquatic habitats, mortality risk reached seasonal lows. Mortality risk also varied with calendar date and was highest during periods when large numbers of Mallards were nesting, suggesting that prey-switching behaviors by common predators may exacerbate risks to adults in all breeding stages. Although prior investments in egg laying and incubation affected mortality risk, most relationships were not consistent with the cost of reproduction hypothesis; birds with extensive prior investments in egg production or incubation typically survived better, suggesting that variation in individual quality drove both relationships. We conclude that for breeding female Mallards, the primary cost of reproduction is a fixed cost associated with placing oneself at risk to predators while incubating nests in terrestrial habitats.

Density dependence and phenological mismatch: consequences for growth and survival of sub-arctic nesting Canada Geese

The extent to which species are plastic in the timing of their reproductive events relative to phenology suggests how climate change might affect their demography. An ecological mismatch between the timing of hatch for avian species and the peak availability in quality and quantity of forage for rapidly growing offspring might ultimately affect recruitment to the breeding population unless individuals can adjust the timing of breeding to adapt to changing phenology. We evaluated effects of goose density, hatch timing relative to forage plant phenology, and weather indices on annual growth of pre-fledging Canada geese (Branta canadensis) from 1993-2010 at Akimiski Island, Nunavut. We found effects of both density and hatch timing relative to forage plant phenology; the earlier that eggs hatched relative to forage plant phenology, the larger the mean gosling size near fledging. Goslings were smallest in years when hatch was latest relative to forage plant phenology, and when local abundance of breeding adults was highest. We found no evidence for a trend in relative hatch timing, but it was apparent that in early springs, Canada geese tended to hatch later relative to vegetation phenology, suggesting that geese were not always able to adjust the timing of nesting as rapidly as vegetation phenology was advanced. Analyses using forage biomass information revealed a positive relationship between gosling size and per capita biomass availability, suggesting a causal mechanism for the density effect. The effects of weather parameters explained additional variation in mean annual gosling size, although total June and July rainfall had a small additive effect on gosling size. Modelling of annual first-year survival probability using mean annual gosling size as an annual covariate revealed a positive relationship, suggesting that reduced gosling growth negatively impacts recruitment.

Serial clustering of extratropical cyclones

The clustering in time (seriality) of extratropical cyclones is responsible for large cumulative insured losses in western Europe, though surprisingly little scientific attention has been given to this important property. This study investigates and quantifies the seriality of extratropical cyclones in the Northern Hemisphere using a point-process approach. A possible mechanism for serial clustering is the time-varying effect of the large-scale flow on individual cyclone tracks. Another mechanism is the generation by one parent cyclone of one or more offspring through secondary cyclogenesis. A long cyclone-track database was constructed for extended October March winters from 1950 to 2003 using 6-h analyses of 850-mb relative vorticity derived from the NCEP NCAR reanalysis. A dispersion statistic based on the varianceto- mean ratio of monthly cyclone counts was used as a measure of clustering. It reveals extensive regions of statistically significant clustering in the European exit region of the North Atlantic storm track and over the central North Pacific. Monthly cyclone counts were regressed on time-varying teleconnection indices with a log-linear Poisson model. Five independent teleconnection patterns were found to be significant factors over Europe: the North Atlantic Oscillation (NAO), the east Atlantic pattern, the Scandinavian pattern, the east Atlantic western Russian pattern, and the polar Eurasian pattern. The NAO alone is not sufficient for explaining the variability of cyclone counts in the North Atlantic region and western Europe. Rate dependence on time-varying teleconnection indices accounts for the variability in monthly cyclone counts, and a cluster process did not need to be invoked.

Evolutionary bi-stability in pathogen transmission mode

Many pathogens transmit to new hosts by both infection (horizontal transmission) and transfer to the infected host's offspring (vertical transmission). These two transmission modes require speci®c adap- tations of the pathogen that can be mutually exclusive, resulting in a trade-off between horizontal and vertical transmission. We show that in mathematical models such trade-offs can lead to the simultaneous existence of two evolutionary stable states (evolutionary bi-stability) of allocation of resources to the two modes of transmission. We also show that jumping between evolutionary stable states can be induced by gradual environmental changes. Using quantitative PCR-based estimates of abundance in seed and vege- tative parts, we show that the pathogen of wheat, Phaeosphaeria nodorum, has jumped between two distinct states of transmission mode twice in the past 160 years, which, based on published evidence, we interpret as adaptation to environmental change. The ®nding of evolutionary bi-stability has impli- cations for human, animal and other plant diseases. An ill-judged change in a disease control programme could cause the pathogen to evolve a new, and possibly more damaging, combination of transmission modes. Similarly, environmental changes can shift the balance between transmission modes, with adverse effects on human, animal and plant health.

Intergenerational effects of birth weight on glucose tolerance and reproductive performance

Women who were themselves small-for-gestational age (SGA) are at a greater risk of adulthood diseases such as non-insulin-dependent diabetes mellitus (NIDDM), and twice at risk of having an SGA baby themselves. The aim of this study was to examine the intergenerational pig. Low (L) and normal (N) birth weight female piglets were followed throughout their first pregnancy (generation 1 (0)). After they had given birth, the growth and development of the lightest (I) and heaviest (n) female piglet from each litter were monitored until approximately 5 months of age (generation 2 (G2)). A glucose tolerance test (GTT) was conducted on G1 pig at similar to 6 months of age and again during late pregnancy; a GTT was also conducted on G2 pigs at similar to 4 months of age. G1 L offspring exhibited impaired glucose metabolism in later life compared to their G1 N sibling but in the next generation a similar scenario was only observed between I and n offspring born to G1 L mothers. Despite G1 L mothers showing greater glucose intolerance in late pregnancy and a decreased litter size, average piglet birth weight was reduced and there was also a large variation in litter weight; this suggests that they were, to some extent, prioritising their nutrient intake towards themselves rather than promoting their reproductive performance. There were numerous relationships between body shape at birth and glucose curve characteristics in later life, which can, to some extent, be used to predict neonatal outcome. In conclusion, intergenerational effects are partly seen in the pig. It is likely that some of the intergenerational influences may be masked due to the pig being a litter-bearing species.