The use of frozen semen to minimize inbreeding in small populations

In this study, we compared the average coancestry and inbreeding levels for two genetic conservation schemes in which frozen semen from a gene bank is used to reduce the inbreeding in a live population. For a simple scheme in which only semen of generation-0 (G0) sires is used, the level of inbreeding asymptotes to 1/(2N), where N is the number of newborn sires in the base generation and rate of inbreeding goes to zero. However, when only sires of G0 are selected, all genes will eventually descend from the founder sires and all genes from the founder dams are lost. We propose an alternative scheme in which N sires from generation 1 (G1), as well as the N sires from G0, have semen conserved, and the semen of G0 and G1 sires is used for dams of odd and even generation numbers, respectively. With this scheme, the level of inbreeding asymptotes to 1/(3N) and the genes of founder dams are also conserved, because 50% of the genes of sires of G1 are derived from the founder dams. A computer simulation study shows that this is the optimum design to minimize inbreeding, even if semen from later generations is available

SNPMace – A meta-analysis to estimate SNP effects by combining results from multiple countries

Selection of bulls and cows is increasingly made on genomic estimated breeding values (GEBVs) calculated from their SNP genotypes and the estimated effects of each SNP. To obtain the most accurate GEBVs a large training population of animals with phenotypes and genotypes is needed. For some traits, some breeds and some countries such a large training population is not available. In these cases it would increase the accuracy of GEBVs if information from multiple countries and breeds were combined. This paper describes a meta-analysis to combine SNP effects from multiple countries. A project to test this procedure is under way and, if successful, may result in a new Interbull service

Effect of Genetic Architecture on Accuracy of Multi Breed Genomic Prediction

Objectives were to investigate effect of genetic architecture and including random across and within breed effects in GBLUP on accuracy of multi breed genomic prediction. High-density genotypes and imputed synonymous, missense and premature stop codon mutations using sequence data were available for 3000 Holstein Friesians and 3000 Jerseys. Phenotypes of traits with different genetic architectures, regarding allele frequency spectra and number of breed specific QTL, were simulated by sampling 100 QTL from a mutation class. Accuracies of genomic breeding values were estimated using GBLUP including random across and within breed effects. Increase in accuracy by adding individuals of another breed to the reference population and accuracy of across breed genomic prediction was low. Genetic architecture influenced accuracies; accuracies reduced when QTL allele frequencies were lower and QTL were more breed specific. Including a random within breed effect did not affect accuracies

Dynamics of tournaments: the soccer case

A random walk-like model is considered to discuss statistical aspects of tournaments. The model is applied to soccer leagues with emphasis on the scores. This competitive system was computationally simulated and the results are compared with empirical data from the English, the German and the Spanish leagues and showed a good agreement with them. The present approach enabled us to characterize a diffusion where the scores are not normally distributed, having a short and asymmetric tail extending towards more positive values. We argue that this non-Gaussian behavior is related with the difference between the teams and with the asymmetry of the scores system. In addition, we compared two tournament systems: the all-play-all and the elimination tournaments.Comment: To appear in EPJ

Geometric origin of mechanical properties of granular materials

Some remarkable generic properties, related to isostaticity and potential energy minimization, of equilibrium configurations of assemblies of rigid, frictionless grains are studied. Isostaticity -the uniqueness of the forces, once the list of contacts is known- is established in a quite general context, and the important distinction between isostatic problems under given external loads and isostatic (rigid) structures is presented. Complete rigidity is only guaranteed, on stability grounds, in the case of spherical cohesionless grains. Otherwise, the network of contacts might deform elastically in response to load increments, even though grains are rigid. This sets an uuper bound on the contact coordination number. The approximation of small displacements (ASD) allows to draw analogies with other model systems studied in statistical mechanics, such as minimum paths on a lattice. It also entails the uniqueness of the equilibrium state (the list of contacts itself is geometrically determined) for cohesionless grains, and thus the absence of plastic dissipation. Plasticity and hysteresis are due to the lack of such uniqueness and may stem, apart from intergranular friction, from small, but finite, rearrangements, in which the system jumps between two distinct potential energy minima, or from bounded tensile contact forces. The response to load increments is discussed. On the basis of past numerical studies, we argue that, if the ASD is valid, the macroscopic displacement field is the solution to an elliptic boundary value problem (akin to the Stokes problem).Comment: RevTex, 40 pages, 26 figures. Close to published paper. Misprints and minor errors correcte

Relativistic Heavy--Ion Collisions in the Dynamical String--Parton Model

We develop and extend the dynamical string parton model. This model, which is based on the salient features of QCD, uses classical Nambu-Got\=o strings with the endpoints identified as partons, an invariant string breaking model of the hadronization process, and interactions described as quark-quark interactions. In this work, the original model is extended to include a phenomenological quantization of the mass of the strings, an analytical technique for treating the incident nucleons as a distribution of string configurations determined by the experimentally measured structure function, the inclusion of the gluonic content of the nucleon through the introduction of purely gluonic strings, and the use of a hard parton-parton interaction taken from perturbative QCD combined with a phenomenological soft interaction. The limited number of parameters in the model are adjusted to $e^+e^-$ and $p$--$p$ data. Utilizing these parameters, the first calculations of the model for $p$--$A$ and $A$--$A$ collisions are presented and found to be in reasonable agreement with a broad set of data.Comment: 26 pages of text with 23 Postscript figures placed in tex

South African food allergy consensus document 2014

The prevalence of food allergy is increasing worldwide and is an important cause of anaphylaxis. There are no local South African food allergy guidelines. This document was devised by the Allergy Society of South Africa (ALLSA), the South African Gastroenterology Society (SAGES) and the Association for Dietetics in South Africa (ADSA). Subjects may have reactions to more than one food, and different types and severity of reactions to different foods may coexist in one individual. A detailed history directed at identifying the type and severity of possible reactions is essential for every food allergen under consideration. Skin-prick tests and specific immunoglobulin E (IgE) (ImmunoCAP) tests prove IgE sensitisation rather than clinical reactivity. The magnitude of sensitisation combined with the history may be sufficient to ascribe causality, but where this is not possible an incremental oral food challenge may be required to assess tolerance or clinical allergy. For milder non-IgE-mediated conditions a diagnostic elimination diet may be followed with food re-introduction at home to assess causality. The primary therapy for food allergy is strict avoidance of the offending food/s, taking into account nutritional status and provision of alternative sources of nutrients. Acute management of severe reactions requires prompt intramuscular administration of adrenaline 0.01 mg/kg and basic resuscitation. Adjunctive therapy includes antihistamines, bronchodilators and corticosteroids. Subjects with food allergy require risk assessment and those at increased risk for future severe reactions require the implementation of risk-reduction strategies, including education of the patient, families and all caregivers (including teachers), the provision of a written emergency action plan, a MedicAlert necklace or bracelet and injectable adrenaline (preferably via auto-injector) where necessary.http://www.samj.org.zaam2016Paediatrics and Child Healt

Epidemiology of IgE-mediated food allergy

Despite the large number of foods that may cause immunoglobulin E (IgE)-mediated reactions, most prevalence studies have focused on the most common allergenic foods, i.e. cow’s milk, hen’s egg, peanut, tree nut, wheat, soya, fish and shellfish. Food allergy peaks during the first two years of life, and then diminishes towards late childhood as tolerance to several foods develops. Based on meta-analyses and large population-based studies, the true prevalence of food allergy varies from 1% to >10%, depending on the geographical area and age of the patient. The prevalence of food allergy in South Africa (SA) is currently being studied. The prevalence of IgE-mediated food allergy in SA children with moderate-to-severe atopic dermatitis is 40%; however, this represents a high-risk population for food allergy. Preliminary data from the South African Food Sensitisation and Food Allergy (SAFFA) study, which is investigating food allergy in an unselected cohort of 1 - 3-year olds, show a prevalence of 11.6% sensitisation to common foods. Food allergy was most common to egg (1.4%) and peanut (1.1%). Food allergy appears to be the most common trigger of anaphylactic reactions in the community, especially in children, in whom food is responsible for ≥85% of such reactions. In adults, shellfish and nut, and in children, peanut, tree nut, milk and egg, are the most common triggers of food-induced anaphylaxis.http://www.samj.org.zahb201