Study of using marker assisted selection on a beef cattle breeding program by model comparison

A data set of a commercial Nellore beef cattle selection program was used to compare breeding models that assumed or not markers effects to estimate the breeding values, when a reduced number of animals have phenotypic, genotypic and pedigree information available. This herd complete data set was composed of 83,404 animals measured for weaning weight (WW), post-weaning gain (PWG), scrotal circumference (SC) and muscle score (MS), corresponding to 116,652 animals in the relationship matrix. Single trait analyses were performed by MTDFREML software to estimate fixed and random effects solutions using this complete data. The additive effects estimated were assumed as the reference breeding values for those animals. The individual observed phenotype of each trait was adjusted for fixed and random effects solutions, except for direct additive effects. The adjusted phenotype composed of the additive and residual parts of observed phenotype was used as dependent variable for models' comparison. Among all measured animals of this herd, only 3160 animals were genotyped for 106 SNP markers. Three models were compared in terms of changes on animals' rank, global fit and predictive ability. Model 1 included only polygenic effects, model 2 included only markers effects and model 3 included both polygenic and markers effects. Bayesian inference via Markov chain Monte Carlo methods performed by TM software was used to analyze the data for model comparison. Two different priors were adopted for markers effects in models 2 and 3, the first prior assumed was a uniform distribution (U) and, as a second prior, was assumed that markers effects were distributed as normal (N). Higher rank correlation coefficients were observed for models 3_U and 3_N, indicating a greater similarity of these models animals' rank and the rank based on the reference breeding values. Model 3_N presented a better global fit, as demonstrated by its low DIC. The best models in terms of predictive ability were models 1 and 3_N. Differences due prior assumed to markers effects in models 2 and 3 could be attributed to the better ability of normal prior in handle with collinear effects. The models 2_U and 2_N presented the worst performance, indicating that this small set of markers should not be used to genetically evaluate animals with no data, since its predictive ability is restricted. In conclusion, model 3_N presented a slight superiority when a reduce number of animals have phenotypic, genotypic and pedigree information. It could be attributed to the variation retained by markers and polygenic effects assumed together and the normal prior assumed to markers effects, that deals better with the collinearity between markers. (C) 2012 Elsevier B.V. All rights reserved.

Contribution and perspectives of quantitative genetics to plant breeding in Brazil

The purpose of this article is to show how quantitative genetics has contributed to the huge genetic progress obtained in plant breeding in Brazil in the last forty years. The information obtained through quantitative genetics has given Brazilian breeders the possibility of responding to innumerable questions in their work in a much more informative way, such as the use or not of hybrid cultivars, which segregating population to use, which breeding method to employ, alternatives for improving the efficiency of selection programs, and how to handle the data of progeny and/or cultivars evaluations to identify the most stable ones and thus improve recommendations.

Using Machine Learning Classifiers to Assist Healthcare-Related Decisions: Classification of Electronic Patient Records

Surveillance Levels (SLs) are categories for medical patients (used in Brazil) that represent different types of medical recommendations. SLs are defined according to risk factors and the medical and developmental history of patients. Each SL is associated with specific educational and clinical measures. The objective of the present paper was to verify computer-aided, automatic assignment of SLs. The present paper proposes a computer-aided approach for automatic recommendation of SLs. The approach is based on the classification of information from patient electronic records. For this purpose, a software architecture composed of three layers was developed. The architecture is formed by a classification layer that includes a linguistic module and machine learning classification modules. The classification layer allows for the use of different classification methods, including the use of preprocessed, normalized language data drawn from the linguistic module. We report the verification and validation of the software architecture in a Brazilian pediatric healthcare institution. The results indicate that selection of attributes can have a great effect on the performance of the system. Nonetheless, our automatic recommendation of surveillance level can still benefit from improvements in processing procedures when the linguistic module is applied prior to classification. Results from our efforts can be applied to different types of medical systems. The results of systems supported by the framework presented in this paper may be used by healthcare and governmental institutions to improve healthcare services in terms of establishing preventive measures and alerting authorities about the possibility of an epidemic.

Batrachochytrium dendrobatidis in amphibians confiscated from illegal wildlife trade and used in an ex situ breeding program in Brazil

This paper describes an outbreak of chytridiomycosis affecting a group of Dendrobates tinctorius, a Neotropical anuran species, confiscated from the illegal wildlife trade and housed in a private zoo in Brazil as part of an ex situ breeding program. We examined histological sections of the skin of 30 D. tinctorius and 20 Adelphobates galactonotus individuals. Twenty D. tinctorius (66.7%) and none of the A. galactonotus were positive for Batrachochytrium dendrobatidis (Bd). Multiple development stages of Bd infection were observed. The reasons for the interspecific difference in the rate of infection could not be determined, and further studies are advised. Because the examined population consisted of confiscated frogs, detailed epidemiological aspects could not be investigated, and the source of the fungus remains uncertain. The existence of ex situ amphibian populations is important for protecting species at higher risk in the wild, and ex situ amphibian conservation and breeding programs in Brazil may be established using confiscated frogs as founders. However, this paper alerts these programs to the urgency of strict quarantine procedures to prevent the introduction of potential pathogens, particularly Bd, into ex situ conservation programs.

Morphological, molecular and cross-breeding analysis of geographic populations of coconut-mite associated predatory mites identified as Neoseiulus baraki: evidence for cryptic species?

Surveys were conducted in Brazil, Benin and Tanzania to collect predatory mites as candidates for control of the coconut mite Aceria guerreronis Keifer, a serious pest of coconut fruits. At all locations surveyed, one of the most dominant predators on infested coconut fruits was identified as Neoseiulus baraki Athias-Henriot, based on morphological similarity with regard to taxonomically relevant characters. However, scrutiny of our own and published descriptions suggests that consistent morphological differences may exist between the Benin population and those from the other geographic origins. In this study, we combined three methods to assess whether these populations belong to one species or a few distinct, yet closely related species. First, multivariate analysis of 32 morphological characters showed that the Benin population differed from the other three populations. Second, DNA sequence analysis based on the mitochondrial cytochrome oxidase subunit I (COI) showed the same difference between these populations. Third, cross-breeding between populations was unsuccessful in all combinations. These data provide evidence for the existence of cryptic species. Subsequent morphological research showed that the Benin population can be distinguished from the others by a new character (not included in the multivariate analysis), viz. the number of teeth on the fixed digit of the female chelicera.

Decisions on Temporal Sampling Protocol Influence the Detection of Ecological Patterns

Within-site variability in species detectability is a problem common to many biodiversity assessments and can strongly bias the results. Such variability can be caused by many factors, including simple counting inaccuracies, which can be solved by increasing sample size, or by temporal changes in species behavior, meaning that the way the temporal sampling protocol is designed is also very important. Here we use the example of mist-netted tropical birds to determine how design decisions in the temporal sampling protocol can alter the data collected and how these changes might affect the detection of ecological patterns, such as the species-area relationship (SAR). Using data from almost 3400 birds captured from 21,000 net-hours at 31 sites in the Brazilian Atlantic Forest, we found that the magnitude of ecological trends remained fairly stable, but the probability of detecting statistically significant ecological patterns varied depending on sampling effort, time of day and season in which sampling was conducted. For example, more species were detected in the wet season, but the SAR was strongest in the dry season. We found that the temporal distribution of sampling effort was more important than its total amount, discovering that similar ecological results could have been obtained with one-third of the total effort, as long as each site had been equally sampled over 2 yr. We discuss that projects with the same sampling effort and spatial design, but with different temporal sampling protocol are likely to report different ecological patterns, which may ultimately lead to inappropriate conservation strategies.

The influence of captive breeding on the fatty acid profiles of Salminus hilarii (Characiformes: Characidae) eggs and larvae

In addition to the strong influence of the broodstock diet on the development and survival of offspring, domestication may also interfere with the larval life success. We obtained eggs from wild and domesticated Salminus hilarii females and domesticated males. Wild females were caught in the Tiete River and tributaries, and the domesticated females were born three years before the beginning of the experiment in the Ponte Nova Fish Farm. Animals from both groups were fed with the same feed to exclude feed variables. The eggs and larvae were sampled at 0, 8, 16, and 28 h after spawning (HAS), with the last sampling (28 HAS) coinciding with hatching time. After hatching, samplings proceeded at 32, 48, 66, and 96 HAS, with the last sampling (96 HAS) corresponding to the end of yolk sac consumption. Finally, the last experimental period was during the larvae exogenous feeding phase, at 102, 118, 166, and 214 HAS. Our data revealed that domestication of S. hilarii females influenced fatty acid (FA) metabolism during embryo and larva development. However, the structure of membrane phospholipid FA remained mostly stable, with changes principally in the neutral fraction. When the external conditions, mainly water and feed quality, remained constant, domestication of S. hilarii females did not significantly affect the structural FA composition but influenced the selectivity of consumption and/or storage of specific FA.

Work activities as a resource for work organization design and for strategic decisions?

This paper proposes a discussion about the possibilities to link strategic decisions to working activities performed by workers. In that sense contributions from activities analysis could be considered in order to design and manage production.

Management practices and influences on IT architecture decisions: a case study in a telecom company

The study aims to analyze the IT architecture management practices associated with their degree of maturity and the influence of institutional and strategic factors on the decisions involved through a case study in a large telecom organization. The case study allowed us to identify practices that led the company to its current stage of maturity and identify practices that can lead the company to the next stage. The strategic influence was mentioned by most respondents and the institutional influence was present in decisions related to innovation and those dealing with a higher level of uncertainties.

Contribution of graduate programs in plant breeding to the education of plant breeders in Brazil

The success of agribusiness in Brazil in recent decades is unquestionable. Although the country has always had favorable conditions for agriculture (land, water and climate), this success has only come about recently, due to scientific research, which has resulted in considerable increases in yield and in improvement of product quality, as well as making the occupation of new agricultural frontiers possible. A decisive factor for development of agriculture in the country was the creation of EMBRAPA in 1973, which, in a few years, led to considerable demand for researchers with training in graduate programs. Among them are plant breeders, who came to exercise their activity throughout the country and in all ecosystems. The training of plant breeders was only possible because, as from the middle of the 1960s, the country began a wide-ranging education program, with the creation of several graduate programs in genetics and plant breeding.

Cognitive and affective processes in social actions and decisions

The question of how we make, and how we should make judgments and decisions has occupied thinkers for many centuries. This thesis has the aim to add new evidences to clarify the brain’s mechanisms for decisions. The cognitive and the emotional processes of social actions and decisions are investigated with the aim to understand which brain areas are mostly involved. Four experimental studies are presented. A specific kind of population is involved in the first study (as well as in study III) concerning patients with lesion of ventromedial prefrontal cortex (vmPFC). This region is collocated in the ventral surface of frontal lobe, and it seems have an important role in social and moral decision in forecasting the negative emotional consequences of choice. In study I, it is examined whether emotions, specifically social emotions subserved by the vmPFC, affect people’s willingness to trust others. In study II is observed how incidental emotions could encourage trusting behaviour, especially when individuals are not aware of emotive stimulation. Study III has the aim to gather a direct psychophysiological evidence, both in healthy and neurologically impaired individuals, that emotions are crucially involved in shaping moral judgment, by preventing moral violations. Study IV explores how the moral meaning of a decision and its subsequent action can modulate the basic component of action such as sense of agency.

Veterinary drugs in drinking water used for pharmaceutical treatments in breeding farms

Water is susceptible to be used for numerous purposes, including edible, both for humans and animals. In the food animal production, drinking water is frequently used as a way to carry out the most common pharmacological treatments. In these cases, there are many variables which could degrade drugs dissolved in this mean, even when properly arranged pharmaceutical formulations are used. In fact, although a product obtains a Marketing Authorization through appropriate laboratory studies both drug stability and solubility, on the other hand the solubility of the same drug in natural water used as a drinking water is not documented. In the present study has been evaluated the dissolution kinetics (at 0 hours and 24 hours) of products, having oxytetracycline and tylosin as active ingredient, used in drinking water samples in order to see how the different physical and chemical factors that characterize the drinking water may affect therapeutic efficacy. In fact, multiple factors, also of little relevance if individually considered, are able to adversely affect the pharmacological treatment carried out in drinking water.

Agricultural Genetics and Plant Breeding in Early Twentieth-Century Italy

This thesis is about plant breeding in Early 20th-Century Italy. The stories of the two most prominent Italian plant-breeders of the time, Nazareno Strampelli and Francesco Todaro, are used to explore a fragment of the often-neglected history of Italian agricultural research. While Italy was not at the forefront of agricultural innovation, research programs aimed at varietal innovation did emerge in the country, along with an early diffusion of Mendelism. Using philosophical as well as historical analysis, plant breeding is analysed throughout this thesis as a process: a sequence of steps that lays on practical skills and theoretical assumptions, acting on various elements of production. Systematic plant-breeding programs in Italy started from small individual efforts, attracting more and more resources until they became a crucial part of the fascist regime's infamous agricultural policy. Hybrid varieties developed in the early 20th century survived World War II and are now ancestors of the varieties that are still cultivated today. Despite this relevance, the history of Italian wheat hybrids is today largely forgotten: this thesis is an effort to re-evaluate a part of it. The research did allow previously unknown or neglected facts to emerge, giving a new perspective on the infamous alliance between plant-breeding programs and the fascist regime. This thesis undertakes an analysis of Italian plant-breeding programs as processes. Those processes had a practical as well as a theoretical side, and involved various elements of production. Although a complete history of Italian plant breeding still remains to be written, the Italian case can now be considered along with the other case-studies that other scholars have developed in the history of plant breeding. The hope is that this historical and philosophical analysis will contribute to the on-going effort to understand the history of plants.

Lipid quality and oxidative stability in food products from animal origin, as affected by breeding factor

Nowadays it is requested more investigations on alternative rearing systems that are able to improve poultry welfare and to warrant high-quality and safe meat products. This thesis work was focused on the evaluation of the oxidative stability of poultry meats, obtained with different rearing systems, diets (supplemented with bioactive compounds), and packaging conditions. The thesis work was divided into the following parts: - Evaluation of the effects of different rearing systems on the quality, fatty acid composition and oxidative stability of poultry thigh and breast meat belonging to different product categories (“rotisserie” and “cut-up” carcasses); - Evaluation of the effects of different rearing systems and packaging conditions on the shelf-life of poultry thigh meat stored at 4°C for 14 days, and the effects of feed supplementation with thymol (control diet and diet with 2 different concentration of thymol) and packaging conditions on lipid oxidation of poultry thigh meat shelf-life (stored at 4°C for 14 days). The oxidative stability of poultry meat was studied by means of the spectrophotometric determinations of peroxide value and thiobarbituric acid reactive substances. - Evaluation of anti-inflammatory effects of different flavonoids (thymol, luteolin, tangeretin, sulforaphane, polymethoxyflavones, curcumin derivates) to detect their biological activity in LPS-stimulated RAW 264.7 macrophage cells in vitro, in order to study more in depth their action mechanisms. It was evaluated the cell vitality (MTT assay), nitrite concentration and protein profile. The study was focused on the identification of potential dietary bioactive compounds in order to investigate their biological activity and possible synergic effects, and to develop new suitable strategies for long-term promotion of human health, in particular against cancer.

Sustainable improvement of water networks : to achieve best decisions for rehabilitation plans using advanced GIS and statistical techniques

Many of developing countries are facing crisis in water management due to increasing of population, water scarcity, water contaminations and effects of world economic crisis. Water distribution systems in developing countries are facing many challenges of efficient repair and rehabilitation since the information of water network is very limited, which makes the rehabilitation assessment plans very difficult. Sufficient information with high technology in developed countries makes the assessment for rehabilitation easy. Developing countries have many difficulties to assess the water network causing system failure, deterioration of mains and bad water quality in the network due to pipe corrosion and deterioration. The limited information brought into focus the urgent need to develop economical assessment for rehabilitation of water distribution systems adapted to water utilities. Gaza Strip is subject to a first case study, suffering from severe shortage in the water supply and environmental problems and contamination of underground water resources. This research focuses on improvement of water supply network to reduce the water losses in water network based on limited database using techniques of ArcGIS and commercial water network software (WaterCAD). A new approach for rehabilitation water pipes has been presented in Gaza city case study. Integrated rehabilitation assessment model has been developed for rehabilitation water pipes including three components; hydraulic assessment model, Physical assessment model and Structural assessment model. WaterCAD model has been developed with integrated in ArcGIS to produce the hydraulic assessment model for water network. The model have been designed based on pipe condition assessment with 100 score points as a maximum points for pipe condition. As results from this model, we can indicate that 40% of water pipeline have score points less than 50 points and about 10% of total pipes length have less than 30 score points. By using this model, the rehabilitation plans for each region in Gaza city can be achieved based on available budget and condition of pipes. The second case study is Kuala Lumpur Case from semi-developed countries, which has been used to develop an approach to improve the water network under crucial conditions using, advanced statistical and GIS techniques. Kuala Lumpur (KL) has water losses about 40% and high failure rate, which make severe problem. This case can represent cases in South Asia countries. Kuala Lumpur faced big challenges to reduce the water losses in water network during last 5 years. One of these challenges is high deterioration of asbestos cement (AC) pipes. They need to replace more than 6500 km of AC pipes, which need a huge budget to be achieved. Asbestos cement is subject to deterioration due to various chemical processes that either leach out the cement material or penetrate the concrete to form products that weaken the cement matrix. This case presents an approach for geo-statistical model for modelling pipe failures in a water distribution network. Database of Syabas Company (Kuala Lumpur water company) has been used in developing the model. The statistical models have been calibrated, verified and used to predict failures for both networks and individual pipes. The mathematical formulation developed for failure frequency in Kuala Lumpur was based on different pipeline characteristics, reflecting several factors such as pipe diameter, length, pressure and failure history. Generalized linear model have been applied to predict pipe failures based on District Meter Zone (DMZ) and individual pipe levels. Based on Kuala Lumpur case study, several outputs and implications have been achieved. Correlations between spatial and temporal intervals of pipe failures also have been done using ArcGIS software. Water Pipe Assessment Model (WPAM) has been developed using the analysis of historical pipe failure in Kuala Lumpur which prioritizing the pipe rehabilitation candidates based on ranking system. Frankfurt Water Network in Germany is the third main case study. This case makes an overview for Survival analysis and neural network methods used in water network. Rehabilitation strategies of water pipes have been developed for Frankfurt water network in cooperation with Mainova (Frankfurt Water Company). This thesis also presents a methodology of technical condition assessment of plastic pipes based on simple analysis. This thesis aims to make contribution to improve the prediction of pipe failures in water networks using Geographic Information System (GIS) and Decision Support System (DSS). The output from the technical condition assessment model can be used to estimate future budget needs for rehabilitation and to define pipes with high priority for replacement based on poor condition. rn