A meta-frontier approach to measuring technical efficiency and technology gaps in beef cattle production in Argentina

In this paper the stochastic metafrontier method is applied to estimate technical efficiency (TE) and metatechnology ratios (MTR), in beef cattle production for three distinct regions in Argentina. A deterministic stochastic metafrontier production function model is estimated that envelops the individual stochastic frontiers of the three regions. Our results show that firms from Pampean region, the most favored in terms of environment conditions, have an average (TE) of 53.7per cent, meanwhile for others regions the TE is around 58.966.97per cent. The average MTR for Pampean region is 96.8per cent, in contrast, the others regions have an average MTR of 42per cent. Our results suggest that, farms in the Pampean region could improve their performance through a better management using the available technologies and resources. In regions II and III the improvement of the productivity is likely to require additional investment in research to adapt and develop new technologies.Instituto de EconomíaFil: Brescia, Victor. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Economía; ArgentinaFil: Lema, Rolando Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Economía; ArgentinaFil: Gatti, Nicolás. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Economía; Argentin

Block network mapping approach to quantitative trait locus analysis

BACKGROUND: Advances in experimental biology have enabled the collection of enormous troves of data on genomic variation in living organisms. The interpretation of this data to extract actionable information is one of the keys to developing novel therapeutic strategies to treat complex diseases. Network organization of biological data overcomes measurement noise in several biological contexts. Does a network approach, combining information about the linear organization of genomic markers with correlative information on these markers in a Bayesian formulation, lead to an analytic method with higher power for detecting quantitative trait loci? RESULTS: Block Network Mapping, combining Similarity Network Fusion (Wang et al., NM 11:333-337, 2014) with a Bayesian locus likelihood evaluation, leads to large improvements in area under the receiver operating characteristic and power over interval mapping with expectation maximization. The method has a monotonically decreasing false discovery rate as a function of effect size, unlike interval mapping. CONCLUSIONS: Block Network Mapping provides an alternative data-driven approach to mapping quantitative trait loci that leverages correlations in the sampled genotypes. The evaluation methodology can be combined with existing approaches such as Interval Mapping. Python scripts are available at http://lbm.niddk.nih.gov/vipulp/ . Genotype data is available at http://churchill-lab.jax.org/website/GattiDOQTL . BMC Bioinformatics 2016 Dec 22; 17(1):544

Genome-level analysis of genetic regulation of liver gene expression networks

The liver is the primary site for metabolism of nutrients, drugs and chemical agents. While metabolic pathways are complex and tightly regulated, genetic variation among individuals, reflected in variation in gene expression levels, introduces complexity into research on liver disease. This study aimed to dissect genetic networks that control liver gene expression by combining large-scale quantitative mRNA expression analysis with genetic mapping in a reference population of BXD recombinant inbred mouse strains for which extensive SNP, haplotype and phenotypic data is publicly available. We profiled gene expression in livers of naive mice of both sexes from C57BL/6J, DBA/2J, B6D2F1, and 37 BXD strains using Agilent oligonucleotide microarrays. This data was used to map quantitative trait loci (QTLs) responsible for variation in expression of about 19,000 transcripts. We identified polymorphic cis- and trans-acting loci, including several loci that control expression of large numbers of genes in liver

Instantaneous band gap collapse in photoexcited monoclinic VO2_2 due to photocarrier doping

Using femtosecond time-resolved photoelectron spectroscopy we demonstrate that photoexcitation transforms monoclinic VO$_2$ quasi-instantaneously into a metal. Thereby, we exclude an 80 femtosecond structural bottleneck for the photoinduced electronic phase transition of VO$_2$. First-principles many-body perturbation theory calculations reveal a high sensitivity of the VO$_2$ bandgap to variations of the dynamically screened Coulomb interaction, supporting a fully electronically driven isostructral insulator-to-metal transition. We thus conclude that the ultrafast band structure renormalization is caused by photoexcitation of carriers from localized V 3d valence states, strongly changing the screening \emph{before} significant hot-carrier relaxation or ionic motion has occurred

Nine quick tips for efficient bioinformatics curriculum development and training.

Biomedical research is becoming increasingly data driven. New technologies that generate large-scale, complex data are continually emerging and evolving. As a result, there is a concurrent need for training researchers to use and understand new computational tools. Here we describe an efficient and effective approach to developing curriculum materials that can be deployed in a research environment to meet this need

Estimación no paramétrica de los componentes del cambio en la productividad agrícola de Argentina y países del Cono Sur 1961-2012

El trabajo aplica una metodología no paramétrica para estimar índices de Productividad Total de Factores (PTF) y descomponer el cambio en sus principales componentes: cambio técnico, eficiencia técnica y eficiencia de escala. Se presentan estimaciones para la agricultura argentina y los países del Cono Sur utilizando datos de la base FAOSTAT. Los datos corresponden al período 1961-2012 para los cinco países del Cono Sur, y constituyen un panel balanceado de datos que permiten analizar la evolución de eficiencia y productividad de los países seleccionados. La metodología de cálculo sigue el enfoque presentado en O'Donnell (2008) para calcular índices de tipo Fare-Primont de productividad y se utiliza el programa DPIN 3.0 para la estimación. Los resultados comparativos muestran que la performance de Argentina ha sido relativamente favorable en términos de PTF, aunque se observa un menor crecimiento relativo de la producción en los últimos años. Se estimó que los determinantes más dinámicos del comportamiento de la PTF de Argentina en el largo plazo han sido el cambio en escala y el cambio tecnológico, mientras que la eficiencia muestra un resultado negativo.Instituto de EconomíaFil: Lema, Rolando Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigación en Ciencias Políticas, Económicas y Sociales. Instituto de Economía; ArgentinaFil: Gatti, Nicolás. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro de Investigación en Ciencias Políticas, Económicas y Sociales. Instituto de Economía; Argentin

Cleaning Genotype Data from Diversity Outbred Mice.

Data cleaning is an important first step in most statistical analyses, including efforts to map the genetic loci that contribute to variation in quantitative traits. Here we illustrate approaches to quality control and cleaning of array-based genotyping data for multiparent populations (experimental crosses derived from more than two founder strains), using MegaMUGA array data from a set of 291 Diversity Outbred (DO) mice. Our approach employs data visualizations that can reveal problems at the level of individual mice or with individual SNP markers. We find that the proportion of missing genotypes for each mouse is an effective indicator of sample quality. We use microarray probe intensities for SNPs on the X and Y chromosomes to confirm the sex of each mouse, and we use the proportion of matching SNP genotypes between pairs of mice to detect sample duplicates. We use a hidden Markov model (HMM) reconstruction of the founder haplotype mosaic across each mouse genome to estimate the number of crossovers and to identify potential genotyping errors. To evaluate marker quality, we find that missing data and genotyping error rates are the most effective diagnostics. We also examine the SNP genotype frequencies with markers grouped according to their minor allele frequency in the founder strains. For markers with high apparent error rates, a scatterplot of the allele-specific probe intensities can reveal the underlying cause of incorrect genotype calls. The decision to include or exclude low-quality samples can have a significant impact on the mapping results for a given study. We find that the impact of low-quality markers on a given study is often minimal, but reporting problematic markers can improve the utility of the genotyping array across many studies

Charge transfer of polyatomic molecules in ion-atom hybrid traps: Stereodynamics in the millikelvin regime

Rate constants for the charge transfer reaction between N${}_{2}$H${}^{+}$ and Rb in the mK regime are measured in an ion-atom hybrid trap and are found to be lower than the Langevin capture limit. Multireference ab initio computation of the potential energy surfaces involved in the reaction reveals that the low-temperature charge transfer is hindered by short-range features highly dependent on the collision angle and is promoted by a deformation of the molecular frame. The present study highlights the importance of polyatomic effects and of stereodynamics in cold molecular ion-neutral collisions.Comment: See supplemental material for details on electronic structure methods, estimates of transition probabilities and timescales, and other PES cut

O jogo da captura da princesa e a introdução da noção de árvore de possibilidades

Resumo: Esse artigo teve como objetivo descrever um relato acerca da elaboração e proposição de um jogo de tabuleiro, para introduzir a noção de árvore de possibilidades, para alunos do nono ano do Ensino Fundamental. A metodologia utilizada foi a pesquisa-ação, na qual os pesquisadores intervieram sobre o objeto pesquisado. O jogo foi proposto em três sessões de quarenta e cinco minutos cada uma. Na primeira, os pesquisadores apresentaram o jogo e explicaram as regras, na segunda houve uma intervenção, com vistas a mostrar uma estratégia de jogo mais efetiva (o conhecimento sobre árvore de possibilidades) e na terceira foi pedido que jogassem novamente. Como resultados, foi possível observar que a intervenção dos pesquisadores foi capaz de fazer com que os estudantes mudassem suas estratégias de jogo, o que pode significar que eles atribuíram significado a noção de árvore de possibilidades, de maneira lúdica.Palavras-chave: Jogo de Tabuleiro; Combinatória; Ensino Fundamental. The princess's capture game and the introduction of the tree notion of possibilitiesAbstract: This article aimed to describe a story about the elaboration and proposal of a board game, to introduce the notion of tree of possibilities, for students of the ninth grade of elementary school. The methodology used was action research, in which the researchers intervened on the researched object. The game was proposed in three sessions of forty-five minutes each. In the first, the researchers presented the game and explained the rules, in the second there was an intervention, with a view to showing a more effective game strategy (knowledge about the tree of possibilities) and in the third, they were asked to play again. As a result, it was possible to observe that the researchers' intervention was able to make students change their game strategies, which may mean that they attributed meaning to the notion of possibilities tree, in a playful way.Keywords: Board Game; Combinatorial; Elementary School.