Introduction and Overview

Global Agricultural Trade and Developing Countries explores the outstanding issues in global agricultural trade policy and evolving world production and trade patterns. This book presents research findings based on a series of commodity studies of significant economic importance to developing countries. Setting the stage with background chapters and investigations of cross-cutting issues, the authors describe trade and domestic policy regimes affecting agricultural and food markets and analyze product standards and compliance costs and their effects on agricultural and food trade. They then examine the impact and effectiveness of preferences and review the evidence on attempts to decouple agricultural support from agricultural output. Finally, they assess the potential gains from global liberalization in agricultural and food markets, and their sensitivity to various assumptions. Within this broad context of global agricultural policies and reforms, the authors then present detailed studies of commodity markets that feature distorted policy regimes among industrial and developing countries or that are important contributors to exports of developing countries. The commodities analyzed are sugar, dairy, rice, wheat, groundnuts, fruits and vegetables, cotton, seafood, and coffee. These commodity studies analyze current policy regimes in key producing and consuming countries, document the magnitude of these distortions, and estimate the distributional impacts-winners and losers-of trade and domestic policy reforms as well as their impact on trade flows and production location. Global Agricultural Trade and Developing Countries will aid policymakers and researchers in approaching global negotiations and in evaluating domestic policies on agriculture. This book compliments the findings of Agriculture and the WTO: Creating a Trading System for Development.

Maximum likelihood estimation of Gaussian mixture models using stochastic search

Cataloged from PDF version of article.Gaussian mixture models (GMM), commonly used in pattern recognition and machine learning, provide a flexible probabilistic model for the data. The conventional expectation-maximization (EM) algorithm for the maximum likelihood estimation of the parameters of GMMs is very sensitive to initialization and easily gets trapped in local maxima. Stochastic search algorithms have been popular alternatives for global optimization but their uses for GMM estimation have been limited to constrained models using identity or diagonal covariance matrices. Our major contributions in this paper are twofold. First, we present a novel parametrization for arbitrary covariance matrices that allow independent updating of individual parameters while retaining validity of the resultant matrices. Second, we propose an effective parameter matching technique to mitigate the issues related with the existence of multiple candidate solutions that are equivalent under permutations of the GMM components. Experiments on synthetic and real data sets show that the proposed framework has a robust performance and achieves significantly higher likelihood values than the EM algorithm. (C) 2012 Elsevier Ltd. All rights reserved

Tsetse fly (Glossina pallidipes) midgut responses to Trypanosoma brucei challenge

Abstract Background Tsetse flies (Glossina spp.) are the prominent vector of African trypanosome parasites (Trypanosoma spp.) in sub-Saharan Africa, and Glossina pallidipes is the most widely distributed species in Kenya. This species displays strong resistance to infection by parasites, which are typically eliminated in the midgut shortly after acquisition from the mammalian host. Although extensive molecular information on immunity for the related species Glossina morsitans morsitans exists, similar information is scarce for G. pallidipes. Methods To determine temporal transcriptional responses of G. pallidipes to Trypanosoma brucei brucei challenge, we conducted Illumina based RNA-seq on midgut organ and carcass from teneral females G. pallidipes at 24 and 48 h post-challenge (hpc) with T. b. brucei relative to their respective controls that received normal blood meals (without the parasite). We used a suite of bioinformatics tools to determine differentially expressed and enriched transcripts between and among tissues, and to identify expanded transcripts in G. pallidipes relative to their orthologs G. m. morsitans. Results Midgut transcripts induced at 24 hpc encoded proteins were associated with lipid remodelling, proteolysis, collagen metabolism, apoptosis, and cell growth. Midgut transcripts induced at 48 hpc encoded proteins linked to embryonic growth and development, serine endopeptidases and proteosomal degradation of the target protein, mRNA translation and neuronal development. Temporal expression of immune responsive transcripts at 48 relative to 24 hpc was pronounced, indicative of a gradual induction of host immune responses the following challenge. We also searched for G. m. morsitans orthologous groups that may have experienced expansions in the G. pallidipes genome. We identified ten expanded groups in G. pallidipes with putative immunity-related functions, which may play a role in the higher refractoriness exhibited by this species. Conclusions There appears to be a lack of strong immune responses elicited by gut epithelia of teneral adults. This in combination with a compromised peritrophic matrix at this stage during the initial phase of T. b. brucei challenge may facilitate the increased parasite infection establishment noted in teneral flies relative to older adults. Although teneral flies are more susceptible than older adults, the majority of tenerals are still able to eliminate parasite infections. Hence, robust responses elicited at a later time point, such as 72 hpc, may clear parasite infections from the majority of flies. The expanded G. m. morsitans orthologous groups in G. pallidipes may also be functionally associated with the enhanced refractoriness to trypanosome infections reported in G. pallidipes relative to G. m. morsitans

Final structure & design parameters of TARLA RF system

Doğan, Mehmet Sinan (Dogus Author) -- Conference full title: 5th International Particle Accelerator Conference, IPAC 2014; International Congress Center DresdenDresden; Germany; 15 June 2014 through 20 June 2014Turkish Accelerator and Radiation Laboratory in Ankara (TARLA) is an oscillator mode IR-FEL facility which is under construction since 2011. ELBE licensed superconducting modules housing TESLA RF cavities have been manufacturing for one year and the first module will be delivered in 2015. He Cryogenic System has also started to be manufacturing at similar time with the accelerator structures. It will be delivered in 2014. High Power RF amplifiers are started to tender procedures and delivery time is planning as 2015. The installation of high power transmission lines have to be completed at the same time with the delivery date of HPRF amplifiers to test the cavities and amplifiers. In this study, the final structural design of high power RF transmission lines and design parameters of RF amplifiers for TARLA is discussed

Integrating biological pathways and genomic profiles with ChiBE 2

Cataloged from PDF version of article.Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets. Results: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks. Conclusions: ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers

<i>Trypanosoma brucei rhodesiense</i> transmitted by a single tsetse fly bite in vervet monkeys as a model of human African trypanosomiasis

Sleeping sickness is caused by a species of trypanosome blood parasite that is transmitted by tsetse flies. To understand better how infection with this parasite leads to disease, we provide here the most detailed description yet of the course of infection and disease onset in vervet monkeys. One infected tsetse fly was allowed to feed on each host individual, and in all cases infections were successful. The characteristics of infection and disease were similar in all hosts, but the rate of progression varied considerably. Parasites were first detected in the blood 4-10 days after infection, showing that migration of parasites from the site of fly bite was very rapid. Anaemia was a key feature of disease, with a reduction in the numbers and average size of red blood cells and associated decline in numbers of platelets and white blood cells. One to six weeks after infection, parasites were observed in the cerebrospinal fluid (CSF), indicating that they had moved from the blood into the brain; this was associated with a white cell infiltration. This study shows that fly-transmitted infection in vervets accurately mimics human disease and provides a robust model to understand better how sleeping sickness develops

Properties of 42 Solar-type Kepler Targets from the Asteroseismic Modeling Portal

Recently the number of main-sequence and subgiant stars exhibiting solar-like oscillations that are resolved into individual mode frequencies has increased dramatically. While only a few such data sets were available for detailed modeling just a decade ago, the Kepler mission has produced suitable observations for hundreds of new targets. This rapid expansion in observational capacity has been accompanied by a shift in analysis and modeling strategies to yield uniform sets of derived stellar properties more quickly and easily. We use previously published asteroseismic and spectroscopic data sets to provide a uniform analysis of 42 solar-type Kepler targets from the Asteroseismic Modeling Portal (AMP). We find that fitting the individual frequencies typically doubles the precision of the asteroseismic radius, mass and age compared to grid-based modeling of the global oscillation properties, and improves the precision of the radius and mass by about a factor of three over empirical scaling relations. We demonstrate the utility of the derived properties with several applications.Comment: 12 emulateapj pages, 9 figures, 1 online-only extended figure, 1 table, ApJS accepted (typo corrected in Eq.8

The cBio cancer Genomics portal: An open platform for exploring multidimensional cancer genomics data

Cataloged from PDF version of article.The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications. © 2012 American Association for Cancer Research

Incorporating scale dependence in disease burden estimates:the case of human African trypanosomiasis in Uganda

The WHO has established the disability-adjusted life year (DALY) as a metric for measuring the burden of human disease and injury globally. However, most DALY estimates have been calculated as national totals. We mapped spatial variation in the burden of human African trypanosomiasis (HAT) in Uganda for the years 2000-2009. This represents the first geographically delimited estimation of HAT disease burden at the sub-country scale.Disability-adjusted life-year (DALY) totals for HAT were estimated based on modelled age and mortality distributions, mapped using Geographic Information Systems (GIS) software, and summarised by parish and district. While the national total burden of HAT is low relative to other conditions, high-impact districts in Uganda had DALY rates comparable to the national burden rates for major infectious diseases. The calculated average national DALY rate for 2000-2009 was 486.3 DALYs/100 000 persons/year, whereas three districts afflicted by rhodesiense HAT in southeastern Uganda had burden rates above 5000 DALYs/100 000 persons/year, comparable to national GBD 2004 average burden rates for malaria and HIV/AIDS.These results provide updated and improved estimates of HAT burden across Uganda, taking into account sensitivity to under-reporting. Our results highlight the critical importance of spatial scale in disease burden analyses. National aggregations of disease burden have resulted in an implied bias against highly focal diseases for which geographically targeted interventions may be feasible and cost-effective. This has significant implications for the use of DALY estimates to prioritize disease interventions and inform cost-benefit analyses