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  • Articles  (300)
  • Food Policy
  • Genomics
  • Oxford University Press  (157)
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  • 1
    Publication Date: 2015-08-11
    Description: The Special Supplemental Nutrition Program for Women, Infants and Children (WIC) Program is a key part of America's safety net, but its structure fails to incentivize participants to be cost-conscious in their purchases and may cause retailers to attach excessive markups to WIC products. We investigate cost containment in the WIC Program, with a focus on California. Results show that smaller vendors often charge considerably higher prices for WIC foods than their larger counterparts. However, larger vendors do not mark up WIC foods more or promote them less than comparable control products. Cost containment can be improved by targeting WIC Program sales to larger vendors when it is possible to do so without compromising participant access, and using large-vendor prices as a benchmark to limit prices set by smaller vendors.
    Keywords: D12 - Consumer Economics: Empirical Analysis, I38 - Government Policy ; Provision and Effects of Welfare Programs, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 2
    Publication Date: 2015-09-19
    Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2015-08-29
    Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
    Keywords: Genomics
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    Topics: Biology
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  • 4
    Publication Date: 2015-05-29
    Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
    Keywords: Genomics
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  • 5
    Publication Date: 2015-05-26
    Description: With the enactment of Regulation (EC) No. 1924/2006, 20 December 2006, ‘ On nutrition and health claims made on foods ’ several health claims can no longer be used on food products in European markets. We simulate the overall impact of the regulation on consumers and producers using the Italian yogurt market as a case study, and data prior to the introduction of the policy. We quantify welfare losses incurred if accepted claims were false, and simulate scenarios where rejected truthful health claims are removed, considering also the case where the products carrying them exit the market. We find that consumers can incur large welfare losses if approved claims are untruthful; if truthful claims are instead denied both consumers and producers may incur losses, with consumers being penalised more than producers.
    Keywords: L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, M38 - Government Policy and Regulation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 6
    Publication Date: 2016-07-09
    Description: Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
    Keywords: Genomics
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  • 7
    Publication Date: 2016-07-28
    Description: Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these ‘repressed transcripts’ have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies.
    Keywords: Genomics
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  • 8
    Publication Date: 2013-06-08
    Description: DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging owing to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of cytosine–guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.
    Keywords: Genomics
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  • 9
    Publication Date: 2015-05-12
    Description: China has long struggled to achieve food security. In the era of a planned economy, local self-sufficiency was dictated by policy. With China's transition to a market economy, however, different policy schemes have been utilized, with greater emphasis placed on the role of market forces, especially in conjunction with China's accession to the World Trade Organization in 2001. Nevertheless, self-sufficiency in grain production remains a deeply rooted goal, and interventionist measures geared towards its achievement are still viewed as the most direct and effective means of food security. This paper examines how the well-being of China's rural population, proxied by measures of food consumption, is affected by the promotion of grain production. Our findings suggest that targeted households bear a disproportionate burden of food security policy, as it is currently implemented.
    Keywords: O12 - Microeconomic Analyses of Economic Development, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 10
    Publication Date: 2015-05-12
    Description: Policymakers have dedicated increasing attention to whether Americans have access to healthful food. As a result, various methods for measuring food store access at the national level have been developed to identify areas that lack access. However, these methods face definitional, data, and methodological limitations. The focus on neighborhoods instead of individuals underestimates the barriers that some individuals face in accessing healthy food, and overestimates the problem in other neighborhoods. This paper reviews and critiques currently available national-level measures of food access. While multiple measures of food access are needed to understand the problem, we recommend greater attention be paid to individual measures of food store access.
    Keywords: I14 - Health and Inequality, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 11
    Publication Date: 2015-05-12
    Description: The Canadian farm share for five crop-based products and seven livestock-based products from 1997 to 2010 is calculated using a supply chain IO analysis. Significant differences exist in farm shares across food commodities with higher farm shares for livestock products and lower farm shares for grain-based products. The decline in the Canadian farm share for food consumed at home is driven in large part by the food purchasing habits of consumers. This paper also addresses the hypothesis that the decline in the Canadian farm share could be partially driven by rising input costs in post-farmgate processes or rising input costs that have greater impact on downstream sectors than primary agricultural producers. Three experiments were conducted to assess the impact of an increase in the cost of corn, energy, and farm labor would have on commodity output prices, farm returns, food expenditure, and farm share. In all three cases, the overall farm share increases, albeit by a small amount, suggesting that these shocks have a larger relative impact on the prices of agricultural commodities than the prices of marketing commodities used in post-farmgate activities. A two-period comparison of these simulations shows that energy (corn and farm labour) price shocks would have had a greater (lower) impact on the farm share in 2007 than 1997.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 12
    Publication Date: 2015-05-12
    Description: Household food insecurity in the United States has reached its highest levels to date. As public and private initiatives have emerged to help improve diets by fostering access to food, the availability of more food stores may result in lower levels of food insecurity. In this article, we assess the relationship between adult food insecurity and food store density in metropolitan areas of the United States. We find that while small grocery/convenience stores show a mitigating effect on adult food insecurity across different samples of households, the effects of large supermarkets/grocery stores and supercenters vary. We also find that Supplemental Nutrition Assistance Program participation and food access can have a simultaneously beneficial effect in reducing adult food insecurity. Implications for policies aiming to improve food security by fostering access to food stores are discussed.
    Keywords: I14 - Health and Inequality, L81 - Retail and Wholesale Trade ; e-Commerce, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 13
    Publication Date: 2014-12-17
    Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Keywords: Genomics
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    Topics: Biology
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  • 14
    Publication Date: 2014-12-17
    Description: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
    Keywords: Genomics
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  • 15
    Publication Date: 2015-04-02
    Description: With read lengths of currently up to 2 x 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.
    Keywords: Genomics
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  • 16
    Publication Date: 2015-04-02
    Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
    Keywords: Genomics
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  • 17
    Publication Date: 2015-12-29
    Description: This article empirically investigates the impact of trade barriers on the world wine trade focusing on trade costs impeding exports, including transport, tariffs, technical barriers and sanitary and phytosanitary (SPS) standards. A gravity model is estimated using data from the main importing and exporting countries for the years 1997–2010. The Poison pseudo-maximum likelihood estimator accounts for heteroskedasticity and the presence of zero trade flows. Our results identify which regulations can adversely affect trade providing useful information to policy-makers involved in negotiations on trade frictions. While SPS measures do not seem to obstruct exports, technical barriers have a varying impact on trade. A decreasing trend for tariffs has largely been compensated by more stringent technical barriers. The overall result is that frictions in the world wine trade have not changed during the past 15 years.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 18
    Publication Date: 2016-01-09
    Description: Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.
    Keywords: Genomics
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  • 19
    Publication Date: 2015-08-29
    Description: Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied ‘gold standard’ haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.
    Keywords: Genomics
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  • 20
    Publication Date: 2015-07-10
    Description: In many developing countries, supermarkets are expanding rapidly. This affects farmers’ marketing options. Previous studies have analyzed welfare effects of smallholder participation in supermarket channels from a static perspective, using cross-section data. We develop a conceptual framework and use panel data to better understand participation and impact dynamics. The analysis focuses on vegetable producers in Kenya. Participation in supermarket channels is associated with income gains. However, many farmers have dropped out of the supermarket channel due to various constraints. The initial income gains cannot be sustained when returning to the traditional market. Organizational support may be needed to avoid widening income disparities.
    Keywords: L24 - Contracting Out ; Joint Ventures ; Technology Licensing, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 21
    Publication Date: 2015-07-12
    Description: Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.
    Keywords: Genomics
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  • 22
    Publication Date: 2015-07-15
    Description: Although the importance of diet quality for improving child health is widely recognized, the roles of environmental factors and the absorption of nutrients for children's physical growth and morbidity have not been adequately integrated into a policy framework. Moreover, nutrient intakes gradually affect child health, so it is helpful to use alternative tools to evaluate short-term interventions versus long-term food policies. This article emphasizes the role of diet quality reflected in the intake of nutrients such as protein, calcium, and iron for children's physical growth. Vitamins A and C are important for reducing morbidity. Children's growth and morbidity affect their cognitive development, which is critical for the future supply of skilled labor and economic growth. Evidence on these issues from countries such as Bangladesh, India, Kenya, the Philippines, and Tanzania is summarized. The supply of nutritious foods is appraised from the viewpoint of improving diet quality. Finally, the roles of educational campaigns and indirect taxes on unhealthy processed foods consumed by the affluent in developing countries are discussed.
    Keywords: O12 - Microeconomic Analyses of Economic Development, I15 - Health and Economic Development, I25 - Education and Economic Development, J10 - General, Q01 - Sustainable Development, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0257-3032
    Electronic ISSN: 1564-6971
    Topics: Economics
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  • 23
    Publication Date: 2016-08-20
    Description: Concerns about the growing prevalence of obesity worldwide have led researchers and policy makers to investigate the potential health impact of fiscal policies such as taxes on unhealthy foods. A common instrument used to measure the relationship between food prices and food consumption is the price elasticity of demand. Using meta-regression analysis we assessed how differences in methodological approaches to estimating demand affected food price elasticities. Most methodological differences had a statistically significant impact on elasticity estimates, which stresses the importance of using meta-estimates or testing the sensitivity of simulation outcomes to a range of elasticity parameters before drawing policy conclusions.
    Keywords: D11 - Consumer Economics: Theory, H31 - Household, Q18 - Agricultural Policy ; Food Policy
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    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 24
    Publication Date: 2016-08-20
    Description: Advanced sequencing technologies have generated a plethora of data for many chromatin marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal utility of those data. A major challenge is to quantitatively model the epigenetic dynamics across both the genome and many cell types for understanding their impacts on differential gene regulation and disease. We introduce IDEAS, an i ntegrative and d iscriminative e pigenome a nnotation s ystem, for jointly characterizing epigenetic landscapes in many cell types and detecting differential regulatory regions. A key distinction between our method and existing state-of-the-art algorithms is that IDEAS integrates epigenomes of many cell types simultaneously in a way that preserves the position-dependent and cell type-specific information at fine scales, thereby greatly improving segmentation accuracy and producing comparable annotations across cell types.
    Keywords: Genomics
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  • 25
    Publication Date: 2016-09-03
    Description: A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 x 10 –4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 x 10 –5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS 1 , IS 2 , IS 5 and IS 186 . Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS 186 target-sites, 5'-GGGG(N6/N7)CCCC-3'. We also detected 48 long deletions not involving IS elements.
    Keywords: Genomics
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  • 26
    Publication Date: 2016-08-20
    Description: This paper reviews the situation in the agricultural sector and food security in Cuba, and particularly the transformations that have (not) taken place since 1990. We compare the Cuban transition with transitions in other "transition countries" and show that Cuba does not easily fit into one of the transition patterns, and, in a way, has characteristics of "a bit of everything". To conclude, we discuss the (potential) effects of the recent policy changes and the new economic reforms that were announced.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, P21 - Planning, Coordination, and Reform, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 27
    Publication Date: 2016-07-09
    Description: If agricultural subsidies are largely capitalized into farmland values through their effect on rental rates, then expanding support for agriculture may not benefit farmers who rent the land they farm. Existing evidence on the incidence of subsidies on cash rental rates is mixed. Identification is obscured by unobserved or imprecisely measured factors that tend to be correlated with subsidies, especially land quality and time-varying factors like commodity prices and adverse weather events. A problem that has received less attention is the fact that subsidies and land quality on rented land may differ from owned land. Since most farms possess both rented and owned acreage, farm-level measures of subsidies, land values, and rental rates may bias estimated incidence. Using a new, field-level data set that, for the first time, precisely links subsidies to land parcels, we show that this bias is considerable: where farm-level estimates suggest an incidence of 42–49 cents of the marginal subsidy dollar, field-level estimates from the same farms indicate that landlords capture just 20–28 cents. The size of the farm and the duration of the rental arrangement have substantial effects. Incidence falls by 5–15 cents when doubling total operated acres, and the incidence falls by 0.1–0.8 cents with each additional year of the rental arrangement. Low incidence of subsidies on rents combined with the farm-size and duration effects suggest that farmers renting land have monopsony power.
    Keywords: H22 - Incidence, Q14 - Agricultural Finance, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 28
    Publication Date: 2016-07-09
    Description: Many countries adjust their trade policies counter-cyclically with food prices, to the extent that the use of restrictions by food-exporting countries has occasionally threatened the food security of food-importing countries. These trade policies are inconsistent with the terms-of-trade motivation often retained to characterize the payoff frontier of self-enforcing trade agreements, as they can worsen the terms of trade of the countries that apply them. This article analyzes trade policy coordination when trade policies are driven by terms-of-trade effects and a desire to reduce domestic food price volatility. This framework implies that importing and exporting countries have incentives to deviate from cooperation at different periods: the latter when prices are high and the former when prices are low. Since staple food prices tend to have asymmetric distributions, with more prices below than above the mean but with occasional spikes, a self-enforcing agreement generates asymmetric outcomes. Without cooperation, an importing country uses its trade policy more frequently because of the concentration of prices below the mean, but an exporting country has a greater incentive to deviate from a cooperative trade policy because positive deviations from the mean price are larger than negative ones. Thus, the asymmetry of the distribution of commodity prices can make it more difficult to discipline export taxes than tariffs in trade agreements.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 29
    Publication Date: 2016-07-09
    Description: We analyze the effects of the interactions that the two pillars of the European Union Common Agricultural Policy—market support and rural development—have on farmers’ uptake of organic farming practices. Special attention is given to the 2003 reform, which substantially altered the relative importance of the two types of support by decoupling direct agricultural payments from the production of a specific crop. In our empirical analysis we study the case of Sweden, making use of the variation in the timing of farmers’ decisions regarding participation in support programs. We estimate a dynamic non-linear unobserved effects probit model to account for unobserved individual heterogeneity and state dependence. Our results indicate the existence of a negative effect of the market support system in place when organic farming techniques were adopted before the 2003 reform. However, this effect is reversed by the introduction of decoupling. Furthermore, the effects of support differ between certified and non-certified organic production: both pillars have significant effects on non-certified organic farming, whereas certified organic farming is exclusively driven by agro-environmental subsidies.
    Keywords: C23 - Models with Panel Data, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 30
    Publication Date: 2015-04-21
    Description: Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact .
    Keywords: Genomics
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    Topics: Biology
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  • 31
    Publication Date: 2015-05-20
    Description: Analysis of rewired upstream subnetworks impacting downstream differential gene expression aids the delineation of evolving molecular mechanisms. Cumulative statistics based on conventional differential correlation are limited for subnetwork rewiring analysis since rewiring is not necessarily equivalent to change in correlation coefficients. Here we present a computational method ChiNet to quantify subnetwork rewiring by statistical heterogeneity that enables detection of potential genotype changes causing altered transcription regulation in evolving organisms. Given a differentially expressed downstream gene set, ChiNet backtracks a rewired upstream subnetwork from a super-network including gene interactions known to occur under various molecular contexts. We benchmarked ChiNet for its high accuracy in distinguishing rewired artificial subnetworks, in silico yeast transcription-metabolic subnetworks, and rewired transcription subnetworks for Candida albicans versus Saccharomyces cerevisiae , against two differential-correlation based subnetwork rewiring approaches. Then, using transcriptome data from tolerant S. cerevisiae strain NRRL Y-50049 and a wild-type intolerant strain, ChiNet identified 44 metabolic pathways affected by rewired transcription subnetworks anchored to major adaptively activated transcription factor genes YAP1 , RPN4 , SFP1 and ROX1 , in response to toxic chemical challenges involved in lignocellulose-to-biofuels conversion. These findings support the use of ChiNet in rewiring analysis of subnetworks where differential interaction patterns resulting from divergent nonlinear dynamics abound.
    Keywords: Genomics
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  • 32
    Publication Date: 2015-05-26
    Description: The European Union (EU) is the world's largest wine producer, as well as the world's most regulated wine market. In 2007, the EU decided on a major reform of its wine policy. A crucial element was the abolishment of a system of planting rights to limit the planting of vineyards. However, after intense lobbying by opponents of the liberalisation, this decision was reversed in 2013. Despite the importance of planting rights in European (and hence global) wine production, and despite the fierce debates surrounding the reforms, no model exists to study the effects of this policy. We develop the first theoretical model of planting rights, integrating the markets for land, planting rights and wine to analyse efficiency and distributional effects. We use the model to study the effects of differences among EU member states in restrictions on trade in planting rights, the role of government reserves and the impact of imperfect enforcement.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 33
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2015-04-18
    Description: The prospects for plant variety protection to deliver improved varieties of self-pollinating crops is assessed using the experience of the Australian wheat breeding sector as a natural experiment. The analysis is based on detailed new data on the agronomic performance of all wheat varieties released by Australian breeders between 1976 and 2011. The results indicate that plant variety protection, and associated reforms, led to a substantial fall in breeder output. Qualitative evidence indicates that this was caused by a combination of fewer research spillovers, lower release standards, and a possible fall in total investment in breeding.
    Keywords: O34 - Intellectual Property Rights, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 34
    Publication Date: 2015-06-24
    Description: Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein–RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein–rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a ‘proof of concept’ that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites.
    Keywords: Genomics
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  • 35
    Publication Date: 2015-02-18
    Description: The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins , implemented in Python and C and supported on Linux and Mac OS X.
    Keywords: Genomics
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  • 36
    Publication Date: 2015-02-18
    Description: Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
    Keywords: Genomics
    Print ISSN: 0305-1048
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  • 37
    Publication Date: 2015-02-11
    Description: Excess returns to producers insured by the Federal Crop Insurance Corporation can arise due to asymmetric information or from the design of the insurance programs themselves. Using unique, unit-level crop insurance contract data for major crops such as corn, soybeans, and wheat in five growing regions, we find evidence that producers in most regions may profit by selecting optional units, buy-up coverage, or by using transitional yields to participate in the federal crop insurance program. We also find evidence that advantages increase with land resource heterogeneity. However, the results do not support hypotheses that producers profit by selecting revenue insurance, nor that high levels of government "incompetence" exist in the design and administration of the crop insurance system.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 38
    Publication Date: 2015-02-11
    Description: We analyze the various welfare costs, transfers, trade, and employment consequences of the current U.S. sugar program for U.S. consumers, other sugar users, sugar refiners, cane and beet growing and processing industries, other associated agricultural sectors, and world markets. The removal of the sugar program would increase U.S. consumers' welfare by $2.9 to $3.5 billion each year and generate a modest job creation of 17,000 to 20,000 new jobs in food manufacturing and related industries. Imports of sugar containing products would fall dramatically, especially confectioneries substituting for domestic inputs under the sugar program. Sugar imports would rise substantially to 5–6 million short tons raw sugar equivalent. World sugar price increases would be minor, equivalent to about 1 cent per pound.
    Keywords: F13 - Trade Policy ; International Trade Organizations, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 39
    Publication Date: 2014-12-03
    Description: This study presents evidence from a survey and choice experiment on the preferences of Hispanic immigrants who entered the United States illegally for different immigration reform proposal attributes. Key components of the current competing US Senate and House immigration reform bills are considered including pathways to legal permanent residence, temporary work visas, family visitation rights, and access to medical care. The results quantify the value Hispanic immigrants place on different policy attributes and suggest that longer-term work visas are highly valued. Ability to legally work in the United States and a pathway to citizenship are substantially more valued than social services such as medical care and social security benefits.
    Keywords: J15 - Economics of Minorities and Races ; Non-labor Discrimination, K37 - Immigration Law, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 40
    Publication Date: 2015-07-10
    Description: Existing analyses of market participation are based on a "double-hurdle" modeling approach. Such models are appropriate only when all members of the population of interest actually produce the good. In some contexts, however (e.g., smallholder farmers), many members of the population do not produce particular goods that they could produce and that their neighbors do produce. Policies influencing market participation among producers may thus also induce additional farmers to become producers. Previous double-hurdle approaches do not allow explicitly for this possibility. To address these limitations, this article presents a "triple-hurdle" approach with an initial stage that includes nonproducers. The model is used to identify the factors associated with Kenyan smallholder farmers choosing to participate in dairy production, and the role that these producers choose to play (or not) in the marketplace. In the midst of debates underway over the privatization of the parastatal Kenya Creameries Company, new knowledge about smallholder participation in dairy could be an important contribution. Results suggest the importance of rural electrification, training, and improved grazing practices. We find that expected net sales are significantly higher when farmers have access to informal private markets. We also describe a version of the ordered tobit model that includes nonproducers and is nested in our triple-hurdle model. A likelihood ratio test shows the latter to be a significantly better fit to our data. We discuss how insights gained from this study differ from the insights that would come from a double-hurdle ordered tobit that also includes nonproducers.
    Keywords: C51 - Model Construction and Estimation, C81 - Methodology for Collecting, Estimating, and Organizing Microeconomic Data, O12 - Microeconomic Analyses of Economic Development, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 41
    Publication Date: 2015-07-10
    Description: This article argues that the structure of the Vietnamese rice export system is, in political economy terms, a rational response to the volatility present in the international rice market. In particular, it is argued that the Vietnamese Food Agency, along with VINAFOOD-1 and VINAFOOD-2, have been structured so that they can benefit from the domestic demands for export restrictions anticipated to occur as a consequence of international price volatility and the psychological demand of consumers for price stability. In turn, the actions of these agencies also contribute to international price volatility and the resulting demand for export restrictions. Since the political and economic elite in Vietnam obtain both political and economic power from this system, it is unlikely to be replaced with more effective and efficient policies to combat domestic price volatility. Thus, continued volatility in the price of rice can be expected.
    Keywords: N55 - Asia including Middle East, P26 - Political Economy ; Property Rights, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 42
    Publication Date: 2015-07-10
    Description: The dimensions that define a food product have expanded rapidly to include characteristics of the production process, marketing arrangements, and implications that production and consumption of the product have for the environment. Some market intermediaries have responded by requiring that their suppliers abide by restrictive production practices. We examine the economic effects of such restrictions and apply this analysis to limitations on the use of antibiotics in U.S. pork production. Results from conceptual and simulation analyses show that, in the absence of demand growth, less pork is sold due to higher costs in the restricted segment, and both pork consumers (on average) and producers are harmed. Demand growth of between 6–11% from adding new consumers who will consume the restricted (antibiotic-free) product but not the conventional product is needed to return consumer surplus to the level in the base case, and between 2–4% demand growth was required to return producer surplus to base. When restricted and conventional products are modeled using a vertical differentiation framework, results depend importantly on the ease with which consumers can switch to a seller who offers their desired product type. Significant distributional impacts among consumers are present when switching costs are prohibitive.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 43
    Publication Date: 2012-12-28
    Description: Sometimes, authorities are unable to rapidly identify the origin of a tainted product. In such cases, recalls or warnings often apply to all suppliers, even to those that had not contributed to the contamination. Traceability enables more targeted recalls by identifying the product's origin more specifically. In this article, we show how increased traceability protects the reputation of industries by limiting the size of recalls. We show the relationships between traceability and the level of food safety with many identical small farms in a competitive industry and for an industry using collective action to set rules and standards.
    Keywords: D21 - Firm Behavior, Q10 - General, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 44
    Publication Date: 2012-08-03
    Description: This paper analyses the impact of the recent decision by the European Union to ‘decouple’ agricultural support payments from agricultural production on Irish farmers' land market decisions. The land market participation decisions of Irish farmers are modelled using a dynamic probit model, while the extent of participation decisions is modelled using a dynamic tobit model. Decoupling does not appear to have significantly altered farmers' land market decisions. One likely explanation for this is the cross-compliance obligation for farmers to maintain land in a state fit for agricultural production in order to receive their full payments.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 45
    Publication Date: 2015-09-12
    Description: This article examines bilateral trade patterns in the Asia-Pacific using a new model in which comparative advantage within the agricultural sector is linked to agro-ecological characteristics, and trade costs are product-specific. Bilateral market share is a function of productivity and trade costs. However, countries with similar land and climate characteristics systematically have high productivity in similar products making them disproportionately sensitive to changes in each other's trade costs. We use a random coefficients logit model to estimate a parametric distribution of comparative advantage and trade costs across products and calculate regional trade liberalization elasticities for each exporter in each import market. Unlike most existing models, the value of the elasticity depends on the degree to which liberalization includes competitors with similar comparative advantage within the agricultural sector. We find disproportionately larger trade elasticities under China-led liberalization relative to U.S.-led liberalization among close U.S. competitors compared to countries whose agricultural products are unlikely to compete head-to-head with U.S. exports. For the United States, we find that the "lost opportunity" cost of exclusion from regional liberalization is increasing in the extent to which its close competitors gain new access.
    Keywords: F13 - Trade Policy ; International Trade Organizations, F14 - Country and Industry Studies of Trade, F15 - Economic Integration, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 46
    Publication Date: 2015-09-12
    Description: Contracts between farmers and intermediaries and crop insurers are important means for farmers to mitigate risks in modern U.S. agriculture. In this paper, we investigate the effect of crop insurance enrollment on contract terms and farmers’ participation in marketing contracts. Following Ligon (2003) , we set up a mechanism design framework to demonstrate an intermediary's contract design problem, where farmers are assumed to be utility maximizing agents. We depict farmers’ optimal choices of insurance coverage using the specification developed by Babcock (2012) . Our model shows that improved terms of crop insurance (lower premiums, higher subsidies) make contracts less appealing to farmers as mechanisms for mitigating risk. Therefore, intermediaries may revise their contract offers so that they are more attractive. However, improvements in contract terms are limited by their cost to the intermediaries and will not lead to expanded participation in contracts.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 47
    Publication Date: 2016-02-20
    Description: Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
    Keywords: Genomics
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  • 48
    Publication Date: 2016-02-20
    Description: Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts ( trans -spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (〉98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans -spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans -spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
    Keywords: Genomics
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  • 49
    Publication Date: 2015-10-31
    Description: We consider how cost heterogeneity and market power affect voting power in producer referenda for mandatory agricultural marketing organisations with generic promotion programmes in the United States. We measure voting power using the Banzhaf Power Index and propose a new version of this index based on the profit-maximising theory of the firm that provides an improved estimate of voting power. Examining several types of demand shifts and voting rules, we find that both Banzhaf Power and our new measure vary considerably depending on the market structure and level of cost heterogeneity.
    Keywords: D71 - Social Choice ; Clubs ; Committees ; Associations, D72 - Models of Political Processes: Rent-Seeking, Elections, Legislatures, and Voting Behavior, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 50
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2015-11-06
    Description: I compare the distribution of risk attitudes of farm owners in the United States to nonfarm business owners and the general population using a measure of risk tolerance collected from national surveys. I find that farmers are significantly more tolerant of risk than the general population, though they are significantly less tolerant of risk than nonfarm business owners. Once demographic differences are controlled, farm and nonfarm business owners are more similar in their risk attitudes and both groups remain significantly more risk tolerant than the general population. First-generation farmers display greater risk tolerance than farmers who inherit operations from family members, as do farmers who have just begun operating a farm; neither pattern emerges among nonfarm business owners. The most risk tolerant farmers are young and male with larger operations, higher incomes, less formal education and close proximity to metropolitan centers. Among farmers, those with less diversified operations and those with specialty enterprises are more risk tolerant than other types of farmers. Crop farmers are less risk tolerant than fruit and vegetable farmers or farmers with specialty enterprises, while farmers who receive government payments or buy enterprise insurance are not significantly different in risk tolerance from farmers who eschew such opportunities. These findings stimulate questions about how farm programs and the distinct challenges of entry in the production agriculture sector shape the underlying distribution of key farmer characteristics such as risk tolerance.
    Keywords: D81 - Criteria for Decision-Making under Risk and Uncertainty, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 51
    Publication Date: 2015-12-02
    Description: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.
    Keywords: Genomics
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    Topics: Biology
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  • 52
    Publication Date: 2015-12-13
    Description: Families in low-income neighborhoods sometimes lack access to supermarkets that provide a broad range of healthy foods. We investigate whether these so called "food deserts" play a role in childhood obesity using a statewide panel data set of Arkansas elementary schoolchildren. We use fixed-effects panel data regression models to estimate the average food desert effect. We next compare children who left (entered) food deserts to children who were always (never) in food deserts and homogenize samples for those whose food desert status changed as a result of a change in residence and those whose status changed only as a consequence of the entry or exit of a supermarket. We present evidence that exposure to food deserts is associated with higher z-scores for body mass index. On average, this is in the neighborhood of 0.04 standard deviations. The strongest evidence and largest association is among urban students and especially those that transition into food deserts from non-deserts. Our food desert estimates are similar in magnitude to findings reported in earlier work on diet and lifestyle interventions targeting similarly aged schoolchildren. That said, we are unable to conclude that the estimated food desert effect is causal because many of the transitions into or out of food deserts result from a change in residence, an event that is endogenous to the child's household. However, there is evidence that food deserts are a risk indicator and that food desert areas may be obesogenic in ways that other low-income neighborhoods are not.
    Keywords: I14 - Health and Inequality, I19 - Other, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 53
    Publication Date: 2011-11-24
    Description: This paper evaluates the farm-level supply and income effects from removing milk quotas and reducing producer prices with increasing direct compensatory payments. Using a panel of Belgian dairy farms, we first estimate a multi-output multi-input flexible cost function that generates a U-shaped marginal cost curve for each farm of the sample. We then embed each farm cost function in a profit-maximisation programming model that is built and calibrated for each farm in the sample. Accounting for farm heterogeneity, the simulations show how dairy farms without quotas may respond differently to changes in prices and structural changes that may take place within the dairy sector. A quota removal with a 20 per cent reduction in milk prices keeps aggregate milk supply and farm income at about the same level of the 2006 reference year.
    Keywords: C33 - Models with Panel Data, C63 - Computational Techniques, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 54
    Publication Date: 2011-11-24
    Description: This paper analyses the impact of milk quotas on the size structure of dairy herds in two major EU milk-producing member states, Germany and the Netherlands, using Markov chain models. Four mobility indicators characterising structural change are developed and calculated. Structural change in the dairy sector as measured by the mobility measures is found to be affected by the milk quota scheme. In the quota period, mobility out of dairying is lower, but the overall and upward mobility increase. This effect is stronger in the Netherlands than in West Germany.
    Keywords: D92 - Intertemporal Firm Choice and Growth, Investment, or Financing, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 55
    Publication Date: 2011-11-24
    Description: We use a stochastic dynamic programming model to simulate the market implications of alternative foot and mouth disease scenarios in the Finnish pig sector. The model considers the dynamics of animal stock adjustment and price movements when the duration of export disruptions is unknown. Explicit treatment of these issues is crucial in the economic analysis of livestock epidemics, especially if there is a risk of a prolonged export ban. Results suggest that the risk of a prolonged ban increases disease losses considerably. It also increases economic benefits from production adjustments.
    Keywords: C61 - Optimization Techniques ; Programming Models ; Dynamic Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 56
    Publication Date: 2011-11-24
    Description: Consumers' preferences for food safety characteristics are investigated with a particular focus on the existence of an embedding effect. Embedding exists if consumer valuation of food safety is insensitive to scope. We conduct between-attribute external tests for embedding in two choice experiments concerning the value of food safety attributes in minced pork and chicken breasts. We find no evidence of embedding neither when using food safety attributes that are not close substitutes and which exhibit both private and public good characteristics, nor when using food safety attributes that are closer substitutes and which have primarily private good characteristics.
    Keywords: Q10 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 57
    Publication Date: 2011-11-24
    Description: In this article, we present one of the first real-world empirical applications of state-contingent production theory. Our state-contingent behavioural model allows us to analyse production under both inefficiency and uncertainty without regard to the nature of producer risk preferences. Using farm data for Finland, we estimate a flexible production model that permits substitutability between state-contingent outputs. We test empirically and reject an assumption that has been implicit in almost all efficiency studies conducted in the last three decades, namely that the production technology is output-cubical, i.e. that outputs are not substitutable between states of nature.
    Keywords: D81 - Criteria for Decision-Making under Risk and Uncertainty, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 58
    Publication Date: 2011-11-24
    Description: In this paper, a modelling approach is developed for the treatment of ‘don't know’(DK) responses, within choice experiments (CEs). A DK option is motivated by the need to allow respondents the opportunity to express uncertainty. Our model explains a DK using an entropy measure of the similarity between options given to respondents within the CE. We illustrate our model by applying it to a CE examining consumer preferences for nutrient contents in food. We find that similarity between options in a given choice set does explain the tendency for respondents to report DK.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 59
    Publication Date: 2011-11-24
    Description: Economists frequently use choice experiments (CEs) to evaluate demand for new attributes in food products. Using a split-sample experimental design focused on demand for pork chop attributes, we find consumer inferences regarding food safety and quality to impact estimates of marginal willingness to pay, market participation, policy appropriateness and consumer welfare effects. Our results suggest that interpretation of findings should be noted as conditional on attributes included in original analyses. A split-sample experimental approach involving multiple CE designs is described and suggested to practitioners to better consider consumer inference effects in future studies.
    Keywords: B40 - General, D12 - Consumer Economics: Empirical Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 60
    Publication Date: 2012-03-08
    Description: Economists have long relied on utilitarian principles in carrying out cost–benefit analysis, but such utilitarianism is typically limited to the well-being of humans. Some prominent philosophers have argued such an approach is unjustifiably speciesist, but what are the consequences of including animal well-being in cost–benefit analysis? This paper considers this question in the context of human altruism towards animals in which people's concerns for the well-being of animals create an externality. After uncovering some conceptual challenges involved in carrying out cost–benefit analysis on animal welfare policies, we report the results of a novel experiment used to measure the public-good value of farm animal welfare, and show that although the average value in our sample is quite large, the result is due to the preferences of only a small subset of the subjects.
    Keywords: C91 - Laboratory, Individual Behavior, D61 - Allocative Efficiency ; Cost-Benefit Analysis, D64 - Altruism, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 61
    Publication Date: 2014-01-22
    Description: Crop insurance is similar to flood and hurricane insurance in that spatially correlated weather tends to cause violations of the independence assumption. Ideally, one would seek to pool uncorrelated risk drawn from the same distribution in crop insurance. This article proposes a testing procedure for the cross-sectional pooling of group units, and empirically analyzes whether the proposed test improves out-of-sample rating performance. We utilize a balanced panel of U.S. county-level corn yields for 510 counties, and the results of an out-of-sample crop insurance rating performance exercise provide economic significance to the proposed pooling methodology and results.
    Keywords: C12 - Hypothesis Testing, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 62
    Publication Date: 2014-01-22
    Description: Is low input use by poor, smallholder farmers caused by time-inconsistent behavior or by limited ability to buy inputs? Are input subsidies the best solution to stimulate input demand or are there smarter solutions? These issues are investigated by combining survey data, stated preference questions, and randomized experiments in Malawi. The demand for fertilizer at harvest time and at planting time, farm gate shadow prices for fertilizer, and the gap between the willingness-to-accept (WTA) and willingness-to-pay (WTP) prices for a standard input package were investigated. Significant effects of timing and of cash constraints were found, suggesting the possibility that smarter designs exist, such as distribution of smaller packages from harvest time to planting time.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 63
    Publication Date: 2014-01-23
    Description: This paper studies the effect of political regime transitions on public policy using a new data set on global agricultural and food policies over a 50-year period (including data from 74 developing and developed countries over the 1955–2005 period). We find evidence that democratization leads to a reduction of agricultural taxation, an increase in agricultural subsidization, or both. The empirical findings are consistent with the predictions of the median voter model because political transitions occurred primarily in countries with a majority of farmers. The results are robust to different specifications, estimation approaches, and variable definitions.
    Keywords: D72 - Models of Political Processes: Rent-Seeking, Elections, Legislatures, and Voting Behavior, F13 - Trade Policy ; International Trade Organizations, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, P16 - Political Economy, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0258-6770
    Electronic ISSN: 1564-698X
    Topics: Economics
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  • 64
    Publication Date: 2014-01-23
    Description: In times of highly volatile commodity markets, governments often try to protect their populations from rapidly rising food prices, which can be particularly harmful for the poor. A potential solution for food-deficit countries is to hold strategic reserves that can be called on when international prices spike. But how large should strategic stockpiles be, and what rules should govern their release? In this paper, we develop a dynamic competitive storage model for wheat in the Middle East and North Africa region, where imported wheat is the most significant component of the average diet. We analyze a strategy that sets aside wheat stockpiles, which can be used to keep domestic prices below a targeted price. Our analysis shows that if the target price is set high and reserves are adequate, the strategy can be effective and robust. Contrary to most interventions, strategic storage policies are counter-cyclical, and when the importing region is sufficiently large, a regional policy can smooth global prices. Simulations indicate that this is the case for the Middle East and North Africa region. Nevertheless, the policy is more costly than a procyclical policy similar to food stamps that uses targeted transfers to directly offset high prices with a subsidy.
    Keywords: F10 - General, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0258-6770
    Electronic ISSN: 1564-698X
    Topics: Economics
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  • 65
    Publication Date: 2013-12-07
    Description: Identity by descent (IBD) can be reliably detected for long shared DNA segments, which are found in related individuals. However, many studies contain cohorts of unrelated individuals that share only short IBD segments. New sequencing technologies facilitate identification of short IBD segments through rare variants, which convey more information on IBD than common variants. Current IBD detection methods, however, are not designed to use rare variants for the detection of short IBD segments. Short IBD segments reveal genetic structures at high resolution. Therefore, they can help to improve imputation and phasing, to increase genotyping accuracy for low-coverage sequencing and to increase the power of association studies. Since short IBD segments are further assumed to be old, they can shed light on the evolutionary history of humans. We propose HapFABIA, a computational method that applies biclustering to identify very short IBD segments characterized by rare variants. HapFABIA is designed to detect short IBD segments in genotype data that were obtained from next-generation sequencing, but can also be applied to DNA microarray data. Especially in next-generation sequencing data, HapFABIA exploits rare variants for IBD detection. HapFABIA significantly outperformed competing algorithms at detecting short IBD segments on artificial and simulated data with rare variants. HapFABIA identified 160 588 different short IBD segments characterized by rare variants with a median length of 23 kb (mean 24 kb) in data for chromosome 1 of the 1000 Genomes Project. These short IBD segments contain 752 000 single nucleotide variants (SNVs), which account for 39% of the rare variants and 23.5% of all variants. The vast majority—152 000 IBD segments—are shared by Africans, while only 19 000 and 11 000 are shared by Europeans and Asians, respectively. IBD segments that match the Denisova or the Neandertal genome are found significantly more often in Asians and Europeans but also, in some cases exclusively, in Africans. The lengths of IBD segments and their sharing between continental populations indicate that many short IBD segments from chromosome 1 existed before humans migrated out of Africa. Thus, rare variants that tag these short IBD segments predate human migration from Africa. The software package HapFABIA is available from Bioconductor. All data sets, result files and programs for data simulation, preprocessing and evaluation are supplied at http://www.bioinf.jku.at/research/short-IBD .
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 66
    Publication Date: 2013-12-07
    Description: Glioma is the most common and fatal primary brain tumour with poor prognosis; however, the functional roles of miRNAs in glioma malignant progression are insufficiently understood. Here, we used an integrated approach to identify miRNA functional targets during glioma malignant progression by combining the paired expression profiles of miRNAs and mRNAs across 160 Chinese glioma patients, and further constructed the functional miRNA–mRNA regulatory network. As a result, most tumour-suppressive miRNAs in glioma progression were newly discovered, whose functions were widely involved in gliomagenesis. Moreover, three miRNA signatures, with different combinations of hub miRNAs (regulations≥30) were constructed, which could independently predict the survival of patients with all gliomas, high-grade glioma and glioblastoma. Our network-based method increased the ability to identify the prognostic biomarkers, when compared with the traditional method and random conditions. Hsa-miR-524-5p and hsa-miR-628-5p, shared by these three signatures, acted as protective factors and their expression decreased gradually during glioma progression. Functional analysis of these miRNA signatures highlighted their critical roles in cell cycle and cell proliferation in glioblastoma malignant progression, especially hsa-miR-524-5p and hsa-miR-628-5p exhibited dominant regulatory activities. Therefore, network-based biomarkers are expected to be more effective and provide deep insights into the molecular mechanism of glioma malignant progression.
    Keywords: Genomics
    Print ISSN: 0305-1048
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    Topics: Biology
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  • 67
    Publication Date: 2014-03-21
    Description: The Minnesota Food Network is a limited liability company comprised of 52 farmers producing a variety of high-quality, sustainably produced agricultural products in southern Minnesota. The network's goal is to develop a regional food system to provide locally grown food at a price that "is fair" to both consumers and producers. This case outlines the challenges that the network faces in their efforts to expand to take advantage of a market opportunity. One of their biggest challenges is that they face high operating costs because of their disaggregated distribution system and need to purchase a distribution and storage facility and two vehicles. They will fund the purchase of a building through an angel investor. An angel investor is necessary because the network cannot sustain traditional loan payments in its current form. Students are asked to consider a number of questions pertaining to the decisions in this case outlined in the final section of the case study.
    Keywords: A22 - Undergraduate, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 68
    Publication Date: 2014-03-21
    Description: Simulated prices from a stochastic storage model are used to examine the price impacts of speculation by rational investors who diversify their financial portfolios by holding agricultural commodity futures. The main result is that rather than destabilizing commodity prices, as is commonly believed, portfolio speculation actually reduces price volatility. Portfolio speculation can potentially destabilize a commodity's price because the additional demand for long futures by speculators is expected to drive up the cash price during both periods of low net demand, when the cash price is below average, and periods of high net demand, when the cash price is above average. Our theoretical analysis demonstrates that the higher level of inventory that is associated with portfolio speculation results in a larger release of stocks during periods of high net demand. The price simulations reveal that this stock adjustment effect is strong since overall price volatility is smaller rather than larger with portfolio speculation.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q14 - Agricultural Finance, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 69
    Publication Date: 2014-02-11
    Description: A major challenge in cancer genomics is uncovering genes with an active role in tumorigenesis from a potentially large pool of mutated genes across patient samples. Here we focus on the interactions that proteins make with nucleic acids, small molecules, ions and peptides, and show that residues within proteins that are involved in these interactions are more frequently affected by mutations observed in large-scale cancer genomic data than are other residues. We leverage this observation to predict genes that play a functionally important role in cancers by introducing a computational pipeline ( http://canbind.princeton.edu ) for mapping large-scale cancer exome data across patients onto protein structures, and automatically extracting proteins with an enriched number of mutations affecting their nucleic acid, small molecule, ion or peptide binding sites. Using this computational approach, we show that many previously known genes implicated in cancers are enriched in mutations within the binding sites of their encoded proteins. By focusing on functionally relevant portions of proteins—specifically those known to be involved in molecular interactions—our approach is particularly well suited to detect infrequent mutations that may nonetheless be important in cancer, and should aid in expanding our functional understanding of the genomic landscape of cancer.
    Keywords: Genomics
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    Topics: Biology
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  • 70
    Publication Date: 2014-04-03
    Description: Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea ( Arabidopsis petraea subsp. umbrosa ), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica . The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated ( r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses.
    Keywords: Genomics
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    Topics: Biology
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  • 71
    Publication Date: 2014-04-05
    Description: This paper uses framed choice experiments to examine the preferences of smallholder farmers in Malawi regarding alternative policy-based incentives to adopt conservation practices that reduce soil erosion and increase yields. The policy incentives offered in the choice experiments included an ideal index-based crop insurance contract, an index insurance contract with basis risk, cash payments, and fertilizer subsidies. Prior to implementing the choice experiments, the farmers participated in a workshop utilizing small group-based dynamic learning games that demonstrated how index-based crop insurance contracts function. The choice experiment results indicate that most farmers preferred cash payments to index insurance contracts, even when the insurance contracts offered substantially higher expected returns. Further, more risk averse farmers were more likely to prefer cash payments than less risk averse and risk loving farmers.
    Keywords: C93 - Field Experiments, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 72
    Publication Date: 2014-04-05
    Description: We develop a dynamic model to assess the effects of policy expectations on crop supply and illustrate the approach with estimates of the effects of base updating in U.S. crop programs. For corn and soybeans in the Corn Belt, the effect of base updating is relatively small because relevant crop alternatives are subject to similar policies and the alternatives are substitutes in production. Increasing acreage of one program crop to capture future payments from base updating reduces future payments from the alternative crop. We also use our model to assess the effect of base updating on acreage response to prices.
    Keywords: Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 73
    Publication Date: 2014-04-05
    Description: A substantial share of U.S. hog producers incorporate antimicrobial drugs into their livestock's feed or water at sub-therapeutic levels to promote feed efficiency and weight gain. Recently, in response to concerns that the overuse of antibiotics in livestock could promote the development of antimicrobial drug-resistant bacteria, the U.S. Food and Drug Administration adopted a strategy to phase out the use of antibiotics for production purposes. This study uses a stochastic frontier model and data from the 2009 USDA Agricultural Resource Management Survey of feeder-to-finish hog producers to estimate the potential effects on hog output and output variability resulting from a ban on antibiotics used for growth promotion. We use propensity score nearest neighbor matching to create a balanced sample of sub-therapeutic antibiotic (STA) users and nonusers. We estimate the frontier model for the pooled sample and separately for users and non-users—which allows for a flexible interaction between STA use and the production technology. Point estimates for the matched sample indicate that STA use has a small positive effect on productivity and production risk, increasing output by 1.0–1.3% and reducing the standard deviation of unexplained output by 1.4%. The results indicate that improvements in productivity resulted exclusively from technological improvement rather than from an increase in technical efficiency.
    Keywords: D24 - Production ; Cost ; Capital and Total Factor Productivity ; Capacity, I18 - Government Policy ; Regulation ; Public Health, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 74
    Publication Date: 2011-12-27
    Description: We investigate farm size inequality in France using agricultural censuses and farm structure surveys at the NUTS3 level (‘départements’) during the period 1970–2007. Using calculated Gini coefficients, we show that farm size inequality has not systematically increased in France. An econometric analysis of the determinants of farm size inequality reveals that policy measures significantly affected farm size inequality, with most of the measures considered decreasing it. Empirical results suggest that the main contributor was the activity of the SAFER (Société d'Aménagement Foncier et d'Etablissement Rural), a specific feature of the French farm structural policy aimed at regulating rural land management. Besides, this research highlights the great complexity of the dynamics underlying the evolution of farm size distribution.
    Keywords: D30 - General, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 75
    Publication Date: 2011-12-27
    Description: This paper analyses implementation policies of environmental quota trade, with the Flemish nutrient production rights as an example. Implementation policies concern the transaction quantity, quota reduction and prevention of speculation. They are analysed with a static and a dynamic multi-agent quota trade model. The static model with discrete non-auctioned quota trade shows that the obligation for quota sellers to entirely stop their production stimulates structural change. The dynamic model version indicates that a flat rate reduction on traded quota and measures taken to prevent speculation combined with too low penalties for overuse stimulate the total production.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 76
    Publication Date: 2011-12-27
    Description: European cattle markets have recently undergone significant change. We explore the simultaneous impacts of agricultural policy reform and the occurrence of an animal health crisis on spatial interdependencies of calf prices of four major European Union markets. The markets are found to be integrated. Price shocks are rapidly absorbed. We find that the member state specific implementations of the 2003 Common Agricultural Policy reforms significantly affected prices of both the national market and of other member states. The blue tongue disease further induced structural change. Using counterfactual scenarios, we show that the decoupling of payments from production led to reduced calf prices.
    Keywords: C32 - Time-Series Models, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 77
    Publication Date: 2011-12-27
    Description: We apply a spatial price equilibrium model of the world sugar market to simulate an abolition of the European Union (EU) quota system in 2015/16. To overcome the normative nature of the approach, we calibrate the model by attaching a non-linear cost term to each trade flow. This is in some regards similar to positive mathematical programming. We suggest an economic interpretation and an econometric specification of the cost term. EU sugar production is simulated to increase from 13.3 to 15.5 million tons in case of quota abolition by 2019/20. Ten member states increase production, nine reduce it. Preferential imports are significantly reduced. Simulated effects are found to be more pronounced the higher the world market price.
    Keywords: F11 - Neoclassical Models of Trade, F17 - Trade Forecasting and Simulation, Q17 - Agriculture in International Trade, Q18 - Agricultural Policy ; Food Policy
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 78
    Publication Date: 2014-11-11
    Description: This paper deals with the determinants of out-farm migration across the European Union (EU) regions focusing on the role played by CAP payments. We add to the existing literature in three main directions. First, our analysis has broad coverage (150 EU regions over the 1990–2009 period); second, we work on the entire portfolio of CAP instruments; third, we rely on modern panel data methods. Results show that standard drivers, such as the relative income and the relative labour share, are important determinants of out-farm migration. Overall, CAP payments significantly contributed to maintain job in agriculture, though the magnitude of the economic effect has been quite moderate and heterogeneous across policy instruments. Pillar I subsidies exerted an effect more than two times greater than that of Pillar II payments.
    Keywords: J21 - Labor Force and Employment, Size, and Structure, J43 - Agricultural Labor Markets, J60 - General, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 79
    Publication Date: 2014-12-03
    Description: Decoupled direct payments to farmers were introduced in the European Union (EU) in the form of the Single Payment Scheme (SPS) in 2005. The 2013 Common Agriculture Policy (CAP) reform changed both the implementation of the SPS and its budget. We assess the possible effects of the 2013 CAP reform on EU land markets, particularly the capitalization of the SPS in land rental values. Our analyses suggest that the implementation details of the 2013 CAP reform will largely determine the impact of the SPS on land markets. The key considerations are the reference period for entitlement allocation, regionalization, payment differentiation, and budgetary changes. Our analysis also implies that a number of relatively minor policy changes could have substantial impacts on land markets.
    Keywords: H22 - Incidence, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 80
    Publication Date: 2014-09-06
    Description: We examine the effect that investments in education have on household expenditure on fruits and vegetables using a two-stage model that accounts for differences in ability and heterogeneous returns to education. For this, we use the 2008 Consumer Expenditure Survey for the United States. We find that higher levels of education contribute to greater household expenditures on both fresh and processed fruits and vegetables. We find a nonlinear effect on fresh fruits and vegetables, indicating that education impacts the quality of purchases as well. Although nutritional education is often touted as important for a healthful diet, these results highlight how investments in human capital via formal education can potentially improve dietary quality as well.
    Keywords: I12 - Health Production, I20 - General, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 81
    Publication Date: 2014-09-06
    Description: In this article, we explore how using imputed income data in the Survey of Income and Program Participation affects the observed relationship between household income volatility and food insufficiency. We find that measuring income volatility using imputed income data substantially understates the association between large drops in household income and food insufficiency. After excluding observations with imputed income, large drops in income are associated with a 2.1–percentage point increased probability of food insufficiency, or a 31% higher likelihood of food insufficiency.
    Keywords: C18 - Methodological Issues: General, C81 - Methodology for Collecting, Estimating, and Organizing Microeconomic Data, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 82
    Publication Date: 2014-09-06
    Description: This research explores the viability of an alternative design for crop insurance based upon farmer-owned savings accounts that are regulated, monitored, and marginally assisted by the government. Such accounts could be an effective risk management tool for many farmers and could operate without major government subsidization. Relative to the current program, the proposed design should exhibit minimal moral hazard and adverse selection problems, and since farm-level risk does not have to be priced, the proposed design eliminates the premium rating difficulties that weaken actuarial soundness and trigger the need for substantial external subsidies. In addition, administrative costs should be considerably lower.
    Keywords: Q14 - Agricultural Finance, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 83
    Publication Date: 2014-09-06
    Description: The recent spikes of global food prices induced a rapid increase in mass media coverage, public policy attention, and donor funding for food security and for agriculture and rural poverty. This has occurred while the shift from low to high food prices has induced a shift in (demographic or social) location of the hunger and poverty effects, but the total number of undernourished and poor people has declined over the same period. We suggest that the observed pattern can be explained by the presence of a global urban bias on agriculture and food policy in developing countries, and we discuss whether this global urban bias may actually benefit poor farmers. We argue that the food price spikes have succeeded where others have failed in the past: to move the problems of poor and hungry farmers to the top of the policy agenda and to induce development and donor strategies to help them.
    Keywords: F35 - Foreign Aid, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 84
    Publication Date: 2014-12-13
    Description: Are labels good or bad for consumers and firms? The answer may seem straightforward since labels improve information, yet economic theory reveals situations where their introduction reduces the welfare of at least some market participants. This essay reviews the theoretical literature on labels in order to identify and explain the main reasons that may cause labeling to produce undesirable side-effects. In contrast to earlier reviews that either concentrate on narrow topics or treat the subject in a more or less informal way, we bring together the main results from all the relevant topics by presenting and discussing the assumptions and model-building techniques that underpin them. The advantage of this approach is that it identifies the origin of the differences between results, thus allowing the synthesis of results that sometimes appear even to be contradictory. We focus on "quality labels" and examine the impact of labeling on market structure, the side-effects of costly certification, issues related to the label's trustworthiness, the rationale for mandatory vs. voluntary labeling, the level at which the label's standard is set according to the agency that selects it, the political economy of labels, that is, pro- or anti-label lobbying, lobbying to affect the label's standard, and lobbying in favor or against the label's mandatory imposition. These topics cover a wide range of applications, including Genetically Modified Organism (GMOs), organic produce, geographic indicators, controlled origin, eco-labels, etc. We conclude by identifying topics that require further research.
    Keywords: L15 - Information and Product Quality ; Standardization and Compatibility, L50 - General, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 85
    Publication Date: 2014-12-13
    Description: Can food prices cause social unrest? Throughout history, riots have frequently broken out, ostensibly as a consequence of high food prices. Using monthly data at the international level, this article studies the impact of food prices – food price levels as well as food price volatility – on social unrest. Because food prices and social unrest are jointly determined, data on natural disasters are used to identify the causal relationship flowing from food price levels to social unrest. Results indicate that for the period 1990–2011, food price increases have led to increases in social unrest, whereas food price volatility has not been associated with increases in social unrest. These results are robust to alternative definitions of social unrest, to using real or nominal prices, to using commodity-specific price indices instead of aggregated price indices, to alternative definitions of the instrumental variable, to alternative definitions of volatility, and to controlling for non-food-related social unrest.
    Keywords: D74 - Conflict ; Conflict Resolution ; Alliances, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 86
    Publication Date: 2015-03-14
    Description: This study examines the relationship between the use of modern food retailers and health outcomes using data from a survey of 1,180 urban households in Indonesia. The dependent variables include adult and child body-mass index and the share of individuals overweight and obese. After controlling for individual and household characteristics and using standard and Lewbel instrumental variable approaches to control for unobservable characteristics, we do not find a statistically significant relationship between use of supermarkets and adult nutrition measures. On the other hand, there is mixed evidence for a negative effect of supermarkets on child nutrition, particularly for those in high-income households.
    Keywords: I15 - Health and Economic Development, P46 - Consumer Economics ; Welfare and Poverty, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 87
    Publication Date: 2015-03-14
    Description: This paper investigates the effect of items’ physical position in the best-worst scaling technique. Although the best-worst scaling technique has been widely used in many fields, the literature has largely overlooked the phenomenon of consumers’ adoption of processing strategies while making their best-worst choices. We examine this issue in the context of consumers’ trust in institutions to provide information about a new food technology, nanotechnology, and its use in food processing. Our results show that approximately half of the consumers used position as a schematic cue when making choices. We find the position bias was particularly strong when consumers chose their most trustworthy institution compared to their least trustworthy institution. In light of our findings, we recommend that researchers in the field be aware of the possibility of position bias when designing best-worst scaling surveys. We also encourage researchers who have already collected best-worst data to investigate whether their data shows such heuristics.
    Keywords: C25 - Discrete Regression and Qualitative Choice Models, D12 - Consumer Economics: Empirical Analysis, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 88
    Publication Date: 2015-03-14
    Description: Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demonstrate EvoTol's ability to identify known disease-causing genes is unmatched by competing methods. Application of EvoTol to the human interactome revealed networks enriched for genes intolerant to protein sequence variation, informing novel polygenic contributions to human disease.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 89
    Publication Date: 2015-03-14
    Description: Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo . However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF–DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF–DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 90
    Publication Date: 2012-10-10
    Description: Enriching target sequences in sequencing libraries via capture hybridization to bait/probes is an efficient means of leveraging the capabilities of next-generation sequencing for obtaining sequence data from target regions of interest. However, homologous sequences from non-target regions may also be enriched by such methods. Here we investigate the fidelity of capture enrichment for complete mitochondrial DNA (mtDNA) genome sequencing by analyzing sequence data for nuclear copies of mtDNA (NUMTs). Using capture-enriched sequencing data from a mitochondria-free cell line and the parental cell line, and from samples previously sequenced from long-range PCR products, we demonstrate that NUMT alleles are indeed present in capture-enriched sequence data, but at low enough levels to not influence calling the authentic mtDNA genome sequence. However, distinguishing NUMT alleles from true low-level mutations (e.g. heteroplasmy) is more challenging. We develop here a computational method to distinguish NUMT alleles from heteroplasmies, using sequence data from artificial mixtures to optimize the method.
    Keywords: Genomics
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    Topics: Biology
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  • 91
    Publication Date: 2012-10-10
    Description: Single nucleotide polymorphisms (SNPs) are increasingly used to tag genetic loci associated with phenotypes such as risk of complex diseases. Technically, this is done genome-wide without prior restriction or knowledge of biological feasibility in scans referred to as genome-wide association studies (GWAS). Depending on the linkage disequilibrium (LD) structure at a particular locus, such tagSNPs may be surrogates for many thousands of other SNPs, and it is difficult to distinguish those that may play a functional role in the phenotype from those simply genetically linked. Because a large proportion of tagSNPs have been identified within non-coding regions of the genome, distinguishing functional from non-functional SNPs has been an even greater challenge. A strategy was recently proposed that prioritizes surrogate SNPs based on non-coding chromatin and epigenomic mapping techniques that have become feasible with the advent of massively parallel sequencing. Here, we introduce an R/Bioconductor software package that enables the identification of candidate functional SNPs by integrating information from tagSNP locations, lists of linked SNPs from the 1000 genomes project and locations of chromatin features which may have functional significance. Availability: FunciSNP is available from Bioconductor (bioconductor.org).
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 92
    Publication Date: 2014-07-03
    Description: Up to now, most nutritional policies have been set up to inform consumers about the health benefits induced by more balanced diets. Reviews of the impacts of these policies show that the effects are often modest. This has led governments to implement, in more recent times, policies focused on the market environment, especially on the characteristics of the food supply. The goal of this paper is to review theoretical and empirical studies focusing on changes in the food supply induced by alternative policies, and to attempt to draw from them policy guidelines and conjectures to test in future research.
    Keywords: I38 - Government Policy ; Provision and Effects of Welfare Programs, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 93
    Publication Date: 2014-07-03
    Description: With the rise of behavioural economics has come the belief that decision-making biases justify paternalistic policies. Such views challenge the notion of consumer sovereignty and the validity of traditional approaches of economic welfare analysis. While behavioural economics might improve the effectiveness of policies that are already justified on some other market-failure grounds, this article argues that the existence of cognitive failures, alone, do not justify government regulation. If one abandons the idea that consumers know what is in their best interest, judging the merits of policies becomes arbitrary and reflects only what a paternalist wants for others. The typical behavioural economic experiment occurs with college students devoid of real-world context. The biases found in such setting may not extrapolate well to conditions where people have more experience and knowledge, and where they can learn from past mistakes. Even when behavioural biases persist in the ‘real world’, consumers face incentives to engage in activities that protect them from the adverse consequences of the biases, and public policies that shield people from such consequences reduce incentives to self-regulate. The article concludes with some ideas for future research and a discussion of the merits of freedom of choice.
    Keywords: D03 - Behavioral Economics ; Underlying Principles, I18 - Government Policy ; Regulation ; Public Health, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 94
    Publication Date: 2013-07-31
    Description: In consequence of strong changes in general economic conditions, adjustments in the agricultural sector can be expected. To date, however, there are only few policy impact analyses on agricultural investments in a dynamic-stochastic context. The objective of this paper is to develop a real options market model which allows the impact assessment of different political schemes. The model combines genetic algorithms and stochastic simulation. Simulations of the model show that investment subsidies and production ceilings are preferable to price floors because the welfare is less reduced for a given stimulation of the willingness to invest.
    Keywords: D81 - Criteria for Decision-Making under Risk and Uncertainty, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 95
    Publication Date: 2013-07-31
    Description: The aim of this paper is to study farmers' participation in rural development policy (RDP) measures. We investigate to what extent regional RDP priorities are driven by regional characteristics and moreover, whether regional-level policy priorities help to explain farmers' participation in RDP measures. We estimate a multilevel binary choice model that includes both farm-level and regional-level explanatory variables. We conclude that regional governments select RDP priorities based on the specific features of their region. Regional policy priorities play an important role in explaining farmers' participation in agri-environmental schemes but not in measures aimed at improving farmer competitiveness.
    Keywords: Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 96
    Publication Date: 2013-07-31
    Description: The distinction between single farm payments (SFP) and counter-cyclical payments (CCPs) is mainly based on theory. Due to a lack of empirical comparative studies between these payments, it is difficult to confirm the claim that CCPs are more distorting. This paper provides a comparative analysis of these payments and quantifies the impact of such payments in the presence of debt constraints. The main findings are that CCPs are more distorting than SFP. However, the magnitude of the impact estimates is not as large as suggested by the different treatment received by both support programmes in the WTO negotiations.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 97
    Publication Date: 2014-04-15
    Description: Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 98
    Publication Date: 2014-09-02
    Description: We examine enrollment in the U.S. Medicaid and Supplemental Nutrition Assistance Programs (SNAP) and find that while SNAP-eligible adults in poor physical health and with multiple chronic conditions are more likely to jointly enroll in SNAP and Medicaid, they are less likely to enroll in SNAP alone. We also find that the conditional probability of SNAP enrollment given Medicaid participation is higher for individuals with multiple chronic conditions. As a result, the expansion of Medicaid and state policies that promote enrollment coordination between SNAP and Medicaid are expected to increase the number of individuals in SNAP with chronic medical conditions.
    Keywords: I10 - General, I38 - Government Policy ; Provision and Effects of Welfare Programs, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 99
    Publication Date: 2014-09-02
    Description: At odds with a vast body of economic evidence reporting exceptionally high rates of return to investments in agricultural research and development (R&D), growth in public R&D spending for food and agriculture has slowed in numerous, especially rich, countries worldwide. The observed R&D spending behavior is consistent with a determination that the reported rates of return are perceived as implausible by policy makers. We examine this notion by scrutinizing 2,242 investment evaluations reported in 372 separate studies from 1958 to 2011. We find that the internal rate of return (IRR) is the predominant summary measure of investment performance used in the literature despite methodological criticisms dating back more than a half century. The reported IRRs imply rates of return that are implausibly high. We investigate the reasons for these implausibly high estimates by analytically comparing the IRR to the modified internal rate of return (MIRR). The MIRR addresses several methodological concerns with using the IRR, has the intuitive interpretation as the annual compounding interest rate paid by an investment, and is directly related to the benefit–cost ratio. To obtain more credible rate of return estimates, we then develop a novel method for recalibrating previously reported IRR estimates using the MIRR when there is limited information on an investment's stream of benefits and costs. Our recalibrated estimates of the rate of return are more modest (median of 9.8% versus 39% per year); however, they are still substantial enough to question the current scaling back of public agricultural R&D spending in many countries.
    Keywords: O22 - Project Analysis, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 100
    Publication Date: 2014-08-02
    Description: We measure impacts of liberalising European agriculture on farm income distribution in western Germany. Unlike previous studies, we do not treat market income and policy support as independent income sources. We jointly apply a partial equilibrium and a programming model and find that liberalisation increases inequality in relative terms though it decreases inequality in absolute terms. In particular, we analyse the relevance of taking into account policy-induced production and market responses in an ex-ante inequality analysis. We find that although their inclusion generally does not affect the direction of distributional effects, it may have considerable impact on their magnitude.
    Keywords: D31 - Personal Income, Wealth, and Their Distributions, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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