ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Cooperatives  (41)
  • Computational Methods  (26)
  • Oxford University Press  (67)
  • 2010-2014  (67)
  • 1
    facet.materialart.
    Unknown
    TrAp: a tree approach for fingerprinting subclonal tumor composition (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Dynalign II: common secondary structure prediction for RNA homologs with domain insertions (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    Product quality in the agri-food chain: do cooperatives offer high-quality wine? (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Description: We investigate the impact of decentralised decision-making on product quality. Comparing a cooperative and an investor-owned firm suggests that members of the cooperative have an incentive to produce too much and to free-ride on quality. Whether or not cooperatives deliver higher quality products depends on the way in which the quality of the final product is determined from the quality levels of the inputs delivered (quality aggregation) as well as the number of members of the cooperative. Empirical evidence on the Austrian wine market suggests that wines produced by cooperatives tend to be of significantly lower quality, ceteris paribus .
    Keywords: D22 - Firm Behavior: Empirical Analysis, D23 - Organizational Behavior ; Transaction Costs ; Property Rights, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    Farmers' satisfaction and intention to continue membership in agricultural marketing co-operatives: neoclassical versus transaction cost considerations (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-26
    Description: The survival of agricultural marketing co-operatives depends on their capability of satisfying and maintaining their base of farmer members. Hypotheses regarding these two success factors are developed in neoclassical economics and transaction cost economics. They are tested with a survey of 321 members of marketing co-operatives specialising in fresh fruits and vegetables. Our results show support for both perspectives. Price paid to farmers is important for their satisfaction with the co-operative. Farmers' perceptions of transaction costs are even more important.
    Keywords: D22 - Firm Behavior: Empirical Analysis, D23 - Organizational Behavior ; Transaction Costs ; Property Rights, P13 - Cooperative Enterprises, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Combining discrete and continuous mixing distributions to identify niche markets for food (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-26
    Description: This paper explores the demand and willingness to pay (WTP) for value-added services to chicken. Since the demand for such services are likely to be highly segmented and often applies only to a market niche, models based on assumptions of homogeneity among consumers are likely to be inappropriate. For this reason, this paper combines discrete and continuous mixing distributions to concurrently identify the size of the niche market and the heterogeneity among consumers within the market niche. Failing to account for the niche market nature of value-added services is shown to have implications for predictions of WTP, demand and total revenue.
    Keywords: C25 - Discrete Regression and Qualitative Choice Models, D12 - Consumer Economics: Empirical Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Efficient motif search in ranked lists and applications to variable gap motifs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Sequence elements, at all levels—DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their coverage and ability to address large motif spaces. We develop and present statistical and algorithmic approaches that take as input ranked lists of sequences and return significant motifs. The efficiency of our approach, based on suffix trees, allows searches over motif spaces that are not covered by existing tools. This includes searching variable gap motifs—two half sites with a flexible length gap in between—and searching long motifs over large alphabets. We used our approach to analyze several high-throughput measurement data sets and report some validation results as well as novel suggested motifs and motif refinements. We suggest a refinement of the known estrogen receptor 1 motif in humans, where we observe gaps other than three nucleotides that also serve as significant recognition sites, as well as a variable length motif related to potential tyrosine phosphorylation.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Inference of modules associated to eQTLs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Cataloging the association of transcripts to genetic variants in recent years holds the promise for functional dissection of regulatory structure of human transcription. Here, we present a novel approach, which aims at elucidating the joint relationships between transcripts and single-nucleotide polymorphisms (SNPs). This entails detection and analysis of modules of transcripts, each weakly associated to a single genetic variant, together exposing a high-confidence association signal between the module and this ‘main’ SNP. To explore how transcripts in a module are related to causative loci for that module, we represent such dependencies by a graphical model. We applied our method to the existing data on genetics of gene expression in the liver. The modules are significantly more, larger and denser than found in permuted data. Quantification of the confidence in a module as a likelihood score, allows us to detect transcripts that do not reach genome-wide significance level. Topological analysis of each module identifies novel insights regarding the flow of causality between the main SNP and transcripts. We observe similar annotations of modules from two sources of information: the enrichment of a module in gene subsets and locus annotation of the genetic variants. This and further phenotypic analysis provide a validation for our methodology.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 11
    facet.materialart.
    Unknown
    Phase variable genes of Campylobacter jejuni exhibit high mutation rates and specific mutational patterns but mutability is not the major determinant of population structure during host colonization (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-22
    Description: Phase variation of surface structures occurs in diverse bacterial species due to stochastic, high frequency, reversible mutations. Multiple genes of Campylobacter jejuni are subject to phase variable gene expression due to mutations in polyC/G tracts. A modal length of nine repeats was detected for polyC/G tracts within C. jejuni genomes. Switching rates for these tracts were measured using chromosomally-located reporter constructs and high rates were observed for cj1139 (G8) and cj0031 (G9). Alteration of the cj1139 tract from G8 to G11 increased mutability 10-fold and changed the mutational pattern from predominantly insertions to mainly deletions. Using a multiplex PCR, major changes were detected in ‘on/off’ status for some phase variable genes during passage of C. jejuni in chickens. Utilization of observed switching rates in a stochastic, theoretical model of phase variation demonstrated links between mutability and genetic diversity but could not replicate observed population diversity. We propose that modal repeat numbers have evolved in C. jejuni genomes due to molecular drivers associated with the mutational patterns of these polyC/G repeats, rather than by selection for particular switching rates, and that factors other than mutational drift are responsible for generating genetic diversity during host colonization by this bacterial pathogen.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 12
    facet.materialart.
    Unknown
    eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-13
    Description: Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5'-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20 mutant have relatively high averaged 5'-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5'-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 13
    facet.materialart.
    Unknown
    Identification of activated cryptic 5' splice sites using structure profiles and odds measure (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-23
    Description: The activation of cryptic 5' splice sites (5' SSs) is often related to human hereditary diseases. The DNA-based mutation screening strategies are commonly used to recognize the cryptic 5' SSs, because features of the local DNA sequence can influence the choice of cryptic 5' SSs. To improve the identification of the cryptic 5' SSs, we developed a structure-based method, named SPO (structure profiles and odds measure), which combines two parameters, the structural feature derived from hydroxyl radical cleavage pattern and odds measure, to assess the likelihood of a cryptic 5' SS activation in competing with its paired authentic 5' SS. Compared to the current tools for identifying activated cryptic 5' SSs, the SPO algorithm achieves higher prediction accuracy than the other methods, including MaxEnt, MDD, Markov model, weight matrix model, Shapiro and Senapathy matrix, R i and G . In addition, the predicted SPO scores from the SPO algorithm exhibited a greater degree of correlation with the strength of cryptic 5' SS activation than that measured from the other seven methods. In conclusion, the SPO algorithm provides an optimal identification of cryptic 5' SSs, can be applied in designing mutagenesis experiments for various splicing events and may be helpful to investigate the relationship between structural variants and human hereditary diseases.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 14
    facet.materialart.
    Unknown
    Modelling pig sector dynamic adjustment to livestock epidemics with stochastic-duration trade disruptions (2011)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 15
    facet.materialart.
    Unknown
    Is embedding entailed in consumer valuation of food safety characteristics? (2011)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 16
    facet.materialart.
    Unknown
    Intangible expenses: a solution to increase the French wine industry performance? (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: This paper presents an empirical investigation of the link between intangible expenses of French wine companies and their financial performance. A flexible moment-based approach is used to analyse the impact of tangible and intangible expenses on the mean, variance and skewness of profit. Econometric evidence shows that a high level of intangible expenses has a positive impact on performance by increasing the expected profit and reducing variance risk. A lower level of intangible expenses reduces risk and mean of profit of corporations. This study provides insights on the use of intangible expenses as a risk management tool.
    Keywords: G32 - Financing Policy ; Financial Risk and Risk Management ; Capital and Ownership Structure, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 17
    facet.materialart.
    Unknown
    Consumer inferences of food safety and quality (2011)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 18
    facet.materialart.
    Unknown
    Consumers' preferences for geographical origin labels: evidence from the Canadian olive oil market (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: Geographical origin labels are important information and marketing tools and have recently become a central component of EU agricultural promotion. We consider demand in a non-EU export market for two distinct label types: country of origin (COO) and geographical indications (GIs). Additionally, two types of GIs, ‘protected designations of origin’ (PDOs) and ‘protected GIs’ (PGIs) are considered. Empirical findings indicate consumers’ willingness to pay varies with the oil's COO and is greater for GIs than for non-GIs from a given country. Weaker evidence that consumers value PDOs more than PGIs is also found.
    Keywords: C25 - Discrete Regression and Qualitative Choice Models, D12 - Consumer Economics: Empirical Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 19
    facet.materialart.
    Unknown
    Chain interdependencies, measurement problems and efficient governance structure: cooperatives versus publicly listed firms (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-08
    Description: We determine the circumstances when the absence of public listing, often believed to be a disadvantage, makes a cooperative the unique efficient governance structure. This is established in a multi-task principal–agent model, capturing that cooperatives are not publicly listed and their CEOs have to bring the downstream enterprise to value as well as to serve upstream member interests. Not having a public listing prevents the CEO from choosing the level of the downstream activities too high. Cooperatives are uniquely efficient when the upstream marginal product multiplied with a function increasing in the strength of the chain complementarities is higher than the downstream marginal product.
    Keywords: D21 - Firm Behavior, L23 - Organization of Production, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 20
    facet.materialart.
    Unknown
    Is producing a private label counterproductive for a branded manufacturer? (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-08
    Description: Branded food manufacturers vindicate the use of excess production capacities to justify their production of retailers’ brands. We study the distributor's and food manufacturer's private label (PL) strategy for production within a framework featuring endogenous store brand quality, bargaining power, possible differences in production technology and potential capacity constraints for the branded manufacturer. Depending on the structure of capacity constraint (applying to both products or to the PL only), we find that the retailer may prefer to choose an independent firm for the production of the store brand whereas the branded manufacturer is chosen in the case of excess capacity.
    Keywords: L11 - Production, Pricing, and Market Structure ; Size Distribution of Firms, L13 - Oligopoly and Other Imperfect Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 21
    facet.materialart.
    Unknown
    Cooperation against theft: A test of incentives for water management In Tunisia (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-22
    Description: Water theft carried out by manipulating water meters constrains volumetric pricing in semi-arid regions. Cooperative management can reduce theft and improve incentives for efficient water use by inducing peer monitoring. Using a theoretical model, we show that theft is more likely when prices are high, punishments are weak, and cooperatives are large. We also show how cooperative membership and punishment levels are determined endogenously by constraints on monitoring. We test the model on data from Tunisia for the years 2001–2003, relying on instruments that proxy for unobservable monitoring costs. The results confirm that well-designed incentives can reduce theft, and that constraints on monitoring costs affect institutional design.
    Keywords: D82 - Asymmetric and Private Information, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q15 - Land Ownership and Tenure ; Land Reform ; Land Use ; Irrigation, Q25 - Water
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 22
    facet.materialart.
    Unknown
    MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ~10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 23
    facet.materialart.
    Unknown
    The Behavior of Bid-Ask Spreads in the Electronically-Traded Corn Futures Market (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-21
    Description: This is the first paper to analyze liquidity costs in agricultural futures markets based on the observed bid-ask spread (BAS) faced by market participants. The results reveal a highly liquid corn market that mostly offers order execution at minimum cost. The BAS responds negatively to volume and positively to price volatility, but also affects volume traded and price volatility. While statistically significant, these responses on a cents/bushel or a percentage basis are generally small. Liquidity costs are also virtually impervious to short-term changes in demand for spreading and trend-following trader activity, as well as differences from day-of-the-week changes in market activity. Much larger cents/bushel and percentage changes in BAS occur during commodity index trader roll periods and on USDA report release days. The roll period findings indicate a sunshine trading effect, while announcement effects identify the importance of unexpected information and adverse selection on order execution costs. Overall, our research demonstrates that the transition to electronic trading in the corn futures market has led to low and stable liquidity costs, despite the market turbulence in 2008–2009.
    Keywords: C36- Instrumental Variables (IV) Estimation, G12 - Asset Pricing ; Trading volume ; Bond Interest Rates, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 24
    facet.materialart.
    Unknown
    Angel Investment and Collective Agricultural Marketing: The Case of the Minnesota Food Network (2014)
    Oxford University Press
    Details
    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
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 25
    facet.materialart.
    Unknown
    Social Networks and New Product Choice (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-21
    Description: To successfully market new products in a social network it is essential to identify influential individuals whose product recommendations influence the consumption choices of their peers. In this study, we use spatial econometric methods to determine how individuals revise their preferences for product attributes when exposed to product recommendations from peers, and how different individuals who vary in their degree of network connectedness exert influence on the product choices of others. We find evidence that consumers look to others for guidance from peers in their preference for subjective, taste-specific parameters, but tend not to respond to peer price choices. Our spatial methods allow us to empirically determine the influence exerted by individual members on the consumption choices of other members of the social network. We find that connected members of the social network are not always the most influential in revising the consumption choices of others. Our estimates reveal that network proximity explains only 8.8% of influence.
    Keywords: D12 - Consumer Economics: Empirical Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 26
    facet.materialart.
    Unknown
    Identifying RNA-binding residues based on evolutionary conserved structural and energetic features (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-11
    Description: Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the structures of homologous proteins belonging to the same family contain useful information because functionally important residues are expected to preserve physico-chemical, structural and energetic features. This information forms the basis of our method, which detects RNA-binding residues of a given RNA-binding protein as those residues that preserve physico-chemical, structural and energetic features in its homologs. Tests on 81 RNA-bound and 35 RNA-free protein structures showed that our method yields a higher fraction of true RNA-binding residues (higher precision) than two structure-based and two sequence-based machine-learning methods. Because the method requires no training data set and has no parameters, its precision does not degrade when applied to ‘novel’ protein sequences unlike methods that are parameterized for a given training data set. It was used to predict the ‘unknown’ RNA-binding residues in the C-terminal RNA-binding domain of human CPEB3. The two predicted residues, F430 and F474, were experimentally verified to bind RNA, in particular F430, whose mutation to alanine or asparagine nearly abolished RNA binding. The method has been implemented in a webserver called DR_bind1, which is freely available with no login requirement at http://drbind.limlab.ibms.sinica.edu.tw .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 27
    facet.materialart.
    Unknown
    Behavioral Responses and the Impact of New Agricultural Technologies: Evidence from a Double-blind Field Experiment in Tanzania (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-05
    Description: Randomized controlled trials (RCTs) in the social sciences are typically not double-blind, so participants know they are "treated" and will adjust their behavior accordingly. Such effort responses complicate the assessment of impact. To gauge the potential magnitude of effort responses we implement a conventional RCT and double-blind trial in rural Tanzania, and randomly allocate modern and traditional cowpea seed varieties to a sample of farmers. Effort responses can be quantitatively important—for our case they explain the entire "treatment effect on the treated" as measured in a conventional economic RCT. Specifically, harvests are the same for people who know they received the modern seeds and for people who did not know what type of seeds they got; however, people who knew they had received the traditional seeds did much worse. Importantly, we also find that most of the behavioral response is unobserved by the analyst, or at least not readily captured using coarse, standard controls.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 28
    facet.materialart.
    Unknown
    Structural change in European calf markets: decoupling and the blue tongue disease (2011)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 29
    facet.materialart.
    Unknown
    Complete RNA inverse folding: computational design of functional hammerhead ribozymes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-10
    Description: Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold , which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold , we design ten cis -cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis -cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/ .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 30
    facet.materialart.
    Unknown
    Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-27
    Description: While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 31
    facet.materialart.
    Unknown
    Gone in Ten Minutes: Intraday Evidence of Announcement Effects in the Electronic Corn Futures Market (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-06
    Description: This article investigates the announcement effects of major USDA reports using intraday Chicago Board of Trade corn futures prices and trading volume from the electronic trading platform for July 2009 to May 2012. Focusing on intraday market reactions, we analyze the extent to which new information impacts and is rapidly reflected in prices. Results show that USDA reports contain substantial information for market participants. Strongest price reactions to the releases are found immediately after the market opens, and market reactions persist for approximately ten minutes. The electronic corn futures market quickly incorporates this new public information, and little evidence exists to support systematic under- or overreactions in prices. Other more subtle reactions occur in the last trading session before USDA announcements as traders adjust their market exposure in anticipation of the release.
    Keywords: D80 - General, G14 - Information and Market Efficiency ; Event Studies, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 32
    facet.materialart.
    Unknown
    Determinants of Occupational Safety for Agribusiness Workers (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-06
    Description: Increases in crop yields and changing cropping patterns have placed stress on agribusiness handling and storage facilities. The objective of this research is to gain insight into the relationship between safety culture and safety performance, and to identify the determinants of safety culture in agribusinesses. The research suggests that investments in labor inputs such as increased training, consistent discipline, and recognition of safety achievements all increase safety culture. Furthermore, improvements in employee perceptions of safety culture have a positive impact on reducing employee injuries. Congress has recently funded nine centers to work on occupational health and safety research in agriculture, fisheries, and forestry.
    Keywords: J43 - Agricultural Labor Markets, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 33
    facet.materialart.
    Unknown
    Futures Market Failure? (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: In a well-functioning futures market, the futures price at expiration equals the price of the underlying asset. This condition failed to hold in grain markets for most of 2005-2010, calling into question the ability of these markets to perform their price discovery and risk management functions. During this period, futures contracts expired up to 35% above the cash grain price. We develop a dynamic rational expectations model of commodity storage that explains how these recent convergence failures were generated by the institutional structure of the delivery system. When delivery occurs on a grain futures contract, the firm on the short side of the market provides a delivery instrument (a warehouse receipt or shipping certificate) to the firm on the long side of the market. The firm taking delivery may hold the delivery instrument indefinitely, providing it pays a daily storage rate. The futures exchange sets the maximum allowable storage rate at a fixed value. We show that non-convergence arises in equilibrium when the market price of physical grain storage exceeds the maximum storage rate on delivery instruments. We call the difference between the price of carrying physical grain and the maximum storage rate the wedge , and demonstrate theoretically and empirically that the magnitude of the non-convergence equals the expected present discounted value of a function of future wedges.
    Keywords: G13 - Contingent Pricing ; Futures Pricing, G14 - Information and Market Efficiency ; Event Studies, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 34
    facet.materialart.
    Unknown
    An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 35
    facet.materialart.
    Unknown
    Price Explosiveness, Speculation, and Grain Futures Prices (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-13
    Description: A recently developed testing procedure is used to detect and date-stamp explosive episodes ("bubbles") in corn, soybean, and wheat futures markets during 2004–2013. We find that the markets experienced price explosiveness only approximately two percent of the time and, when bubbles do occur, they are generally short-lived and small in magnitude. The correspondence between observed price spikes and bubbles is rather low, with a large portion of the price explosiveness occurring during downward price movements. Commodity index trader positions do not significantly affect the probability of a positive bubble occurring in grain futures markets, which directly contradicts the argument (the "Masters Hypothesis") that waves of index investment distorted underlying supply-and-demand relationships and led to a series of massive bubbles in agricultural futures markets. In addition, commodity index trader positions tend to reduce negative bubble occurrence, while general speculative activity as measured by Working's T reduces the probability of a positive bubble. There is some evidence that the positions of noncommercial traders have a direct effect on positive bubble occurrence, but the effect declines when accounting for the composition of other traders in the market. Overall, speculation has little effect or negative effects on price explosiveness. Finally, positive bubbles are more likely to occur in the presence of low inventories, strong exports, a weak U.S. dollar, and booming economic growth, whereas negative bubbles are more likely to occur with large inventories, weak exports, and stagnant economic growth.
    Keywords: D84 - Expectations ; Speculations, G12 - Asset Pricing ; Trading volume ; Bond Interest Rates, G13 - Contingent Pricing ; Futures Pricing, G14 - Information and Market Efficiency ; Event Studies, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q41 - Demand and Supply
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 36
    facet.materialart.
    Unknown
    Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-10
    Description: The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 37
    facet.materialart.
    Unknown
    Strain/species identification in metagenomes using genome-specific markers (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: Shotgun metagenome sequencing has become a fast, cheap and high-throughput technology for characterizing microbial communities in complex environments and human body sites. However, accurate identification of microorganisms at the strain/species level remains extremely challenging. We present a novel k -mer-based approach, termed GSMer, that identifies genome-specific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/species-level identification in metagenomes. Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and 11 736 360 species-specific GSMs were identified for 4088 strains and 2005 species (4933 strains), respectively. The GSMs were first evaluated against mock community metagenomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that the identified GSMs were specific to their targeting genomes. Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GSMs per strain were sufficient to identify most microbial strains with ≥0.25 x coverage, and 10% of selected GSMs in a database should be detected for confident positive callings. Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 38
    facet.materialart.
    Unknown
    Adapting Contract Theory to Fit Contract Farming (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: This article discusses the current state of contract theory and its usefulness for conceptualizing issues related to agricultural contracting. The paper will explore the limitations of existing theory for applied work, and what methodological improvements are needed to enhance the usefulness of the theory to agricultural economists. One pervasive problem is that the economic literature on contracts is rather fragmented and the various methodological strands are narrow in their focus. As such, agricultural economists should engage in methodological research to develop applied contracting models that can capture higher-order features of real-world agricultural contracts while delivering generalizable comparative statics predictions because contracting continues to expand along the entire modern food marketing channel. In the latter part of this article, a simple model is developed to illustrate how classic methodological approaches can be combined with recent developments in contract and game theory to construct applied theory models that are useful for capturing some important features of agricultural contracts.
    Keywords: D43 - Oligopoly and Other Forms of Market Imperfection, D82 - Asymmetric and Private Information, D86 - Economics of Contract: Theory, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 39
    facet.materialart.
    Unknown
    Information, Mobile Telephony, and Traders' Search Behavior in Niger (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: Information and communications technologies have spread rapidly in developing countries. We investigate the impact of mobile phones on traders' search behavior in Niger by constructing a theoretical model of search in which traders engage in sequential search for the optimal sales price. Using a trader panel dataset spanning 2005–2007, we find empirical support for the model in that the duration of mobile phone coverage is associated with increased search activity. This effect evolves dynamically over time and is stronger for larger traders, who engage in arbitrage over longer distances. Results provide empirical evidence for the observed linkages between mobile telephony and price dispersion.
    Keywords: O10 - General, O30 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 40
    facet.materialart.
    Unknown
    Characterizing RNA ensembles from NMR data with kinematic models (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 41
    facet.materialart.
    Unknown
    Quantitative models for accelerated protein dissociation from nucleosomal DNA (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-02
    Description: Binding of transcription factors to their binding sites in promoter regions is the fundamental event in transcriptional gene regulation. When a transcription factor binding site is located within a nucleosome, the DNA has to partially unwrap from the nucleosome to allow transcription factor binding. This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure. Recently a second mechanism has been reported where transcription factor off-rates are dramatically increased when binding to target sites within the nucleosome. There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA. We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase. Our results suggest a general mechanism how nucleosomes increase transcription factor dissociation to promote exchange of transcription factors and regulate gene expression.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 42
    facet.materialart.
    Unknown
    SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-15
    Description: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A , a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 43
    facet.materialart.
    Unknown
    Distinguishing beliefs from preferences in food choice (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-02
    Description: In the past two decades, there has been an explosion of studies eliciting consumer willingness-to-pay for food attributes; however, this work has largely refrained from drawing a distinction between preferences for health, safety and quality on the one hand and consumers' subjective beliefs that the products studied possess these attributes, on the other. Using data from three experimental studies, along with structural economic models, we show that controlling for subjective beliefs can substantively alter the interpretation of results and the ultimate implications derived from a study. The results suggest the need to measure subjective beliefs in studies of consumer choice and to utilise the measures when making policy and marketing recommendations.
    Keywords: C91 - Laboratory, Individual Behavior, D83 - Search ; Learning ; Information and Knowledge ; Communication ; Belief, 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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 44
    facet.materialart.
    Unknown
    r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-16
    Description: The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of long-range genomic interactions, via the generation of ligation products between DNA sequences, which are closely juxtaposed in vivo . These interactions involve promoter regions, enhancers and other regulatory and structural elements of chromosomes and can reveal key details of the regulation of gene expression. 3C-seq is a variant of the method for the detection of interactions between one chosen genomic element (viewpoint) and the rest of the genome. We present r3Cseq , an R/Bioconductor package designed to perform 3C-seq data analysis in a number of different experimental designs. The package reads a common aligned read input format, provides data normalization, allows the visualization of candidate interaction regions and detects statistically significant chromatin interactions, thus greatly facilitating hypothesis generation and the interpretation of experimental results. We further demonstrate its use on a series of real-world applications.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 45
    facet.materialart.
    Unknown
    Consumer preferences for local production and other value-added label claims for a processed food product (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-29
    Description: Using stated preference data from Kentucky and Ohio, USA, we estimate consumer willingness-to-pay for varieties of a processed food product (blackberry jam) that are differentiated with respect to their local production labelling and a series of other value-added claims. Results show that consumers were willing to pay more for the product indicating locally produced, produced in their state or in a well-identified multi-state region. Consumers were willing to purchase organic products, although there might be some confusion as to the meaning of the organic logo. Our results also supported the notion that consumers are willing to support small family farms.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 46
    facet.materialart.
    Unknown
    Dairy supply chain modernisation in Poland: what about those not keeping pace? (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-29
    Description: This paper studies the determinants and consequences of heterogeneous market participation among Polish dairy farmers using a unique data set on supply chain characteristics and individuals with different market relationships. It investigates factors that cause households not to participate in the market and then estimates farm orientation effects on revenues, using semi-parametric methods. The key finding is that farms maintaining commercial dairy business were better off than those who ceased milk sales. However, detailed analysis shows that this difference could be attributed to supply chain modernisation and becomes insignificant once subsistence farmers are compared to commercial farms supplying the traditional marketing channel.
    Keywords: D22 - Firm Behavior: Empirical Analysis, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 47
    facet.materialart.
    Unknown
    The Impact of Credit Constraints on Farm Households: Survey Results from India and China (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-22
    Description: India and China have the largest farm-household populations in the world—populations that are also among the poorest. Among the many factors that affect farm livelihoods, access to credit has been identified as a significant barrier preventing the escape from poverty. While there has been significant research on credit constraints in developing countries, there is surprisingly little information pertaining to the actual impacts of credit constraints on household well-being. The objective of this paper is to investigate the impacts of credit constraints on various factors affecting farm households, such as physical and human capital formation, agricultural inputs applications, consumption smoothing, and wage-seeking behavior using direct elicitation. This paper contributes to the literature and policy debates by comparing the effects of credit constraints in China and India as surveyed in 2008–2009. The analytical results and data demonstrate that binding credit constraints adversely affect a broad range of production and livelihood choices. We empirically show that credit constraints negatively affect food consumption, farm input applications, and health and educational attainments.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, O17 - Formal and Informal Sectors ; Shadow Economy ; Institutional Arrangements, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 48
    facet.materialart.
    Unknown
    Consumer Response to "Contains" and "Free of" Labeling: Evidence from Lab Experiments (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-22
    Description: Using a lab experiment with 351 adult non-student subjects, we investigate the impact of labels and secondary information on willingness to pay (WTP) for foods that use various ingredients and processes that have been the subject of food policy discussions. We find a distinct asymmetry of WTP sensitivity between "Contains X" and "Free of X" labels with negatively-framed secondary information. The "Free of X" label has an impact only when secondary information is provided, and the negative impact of "Contains X" is mitigated by secondary information. We also consider how the results of our study can inform the ongoing debate about mandatory food labeling regulations in the United States: if mandatory labeling is adopted, providing additional information about what the product contains would significantly lessen the negative impact on demand.
    Keywords: M31 - Marketing, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 49
    facet.materialart.
    Unknown
    Road Block to Risk Management -- Investigating Class I Milk Cross-Hedging Opportunities (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-22
    Description: This study examines the risk management opportunities for fluid milk market participants in the United States through the use of milk futures contracts. We estimate the nature of basis risk from 2002–2011 using modern time-series and econometric techniques. The results of this investigation reveal that at sufficient hedging intervals, using class III manufacturing milk futures contracts to cross-hedge fluid milk has the ability to reduce risk and provide revenue stability to market participants. When used in conjunction with milk futures, prediction algorithms for the closing basis facilitate more direct management of fluid milk price risk.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, 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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 50
    facet.materialart.
    Unknown
    Tails Curtailed: Accounting for Nonlinear Dependence in Pricing Margin Insurance for Dairy Farmers (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: Livestock Gross Margin Insurance for Dairy Cattle (LGM-Dairy) is a risk management tool for protecting milk income over feed cost margins. In this article, we examine the assumptions underpinning the method used to determine LGM-Dairy premiums. Analysis of the milk–feed dependence structure is conducted using copula methods, a rich set of tools that allow modelers to capture nonlinearities in dependence among variables of interest. We find a significant relationship between milk and feed prices that increases with time-to-maturity and severity of negative price shocks. Extremal, or tail, dependence is the propensity of dependence to concentrate in the tails of a distribution. A common theme in financial and actuarial applications and in agricultural crop revenue insurance is that tail dependence increases the risk to the underwriter and results in higher insurance premiums. We present, to our knowledge, the first case in which tail dependence may actually reduce actuarially fair premiums for an agricultural risk insurance product. We examine hedging effectiveness with LGM-Dairy and show that, even in the absence of basis or production risk, hedging horizon plays an important role in the ability of this tool to smooth farm income over feed cost margins over time. Rating methodology that accounts for tail dependence between milk and feed prices extends the optimal hedging horizon and increases hedging effectiveness of the LGM-Dairy program.
    Keywords: G13 - Contingent Pricing ; Futures Pricing, 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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 51
    facet.materialart.
    Unknown
    Impact of Third-party Contract Enforcement in Agricultural Markets--A Field Experiment in Vietnam (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: We study the effect of alleviating the information asymmetry regarding product quality that is widespread in contracts between agricultural producers and buyers in developing countries. Opportunistic buyers may underreport quality levels to farmers to reduce the price that they have to pay. In response, farmers may curb investment, thereby negatively affecting farm productivity. In an experiment, we entitle randomly selected smallholder dairy farmers in Vietnam, who are contracted by a large company, to independently verify milk testing results. Results indicate that treatment farmers use 12% more inputs, and they also increase their output significantly. Some wider research and policy implications are discussed.
    Keywords: C93 - Field Experiments, D82 - Asymmetric and Private Information, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 52
    facet.materialart.
    Unknown
    Strength of Protection for Geographical Indications: Promotion Incentives and Welfare Effects (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: We address the question of how the strength of protection for geographical indications (GIs) affects the GI industry's promotion incentives, equilibrium market outcomes, and the distribution of welfare. Geographical indication producers engage in informative advertising by associating their true quality premium (relative to a substitute product) with a specific label emphasizing the GI's geographic origin. The extent to which the names/words of the GI label can be used and/or imitated by competing products—which depends on the strength of GI protection—determines how informative the GI promotion messages can be. Consumers’ heterogeneous preferences (vis-à-vis the GI quality premium) are modeled in a vertically differentiated framework. Both the GI industry and the substitute product industry are assumed to be competitive (with free entry). The model is calibrated and solved for alternative parameter values. Results show that producers of the GI and of the lower-quality substitute good have divergent interests: GI producers are better off with full protection, whereas the substitute good's producers prefer intermediate levels of protection (but they never prefer zero protection because they benefit indirectly if the GI producers’ incentives to promote are preserved). For consumers and aggregate welfare, the preferred level of protection depends on the model's parameters, with an intermediate level of protection being optimal in many circumstances.
    Keywords: D23 - Organizational Behavior ; Transaction Costs ; Property Rights, L15 - Information and Product Quality ; Standardization and Compatibility, M37 - Advertising, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 53
    facet.materialart.
    Unknown
    Pass-Through and Consumer Search: An Empirical Analysis (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: Retail-price pass-through is one of the most important issues facing manufacturers of consumer packaged goods. Although retailers tend to pass higher wholesale prices through to consumers quickly and completely, they often do not pass on trade promotions. Currently, asymmetric pass-through is commonly thought to result from retailers’ exercise of market power. Alternatively, it may be because of consumer search behavior and retailers’ competitive response. We test this theory using a panel threshold asymmetric error-correction model applied to wholesale and retail scanner data for ready-to-eat cereal for a number of retailers in the Los Angeles metropolitan market. We find that consumer search behavior contributes significantly to imperfect pass-through. By allowing pass-through to depend on market power and consumer search costs, we find results that are contrary to the conventional wisdom. Namely, market power causes retail prices to fall quickly and rise slowly, whereas consumer search behavior causes retail prices to rise quickly and fall slowly—precisely the "rockets and feathers" phenomenon.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, L13 - Oligopoly and Other Imperfect Markets, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 54
    facet.materialart.
    Unknown
    Measuring Benefits from a Marketing Cooperative in the Copper River Fishery (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: The degradation of product quality is one form of rent dissipation resulting from incomplete property rights in fisheries. Industry structure and information asymmetries can also lead to underinvestment in product quality, even when property rights are well defined. In this article we empirically examine whether the voluntary formation of a marketing cooperative was able to mitigate market failures that led to the production of inferior-quality fish. Specifically, we use a difference-in-differences estimation strategy to measure the impact that the Copper River Fishermen's Cooperative, an Alaskan salmon marketing cooperative, had on ex-vessel salmon prices and salmon quality measures. We find that the cooperative was able to improve product quality, as well as attract and sustain a higher price for its salmon. Our findings provide empirical support for many of the key tenets of cooperative theory. Specifically, we find evidence that marketing cooperatives can address existing market failures, that marketing cooperatives can have advantages in high-quality product markets, and that over time, as a result of their success, marketing cooperatives may lead to lasting producer benefits even though they become obsolete due to nonmember free-riding.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q22 - Fishery ; Aquaculture
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 55
    facet.materialart.
    Unknown
    Does Organic Command a Premium When the Food is Already Local? (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: The emergence of community supported agriculture (CSA) farms has been recognized as a new way for small farms to remain competitive while engaging in their local community through direct marketing. In this study, we report on first revealed preference valuation of CSA attributes using data on share prices and CSA characteristics for the summer 2012 growing season. Using data covering 453 CSA farms in Michigan, New York, Ohio, and Pennsylvania, we develop a hedonic model based on firm-level prices to reveal consumer valuations of CSA attributes, including various types of organic certification. We also test for competition in the CSA market using a model of firm entry to evaluate whether firms appear perfectly competitive, which is a requirement when using firm-level prices in our hedonic analysis. Our results reveal a price premium of approximately 7% for USDA organic certification, although this value is heterogeneous across states. We find no premium associated with competing certified naturally grown programs. Finally, we find that CSA farms exhibit little market power and appear to act competitively even with few market entrants.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q51 - Valuation of Environmental Effects
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 56
    facet.materialart.
    Unknown
    Automated 3D structure composition for large RNAs (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-08
    Description: Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 57
    facet.materialart.
    Unknown
    Will geographical indications supply excessive quality? (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-03
    Description: This study investigates the choice of quality by producer organisations (POs) in charge of defining product specifications for geographical indications. The model assumes that the PO chooses the quality level that maximises joint producer profits in anticipation of the competitive equilibrium that arises once quality is set. Using a fairly general variant of the vertical differentiation model and a flexible specification of production costs, we show that the PO has an incentive to supply quality in excess of the socially optimal level.
    Keywords: L15 - Information and Product Quality ; Standardization and Compatibility, L44 - Antitrust Policy and Public Enterprises, Nonprofit Institutions, and Professional Organization, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 58
    facet.materialart.
    Unknown
    Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-27
    Description: Programmed –1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slippery sequence, where the ribosome changes frame, and a stimulatory RNA structure, a stem–loop or RNA pseudoknot. Antisense oligonucleotides annealed appropriately 3' of a slippery sequence have also shown activity in frameshifting, at least in vitro . Here we examined frameshifting at the U 6 A slippery sequence of the HIV gag/pol signal and found high levels of both –1 and –2 frameshifting with stem–loop, pseudoknot or antisense oligonucleotide stimulators. By examining –1 and –2 frameshifting outcomes on mRNAs with varying slippery sequence-stimulatory RNA spacing distances, we found that –2 frameshifting was optimal at a spacer length 1–2 nucleotides shorter than that optimal for –1 frameshifting with all stimulatory RNAs tested. We propose that the shorter spacer increases the tension on the mRNA such that when the tRNA detaches, it more readily enters the –2 frame on the U 6 A heptamer. We propose that mRNA tension is central to frameshifting, whether promoted by stem–loop, pseudoknot or antisense oligonucleotide stimulator.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 59
    facet.materialart.
    Unknown
    Co-clustering phenome-genome for phenotype classification and disease gene discovery (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-24
    Description: Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped 〉2000 phenotype–gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this article, a regularized non-negative matrix tri-factorization (R-NMTF) algorithm is introduced to co-cluster phenotypes and genes, and simultaneously detect associations between the detected phenotype clusters and gene clusters. The R-NMTF algorithm factorizes the phenotype–gene association matrix under the prior knowledge from phenotype similarity network and protein–protein interaction network, supervised by the label information from known disease classes and biological pathways. In the experiments on disease phenotype–gene associations in OMIM and KEGG disease pathways, R-NMTF significantly improved the classification of disease phenotypes and disease pathway genes compared with support vector machines and Label Propagation in cross-validation on the annotated phenotypes and genes. The newly predicted phenotypes in each disease class are highly consistent with human phenotype ontology annotations. The roles of the new member genes in the disease pathways are examined and validated in the protein–protein interaction subnetworks. Extensive literature review also confirmed many new members of the disease classes and pathways as well as the predicted associations between disease phenotype classes and pathways.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 60
    facet.materialart.
    Unknown
    A global sampling approach to designing and reengineering RNA secondary structures (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-04
    Description: The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign , a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 61
    facet.materialart.
    Unknown
    Functional impact bias reveals cancer drivers (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-25
    Description: Identifying cancer driver genes and pathways among all somatic mutations detected in a cohort of tumors is a key challenge in cancer genomics. Traditionally, this is done by prioritizing genes according to the recurrence of alterations that they bear. However, this approach has some known limitations, such as the difficulty to correctly estimate the background mutation rate, and the fact that it cannot identify lowly recurrently mutated driver genes. Here we present a novel approach, Oncodrive-fm, to detect candidate cancer drivers which does not rely on recurrence. First, we hypothesized that any bias toward the accumulation of variants with high functional impact observed in a gene or group of genes may be an indication of positive selection and can thus be used to detect candidate driver genes or gene modules. Next, we developed a method to measure this bias (FM bias) and applied it to three datasets of tumor somatic variants. As a proof of concept of our hypothesis we show that most of the highly recurrent and well-known cancer genes exhibit a clear FM bias. Moreover, this novel approach avoids some known limitations of recurrence-based approaches, and can successfully identify lowly recurrent candidate cancer drivers.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 62
    facet.materialart.
    Unknown
    Who are consuming food away from home and where? Results from the Consumer Expenditure Surveys (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Description: This paper investigates household expenditures on food away from home by type of facility. A system of expenditures at full-service restaurants, fast-food restaurants and other facilities are estimated with a multivariate sample selection procedure, for three types of households by household composition. Statistical significance of error correlations suggests endogeneity of sample selectivity and justifies estimation of the equations in a system to improve statistical efficiency. Differentiated effects of economic and demographic factors are found on expenditures at different facilities and across household types. Findings on the roles of economic and socio-demographic factors can inform marketing strategies and policy deliberations.
    Keywords: C31 - Cross-Sectional Models ; Spatial Models ; Treatment Effect Models, D12 - Consumer Economics: Empirical Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 63
    facet.materialart.
    Unknown
    Quality labels and firm survival: some first empirical evidence (2013)
    Oxford University Press
    Details
    Publication Date: 2013-05-31
    Description: European Union regulation on quality food products (protected designations of origin (PDO) labelling) is expected to sustain competitiveness within the agricultural sector. This paper examines the impact of this policy on the survival of cheese firms over the period 1990–2006 in France. We show that such a policy (Appellation d'Origine Controlée) reduces exiting risk for smaller firms. However, smaller firms still have a lower survival rate compared with larger ones that cannot be compensated by the quality label effect.
    Keywords: L10 - 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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 64
    facet.materialart.
    Unknown
    Testing hypothetical bias with a real choice experiment using respondents' own money (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-24
    Description: The investigation of hypothetical bias in choice experiments (CEs) has typically been conducted in the laboratory with only minimal field experiments. Moreover, it is common practice to provide an initial endowment (money or coupons) to respondents. In this research, we employed a between-subject CE in a supermarket with three different treatments (i.e. hypothetical, hypothetical with cheap talk script and real). With the ‘real’ treatment, we required respondents to use their own money when making a payment. The proposed incentive-compatible mechanism mimics as close as possible the everyday purchasing situation. Results confirm the presence of hypothetical bias and the mixed effectiveness of a cheap talk script.
    Keywords: D12 - Consumer Economics: Empirical Analysis, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 65
    facet.materialart.
    Unknown
    Demand for food-away-from-home: a multiple-discrete-continuous extreme value model (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-24
    Description: Policymakers have suggested the use of taxes to raise the relative cost of buying fast food. Yet, little is known of the structure of demand for food-away-from-home (FAFH) in general. This study provides estimates of the price-elasticity of demand for four different types of FAFH using a new data set from NPD, Inc. and an econometric approach that accounts for the multiple-discrete–continuous nature of FAFH demand. We find that cross-price elasticities of demand are small, so consumers are unwilling to substitute between food-at-home and any type of FAFH or among types of FAFH. Therefore, taxing fast food may be effective in reducing the number of fast food visits and shifting consumption to at-home meals.
    Keywords: C35 - Discrete Regression and Qualitative Choice Models, D12 - Consumer Economics: Empirical Analysis, I18 - Government Policy ; Regulation ; Public Health, 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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 66
    facet.materialart.
    Unknown
    Willingness to pay for pesticide reduction in the EU: nothing but organic? (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-24
    Description: Using experimental auctions carried out on apples in different European countries, this paper contributes to the assessment of consumer willingness to pay for the reduction of pesticides. We study several systems of good agricultural practices, possibly signalled to consumers, ranging from Integrated Pest Management certifications to organic production methods. The results show a relatively homogeneous behaviour of European consumers and reveal that improving the information on pesticide reduction may have unintended consequences. Results also suggest that taste characteristics and reference to a Protected Denomination of Origin should not be overlooked.
    Keywords: C91 - Laboratory, Individual Behavior, D12 - Consumer Economics: Empirical Analysis, Q01 - Sustainable Development, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 67
    facet.materialart.
    Unknown
    Capitalisation of Single Farm Payment on farm price: an analysis of Swedish farm prices using farm-level data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-07
    Description: This paper estimates capitalisation effects of farm attributes with a particular focus on the decoupled Single Farm Payment (SFP) on prices. The spatial analysis employs a sample of mainly small- and medium-sized Swedish farm transactions sold all across Sweden; the results from a spatial multiple-membership model suggest that decoupled SFP has no influence on farm prices. Prices are profoundly influenced by residential characteristics and accessibility to urban amenities. Spatial heterogeneity is found for both regional and local levels, and a large spatial spillover effect is found between neighbouring farms. Results are confirmed by sensitivity analyses.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, R38 - Government Policies ; Regulatory Policies
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...