bluuebunny/crossref_metadata_2025_split huggingface dataset:
Varietal Intensities and Similarities of the World's Wine Regions
Authors: Anderson Kym 
Published: June 2012

AbstractThis paper examines empirically two distinguishing aspects of the world's wine regions: their degree of specialization in certain varieties, as measured by a varietal intensity index; and their similarity with the varietal mix of other regions, as measured by a varietal-based regional similarity index. Twelve of the most important wine-producing countries, that together account for all but one-eighth of the world's winegrapes, are included in the analysis. The data refer to circa 2000 (or 1999 for EU member countries, since that is their most recent census data). These indexes provide a baseline against which to compare more recent and future vintages. They will be especially useful as producers and regulators respond at varying speeds to the impacts of climate changes, in addition to market developments, on the optimal location of production of different varieties around the world. (JEL Classifications: D24, L66, Q13, Q15)
The Market Share of Wine in Denmark
Authors: Milhøj Anders 
Published: June 2012

AbstractThis paper analyzes the position of wine in the Danish alcohol market from 1978 to 2008. During this time period the market share of wine has doubled, assumingly due to a tax-induced change in relative prices as well as behavioral changes. This paper models the yearly observed market share of wine by unobserved component models which allow for adaptive trends including regressions with time varying coefficients. I find that the market share of wine has a steady upward trend even if it was temporarily broken by a tax reduction for liquor in 2001. (JEL Classification: C22, D11, L66)
The Agricultural and Food Trade in the First Globalization: Spanish Table Wine Exports 1871 to 1935 – A Case Study
Authors: Pinilla Vicente , Serrano Raúl 
Published: June 2012

AbstractThe objective of the present study is to analyze the overall trajectory of Spanish table wine exports during the period 1871–1935 and provide convincing explanations of the pattern. Thus, we employ an approach that takes all of the possible explanatory factors into account, instead of adopting a narrower approach which focuses on a single principal factor. The methodology employed consists of using a gravity model to explain trade flows in Spanish table wine. Our results highlight the key role of trade policies in the determination of export possibilities and the difficulties derived from the export of products which are characterized by the low or non-existent change in demand when income changes. These results may shed a little more light on the determinants of trade in the first phase of globalization. (JEL Classification: F14, N73, N74, Q17)
From Bayes to the Just Noticeable Difference to Effect Sizes: A Note to Understanding the Clinical and Statistical Significance of Oenologic Research Findings
Authors: Cicchetti Domenic V. 
Published: June 2012

AbstractThe objectives of this paper are (1) to broaden the concept and importance of differentiating statistical significance from clinical or practical significance that was introduced in a recent oenologie application that appeared in this Journal (Cicchetti, 2007); (2) to highlight the major contribution of Economics to the clinical-statistical significance differentiation; (3) to provide oenologie researchers with the tools to accomplish this objective; and (4) to provide examples of oenologie applications using these biostatistical tools. Results indicate that the terms clinical significance, effect sizes, the just noticeable difference between stimuli, and the economic term marginal utility are conceptually related and when applied to the results of oenologie research, offer a richness of interpretation that levels of statistical significance alone cannot provide. (JEL Classification: C0, C1)
Natural Endowments, Production Technologies and the Quality of Wines in Bordeaux. Does Terroir Matter?
Authors: Gergaud Olivier , Ginsburgh Victor 
Published: June 2012

AbstractWe study whether quality assessments made by wine experts and by consumers (based on prices obtained at auction between 1980 and 1992), can be explained by variables describing endowments (land characteristics, exposures of vineyards) and technologies (from grape varieties and picking, to bottled wines). However, since technological choices are likely to depend on endowments, the effects can only be identified using an instrumental variables approach. We show that technological choices affect quality much more than natural endowments, the effect of which is negligible. (JEL Classification: L66, Q12, Q13, Q16)
Prohibition and Repeal: A Short History of the Wine Industry's Regulation in the United States
Authors: Beliveau Barbara C. , Rouse M. Elizabeth 
Published: June 2012

AbstractThe United States wine industry has experienced tremendous growth in the past twenty-five years. The number of wineries in the United States has grown to almost 5000, located in all fifty states, and creating over a million full time jobs. Alcohol distribution laws that hinge on the Supreme Court's reconciliation of the Twenty-first Amendment and the Commerce Clause have significantly hindered the industry's ability to expand. Current interpretations of the 21stAmendment give states unprecedented freedom to regulate interstate commerce in alcoholic beverages. The resulting regulatory diversity presents problems both domestically and internationally. (JEL Classification: K2, L5, N4)
The Economic Impact of the Wine Industry on Hotels and Restaurants: Evidence from Washington State
Authors: Storchmann Karl 
Published: June 2012

AbstractWashington State enjoys an extraordinarily fast growing wine industry and is now the second largest wine producing state in the U.S. This paper examines the impact of this growth on the revenue of hotels and restaurants. Employing a dynamic quarterly panel model at the county level we show that the regional reputation as high quality wine county, as expressed by critical wine points in the national wine press, has a significant effect on the tourism industry. For Walla Walla, the most prominent wine county in the state, less than 17% of all restaurant and approximately 40% of all hotel revenue is tied to the wine cluster (2007). However, regional reputation is not long-living and needs constant replenishment. (JEL Classification: R11, R15, Q19)
Beer in Good Times and Bad: A U.S. State-Level Analysis of Economic Conditions and Alcohol Consumption
Authors: Freeman Donald G. 
Published: June 2012

AbstractData on U.S. state-level beer shipments from 1970 to 2007 provided by The Beer Institute are used to estimate pooled time-series models of annual consumption regressed on economic and demographic variables, using the common correlated effects (CCE) estimators to control for unobserved common effects and to allow for heterogeneous responses across units. Beer is found to be a procyclical good, varying negatively with the state unemployment rate. Previous findings for the negative effect of excise taxes on consumption are supported, though the estimated elasticities are smaller than those reported in earlier research. Demographics have a significant and material effect on consumption, with larger shares of young adults in the population implying greater consumption of beer per capita. (JEL Classification: D12, C23)
Fluid upwelling beneath arc volcanoes above the subducting Philippine Sea Plate: Evidence from regional electrical resistivity structure
Authors: Hata Maki , Oshiman Naoto , Yoshimura Ryokei , Tanaka Yoshikazu , Uyeshima Makoto 
Published: June 2012

At subduction zones, aqueous fluids released from the subducting slab play an important role in island arc volcanism, triggering partial melting and accretion magmatism. We used the Network‐magnetotelluric (MT) method to obtain the deep (>100 km), large‐scale electrical resistivity structure beneath Kyushu, Japan, with the aim of identifying regions of deep fluids and magma that feeds subduction zone volcanoes in the region. Network‐MT observations, in which dipoles of about 10–30 km in length were used to measure the electric potential difference, were performed over all of Kyushu, in the Southwest Japan Arc, where the Philippine Sea Plate (PSP) is subducting beneath the Eurasian Plate at a high angle. Using the Network‐MT data, we obtained the large‐scale electrical resistivity structure along four profiles across each of four Quaternary active volcanoes at the volcanic front of the Kyushu subduction zone. The resistivity models have two features in common: a conductor beneath each volcano, whose base extends to the backarc side, and a resistor along the hinge line of the subducting PSP in the forearc. The conductor indicates regions of fluid released from the slab or partial melting of the mantle, representing a magma source for subduction zone volcanoes in this region.
Transport of thermal‐energy ionospheric oxygen (O+) ions between the ionosphere and the plasma sheet and ring current at quiet times preceding magnetic storms
Authors: Yau Andrew W. , Howarth Andrew , Peterson W. K. , Abe Takumi 
Published: June 2012

The presence of energetic O+ ions in the ring current at the onset of a magnetic storm prompts the question of the possible role of “in‐transit” ionospheric O+ ions between the ionosphere and the plasma sheet and ring current in the quiet periods immediately preceding the main phase of a magnetic storm. Thermal‐energy O+ ions are often observed in the quiet time high‐altitude (>7000 km) polar ionosphere on Akebono, at temperatures of ∼0.2–0.3 eV and flow velocities of a few km/s. In this paper, we use single‐particle trajectory simulation to study the transport of these ions in the periods preceding a number of large magnetic storms (Dst < −100 nT). Our simulation shows that due to centrifugal ion acceleration at higher altitudes (above ∼3 RE altitude), about 10–20% of polar wind and other low‐energy O+ ions reaches the plasma sheet during such periods; the actual percentage is a factor of ∼3 larger in the dusk sector on average compared with the dawn sector and dependent on the IMF and the O+ ion temperature. This provides a low but non‐negligible flux of O+ ions between the ionosphere and the plasma sheet and ring current, which is believed to constitute a significant “in‐transit” oxygen ion population over a period of a few (∼4) hours preceding a magnetic storm. Such a population could explain the presence of energetic O+ ions at the onset of the main phase of the storm, when the heavy ions could potentially modify the evolution of the ring current.
Weighted pooling—practical and cost-effective techniques for pooled high-throughput sequencing
Authors: Golan David , Erlich Yaniv , Rosset Saharon 
Published: June 2012

Abstract
Motivation: Despite the rapid decline in sequencing costs, sequencing large cohorts of individuals is still prohibitively expensive. Recently, several sophisticated pooling designs were suggested that can identify carriers of rare alleles in large cohorts with a significantly smaller number of pools, thus dramatically reducing the cost of such large-scale sequencing projects. These approaches use combinatorial pooling designs where each individual is either present or absent from a pool. One can then infer the number of carriers in a pool, and by combining information across pools, reconstruct the identity of the carriers.
Results: We show that one can gain further efficiency and cost reduction by using ‘weighted’ designs, in which different individuals donate different amounts of DNA to the pools. Intuitively, in this situation, the number of mutant reads in a pool does not only indicate the number of carriers, but also their identity.
We describe and study a powerful example of such weighted designs, using non-overlapping pools. We demonstrate that this approach is not only easier to implement and analyze but is also competitive in terms of accuracy with combinatorial designs when identifying rare variants, and is superior when sequencing common variants.
We then discuss how weighting can be incorporated into existing combinatorial designs to increase their accuracy and demonstrate the resulting improvement using simulations. Finally, we argue that weighted designs have enough power to facilitate detection of common alleles, so they can be used as a cornerstone of whole-exome sequencing projects.
Contact: saharon@post.tau.ac.il
Identification of sequence–structure RNA binding motifs for SELEX-derived aptamers
Authors: Hoinka Jan , Zotenko Elena , Friedman Adam , Sauna Zuben E. , Przytycka Teresa M. 
Published: June 2012

AbstractMotivation: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computational approaches. At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process.Results: To close this gap we developed, Aptamotif, a computational method for the identification of sequence–structure motifs in SELEX-derived aptamers. To increase the chances of identifying functional motifs, Aptamotif uses an ensemble-based approach. We validated the method using two published aptamer datasets containing experimentally determined motifs of increasing complexity. We were able to recreate the author's findings to a high degree, thus proving the capability of our approach to identify binding motifs in SELEX data. Additionally, using our new experimental dataset, we illustrate the application of Aptamotif to elucidate several properties of the selection process.Contact: przytyck@ncbi.nlm.nih.gov, Zuben.Sauna@fda.hhs.gov
A conditional neural fields model for protein threading
Authors: Ma Jianzhu , Peng Jian , Wang Sheng , Xu Jinbo 
Published: June 2012

Abstract
Motivation: Alignment errors are still the main bottleneck for current template-based protein modeling (TM) methods, including protein threading and homology modeling, especially when the sequence identity between two proteins under consideration is low (&lt;30%).
Results: We present a novel protein threading method, CNFpred, which achieves much more accurate sequence–template alignment by employing a probabilistic graphical model called a Conditional Neural Field (CNF), which aligns one protein sequence to its remote template using a non-linear scoring function. This scoring function accounts for correlation among a variety of protein sequence and structure features, makes use of information in the neighborhood of two residues to be aligned, and is thus much more sensitive than the widely used linear or profile-based scoring function. To train this CNF threading model, we employ a novel quality-sensitive method, instead of the standard maximum-likelihood method, to maximize directly the expected quality of the training set. Experimental results show that CNFpred generates significantly better alignments than the best profile-based and threading methods on several public (but small) benchmarks as well as our own large dataset. CNFpred outperforms others regardless of the lengths or classes of proteins, and works particularly well for proteins with sparse sequence profiles due to the effective utilization of structure information. Our methodology can also be adapted to protein sequence alignment.
Contact: j3xu@ttic.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SEQuel: improving the accuracy of genome assemblies
Authors: Ronen Roy , Boucher Christina , Chitsaz Hamidreza , Pevzner Pavel 
Published: June 2012

Abstract
Motivation: Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.
Results: SEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell Escherichia coli data by almost half, and corrected between 30% and 94% of the substitution errors. Further, we show SEQuel is imperative to improving single-cell assembly, which is inherently more challenging due to higher error rates and non-uniform coverage; over half of the small indels, and substitution errors in the single-cell assemblies were corrected. We apply SEQuel to the recently assembled Deltaproteobacterium SAR324 genome, which is the first bacterial genome with a comprehensive single-cell genome assembly, and make over 800 changes (insertions, deletions and substitutions) to refine this assembly.
Availability: SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at http://bix.ucsd.edu/SEQuel/.
Contact: ppevzner@cs.ucsd.edu
Minimum message length inference of secondary structure from protein coordinate data
Authors: Konagurthu Arun S. , Lesk Arthur M. , Allison Lloyd 
Published: June 2012

Abstract
Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data.
Results: We report a new method to infer secondary structure based on the Bayesian method of minimum message length inference. It treats assignments of secondary structure as hypotheses that explain the given coordinate data. The method seeks to maximize the joint probability of a hypothesis and the data. There is a natural null hypothesis and any assignment that cannot better it is unacceptable. We developed a program SST based on this approach and compared it with popular programs, such as DSSP and STRIDE among others. Our evaluation suggests that SST gives reliable assignments even on low-resolution structures.
Availability: http://www.csse.monash.edu.au/~karun/sst
Contact: arun.konagurthu@monash.edu (or lloyd.allison@monash.edu)
Protein subcellular location pattern classification in cellular images using latent discriminative models
Authors: Li Jieyue , Xiong Liang , Schneider Jeff , Murphy Robert F. 
Published: June 2012

Abstract
Motivation: Knowledge of the subcellular location of a protein is crucial for understanding its functions. The subcellular pattern of a protein is typically represented as the set of cellular components in which it is located, and an important task is to determine this set from microscope images. In this article, we address this classification problem using confocal immunofluorescence images from the Human Protein Atlas (HPA) project. The HPA contains images of cells stained for many proteins; each is also stained for three reference components, but there are many other components that are invisible. Given one such cell, the task is to classify the pattern type of the stained protein. We first randomly select local image regions within the cells, and then extract various carefully designed features from these regions. This region-based approach enables us to explicitly study the relationship between proteins and different cell components, as well as the interactions between these components. To achieve these two goals, we propose two discriminative models that extend logistic regression with structured latent variables. The first model allows the same protein pattern class to be expressed differently according to the underlying components in different regions. The second model further captures the spatial dependencies between the components within the same cell so that we can better infer these components. To learn these models, we propose a fast approximate algorithm for inference, and then use gradient-based methods to maximize the data likelihood.
Results: In the experiments, we show that the proposed models help improve the classification accuracies on synthetic data and real cellular images. The best overall accuracy we report in this article for classifying 942 proteins into 13 classes of patterns is about 84.6%, which to our knowledge is the best so far. In addition, the dependencies learned are consistent with prior knowledge of cell organization.
Availability: http://murphylab.web.cmu.edu/software/.
Contact: Jeff.Schneider@cs.cmu.edu, murphy@cmu.edu
Incorporating prior information into association studies
Authors: Darnell Gregory , Duong Dat , Han Buhm , Eskin Eleazar 
Published: June 2012

Abstract
Summary: Recent technological developments in measuring genetic variation have ushered in an era of genome-wide association studies which have discovered many genes involved in human disease. Current methods to perform association studies collect genetic information and compare the frequency of variants in individuals with and without the disease. Standard approaches do not take into account any information on whether or not a given variant is likely to have an effect on the disease. We propose a novel method for computing an association statistic which takes into account prior information. Our method improves both power and resolution by 8% and 27%, respectively, over traditional methods for performing association studies when applied to simulations using the HapMap data. Advantages of our method are that it is as simple to apply to association studies as standard methods, the results of the method are interpretable as the method reports p-values, and the method is optimal in its use of prior information in regards to statistical power.
Availability: The method presented herein is available at http://masa.cs.ucla.edu
Contact: eeskin@cs.ucla.edu