bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alcohol Consumption and Liver Cirrhosis Mortality: New Evidence from a Panel Data Analysis for Sixteen European Countries
Authors: Bentzen Jan , Smith Valdemar 
Published: June 2012

AbstractEmpirical evidence gives support to a close association between liver cirrhosis mortality and the intake of alcohol. The present analysis draws on a panel data set for sixteen European countries from 1970–2006 where both alcohol consumption and liver cirrhosis seem best described as trend-stationary variables. Consequently, a flexible non-linear functional form with country fixed effects including linear trends is applied in the analysis. It is argued that fewer restrictions on the relationship between liver cirrhosis mortality and alcohol consumption are appropriate for empirical modeling. The conclusion is that the total level of alcohol consumption as well as the specific beverages – beer, wine and spirits – contribute to liver cirrhosis mortality, but the present study also reveals that addressing the question of panel unit roots directly and in this case subsequently applying a trend-stationary modeling methodology reduces the estimates of the impacts from alcohol consumption to liver cirrhosis. Finally, more restrictive alcohol policies seem to have influenced the country-specific development in cirrhosis mortality positively. (JEL Classification: 110)
An Examination of Judge Reliability at a major U.S. Wine Competition
Authors: Hodgson Robert T. 
Published: June 2012

AbstractWine judge performance at a major wine competition has been analyzed from 2005 to 2008 using replicate samples. Each panel of four expert judges received a flight of 30 wines imbedded with triplicate samples poured from the same bottle. Between 65 and 70 judges were tested each year. About 10 percent of the judges were able to replicate their score within a single medal group. Another 10 percent, on occasion, scored the same wine Bronze to Gold. Judges tend to be more consistent in what they don't like than what they do. An analysis of variance covering every panel over the study period indicates only about half of the panels presented awards based solely on wine quality. (JEL Classification: Q13, Q19)
Hedging Adverse Bioclimatic Conditions Employing a Short Condor Position
Authors: Cyr Don , Kusy Martin , Shaw Anthony B. 
Published: June 2012

AbstractWeather derivatives are a relatively new form of financial security, providing firms with the ability to hedge the impact of weather related risks to their activities. Participants in the energy industry have employed standardized temperature contracts trading on organized exchanges since 1999, and the availability and use of non-standardized contracts designed for specialized weather related risks is growing dramatically. The primary goal of this paper is to consider the potential design and use of a weather contract to hedge the risks faced in viticulture as measured by bioclimatic indices. Specifically we examine the Winkler and Huglin bioclimatic indices over a 43 year period for the Niagara region of Ontario, Canada's largest wine producing region, and identify a mixed jump diffusion stochastic process for cumulative growing season index values. We then employ Monte Carlo simulation to derive a range of benchmark prices for a “short condor” contract employing the Huglin index as the underlying variable. The results show that valuable hedging opportunities can be provided by such contracts. (JEL Classification: G13, G32, Q14, Q51, Q54)
Estimating the Demand for Wine Using Instrumental Variable Techniques
Authors: Cuellar Steven S. , Huffman Ryan 
Published: June 2012

AbstractThe demand for wine is generally estimated on an aggregate level as a single commodity. However, as recent history shows us, the demand for wine not only varies considerably by varietal, but also by price point within each varietal. As a result, although estimates of the demand for wine may be beneficial to the wine industry as a whole, they provide little benefit to individual wine producers. Using scan data of purchases from US retail chain stores, this paper uses store keeping unit (sku) level data to overcome the limitations of prior research on the demand for wine by providing estimates for the demand for wine by varietal and price point. We also provide estimates of own price effects, income effects by color, varietal and price segment. Problems of endogeneity inherent in demand estimation are corrected by utilizing a novel instrumental variable technique using grape prices as the instrument. (JEL Classification: C23, D12)
The U.S. Beer Industry: Concentration, Fragmentation, and a Nexus with Wine
Authors: Elzinga Kenneth G. 
Published: June 2012

AbstractThe U.S. Beer industry has undergone two periods of major structural change in the post-World War II period. The first period, 1950–1980, was one of consolidation in which concentration increased dramatically. Since this period, combinations among leading brewers took place that would not have passed antitrust scrutiny earlier. The second period, from 1980 on, is one of fragmentation, marked by the entry of many craft brewers and increased product heterogeneity. The fragmentation has brought about consumption complementarities between wine and beer that never existed before. The wine and beer industry both face distributional inefficiencies sustained by state regulatory provisions that were a consequence of ending prohibition in the United States. Each of these topics is explored in this paper. (JEL Classification: L66, M37)
A potential vorticity perspective on the motion of a mid‐latitude winter storm
Authors: Rivière G. , Arbogast P. , Lapeyre G. , Maynard K. 
Published: June 2012

The motion of mid‐latitude surface cyclones relative to the jet streams is of particular interest because of the commonly observed strong and rapid deepening they undergo when they cross the upper‐level jet axis. The purpose of the present study is to validate a recent theory that may explain this motion which is a generalization of the so‐called beta drift in the mid‐latitude baroclinic context. According to this theory, the key parameter controlling the movement of a surface cyclone across the mean tropospheric jet is the vertically averaged potential vorticity (PV) gradient associated with the jet. To test this theoretical result, numerical sensitivity experiments are performed using the Météo‐France global operational forecast model ARPEGE‐IFS for the particular case of the storm Xynthia (26–28 February 2010). The control forecast, starting from the operational analysis almost 2 days before the storm hit France, represents the trajectory of the storm quite well, together with the deepening during the crossing of the upper‐level jet axis. A PV‐inversion tool is used to modify the vertically averaged PV gradient of the initial state. As expected from the theory, when the PV gradient is intensified, there is a quicker displacement of the surface cyclone toward the jet axis and the jet‐crossing phase occurs earlier than in the control forecast. The opposite occurs for a reduced PV gradient. The interpretation is that an enhanced PV gradient reinforces the dipolar PV anomaly located at upper levels which, in turn, advects the surface cyclone faster towards the jet axis.
Using Fyke-Net Capture Data to Assess Daily Trends in Abundance of Spawning Rio Grande Silvery Minnow
Authors: Gonzales Eric J. , Haggerty Grace M. , Lundahl Anders 
Published: June 2012

Abstract
Assessments of the assumptions underlying catch-per-unit-effort (CPUE) data are necessary to determine whether catch data provide a reliable relative abundance metric. Rio Grande silvery minnow Hybognathus amarus were collected with fyke nets from seasonally flooded habitats of the Rio Grande in New Mexico to determine habitat use by the species during spring runoff in May and June of 2008 and 2009. The CPUE was calculated as fish/h to assess relative abundance among sites and sampling dates due to differences between the durations of the samples in 2008 and 2009. The assumption that the number of fish captured with fyke nets is proportional to effort was assessed by using a multiple-regression model. Catch per unit effort was also compared over the course of a day to determine whether diel differences in catch rate exist. Catch of Rio Grande silvery minnow increased with fyke-net soak time during 2008 and 2009; however, the proportion of the variability explained by the model was greater for 2009 than for 2008. The CPUE did not differ among 24-h collections at high density (mean = 8.24 fish/h) or low density (mean = 0.12 fish/h) sites. These results indicate that fyke-net catches of Rio Grande silvery minnow are proportional to soak time, and calculation of CPUE as fish/h may be used to compare the relative abundance of the species among and between fyke-net samples collected from seasonally flooded habitats.
Received June 20, 2011; accepted February 1, 2012
How networks change with time
Authors: Park Yongjin , Bader Joel S. 
Published: June 2012

Abstract
Motivation: Biological networks change in response to genetic and environmental cues. Changes are reflected in the abundances of biomolecules, the composition of protein complexes and other descriptors of the biological state. Methods to infer the dynamic state of a cell would have great value for understanding how cells change over time to accomplish biological goals.
Results: A new method predicts the dynamic state of protein complexes in a cell, with protein expression inferred from transcription profile time courses and protein complexes inferred by joint analysis of protein co-expression and protein–protein interaction maps. Two algorithmic advances are presented: a new method, DHAC (Dynamical Hierarchical Agglomerative Clustering), for clustering time-evolving networks; and a companion method, MATCH-EM, for matching corresponding clusters across time points. With link prediction as an objective assessment metric, DHAC provides a substantial advance over existing clustering methods. An application to the yeast metabolic cycle demonstrates how waves of gene expression correspond to individual protein complexes. Our results suggest regulatory mechanisms for assembling the mitochondrial ribosome and illustrate dynamic changes in the components of the nuclear pore.
Availability: All source code and data are available under the Boost Software License as supplementary material, at www.baderzone.org, and at sourceforge.net/projects/dhacdist
Contact: joel.bader@jhu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Joint stage recognition and anatomical annotation of drosophila gene expression patterns
Authors: Cai Xiao , Wang Hua , Huang Heng , Ding Chris 
Published: June 2012

Abstract
Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms.
Results: In this article, we propose a novel computational model for jointly stage classification and anatomical terms annotation of Drosophila gene expression patterns. We propose a novel Tri-Relational Graph (TG) model that comprises the data graph, anatomical term graph, developmental stage term graph, and connect them by two additional graphs induced from stage or annotation label assignments. Upon the TG model, we introduce a Preferential Random Walk (PRW) method to jointly recognize developmental stage and annotate anatomical terms by utilizing the interrelations between two tasks. The experimental results on two refined BDGP datasets demonstrate that our joint learning method can achieve superior prediction results on both tasks than the state-of-the-art methods.
Availability: http://ranger.uta.edu/%7eheng/Drosophila/
Contact: heng@uta.edu
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
Authors: Bansal Mukul S. , Alm Eric J. , Kellis Manolis 
Published: June 2012

Abstract
Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.
Results: We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods.
Availability: Our programs can be freely downloaded from http://compbio.mit.edu/ranger-dtl/.
Contact: mukul@csail.mit.edu; manoli@mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs
Authors: Lee Seunghak , Xing Eric P. 
Published: June 2012

AbstractMotivation: As many complex disease and expression phenotypes are the outcome of intricate perturbation of molecular networks underlying gene regulation resulted from interdependent genome variations, association mapping of causal QTLs or expression quantitative trait loci must consider both additive and epistatic effects of multiple candidate genotypes. This problem poses a significant challenge to contemporary genome-wide-association (GWA) mapping technologies because of its computational complexity. Fortunately, a plethora of recent developments in biological network community, especially the availability of genetic interaction networks, make it possible to construct informative priors of complex interactions between genotypes, which can substantially reduce the complexity and increase the statistical power of GWA inference.Results: In this article, we consider the problem of learning a multitask regression model while taking advantage of the prior information on structures on both the inputs (genetic variations) and outputs (expression levels). We propose a novel regularization scheme over multitask regression called jointly structured input–output lasso based on an ℓ1/ℓ2 norm, which allows shared sparsity patterns for related inputs and outputs to be optimally estimated. Such patterns capture multiple related single nucleotide polymorphisms (SNPs) that jointly influence multiple-related expression traits. In addition, we generalize this new multitask regression to structurally regularized polynomial regression to detect epistatic interactions with manageable complexity by exploiting the prior knowledge on candidate SNPs for epistatic effects from biological experiments. We demonstrate our method on simulated and yeast eQTL datasets.Availability: Software is available at http://www.sailing.cs.cmu.edu/.Contact: epxing@cs.cmu.edu
Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning
Authors: Wang Hua , Nie Feiping , Huang Heng , Risacher Shannon L. , Saykin Andrew J. , Shen Li ,   For the Alzheimer's Disease Neuroimaging Initiative
Published: June 2012

AbstractMotivation: Recent advances in brain imaging and high-throughput genotyping techniques enable new approaches to study the influence of genetic and anatomical variations on brain functions and disorders. Traditional association studies typically perform independent and pairwise analysis among neuroimaging measures, cognitive scores and disease status, and ignore the important underlying interacting relationships between these units.Results: To overcome this limitation, in this article, we propose a new sparse multimodal multitask learning method to reveal complex relationships from gene to brain to symptom. Our main contributions are three-fold: (i) introducing combined structured sparsity regularizations into multimodal multitask learning to integrate multidimensional heterogeneous imaging genetics data and identify multimodal biomarkers; (ii) utilizing a joint classification and regression learning model to identify disease-sensitive and cognition-relevant biomarkers; (iii) deriving a new efficient optimization algorithm to solve our non-smooth objective function and providing rigorous theoretical analysis on the global optimum convergency. Using the imaging genetics data from the Alzheimer's Disease Neuroimaging Initiative database, the effectiveness of the proposed method is demonstrated by clearly improved performance on predicting both cognitive scores and disease status. The identified multimodal biomarkers could predict not only disease status but also cognitive function to help elucidate the biological pathway from gene to brain structure and function, and to cognition and disease.Availability: Software is publicly available at: http://ranger.uta.edu/%7eheng/multimodal/Contact: heng@uta.edu; shenli@iupui.edu
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease
Authors: Patel Chirag J. , Chen Rong , Butte Atul J. 
Published: June 2012

AbstractMotivation: Complex diseases, such as Type 2 Diabetes Mellitus (T2D), result from the interplay of both environmental and genetic factors. However, most studies investigate either the genetics or the environment and there are a few that study their possible interaction in context of disease. One key challenge in documenting interactions between genes and environment includes choosing which of each to test jointly. Here, we attempt to address this challenge through a data-driven integration of epidemiological and toxicological studies. Specifically, we derive lists of candidate interacting genetic and environmental factors by integrating findings from genome-wide and environment-wide association studies. Next, we search for evidence of toxicological relationships between these genetic and environmental factors that may have an etiological role in the disease. We illustrate our method by selecting candidate interacting factors for T2D.Contact: abutte@stanford.edu
Xenome—a tool for classifying reads from xenograft samples
Authors: Conway Thomas , Wazny Jeremy , Bromage Andrew , Tymms Martin , Sooraj Dhanya , Williams Elizabeth D. , Beresford-Smith Bryan 
Published: June 2012

Abstract
Motivation: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed.
Results: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.
Availability: Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics
Contact: tom.conway@nicta.com.au
Randomised clinical trial: Lactobacillus reuteri DSM 17938 vs. placebo in children with acute diarrhoea ‐ a double‐blind study
Authors: Francavilla R. , Lionetti E. , Castellaneta S. , Ciruzzi F. , Indrio F. , Masciale A. , Fontana C. , La Rosa M. M. , Cavallo L. , Francavilla A 
Published: June 2012

SummaryBackgroundProbiotics may be of help for the management of acute diarrhoea, however, the effect is strain specific and efficacy needs to be proven.AimTo test the efficacy and safety of
Lactobacillus reuteri
DSM 17938 derived from
L. reuteri
ATCC 55730 in children with acute diarrhoea. Primary outcomes were the rate of unresolved diarrhoea after 3 days of treatment and duration of diarrhoea.MethodsChildren (6–36 months), hospitalised in three paediatric hospitals in Southern Italy for acute diarrhoea with clinical signs of dehydration were randomised to receive in a double‐blind fashion either
L. reuteri (dose of 4 × 108 colony‐forming units/die) or placebo.ResultsOut of 96 eligible children, 74 were enrolled, five patients were withdrawn; 35 in the
L. reuteri group and 34 in the placebo group.
Lactobacillus reuteri significantly reduced the duration of watery diarrhoea as compared with placebo (2.1 ± 1.7 days vs. 3.3 ± 2.1 days; P < 0.03); on day two and three of treatment watery diarrhoea persisted in 82% and 74% of the placebo and 55% and 45% of the
L. reuteri recipients respectively (P < 0.01; P < 0.03). Finally, children receiving
L. reuteri had a significantly lower relapse rate of diarrhoea (15% vs. 42%; P < 0.03). There was not a significant difference in hospital stay between the groups. No adverse events were recorded.ConclusionOur study shows that
L
. reuteri
DSM 17938 as an adjunct to rehydration therapy is efficacious in the treatment of acute diarrhoea reducing the frequency, duration and recrudescence rate of the disease.