bluuebunny/crossref_metadata_2025 huggingface dataset:
Wine Quality, Wine Prices, and the Weather: Is Napa “Different”?
Authors: Ramirez Carlos D.
Published: June 2012

This paper uses a large longitudinal database (nearly 6,000 observations) of all cabernet sauvignon wines rated byWine Spectatorfrom 1970 to 2004 in the Napa Valley region of California to investigate whether a quality-weather relationship and a price-weather relationship exist and, if so, whether they occur in a linear, quadratic, or log-linear fashion. The paper examines three different models of wine rating and wine prices to study the effect of weather variations. The results suggest that the weather affects both quality and wine prices, but the results are much stronger for prices than for ratings. A log-linear model can explain nearly 92 percent of the variation in wine prices, but only about 28 percent of the variation in wine ratings. (JEL Classification: C23, Q54)
The Importance of Australian Corporate Brand and Grape Varietal Wines: Hedonic Pricing in the British Columbia Wine Market
Authors: Carew Richard , Florkowski Wojciech J.
Published: June 2012

A hedonic analysis is applied to a unique data set of Australian wines imported by the British Columbia Liquor Distribution Branch. The data included the important corporate red wine brands produced in Australia. Hedonic price functions are estimated for red Australian wines to show how price premia associated with the attributes of wine brands including the grape variety and alcohol content differ by corporate brands. Results show the positive effects on price of highly reputable brands, positive effect of grape variety Shiraz, and premia for alcohol content. (JEL Classification: D49, L15, L66, QII)
Wine as an Alternative Asset Class
Authors: Masset Philippe , Henderson Caroline
Published: June 2012

Using a dataset that spans the period 1996 to 2007 and contains transaction prices for all reported auctions at the Chicago Wine Company, we analyze how the prices of high-end wines have evolved during this time period. The best wines according to characteristics like vintage, rating and ranking earn higher returns and tend to have a lower variance than poorer wines. Nevertheless, the different categories of wines seem to follow a rather similar trend over the long run. Wine returns are only slightly correlated with other assets and can consequently be used to reduce the risk of an equity portfolio. Wine looks even more attractive when the investor also has concerns about the skewness of his portfolio. However, the part to be invested in wine is reduced once the kurtosis is included into the analysis. Finally, it seems advisable to diversify across different wine categories as their short-run movements are partially independent of each other. First growths and wines rated as extraordinary by Robert Parker deliver the best tradeoff in terms of portfolio expected returns, variance, skewness and kurtosis for most investor preference settings under consideration. (JEL Classification: C60, G11, Q11)
Wine Investment and Portfolio Diversification Gains
Authors: Fogarty James J.
Published: June 2012

The existing literature on the return to wine is mixed. Some studies have found wine to be an unattractive investment option and others have found wine to be an investment class that provides excess risk adjusted returns. However, provided the return to wine does not have a strong positive correlation with standard financial assets, even if the return to wine is low, it is possible that including wine in an investment portfolio will provide a diversification benefit. Here the repeat sales regression methodology is used to estimate the return to Australian wine, and the return is shown to be lower than for standard financial assets. Several measures are then used to show that despite the return to Australian wine being lower than the return to standard financial assets, wine does provide a modest diversification benefit. (JEL Classification: G11, G12)
Improving Experts' Wine Quality Judgments: Two Heads Are Better than One
Authors: Ashton Robert H.
Published: June 2012

This paper reports an analysis of data from the “Judgment of Paris,” the 1976 blind tasting of California and French wines that revolutionized the wine world. Using both empirical and analytical methods, I demonstrate that the wine quality judgments of the renowned experts who participated in the Paris tasting would have been improved simply by averaging the quality ratings of two or more of the judges. Moreover, I explore bothhow manyof the Paris judges should be included in the average andwhich onesthey should be. The results have implications for the practical issue of choosing judges to include in tasting panels that award prizes or provide expert advice to consumers, as well as for better understanding the variability in the price-quality association across hedonic wine pricing studies. (JEL Classification: C93)
Guest Editors' Introduction to Symposium
Authors: Swinnen Johan F.M. , Vandemoortele Thijs , Vanormelingen Stijn
Published: June 2012

This symposium in the Journal of Wine Economics contains a series of articles on various aspects of the economics of beer and brewing. Today, wine and beer are the two most widely consumed alcoholic beverages in the world. Beer consumption is larger than wine consumption both in terms of volume and value. In 2007 global beer consumption reached 174 billion liters compared to 24 billion liters for wine. The global value of beer amounted to 153 billion US dollars, which was roughly double the global value of wine – around 75 billion US dollars (Colen and Swinnen, 2011).
W.S. Gosset and Some Neglected Concepts in Experimental Statistics: Guinnessometrics II
Authors: Ziliak Stephen T.
Published: June 2012

Student's exacting theory of errors, both random and real, marked a significant advance over ambiguous reports of plant life and fermentation asserted by chemists from Priestley and Lavoisier down to Pasteur and Johannsen, working at the Carlsberg Laboratory. One reason seems to be that William Sealy Gosset (1876–1937) aka “Student” – he of Student'st-table and test of statistical significance – rejected artificial rules about sample size, experimental design, and the level of significance, and took instead an economic approach to the logic of decisions made under uncertainty. In his job as Apprentice Brewer, Head Experimental Brewer, and finally Head Brewer of Guinness, Student produced small samples of experimental barley, malt, and hops, seeking guidance for industrial quality control and maximum expected profit at the large scale brewery. In the process Student invented or inspired half of modern statistics. This article draws on original archival evidence, shedding light on several core yet neglected aspects of Student's methods, that is, Guinnessometrics, not discussed by Ronald A. Fisher (1890–1962). The focus is on Student's small sample, economic approach to real error minimization, particularly in field and laboratory experiments he conducted on barley and malt, 1904 to 1937. Balanced designs of experiments, he found, are more efficient than random and have higher power to detect large and real treatment differences in a series of repeated and independent experiments. Student's world-class achievement poses a challenge to every science. Should statistical methods – such as the choice of sample size, experimental design, and level of significance – follow the purpose of the experiment, rather than the other way around? (JEL classification codes: C10, C90, C93, L66)
Reliability of Coulomb stress changes inferred from correlated uncertainties of finite‐fault source models
Authors: Woessner J. , Jónsson S. , Sudhaus H. , Baumann C.
Published: June 2012

Static stress transfer is one physical mechanism to explain triggered seismicity. Coseismic stress‐change calculations strongly depend on the parameterization of the causative finite‐fault source model. These models are uncertain due to uncertainties in input data, model assumptions, and modeling procedures. However, fault model uncertainties have usually been ignored in stress‐triggering studies and have not been propagated to assess the reliability of Coulomb failure stress change (ΔCFS) calculations. We show how these uncertainties can be used to provide confidence intervals for co‐seismic ΔCFS‐values. We demonstrate this for the MW = 5.9 June 2000 Kleifarvatn earthquake in southwest Iceland and systematically map these uncertainties. A set of 2500 candidate source models from the full posterior fault‐parameter distribution was used to compute 2500 ΔCFS maps. We assess the reliability of the ΔCFS‐values from the coefficient of variation (CV) and deem ΔCFS‐values to be reliable where they are at least twice as large as the standard deviation (CV ≤ 0.5). Unreliable ΔCFS‐values are found near the causative fault and between lobes of positive and negative stress change, where a small change in fault strike causes ΔCFS‐values to change sign. The most reliable ΔCFS‐values are found away from the source fault in the middle of positive and negative ΔCFS‐lobes, a likely general pattern. Using the reliability criterion, our results support the static stress‐triggering hypothesis. Nevertheless, our analysis also suggests that results from previous stress‐triggering studies not considering source model uncertainties may have lead to a biased interpretation of the importance of static stress‐triggering.
Role of sea surface temperature and wind convergence in regulating convection over the tropical Indian Ocean
Authors: Meenu S. , Parameswaran K. , Rajeev K.
Published: June 2012

The notions that (a) the frequency of occurrence of clouds is little affected by the sea surface temperature (SST) over the warm tropical oceans when it is maintained above ∼27.5°C and (b) over these regions the cloudiness is mainly governed by the large‐scale atmospheric dynamics, are well‐founded. This study investigates the association among SST, atmospheric wind divergence, vertical wind and cloudiness (convection) over the Arabian Sea, the Bay of Bengal and the tropical Indian Ocean during different seasons. Analysis carried out on data from all the above regions during 1996–2008 shows that the cloudiness and cloud top altitude increase with SST for SST > 26.5°C and become saturated for SST in the range of 28.5–29.75°C. Further increases in SST reduce cloudiness. Similar variations are obtained by analyzing the data during the Asian summer monsoon season (June–September) alone. In contrast, the cloudiness and cloud top altitude increase with SST even for SST > 29.5°C during winter (December–February). The base value of SST for a significant enhancement in cloudiness during winter is found to be ∼1°C larger than that during the summer monsoon season. Seasonal variations in the SST‐dependence of cloudiness over warm oceanic regions are primarily due to changes in the large‐scale atmospheric circulation which plays a pivotal role in regulating cloudiness, especially through surface‐level moisture convergence, mid‐tropospheric vertical winds, upper tropospheric divergence and orographic effects in the upwind direction. Regions of the warmest SST, maximum surface wind convergence and the largest cloudiness are generally not collocated.
Partnering to improve undergraduate teaching: NAGT and AGU join forces
Authors: Treworgy Janis , Wright Elizabeth , Manduca Cathryn
Published: June 2012

To live sustainably on the planet, we must understand its workings, its effect on us, and our effect on it. This requires not only research but also broad education that supports informed personal and political decision making and creates the geoscience workforce of tomorrow. AGU brings together Earth and space scientists not only to support scientific research but also to promote society's use of that science. Currently, AGU's outreach programing is focused on improving members' ability to communicate scientific research results more broadly.
Connolly and Hirschmann receive 2011 N. L. Bowen Awards: Response from Marc M. Hirschmann
Authors: Hirschmann Marc M.
Published: June 2012

James A. Connolly and Marc M. Hirschmann received the 2011 N. L. Bowen Award at the 2011 AGU Fall Meeting, held 5–9 December in San Francisco, Calif. The award recognizes “outstanding contributions to volcanology, geochemistry, or petrology.”
Annual Arctic sea ice less reflective than old ice
Authors: Schultz Colin
Published: June 2012

In the Arctic Ocean the blanket of permanent sea ice is being progressively replaced by a transient winter cover. In recent years the extent of the northern ocean's ice cover has declined. The summer melt season is starting earlier, the winter freeze is happening later, the areal extent of the ice has decreased, and more ice is failing to last through the summer. A key uncertainty in this ongoing climate transformation is how seasonal sea ice affects and responds to climate dynamics as compared to the traditional multiyear sea ice. Tackling an important branch of this issue, Perovich and Polashenski analyze how the albedo of seasonal sea ice changes throughout the summer melt season. The ice's albedo affects how much sunlight enters the system and hence influences biological productivity, ice extent, and future rates of warming.
Tropical SST and Sahel rainfall: A non‐stationary relationship
Authors: Losada T. , Rodriguez‐Fonseca B. , Mohino E. , Bader J. , Janicot S. , Mechoso C. R.
Published: June 2012

Sea surface temperature (SST) anomalies in the tropical Atlantic have been associated with precipitation anomalies in West Africa that form a dipole pattern with centers over the Sahel and the Gulf of Guinea. Whilst this was clear before the 1970's, the dipole pattern almost disappeared after that date, as the anti‐correlation between rainfall anomalies in the Sahel and Guinea dropped abruptly. Simultaneously, the anti‐correlations between Sahel rainfall and tropical Pacific SSTs strengthened. It has been posited that these changes after the 1970's developed as rainfall over West Africa started to co‐vary with SSTs in the global tropics. In this co‐variability, enhanced summer rainfall over West Africa with a monopole pattern corresponds to warmer SSTs in the tropical Atlantic and Maritime Continent, and colder SSTs in the tropical Pacific and western Indian Oceans. The present paper describes the hitherto unexplored seasonal evolution of this co‐variability and the physical mechanisms at work. Sensitivity experiments with two atmospheric general circulation models demonstrate that, after the 1970's, the impacts of SST anomalies in the Indo‐Pacific counteract those in the Atlantic in terms of generating rainfall anomalies over the Sahel, and that this superposition of effects is primarily linear. Therefore, at interannual timescales, the change in the patterns of co‐variability between West African rainfall and tropical SSTs can explain the non‐stationary relationship between the anomalies in these two fields.
Geologic relationships between gray hematite, sulfates, and clays in Capri Chasma
Authors: Weitz Catherine M. , Noe Dobrea Eldar Z. , Lane Melissa D. , Knudson Amy T.
Published: June 2012

We used emissivity spectra from the Thermal Emission Spectrometer (TES) to identify the signature of crystalline gray hematite in Capri Chasma. Geologic units associated with major concentrations of hematite were then mapped using HiRISE, CRISM, and CTX images from the Mars Reconnaissance Orbiter (MRO). Along the northern portion of the Interior Layered Deposit (ILD), a lower polyhydrated sulfate (PHS) unit lies beneath a thicker kieserite unit, above which is a thinner upper PHS. An exposure at the thickest central portion of the ILD reveals additional sulfates, including a middle PHS, a mixture of lower hydration states PHS, and an intercalated unit comprised of kieserite and szomolnokite. We interpret these compositional transitions to reflect either changes in aqueous chemistry (e.g., iron levels and salinity) during groundwater upwelling events or successively buried layers of dust, ice and volcanic aerosols laid down over obliquity cycles. In addition to these sulfates, we identified a few small mounds along the chasma floor composed of either mixtures of ferric hydroxysulfate and Fe/Mg‐smectites, or possible opal, leached clays, and Fe/Mg‐smectites. Gray hematite is strongly spatially correlated to kieserite‐bearing slopes within the ILD and mantled PHS along the northern chasma floor. These results are consistent with sulfate and hematite formation found elsewhere on Mars, including Meridiani Planum, Aram Chaos, and several other chasmata and chaos regions within Valles Marineris.
The Fate of the Generalist: Edward L. Walker (1914−1997) as a Case Study
Authors: Dewsbury Donald A.
Published: June 2012

Psychology has become a field for specialists. I explore the fate of a generalist who did not fit this image, Edward L. Walker. Walker was president of both a regional society and a division of the American Psychological Association, author of 11 books, counselor to many graduate students, and a mainstay in a top psychology department. He received a Career Research Award from the National Institute of Mental Health. He contributed to the study of learning and motivation, aesthetics, the science of psychiatry, social psychology, and more. Yet, on his death, there appeared no obituaries in the psychology national media. One reason may be the very breadth of his interests.
Systematic interaction analysis of human lipocalin-type prostaglandin D synthase with small lipophilic ligands
Authors: Kume Satoshi , Lee Young-Ho , Miyamoto Yuya , Fukada Harumi , Goto Yuji , Inui Takashi
Published: June 2012

L-PGDS [lipocalin-type PG (prostaglandin) D synthase] is a multi-functional protein, acting as a PGD2-producing enzyme and a lipid-transporter. In the present study, we focus on the function of L-PGDS as an extracellular transporter for small lipophilic molecules. We characterize the binding mechanism of human L-PGDS for the molecules, especially binding affinity stoichiometry and driving force, using tryptophan fluorescence quenching, ICD (induced circular dichroism) and ITC (isothermal titration calorimetry). The tryptophan fluorescence quenching measurements revealed that haem metabolites such as haemin, biliverdin and bilirubin bind to L-PGDS with significantly higher affinities than the other small lipophilic ligands examined, showing dissociation constant (Kd) values from 17.0 to 20.9 nM. We focused particularly on the extra-specificities of haem metabolites and L-PGDS. The ITC and ICD data revealed that two molecules of the haem metabolites bind to L-PGDS with high and low affinities, showing Kd values from 2.8 to 18.1 nM and from 0.209 to 1.63 μM respectively. The thermodynamic parameters for the interactions revealed that the contributions of enthalpy and entropy change were considerably different for each haem metabolite even when the Gibbs energy change was the same. Thus we believe that the binding energy of haem metabolites to L-PGDS is optimized by balancing enthalpy and entropy change.
Oxytetracycline Pharmacokinetics in Rainbow Trout during and after an Orally Administered Medicated Feed Regimen
Authors: Miller Ron A. , Pelsor Francis R. , Kane Andrew S. , Reimschuessel Renate
Published: June 2012

The pharmacokinetic–pharmacodynamic predictor of antimicrobial activity for tetracyclines is reported to be the area under the concentration–time curve at steady state (AUCss) divided by the minimal inhibitory concentration of the targeted pathogen. Here, we estimate AUCss values for oxytetracycline (OTC) in serum of rainbow trout Oncorhynchus mykiss by using a destructive sampling study design. Seventy-two rainbow trout were fed OTC-medicated feed at 74.7 ± 1.5 mg/kg (mean ± SD) body weight (BW) by oral gavage for 10 consecutive days. Serum was collected from nine fish at 1, 3, 6, 8, 10, 12, 15, and 22 d after dosing began. Serum OTC concentrations were measured by high-performance liquid chromatography with a 0.01-μg/mL limit of detection. The average OTC AUCss was 29.2 μg × h/mL and was estimated using nonlinear mixed-effects modeling and bootstrap resampling techniques. The elimination half-life was estimated as 85.0 h, and the fraction of steady state achieved was estimated as 0.85. The calculated AUCss (24.8 μg × h/mL) following 10 d of oral dosing with 75 mg OTC/kg BW was less than the estimated AUCss. Results suggest that the pharmacokinetics of OTC exposure, including the AUCss, is better evaluated by using multiday dosimetry than by using a standard single-dose protocol.

Received September 29, 2011; accepted January 30, 2012
Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase
Authors: Rubenstein Eric M. , Kreft Stefan G. , Greenblatt Wesley , Swanson Robert , Hochstrasser Mark
Published: June 2012

Little is known about quality control of proteins that aberrantly or persistently engage the endoplasmic reticulum (ER)-localized translocon en route to membrane localization or the secretory pathway. Hrd1 and Doa10, the primary ubiquitin ligases that function in ER-associated degradation (ERAD) in yeast, target distinct subsets of misfolded or otherwise abnormal proteins based primarily on degradation signal (degron) location. We report the surprising observation that fusing Deg1, a cytoplasmic degron normally recognized by Doa10, to the Sec62 membrane protein rendered the protein a Hrd1 substrate. Hrd1-dependent degradation occurred when Deg1-Sec62 aberrantly engaged the Sec61 translocon channel and underwent topological rearrangement. Mutations that prevent translocon engagement caused a reversion to Doa10-dependent degradation. Similarly, a variant of apolipoprotein B, a protein known to be cotranslocationally targeted for proteasomal degradation, was also a Hrd1 substrate. Hrd1 therefore likely plays a general role in targeting proteins that persistently associate with and potentially obstruct the translocon.
Recurrence coefficients of generalized Charlier polynomials and the fifth Painlevé equation
Authors: Filipuk Galina , Van Assche Walter
Published: June 2012

We investigate generalizations of the Charlier polynomials on the lattice

N

\mathbb {N}

, on the shifted lattice

N

+
1
−
β

\mathbb {N}+1-\beta

, and on the bi-lattice

N

∪

\mathbb {N}\;\cup

(

N

+
1
−
β
)

(\mathbb {N}+1-\beta )

. We show that the coefficients of the three-term recurrence relation for the orthogonal polynomials are related to solutions of the fifth Painlevé equation P

V

_{\mathrm {V}}

(which can be transformed to the third Painlevé equation). Initial conditions for different lattices can be transformed to the classical solutions of P

V

_{\mathrm {V}}

with special values of the parameters.
Recognition models to predict DNA-binding specificities of homeodomain proteins
Authors: Christensen Ryan G. , Enuameh Metewo Selase , Noyes Marcus B. , Brodsky Michael H. , Wolfe Scot A. , Stormo Gary D.
Published: June 2012

Motivation: Recognition models for protein-DNA interactions, which allow the prediction of specificity for a DNA-binding domain based only on its sequence or the alteration of specificity through rational design, have long been a goal of computational biology. There has been some progress in constructing useful models, especially for C2H2 zinc finger proteins, but it remains a challenging problem with ample room for improvement. For most families of transcription factors the best available methods utilize k-nearest neighbor (KNN) algorithms to make specificity predictions based on the average of the specificities of the k most similar proteins with defined specificities. Homeodomain (HD) proteins are the second most abundant family of transcription factors, after zinc fingers, in most metazoan genomes, and as a consequence an effective recognition model for this family would facilitate predictive models of many transcriptional regulatory networks within these genomes.

Results: Using extensive experimental data, we have tested several machine learning approaches and find that both support vector machines and random forests (RFs) can produce recognition models for HD proteins that are significant improvements over KNN-based methods. Cross-validation analyses show that the resulting models are capable of predicting specificities with high accuracy. We have produced a web-based prediction tool, PreMoTF (Predicted Motifs for Transcription Factors) (http://stormo.wustl.edu/PreMoTF), for predicting position frequency matrices from protein sequence using a RF-based model.

Contact:  stormo@wustl.edu
Matching experiments across species using expression values and textual information
Authors: Wise Aaron , Oltvai Zoltán N. , Bar−Joseph Ziv
Published: June 2012

Motivation: With the vast increase in the number of gene expression datasets deposited in public databases, novel techniques are required to analyze and mine this wealth of data. Similar to the way BLAST enables cross-species comparison of sequence data, tools that enable cross-species expression comparison will allow us to better utilize these datasets: cross-species expression comparison enables us to address questions in evolution and development, and further allows the identification of disease-related genes and pathways that play similar roles in humans and model organisms. Unlike sequence, which is static, expression data changes over time and under different conditions. Thus, a prerequisite for performing cross-species analysis is the ability to match experiments across species.

Results: To enable better cross-species comparisons, we developed methods for automatically identifying pairs of similar expression datasets across species. Our method uses a co-training algorithm to combine a model of expression similarity with a model of the text which accompanies the expression experiments. The co-training method outperforms previous methods based on expression similarity alone. Using expert analysis, we show that the new matches identified by our method indeed capture biological similarities across species. We then use the matched expression pairs between human and mouse to recover known and novel cycling genes as well as to identify genes with possible involvement in diabetes. By providing the ability to identify novel candidate genes in model organisms, our method opens the door to new models for studying diseases.

Availability: Source code and supplementary information is available at: www.andrew.cmu.edu/user/aaronwis/cotrain12.

Contact:  zivbj@cs.cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model
Authors: Polishko Anton , Ponts Nadia , Le Roch Karine G. , Lonardi Stefano
Published: June 2012

Motivation: Nucleosomes are the basic elements of chromatin structure. They control the packaging of DNA and play a critical role in gene regulation by allowing physical access to transcription factors. The advent of second-generation sequencing has enabled landmark genome-wide studies of nucleosome positions for several model organisms. Current methods to determine nucleosome positioning first compute an occupancy coverage profile by mapping nucleosome-enriched sequenced reads to a reference genome; then, nucleosomes are placed according to the peaks of the coverage profile. These methods are quite accurate on placing isolated nucleosomes, but they do not properly handle more complex configurations. Also, they can only provide the positions of nucleosomes and their occupancy level, whereas it is very beneficial to supply molecular biologists additional information about nucleosomes like the probability of placement, the size of DNA fragments enriched for nucleosomes and/or whether nucleosomes are well positioned or ‘fuzzy’ in the sequenced cell sample.

Results: We address these issues by providing a novel method based on a parametric probabilistic model. An expectation maximization algorithm is used to infer the parameters of the mixture of distributions. We compare the performance of our method on two real datasets against Template Filtering, which is considered the current state-of-the-art. On synthetic data, we show that our method can resolve more accurately complex configurations of nucleosomes, and it is more robust to user-defined parameters. On real data, we show that our method detects a significantly higher number of nucleosomes.

Availability: Visit http://www.cs.ucr.edu/~polishka

Contact:  stelo@cs.ucr.edu or polishka@cs.ucr.edu
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
Authors: Disfani Fatemeh Miri , Hsu Wei-Lun , Mizianty Marcin J. , Oldfield Christopher J. , Xue Bin , Dunker A. Keith , Uversky Vladimir N. , Kurgan Lukasz
Published: June 2012

Motivation: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains.

Results: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build and empirically compare our method. MoRFpred utilizes a novel design in which annotations generated by sequence alignment are fused with predictions generated by a Support Vector Machine (SVM), which uses a custom designed set of sequence-derived features. The features provide information about evolutionary profiles, selected physiochemical properties of amino acids, and predicted disorder, solvent accessibility and B-factors. Empirical evaluation on several datasets shows that MoRFpred outperforms related methods: α-MoRF-Pred that predicts α-MoRFs and ANCHOR which finds disordered regions that become ordered when bound to a globular partner. We show that our predicted (new) MoRF regions have non-random sequence similarity with native MoRFs. We use this observation along with the fact that predictions with higher probability are more accurate to identify putative MoRF regions. We also identify a few sequence-derived hallmarks of MoRFs. They are characterized by dips in the disorder predictions and higher hydrophobicity and stability when compared to adjacent (in the chain) residues.

Availability:  http://biomine.ece.ualberta.ca/MoRFpred/; http://biomine.ece.ualberta.ca/MoRFpred/Supplement.pdf

Contact:  lkurgan@ece.ualberta.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
A single source k-shortest paths algorithm to infer regulatory pathways in a gene network
Authors: Shih Yu-Keng , Parthasarathy Srinivasan
Published: June 2012

Motivation: Inferring the underlying regulatory pathways within a gene interaction network is a fundamental problem in Systems Biology to help understand the complex interactions and the regulation and flow of information within a system-of-interest. Given a weighted gene network and a gene in this network, the goal of an inference algorithm is to identify the potential regulatory pathways passing through this gene.

Results: In a departure from previous approaches that largely rely on the random walk model, we propose a novel single-source k-shortest paths based algorithm to address this inference problem. An important element of our approach is to explicitly account for and enhance the diversity of paths discovered by our algorithm. The intuition here is that diversity in paths can help enrich different functions and thereby better position one to understand the underlying system-of-interest. Results on the yeast gene network demonstrate the utility of the proposed approach over extant state-of-the-art inference algorithms. Beyond utility, our algorithm achieves a significant speedup over these baselines.

Availability: All data and codes are freely available upon request.

Contact:  srini@cse.ohio-state.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores
Authors: Hochbaum Dorit S. , Hsu Chun-Nan , Yang Yan T.
Published: June 2012

Motivation: The recent development of high-throughput drug profiling (high content screening or HCS) provides a large amount of quantitative multidimensional data. Despite its potentials, it poses several challenges for academia and industry analysts alike. This is especially true for ranking the effectiveness of several drugs from many thousands of images directly. This paper introduces, for the first time, a new framework for automatically ordering the performance of drugs, called fractional adjusted bi-partitional score (FABS). This general strategy takes advantage of graph-based formulations and solutions and avoids many shortfalls of traditionally used methods in practice. We experimented with FABS framework by implementing it with a specific algorithm, a variant of normalized cut—normalized cut prime (FABS-NC′), producing a ranking of drugs. This algorithm is known to run in polynomial time and therefore can scale well in high-throughput applications.

Results: We compare the performance of FABS-NC′ to other methods that could be used for drugs ranking. We devise two variants of the FABS algorithm: FABS-SVM that utilizes support vector machine (SVM) as black box, and FABS-Spectral that utilizes the eigenvector technique (spectral) as black box. We compare the performance of FABS-NC′ also to three other methods that have been previously considered: center ranking (Center), PCA ranking (PCA), and graph transition energy method (GTEM). The conclusion is encouraging: FABS-NC′ consistently outperforms all these five alternatives. FABS-SVM has the second best performance among these six methods, but is far behind FABS-NC′: In some cases FABS-NC′ produces over half correctly predicted ranking experiment trials than FABS-SVM.

Availability: The system and data for the evaluation reported here will be made available upon request to the authors after this manuscript is accepted for publication.

Contact:  yxy128@berkeley.edu
DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism
Authors: Aguiar Derek , Halldórsson Bjarni V. , Morrow Eric M. , Istrail Sorin
Published: June 2012

Motivation: The understanding of the genetic determinants of complex disease is undergoing a paradigm shift. Genetic heterogeneity of rare mutations with deleterious effects is more commonly being viewed as a major component of disease. Autism is an excellent example where research is active in identifying matches between the phenotypic and genomic heterogeneities. A considerable portion of autism appears to be correlated with copy number variation, which is not directly probed by single nucleotide polymorphism (SNP) array or sequencing technologies. Identifying the genetic heterogeneity of small deletions remains a major unresolved computational problem partly due to the inability of algorithms to detect them.

Results: In this article, we present an algorithmic framework, which we term DELISHUS, that implements three exact algorithms for inferring regions of hemizygosity containing genomic deletions of all sizes and frequencies in SNP genotype data. We implement an efficient backtracking algorithm—that processes a 1 billion entry genome-wide association study SNP matrix in a few minutes—to compute all inherited deletions in a dataset. We further extend our model to give an efficient algorithm for detecting de novo deletions. Finally, given a set of called deletions, we also give a polynomial time algorithm for computing the critical regions of recurrent deletions. DELISHUS achieves significantly lower false-positive rates and higher power than previously published algorithms partly because it considers all individuals in the sample simultaneously. DELISHUS may be applied to SNP array or sequencing data to identify the deletion spectrum for family-based association studies.

Availability: DELISHUS is available at http://www.brown.edu/Research/Istrail_Lab/.

Contact:  Eric_Morrow@brown.edu and Sorin_Istrail@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Unidirectional crystal growth and crystalline perfection ofL-arginine phosphate monohydrate
Authors: Riscob B. , Shakir Mohd , Vijayan N. , Maurya K. K. , Wahab M. A. , Bhagavannarayana G.
Published: June 2012

A large (∼20 mm diameter and 80 mm length) single crystal of L-arginine phosphate monohydrate (LAP) has been grown for the first time by the unidirectional Sankaranarayanan–Ramasamy method in an aqueous medium in a specially designed constant-temperature bath. The crystal structure has been confirmed by powder X-ray diffraction. The crystalline perfection was assessed by high-resolution X-ray diffractometry (HRXRD) which found that the quality of the grown single crystal is quite good. HRXRD studies along different directions show that the crystal contains a low density of edge-type dislocations formed along the growth direction. The thermal stability was assessed using thermogravimetric/differential thermal analysis. The mechanical behaviour was studied using an Omnitech micro-hardness tester. The dielectric studies were carried out over a wide frequency range of 10 Hz to 5 MHz at room temperature. The characterization studies reveal that the grown bulk single crystal of LAP is suitable for device applications.
FraGen: a computer program for real-space structure solution of extended inorganic frameworks
Authors: Li Yi , Yu Jihong , Xu Ruren
Published: June 2012

TheFraGen(framework generator) program has been developed for real-space structure solution. It has been designed especially for the generation of extended inorganic frameworks in a given unit cell.FraGenis based on the parallel tempering global optimization method. Various restraints can be introduced intoFraGen, such as restraints on bonding geometry, relative reflection intensities and three-dimensional density maps. The basic inputs forFraGenare the space group and cell parameters. The number of unique atoms is not a necessary input, since it can be estimated from certain constraints.FraGenalso has the ability to exit unpromising simulation cycles to save computation time for promising ones. Program features, methods and three examples are demonstrated. TheFraGenprogram for the Windows platform is available from the authors upon request.
Exploring the Needs of Socially Excluded Young Men
Authors: Rondón Janeet , Campbell James , Galway Karen , Leavey Gerard
Published: June 2012

In recent years, social exclusion has gained the attention of governments around the world. This paper reports on a qualitative study involving 27 young men aged 14–19 years experiencing particular forms of exclusion in the context of Northern Irish society. The study used a focus group methodology to elicit their views with the aim of exploring both emotional and psychological needs and the structural factors that may contribute to their experiences of social exclusion. The findings reveal a range of unmet social and psychological needs, the impact of sectarianism and segregation, and a paucity of support systems in place. The paper concludes by making recommendations about how policy‐makers and practitioners could find more imaginative ways of engaging such vulnerable young men to reduce social exclusion.
Seasonal interactions between photoperiod and maternal effects determine offspring phenotype inFranklin's gull
Authors: Clark Mark E. , Reed Wendy L.
Published: June 2012

1.When predictable seasonal changes affect offspring fitness, we expect offspring to evolve phenotypes that minimize the costs of seasonal variation in timing of breeding. For species with parental care during embryonic development, offspring receive seasonal cues of the environment from parents that are biased by their parent's fitness (which is not equivalent to offspring fitness). Therefore, mechanisms enabling offspring to detect environmental cues independent of parents should be strongly favoured.

2.We experimentally evaluated the ability of avian embryos to integrate cues of season from photoperiod and maternal environments present in eggs to produce seasonal variation in phenotypes among Franklin's gull (Leucophaeus pipixcan) hatchlings. Eggs were collected early and late in the season and some were separated into their component parts and others were incubated under short (early season) and long (late season) photoperiods. After hatching, we measured the structural size of the chicks and the amount of yolk sac reserves.

3.We found that hatchling size, a phenotype linked with fitness, is sensitive to both egg contents provided by mothers and photoperiod, and development time decreases across the season. The effects of integrating cues of season from eggs and photoperiod on offspring phenotype are complex, and when cues of season from eggs are mismatched with cues of season from photoperiod, alternate phenotypes are created.

4.We also found that seasonal variation in egg size, yolk, albumen or shell content of the eggs do not account for the seasonal maternal egg effect on hatchling size. This seasonal maternal effect could be a result of other egg constituents or reflect heritable variation in timing of breeding that is linked with offspring size.

5.Changes in breeding phenology of adults could result in a mismatch between cues from parents and photoperiod cues of season. For example, if breeding seasons advanced such that late season birds initiate breeding at an early season photoperiod, offspring would then be integrating maternal cues of late season with photoperiod cues of early season and alter their phenotypes. We expect our results to initiate new studies on how vertebrate embryos integrate environmental cues with maternal effects and offspring responses to optimize the expression of offspring phenotype.
Characteristics of gelling agent substituted fruit jam: studies on the textural, optical, physicochemical and sensory properties
Authors: Javanmard Marjan , Chin Nyuk Ling , Mirhosseini Seyed Hamed , Endan Johari
Published: June 2012

A series of mango jams were prepared using different hydrocolloid solutions (high methoxyl pectin (HMP), carboxymethyl cellulose (CMC), and sago starch) as gelling agents to investigate the effect of hydrocolloid type, hydrocolloid concentration, and freeze‐thaw treatment on the physicochemical, optical, textural, and sensory characteristics. The optical properties results revealed that the total colour change (ΔE) of the sago starch‐based mango jam samples displayed higher values in comparison with samples prepared with HMP and CMC. The textural parameters (hardness, work of shear, stickiness, and work of adhesion) increased with hydrocolloid concentration but decreased with the freeze‐thaw treatment except for sago starch‐based mango jams. The overall acceptability of mango jams containing 6% sago starch was rated similarly to the samples prepared with 0.7% HMP and 0.5% CMC. Principle component analysis revealed that it could be used as an effective tool to segregate characteristics related to fruit jam manufacture.
Nitrite and nitrate in fresh meats: a contribution to the estimation of admissible maximum limits to introduce in directive 95/2/EC
Authors: Iammarino Marco , Di Taranto Aurelia
Published: June 2012

Nitrite and nitrate are food preservatives not allowed in fresh meat preparations. Two hundred fresh meat samples were analysed to evaluate the natural presence of nitrite and nitrate and estimate the maximum concentrations to considerate as ‘natural’ and to admit in fresh meat preparations. The analyses were carried out by a validated ion chromatography method, and the ‘positive’ samples were confirmed by an alternative ion chromatography method. Nitrite residues were not detected. Quantifiable nitrate concentrations, ranging from 10.2 to 36.5 mg kg−1, were found in nineteen samples. In chicken meat samples, nitrate residues were not detected. Taking into account the distribution of nitrate concentrations, it is possible to suggest a maximum admissible limit of 30.0 mg kg−1 in beef and pork meats; in equine meats, this limit may be increased to 40.0 mg kg−1. Below these values, the samples can be considered as ‘compliant’.
Predation risk and food: opposite effects on overwintering survival and onset of breeding in a boreal rodent
Authors: Haapakoski Marko , Sundell Janne , Ylönen Hannu
Published: June 2012

1. In seasonal environments, optimal onset of breeding and survival plays major roles in individual fitness. Many physiological and behavioural factors related to breeding increase the risk of predation; thus, breeding decisions should be based on current risks and benefits. According to life‐history theory, if current predation risk is high and breeding itself increases the risk, it may be beneficial to postpone breeding.

2. During winter in northern hemispheres, food availability is limited and is at its lowest just prior to the onset of breeding in spring. Food constraint may lead to poor condition and reduced ability to start breeding.

3. We studied the effects of food and predation risk on winter survival and onset of breeding in a common boreal rodent, the bank vole (Myodes glareolus). In a 2 × 2 factorial experiment, we manipulated food availability (food supplemented or not) and predation risk (presence/absence of predator odour) in 20 large outdoor enclosures in central Finland.

4. Survival probabilities were highest in no predation risk treatments, whereas they were lowest in the predator risk treatment. The same trend was observed in vole densities and the weight change in individuals. Voles with food addition bred earlier than in the other treatments.

5. We conclude that during energy constrained harsh conditions in winter, predation risk causes behavioural changes throughout the winter and has significant negative survival and fitness effects for small mammals, reflected as delay in the start of breeding.
An interdisciplinary educational trial for adolescent health and development in urbanising China
Authors: Zang Yu‐Li , Liu Qian , Pu Lin‐Zhe
Published: June 2012

Aims and objectives.  To evaluate the effects on master student participants of an intensive interdisciplinary educational programme aiming at improving adolescent health and development services in urbanising China.

Background.  There is a need for interdisciplinary education and collaborative practice in health, but few educational programmes have been reported.

Design.  Experimental design including a qualitative component.

Methods.  Purposive sampling was used to identify master students in relevant disciplinary areas for the four‐day classroom learning, four‐day field learning and a half‐day reflection, focusing on key aspects of adolescent health and development in the face of rapid urbanisation. Data about family function, cognitive development, adolescent health and development competency, and difficulties caused by health conditions were collected using quantitative and qualitative methods.

Result.  Master student participants reported positive outcomes in adolescent health and development competency, and cognitive development. Six themes were identified about the programme and its impact: ‘programme evaluation’, ‘programme characteristics’, ‘changed views about nursing and nurses’, ‘lessons learned’, ‘participation benefits’ and ‘suggestions for future action’.

Conclusion.  Interdisciplinary educational programmes are possible and beneficial at masters level but may be very challenging given the need for administrative, financial and human resources.

Relevance to clinical practice.  Interdisciplinary educational programmes require to start with small health sector trials to accumulate evidence and skills. Faculty development is a prerequisite for such programmes towards collaborative practice.