Berkeley Electronic Press

Graph Selection with GGMselect

Christophe Giraud et al. — Fri, 10 Feb 2012 10:30:38 PST

Applications on inference of biological networks have raised a strong interest in the problem of graph estimation in high-dimensional Gaussian graphical models. To handle this problem, we propose a two-stage procedure which first builds a family of candidate graphs from the data, and then selects one graph among this family according to a dedicated criterion. This estimation procedure is shown to be consistent in a high-dimensional setting, and its risk is controlled by a non-asymptotic oracle-like inequality. The procedure is tested on a real data set concerning gene expression data, and its performances are assessed on the basis of a large numerical study.

The procedure is implemented in the R-package GGMselect available on the CRAN.

Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry

Stephen O. Nyangoma et al. — Fri, 10 Feb 2012 10:30:35 PST

In cancer clinical proteomics, MALDI and SELDI profiling are used to search for biomarkers of potentially curable early-stage disease. A given number of samples must be analysed in order to detect clinically relevant differences between cancers and controls, with adequate statistical power. From clinical proteomic profiling studies, expression data for each peak (protein or peptide) from two or more clinically defined groups of subjects are typically available. Typically, both exposure and confounder information on each subject are also available, and usually the samples are not from randomized subjects. Moreover, the data is usually available in replicate. At the design stage, however, covariates are not typically available and are often ignored in sample size calculations. This leads to the use of insufficient numbers of samples and reduced power when there are imbalances in the numbers of subjects between different phenotypic groups. A method is proposed for accommodating information on covariates, data imbalances and design-characteristics, such as the technical replication and the observational nature of these studies, in sample size calculations. It assumes knowledge of a joint distribution for the protein expression values and the covariates. When discretized covariates are considered, the effect of the covariates enters the calculations as a function of the proportions of subjects with specific attributes. This makes it relatively straightforward (even when pilot data on subject covariates is unavailable) to specify and to adjust for the effect of the expected heterogeneities. The new method suggests certain experimental designs which lead to the use of a smaller number of samples when planning a study. Analysis of data from the proteomic profiling of colorectal cancer reveals that fewer samples are needed when a study is balanced than when it is unbalanced, and when the IMAC30 chip-type is used. The method is implemented in the clippda package and is available in R at: http://www.bioconductor.org/help/bioc-views/release/bioc/html/clippda.html.

A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification

John P. Ferguson et al. — Fri, 10 Feb 2012 10:30:31 PST

Most approaches for analyzing ChIP-Seq data are focused on inferring exact protein binding sites from a single library. However, frequently multiple ChIP-Seq libraries derived from differing cell lines or tissue types from the same individual may be available. In such a situation, a separate analysis for each tissue or cell line may be inefficient. Here, we describe a novel method to analyze such data that intelligently uses the joint information from multiple related ChIP-Seq libraries. We present our method as a two-stage procedure. First, separate single cell line analysis is performed for each cell line. Here, we use a novel mixture regression approach to infer the subset of genes that are most likely to be involved in protein binding in each cell line. In the second step, we combine the separate single cell line analyses using an Empirical Bayes algorithm that implicitly incorporates inter-cell line correlation. We demonstrate the usefulness of our method using both simulated data, as well as real H3K4me3 and H3K27me3 histone methylation libraries.

Effect of Gluten Powder on the Quality of Fresh Spaghetti Made with Farina

Mahsa Majzoobi et al. — Thu, 09 Feb 2012 04:36:50 PST

The objective of this study was to improve the quality of fresh spaghetti made from ordinary wheat flour using gluten powder at different levels (0.0, 0.5, 1.5 and 3.0%, w/w, flour basis). The spaghetti dough was evaluated by a Brabender Farinograph. The results indicated that with increasing the gluten level, peak, stability time and consistency of the dough increased. The results of creep test (carried out using a Texture Analyser) showed that with increasing the gluten content, elasticity of the dough increased while its viscosity decreased. Increasing the gluten level reduced the cooking loss and increased the water absorption of the samples cooked in distilled or salted water (2% NaCl). The hardness and the color of the uncooked and cooked spaghettis improved with increasing the gluten content. The sample containing 3% gluten powder cooked in salted water received the highest score for its sensory attributes.

Effects of Fermentation on Nutritional and Functional Properties of Soybean, Maize, and Germinated Sorghum Composite Flour

Nicole Murekatete et al. — Thu, 09 Feb 2012 04:36:46 PST

Sorghum germination resulted in a substantial tannin loss (95.7 %). Proximate composition, titratable acidity, pasting properties, in vitro protein digestibility, and protein solubility were studied post fermentation (Saccharomyces Cerevisiae) of the blended soybean, maize, and germinated sorghum flours. The pH progressively decreased with fermentation time, while titratable acidity increased from 0.029 to 0.118 ml/ml. Crude protein content increased with fermentation (251.7-274.8 mg/g) as a result of a shift in the dry matter composition. In-vitro protein digestibility markedly increased (12 %) as a result of fermentation. Protein solubility curves were above 30% of which highest for both fermented (12 and 24 hours) and unfermented composite flours were at pH 12 (51.77-77.64%) and lowest at pH 4 (30.31-35.98%). SDS-PAGE showed that protein hydrolysis occurred during fermentation over 12 and 24 hours. Unfermented composite flour was potentially stable as food ingredient due to its pasting stability, but the fermented flour low viscosity potential was preferred in this study as more flour will be used during porridge making, hence giving a food with a high nutrient density.

Optimal Alcohol Taxes for Australia

James J. Fogarty — Sun, 05 Feb 2012 17:13:42 PST

The 2010 Australian government tax review suggested Australia move to a uniform excise tax rate for all alcoholic beverages. Here, a model is presented and calibrated that shows the optimal per litre of pure alcohol (LAL) tax rates for beer, wine, spirits, and ready-to-drink spirits are substantially different to both current alcohol tax rates and the uniform tax rate recommended by the tax review. Specifically, given an individual consumer utility model, the best estimate values of the welfare maximising LAL tax rates are: $37 for beer, $11 for wine, $50 for spirits, and $77 for ready-to-drink spirits. The variation in the optimal tax rate across beverage types flows from differences in the externality costs associated with the consumption of each beverage type, and differences in the proportion of moderate consumption and abusive consumption associated with each beverage type. In addition, it is shown that the optimal tax rates are influenced by the range of costs that are considered to be externality costs, and the relative price responsiveness of abusers and moderate consumers.

Why and When "Flawed" Social Network Analyses Still Yield Valid Tests of no Contagion

Tyler J. VanderWeele et al. — Sat, 04 Feb 2012 14:43:11 PST

Lyons (2011) offered several critiques of the social network analyses of Christakis and Fowler, including issues of confounding, model inconsistency, and statistical dependence in networks. Here we show that in some settings, social network analyses of the type employed by Christakis and Fowler will still yield valid tests of the null of no social contagion, even though estimates and confidence intervals may not be valid. In particular, we show that if the alter's state is lagged by an additional period, then under the null of no contagion, the problems of model inconsistency and statistical dependence effectively disappear which allow for testing for contagion. Our results clarify the setting in which even "flawed" social network analyses are still useful for assessing social contagion and social influence.

Clean Synthesis of 2-Methylglycidol over a Novel Titanosilica Catalyst – Ti-MWW under Autogenic Pressure

Anna Fajdek et al. — Fri, 03 Feb 2012 18:46:51 PST

In this work the epoxidation of methallyl alcohol (MAA) with 30 wt% H₂O₂ over the Ti-MWW catalyst has been studied. The significant parameters for the MAA epoxidation were established as temperature (20-120°C), the molar ratio of MAA/H₂O₂ (1:1-5:1), methanol (solvent) concentration (5-90 wt%), Ti-MWW catalyst concentration (0-5.0 wt%), reaction time (5-300 min) and intensity of stirring (0-500 rpm). The process of MAA epoxidation was carried out the most effective at temperature of 100°C, the molar ratio of MAA/H₂O₂=1:1, methanol concentration of 40 wt%, the catalyst concentration of 2 wt%, the reaction time of 15 min and with the stirring intensity over 350 rpm. These the best technological parameters (mild and relatively safe) allow to obtain the selectivity of transformation to 2MG 37 mol%, the MAA conversion 52 mol%, and the selectivity of transformation to organic compounds in relation to H₂O₂ consumed 48 mol%.

Multiobjective Optimization of an Industrial Styrene Reactor Using the Dual Population Evolutionary Algorithm (DPEA)

Salim Fettaka et al. — Fri, 03 Feb 2012 18:46:48 PST

In the last few years, multiobjective evolutionary algorithms (MOEAs) have gained significant interest as a reliable option to optimize problems with conflicting objectives in science and engineering. These algorithms generate an optimal set of trade-off solutions referred to as the Pareto domain. In this investigation, a MOEA was used to optimize simultaneously conflicting design variables of an industrial styrene reactor. The dual population evolutionary algorithm (DPEA) was implemented to optimize the productivity, yield, and selectivity of styrene. To evaluate the robustness and versatility of the algorithm, two and three objective optimization case studies were conducted for three different configurations of the reactor: adiabatic, steam-injected, and isothermal.

Results indicated that DPEA is a robust optimization strategy to generate a well-defined Pareto domain with a wide range of solutions. In addition, the Pareto-optimal solutions of the steam-injected configuration were superior to the adiabatic reactor and to a portion of the isothermal configuration. The optimal operating conditions corresponding to the Pareto domains were also slightly better in terms of profit when compared with previously published studies. The Pareto domains were then ranked using the Net Flow Method (NFM), a ranking algorithm that incorporates the knowledge and preferences of an expert into the optimization routine.

MHD Flow of an Oldroyd-B Fluid Through a Porous Channel

Tasawar Hayat et al. — Fri, 03 Feb 2012 18:46:41 PST

This paper discusses the hydromagnetic boundary layer flow of an Oldroyd-B fluid in a porous channel. Both suction and injection (blowing) cases are considered. Appropriate similarity transformations are invoked to convert the partial differential equations into ordinary ones. Homotopy analysis method (HAM) is used for the presentation of analytic solution of the nonlinear differential system. Graphical results provide the salient features of the embedded flow parameters which include the Reynolds number, the Deborah numbers, and the Hartman number. Comparison between the existing numerical solution in a Maxwell fluid and present deduced series solution in a limiting sense is excellent.

Organizational Redesign, Information Technologies and Workplace Productivity

Benoit Dostie et al. — Fri, 03 Feb 2012 07:31:47 PST

Using a large, longitudinal, nationally representative workplace-level data-set, we explore the productivity gains associated with computer use and organizational redesign. The empirical strategy involves the estimation of a production function, augmented to account for technology use and organizational design, correcting for unobserved heterogeneity. Our first-difference and GMM estimates suggest that the productivity premium associated with computer use is not statistically different from zero. Neither is there any evidence to support the idea that complementarities between computer use and organizational redesign have any substantial bearing on productivity.

Behavioral Responses of Patients in AIDS Treatment Programs: Sexual Behavior in Kenya

Harsha Thirumurthy et al. — Tue, 31 Jan 2012 12:47:15 PST

We estimate changes in sexual behavior for HIV-positive individuals enrolled in an AIDS treatment program using longitudinal household survey data collected in western Kenya. We find that sexual activity is lowest at the time that treatment is initiated and increases significantly in the subsequent six months, consistent with the health improvements that result from ART treatment. More importantly, we find large and significant increases of 10 to 30 percentage points in the reported use of condoms during last sexual intercourse. The increases in condom use appear to be driven primarily by a program effect, applying to all HIV clinic patients regardless of treatment status.

Why do Firms Hold Oil Stockpiles?

Charles F. Mason — Tue, 31 Jan 2012 06:14:14 PST

Persistent and significant privately-held stockpiles of crude oil have long been an important empirical regularity in the United States. Such stockpiles would not rationally be held in a traditional Hotelling-style model. How then can the existence of these inventories be explained? In the presence of sufficiently stochastic prices, oil extracting firms have an incentive to hold inventories to smooth production over time. An alternative explanation is related to a speculative motive - firms hold stockpiles intending to cash in on periods of particularly high prices. I argue that empirical evidence supports the former but not the latter explanation.

Graduating High School in a Recession: Work, Education, and Home Production

Brad J. Hershbein — Tue, 31 Jan 2012 05:11:06 PST

This paper explores how high school graduate men and women vary in their behavioral responses to beginning labor market entry during a recession. In contrast with previous related literature that found a substantial negative wage impact but minimal employment impact in samples of highly educated men, the empirical evidence presented here suggests a different outcome for the less well educated, and between the sexes. Women, but not men, who graduate high school in an adverse labor market are less likely to be in the workforce for the next four years, but longer-term effects are minimal. Further, while men increase their enrollment as a short-run response to weak labor demand, women do not; instead, they appear temporarily to substitute into home production. Women's wages are less affected than men's, and both groups' wages are less affected than the college graduates previously studied.

Evaluating the Impacts of the EU-ETS on Prices, Investments and Profits of the Italian Electricity Market

Francesca Bonenti et al. — Tue, 31 Jan 2012 04:48:09 PST

In this paper we investigate the economic impacts of the European Emission Trading Scheme (EU-ETS) on the Italian electricity market by a power generation expansion model. In particular, we assume that generators make their capacity expansion decisions in a Cournot or in a perfect competition manner. This model is used to measure the effects of the EU-ETS Directives on electricity prices and demand, investments and generators' profits both in an oligopolistic and in a perfectly competitive organization of the power market. We adopt a technological representation of the energy market which is discretized into six geographical zones (North, Center-North, Center-South, South, Sicily, Sardinia) and five virtual poles (Monfalcone, Foggia, Brindisi, Rossano, Priolo) with limited production for a total of eleven zones. We assume that generators operate in different zones connected by interconnections with limited capacity and produce energy by running existing or new plants in which they directly invest. We consider several investment scenarios under the CO2 regulation with and without incentives to renewables. The scenarios also include simulations on future effects of the third EU-ETS phase on the system. Our analysis shows that perfect competition induces generators to invest more than in an oligopolistic framework, but in both market configurations, investments are mainly concentrated in fossil-red plants (CCGT and coal), leaving a small proportion to new wind plants. This happens also in presence of incentives given to renewable technologies. We can thus conclude that investments in a secure and efficient technology like CCGT are preferable compared to those in renewables that cannot be used with continuity. This investment policy affects electricity prices that significantly increase in 2020 compared to their 2009 levels. The raise of electricity prices in 2020 is particularly favorable for generators operating as Cournot players which are able to increase their profits compared to 2009, despite the full auctioning system foreseen for the allocation of CO2 allowance to the power sector in the third EU-ETS phase. The solution of the overall system is found by exploiting the mixed complementarity theoretical framework and solution algorithms. The developed model is implemented as complementarity problems and solved in GAMS using the PATH solver.

Combining Climate and Energy Policies: Synergies or Antagonism? Modeling interactions with energy efficiency instruments

Oskar Lecuyer et al. — Tue, 31 Jan 2012 03:42:44 PST

In addition to the already present Climate and Energy package, the European Union (EU) plans to include a binding target to reduce energy consumption. We analyze the rationales the EU invokes to justify such an overlapping and develop a minimal common framework to study interactions arising from the combination of instruments reducing emissions, promoting renewable energy (RE) production and reducing energy demand through energy efficiency (EE) investments. We find that although all instruments tend to reduce emissions and a price on carbon tends to give the right incentives for RE and EE too, the combination of more than one instrument leads to significant antagonisms regarding major objectives of the policy package. The model allows to show in a single framework and to quantify the antagonistic effects of the joint promotion of RE and EE. We also show and quantify the effects of this joint promotion on ETS permit price, on wholesale market price and on energy production levels.

Incentives and Stability of International Climate Coalitions: An Integrated Assessment

Valentina Bosetti et al. — Tue, 31 Jan 2012 03:28:17 PST

This paper analyses the incentives to participate in and the stability of international climate coalitions. Using the integrated assessment model WITCH, the analysis of coalitions’ profitability and stability is performed under alternative assumptions concerning the pure rate of time preference, the social welfare aggregator and the extent of climate damages. We focus on the profitability, stability, and “potential stability” of a number of coalitions which are “potentially effective” in reducing emissions. We find that only the grand coalition under a specific sets of assumptions finds it optimal to stabilise GHG concentration below 550 ppm CO2-eq. However, the grand coalition is found not to be stable, not even “potentially stable” even through an adequate set of transfers. However, there exist potentially stable coalitions, but of smaller size, which are also potentially environmentally effective. Depending on the assumptions made, they could achieve up to 600 ppm CO2-eq. More ambitious targets lead to the collapse of the coalition.

Designing Carbon Taxation Schemes for Automobiles: A Simulation Exercise for Germany

Adamos Adamou et al. — Tue, 31 Jan 2012 03:21:44 PST

Vehicle taxation based on CO2 emissions is increasingly being adopted worldwide in order to shift consumer purchases to low-carbon cars, yet little is known about the effectiveness and overall economic impact of these schemes. We focus on feebate schemes, which impose a fee on high-carbon vehicles and give a rebate to purchasers of low-carbon automobiles. e estimate a discrete choice model of demand for automobiles in Germany and simulate the impact of alternative feebate schemes on emissions, consumer welfare, public revenues and firm profits. The analysis shows that a well-designed scheme can lead to emission reductions without reducing overall welfare.

The Environment and Directed Technical Change: Comment

Jean-Charles Hourcade et al. — Tue, 31 Jan 2012 03:12:35 PST

This paper discusses the growth model with environmental constraints recently presented in (Acemoglu et al., 2011) which focuses on the redirection of technical change by climate policies with research subsidies and a carbon tax. First, Acemoglu et al.'s model and chosen parameters yield numerical results that do not support the conclusion that ambitious climate policies can be conducted “without sacrificing (much or any) long-run growth”. Second, they select unrealistic key parameters for carbon sinks and elasticity of substitution. We find that more realistic parameters lead to very different results. Third, the model leads to an unrealistic conclusion when used to analyse endogenous growth, suggesting specification problems.

Work Values in Western and Eastern Europe

Benno Torgler — Tue, 31 Jan 2012 03:12:34 PST

The paper reports on work values in Europe. At the country level we find that job satisfaction is related to lower working hours, higher well-being, and a higher GDP per capita. Moving to the micro level, we turn our attention from job satisfaction to analyse empirically work centrality and work value dimensions (without exploring empirically job satisfaction) related to intrinsic and extrinsic values, power and social elements. The results indicate substantial differences between Eastern and Western Europe. Socio-demographic factors, education, income, religiosity and religious denomination are significant influences. We find additional differences between Eastern and Western Europe regarding work-leisure and work-family centrality that could be driven by institutional conditions. Furthermore, hierarchical cluster analyses report further levels of dissimilarity among European countries.