De novo construction of polyploid linkage maps using discrete graphical models

Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. We propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a nonparanormal skeptic approach. Linkage groups (LGs), typically chromosomes, and the order of markers in each LG are determined by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors and are incomplete. We apply the proposed method to two genotype datasets: barley and potato from diploid and polypoid populations, respectively. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We have implemented the method in the R package netgwas.Comment: 25 pages, 7 figure

A Conceptual UX-aware Model of Requirements

User eXperience (UX) is becoming increasingly important for success of software products. Yet, many companies still face various challenges in their work with UX. Part of these challenges relate to inadequate knowledge and awareness of UX and that current UX models are commonly not practical nor well integrated into existing Software Engineering (SE) models and concepts. Therefore, we present a conceptual UX-aware model of requirements for software development practitioners. This layered model shows the interrelation between UX and functional and quality requirements. The model is developed based on current models of UX and software quality characteristics. Through the model we highlight the main differences between various requirement types in particular essentially subjective and accidentally subjective quality requirements. We also present the result of an initial validation of the model through interviews with 12 practitioners and researchers. Our results show that the model can raise practitioners' knowledge and awareness of UX in particular in relation to requirement and testing activities. It can also facilitate UX-related communication among stakeholders with different backgrounds.Comment: 6th International Working Conference on Human-Centred Software Engineerin

netgwas: An R Package for Network-Based Genome-Wide Association Studies

Graphical models are powerful tools for modeling and making statistical inferences regarding complex associations among variables in multivariate data. In this paper we introduce the R package netgwas, which is designed based on undirected graphical models to accomplish three important and interrelated goals in genetics: constructing linkage map, reconstructing linkage disequilibrium (LD) networks from multi-loci genotype data, and detecting high-dimensional genotype-phenotype networks. The netgwas package deals with species with any chromosome copy number in a unified way, unlike other software. It implements recent improvements in both linkage map construction (Behrouzi and Wit, 2018), and reconstructing conditional independence network for non-Gaussian continuous data, discrete data, and mixed discrete-and-continuous data (Behrouzi and Wit, 2017). Such datasets routinely occur in genetics and genomics such as genotype data, and genotype-phenotype data. We demonstrate the value of our package functionality by applying it to various multivariate example datasets taken from the literature. We show, in particular, that our package allows a more realistic analysis of data, as it adjusts for the effect of all other variables while performing pairwise associations. This feature controls for spurious associations between variables that can arise from classical multiple testing approach. This paper includes a brief overview of the statistical methods which have been implemented in the package. The main body of the paper explains how to use the package. The package uses a parallelization strategy on multi-core processors to speed-up computations for large datasets. In addition, it contains several functions for simulation and visualization. The netgwas package is freely available at https://cran.r-project.org/web/packages/netgwasComment: 32 pages, 9 figures; due to the limitation "The abstract field cannot be longer than 1,920 characters", the abstract appearing here is slightly shorter than that in the PDF fil

Nothing new under the sun, or the moon, or both

PC and CR were supported by the PRIN grant 2010RP5RNM_001 from the Italian Ministry of University./nLB was supported by MINECO grant PSI2012-31961

Impact of the components of Mediterranean nutrition regimen on long-term prognosis of diabetic patients with coronary artery disease

BACKGROUND: The impact of different nutritional regimens on long-term prognosis and outcome in diabetic patients with coronary artery disease (CAD) has been questioned. Therefore, the objective of the present study was to determine the effects of different nutritional components of Mediterranean regimen on long-term cardiovascular events in diabetic patients with CAD in the Iranian population. METHODS: In a prospective cohort study, we recruited 233 consecutive patients with the diagnosis of type 2 diabetes mellitus and with at least 6 months of documented CAD. Nutritional assessment was obtained by a validated semi-quantitative food frequency questionnaire (FFQ) and the diet score was calculated on the basis of the Mediterranean diet quality index (Med-DQI). For Assessing long-term CAD prognosis, the patients were followed by telephone for one year. The study endpoint was long-term Major Adverse Cardiac and Cerebrovascular event (MACCE). RESULTS: Death was observed in 19 patients (8.2) during the one-year follow-up. Two patients (0.9) suffered non-fatal myocardial infarction and 14 (6.0) needed revascularization within 1 year after discharge from hospital. Overall MACCE within one year in the study population was 12.4. There were significant differences between number of deaths and dietary scores of saturated fatty acid, cholesterol, meats, fish, and fruit and vegetables (P < 0.05). Moreover, significant differences were found between MACCE rate and dietary scores of saturated fatty acid, cholesterol, and fruit and vegetables (P < 0.05). Using multivariate logistic regression models, Mediterranean dietary regimen could effectively predict long-term death as well as MACCE adjusted for gender and age variables. CONCLUSION: Mediterranean dietary regimens, including low level of cholesterol and saturated fatty acid, can effectively improve long-term outcome including death and MACCE in diabetic patients with CAD

Investigating the role of "Italian Origin" claim and other key attributes in price determination: A hedonic pricing study in the olive oil markets of Italy and Sweden

openWith high competition and a saturated market in the food sector, particularly in Mediterranean foods, deep analysis and creativity in strategic decisions play a powerful and inevitable role. The determining characteristics of the olive oil market, or in other words, extrinsic values are the undertakers for the final price fluctuations which are exposed to consumer purchases. Geographical indication, organic labels or Italian claims perform crucial roles in the olive oil dynamic pricing and these players demonstrate different behavior in different countries of the European Union or even the regions in one country like Italy. Variation in the food industry increases consumer expectations around the world where most of the time, competition among producers takes place in the export destination. Italian growers who produce thousands of tons of Extra Virgin Olive Oil over the years, employ native values of Italian olives to provide the premium quality while they must monitor challenges such as disease, climate change or other incidents. Also simultaneous export and import in this sector implies the relevance of olive oil trade flow and the strong impacts of that on the economic dimensions in southern European countries. Wine, citrus fruits and fresh vegetables, pork, cheese, and pasta are the other foodstuffs that improve the international market even in non-EU countries, using the hectares of profitable landscapes. Results show the importance of utilizing hedonic pricing where different values detect consumer preferences. Therefore, in this research, the prices of Extra Virgin Olive Oil in Italy and Sweden are analyzed to investigate differences.With high competition and a saturated market in the food sector, particularly in Mediterranean foods, deep analysis and creativity in strategic decisions play a powerful and inevitable role. The determining characteristics of the olive oil market, or in other words, extrinsic values are the undertakers for the final price fluctuations which are exposed to consumer purchases. Geographical indication, organic labels or Italian claims perform crucial roles in the olive oil dynamic pricing and these players demonstrate different behavior in different countries of the European Union or even the regions in one country like Italy. Variation in the food industry increases consumer expectations around the world where most of the time, competition among producers takes place in the export destination. Italian growers who produce thousands of tons of Extra Virgin Olive Oil over the years, employ native values of Italian olives to provide the premium quality while they must monitor challenges such as disease, climate change or other incidents. Also simultaneous export and import in this sector implies the relevance of olive oil trade flow and the strong impacts of that on the economic dimensions in southern European countries. Wine, citrus fruits and fresh vegetables, pork, cheese, and pasta are the other foodstuffs that improve the international market even in non-EU countries, using the hectares of profitable landscapes. Results show the importance of utilizing hedonic pricing where different values detect consumer preferences. Therefore, in this research, the prices of Extra Virgin Olive Oil in Italy and Sweden are analyzed to investigate differences

Theoretical Modeling, Experimental Observation, and Reliability Analysis of Flow-induced Oscillations in Offshore Wind Turbine Blades

Offshore wind energy has been growing rapidly due to its capacity for utilizing much larger turbines and thus higher power generation compared to onshore. With the increasing size of offshore wind turbine rotors, the design criteria used for the blades may also evolve. Increased flexibility in blades causes them to be more susceptible to experiencing flow-induced instability. One of the destructive aero-elastic instabilities that can occur in flexible structures subjected to aerodynamic loading is coupled-mode flutter. Coupled-mode flutter instability has not been a design driver in the current wind turbine blades, however, considering the industry tendency in utilizing longer and lighter blades, it needs very closeattention. Long-span bridges, aircrafts and turbomachines are the most common engineering devices subject to flutter. In recent years, a few studies have focused on flutter instability in wind turbine blades. Coupled-mode flutter in wind turbine blades is the result of the interaction between a torsional mode and a flapwise mode. The two structural modes coalesce at a critical flow velocity and result in a negative damping that cannot be compensated by structural damping. Contrary to the stall flutter which is the result of separation and reattachment of the flow due to high angles of attack, classical flutter occurs in the attached flow regime and may occur in pitch-regulated wind turbines. The aim of this thesis is to provide a thorough study of the coupled-mode flutter in wind turbine blades. For this purpose coupled-mode flutter is studied both through theoretical modeling and wind tunnel experimentations. Parametric studies are performed on three MW-size wind turbine blades and it is shown that the ratio between the torsional and flapwise natural frequencies, as well as the magnitude of the 1st torsional natural frequency significantly influence the onset of flutter. To investigate the influence of uncertainty in system’s parameters on the onset of flutter, Monte Carlo simulations are conducted assuming randomness in both flow forces and structural properties. It is shown that the safety margin between the flutter onset and the rated rotor speed shrinks and in some cases vanishes when the randomness is considered. Different reliability methods are used to mitigate the Monte Carlo simulations and a new reliability method which is developed, is proven to be a viable substitute for the Monte Carlo with much less computing time. Coupled mode flutter of fixed and rotating highly flexible airfoils is also studied and the influence of static deflection on the flutter characteristic is shown and validated through conducting experiments in a wind tunnel. A small scale wind turbine is designed to study the aero-elastic instabilities in rotating blades. A set of experiments is carried out in a wind tunnel and the failure of the small scale blades due to the aero-elastic instability is captured