Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans

We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of D. yakuba, and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting deleterious impacts are common. D. simulans shows larger numbers of whole gene duplications in comparison to larger proportions of gene fragments in D. yakuba. D. simulans displays an excess of high frequency variants on the X chromosome, consistent with adaptive evolution through duplications on the D. simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D. yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited non-coding sequence in D. yakuba and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these results suggest that tandem duplications often result in complex variation beyond whole gene duplications that offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease, as well as to adaptive evolutionary change.Comment: Revised Version- Accepted at Molecular Biology and Evolutio

Automated design of robust discriminant analysis classifier for foot pressure lesions using kinematic data

In the recent years, the use of motion tracking systems for acquisition of functional biomechanical gait data, has received increasing interest due to the richness and accuracy of the measured kinematic information. However, costs frequently restrict the number of subjects employed, and this makes the dimensionality of the collected data far higher than the available samples. This paper applies discriminant analysis algorithms to the classification of patients with different types of foot lesions, in order to establish an association between foot motion and lesion formation. With primary attention to small sample size situations, we compare different types of Bayesian classifiers and evaluate their performance with various dimensionality reduction techniques for feature extraction, as well as search methods for selection of raw kinematic variables. Finally, we propose a novel integrated method which fine-tunes the classifier parameters and selects the most relevant kinematic variables simultaneously. Performance comparisons are using robust resampling techniques such as Bootstrap$632+$and k-fold cross-validation. Results from experimentations with lesion subjects suffering from pathological plantar hyperkeratosis, show that the proposed method can lead to$sim 96$correct classification rates with less than 10% of the original features

VIRTUE : integrating CFD ship design

Novel ship concepts, increasing size and speed, and strong competition in the global maritime market require that a ship's hydrodynamic performance be studied at the highest level of sophistication. All hydrodynamic aspects need to be considered so as to optimize trade-offs between resistance, propulsion (and cavitation), seakeeping or manoeuvring. VIRTUE takes a holistic approach to hydrodynamic design and focuses on integrating advanced CFD tools in a software platform that can control and launch multi-objective hydrodynamic design projects. In this paper current practice, future requirements and a potential software integration platform are presented. The necessity of parametric modelling as a means of effectively generating and efficiently varying geometry, and the added-value of advanced visualization, is discussed. An illustrating example is given as a test case, a container carrier investigation, and the requirements and a proposed architecture for the platform are outlined

A Learning Algorithm based on High School Teaching Wisdom

A learning algorithm based on primary school teaching and learning is presented. The methodology is to continuously evaluate a student and to give them training on the examples for which they repeatedly fail, until, they can correctly answer all types of questions. This incremental learning procedure produces better learning curves by demanding the student to optimally dedicate their learning time on the failed examples. When used in machine learning, the algorithm is found to train a machine on a data with maximum variance in the feature space so that the generalization ability of the network improves. The algorithm has interesting applications in data mining, model evaluations and rare objects discovery

On the Interface Between LENS® Deposited Stainless Steel 304L Repair Geometry and Cast or Machined Components

Laser Engineered Net Shaping™ (LENS®) is being evaluated for use as a metal component repair/modification process. A component of the evaluation is to better understand the characteristics of the interface between LENS deposited material and the substrate on which it is deposited. A processing and metallurgical evaluation was made on LENS processed material fabricated for component qualification tests. A process parameter evaluation was used to determine optimum build parameters and these parameters were used in the fabrication of tensile test specimens to study the characteristics of the interface between LENS deposited material and several types of substrates. Analyses of the interface included mechanical properties, microstructure, and metallurgical integrity. Test samples were determined for a variety of geometric configurations associated with interfaces between LENS deposited material and both wrought base material or previously deposited LENS material. Thirteen different interface configurations were fabricated for evaluation representing a spectrum of deposition conditions from complete part build, to hybrid substrate-LENS builds, to repair builds for damaged or re-designed housings. Good mechanical properties and full density were observed for all configurations. When tested to failure, fracture occurred by ductile microvoid coalescence. The repair and hybrid interfaces showed the same metallurgical integrity as, and had properties similar to, monolithic LENS deposits.Mechanical Engineerin

Configurations of market environments, competitive strategies, manufacturing technologies and human resource management policies : a two-industry and two-country analysis of fit

In this paper an attempt is made to gain further insight into the environment-strategy-structure- performance linkages. A framework is developed to relate managers’ perceptions of their market environment and competitive strategies to the (advanced) production technologies and human resource management (HRM) policies their firms have adopted. Data from twelve Dutch and eight British companies in the food & drink and chemical industries reveal that firms with coherent environment-strategy-technology-HRM ''gestalts'' outperform rivals with incoherent profiles. Additionally, refined typologies of manufacturing technologies and HRM policies are proposed.management and organization theory ;