Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

The Design and Implementation of a SD Card File System

SD card (Secure Digital Memory Card) is widely used in portable storage medium. Currently, latest researches on SD card, are mainly SD card controller based on FPGA (Field Programmable Gate Array). Most of them are relying on API interface (Application Programming Interface), AHB bus (Advanced High performance Bus), etc. They are dedicated to the realization of ultra high speed communication between SD card and upper systems. Studies about SD card controller, really play a vital role in the field of high speed cameras and other sub-areas of expertise. This design of FPGA-based file systems and SD2.0 IP (Intellectual Property core) does not only exhibit a nice transmission rate, but also achieve the systematic management of files, while retaining a strong portability and practicality. The file system design and implementation on a SD card covers the main three IP innovation points. First, the combination and integration of file system and SD card controller, makes the overall system highly integrated and practical. The popular SD2.0 protocol is implemented for communication channels. Pure digital logic design based on VHDL (Very-High-Speed Integrated Circuit Hardware Description Language), integrates the SD card controller in hardware layer and the FAT32 file system for the entire system. Secondly, the document management system mechanism makes document processing more convenient and easy. Especially for small files in batch processing, it can ease the pressure of upper system to frequently access and process them, thereby enhancing the overall efficiency of systems. Finally, digital design ensures the superior performance. For transmission security, CRC (Cyclic Redundancy Check) algorithm is for data transmission protection. Design of each module is platform-independent of macro cells, and keeps a better portability. Custom integrated instructions and interfaces may facilitate easily to use. Finally, the actual test went through multi-platform method, Xilinx and Altera FPGA developing platforms. The timing simulation and debugging of each module was covered. Finally, Test results show that the designed FPGA-based file system IP on SD card can support SD card, TF card and Micro SD with 2.0 protocols, and the successful implementation of systematic management for stored files, and supports SD bus mode. Data read and write rates in Kingston class10 card is approximately 24.27MB/s and 16.94MB/s.

EXAMINING THE IMPLEMENTATION CHALLENGES OF PROJECT-BASED LEARNING: A CASE STUDY

Title of Thesis: Thesis directed by: ABSTRACT EXAMINING THE IMPLEMENTATION CHALLENGES OF PROJECT-BASED LEARNING: A CASE STUDY Stefan Frederick Brooks, Master of Education, 2016 Professor and Chair Francine Hultgren Teaching and Learning, Policy and Leadership Department Project-based learning (PjBL) is a common instructional strategy to consider for educators, scholars, and advocates who focus on education reform. Previous research on PjBL has focused on its effectiveness, but a limited amount of research exists on the implementation challenges. This exploratory case study examines an attempted project- based learning implementation in one chemistry classroom at a private school that fully supports PjBL for most subjects with limited use in mathematics. During the course of the study, the teacher used a modified version of PjBL. Specifically, he implemented some of the elements of PjBL, such as a driving theme and a public presentation of projects, with the support of traditional instructional methods due to the context of the classroom. The findings of this study emphasize the teacher’s experience with implementing some of the PjBL components and how the inherent implementation challenges affected his practice.

Outcome of childhood malignancies at the University of Port Harcourt Teaching Hospital: a call for implementation of palliative care.

Background: Cancers in children are yet to be recognised as an important cause of childhood morbidity and mortality in developing countries where more than 70% of the world annual cases occur. Despite the limited resources and whatever the projected outcome, children with cancer need treatment, be it curative or palliative. Objectives: To determine outcome of cancers in children at the UPTH; identify factors that influence outcome, highlight the need for palliative care. Method: A retrospective study of cases of childhood malignancies admitted into Paediatric Oncology unit of UPTH over a two year period. Clinical profile of patients and outcome were analyzed using SPSS version 20.0. Results: Sixty cases were analysed: 35(58.3%) males, 25(41.7%) females giving a M:F ratio of 1.4:1. Under-fives constituted 55%. Twenty-seven (45%) patients presented within 4 weeks of onset of symptoms. Median duration of symptoms before presentation was 8 weeks while 36 (60%) had metastatic disease at diagnosis. Twenty patients (33.3%) defaulted with or without specific treatment. Mortality was recorded in 26(43.4%) of cases. Conclusion: There were more cases of cancer amongst under-fives with male preponderance. Late presentation, financial constraints and high default rate were contributory factors to poor outcome in most cases. Lack of palliative care left many families to face their sufferings.

A three-dimensional representation method for noisy point clouds based on growing self-organizing maps accelerated on GPUs

The research described in this thesis was motivated by the need of a robust model capable of representing 3D data obtained with 3D sensors, which are inherently noisy. In addition, time constraints have to be considered as these sensors are capable of providing a 3D data stream in real time. This thesis proposed the use of Self-Organizing Maps (SOMs) as a 3D representation model. In particular, we proposed the use of the Growing Neural Gas (GNG) network, which has been successfully used for clustering, pattern recognition and topology representation of multi-dimensional data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models, without considering time constraints. It is proposed a hardware implementation leveraging the computing power of modern GPUs, which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). The proposed methods were applied to different problem and applications in the area of computer vision such as the recognition and localization of objects, visual surveillance or 3D reconstruction.

Adolescent physical activity: does implementation intention have a role?

BACKGROUND: The current study tested the utility of an integrated social cognitive model to predict physical activity (PA) intentions and behavior in New Zealand adolescents. METHOD: Seventy-two adolescents (mean age = 16.92, SD = 0.66) completed measures consistent with the integrated model (attitude, subjective norm, perceived behavioral control [PBC], goal intention, task-efficacy, barrier efficacy, and implementation intention). Pedometer data (Yamax SW200 pedometer) were collected for 7 days, and a self-report 7-day recall questionnaire was administered at the end of this week. A series of hierarchical regression analyses were conducted to examine the contribution of the model to PA goal intention, implementation intention, self-reported and objective PA. RESULTS: The integrated model accounted for 41% of goal intention, 33% of implementation intention, and 41% and 18% of subjectively and objectively measured PA, respectively. PBC had the strongest association with goal intention whereas attitude had the strongest association with implementation intention. Task-efficacy made the greatest contribution to objectively measured PA, whereas implementation intention had the strongest association with subjectively measured PA. CONCLUSION: These findings have implications regarding PA measurement in adolescent populations, and suggest that social cognitive variables play an important role in adolescent PA. Recommendations for future research are discussed.

A hybrid simulated annealing and perturb and observe method for maximum power point tracking in PV systems under partial shading conditions

This paper presents a hybrid method for Maximum Power Point Tracking (MPPT) of a Photovoltaic (PV) system which experiences non-uniform environmental conditions or partial shading conditions. The hybrid method combines two simple techniques with complementary strengths in achieving Global MPPT. Simulated Annealing (SA) has only recently been applied to PV MPPT and is very effective at locating global maxima with limited implementation complexity. Perturb and Observe (P&O) is a very common technique which provides continuous tracking of the MPP in a simple and easy to implement manner. The P&O method is generally incapable of locating global maxima, and the SA based method is unable to perform continuous searching. By merging these techniques in a hybrid MPPT method consisting of a global searching stage and a local searching stage, the tracking performance is improved compared to what each technique could achieve independently. Simulation results are presented to demonstrate the effectiveness of the proposed hybrid technique.

Analysis of reverse logistics implementation practices by South Australian construction organisations

Purpose – A large number of benefits have been reported when reverse logistics (RL) is fully implemented in the construction industry. However, RL is yet to become common place in the construction sector, particularly in Australia. The particular sub-sector in which RL operates is small and weak and the remainder of the sector must embrace and accommodate it comfortably. Research is lacking on how to promoting RL in the construction industry. Very little has been done to identify the current practices that have the potential to promote RL industry-wide. The purpose of this paper is to identify the practices that work well in the sector, a strategy could be mapped out to promote RL to all stakeholders. Design/methodology/approach – In order to fill the above gap, the present study used a mixed method approach to gather and evaluate current practices and their potential to promote RL in South Australia’s construction industry. Practices that were identified using a comprehensive literature review were evaluated with a questionnaire survey and series of interviews involving construction professionals. Findings – The findings are that practices facilitating deconstruction is the most important, followed by practices facilitating the use of salvaged materials in new construction to promote RL in South Australia. Awareness of deconstruction benefits, challenges and procedures at the organisation level and facilities and services at industry level were associated with RL implementation. Availability of salvaged materials in the market was found to influence its use in new construction and as a consequence its demand. Designing for reverse logistics is another practice that could facilitate deconstruction and the onus of its promotion lies mainly with the designers. Research limitations/implications – This research was confined to one state in Australia. As such the generalisation to other states and other countries should be treated cautiously. Practical implications – The findings of this study can help inform the industry and its stakeholders on areas that they need to concentrate more on to make the South Australian construction industry a fully RL integrated one. To that end the authors propose some recommendations arising from the findings reported here. Originality/value – This study makes a contribution to the body of knowledge on reserve logistics within a previously unexplored South Australian context. In addition, the study provides valuable insights into the contribution of RL practices to the construction industry.

SIMULATING LARGE DEFORMATION OF INTRANEURAL GANGLION CYST USING FINITE ELEMENT METHOD

Intraneural Ganglion Cyst is disorder observed in the nerve injury, it is still unknown and very difficult to predict its propagation in the human body so many times it is referred as an unsolved history. The treatments for this disorder are to remove the cystic substance from the nerve by a surgery. However these treatments may result in neuropathic pain and recurrence of the cyst. The articular theory proposed by Spinner et al., (Spinner et al. 2003) considers the neurological deficit in Common Peroneal Nerve (CPN) branch of the sciatic nerve and adds that in addition to the treatment, ligation of articular branch results into foolproof eradication of the deficit. Mechanical modeling of the affected nerve cross section will reinforce the articular theory (Spinner et al. 2003). As the cyst propagates, it compresses the neighboring fascicles and the nerve cross section appears like a signet ring. Hence, in order to mechanically model the affected nerve cross section; computational methods capable of modeling excessively large deformations are required. Traditional FEM produces distorted elements while modeling such deformations, resulting into inaccuracies and premature termination of the analysis. The methods described in research report have the capability to simulate large deformation. The results obtained from this research shows significant deformation as compared to the deformation observed in the conventional finite element models. The report elaborates the neurological deficit followed by detail explanation of the Smoothed Particle Hydrodynamic approach. Finally, the results show the large deformation in stages and also the successful implementation of the SPH method for the large deformation of the biological organ like the Intra-neural ganglion cyst.

A real time electromagnetic analysis of electric machines for educational purposes and laboratory implementation

This thesis presents a system for visually analyzing the electromagnetic fields of the electrical machines in the energy conversion laboratory. The system basically utilizes the finite element method to achieve a real-time effect in the analysis of electrical machines during hands-on experimentation. The system developed is a tool to support the student's understanding of the electromagnetic field by calculating performance measures and operational concepts pertaining to the practical study of electrical machines. Energy conversion courses are fundamental in electrical engineering. The laboratory is conducted oriented to facilitate the practical application of the theory presented in class, enabling the student to use electromagnetic field solutions obtained numerically to calculate performance measures and operating characteristics. Laboratory experiments are utilized to help the students understand the electromagnetic concepts by the use of this visual and interactive analysis system. In this system, this understanding is accomplished while hands-on experimentation takes place in real-time.

Meshfree Method for Prediction of Thermal Properties of Porous Ceramic Materials

In the presented thesis work, meshfree method with distance fields is applied to create a novel computational approach which enables inclusion of the realistic geometric models of the microstructure and liberates Finite Element Analysis(FEA) from thedependance on and limitations of meshing of fine microstructural feature such as splats and porosity.Manufacturing processes of ceramics produce materials with complex porosity microstructure.Geometry of pores, their size and location substantially affect macro scale physical properties of the material. Complex structure and geometry of the pores severely limit application of modern Finite Element Analysis methods because they require construction of spatial grids (meshes) that conform to the geometric shape of the structure. As a result, there are virtually no effective tools available for predicting overall mechanical and thermal properties of porous materials based on their microstructure. This thesis is a separate handling and controls of geometric and physical computational models that are seamlessly combined at solution run time. Using the proposedapproach we will determine the effective thermal conductivity tensor of real porous ceramic materials featuring both isotropic and anisotropic thermal properties. This work involved development and implementation of numerical algorithms, data structure, and software.

Development of a Coupling Model for Fluid-Structure Interaction using the Mesh-free Finite Element Method and the Lattice Boltzmann Method

In the presented thesis work, the meshfree method with distance fields was coupled with the lattice Boltzmann method to obtain solutions of fluid-structure interaction problems. The thesis work involved development and implementation of numerical algorithms, data structure, and software. Numerical and computational properties of the coupling algorithm combining the meshfree method with distance fields and the lattice Boltzmann method were investigated. Convergence and accuracy of the methodology was validated by analytical solutions. The research was focused on fluid-structure interaction solutions in complex, mesh-resistant domains as both the lattice Boltzmann method and the meshfree method with distance fields are particularly adept in these situations. Furthermore, the fluid solution provided by the lattice Boltzmann method is massively scalable, allowing extensive use of cutting edge parallel computing resources to accelerate this phase of the solution process. The meshfree method with distance fields allows for exact satisfaction of boundary conditions making it possible to exactly capture the effects of the fluid field on the solid structure.

Implementation of dual stack technique for reducing leakage and dynamic power

This paper deals with proposal of a new dual stack approach for reducing both leakage and dynamic powers. The development of digital integrated circuits is challenged by higher power consumption. Thecombination of higher clock speeds, greater functional integration, and smaller process geometries has contributed to significant growth in power density. Scaling improves transistor density and functionality ona chip. Scaling helps to increase speed and frequency of operation and hence higher performance. As voltages scale downward with the geometries threshold voltages must also decrease to gain the performance advantages of the new technology but leakage current increases exponentially. Today leakage power has become anincreasingly important issue in processor hardware and software design. It can be used in various applications like digital VLSI clocking system, buffers, registers, microprocessors etc. The leakage power increases astechnology is scaled down. In this paper, we propose a new dual stack approach for reducing both leakage and dynamic powers. Moreover, the novel dual stack approach shows the least speed power product whencompared to the existing methods. All well known approach is “Sleep” in this method we reduce leakage power. The proposed Dual Stack approach we reduce more power leakage. Dual Stack approach uses theadvantage of using the two extra pull-up and two extra pull-down transistors in sleep mode either in OFF state or in ON state. Since the Dual Stack portion can be made common to all logic circuitry, less number of transistors is needed to apply a certain logic circuit.The dual stack approach shows the least speed power product among all methods. The Dual Stack technique provides new ways to designers who require ultra-low leakage power consumption with much less speedpower product.