Over the past few years, DNA sequencing technology has been advancing at such a fast pace that computer hardware and software can hardly meet the ever-increasing demand for sequence analysis. A natural approach to boost analysis efficiency is parallelization, which divides the problem into smaller ones that are to be solved simultaneously on multiple execution units. Common architectures such as multi-core CPUs and clusters can increase the throughput to some extent, but the hardware setup and maintenance costs are prohibitive. Fortunately, the newly emerged general-purpose GPU programming paradigm gives us a low-cost alternative for parallelization. This thesis presents GPU-accelerated algorithms for several problems in bioinformatics, along with implementations to demonstrate their power in handling enormous totally different limitations and optimization techniques than the CPU. The first tool presented is SOAP3-dp, which is a DNA short-read aligner highly optimized for speed. Prior to SOAP3-DP, the fastest short-read aligner was its predecessor SOAP2, which was capable of aligning 1 million 100-bp reads in 5 minutes. SOAP3-dp beats this record by aligning the same volume in only 10 seconds. The key to unlocking this unprecedented speed is the revamped BWT engine underlying SOAP3-dp. All data structures and associated operations have been tailor made for the GPU to achieve optimized performance. Experiments show that SOAP3-dp not only excels in speed, but also outperforms other aligners in both alignment sensitivity and accuracy. The next tools are for constructing data structures, namely Burrows-Wheeler transform (BWT) and de Bruijn graphs (DBGs), to facilitate genome assembly of short reads, especially large metagenomics data. The BWT index for a set of short reads has recently found its use in string-graph assemblers [44], as it provides a succinct way of representing huge string graphs which would otherwise exceed the main memory limit. Constructing the BWT index for a million reads is by itself not an easy task, let alone optimize for the GPU. Another class of assemblers, the DBG-based assemblers, also faces the same problem. This thesis presents construction algorithms for both the BWT and DBGs in a succinct form. In our experiments, we constructed the succinct DBG for a metagenomics data set with over 200 gigabases in 3 hours, and the resulting DBG only consumed 31.2 GB of memory. We also constructed the BWT index for 10 million 100-bp reads in 40 minutes using 4 quad-core machines. Lastly, we introduce a SNP detection tool, iSNPcall, which detects SNPs from a set of reads. Given a set of user-supplied annotated SNPs, iSNPcall focuses only on alignments covering these SNPs, which greatly accelerates the detection of SNPs at the prescribed loci. The annotated SNPs also helps us distinguish sequencing errors from authentic SNPs alleles easily. This is in contrast to the traditional de novo method which aligns reads onto the reference genome and then filters inauthentic mismatches according to some probabilities. After comparing on several applications, iSNPcall was found to give a higher accuracy than the de novo method, especially for samples with low coverage. / published_or_final_version / Computer Science / Doctoral / Doctor of Philosophy

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The thesis deals with systems consisting of marine cables and subsea units. Such systems have wide applications in offshore subsea operations. After a general introduction, the thesis sets out to analyse both the static and dynamic behaviours of the system under various environmental and operational conditions. It endeavours to pursue a fundamental approach in order to reveal the basic characteristics of the system, in addition to developing numerical algorithms for predicting performance. The analysis of behaviour of marine cables consists of the following parts: Statics A semi-analytic approach is developed to predict the equilibrium configurations of marine cables. One-dimensional dynamics Using a coordinate transformation, the method can predict the unsteady dynamic behaviour of systems where the length of cable varies. Two-dimensional dynamics The methodology adopted in the one-dimension analysis is extended to a more general case. Three-dimensional dynamics An alternative approach based upon a lumped mass model is developed. Mathematical analysis reveals many interesting characteristics of the model. By applying modern control theory, a novel heave compensation mechanism is developed for marine systems of cables and subsea units. This mechanism involves an actively controlled winch system. A framework of optimal stochastic control is outlined for integrating all the elements of surface supported subsea operations. The thesis presents a variety of numerical examples in domenstrating the validity of the approaches adopted, along with discussions. Further developments are also recommended.

The events of September 11, 2001 marked a paradigm shift in the strategy within all levels of law enforcement in the United States. Intelligence became the watchword of the day and with it, the movement to incorporate strategic and tactical information in daily policing. Yet while the philosophy was clear, the method and manner to which agencies were left to achieve these goals was much less designed. The federal government allocated funds to assist help agencies incorporate an intelligence function in their daily operations but which agencies and to what degree remains unclear even today. This study seeks to determine the current state of use of intelligence in municipal law enforcement agencies in the State of Texas ten years after 9/11. Through use of a survey, it assesses the frequency of use of intelligence units in local police departments in the State of Texas, identifies commonalities in their structure, and determines the state of their effectiveness.

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Science in Physiotherapy Johannesburg, 2017 / Background: Burns are a significant cause of paediatric injuries, particularly in low and middle-income countries, where more than 90% of burn-related paediatric deaths occur. Physiotherapy is an essential, sometimes painful, component of burn rehabilitation therapy. The popularity of the video game use in burns rehabilitation has grown because, in addition to facilitating range of motion (ROM) in an effort to prevent joint contracture formation, the virtual imaging characteristics of these games provides additional benefit of distraction from pain. Video games provide a more efficient, effective and enjoyable method training, and are a helpful adjunct to rehabilitation. Aim: To investigate the effect of using the Xbox Kinect™ on discharge outcomes and early activity levels of children in the Paediatric Burns Unit (PBU) at Chris Hani Baragwanath Academic Hospital (CHBAH) Methods: This non-equivalent post-test only control group design study took place over a period of time until the total number of children required was achieved for each group. The control group was the first group of children recruited to the study and received standard physiotherapy treatment and rehabilitation. The experimental group was the second group of children recruited to the study who received standard physiotherapy treatment and rehabilitation as well as the Xbox Kinect™. Comparisons were made only after the intervention and analysed. Outcome measures for each participant were ROM, Activities Scale for Kids© participation (ASK©p) and a modified Wong-Baker FACES® enjoyment rating scale. On discharge from the unit, ROM assessments and the modified Wong-Baker FACES® enjoyment rating scale were administered. On follow-up one week post discharge, ROM re-assessments were done and the ASK©p was administered. A questionnaire regarding the use of the Xbox Kinect™ was completed by health professionals working within the PBU. Results: Seventy children were recruited into the study of which the data for 66 were analysed. Thirty five children were part of the control group and 31 were part of the Xbox intervention group. No significant difference was found between groups regarding demographic characteristics, the median age was seven years old and 55% of the participants were male. There was one mortality and five children in total were lost to follow up. The majority burns were as a result of hot water attributing to more than 50% of admissions, followed by flame burns (30%) and electrical burns (12%). This study population showed an overall total burn surface area (TBSA) of nine percent which were superficial partial in depth; this is seen as a minor burn injury. Forty percent were seen to have moderate-severe injury and three children were considered to have severe major burns > 30 % TBSA. We observed a greater proportion of injury involving the lower limbs (23.10%) and upper limbs (21.10%), followed by injury involving the trunk (11.40%), buttocks and genitalia (7.50%) and the head and neck regions (6.80%). There was no difference in length of stay (LoS) or the chance of Intensive Care Unit (ICU) stay between the two groups. In the intervention group 75% of the children received 2 or more Xbox Kinect™ sessions. The Xbox Kinect™ was shown to be significant in achieving higher active range of movement (AROM) at discharge (p< 0.01) and at follow up (p< 0.01), and highlights the advantages it has in providing a more amusing and comfortable option as part of the burns rehabilitation process. By allowing the children to be more engaged in the Xbox Kinect™ experience and games, they were distracted and thus experienced less pain. In this study we found that TBSA% was a predictor of ASK©p scores (p= 0.03), thus the higher the burn percentage the lower the ASK©p scores. We also found that age (p= 0.05) and AROM (p= 0.04) were associated with ASK©p scores, thus the younger the child or a child with reduced AROM would have lower ASK©p scores. Fun and enjoyment (p<0.01) was found to be significant in this study, thus highlighting the fun and enjoyment factor the Xbox Kinect™ offers as part of therapy and as an adjunct to burns rehabilitation. Thirty one questionnaires regarding the value and use of the Xbox Kinect™ were completed by health professionals working within the PBU. Many highlighted the value of fun, enjoyment and distraction the Xbox Kinect™ offered as part of the rehabilitation, as well as assisting in achieving more AROM but also indicated that the Xbox Kinect™ sessions still needed to be supervised and guided. Conclusion: This study was the first study done in South Africa involving video game technology during physiotherapy within the paediatric burns population. The use of the Xbox Kinect™ as seen in this study has proven to be beneficial and a useful adjunct to burns rehabilitation within in the paediatric burns population. This distraction and decline in pain assists in reducing the fear associated with movement these burns children experience and assist in improvements related to activity and ultimately age-appropriate play and activities of daily living (ADLs). / MT2017

The timing of harvest aid application on cotton (Gossypium hirsutum L.) is critical, and poses potential problems when mistimed. The consequences of premature harvest aid application could result in reduced profit to the grower through the need for additional applications, reduced lint yield, poor fiber quality, and/or delayed harvest. A delayed application of harvest aid materials may also reduce lint yield and fiber quality if late season inclement weather patterns are established. Currently, there are many methods utilized for determining application of harvest aid materials. One method utilizes accumulated heat units, or growing degree days (HU or DD60??s), following plant physiological maturity. Physiological maturity (cutout) is identified as nodes above white flower equals 5 (NAWF=5). This method triggers the application of harvest aid chemicals when 850 HU have been accumulated beyond cutout. Due to differing environmental and edaphic characteristics across the Cotton Belt, application of harvest aid chemicals at this time may be premature in terms of optimizing lint yield and fiber quality. A two-year study was established to determine the proper timing of harvest aid application for picker harvested cotton in south central Texas. The design utilized a split-plot with four replications. The main plots consisted of three nodal positions(NAWF=3, 4, and 5), and the subplots were five HU accumulations (650, 750, 850, 950, and 1050) that corresponded to each of the nodal positions. In both years, lint yields increased with an increase in HU accumulation. Greater yields were achieved when HU accumulation was initiated after NAWF = 4. This two-year study indicates that harvest aid applications made at NAWF = 4 plus 1050 HU would optimize yield potential for picker harvested cotton in south central Texas.

Thesis (Ph. D.)--Lehigh University, 2004. / Includes vita. Includes bibliographical references (leaves 205-221).

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