As improving technology is making it easier to select or engineer DNA sequences that produce dangerous proteins, it is important to be able to predict whether a novel DNA sequence is potentially dangerous by determining its taxonomic identity and functional characteristics. These tasks can be facilitated by the ever increasing amounts of available biological data. Unfortunately, though, these growing databases can be difficult to take full advantage of due to the corresponding increase in computational and storage costs. Entropy scaling algorithms and data structures present an approach that can expedite this type of analysis by scaling with the amount of entropy contained in the database instead of scaling with the size of the database. Because sets of DNA and protein sequences are biologically meaningful instead of being random, they demonstrate some amount of structure instead of being purely random. As biological databases grow, taking advantage of this structure can be extremely beneficial. The entropy scaling sequence similarity search algorithm introduced here demonstrates this by accelerating the biological sequence search tools BLAST and DIAMOND. Tests of the implementation of this algorithm shows that while this approach can lead to improved query times, constructing the required entropy scaling indices is difficult and expensive. To improve performance and remove this bottleneck, I investigate several ideas for accelerating building indices that support entropy scaling searches. The results of these tests identify key tradeoffs and demonstrate that there is potential in using these techniques for sequence similarity searches. / Master of Science / As biological organisms are created and discovered, it is important to compare their genetic information to known organisms in order to detect possible harmful or dangerous properties. However, the collection of published genetic information from known organisms is huge and growing rapidly, making it difficult to search. This thesis shows that it might be possible to use the non-random properties of biological information to increase the speed and efficiency of searches; that is, because genetic sequences are not random but have common structures, the increase of known data does not mean a proportional increase in complexity, known as entropy. Specifically, when comparing a new sequence to a set of previously known sequences, it is important to choose the correct algorithms for comparing the similarity of two sequences, also known as the distance between them. This thesis explores the performance of entropy scaling algorithm compared to several conventional tools.

Dynamic voltage and frequency scaling (DVFS) is an extensively studied energy manage ment technique, which aims to reduce the energy consumption of computing platforms by dynamically scaling the CPU frequency. Real-Time DVFS (RT-DVFS) is a branch of DVFS, which reduces CPU energy consumption through DVFS, while at the same time ensures that task time constraints are satisfied by constructing appropriate real-time task schedules. The literature presents numerous RT-DVFS scheduling algorithms, which employ different techniques to utilize the CPU idle time to scale the frequency. Many of these algorithms have been experimentally studied through simulations, but have not been implemented on real hardware platforms. Though simulation-based experimental studies can provide a first-order understanding, implementation-based studies can reveal actual timeliness and energy consumption behaviours. This is particularly important, when it is difficult to devise accurate simulation models of hardware, which is increasingly the case with modern systems. In this thesis, we study the timeliness and energy consumption behaviours of fourteen state- of-the-art RT-DVFS schedulers by implementing and evaluating them on two hardware platforms. The schedulers include CC-EDF, LA-EDF, REUA, DRA andd AGR1 among others, and the hardware platforms include ASUS laptop with the Intel I5 processor and a mother- board with the AMD Zacate processor. We implemented these schedulers in the ChronOS real-time Linux kernel and measured their actual timeliness and energy behaviours under a range of workloads including CPU-intensive, memory-intensive, mutual exclusion lock-intensive, and processor-underloaded and overloaded workloads. Our studies reveal that measuring the CPU power consumption as the cube of CPU frequency can lead to incorrect conclusions. In particular, it ignores the idle state CPU power consumption, which is orders of magnitude smaller than the active power consumption. Consequently, power savings obtained by exclusively optimizing active power consumption (i.e., RT-DVFS) may be offset by completing tasks sooner by running them at the highest frequency and transitioning to the idle state earlier (i.e., no DVFS). Thus, the active power consumption savings of the RT-DVFS techniques' that we report are orders of magnitude smaller than their simulation-based savings reported in the literature. / Master of Science

A comparison of available fluid-to-fluid scaling laws for scaling convective heat transfer at supercritical pressures showed that the ones suggested by Zahlan, Groeneveld and Tavoularis (ZGT) have some advantages. The applicability of the ZGT laws was tested for pairs of fluids including carbon dioxide, water or Refrigerant R134a. The conditions of previous measurements taken in the Supercritical University of Ottawa Loop with CO2 flowing vertically upwards in an electrically heated tube with 8 mm ID were scaled to equivalent conditions in R134a and new measurements of the heat transfer coefficient (HTC) were taken in the same tube using the latter fluid. The inlet pressure was 1.13 times the critical pressure (4.06 MPa), the mass flux was in the range from 212 kg/m^2 s to 1609 kg/m^2 s, the heat flux was in the range from 2 kW/m^2 to 137 kW/m^2, and the inlet temperature was in the range from 62 ℃ to 105 ℃. The HTC at equivalent conditions in water was also determined with the use of transcritical look-up tables. Average and linearly varying corrections to the ZGT scaling laws were derived by statistical analysis for each pair of fluids under NHT or DHT conditions. Such corrections reduced the standard deviation of the scaling error but did not eliminate the presence of large errors under many sets of conditions. As expected, scaling errors were in general larger for DHT than NHT conditions. The present results did not reveal any systematic and correctable dependence of the scaling error upon the mass flux or heat flux but showed that scaling errors became particularly large as the bulk temperature T_b approached the pseudocritical temperature T_pc. In conclusion, the ZGT scaling laws appear to be fairly accurate for the three pairs of fluids considered in the liquid-like region with T_b/T_pc ≤ 0.94 and possibly in the gas-like region with T_b/T_pc ≥ 1.02, whereas outside this range scaling errors could be significant. It was also found that the ZGT scaling laws do not scale accurately the onset of DHT in different fluids.

abstract: Body size plays a pervasive role in determining physiological and behavioral performance across animals. It is generally thought that smaller animals are limited in performance measures compared to larger animals; yet, the vast majority of animals on earth are small and evolutionary trends like miniaturization occur in every animal clade. Therefore, there must be some evolutionary advantages to being small and/or compensatory mechanisms that allow small animals to compete with larger species. In this dissertation I specifically explore the scaling of flight performance (flight metabolic rate, wing beat frequency, load-carrying capacity) and learning behaviors (visual differentiation visual Y-maze learning) across stingless bee species that vary by three orders of magnitude in body size. I also test whether eye morphology and calculated visual acuity match visual differentiation and learning abilities using honeybees and stingless bees. In order to determine what morphological and physiological factors contribute to scaling of these performance parameters I measure the scaling of head, thorax, and abdomen mass, wing size, brain size, and eye size. I find that small stingless bee species are not limited in visual learning compared to larger species, and even have some energetic advantages in flight. These insights are essential to understanding how small size evolved repeatedly in all animal clades and why it persists. Finally, I test flight performance across stingless bee species while varying temperature in accordance with thermal changes that are predicted with climate change. I find that thermal performance curves varied greatly among species, that smaller species conform closely to air temperature, and that larger bees may be better equipped to cope with rising temperatures due to more frequent exposure to high temperatures. This information may help us predict whether small or large species might fare better in future thermal climate conditions, and which body-size related traits might be expected to evolve. / Dissertation/Thesis / Doctoral Dissertation Biology 2018

This study examined the validity of various scaling methods, isometric mid-thigh pull (IMTP) peak force using various scaling methods, and the relationships between IMTP peak force and countermovement jump height. Fifty-one collegiate baseball and soccer athletes performed two maximal IMTPs. Absolute peak force was compared between teams and when data were scaled using ratio (RS), traditional allometric (ALLOTrad), and fitted allometric (ALLOFit) scaling. ALLOTrad and ALLOFit validity was violated because different derived exponents existed for baseball (b = 0.20) and soccer (b = 1.20). Soccer athletes produced greater RS peak force compared to baseball (p = 0.012), while no difference existed with absolute, ALLOTrad or ALLOFit (all p > 0.05) peak force. Moderate relationships existed between body mass and absolute (r = 0.402, p = 0.003) and RS (r = -0.328, p = 0.019) peak force, while trivial relationships existed with ALLOTrad and ALLOFit (both r < -0.10, p > 0.05). Trivial relationships existed between countermovement jump height and absolute, RS, ALLOTrad, and ALLOFit (all r < 0.20, p > 0.05) peak force. The current dataset violated allometric scaling assumptions, making it inappropriate to use ALLOTrad and ALLOFit scaling. Practitioners must understand the assumptions, limitations, and purpose of scaling methods.

Alcohol expectancies have been shown to be predictive of risk for alcohol problems. Experimental research studies have challenged participants' expectancies with the end result demonstrating a mediational effect on participant drinking. Cognitive research using priming and word recognition tasks have led to the theory that expectancies operate in an associative network. Using dissimilarities information this network has been mapped using multidimensional scaling. The current techniques for collecting dissimilarities information directly in alcohol expectancy research has been limited to the use of the paired comparisons tasks. In order to investigate the utility of a different similarities task a comparison was made between a card sorting task and paired comparisons. The overall comparisons of matrices and Individual Difference Scaling (INDSCAL; Carroll & Chang, 1970) results followed the expected trends and generally supported the hypotheses that the two methods would provide essentially the same information. However, a possible method effect for gender was observed. The method effect was seen when comparing across methods within the females dichotomized by drinker category. Further studies are necessary to replicate these findings and to attempt to identify which method has the effect.

Title from PDF of title page. / Document formatted into pages; contains 64 pages. / Thesis (M.A.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Alcohol expectancies have been shown to be predictive of risk for alcohol problems. Experimental research studies have challenged participants' expectancies with the end result demonstrating a mediational effect on participant drinking. Cognitive research using priming and word recognition tasks have led to the theory that expectancies operate in an associative network. Using dissimilarities information this network has been mapped using multidimensional scaling. The current techniques for collecting dissimilarities information directly in alcohol expectancy research has been limited to the use of the paired comparisons tasks. In order to investigate the utility of a different similarities task a comparison was made between a card sorting task and paired comparisons. / ABSTRACT: The overall comparisons of matrices and Individual Difference Scaling (INDSCAL; Carroll & Chang, 1970) results followed the expected trends and generally supported the hypotheses that the two methods would provide essentially the same information. However, a possible method effect for gender was observed. The method effect was seen when comparing across methods within the females dichotomized by drinker category. Further studies are necessary to replicate these findings and to attempt to identify which method has the effect. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Branches of complexity theory have been widely employed in geographic information systems (GIS) to explore phenomena that appear in urban environments. Among these, space syntax, as an urban morphological application of complexity theory, has attracted increasing attention in recent years. Accordingly, many computer-based tools have been developed to realize related analysis spatially, especially those that can be integrated as functions with GIS. In this thesis, a space syntax tool – Axwoman – is redeveloped and tested as an extension of ESRI ArcGIS Desktop in order to fulfill certain specific needs in urban morphological analysis. It is primarily used to calculate all space syntax measures for several urban systems and to explore the relationships between these measures. To meet the needs for this new version of Axwoman, several functions have been updated and changed, for drawing, coloring, and classifying axial lines as maps for visual thinking; ticking overpasses and excluding them from computing space syntax parameters; and integrating AxialGen and Axwoman. In accordance with this, several case studies have been performed on the urban street networks in large cities. In this paper, Stockholm was chosen as the study object at both the urban level and the building level. After the scaling analysis and time efficiency analysis, the results are also interpreted from a structural point of view and in terms of how the function of space is subject to its morphological structure. Finally, the connectivity of axial lines (a spatial measurement in space syntax theory) was found to follow a power-law distribution. Through this work, the new edition of Axwoman generating satisfactory outputs, the research have proved that the connectivity of axial lines follows a lognormal distribution or a power-law-like distribution, which is one of the heavy-tailed distributions. In addition, it was have found that axial lines better for capture the underlying urban morphologies showed in their study on redefining the generated axial lines from street center lines. Moreover, fewer longest axial lines will show up on the maps, just as coincidental as the shape of mental maps, which proved that the axial line representations can be a powerful tool for urban studies.

In modern digital audio applications, a continuous audio signal stream is sampled at a fixed sampling rate, which is always greater than twice the highest frequency of the input signal, to prevent aliasing. A more energy efficient approach is to dynamically change the sampling rate based on the input signal. In the dynamic sampling rate technique, fewer samples are processed when there is little frequency content in the samples. The perceived quality of the signal is unchanged in this technique. Processing fewer samples involves less computation work; therefore processor speed and voltage can be reduced. This reduction in processor speed and voltage has been shown to reduce power consumption by up to 40% less than if the audio stream had been run at a fixed sampling rate.

Thesis (M.S.)--University of Michigan, 1966.