published_or_final_version / Mechanical Engineering / Master / Master of Philosophy

Graduate

Pathology congruent information-processing biases, the tendency for the information processing system to consistently favour materials whose content corresponds to the pathology’s symptoms and concerns, had been found to be implicated in the aetiology and maintenance of multiple clinical disorders, with ample research established in emotional disorders. Relatively, little work had been done on psychosis, in which research to date on biased interpretation mainly focused on interpretation of auditory hallucinations and the associated distress. The aim of the current study was to evaluate the effects of pathology congruent interpretation bias in paranoia on the prediction of psychosis proneness, the subclinical manifestation of psychosis phenotypes. Cross-sectional data on biased information processing and psychosis proneness were collected from 154 individuals recruited in the normal population via cognitive and self-report measures. A series of hierarchical regression analyses were performed and results suggest that negative information processing bias significantly contributes to the prediction of psychosis proneness. There is also evidence that interpretation bias plays a mediating role in the prediction of psychosis proneness only when the direction of bias was congruent to the pathology’s symptoms and concerns. The discerned mediating role of pathology congruent interpretation bias contributes to the understanding of the mechanisms underlying psychosis proneness. Its clinical implications in terms early identification and target for intervention are further discussed. / published_or_final_version / Clinical Psychology / Master / Master of Social Sciences

The establishment of copyright protection systems aims to achieve two important purposes; to stimulate the incentive for creation by granting authors a series of exclusive rights on the one hand, and promote the progress of culture and public welfare by establishing a series of limitations on these exclusive rights so that the flow of information and dissemination of knowledge will not be hindered on the other hand. There is always a close relationship between technology development and copyright law. The emergence of personal computers and the internet has brought about a distinct wave of technological innovation that has reshaped copyright laws by empowering anyone with a connection to flawless, inexpensive and instantaneous reproduction and distribution of works of authorship. Such technological advancement changes the interests of copyright owners and public users. Users are exposed to more opportunities brought about by digital network technology to obtain access and exploit copyrightable works. If copyright laws do not expand their protected subject matters and categories of exclusive rights, authors cannot be adequately compensated under the digital network environment. Copyright laws can no longer function as an incentive for creation if there is a lack of revision and appropriate expansion. Hence, copyright laws need to extend protection to new subject matters, such as computer programs and databases; grant right holders new kinds of rights, such as right of rental and right to network dissemination of information; establish indirect infringing liability for internet service providers; and expand protection to technological measures. However, copyright expansion should not be unlimited and should cease when appropriate access to various works and future creations is at risk. Expansion of copyright protection is only justified when the access and use of works by the public threaten the incentive of authors to create and reap economic rewards. Overexpansion of copyright protection would again disrupt the balance if access to works is narrowly restricted. Overprotection of copyrights will not only obstruct access to original works, but will also inhibit future creations based on the original works. Based on comparative research on international and regional conventions as well as laws, regulations, policies and cases among different jurisdictions, this thesis intends to suggest proposals to recover the balance of interests among copyright holders, technological intermediaries and public users in terms of accessing, distributing and exploiting copyrighted works. Four specific issues are discussed in the thesis: the anti-circumvention rules for protection of technological measures; indirect infringing liability for internet service providers and safe harbor regulations; copyright limitations and exceptions especially under the digital network environment; and digital commons projects which promote distribution and adaptation of copyrighted works placed under voluntary licensing schemes. The analysis of these issues and corresponding proposals for reform are not only to reverse the worldwide copyright expansion trend so as to make copyright laws appropriately respond to digital network challenges and the emerging remix culture in general, but also to induce China to rethink and amend her copyright system so as to restore a robust public domain where existing information and data can be used to produce future intellectual assets. / published_or_final_version / Law / Doctoral / Doctor of Philosophy

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

abstract / Computer Science / Doctoral / Doctor of Philosophy

abstract / Electrical and Electronic Engineering / Doctoral / Doctor of Philosophy

This study was undertaken to determine the sensory differences in high pressure vs. heat processed food systems after storage at ambient and refrigerated temperatures as determined by a trained sensory panel. Spanish rice and spaghetti with meat sauce were prepared and treated with heat and with high pressure processing (HHP). A citrus fruit mix consisting of pieces of orange, grapefruit, and pineapple was processed by mild heat and HHP, and heat alone. One day after processing, treated products were tested along with untreated controls. Products were stored at either 22°C or 3°C, and tested at 10, 30, 60, 90, and 120 days. Sensory testing was done by a panel trained in a QDA-type method, and data was analyzed by univariate and multivariate methods. For spaghetti with meat sauce, significant differences (p>0.05) were found between processing methods stored at the same temperature in appearance and texture attributes, with the high pressure processed samples closer to unstored product than those treated by heat. Differences in treatments first appeared in 'dry appearance' at 10 days, and by 120 days there were differences in 'tomato integrity', 'pasta integrity', 'brightness of color', and 'firmness of pasta' as well. Most of these differences were due to the stickiness caused by the extra amylose leaking out of the heat treated pasta over time. For Spanish rice, there were no statistically significant differences between samples processed by the two methods and stored at the same temperature. The Spanish rice was formulated with parboiled rice, which allows very little amylose leakage, so it did not show amylose-related effects as the spaghetti with meat sauce did. The fruit mix processed with HPP and mild heat had significantly higher ratings in appearance attributes 'brightness of color' and piece integrity', and lower ratings in 'cooked' descriptors than product treated with heat alone stored at the same temperature. / Graduation date: 2000

The objective of these studies was to develop an analog from surimi that would resemble abalone. Preliminary studies involved the standardization of batter preparation conditions, such as pH adjustment, optimum moisture content and batter mixing time. The texture of a gelled analog prepared with different protein adjuncts egg white, gluten and bovine serum albumin) was compared with cooked abalone for hardness, elasticity, and cohesiveness by a trained sensory evaluation panel and by instrumental methods. Serial levels of sodium carbonate were used to adjust the pH of the sol from pH 6.75 to 7.73. As the pH value rose, the textural strength of kamaboko correspondingly increased. The 0.1% level of sodium carbonate was determined suitable for further use. The moisture level in kamaboko caused significant variations in hardness (P<0.001) and cohesiveness (P<0.001). At the lowest level of moisture tested, 73.24%, gel hardness was greatest (l27N/g); with a 5% increase in moisture, the gel hardness was lower (52N/g). Sol mixing time (solubilization of myofibrillar proteins) was a very important factor to significantly affect gel texture for properties of hardness (P<0.00l), elasticity (P=0.002) and cohesiveness (P<0.001). To produce a strong, elastic and cohesive gel, 30 minutes mixing was required. In serial concentrations (O to 4%), egg white, gluten, and bovine serum albumin, were evaluated for enhancement of textural parameters in order to produce an imitation abalone product. The addition of either egg white or gluten at the two percent level resulted in the greatest hardness and most cohesive gels (P<0.001). Two percent added bovine serum albumin significantly improved gel hardness and elasticity (P=0.003 and P=0.0149, respectively). A shredded gel containing one of three protein adjuncts was effective in varying the final gel texture when incorporated with a surimi-based carrier. In overall parameters, the trained sensory evaluation panel judged the analog gel containing bovine serum albumin texturized chunks (at a 70:30 ratio to carrier) closest to cooked abalone. The instrumental measurements of textural parameters were slightly less discriminating than the trained sensory panel. / Graduation date: 1989

The influence of protein adjuncts and variations in pH on the cook-cool loss, moisture content, and texture of squid gels was investigated. Break force (P [greater than or equal to] .025), deformation to break (P [greater than or equal to] .01) and cook-cool loss (P [greater than or equal to] .001) decreased as the pH of squid gels was adjusted from 6.4 to 8.3 with sodium carbonate. The moisture content of gels increased (P [greater than or equal to] .01) as the pH was elevated. Break force (P [greater than or equal to] .001) and deformation distance to break (P [greater than or equal to] .005) were inversely correlated to gel moisture content. Protein adjuncts (2%) had a significant effect on cook-cool loss, break force and moisture content (P [greater than or equal to] .001, .026, and .018, respectively) of squid gels. Egg white produced an improved water-holding capacity over soy protein isolate and sodium caseinate. The mean cook-cool loss from gels containing egg white was 5.29 + 0.66% which was significantly (P=.05) lower than that of gels containing soy protein isolate (12.41 + 0.17%), no protein adjunct (16.65 + 3.82%) and sodium caseinate (19.75 + 2.42%). Gels containing sodium caseinate had a significantly (p [greater than or equal to] .05) lower moisture content and higher cook-cool loss (P=.05) than gels containing egg white or soy protein isolate. The break force of gels containing sodium caseinate could not be measured because the gels possessed little fracturability when compressed. The break-force of gels containing soy protein isolate or egg white were equal (P=.05), but each was less (P=.05) than observed for control gels. Holding minced squid gel sols at 4°C for 4 and 24 hours before forming and heat-setting into gels, had a significant effect on the force required to break gels (P [greater than or equal to] .001) and expressible moisture (P [greater than or equal to] .006). Control squid gels and gels containing soy protein isolate that were formed after holding for 24 hours required a lower force (P=.05) to break gels than similar gels formed after holding for 4 hours. Holding time did not alter (P [greater than or equal to] .05) moisture content, cook-cool loss or deformation at break. Reduced gel strengths observed for gels held for 24 hours prior to heat-setting was related to protease activity, loss of reactive sulfhydryl functions and/or cold temperature setting. A restructured seafood product was fabricated from mantle and tentacle muscle of squid (Loligo opalescens). Whole squid yielded 37.5 + 1.4% edible mantle and 15.3 + 1.0% tentacle meat; a total yield of 52.2 + 2.4% based upon round weight. A restructured product fabricated from heat-set fibers (60%) and squid sol (40%) yielded 33.4 + 1.0% based upon round weight. A consumer preference panel found no (P [less than or equal to] .05) differences in the product containing different protein adjuncts and judged the product to be, at least, slightly desirable (score of 6.0 on a 9 point scale). Firmness was the only sensory attribute that a trained panel found to be influenced (P [greater than or equal to] .05) by the incorporation of protein adjuncts. The product containing sodium caseinate was judged to be less firm (P=.05) than products incorporating either egg white or soy protein isolate. Trained panel scores for firmness were consistent with measurements for break force. / Graduation date: 1988