published_or_final_version / Industrial Engineering / Master / Master of Science in Engineering

<p>Advances in sequencing technologies constantly improves the throughput andaccuracy of sequencing instruments. Together with this development comes newdemands and opportunities to fully take advantage of the massive amounts of dataproduced within a sequence run. One way of doing this is by analyzing a large set ofsamples in parallel by pooling them together prior to sequencing and associating thereads to the corresponding samples using DNA sequence tags. Amplicon sequencingis a common application for this technique, enabling ultra deep sequencing andidentification of rare allelic variants. However, a common problem for ampliconsequencing projects is formation of unspecific PCR products and primer dimersoccupying large portions of the data sets.</p><p>This thesis is based on two papers exploring these new kinds of possibilities andissues. In the first paper, a method for including thousands of samples in the samesequencing run without dramatically increasing the cost or sample handlingcomplexity is presented. The second paper presents how the amount of high qualitydata from an amplicon sequencing run can be maximized.</p><p>The findings from the first paper shows that a two-tagging system, where the first tagis introduced by PCR and the second tag is introduced by ligation, can be used foreffectively sequence a cohort of 3500 samples using the 454 GS FLX Titaniumchemistry. The tagging procedure allows for simple and easy scalable samplehandling during sequence library preparation. The first PCR introduced tags, that arepresent in both ends of the fragments, enables detection of chimeric formation andhence, avoiding false typing in the data set.</p><p>In the second paper, a FACS-machine is used to sort and enrich target DNA covered emPCR beads. This is facilitated by tagging quality beads using hybridization of afluorescently labeled target specific DNA probe prior to sorting. The system wasevaluated by sequencing two amplicon libraries, one FACS sorted and one standardenriched, on the 454 showing a three-fold increase of quality data obtained.</p> / QC20100907

Job redesign could significantly impact the efficiency was obtained. This survey was comprised of nineteen scales with of the organization. The purpose of this descriptive, comparative study was to describe and compare job characteristics, general job satisfaction, and motivation potential of the job in order to diagnose the job profile of registered nurses, licensed practical nurses, and nursing assistants.The convenience sample consisted of all staff nurses, licensed practical nurses, and nursing assistants working at a 515 bed Department of Veterans Affairs Medical Center in the midwest who voluntarily agreed to complete the Job Diagnostic Survey. A response rate of 36.8% (n = 118) to measure the degree of job characteristics, motivating potential of the job, psychological states, growth need strength, general job satisfaction, and satisfaction context factors present in the current job.Mean scores were computed to measure each variable. All means for each job category were found to be over the midpoint (3.5). Growth need strength was significantly lower than the normative data for RN's and LPN's. Task identity and experienced responsibility for work outcomes were significantly lower than the norm for LPN's assigned to the acute medical area. Motivating potential was significantly lower for nursing assistants assigned to the acute medical and the long term psychiatric area.Adjusting staff assignments to encourage continuity and observation of patient outcomes, and providing direct feedback regarding performance to staff members from nurse managers were implications. Implications include combining tasks to provide a more identifiable job and enable the worker to visualize patient outcomes to a greater degree. Recommendations included further research utilizing the JDS, including comparison of various types of nurse jobs. Statistical analysis in future studies should include comparisons of these different groups. / School of Nursing

Gene set enrichment analysis aims to discover sets of genes, such as biological pathways or protein complexes, which may show moderate but coordinated differentiation across experimental conditions. The existing gene set enrichment approaches utilize single gene statistic as a measure of differentiation for individual genes. These approaches do not utilize any inter-gene correlations, but it has been known that genes in a pathway often interact with each other. Motivated by the need for taking gene dependence into account, we propose a novel gene set enrichment algorithm, where the gene-gene correlation is addressed via a gene-pair representation strategy. Relying on an appropriately defined gene pair statistic, the gene set statistic is formulated using a competitive null hypothesis. Extensive simulation studies show that our proposed approach can correctly control the type I error (false positive rate), and retain good statistical power for detecting true differential expression. The new method is also applied to analyze several gene expression datasets. / October 2016

Challenges encountered in pathogen identification and detection include the genetic heterogeneity of strains within species of some foodborne pathogens, isolation of injured cells, mixed strains or mixed species contamination of foods, and differentiation between viable and dead cells. The first objective of this research was to evaluate an isolation medium that was based on time-delayed release (5 to 6 h) of selective agents in tablet format to a modified Listeria recovery enrichment broth (mLRB) medium for enhanced and rapid recovery of injured Listeria. The second objective involved the use of Fourier transform infrared (FT-IR) spectroscopy and chemometric analysis for the differentiation of: Listeria monocytogenes epidemic clones (ECs); viable versus heat-killed populations; different mixed strains and mixed species of Listeria; and different injury treatments and repair in Listeria populations. Nitrite- or acid-injured Listeria at approximately 10 CFU/ml were recovered in mLRB medium, and cell populations enumerated at various times (12 to 48 h) of incubation at 37oC. Analysis of variance revealed that acid-injured Listeria populations in mLRBS6 (mLRB plus the selective agents at 6 h) were significantly higher (P < 0.05) than those in mLRBS0 (mLRB plus the selective agents at 0 h) at 24 h; however, the differences in populations on these two media were not significant for nitrite-injured Listeria. Cell populations of four strains of Listeria recovered in mLRBTD (mLRB plus the time-delayed release tablets of the selective agents) were significantly higher than when those strains were enriched in the U.S. Food and Drug Administration (FDA), International Organization for Standardization (ISO), and U.S. Department of Agriculture (USDA) broths at 24 h. Comparison between artificially contaminated milk and meat samples with a four-strain cocktail of Listeria resulted in cell populations that were significantly higher (P < 0.05) on mLRBTD for contaminated meat than on mLRBTD for contaminated milk at 24 h. FT-IR spectroscopy in the mid-infrared region (4000 to 600 cm-1) and chemometrics was successfully applied to discriminate L. monocytogenes strains belonging to the same EC (ECII or ECIV) (100% accurate spectral classification), intact and heat-killed populations of each EC strain (100% accurate spectral classification), and spectral wavenumbers 1650 to 1390 cm-1 were used to differentiate heat-killed from intact populations. FT-IR spectroscopy and chemometrics in the wavelength region 1800 to 900 cm-1 could successfully discriminate different mixed strains of L. monocytogenes (98.15% accurate spectral classification) and different mixed species of L. monocytogenes and L. innocua (92.06% accurate spectral classification) from individual strains; Wavelength range 1800 to 900 cm-1 was successfully used to discriminate between intact, acid-injured, and heat-injured Listeria, with repaired cells from acid and heat treatments clustering closer to intact cells (93.33% of spectra accurately classified). Delayed-addition of selective agents to broth medium improves recovery of injured Listeria by allowing repair time, could minimize contamination through manual addition of selective agents, and saves analyst time; FT-IR spectroscopy is a highly discriminatory and reproducible technique that can be used for the differentiation of strains and various physiological states of Listeria.

Unjustified Enrichment in Business Law Abstract The aim of my thesis is to analyse the concept of unjustified enrichment in connection with the commercial law. In fact this topic is usually described in the civil law studies and at the same time the unjustified enrichment is minor topic compared to the obligations arising from the contracts. This is the reason why I have chosen this issue describe and focus on the business aspects. The thesis is composed of seven chapters. Chapter one as an introduction defines basic legislation acts, which I am dealing with throughout the thesis and roughly describes there are changes in connection with the extensive recodification of the Czech private law. Chapter two is subdivided into two parts. Part one focuses on the origin of the unjustified enrichment in Ancient Rome as the base for the civil law. Part two provides an outline of past legislation within the territory of the Czech Republic until its establishment. Chapter three concentrates on the legislation effective until 31 December 2013. It illustrates the approach to decision-making by the Supreme Court including the decision-making in connection with the limitation of rights according to Commercial Code. Chapter four analyses the changes after New Civil Code came into force in relation to commercial law. Here...

The thesis is focused on the legal concept of unjust enrichment specifically in relation to the area of business law. Although the basic legal regulation relevant also for the area of business law was, and even after the adoption of the new private law codes, still remains in the civil code, the thesis endeavors to focus on certain specifics related particularly to the business relations. For these purposes it deals, in less or more detailed manner, also with other legal concepts, which are significant for the topic and closely related (such as limitation of claims resulting from the unjust enrichment, good faith of legal entities, invalidity of legal acts etc.). The thesis analyses legal acts regulating the institution of unjust enrichment for the area of private law, eventually specifically for the business relations. Especially in the areas where the legal text itself is not exhaustive, it supplies also analysis of relatively extensive case law (available so far only in respect of the previous legislation), eventually also the analysis of expert opinions. It draws attention to certain conflicts in interpretation of individual legal provisions. Considering the recent essential change of the private law basis (new private law codes) the thesis provides to a considerable extent comparison of the...

1 ABSTRACT UNJUST ENRICHMENT UNDER ENGLISH AND CZECH LAW The topic of presented thesis is "Unjust Enrichment under English and Czech Law". It aims to provide a comprehensive analysis and comparison of legal rules governing unjust enrichment in English and Czech law. The thesis is systematically divided into four principal chapters which are further subdivided. The first chapter presents an introduction to unjust enrichment. It provides a brief historical overview and a description of legal nature of unjust enrichment. It also aims to bring a basic comparison of the common law system and the civil law system to which English law and Czech law belong. Unjust enrichment on the European level is analysed in the second chapter. Two chosen soft law instruments of the European private law are presented here, namely Draft Common Frame of Reference and Principles of European Law of Unjust Enrichment, which set forth non-binding rules for the functioning of unjust enrichment. The third chapter is focused on the English law of unjust enrichment. It primarily brings the analysis of the requirements of unjust enrichment under English law. These requirements, which are based on the case law of the English courts, are as follows: (1) benefit, (2) at the claimant's expense, (3) unjust factor, and (4) lack of defence....

The paper is titled: Phraseology updates in the contemporary Czech language The aim of this paper is to collect and describe phraseological updates. The collection of materials (resources) took place from January 2013 to June 2015. Updates were sought out from various sources - the media, books, the theater, the internet and landline calls. With the help of professional literature we first limited the theoretical framework of the issue and based on these theoretical attainments we classified the material according to the sources and types of resources from which it originated. In the summary of updates we can see for every idiom update its original version, its type of update, its specific description and its source with a comment specifying its occurrence etc. With the performed analysis we determined that the most common kinds of updates are contamination and lexical updates.

1 Abstract This thesis deals with the institute of unjust enrichment extending to commercial law. It is focused on specific aspects of existence of this institute in commercial law. Particularly it means an issue of the limitation of unjust enrichment claims in business relationships as well as other special elements of unjust enrichment in commercial law regulations such as the question of repayment of the performance caused by the withdrawal, the protection of the company name claims and protection against unfair competition, rights of industrial property and bill of exchange and cheques enrichment. Although the work is primarily based on existing legislation, it is not limited to the examination of the issue from the perspective of re-codification of private law. The thesis analyzes the various provisions of the relevant commercial law regulations whose interpretation is in theory and practice greatly divided, and with their detailed analysis using initially established theoretical basis, trying to make their own suggestions.