Developing and maintaining software is a difficult task, and finding effective methods of understanding software is more necessary now than ever with the last few decades seeing a dramatic climb in the scale of software. Appropriate visualisations may enable greater understanding of the datasets we deal with in software engineering. As an aid for sense-making, visualisation is widely used in daily life (through graphics such as weather maps and road signs), as well as in other research domains, and is thought to be exceedingly beneficial. Unfortunately, there has not been widespread use of the multitude of techniques which have proposed for the software engineering domain. Tag clouds are a simple, text-based visualisation commonly found on the internet. Typically, implementations of tag clouds have not included rich interactive features which are necessary for data exploration. In this thesis, I introduce design considerations and a task set for enabling interaction in a tag cloud visualisation system. These considerations are based on an analysis of challenges in visualising software engineering data, and the perceptive influences of visual properties available in tag clouds. The design and implementation of interactive system Taggle based on these considerations is also presented, along with its broad-based evaluation. Evaluation approaches were informed by a systematic mapping study of previous tag cloud evaluation, providing an overview of existing research in the domain. The design of Taggle was improved following a heuristic evaluation by domain experts. Subsequent evaluations were divided into two parts - experiments focused on the tag cloud visualisation technique itself, and a task-based approach focused on the whole interactive system. As evidenced in the series of evaluative studies, the enhanced tag cloud features incorporated into Taggle enabled faster visual search response time, and the system could be used with minimal training to discover relevant information about an unknown software engineering dataset.

Developing and maintaining software is a difficult task, and finding effective methods of understanding software is more necessary now than ever with the last few decades seeing a dramatic climb in the scale of software. Appropriate visualisations may enable greater understanding of the datasets we deal with in software engineering. As an aid for sense-making, visualisation is widely used in daily life (through graphics such as weather maps and road signs), as well as in other research domains, and is thought to be exceedingly beneficial. Unfortunately, there has not been widespread use of the multitude of techniques which have proposed for the software engineering domain. Tag clouds are a simple, text-based visualisation commonly found on the internet. Typically, implementations of tag clouds have not included rich interactive features which are necessary for data exploration. In this thesis, I introduce design considerations and a task set for enabling interaction in a tag cloud visualisation system. These considerations are based on an analysis of challenges in visualising software engineering data, and the perceptive influences of visual properties available in tag clouds. The design and implementation of interactive system Taggle based on these considerations is also presented, along with its broad-based evaluation. Evaluation approaches were informed by a systematic mapping study of previous tag cloud evaluation, providing an overview of existing research in the domain. The design of Taggle was improved following a heuristic evaluation by domain experts. Subsequent evaluations were divided into two parts - experiments focused on the tag cloud visualisation technique itself, and a task-based approach focused on the whole interactive system. As evidenced in the series of evaluative studies, the enhanced tag cloud features incorporated into Taggle enabled faster visual search response time, and the system could be used with minimal training to discover relevant information about an unknown software engineering dataset.

Over the past ten years, the development of High Throughput (HT) synthetic chemistry techniques has allowed the rapid preparation of libraries of hundreds to thousands of compounds. These tools are now extensively used for drug and material discovery programmes. The subsequent development of analytical capabilities to carry out qualitative and quantitative assessment of the compounds generated by HT synthesis as well as their HT screening has led to a dramatic broadening of the scope of HT techniques, ranging from image based analysis techniques to mass spectrometry (MS). Based on the latter, a range of solid phase and solution phase analytical constructs was developed to enable the qualitative and quantitative assessment of mixtures of small compounds, using positive electrospray MS as the sole analytical tool. A version of the construct allowed HT reactivity profiling to be carried out on a range of ten carboxylic acids, ten aldehydes and ten isonitriles in the Ugi 4-component condensation reaction. The effect of various parameters such as the concentration of the monomers on the reactivity was investigated. The elaboration of a HT Hammett parameter assessment method was made possible by the development of an electrophilic version of the construct. The value of the Hammett value was afforded by means of combinatorial Hammett plots and values were successfully evaluated in a HT mode for around thirty anilines with substituents in the meta and para position of the aromatic ring. Finally, analytical constructs were used in an attempt to evaluate enzyme reaction kinetics via the labelling of peptides and small drug fragment with coded constructs, to afford affinity determinations between the enzyme (protease) and peptidic or fragment based substrates.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Genetic code expansion allows the incorporation of non-canonical amino acids with a variety of new functional groups: fluorescent amino acids,1-3 azides,4-6 alkynes,5-10 and photocrosslinkers.4,11,12 This incorporation requires the evolution of new tRNA/aminoacyl tRNA sythetase pairs. Traditionally screenings of novel tRNA/aminoacyl tRNA synthetase pairs have been done in vivo. While these in vivo screenings have proven robust, they are limited in multiple ways: non-canonical amino acids (ncAAs) must be nontoxic and bioavailable. Furthermore, library size is limited by transformation efficiency. Lastly, in vivo screenings require substantial amounts of the target ncAA, which is often not available in large masses. In vitro screenings bypass these limitations: toxicity and bioavailibilty are no longer concerns. Library size can be expanded by several orders of magnitude as we are no longer limited by transformation efficiency. Lastly, because in vitro transcription/translation reactions are routinely conducted on the μL scale, ncAA usage can be minimized. We set out to use in vitro compartmentalization to further expand the code. In an in vitro compartmentalization screening, the water droplets in a water-in-oil emulsion serve as separate reaction chambers in which individual library members are transcribed and translated. Here we report optimization of S30 transcription/translation reactions. Optimizations include cell lysis method, reaction temperature, template amount, and T7 RNA polymerase amounts. Yields remained low and we transistioned into the use of PURExpress. Fluorohistidines are isosteric with histidine, but not isoelectronic.13 This change in environment results in a reduction of pKa. We set out to synthesize 4-fluorohistidine to use as a pH probe in several target proteins. A synthesis of 4-fluorohistidine was published in 1973.14,15 We were able to improve upon this synthesis by reducing cost and improving yield of a key step in the reaction. Next, small peptides with polyhistidine tags were translated in vitro using our 4-fluorohistidine. We are calling this polyhistidine tag incorporating 4-fluorohistidine our “hexafluorohistag.” Because of the reduced pKa of the 4-fluorohistidine, the hexafluorohistag showed affinity to Nickel-NTA resin even at reduced pH. This allowed for the purification of hexafluorohistagged peptides in the presence of traditional polyhistidine-tagged peptides.

Title: Joining segments in Czech sentences Author: Bc. Josef Čech Department: Institute of Formal and Applied Linguistics Supervisor: doc. RNDr. Vladislav Kuboň Ph.D. e-mail: vk@ufal.mff.cuni.cz Abstract: This thesis follows up segmentation of complex sentences to linguistic motivated objects - segments - and their mutual relations. These relations can be used for next work with segments. Main purpose for mapping relations is their joining into next level unit - clause. Theoretically should be possible to analyse each clause of complex sentence separately. Analysis of set of clauses should be quicker than of analysis whole complex sentence. Segments should be found thanks to linguistic separators and rule approach. Rule approach proves in problem relations between neighbouring segments. This thesis should attest that rule approach is best solution for joining segments into clauses. Position tag of segment was part of this thesis. This tag should be used in methods dealing with segments instead of custom segment. Keyword: segment, clause, tag, joining segments, syntactic analysis

Title: Joining segments in Czech sentences Author: Bc. Josef Čech Department: Institute of Formal and Applied Linguistics Supervisor: doc. RNDr. Vladislav Kuboň Ph.D. e-mail: vk@ufal.mff.cuni.cz Abstract: This thesis follows up segmentation of complex sentences to linguistic motivated objects - segments - and their mutual relations. These relations can be used for next work with segments. Main purpose for mapping relations is their joining into next level unit - clause. Theoretically should be possible to analyze each clause of complex sentence separately. Analysis of set of clauses should be quicker than of analysis whole complex sentence. Segments should be found thanks to linguistic separators and rule approach. Rule approach prove in problem relations between neighbouring segments. This thesis should attest that rule approach is best solution for joining segments into clauses. Position tag of segment was part of this thesis. This tag should be used in metods dealing with segments instead of custom segment. Keyword: segment, clause, tag, joinig segments, syntactic analysis

Doctor of Philosophy / Biochemistry and Molecular Biophysics / Timothy P. Durrett / The membrane bound O-acyltransferase (MBOAT) family contains multi-pass membrane proteins that add fatty acids to different compounds. Despite their importance in economic activity and human health, little is known about the localization of the active site and regions important for determining substrate specificity of MBOATs. Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) is the only known MBOAT enzyme that exhibits a high preference for acetyl-CoA, the shortest possible acyl-CoA. EaDAcT catalyzes the transfer of the acetate group from acetyl-CoA to the sn-3 position of diacylglycerol to form 3-acetyl-1,2-diacyl-sn-glycerol. Our goal was to investigate the structural features and the amino acid residues that define substrate specificity of EaDAcT to provide insights into the mechanism by which MBOAT family controls substrate selection. By mapping the membrane topology of EaDAcT we obtained the first experimentally determined topology model for a plant MBOAT. The EaDAcT model contains four transmembrane domains with both the N- and C- termini oriented toward the endoplasmic reticulum lumen. The MBOAT signature region including the putative active site His-257 of the protein is embedded in the third transmembrane domain close to the interface between the membrane and the cytoplasm. In order to identify amino acid residues important for acetyltransferase activity, we isolated and characterized orthologs of EaDAcT from other acetyl-TAG producing plants. Among them, the acetyltransferase from Euonymus fortunei possessed the highest activity in vivo and in vitro. Mutagenesis of conserved residues of DAcTs revealed that Ser-253, His-257 and Asp-258 are essential for enzyme activity of EaDAcT, suggesting their involvement in the enzyme catalysis. Alteration of residues unique to acetyltransferases did not alter the acyl donor specificity of EaDAcT, implying that multiple amino acids are important for substrate recognition. Together, this work identifies the structural features of EaDAcT and offers an initial view of the amino acids important for activity of the enzyme.

Master of Science / Department of Computing and Information Sciences / Doina Caragea / Over the last decade, the Internet has become an involving medium and user-generated content is continuously growing. Recommender systems that exploit user feedback are widely used in e-commerce and quite necessary for business enhancement. To make use of such user feedback, we propose a new content/collaborative hybrid approach, which is built on top of the recently released hetrec2011-movielens-2k dataset and is an extension of a previously proposed approach, called Weighted Tag Recommender (WTR). The WTR approach makes use of tag information available in hetrec2011-movielens-2k, but it does not use explicit ratings. As opposed to WTR, our modified approach can make use of ratings to capture collaborative filtering and either user-tags, available in the hetrec2011-movielens-2k, or movie keywords retrieved from IMDB, to capture movie content information. We call the two versions of our approach Weighted Tag Rating Recommender (WTRR) and Weighted Keyword Rating Recommender (WKRR), respectively. Movie keywords (which are not user specific) allow us to use all ratings available in hetrec2011-movielens-2k, as WKKR associates the content information from movies with the users, based on their ratings. On the other hand, tags provide more specific information for a user, but limit the usage of the data to the user-movie pairs that have tags (significantly smaller number compared with all pairs that have ratings). Both our keyword and tag representations of users can help alleviate the noise and semantic ambiguity problems inherent in information contributed by users of social networks. Experiments using the WTRR approach on a subset of the dataset (which contains both ratings and tags) show that it slightly outperforms the WKRR approach. However, WKRR can be applied to the whole hetrec2011-movielens-2k dataset and results show that the information from keywords can help build a movie recommender system competitive with other neighborhood based approaches and even with more sophisticated state-of-the-art approaches.

Anti-malware companies analyze large number of files every day. In order to speed up their analysis, many automatized tools were implemented. Detection definitions that detect malicious software are often generated automatically. Information about currently spreading malware is scattered across several tools and they are sometimes too generic. This work proposes a new tool that will aggregate, prioritize, and evaluate all the available information. Due to large amount of incoming data, high performance and scalability of the system is necessary. Files, detection definitions, and other objects will be tagged using the given information directly or inferred. Collected information will be accessible via interface for further analysis and statistics. Everything was implemented, tested and put into production.