The International Linear Collider (ILC) aims to collide electrons and positrons with a centre of mass energy of 500GeV and a luminosity of 2×10³⁴ cm⁻² s⁻¹. To achieve this luminosity, the nominal final emittance of the electron and positron beams have to be below 10μm.rad horizontally and 0.04μm.rad vertically. To prevent the emittance from becoming too large, the main linacs will require alignment at an unprecedented level. The ILC main linacs will be aligned with respect to a reference network which runs along the entire length of the tunnel. The Linear Collider Alignment and Survey (LiCAS) Rapid Tunnel Reference Surveyor (RTRS) is the prototype of a device proposed to survey the ILC reference network. The LiCAS RTRS has several measurement systems; its Frequency Scanning Interferometry (FSI) measurement system is studied in this thesis. The FSI system has three distinct sub-systems: the reference interferometers, the external FSI measurement system and the internal FSI measurement system. The errors on the length of the reference interferometers are shown to be of the order of 1.1μm (0.3ppm). The external FSI measurement system is shown to measure distances close to 0.42m with errors of ±1.9μm stat ±0.16μm syst and the internal FSI measurement system is shown to measure distances close to 4.2m with errors of ±0.24μm stat ±1.6μm syst. A survey of the ILC reference network using laser trackers is simulated without taking account of systematic measurement errors from refraction in the tunnel air. The simulated networks are used to misalign the simulated accelerators in Dispersion Matched Steering (DMS) simulations. The DMS simulations show that only 30% of the simulated accelerators produce an acceptable final corrected vertical emittance. It is further shown that the introduction of long range distance measurements between primary reference markers (PRMs) using GPS, reduces the long range error growth in the network, and that 95% of simulated accelerators give acceptable performance. A simplified network simulation model, which is capable of simulating reference networks surveyed by conventional and novel devices, is produced and compares favorably to full simulations.

The present research sought to expand upon previous research demonstrating that individuals shift their attitudes to match the attitudes of their romantic partner. This research examined whether attitude alignment is influenced, in part, by belonging threats. Participants reported their attitudes about social issues and were randomly assigned to receive a belonging threat (or acceptance) in the form of feedback about their future relationships prior to discussing issues about which they disagreed with their partner. Partners discussed issues that were central to self - peripheral to partner and peripheral to self - central to partner. Attitude alignment was measured following discussion and at a one-week follow-up. Attitude alignment was expected to vary as a function of belonging threat, centrality of issue, and strength of unit relationship. Results did not support hypotheses, but did reveal noteworthy points to be considered for future work in this area.

Thesis advisor: Peter Clote / RNA molecules play important roles in living organisms, such as protein translation, gene regulation, and RNA processing. It is known that RNA secondary structure is a scaffold for tertiary structure leading to extensive amount of interest in RNA secondary structure. This thesis is primarily focused on the development of novel algorithms for the analysis of RNA secondary structure evolution and folding kinetics. We describe a software RNAsampleCDS to generate mRNA sequences coding user-specified peptides overlapping in up to six open reading frames. Sampled mRNAs are then analyzed with other tools to provide an estimate of their secondary structure properties. We investigate homology of RNAs with respect to both sequence and secondary structure information as well. RNAmountAlign an efficient software package for multiple global, local, and semiglobal alignment of RNAs using a weighted combination of sequence and structural similarity with statistical support is presented. Furthermore, we approach RNA folding kinetics from a novel network perspective, presenting algorithms for the shortest path and expected degree of nodes in the network of all secondary structures of an RNA. In these algorithms we consider move set MS2 , allowing addition, removal and shift of base pairs used by several widely-used RNA secondary structure folding kinetics software that implement Gillespie’s algorithm. We describe MS2distance software to compute the shortest MS2 folding trajectory between any two given RNA secondary structures. Moreover, RNAdegree software implements the first algorithm to efficiently compute the expected degree of an RNA MS2 network of secondary structures. The source code for all the software and webservers for RNAmountAlign, MS2distance, and RNAdegree are publicly available at http://bioinformatics.bc.edu/clotelab/. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Title: Multiple sequence alignment using genetic algorithms Author: Zdeněk Pátek Department: Department of Software and Computer Science Education Supervisor: RNDr. František Mráz, CSc. Abstract: The thesis adresses the problem of multiple sequence alignment (MSA). It contains the specication of the proposed method MSAMS that allows to find motifs in biological sequences, to split sequences to blocks using the motifs, to solve MSA on the blocks and nally to assemble the global alignment from the aligned blocks and motifs. Motif search and MSA are both solved using genetic algorithms. The thesis describes the implementation of the method, conguration of its settings, benchmarking on the BAliBASE database and comparison to the ClustalW program. Experimental results showed that MSAMS can discover better alignments than ClustalW. Keywords: multiple sequence alignment, motif nding, genetic algorithms, ClustalW

One of the cultural traditions in Saudi Arabia is that the Saudi female patient has to be accompanied by a third-party on her medical visits, thus giving rise to consultations between three parties. By third-party, I mean a chaperone or a family member who can be a patient’s spouse, parent, adult child, sibling, or relative. This person shares responsibility for the patient’s health and the patient relies on them to support them generally with assistance in terms of their health care needs and especially for medical visits. In this research, I focus on the presence of a third party in medical consultations with reference to patient satisfaction, how patients perceive the role of their chaperones during the medical visit and the nature of three-party medical interactions. To investigate these aspects, a convergent parallel mixed method design was used in order to develop a better understanding of doctor-patient-three party interactions, as no mixed method study has been conducted on these issues in medical consultations in Saudi Arabia. Hence, this study addresses this gap in literature by focusing on the interaction between the Saudi female patients, their male physicians and their chaperones. I have concentrated on the Saudi female patients (from different age groups, i.e. 19-75) for religious and cultural reasons. Therefore, the overall aim of this thesis is to understand the phenomenon of three-party consultations in Saudi Arabia through a variety of aspects including patient satisfaction, patients’ perceptions, and what actually happens in three-party medical interactions (e.g., alignment and epistemic asymmetry). The data for this study included quantitative (i.e. questionnaires) and qualitative (i.e. four open-ended questions and observational and audio-recorded) data collected in one phase from 20 clinics in 3 hospitals in Jeddah in Saudi Arabia (two private and one governmental). A total of 117 female patients along with their chaperones were recruited. Statistical analysis of the questionnaire ratings showed that only patient’s education has a positive effect on patient satisfaction with chaperone involvement. Findings from thematic analysis of the open-ended questions data revealed that patients described three supportive roles of the chaperones, namely emotional, informational and logistical support. The patients’ perceptions regarding their chaperones’ supportive roles are re-evaluated in a real-life context by observing the chaperone’s facilitative role in three-party consultations. Therefore, conversation analysis of the audio-recorded data showed three main patterns of alignment: (1) doctor-patient, (2) chaperone-patient (and patient-chaperone), and (3) chaperone-doctor (and chaperone-patient) alignments. All these actions indicate that the participants were collaboratively involved in the positive interaction and this enhanced patient participation. However, in analysing three exceptional cases from the Chemotherapy and Haematology clinics, it was found that the presence of a chaperone dominates as well as complicates doctor-patient interaction and thus can significantly override or ostracise the patient who does not know her illness. For example, by using the Conversation Analysis approach, various epistemic resources used by the interlocutors (i.e. the oncologist and chaperones) are displayed by which the patient’s epistemic primacy is usurped and her epistemic access is controlled in terms of participation and the amount of information given. In comparing the mixed methods used in this study, congruent and discrepant results are found between the quantitative and qualitative data. In terms of congruent results, overall, the findings of this study concurred on the importance of having a supportive chaperone during a female patient’s medical appointment. Chaperones’ supportive roles appear to differently influence female patients’ symptoms, diagnosis or treatment plan. Chaperones in the current study have provided a useful contribution to the doctor-patient interactions. However, in terms of discrepancy, findings yielded by the conversation analysis (in Chapters 6 and 7) showed a discrepancy between what patients reported (see Chapter 5) about their chaperones’ supportive roles and what their chaperones did in the consultation. For example, the thematic analysis of the open-ended questions found that both genders were equally likely to be active in speaking for the patient. However, the conversation analysis of observational data adds and clarifies to what patients reported about their chaperones speaking on their behalf. The conversation analysis has given a good picture of the chaperone’s supportive role during medical visits in orienting towards patients as being the actual owners of their bodies and illness (see Chapter 6). Therefore, patients were given the chance to present their problem. Chaperones, in working collaboratively with patients and physicians, support the patient and facilitate the physician’s understanding. However, in only two exceptional cases (see Chapter 7) of actual medical interactions, the chaperone acts as a surrogate patient and restricts the patient’s own knowledge of their illness. Therefore, the current study contributes to three important areas, namely: (1) the literature of three-party interactions, (2) three-party interactions in Saudi Arabia, and (3) clinical practices in Saudi Arabia.

Situation faced: Raiffeisen Bank Kosovo, as a subsidiary of Raiffeisen BankInternational AG, providesa wide range of banking products and services to all categories of customers in the private individual and business segments. In the first six months of 2018, the profit of the Bank was 11 Million Euro, being the highest in the banking market. The on-line banking channels has increased significantly and today the customers chose to do more than 80% of transactions through E-Banking, mobile phone,or ATMs. Raiffeisen Bank has started to adopt BPM since 2006 as a systemic and structured approach to analyze, improve, control, and manage processes with the aim to improve the quality of products and services. But, how well is BPM adapted and implemented in the bank, and what is the impact of BPM to the strategic goals? b)Action taken: This paper tackles the problem from two angles. First, a literature review is used to clarify the concept of BPM its scope. Second, semistructured interviews were used to collect data from nine participants covering high positions in Raiffeisen Bank Kosovo. In addition, the Research ffered both an evaluation of the significant aspects of the implementation process, and examinedthe key factors effects on alignment of BPM with organization strategy. c)Results achieved: his study unveils that BPM is well understood and is con-sidered an important practice within the bank. Its implementation is familiar to the top management. Especially, process visualization is a considered a core element within BPM projects. Existing project can further benefit from BPM by applying process ownership and defining responsibilities within the end to end processes in every department were these processes are performed. Moreover, this study collects evidence that strategy objectives can be led by BPM. d)Lessons learned: Experience has taught that there are many challenges whenapplying BPM initiatives. However, once these are applied, they help achieving strategic objectives. Two main challenges of implementing BPM were related to lack of proper IT support and budget needed to cover staff training. This paper recommends that BPM initiatives be strategy driven. It should be treated in a holistic way, including several methodologies like Six Sigma, Lean, and Agile. In this way, the Bank is lead towards thinking how its product or services are delivered to the customers.

An alignment or “fit” between an organization’s objectives and knowledge management (KM) practices should be established in order for the organization to fully utilize its knowledge assets and to derive competitive advantages. The organization should deploy a holistic approach for KM that spans business strategy, information system (IS) strategy, organization culture, and human factors. This research has investigated the strategic alignment between knowledge strategy and business strategy - KMBS-SA and the strategic alignment between knowledge strategy and IS strategy - KMIS-SA in the banking sector among the Gulf Cooperation Council (GCC) countries. Using the proposed model, the study explored the impacts of KMBS-SA and KMIS-SA on the organizational performance. The main hypothesis of this research is that knowledge is the main resource in an organization, and by aligning this resource with the business strategy and IS strategy, the alignment will contribute positively on the performance of the organization. The research model was illustrated in two different conceptualizations hypothesizing the different relationships between knowledge strategies, business strategy and IS strategy. The first conceptualization illustrates the KMBS-SA and KMIS-SA, and an investigation on the contribution of theses alignments on the organizational performance. The second conceptualization of the research model aims at investigating the impact of different types or profiles of KMBS-SA and KMIS-SA on the organizational performance. This study examined different alignments between two profiles of knowledge strategy - Aggressive Knowledge Strategy (AKS) and Conservative Knowledge Strategy (CKS), with various types of business strategy according to Miles and Snow’s (1978) strategic typology, and, the alignment of the two profiles of knowledge strategy with various IS strategy based on the STROIS approach by Chan et al. (1997). Using both conceptualizations, the role of knowledge strategy as a moderator or a mediator in the contribution of the business strategy and IS strategy towards the organizational performance was examined. The primary data for this study was collected through a survey of 106 banks from the six Gulf countries: Kingdom of Bahrain, Kingdom of Saudi Arabia, Kuwait, Qatar, United Arab Emirates (UAE), and Oman. The first overall conclusion demonstrated that there is a strong association between knowledge strategy and business strategy and that KMBS-SA clearly influenced the organizational performance. The second overall result of this research shows that in the context of GCC countries, knowledge strategy received stronger support as moderator of the IS congruence association with performance and that KMIS-SA is the primary determinant of the effectiveness of IS in the GCC banks. From the finding, it is recommended that the GCC banks should take KMBS-SA and KMIS-SA challenge seriously and should consider the alignment implication before moving ahead to implement a strategic plan. Furthermore, the research finding revealed that GCC bank should not ignore the different dimensions of knowledge strategic choices. The banks need to determine different profiles for their knowledge strategy in order to support all aspects of business strategy and IS strategic dimensions that are most important for the organization. They should then direct the organizational knowledge resources to support these profiles. Finally, it is recommended that the banks should define and establish a position in KM in order to oversee the knowledge strategy and KM issues.

This thesis addresses the problem of recognizing solid objects in the three-dimensional world, using two-dimensional shape information extracted from a single image. Objects can be partly occluded and can occur in cluttered scenes. A model based approach is taken, where stored models are matched to an image. The matching problem is separated into two stages, which employ different representations of objects. The first stage uses the smallest possible number of local features to find transformations from a model to an image. This minimizes the amount of search required in recognition. The second stage uses the entire edge contour of an object to verify each transformation. This reduces the chance of finding false matches.

Sketches are commonly used in the early stages of design. Our previous system allows users to sketch mechanical systems that the computer interprets. However, some parts of the mechanical system might be too hard or too complicated to express in the sketch. Adding speech recognition to create a multimodal system would move us toward our goal of creating a more natural user interface. This thesis examines the relationship between the verbal and sketch input, particularly how to segment and align the two inputs. Toward this end, subjects were recorded while they sketched and talked. These recordings were transcribed, and a set of rules to perform segmentation and alignment was created. These rules represent the knowledge that the computer needs to perform segmentation and alignment. The rules successfully interpreted the 24 data sets that they were given.

Sequence alignment has become one of the most common tasks in bioinformatics. Most of the existing sequence alignment methods use general scoring schemes. But these alignments are sometimes not completely relevant because they do not necessarily provide the desired information. It would be extremely difficult, if not impossible, to include any possible objective into an algorithm. Our goal is to allow a working biologist to augment a given alignment with additional information based on their knowledge and objectives.<p></p>In this thesis, we will formally define constraints and compatible constraint sets for an alignment which require some positions of the sequences to be aligned together. Using this approach, one can align some specific segments such as domains within protein sequences by inputting constraints (the positions of the segments on the sequences), and the algorithm will automatically find an optimal alignment in which the segments are aligned together.<p></p>A necessary prerequisite of calculating an alignment is that the constraints inputted be compatible with each other, and we will develop algorithms to check this condition for both pairwise and multiple sequence alignments. The algorithms are based on a depth-first search on a graph that is converted from the constraints and the alignment. We then develop algorithms to perform pairwise and multiple sequence alignments satisfying these compatible constraints.<p></p>Using straightforward dynamic programming for pairwise sequence alignment satisfying a compatible constraint set, an optimal alignment corresponds to a path going through the dynamic programming matrix, and as we are only using single-position constraints, a constraint can be represented as a point on the matrix, so a compatible constraint set is a set of points. We try to determine a new path, rather than the original path, that achieves the highest score which goes through all the compatible constraint set points. The path is a concatenation of sub-paths, so that only the scores in the sub-matrices need to be calculated. This means the time required to get the new path decreases as the number of constraints increases, and it also varies as the positions of the points change. It can be further reduced by using the information from the original alignment, which can offer a significant speed gain.<p></p>We then use exact and progressive algorithms to find multiple sequence alignments satisfying a compatible constraint set, which are extensions of pairwise sequence alignments. With exact algorithms for three sequences, where constraints are represented as lines, we discuss a method to force the optimal path to cross the constraint lines. And with progressive algorithms, we use a set of pairwise alignments satisfying compatible constraints to construct multiple sequence alignments progressively. Because they are more complex, we leave some extensions as future work.