The development of large, software-intensive systems is a complex undertaking that is generally tackled by a divide and conquer strategy. Organizations face thereby the challenge of coordinating the resources which enable the individual aspects of software development, commonly solved by adopting a particular process model. The alignment between requirements engineering (RE) and software testing (ST) activities is of particular interest as those two aspects are intrinsically connected: requirements are an expression of user/customer needs while testing increases the likelihood that those needs are actually satisfied. The work in this thesis is driven by empirical problem identification, analysis and solution development towards two main objectives. The first is to develop an understanding of RE and ST alignment challenges and characteristics. Building this foundation is a necessary step that facilitates the second objective, the development of solutions relevant and scalable to industry practice that improve REST alignment. The research methods employed to work towards these objectives are primarily empirical. Case study research is used to elicit data from practitioners while technical action research and field experiments are conducted to validate the developed  solutions in practice. This thesis contains four main contributions: (1) An in-depth study on REST alignment challenges and practices encountered in industry. (2) A conceptual framework in the form of a taxonomy providing constructs that further our understanding of REST alignment. The taxonomy is operationalized in an assessment framework, REST-bench (3), that was designed to be lightweight and can be applied as a postmortem in closing development projects. (4) An extensive investigation into the potential of information retrieval techniques to improve test coverage, a common REST alignment challenge, resulting in a solution prototype, risk-based testing supported by topic models (RiTTM). REST-bench has been validated in five cases and has shown to be efficient and effective in identifying improvement opportunities in the coordination of RE and ST. Most of the concepts operationalized from the REST taxonomy were found to be useful, validating the conceptual framework. RiTTM, on the other hand, was validated in a single case experiment where it has shown great potential, in particular by identifying test cases that were originally overlooked by expert test engineers, improving effectively test coverage.

This thesis is devoted to two $\mathcal{NP}$-complete combinatorial optimization problems arising in computational biology, the well-studied \emph{multiple sequence alignment} problem and the new formulated \emph{interval constraint coloring} problem. It shows that advanced mathematical programming techniques are capable of solving large scale real-world instances from biology to optimality. Furthermore, it reveals alternative methods that provide approximate solutions. In the first part of the thesis, we present a \emph{Lagrangian relaxation} approach for the multiple sequence alignment (MSA) problem. The multiple alignment is one common mathematical abstraction of the comparison of multiple biological sequences, like DNA, RNA, or protein sequences. If the weight of a multiple alignment is measured by the sum of the projected pairwise weights of all pairs of sequences in the alignment, then finding a multiple alignment of maximum weight is $\mathcal{NP}$-complete if the number of sequences is not fixed. The majority of the available tools for aligning multiple sequences implement heuristic algorithms; no current exact method is able to solve moderately large instances or instances involving sequences exhibiting a lower degree of similarity. We present a branch-and-bound (B\&B) algorithm for the MSA problem.\ignore{the multiple sequence alignment problem.} We approximate the optimal integer solution in the nodes of the B\&B tree by a Lagrangian relaxation of an ILP formulation for MSA relative to an exponential large class of inequalities, that ensure that all pairwise alignments can be incorporated to a multiple alignment. By lifting these constraints prior to dualization the Lagrangian subproblem becomes an \emph{extended pairwise alignment} (EPA) problem: Compute the longest path in an acyclic graph, that is penalized a charge for entering ``obstacles''. We describe an efficient algorithm that solves the EPA problem repetitively to determine near-optimal \emph{Lagrangian multipliers} via subgradient optimization. The reformulation of the dualized constraints with respect to additionally introduced variables improves the convergence rate dramatically. We account for the exponential number of dualized constraints by starting with an empty \emph{constraint pool} in the first iteration to which we add cuts in each iteration, that are most violated by the convex combination of a small number of preceding Lagrangian solutions (including the current solution). In this \emph{relax-and-cut} scheme, only inequalities from the constraint pool are dualized. The interval constraint coloring problem appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy is a method used to obtain information about protein tertiary structure. The output of these experiments provides aggregate data about the exchange rate of residues in overlapping fragments of the protein backbone. These fragments must be re-assembled in order to obtain a global picture of the protein structure. The interval constraint coloring problem is the mathematical abstraction of this re-assembly process. The objective of the interval constraint coloring problem is to assign a color (exchange rate) to a set of integers (protein residues) such that a set of constraints is satisfied. Each constraint is made up of a closed interval (protein fragment) and requirements on the number of elements in the interval that belong to each color class (exchange rates observed in the experiments). We introduce a polyhedral description of the interval constraint coloring problem, which serves as a basis to attack the problem by integer linear programming (ILP) methods and tools, which perform well in practice. Since the goal is to provide biochemists with all possible candidate solutions, we combine related solutions to equivalence classes in an improved ILP formulation in order to reduce the running time of our enumeration algorithm. Moreover, we establish the polynomial-time solvability of the two-color case by the integrality of the linear programming relaxation polytope $\mathcal{P}$, and also present a combinatorial polynomial-time algorithm for this case. We apply this algorithm as a subroutine to approximate solutions to instances with arbitrary but fixed number of colors and achieve an order of magnitude improvement in running time over the (exact) ILP approach. We show that the problem is $\mathcal{NP}$-complete for arbitrary number of colors, and we provide algorithms that, given an instance with $\mathcal{P}\neq\emptyset$, find a coloring that satisfies all the coloring requirements within $\pm 1$ of the prescribed value. In light of our $\mathcal{NP}$-completeness result, this is essentially the best one can hope for. Our approach is based on polyhedral theory and randomized rounding techniques. In practice, data emanating from the experiments are noisy, which normally causes the instance to be infeasible, and, in some cases, even forces $\mathcal{P}$ to be empty. To deal with this problem, the objective of the ILP is to minimize the total sum of absolute deviations from the coloring requirements over all intervals. The combinatorial approach for the two-color case optimizes the same objective function. Furthermore, we use this combinatorial method to compute, in a Lagrangian way, a bound on the minimum total error, which is exploited in a branch-and-bound manner to determine all optimal colorings. Alternatively, we study a variant of the problem in which we want to maximize the number of requirements that are satisfied. We prove that this variant is $\mathcal{APX}$-hard even in the two-color case and thus does not admit a polynomial time approximation scheme (PTAS) unless $\mathcal{P}=\mathcal{NP}$. Therefore, we slightly (by a factor of $(1+\epsilon)$) relax the condition on when a requirement is satisfied and propose a \emph{quasi-polynomial time approximation scheme} (QPTAS) which finds a coloring that ``satisfies'' the requirements of as many intervals as possible.

<p>This thesis addresses assembly issues encountered in optical and fluidic microsystem applications.</p><p>In optics, the first subject concerns the active alignment of components in optical fibersystems. A solution for reducing the cost of optical component assembly while retaining submicron accuracy is to integrate the alignment mechanism onto the optical substrate. A polymer V-shaped actuator is presented that can carry the weight of the large components - on a micromechanical scale - and that can generate movement with six degrees of freedom.</p><p>The second subject in optics is the CMOS-compatible fabrication of monocrystalline silicon micromirror arrays that are intended to serve as CMOS-controlled high-quality spatial light modulators in maskless microlithography systems. A wafer-level assembly method is presented that is based on adhesive wafer bonding whereby a monocrystalline layer is transferred onto a substrate wafer in a CMOS-compatible process without needing bond alignment.</p><p>In fluidics, a hybrid assembly method is introduced that combines two separately micromachined structures to create hotwire anemometers that protrude from a surface with minimum interference with the air flow. The assembled sensor enables one to make accurate time-resolved measurements of the wall shear stress, a quantity that has previously been hard to measure with high time resolution. Also in the field of hotwire anemometers, a method using a hotwire anemometer array is presented for measuring the mass flow, temperature and composition of a gas in a duct.</p><p>In biochemistry, a bio-analysis chip is presented. Single nucleotide polymorphism scoring is performed using dynamic allele-specific hybridization (DASH). Using monolayers of beads, multiplexing based on single-bead analysis is achieved at heating rates more than 20 times faster than conventional DASH provides.</p><p>Space and material e±ciency in packaging are the focus of the other two projects in fluidics. The first introduces an assembly based on layering conductive adhesives for the fabrication of miniature polymer electrolyte membrane fuel cells. The fuel cells made with this low-cost approach perform among the best of their type to date. The second project concerns a new cross-flow microvalve concept. Intended as a step towards the mass production of large-flow I/P converters, the silicon footprint area is minimized by an out-of-plane moving gate and in-plane, half-open pneumatic channels.</p>

Although language usually occurs in an interactive and world-situated context (Clark, 1996), most research on language use to date has studied comprehension and production in isolation. This thesis combines research on comprehension and production, and explores the links between them. Its main focus is on the coordination of visual attention between speakers and listeners, as well as the influence this has on the language they use and the ease with which they understand it. Experiment 1 compared participants’ eye movements during comprehension and production of similar sentences: in a syntactic priming task, they first heard a confederate describe an image using active or passive voice, and then described the same kind of picture themselves (cf. Branigan, Pickering, & Cleland, 2000). As expected, the primary influence on eye movements in both tasks was the unfolding sentence structure. In addition, eye movements during target production were affected by the structure of the prime sentence. Eye movements in comprehension were linked more loosely with speech, reflecting the ongoing integration of listeners’ interpretations with the visual context and other conceptual factors. Experiments 2-7 established a novel paradigm to explore how seeing where a speaker was looking during unscripted production would facilitate identification of the objects they were describing in a photographic scene. Visual coordination in these studies was created artificially through an on-screen cursor which reflected the speaker’s original eye movements (cf. Brennan, Chen, Dickinson, Neider, & Zelinsky, 2007). A series of spatial and temporal manipulations of the link between cursor and speech investigated the respective influences of linguistic and visual information at different points in the comprehension process. Implications and potential future applications are discussed, as well as the relevance of this kind of visual cueing to the processing of real gaze in face-to-face interaction.

Liquid crystals are traditionally aligned via a rubbed substrate. The rubbing creates anisotropic defects and strain in the material which provide an energetically favorable orientation for the liquid crystal (LC). This is a well-developed technology that is used in virtually all liquid crystal displays (LCDs). However, it is only capable of uniform alignment on a large planar substrate. This work utilizes a new class of photoalignment materials (PM) that replace the traditional buffing technique. PMs allow for patterned LC alignment using polarized photo-lithography. Further, instead of using a nematic liquid crystal, a UV curable liquid crystal polymer (LCP) is coated on this patterned alignment material. This generates a cured, aligned, and patterned thin film that has retardance and diattenuation if a dichroic dye is incorporated in the LCP. Using these materials and methods, retarders, polarizers, and polarized fluorescent sources are fabricated with dimensions as small as a few microns. In addition to exploring the material and processing properties of the PM and LCP system, arrays of micropolarizer are fabricated for the construction of a prototype polarization camera, termed an imaging polarimeter. An imaging polarimeter is a device that measures not only the intensity but also the polarization state of a light field. My imaging polarimeter design incorporates a patterned LCP polarizer focal plane array (FPA) that is aligned and mounted to a charge-couple-device (CCD) image sensor. A polarizer FPA allows an individual pixel on a CCD sensor to detect a unique polarization state, such as a specific linear polarization orientation or right or left handed circular polarization. Neighboring pixels are designed to detect different states and each cluster can then estimate the incident polarization state. Results of a linear LCP polarimeter operating in the visible spectrum are presented.

<p>The action of Mung Bean Nuclease (MBN) on DNA makes it possible to clone intact gene fragments from genes of the malaria parasite, Plasmodium. This &ldquo / genease&rdquo / activity has provided a foundation for further investigation of the coding elements of the Plasmodium genome. MBN has been reported to cleave genomic DNA of Plasmodium preferentially at positions before and after genes, but not within gene coding regions. This mechanism has overcome the difficulty encountered in obtaining genes with low expression levels because the cleavage mechanism of the enzyme yields sequences of genes from genomic DNA rather than mRNA. However, as potentially useful as MBN may be, evidence to support its genease activity comes from analysis of a limited number of genes. It is not clear whether this mechanism is specific to certain genes or species of Plasmodia or whether it is a general cleavage mechanism for Plasmodium DNA .There have also been some projects (Nomura et al., 2001 / van Lin, Janse, and Waters, 2000) which have identified MBN generated fragments which contain fragments of genes with both introns and exons, rather than the intact genes expected from MBN-digestion of genomic DNA, which raises concerns about the efficiency of the MBN mechanism in generating complete genes.</p> <p><br /> Using a large-scale, whole genome mapping approach, 7242 MBN generated genome survey sequences (GSSs) have been mapped to determine their position relative to coding sequences within the complete genome sequences of the human malaria parasite Plasmodium falciparum and the incomplete genome of a rodent malaria parasite Plasmodium berghei. The location of MBN cleavage sites was determined with respect to coding regions in orthologous genes, non-coding /intergenic regions and exon-intron boundaries in these two species of Plasmodium. The survey illustrates that for P. falciparum 79% of GSSs had at least one terminal mapping within an ortholog coding sequence and 85% of GSSs which overlapped coding sequence boundaries mapped within 50 bp of the start or end of the gene. Similarly, despite the partial nature of P.berghei genome sequence information, 73% of P.berghei GSSs had at least one terminal mapping within an ortholog coding sequence and 37% of these mapped between 0-50 bp of the start or end of the gene. This indicates that a larger percentage of cleavage sites in both P.falciparum and P.berghei were found proximal to coding regions. Furthermore, 86% of P.falciparum GSSs had at least one terminal mapping within a coding exon and 85% of GSSs which overlapped exon-intron boundaries mapped within 50bp of the exon start and end site. The fact that 11% of GSSs mapped completely to intronic regions, suggests that some introns contain specific cleavage sites sensitive to cleavage and this also indicates that MBN cleavage of Plasmodium DNA does not always yield complete exons.</p> <p><br /> Finally, the results presented herein were obtained from analysis of several thousand Plasmodium genes which have different coding sequences, in different locations on individual chromosomes/contigs in two different species of Plasmodium. Therefore it appears that the MBN mechanism is neither species specific nor is it limited to specific genes.</p>

Šiame darbe analizuotos įvairių laiko eilučių išlyginimo ir panašumo nustatymo metodų pritaikymo galimybės T bangų kaitos (TBK) analizėje, pagerinant Nearing ir Verrier pasiūlytą, modifikuoto slenkančio vidurkio metodą. Pasinaudojant TWA duomenų baze ir generuotais duomenimis surasti labiausiai TBK analizei tinkami išlyginimo ir panašumo vertinimo metodai. TBK, paskaičiuoto naudojant modifikuotą slenkančio vidurkio metodą papildytą TBK analizei tinkamiausiais laiko eilučių išlyginimo ir panašumo nustatymo metodais, tinkamumas širdies ligų diagnostikai patikrintas su duomenimis iš PTB duomenų bazės. Pasiremiant PTB duomenimis rastas galimas biomarkeris širdies ligų diagnostikoje, paskutinių dviejų TBK įverčių, gautų taikant MSVM su atviros pradžios ir pabaigos dinaminio laiko skalės kraipymo su asimetriniu judėjimo šablonu išlyginimą ir panašumą vertinant kaip absoliutinį skirtumą tarp maksimumo taškų, min-max kombinaciją. / T wave alternans (TWA) is a beat-to-beat change in the amplitude or shape of T wave. TWA is one of potential biomarkers for ventricular arrhythmias and can be a sign of serious heart disease. Because there is no gold standard in TWA measuring, modifications of existing methods and new solutions are possible. Modified moving average method, proposed by Nearing and Verrier, is one of mostly used in medical practise, but can give misleading results then T waves is not properly aligned or T wave length and morphology changes because of heart rate variability. It is known, that some ventricular arrhythmias can cause heart rate variability, so this type of error is unwanted, because online TWA measuring can become one of sudden ventricular arrhythmias predictors in the near future. In this work, variuos time series alignment and similarity detection techniques were used to improve TWA measuring and this measure capabilities in heart disease diagnostic were analized. TWA analysis with simulated and real data from ECG databases was performed and potentional biomarker was found by using biomarkers combining method, proposed by Liu, Liu and Halabi. 57.

Methods of controlling molecular rotations using linearly polarized femtosecond and picosecond pulses are considered and analyzed theoretically. These laser pulses, typically in the infrared, are highly non-resonant with respect to the electronic degrees of freedom of the molecules and have intensities of &sim; 10^13 to 10^14 W/cm&sup2;. It is shown how these laser pulses can force small linear molecules to align with the direction of the electric field vector of the laser both in the presence of the laser field as well as after the application of a short laser pulse. Recent experiments on laser-induced molecular alignment are modeled and excellent agreement between experiment and theory is found. Additional methods of controlling molecular rotational dynamics are outlined. The first method considers the forced rotational acceleration of diatomic molecules, called the <i>optical centrifuge</i>. Here, the direction of polarization of a linearly polarized laser field is made to smoothly rotate faster and faster. The molecules, which tend to align with the polarization vector of the laser field, follow the rotation of the laser polarization and are accelerated to high angular momentum. The second method considers the control of field-free rotational dynamics by applying phase shifts to the molecular wave function at select times called <i>fractional revivals</i>. At these select moments, an initially localized wave function splits into several copies of the initial state. Adding phase shifts to the copies then induces interference effects which can be used to control the subsequent evolution of the rotational wave function. This same control scheme has a close link to quantum information and this connection is outlined. Finally, a recently proposed method of controlling the quantum dynamics of the classically chaotic kicked rotor system [J. Gong and P. Brumer, Phys. Rev. Lett. 86, 1741 (2001)] is analyzed from a phase space perspective. It is shown that the proposed quantum control can be linked to small islands of stability in the classical phase space. An experimentally feasible variant of this control scenario using wave packets of molecular alignment is proposed. Two applications of molecular alignment are discussed. The first application uses field-free aligned molecules as a non-linear medium for compression of a laser pulse to the 1 fs regime at optical wavelengths. At such durations, these laser pulses contain nearly a single oscillation of the electric field and represent the shortest laser pulses physically achievable for such frequencies. The second application uses molecular alignment to create a sort of gas phase "molecular crystal" which forms a basis for laser-induced electron diffraction and imaging of the aligned molecules. Here, a first laser pulse aligns the molecules in space. A second laser pulse is then used to ionize outer-shell electrons, accelerate them in the laser field, and steer them back to collide with the parent ion creating a diffraction image with sub-femtosecond and sub-Angstrom resolution.

Over the past few years there has been growing interest in the study of leadership styles and organisational culture. Internal issues and external environment challenge the leadership of manufacturing organisations, Scarborough(2001). The focus of the research was to gain insight into the transformational leadership of manufacturing organisations. Although leadership scholars have generated a significant stream of research on transformational leadership, there has been a lack of attention to the specific features in the context of transformational leadership such as contingency theories, attribution theory, and organisational culture. The study investigates the effects of transformational leadership on situational determinants and organisational culture in manufacturing organisations in Pakistan. Podsakoff et al, (1990) a 23-item measure of transformational leadership inventory questionnaire was employed to evaluate transformational leadership in manufacturing organisations. The objectives of this research study are: Firstly to study transformational leadership in Pakistani manufacturing organisations. Secondly to study transformational leaders' behaviour in manufacturing organisations with respect to situational determinants, i.e., situation strength, attribution theory, feedback, and organisational culture. Thirdly to develop hypotheses concerning the relationship between transformational leadership, and situational determinants and to develop a model of relationship between transformational leadership, situational determinants and organisational culture. Lastly, to suggest further research guidelines for transformational leadership phenomena and leadership in Pakistani manufacturing organisations. Results from the research show that transformational leaders tend to create weak situations for their followers in manufacturing organisations; they favour discretion to their followers and delegate decision-making to followers. Transformational leaders also tend to make external attributions for the causes of poor performance in their organisations, and assume follower's mistake as a learning experience. They try to establish close contact with their followers and seek feedback directly from followers. Transformational leaders favour clan type culture more in their manufacturing organisations; however adhocracy culture is not completely ignored. A new leadership alignment model incorporating various concepts focusing on leadership style, organisational leadership, and situational strength has been introduccd. Results from the data analysis indicate that there is a need to train more leaders in Pakistani manufacturing organisations to benefit from the transformational leadership style, as it has beene stablished that transformational leadershipis an influential form of leadership clearly associated with high levels of individual and organisational performance(, Shamir & Kark, 2002). As pointed out by Bass, (2002) leaders will be prized for their innovativeness, responsiveness, and flexibility, all linked to their frequency of transformational leadership behaviour.

The alignment of information systems (IS) strategies with business strategies has been a managerial priority in modern organisations. Information Technology (IT) governance is an alternative perspective that has recently been used as a management solution that can drive to desired levels of IS/business alignment. From a pragmatic perspective, both IS/business alignment and IT governance appear to be managerial solutions that corporations desire to implement in order to get the most of the business and IT relationship. Empirical research has addressed the idea that effective designs of IT governance enable IS/business alignment, however, the extent of such impact and related interactions are still unclear. This research is focused on those claims to contribute with pragmatic solutions towards IS/business alignment and IT governance by means of collective management practices. This research explored challenges, assumptions and conceptualisations around IS/business alignment and focused on the assessment process of IS-business alignment to identify management practices for both IS/business alignment and IT governance. First, a quantitative analysis from data collected of an international survey was performed. This survey was conducted to identify extreme outcomes of relevant management practices in the IS/business alignment dynamics and links with IT governance. Second, a qualitative analysis from data collected of two leading large companies, one in the manufacturing and other in the financial sector, was performed by using a three-level (strategic, tactical and operational) assessment method. This case research aimed to identify how common relevant management practices interact across strategic, tactical and operational organisational levels. Results of both analyses were integrated to elaborate the constructors of the framework derived from this research, namely ALIS-G. The results from this research can be summarised as follows: First, ALIS-G exhibits four core management practices (IT investment management, budgetary control, strategic and tactical program management, strategic and tactical understanding of IT-business) and four supportive (IT-business planning, IT projects prioritisation, sponsorship & championship and change readiness) to show collective and compelling influence over the IS-business alignment dynamics and the effectiveness of IT governance arrangements. Second, a well-established IT investment management process holds the most substantial positive impact in the IS-business alignment dynamics and design of IT governance arrangements. Finally, results highlights the fact, perhaps obvious, that the arrangement of IT governance and the dynamics of IS/business alignment are very much conditioned by the resilient assignment, allocation and administration of budgets