The multiple sequence alignment (MSA) is a fundamental technique of molecular biology. Biological sequences are aligned with each other vertically in order to show the similarities and differences among them. Due to its importance, many algorithms have been proposed. With dynamic programming, finding the optimal alignment for a pair of sequences can be done in O(n2) time, where n is the length of the two strings. Unfortunately, for the general optimization problem of aligning k sequences of length n , O(nk) time is required. In this thesis, we shall first propose an efficient group alignment method to perform the alignment between two groups of sequences. Then we shall propose a clustering method to build the tree topology for merging. The clustering method is based on the concept that the two sequences having the longest distance should be split into two clusters. By our experiments, both the alignment quality and required time of our algorithm are better than those of NJ (neighbor joining) algorithm and Clustal W algorithm.

This study investigated the electro-optic characteristics of VAN ¡]vertical-alignment nematic¡^liquid crystal device in passive mode, and tried to present the advantage of high contrast ratio which belongs to VA mode. The experiment consisted of three parts: 1. Change different cell thickness¡]d = 12£gm¡B6£gm¡B4.9£gm¡^. 2. Chang LC with the different value of dielectric¡]£G£`= -3.7¡B-6.1¡^. 3. Chang LC with different refraction anisotropy¡]£Gn = 0.15¡B0.078¡^. We drive those samples with different number of duty in passive mode, and to measure the electro-optic characteristics, including VT curve, response time, and contrast ratio. We knew that STN¡]Super Twist Nematic LCD¡^has the drawbacks of lower contrast ratio, higher operational voltage and slower response time within higher duty in passive mode. And the same problem comes with VAN in passive-drive mode, although it is said VAN has the high performance of contrast ratio. The contrast ratio is worse then STN when driving in higher duty. As a result of VAN is kind of ECB mode, its transparency has a big matter with light retardation. We find that in the same condition of driving duty, the value of cell gap or the £Gn become larger, the value of the sharpness and the contrast ratio become larger.

Rubbing alignment has been used popularly in display industry. However, the alignment mechanisms of rubbed polymer are still not well understood. The purpose of this study is to investigate the relationship between anisotropy of rubbed polyimide thin film and liquid crystal alignment. In this study, we discuss the effects of surface energy and RAS on the surface roughness and pretilt angle of liquid crystal molecules. RAS is a non-contact optical probing technique developed originally for real-time, in situ monitoring of semiconductor growth . In this technique the normalized difference in reflectivity along two orthogonal directions is measured. Recently, the prospect of using RAS for process control in the fabrication of liquid crystal devices is investigated. On the other hand, we have known that the magnitude of surface energy is related to the strength of molecular bond. We can obtain the variation of surface properties by measuring the difference of surface energy. We found that the RA signal, pretilt angle and surface roughness are increasing with an increase in rubbing strength, but surface energy was decreased..

This study proposed a numerical algorithm for estimating the angular misalignments between sensors of an ultra short baseline (USBL) positioning system. The algorithm is based on positioning a seabed transponder by moving a vessel along a predetermined straight-line path. Under the scheme of straight-line survey, mathematical representations of positioning error arising from heading, pitch, and roll misalignments were derived, respectively. The effect of each misalignment angle and how the differences can be used to calibrate each misalignment angle in turn are presented. A USBL calibration procedure that takes advantage of the geometry of position errors resulting from angular misalignments is then developed. During the USBL measurement, temporal and spatial variations of sound speed structure in water column are the major error sources. Therefore, this study used the sound speed profile together with a ray tracing method to correct observations of the USBL measurement. In addition, this study developed a method to compensate the effects of cross-track error on the estimation of alignment errors, and this makes the proposed algorithm applicable for using a vessel without dynamic positioning (DP) systems to collect USBL observations. The performance of the algorithm is evaluated through simulation and field experiment. The simulation and experimental results have demonstrated the effectiveness and robustness of the iterative scheme in finding alignment errors. The proposed algorithm yields a very rapid convergence of the solution series; usually the estimates obtained in the first iteration approximate to true values, and only a few iterations are necessary to achieve fairly accurate solutions.

This paper presents a search method of coupling between the laser and fiber , search method to make up through the fiber and the laser inter-position deviation caused optical transmission loss , this search method is applied in the array-alignment is different from the traditional single-alignment , the advantage for the method is simple, through the rough alignment then blind search and angle search , for fiber array find the coupling of the greatest optical power position. In the experiment there are four degrees of freedom to use precise stage to fine-tune the location of fiber array , to reduce losses due to tools to reach precise alignment of purpose ,so we prove our method can achieve the objective of the fiber-optic alignment in our experiments.

Titel: Den strategiska prestationsmätningens utmaningar: En studie i svenska apoteksbranschen   Författare: Anton Greko & Rickard Manneklint   Handledare: Anders Wrenne   Institution: Managementhögskolan, Blekinge Tekniska Högskola   Kurs: Kandidatarbete i företagsekonomi, 15 högskolepoäng   Syfte: Syftet med denna studie är att identifiera de utmaningar som finns på olika organisatoriska nivåer med att upprätthålla strategisk linjering med hjälp av prestationsmätning och därigenom bidra till förståelsen kring prestationsmätningens roll i strategisk linjering.   Metod: I denna studie har vi använt oss av semistrukturerade kvalitativa intervjuer för att samla in det empiriska materialet, gällande prestationsmätning, strategi och strategisk linjering.   Slutsatser: Denna studie har identifierat ett antal utmaningar på olika organisatoriska nivåer med att upprätthålla strategisk linjering med hjälp av prestationsmätning. På ledningsnivå finns främst utmaningar gällande att ständigt diskutera och ompröva prestationsmåttens relevans även då det kan finnas drivkrafter som motarbetar detta. På operativ nivå finns främst utmaningar i att förse operativa chefer med tid, resurser och verktyg för att följa upp mätningar, leda sina medarbetare och påverka prestationsmätningarnas resultat. / Title: The challenges of strategic performance measurement: A study in the Swedish pharmaceutical industry   Authors: Anton Greko & Rickard Manneklint   Supervisor: Anders Wrenne   Department: School of Management, Blekinge Institute of Technology   Course: Bachelor’s thesis in Business Administration, 15 credits   Purpose: The purpose with this study is to identify the challenges that exist at different organizational levels to maintain strategic alignment with performance measurement and thereby contribute to the understanding about the role of performance measurement in strategic alignment.   Method: In this study, we have used semi-structured qualitative interviews to collect the empirical data, regarding performance measurement, strategy and strategic alignment.   Conclusions: This study has identified a number of different challenges at different organizational levels to maintain strategic alignment with performance measurement. At a corporate level, there are challenges mainly about constantly discuss and reevaluate the relevance of the performance measures, even though there might be forces that counteract this. At an operational level, there are challenges mainly about providing the operational managers with time, resources and tools to be able to follow up the measurements, lead their employees and affect the results of the measurements.

To investigate the diversities and abundances of nitrifiers and to apply the highthroughput sequencing technologies to analyze the overall microbial community structures and functions in the wastewater treatment bioreactors were the major objectives of this study. Specifically, this study was conducted: (1) to investigate the diversities and abundances of AOA, AOB and NOB in bioreactors, (2) to explore the bacterial communities in bioreactors using 454 pyrosequencing, and (3) to analyze the metagenomes of activated sludge using Illumina sequencing. A lab-scale nitrification bioreactor was operated for 342 days under low DO (0.15~0.5 mg/L) and high nitrogen loading (0.26~0.52 kg-N/(m3d)). T-RFLP and cloning analysis showed there were only one dominant AOA, AOB and NOB species in the bioreactor, respectively. The amoA gene of the dominant AOA had a similarity of 89.3% with the isolated AOA species Nitrosopumilus maritimus SCM1. The AOB species detected in the bioreactor belonged to Nitrosomonas genus. The abundance of AOB was more than 40 times larger than that of AOA. The percentage of NOB in total bacteria increased from not detectable to 30% when DO changed from 0.15 to 0.5 mg/L. Compared with traditional methods, pyrosequencing analysis of the bacteria in this bioreactor provided unprecedented information. 494 bacterial OTUs was obtained at 3% distance cutoff. Furthermore, 454 pyrosequencing was applied to investigate the bacterial communities of activated sludge samples from 14 WWTPs of Asia (mainland China, Hong Kong, and Singapore) and North America (Canada and the United States). The results revealed huge amounts of OTUs in activated sludge, i.e. 1183~3567 OTUs in one sludge sample at 3% distance cutoff. Clear geographical differences among these samples were observed. The AOB amoA genes in different WWTPs were found quite diverse while the 16S rRNA genes were relatively conserved. To explore microbial community structures and functions in the abovementioned labscale bioreactor and a full-scale bioreactor, over six gigabases of metagenomic sequence data and 150,000 paired-end reads of PCR amplicons were generated from the activated sludge in the two bioreactors on Illumina HiSeq2000 platform. Three kinds of sequences (16S rRNA amplicons, 16S rRNA gene tags and predicted genes) were used to conduct taxonomic assignment and their applicabilities and reliabilities were compared. Specially, based on 16S rRNA and amoA gene sequences, AOB were found more abundant than AOA in the two bioreactors. Furthermore, the analysis of the metabolic profiles and pathways indicated that the overall pathways in the two bioreactors were quite similar. However, the abundances of some specific genes in the two bioreactors were different. In addition, 454 pyrosequencing was also used to detect potentially pathogenic bacteria in environmental samples. It was found most abundant potentially pathogenic bacteria in the WWTPs were affiliated with Aeromonas and Clostridium. Aeromonas veronii, Aeromonas hydrophila and Clostridium perfringens were species most similar to the potentially pathogenic bacteria found in this study. Overall, the percentage of the sequences closely related to known pathogenic bacteria sequences was about 0.16% of the total sequences. Additionally, a Java application (BAND) was developed for graphical visualization of microbial abundance data. / published_or_final_version / Civil Engineering / Doctoral / Doctor of Philosophy

The recent advance of second-generation sequencing technologies has made it possible to generate a vast amount of short read sequences from a DNA (cDNA) sample. Current short read assemblers make use of the de Bruijn graph, in which each vertex is a k-mer and each edge connecting vertex u and vertex v represents u and v appearing in a read consecutively, to produce contigs. There are three major problems for de Bruijn graph assemblers: (1) branch problem, due to errors and repeats; (2) gap problem, due to low or uneven sequencing depth; and (3) error problem, due to sequencing errors. A proper choice of k value is a crucial tradeoff in de Bruijn graph assemblers: a low k value leads to fewer gaps but more branches; a high k value leads to fewer branches but more gaps. In this thesis, I first analyze the fundamental genome assembly problem and then propose an iterative de Bruijn graph assembler (IDBA), which iterates from low to high k values, to construct a de Bruijn graph with fewer branches and fewer gaps than any other de Bruijn graph assembler using a fixed k value. Then, the second-generation sequencing data from metagenomic, single-cell and transcriptome samples is investigated. IDBA is then tailored with special treatments to handle the specific issues for each kind of data. For metagenomic sequencing data, a graph partition algorithm is proposed to separate de Bruijn graph into dense components, which represent similar regions in subspecies from the same species, and multiple sequence alignment is used to produce consensus of each component. For sequencing data with highly uneven depth such as single-cell and metagenomic sequencing data, a method called local assembly is designed to reconstruct missing k-mers in low-depth regions. Then, based on the observation that short and relatively low-depth contigs are more likely erroneous, progressive depth on contigs is used to remove errors in both low-depth and high-depth regions iteratively. For transcriptome sequencing data, a variant of the progressive depth method is adopted to decompose the de Bruijn graph into components corresponding to transcripts from the same gene, and then the transcripts are found in each component by considering the reads and paired-end reads support. Plenty of experiments on both simulated and real data show that IDBA assemblers outperform the existing assemblers by constructing longer contigs with higher completeness and similar or better accuracy. The running time of IDBA assemblers is comparable to existing algorithms, while the memory cost is usually less than the others. / published_or_final_version / Computer Science / Doctoral / Doctor of Philosophy

This research investigates the role of emotion in the persuasion process by establishing a novel relationship between emotion and construal level. Built on cognitive appraisal theories, this research proposes that the certainty appraisal components of emotions exert a direct influence on an individual’s representation of information at a high versus low construal level. The findings indicate that individuals primed to feel emotion low on certainty appraisals construe behaviors or events at a high level and estimate uncertain events as more likely to happen, while those primed to feel emotion high on certainty appraisals characterize behavior or events at a low level and evaluate uncertain events as less likely to occur (Study 1 & Study 2). Further, such a fit (vs. nonfit) between an individual’s emotional state and the construal level at which product benefits in an advertising message are represented lead to a more favorable evaluation of the message and product (Study 3). The findings from this dissertation study also illustrate that uncertainty-related emotion eliciting a high-level construal mindset leads to a cognitive shift toward relying more on nonalignable attribute differences and a greater preference for the nonalignable-better brand although individuals usually rely more on alignable attribute differences and favor the alignable-better brand (Study 4). Accordingly, these outcomes occur because the certainty appraisal components of emotions influence mental construal levels. / text

Rather than measuring aberrations at several locations across the field to quantify the alignment of an optical system, we show how a simple measurement of the pupil mapping can be used to measure the off-axis performance of the system. This method uses the Abbe sine condition to relate the mapping between the entrance and the exit pupils, where the violations of the generalized sine condition are used to determine the pupil mapping error. From this pupil mapping, the linearly field-dependent aberrations can be calculated. One of the advantages to this method is that all of the test equipment can be aligned to the center of the field while making measurements of the off-axis performance, which reduces the uncertainty of the measurement. This advantage is particularly evident with systems or sub-systems that have large inherent aberrations where off-axis alignment tolerances are very tight. Additionally, in the Sine Condition Test (SCTest), the test equipment can be designed to compensate for the native Siedel coma in the system. This makes it more straightforward to measure the linearly field dependence of the aberrations. By reducing or removing coma, the measurement uncertainty is further reduced. This work begins by explaining the background of the Abbe sine condition, derivation of the pupil mapping error, and an overview of linearly field-dependent astigmatism that arises from misalignment. Next, the general method of implementation is discussed, and expanded further by exploring the two different source options: a point source with a grating or a flat-panel display. Experimental results from proof of concept systems are shown for both cases. Next, this dissertation explains how the SCTest can be implemented on more complex systems. Last, this dissertation shows how the linear aberrations, along with constant field-dependent aberrations, can be used to align a system. Here, the application of the alignment version of the SCTest on a three mirror anastigmat (TMA) is discussed. Using simulation, this dissertation then investigates the behavior of the alignment SCTest for various levels of mirror misalignment, mirror fabrication errors, and misalignment of the test equipment. All of these tests show that the alignment SCTest can successfully align an optical system.