Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

Modeling and illustrating requirement prioritization in public e-service development from a value-based perspective

A major problem in e-service development is the prioritization of the requirements of different stakeholders. The main stakeholders are governments and their citizens, all of whom have different and sometimes conflicting requirements. In this paper, the prioritization problem is addressed by combining a value-based approach with an illustration technique. This paper examines the following research question: How can multiple stakeholder requirements be illustrated from a value-based perspective in order to be prioritizable? We used an e-service development case taken from a Swedish municipality to elaborate on our approach. Our contributions are: 1) a model of the relevant domains for requirement prioritization for government, citizens, technology, finances and laws and regulations; and 2) a requirement fulfillment analysis tool (RFA) that consists of a requirement-goal-value matrix (RGV), and a calculation and illustration module (CIM). The model reduces cognitive load, helps developers to focus on value fulfillment in e-service development and supports them in the formulation of requirements. It also offers an input to public policy makers, should they aim to target values in the design of e-services.

Analysis of EnterpriseVoIP Traffic from aWire line IMS System

With the rapid development of telecommunication industry, the IP multimedia Subsystem (IMS) could very well be the panacea for most telecom operators. It is originally defined as the core network for 3G mobile systems by the 3rd Generation Partnership Project (3GPP), the more recent development is merging between fixed line network and wireless networkd This report researchs the characteristic of the IMS data and proposes an IMS characterization analysis. We captured the IMS traffic data with 10 tousands users for about 41 hours. By analyzing the characteristics of the IMS, we know that the most important application in the IMS is VoIP call. Then we use the tool designed by Tsinghua University & Ericsson Company to recognize the data, and the results we got can be used to build the traffic models. From the results of the traffic models, I will get some reasons and conclusion. The traffic model gives out the types of session and types of VoIP call. I bring into a concept—busy hour. This concept is very important because it can help us to know which period is the peak of the VoIP call. The busy hour is from 10:00 to 11:00 in the morning. I also bring into another concept—connection ratio. This concept is significant because it can evaluate whether the VoIP call is good when it use IMS network. By comparing the traffic model with other one’s models, we found the different results from them, both the accuracy and the busy hour. From the contract, we got the advantages of our traffic models.

Validering av Alberta Context Tool (ACT) för bruk inom svensk kommunal äldrevård : Ett verktyg för implementering av evidensbaserad vård

The aim of this study was to conduct an instrument test of the Canadian questionnaire Alberta Context Tool (ACT) version Long-Term care for Swedish conditions. ACT is designed in order to measure the context in the care environment and different behaviours related to the changes in clinical practice. In total, 159 Licensed Practical Nurses (LPNs) and Registered Nurses (RNs) within municipality care of the elderly were included in the survey. The test included the instrument's reliability and face validity.The reliability test was implemented through calculation of Cronbach´s Alpha, and showed internal consistency for five of the scales of the ACT-instrument with Cronbach´s Alpha values ranging between 0,728 and 0,873. However, three dimensions got lower values (0,558 - 0,683).The analysis was carried out with content analysis and carried out for LPNs and RNs in separate groups. The majority of LPNs expressed that it was easy to respond to the questions (56%), while nine percent considered it as difficult. Eleven comments were given about questions that were perceived to be unclear, complicated or contained difficult words. In the RN group only 30 percent considered that the questions were easy to respond to. One third of the RNs considered that part of the questions were unclear, and six RNs expressed also which questions they experienced as unclear. In general, the questions in the ACT were perceived as relevant. The instrument's relevance as a tool to measure contextual factors that influence the implementation of evidence based nursing can also be considered to be determined. By modifying the content in the questionnaire in accordance with what appeared in this survey and to implement yet another test, the instrument should be considered to be relevant for use within Swedish municipality care of the elderly. ACT can be used both as a tool in the work on improvement of clinical practice and as a tool for further research about implementation of evidence based nursing.

Personalized Communications : A Cross Media tool for the future

Personalized communication is when the marketing message is adapted to each individual by using information from a databaseand utilizing it in the various, different media channels available today. That gives the marketer the possibility to create a campaign that cuts through today’s clutter of marketing messages and gets the recipients attention. PODi is a non-profit organization that was started with the aim of contributing knowledge in the field of digital printingtechnologies. They have created a database of case studies showing companies that have successfully implemented personalizedcommunication in their marketing campaigns. The purpose of the project was therefore to analyze PODi case studies with the main objective of finding out if/how successfully the PODi-cases have been and what made them so successful. To collect the data found in the PODi cases the authors did a content analysis with a sample size of 140 PODi cases from the year 2008 to 2010. The study was carried out by analyzing the cases' measurable ways of success: response rate, conversion rate, visited PURL (personalized URL:s) and ROI (Return On Investment). In order to find out if there were any relationships to be found between the measurable result and what type of industry, campaign objective and media vehicle that was used in the campaign, the authors put up different research uestions to explore that. After clustering and merging the collected data the results were found to be quite spread but shows that the averages of response rates, visited PURL and conversion rates were consistently very high. In the study the authors also collected and summarized what the companies themselves claim to be the reasons for success with their marketing campaigns. The resultshows that the creation of a personalized campaign is complex and dependent on many different variables. It is for instance ofgreat importance to have a well thought-out plan with the campaign and to have good data and insights about the customer in order to perform creative personalization. It is also important to make it easy for the recipient to reply, to use several media vehicles for multiple touch points and to have an attractive and clever design.

Immigration, security and the public debate on US language policy : a critical discourse analysis of language attitudes in the United States of America

The narrative of the United States is of a "nation of immigrants" in which the language shift patterns of earlier ethnolinguistic groups have tended towards linguistic assimilation through English. In recent years, however, changes in the demographic landscape and language maintenance by non-English speaking immigrants, particularly Hispanics, have been perceived as threats and have led to calls for an official English language policy.This thesis aims to contribute to the study of language policy making from a societal security perspective as expressed in attitudes regarding language and identity originating in the daily interaction between language groups. The focus is on the role of language and American identity in relation to immigration. The study takes an interdisciplinary approach combining language policy studies, security theory, and critical discourse analysis. The material consists of articles collected from four newspapers, namely USA Today, The New York Times, Los Angeles Times, and San Francisco Chronicle between April 2006 and December 2007.Two discourse types are evident from the analysis namely Loyalty and Efficiency. The former is mainly marked by concerns of national identity and contains speech acts of security related to language shift, choice and English for unity. Immigrants are represented as dehumanised, and harmful. Immigration is given as sovereignty-related, racial, and as war. The discourse type of Efficiency is mainly instrumental and contains speech acts of security related to cost, provision of services, health and safety, and social mobility. Immigrants are further represented as a labour resource. These discourse types reflect how the construction of the linguistic 'we' is expected to be maintained. Loyalty is triggered by arguments that the collective identity is threatened and is itself used in reproducing the collective 'we' through hegemonic expressions of monolingualism in the public space and semi-public space. The denigration of immigrants is used as a tool for enhancing societal security through solidarity and as a possible justification for the denial of minority rights. Also, although language acquisition patterns still follow the historical trend of language shift, factors indicating cultural separateness such as the appearance of speech communities or the use of minority languages in the public space and semi-public space have led to manifestations of intolerance. Examples of discrimination and prejudice towards minority groups indicate that the perception of worth of a shared language differs from the actual worth of dominant language acquisition for integration purposes. The study further indicates that the efficient working of the free market by using minority languages to sell services or buy labour is perceived as conflicting with nation-building notions since it may create separately functioning sub-communities with a new cultural capital recognised as legitimate competence. The discourse types mainly represent securitising moves constructing existential threats. The perception of threat and ideas of national belonging are primarily based on a zero-sum notion favouring monolingualism. Further, the identity of the immigrant individual is seen as dynamic and adaptable to assimilationist measures whereas the identity of the state and its members are perceived as static. Also, the study shows that debates concerning language status are linked to extra-linguistic matters. To conclude, policy makers in the US need to consider the relationship between four factors, namely societal security based on collective identity, individual/human security, human rights, and a changing linguistic demography, for proposed language intervention measures to be successful.

Manipulation in Newspaper Articles : A Political Discourse Analysis of Lexical Choice and Manipulation in Japanese Newspaper Crisis Reporting in the case of North Korea

This paper analyzes some forms of linguistic manipulation in Japanese in newspapers when reporting on North Korea and its nuclear tests. The focus lies on lexical ambiguity in headlines and journalist’s voices in the body of the articles, that results in manipulation of the minds of the readers. The study is based on a corpus of nine articles from two of Japan’s largest newspapers Yomiuri Online and Asahi Shimbun Digital. The linguistic phenomenon that contribute to create manipulation are divided into Short Term Memory impact or Long Term Memory impact and examples will be discussed under each of the categories.The main results of the study are that headlines in Japanese newspapers do not make use of an ambiguous, double grounded structure. However, the articles are filled with explicit and implied attitudes as well as attributed material from people of a high social status, which suggests that manipulation of the long term memory is a tool used in Japanese media.

Motion Cues Analysis for Parkinson Gait Recognition

Background: Previous assessment methods for PG recognition used sensor mechanisms for PG that may cause discomfort. In order to avoid stress of applying wearable sensors, computer vision (CV) based diagnostic systems for PG recognition have been proposed. Main constraints in these methods are the laboratory setup procedures: Novel colored dresses for the patients were specifically designed to segment the test body from a specific colored background. Objective: To develop an image processing tool for home-assessment of Parkinson Gait(PG) by analyzing motion cues extracted during the gait cycles. Methods: The system is based on the idea that a normal body attains equilibrium during the gait by aligning the body posture with the axis of gravity. Due to the rigidity in muscular tone, persons with PD fail to align their bodies with the axis of gravity. The leaned posture of PD patients appears to fall forward. Whereas a normal posture exhibits a constant erect posture throughout the gait. Patients with PD walk with shortened stride angle (less than 15 degrees on average) with high variability in the stride frequency. Whereas a normal gait exhibits a constant stride frequency with an average stride angle of 45 degrees. In order to analyze PG, levodopa-responsive patients and normal controls were videotaped with several gait cycles. First, the test body is segmented in each frame of the gait video based on the pixel contrast from the background to form a silhouette. Next, the center of gravity of this silhouette is calculated. This silhouette is further skeletonized from the video frames to extract the motion cues. Two motion cues were stride frequency based on the cyclic leg motion and the lean frequency based on the angle between the leaned torso tangent and the axis of gravity. The differences in the peaks in stride and lean frequencies between PG and normal gait are calculated using Cosine Similarity measurements. Results: High cosine dissimilarity was observed in the stride and lean frequencies between PG and normal gait. High variations are found in the stride intervals of PG whereas constant stride intervals are found in the normal gait. Conclusions: We propose an algorithm as a source to eliminate laboratory constraints and discomfort during PG analysis. Installing this tool in a home computer with a webcam allows assessment of gait in the home environment.

Extended local labor markets due to high speed trains : Visualization of estimations in the Swedish national travel demand forecasting tool, SAMPERS

Wider economic benefits resulting from extended geographical mobility is one argument for investments in high-speed rail. More specifically, the argument for high-speed trains in Sweden has been that they can help to further spatially extend labor market regions which in turn has a positive effect on growth and development. In this paper the aim is to cartographically visualize the potential size of the labor markets in areas that could be affected by possible future high-speed trains. The visualization is based on the forecasts of labor mobility with public transport made by the Swedish national mobility transport forecasting tool, SAMPERS, for two alternative high-speed rail scenarios. The analysis, not surprisingly, suggests that the largest impact of high-speed trains results in the area where the future high speed rail tracks are planned to be built. This expected effect on local labor market regions of high-speed trains could mean that possible regional economic development effects also are to be expected in this area. However, the results, in general, from the SAMPERS forecasts indicaterelatively small increases in local labor market potentials.

Motion cue analysis for parkinsonian gait recognition

This paper presents a computer-vision based marker-free method for gait-impairment detection in Patients with Parkinson's disease (PWP). The system is based upon the idea that a normal human body attains equilibrium during the gait by aligning the body posture with Axis-of-Gravity (AOG) using feet as the base of support. In contrast, PWP appear to be falling forward as they are less-able to align their body with AOG due to rigid muscular tone. A normal gait exhibits periodic stride-cycles with stride-angle around 45o between the legs, whereas PWP walk with shortened stride-angle with high variability between the stride-cycles. In order to analyze Parkinsonian-gait (PG), subjects were videotaped with several gait-cycles. The subject's body was segmented using a color-segmentation method to form a silhouette. The silhouette was skeletonized for motion cues extraction. The motion cues analyzed were stride-cycles (based on the cyclic leg motion of skeleton) and posture lean (based on the angle between leaned torso of skeleton and AOG). Cosine similarity between an imaginary perfect gait pattern and the subject gait patterns produced 100% recognition rate of PG for 4 normal-controls and 3 PWP. Results suggested that the method is a promising tool to be used for PG assessment in home-environment.