DNA damage in spermatozoa is a crucial contributor to spontaneous abortion, severe genetic disease in the offspring and infertility. The chromatin of spermatozoa is highly compacted, transcriptionally and translationally silent, hence lacking DNA damage response (DDR). DDR foci follow within seconds after a DNA double strand break (DSB) and correlate to an abortive topoisomerase-IIb activity during spermiogenesis. When comparing the DSB frequencies at the two most fragile genomic loci (fragile sites FRA3B, FRA16D) in human and murine spermatozoa with lymphocytes, significantly increased DSB levels were detected in spermatozoa in both species. This corroborates that spermatozoa are more prone to DSBs than somatic cells. When comparing the DSB frequencies at FRA3B/FRA16D in spermatozoa of smokers with non-smokers, two-fold increases were found, probably caused by cigarette smoke components triggering abortive topoisomerase-II¿ activity. The phosphorylated DDR proteins H2AX and ATM were identified in human spermatozoa and murine spermatids using multicolour immunostaining with laser-scanning confocal microscopy (LSCM) and Western blots. Based on significantly increased DDR foci in spermatozoa of smoking men, but lacking DDR foci in response to in vitro challenge with H2O2, an abortive topoisomerase-IIb activity is the likely cause of DDR foci in spermatozoa. As DDR foci are susceptible to cigarette smoke, they can potentially be used as a novel biomarker. When comparing paternal spermatozoa, and lymphocytes as well as maternal and cord lymphocytes from 39 families for DSBs (via high-throughput LSCM pH2AX detection) and DNA fragmentation (Comet assay), significant increases were found in newborns of mothers exposed to environmental tobacco smoke and smoking fathers. When challenging lymphocytes and spermatozoa to different genotoxicants, significantly increased DNA damage in newborns compared to adults was found. This confirms an exceptional vulnerability in newborns, believed to cause increased susceptibly to disease in later life, including cancer. / European Union¿s 6th Framework project Newborns and genotoxic exposure risk (NewGeneris), British Council¿s United Kingdom Indian Education Research Initiative (UKIER)

Security breaches caused by hackers are a significant issue for businesses. This illustrates the need for protection against these attacks. Using a Security Operations Center (SOC) solution to detect attacks against ones corporation is an essential step in doing that. How should businesses deploy their SOC? This thesis compares traditional and modern SOC both by means of a literature study and hands-on experimentation, to evaluate which approach is appropriate for the current situation. The SOC solutions were set up to monitor a simulated office environment, using only free, open-source software. This thesis sheds light on both subtle and significant differences betweenthe two solutions. This thesis also concludes that the time for establishing a traditional SOC has passed. The advantages of utilizing a virtual SOC and its accompanying tool sare too significant to ignore. / Dataintrång orsakade av hackare är ett stort problem för företag. Detta belyser vikten av att ha skydd mot attacker. Användning av en SOC (Security Operations Center) lösning för att upptäcka attacker är ett viktigt steg i denna process. Hur bör företag implementera sin SOC lösning? Denna rapport jämför traditionella och moderna lösningar genom delvis litteraturstudie och sedan ett laborativt moment, för att slutligen komma fram till vilken lösning som passar dagens företag. SOC lösningarna implementerades i syfte att övervaka en simulerad kontorsmiljö. Endast gratis programvara medöppen källkod användes. Rapporten belyser både subtila och större skillnader mellan de två lösningarna. I rapporten framgår slutsatsen att det traditionella sättet att ta fram en SOC lösning på är förlegat. Fördelarna med moderna lösningar och dess tillhörandeverktyg är för omfattande för att inte dra nytta av.

Afin de répondre à l’augmentation des besoins au niveau des ressources hospitalières causées par pandémie de la maladie à coronavirus de 2019 (COVID-19), différents sites non traditionnels (SNT) ont été déployés au Québec et mondialement. Le SNT de la Place Bell a été déployé à Laval durant la première vague de la pandémie et avait comme fonctions de libérer des lits en milieu hospitalier en accueillant des usagers atteints de la COVID-19. Le but de cette étude de cas était d’examiner la capacité du SNT de la Place Bell à remplir ces fonctions. Un devis mixte convergent a été utilisé, incluant une analyse descriptive des données quantitatives ainsi que des entrevues semi-dirigées auprès de sept participants, incluant des professionnels, des non professionnels et un gestionnaire. Malgré un faible taux d’occupation et une ouverture tardive, le SNT a permis de libérer 29% des lits occupés par des usagers atteints de la COVID-19 à l’hôpital. Le cout par nuit au site était plus élevé qu’en centre d’hébergement et de soins de longue durée et que pour un autre SNT dans la province, mais moins élevé qu’en milieu hospitalier. En considérant le risque de transmission de la maladie dans les milieux de vie et qu’une des options alternatives était de garder les usagers en milieu hospitalier, le SNT semble avoir été un choix financier efficient. Le SNT a été un environnement favorable au déploiement d’une plus grande étendue de pratique infirmière, en raison du haut ratio de personnel-patient, l’absence de médecin sur place et l’autoorganisation du travail au site. En conclusion, plusieurs éléments contribuent à l’efficience d’un SNT, dont son déploiement rapide, la composition des équipes, le soutien offert aux employés et l’autonomie et l’indépendance du site. / In order to respond to the rapidly increasing needs in hospital resources caused by the coronavirus disease of 2019 (COVID-19) pandemic, different alternate care sites (ACS) were deployed in Quebec and worldwide. The Place Bell ACS was deployed in Laval during the first wave of the pandemic with the aim of offloading the volume of patients in the hospital by admitting patients with COVID-19. The aim of this case study was to examine the capacity of the Place Bell ACS in achieving these functions. A mixed convergent design was used, including a descriptive analysis of the quantitative data and semi-structured interviews with seven participants including professionals, non-professionals and a manager. Despite the low occupancy rate and the late opening, the ACS was able to free up 29% of the beds occupied by COVID-19 patients at the hospital. The cost per night at the site was greater than that of a residential and long-term care center and of another ACS in the province, but lower than the cost per night in the affiliated hospital. In considering the risk of propagating the virus in certain home environments and an alternative option of keeping the patients in the hospital, the ACS seems to have been an efficient financial option. The high staff-to-patient ratios, the absence of doctors on site and the self-organization of the team’s work contributed to making the ACS a favorable environment to a larger scope of practice for nurses. In conclusion, several elements contribute to the efficiency of an ACS, including its rapid deployment, the team compositions, the support offered to the employees as well as the site’s autonomy and independence.

There are three important greenhouse gases: carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O), which are generated from the domestic wastewater treatment systems, including on-site and off-site sources. On-site emission of greenhouse gases occurs during process of wastewater treatment, while the off-site emission of greenhouse gases occurs during energy using and other supporting activities of the treatment system. The research established model to calculate greenhouse gas emissions from the domestic wastewater treatment systems, was named No.0 MTH model. The No.0 MTH model was based on balance equations of substrate and biomass, biochemical reactions and Monod kinetics equations for biological treatment reactors and writen by programing Scalable language. Model was calibrated and applied on the Yen So wastewater treatment plant, Ha Noi and the results were obtained at 22oC as follows: off-site GHG emission is 29,560 kgCO2-eq/day; on-site GHG emission is 13,534 kgCO2-eq/day, and the rate of on-site emission is 2.506 kgCO2-eq/ kg BOD. Maybe using the No.0 MTH model to calculate greenhouse gas emissions from the domestic wastewater treatment systems with similar biological methods. / Có 3 khí nhà kính quan trọng là khí Cacbonic (CO2), khí Mêtan (CH4), và khí Đinitơ monoxit (N2O) được phát sinh từ hệ thống xử lý nước thải sinh hoạt gồm cả nguồn trực tiếp và gián tiếp. Phát thải trực tiếp khí nhà kính (KHK) xảy ra trong suốt quá trình xử lý còn phát thải gián tiếp khí nhà kính xảy ra trong quá trình sử dụng năng lượng và các hoạt động phụ trợ bên ngoài hệ thống xử lý. Nghiên cứu đã thiết lập mô hình tính toán phát thải khí nhà kính từ hệ thống xử lý nước thải sinh hoạt, được đặt tên là mô hình MTH số 0. Mô hình MTH số 0 đã dựa trên các phương trình cân bằng khối lượng cơ chất và sinh khối, các phản ứng hóa sinh và phương trình Monod đối với các thiết bị xử lý sinh học và được viết trên ngôn ngữ lập trình scala. Mô hình đã được hiệu chỉnh và được áp dụng tính toán tại nhà máy xử lý nước thải sinh hoạt Yên Sở, thành phố Hà Nội và kết quả thu được tại 22oC như sau: phát thải KNK gián tiếp là 29.560 kgCO2-tđ/ngày và phát thải KNK trực tiếp là 13.534 kgCO2-tđ/ngày với tỷ lệ phát thải khí nhà kính trực tiếp là 2,506 kgCO2-tđ/ kgBOD. Có thể sử dụng mô hình MTH số 0 để tính toán phát thải khí nhà kính từ hệ thống xử lý nước thải sinh hoạt bằng phương pháp sinh học tương tự.

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Tomträtt är en nyttjanderätt som bara kan upplåtas av stat, kommun eller om marken i övrigt är i allmän ägo. Upplåtelse av tomträtt måste ske i hel fastighet och kommer att omfatta alla befogenheter som fastigheten har. Tomträttsavgälden fastställs genom ett tomträttsavtal mellan tomträttshavaren och fastighetsägaren. Den avtalade avgälden kommer gälla för en avgäldsperiod om tio eller tjugo år. Friköp av tomträtt innebär att tomträttshavaren förvärvar fastigheten av fastighetsägaren och bildar en småhusfastighet. Hur avgälden och friköpspriset bestäms varierar beroende av vilken kommun som upplåter marken. Syftet med studien var att undersöka den ekonomiska aspekten som friköp av tomträtter medför samt att se under vilken förutsättning det är lönsamt att tomträtten friköps. Studiens syfte kommer besvaras genom att undersöka vilken ekonomisk lönsamhet som en överlåtarsituation kontra innehavarsituation medför ur ett kommunalt perspektiv. Studien avgränsas till att beröra småhustomträtter av typen radhus inom tre geografiska områden i Nacka kommun. Den ekonomiska lönsamheten som tomträtter medför ur en överlåtarsituation respektive en innehavarsituation kommer bedömas med hjälp av det principbeslut gällande tomträttsavgäld och friköpspriser som gäller i Nacka kommun idag. Metoder som används för att besvara forskningsfrågorna utgjordes av en juridisk metod. Beräkningsmetod efter värdeteori samt semistrukturerade intervjuer. Utifrån studiens resultat kan det konstateras att den ekonomiska lönsamheten är störst vid en överlåtelsesituation jämfört med en innehavssituation där skillnaden mellan situationerna är påtaglig. Resultatet påvisar även att kommuner tillämpar olika metoder vid fastställande av tomträttsavgäld och friköpspris vilket medför att den ekonomiska lönsamheten skiljer sig åt mellan kommuner beroende av vilken metod som tillämpas för avgäld och friköp.

I projekteringsfasen utformas en arbetsplatsdispositionsplan (APD-plan), vilket fungerar som en översiktlig illustration av byggarbetsplatsen. Denna ritning visualiserar de byggnader som finns på plats och visar var bland annat upplagsytor för material, transportvägar och bodetablering kan identifieras. För närvarande är 2D-ritningar den dominerande och mest frekvent använda typen av APD-planer. Det finns ytterligare dimensioner som kan adderas på en APD-plan, i denna studie undersöks de nästkommande dimensionerna, volym (3D) samt tidsaspekten (4D). För att analysera de utmaningar, möjligheter och värdet som en APD-plan i 3D och 4D kan medföra samt hur kunskapen och tillgängligheten kan utvecklas för att kontribuera till ett ökande användande av en APD-planering i 3D och 4D. Denna studie har en kvalitativ ansats med sju djupingående intervjuer. Resultatet visar att APD-planering i 3D och 4D ger en tydlig verklighetsbild av byggarbetsplatsens utseende. Vilket möjliggör att risker och fel kan uppmärksammas i ett tidigt skede och genom en simulering kopplat till tidplanen, blir det ett effektivt diskussionsunderlag som kan användas till planering inom det aktuella projektet. För att en implementering och ett fortsatt arbete av 3D och 4D APD-planering ska lyckas, krävs det att organisationerna skapar sig rätt förutsättningar genom att lägga tid och resurser för att etablera en stark kompetens som kan forma ett arbetssätt med APD-planering i 3D och 4D. / During the design phase, a construction site layout plan (CSL-plan) is developed, serving as an overview illustration of the construction site. This plan visualizes the buildings on site and indicates where, among other things such as material storage areas, transport routes, and site offices are located. Currently, 2D drawings are the most frequently used type of CSL-plans. Additional dimensions can be incorporated into an CSL-plan; this study examines the subsequent dimensions: volume (3D) and time (4D). The aim is to analyze the challenges, opportunities, and value that a 3D and 4D APD-plan can offer, and how knowledge and accessibility can be enhanced to encourage greater use of 3D and 4D CSL-planning. This study employs a qualitative approach with seven in-depth interviews. The results suggest that 3D and 4D CSL-planning using various software tools provides a clear, realistic representation of the construction site. This allows risks and errors to be identified at an early stage. Through simulation linked to the schedule, it also becomes an effective discussion framework for project planning. For successful implementation and continued use of 3D and 4D CSL-planning, organizations must create the right conditions by investing time and resources to build strong competencies that can establish an effective workflow with 3D and 4D CSL-planning.

Master of Science / Department of Computing and Information Sciences / Doina Caragea / Several computational biology and bioinformatics problems involve DNA sequence classification using supervised machine learning algorithms. The performance of these algorithms is largely dependent on the availability of labeled data and the approach used to represent DNA sequences as {\it feature vectors}. For many organisms, the labeled DNA data is scarce, while the unlabeled data is easily available. However, for a small number of well-studied model organisms, large amounts of labeled data are available. This calls for {\it domain adaptation} approaches, which can transfer knowledge from a {\it source} domain, for which labeled data is available, to a {\it target} domain, for which large amounts of unlabeled data are available. Intuitively, one approach to domain adaptation can be obtained by extracting and representing the features that the source domain and the target domain sequences share. \emph{Latent Dirichlet Allocation} (LDA) is an unsupervised dimensionality reduction technique that has been successfully used to generate features for sequence data such as text. In this work, we explore the use of LDA for generating predictive DNA sequence features, that can be used in both supervised and domain adaptation frameworks. More precisely, we propose two dimensionality reduction approaches, LDA Words (LDAW) and LDA Distribution (LDAD) for DNA sequences. LDA is a probabilistic model, which is generative in nature, and is used to model collections of discrete data such as document collections. For our problem, a sequence is considered to be a ``document" and k-mers obtained from a sequence are ``document words". We use LDA to model our sequence collection. Given the LDA model, each document can be represented as a distribution over topics (where a topic can be seen as a distribution over k-mers). In the LDAW method, we use the top k-mers in each topic as our features (i.e., k-mers with the highest probability); while in the LDAD method, we use the topic distribution to represent a document as a feature vector. We study LDA-based dimensionality reduction approaches for both supervised DNA sequence classification, as well as domain adaptation approaches. We apply the proposed approaches on the splice site predication problem, which is an important DNA sequence classification problem in the context of genome annotation. In the supervised learning framework, we study the effectiveness of LDAW and LDAD methods by comparing them with a traditional dimensionality reduction technique based on the information gain criterion. In the domain adaptation framework, we study the effect of increasing the evolutionary distances between the source and target organisms, and the effect of using different weights when combining labeled data from the source domain and with labeled data from the target domain. Experimental results show that LDA-based features can be successfully used to perform dimensionality reduction and domain adaptation for DNA sequence classification problems.

Master of Landscape Architecture / Department of Landscape Architecture/Regional and Community Planning / Mary C. Kingery-Page / Placemaking for Socially Resilient Site Design is a project focused on clarifying and characterizing social resilience. This project used ethnographic methods to answer the question: what qualities of place affect the downtown community’s desires for a temporary landscape in Wichita, Kansas? Through literature review this project further defined what social resilience meant at the site scale. Social resilience was operationalized as social systems ability to maintain function while promoting social trust, reciprocity, collaboration, and character between networks of varying scales (Putnam 1995). Literature review provided the foundational knowledge on creative placemaking, a design strategy used to improve community prosperity through a sense of place and imageability (Artscape 2014). Place is determined by a user’s surroundings, and more importantly the memory of social engagement on site (Fleming 2007). Creative placemaking design strategies are valuable and specific to location. Therefore, it was imperative I incorporated ethnographic research methods to answer my focus question. Ethnographic research investigates cultural patterns and themes expressed or observed by a community (LeCompte et al. 1991). This form of research is unconventional for the typical site design process in landscape architecture. However, it proved to be effective in determining the most successful site use and organization. The ethnographic research allowed me to inventory and document user’s most desirable site needs and programming through the stakeholder design charrette and individual interviews. In November 2014 the Wichita Downtown Development Cooperation requested our team as a partner in developing a temporary landscape for downtown Wichita, Kansas. The site was already selected with the intention of becoming Douglas Avenue Pop-Up Park. Funding for this project was awarded to the WDDC in the form of a $146,025 grant from the Knight Foundation. Using an iterative community feedback process with five ethnographic interviews, I reevaluated the WDDC’s initial Pop-Up Park plan resulting from a community charrette. Recurring themes from interviews were identity crisis of downtown, outdoor preference, lack of residential amenities, negative perception of active and public transit, downtown lifestyle, Wichita as a place for families, and lack of nighttime activation. Using the recurring interview themes, I proposed a plan conducive to social resilience.