Cloning, sequence analysis, and expression of cDNA coding for the major house dust mite allergen, Der f 1, in Escherichia coli

Our objective was to clone, express and characterize adult Dermatophagoides farinae group 1 (Der f 1) allergens to further produce recombinant allergens for future clinical applications in order to eliminate side reactions from crude extracts of mites. Based on GenBank data, we designed primers and amplified the cDNA fragment coding for Der f 1 by nested-PCR. After purification and recovery, the cDNA fragment was cloned into the pMD19-T vector. The fragment was then sequenced, subcloned into the plasmid pET28a(+), expressed in Escherichia coli BL21 and identified by Western blotting. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Sequence analysis showed the presence of an open reading frame containing 966 bp that encodes a protein of 321 amino acids. Interestingly, homology analysis showed that the Der p 1 shared more than 87% identity in amino acid sequence with Eur m 1 but only 80% with Der f 1. Furthermore, phylogenetic analyses suggested that D. pteronyssinus was evolutionarily closer to Euroglyphus maynei than to D. farinae, even though D. pteronyssinus and D. farinae belong to the same Dermatophagoides genus. A total of three cysteine peptidase active sites were found in the predicted amino acid sequence, including 127-138 (QGGCGSCWAFSG), 267-277 (NYHAVNIVGYG) and 284-303 (YWIVRNSWDTTWGDSGYGYF). Moreover, secondary structure analysis revealed that Der f 1 contained an a helix (33.96%), an extended strand (17.13%), a ß turn (5.61%), and a random coil (43.30%). A simple three-dimensional model of this protein was constructed using a Swiss-model server. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Alignment and phylogenetic analysis suggests that D. pteronyssinus is evolutionarily more similar to E. maynei than to D. farinae.

Energy aware software for many-core systems

Many-core systems provide a great potential in application performance with the massively parallel structure. Such systems are currently being integrated into most parts of daily life from high-end server farms to desktop systems, laptops and mobile devices. Yet, these systems are facing increasing challenges such as high temperature causing physical damage, high electrical bills both for servers and individual users, unpleasant noise levels due to active cooling and unrealistic battery drainage in mobile devices; factors caused directly by poor energy efficiency. Power management has traditionally been an area of research providing hardware solutions or runtime power management in the operating system in form of frequency governors. Energy awareness in application software is currently non-existent. This means that applications are not involved in the power management decisions, nor does any interface between the applications and the runtime system to provide such facilities exist. Power management in the operating system is therefore performed purely based on indirect implications of software execution, usually referred to as the workload. It often results in over-allocation of resources, hence power waste. This thesis discusses power management strategies in many-core systems in the form of increasing application software awareness of energy efficiency. The presented approach allows meta-data descriptions in the applications and is manifested in two design recommendations: 1) Energy-aware mapping 2) Energy-aware execution which allow the applications to directly influence the power management decisions. The recommendations eliminate over-allocation of resources and increase the energy efficiency of the computing system. Both recommendations are fully supported in a provided interface in combination with a novel power management runtime system called Bricktop. The work presented in this thesis allows both new- and legacy software to execute with the most energy efficient mapping on a many-core CPU and with the most energy efficient performance level. A set of case study examples demonstrate realworld energy savings in a wide range of applications without performance degradation.

Adopting the Vaadin Java framework to rebuild VTT’s Web Interfaces and Database Applications

With the growth in new technologies, using online tools have become an everyday lifestyle. It has a greater impact on researchers as the data obtained from various experiments needs to be analyzed and knowledge of programming has become mandatory even for pure biologists. Hence, VTT came up with a new tool, R Executables (REX) which is a web application designed to provide a graphical interface for biological data functions like Image analysis, Gene expression data analysis, plotting, disease and control studies etc., which employs R functions to provide results. REX provides a user interactive application for the biologists to directly enter the values and run the required analysis with a single click. The program processes the given data in the background and prints results rapidly. Due to growth of data and load on server, the interface has gained problems concerning time consumption, poor GUI, data storage issues, security, minimal user interactive experience and crashes with large amount of data. This thesis handles the methods by which these problems were resolved and made REX a better application for the future. The old REX was developed using Python Django and now, a new programming language, Vaadin has been implemented. Vaadin is a Java framework for developing web applications and the programming language is extremely similar to Java with new rich components. Vaadin provides better security, better speed, good and interactive interface. In this thesis, subset functionalities of REX was selected which includes IST bulk plotting and image segmentation and implemented those using Vaadin. A code of 662 lines was programmed by me which included Vaadin as the front-end handler while R language was used for back-end data retrieval, computing and plotting. The application is optimized to allow further functionalities to be migrated with ease from old REX. Future development is focused on including Hight throughput screening functions along with gene expression database handling

A Study of Privacy Preserving Queries with Bloom Filters

This thesis focuses on the private membership test (PMT) problem and presents three single server protocols to resolve this problem. In the presented solutions, a client can perform an inclusion test for some record x in a server's database, without revealing his record. Moreover after executing the protocols, the contents of server's database remain secret. In each of these solutions, a different cryptographic protocol is utilized to construct a privacy preserving variant of Bloom filter. The three suggested solutions are slightly different from each other, from privacy perspective and also from complexity point of view. Therefore, their use cases are different and it is impossible to choose one that is clearly the best between all three. We present the software developments of the three protocols by utilizing various pseudocodes. The performance of our implementation is measured based on a real case scenario. This thesis is a spin-off from the Academy of Finland research project "Cloud Security Services".

Measuring software security from the design of software

The vast majority of our contemporary society owns a mobile phone, which has resulted in a dramatic rise in the amount of networked computers in recent years. Security issues in the computers have followed the same trend and nearly everyone is now affected by such issues. How could the situation be improved? For software engineers, an obvious answer is to build computer software with security in mind. A problem with building software with security is how to define secure software or how to measure security. This thesis divides the problem into three research questions. First, how can we measure the security of software? Second, what types of tools are available for measuring security? And finally, what do these tools reveal about the security of software? Measuring tools of these kind are commonly called metrics. This thesis is focused on the perspective of software engineers in the software design phase. Focus on the design phase means that code level semantics or programming language specifics are not discussed in this work. Organizational policy, management issues or software development process are also out of the scope. The first two research problems were studied using a literature review while the third was studied using a case study research. The target of the case study was a Java based email server called Apache James, which had details from its changelog and security issues available and the source code was accessible. The research revealed that there is a consensus in the terminology on software security. Security verification activities are commonly divided into evaluation and assurance. The focus of this work was in assurance, which means to verify one’s own work. There are 34 metrics available for security measurements, of which five are evaluation metrics and 29 are assurance metrics. We found, however, that the general quality of these metrics was not good. Only three metrics in the design category passed the inspection criteria and could be used in the case study. The metrics claim to give quantitative information on the security of the software, but in practice they were limited to evaluating different versions of the same software. Apart from being relative, the metrics were unable to detect security issues or point out problems in the design. Furthermore, interpreting the metrics’ results was difficult. In conclusion, the general state of the software security metrics leaves a lot to be desired. The metrics studied had both theoretical and practical issues, and are not suitable for daily engineering workflows. The metrics studied provided a basis for further research, since they pointed out areas where the security metrics were necessary to improve whether verification of security from the design was desired.

Life-related negative customer emotions in real estate agent encounters

The goal of this study was to explore how do customers’ life-related negative emotions affect real estate business. This was divided into two research questions: 1. What life-related negative emotions can be recognised in real estate customer encounters? 2. How do the recognised emotions affect customer encounters and the realtor’s work? 3. How can the realtor take the emotions into account in customer service? The theoretical background consists of two main lines of study: emotions and customer encounters. A wide literary review on emotions research was conducted from a cognitive psychology point of view, focusing on negative emotions. Emotions research was then combined into the field of customer encounters. Qualitative study was chosen as the methodological basis of the study. Empirical material of this study was collected through in-depth interviews with 13 successful Finnish real estate agents. Narrative research was used as a method for the study. Four life-related emotion categories were recognized in real estate customer encounters: sadness, anger, anxiety and shame. These emotions rose from issues varying from death of a close one to divorce and from major changes in life stages to deep emotional attachment to an old home. The study also found that these incidental negative emotions do affect customer encounters and realtors’ work. The emotions affected the decision making of customers and sometimes overshadowed reason. Some emotions made the customer passive and slow to make any decisions, while others made their decision making fast and hasty. Even though the incidental emotions might not have had anything to do with the real estate deal, they could affect the outcome of the customer encounter and the whole real estate deal. Interestingly enough, the study found that not all successful real estate agents knowingly serve customers in an emotional level. The study does, however, suggest that in fact it may be an ethical decision of the customer server to take into account the emotional state of the customer. Attending to the emotional side of customers does not only increase pleasantness of the customer encounter, but may improve and balance customer decision making and prevent hasty decisions possibly leading to improved customer satisfaction. This study also gave practical managerial implications to customer service providers on how negative incidental emotions can be attended to in a customer encounter. This study could be useful not only to real estate agents, but also in other types of customer service, especially with vulnerable populations or other types of home-related business.

Chronique, histoires de la Bible, Vies de saints, Sermons de MAURICE DE SULLY, en français.

Contient : Chronique abrégée depuis la naissance de Jésus-Christ jusqu'en 1304. Cf. Hist. litt. de la France, t. XXXII, p. 240 ; Recueil d'histoires tirées de la Bible : « Bien doivent metre lor entendement tuit cil ki ont sens... » (Genèse, Juges, Rois et Macchabées) ; Vie de Jésus-Christ: « Quant li tans fu raemplis... » ; Vies de saints abrégées, en français ; Sermons de MAURICE DE SULLY, en français. — Le premier de ces sermons débute : « Dominus ac salvator noster, dilectissimi, post passionem salutiferam... Dicit ei pasce oves meas. — Seignor provoire, ceste parole ne fu mie seulement dite à mon signor S. Pierre... » ; « Ce est la ramembrance combien li Crestien furent en servage o les Sarasins. » (Jusqu'en 1290. — Écriture postérieure.) — A la fin (fol. 375): « Ssm scrhtpr tblhs mpsstrbt mfb lhttfrb qsbl». » = Sum scriptor talis mosstrat mea littera qualis

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal

Système de listes de vérification interactives du niveau de conformité des maquettes avec les recommandations des fabricants de plateformes mobiles

L'ensemble de mon travail a été réalisé grâce a l'utilisation de logiciel libre.

Carl Schmitt et la critique de l’universalisme libéral

Ce mémoire porte sur la pensée politique du juriste allemand Carl Schmitt, plus précisément sur sa critique de l’universalisme libéral. Sur la base d’une analyse de ses principaux textes, nous démontrons que la pertinence de cet auteur controversé réside dans le défi renouvelé que présente son antinormativisme pour la pensée politique contemporaine. Nous soutenons qu’il y a chez Schmitt un souci constant de rattacher le droit à l’ordre concret, qu’il soit institué ou reçu. Nous démontrons ensuite comment l’antinormativisme se prolonge en droit international dans la critique de l’universalisme, entendu comme l’ambition de penser le politique à partir de l’humanité comme sujet unique. D’une perspective décisionniste, l’universalisme masque des intérêts impérialistes qu’il convient de dénoncer ; d’une perspective institutionnaliste, l’universalisme néglige l’ordre spatial concret sur lequel repose le droit international. Nous affirmons que Schmitt démontre l’importance de préserver l’autonomie de la science juridique envers la morale et la technique.

Échantillonnage des distributions continues non uniformes en précision arbitraire et protocole pour l'échantillonnage exact distribué des distributions discrètes quantiques

La thèse est divisée principalement en deux parties. La première partie regroupe les chapitres 2 et 3. La deuxième partie regroupe les chapitres 4 et 5. La première partie concerne l'échantillonnage de distributions continues non uniformes garantissant un niveau fixe de précision. Knuth et Yao démontrèrent en 1976 comment échantillonner exactement n'importe quelle distribution discrète en n'ayant recours qu'à une source de bits non biaisés indépendants et identiquement distribués. La première partie de cette thèse généralise en quelque sorte la théorie de Knuth et Yao aux distributions continues non uniformes, une fois la précision fixée. Une borne inférieure ainsi que des bornes supérieures pour des algorithmes génériques comme l'inversion et la discrétisation figurent parmi les résultats de cette première partie. De plus, une nouvelle preuve simple du résultat principal de l'article original de Knuth et Yao figure parmi les résultats de cette thèse. La deuxième partie concerne la résolution d'un problème en théorie de la complexité de la communication, un problème qui naquit avec l'avènement de l'informatique quantique. Étant donné une distribution discrète paramétrée par un vecteur réel de dimension N et un réseau de N ordinateurs ayant accès à une source de bits non biaisés indépendants et identiquement distribués où chaque ordinateur possède un et un seul des N paramètres, un protocole distribué est établi afin d'échantillonner exactement ladite distribution.

Analysis of Some Queueing Models Related To N-Policy: Operations Research

This study is about the analysis of some queueing models related to N-policy.The optimal value the queue size has to attain in order to turn on a single server, assuming that the policy is to turn on a single server when the queue size reaches a certain number, N, and turn him off when the system is empty.The operating policy is the usual N-policy, but with random N and in model 2, a system similar to the one described here.This study analyses “ Tandem queue with two servers”.Here assume that the first server is a specialized one.In a queueing system,under N-policy ,the server will be on vacation until N units accumulate for the first time after becoming idle.A modified version of the N-policy for an M│M│1 queueing system is considered here.The novel feature of this model is that a busy service unit prevents the access of new customers to servers further down the line.It is deals with a queueing model consisting of two servers connected in series with a finite intermediate waiting room of capacity k.Here assume that server I is a specialized server.For this model ,the steady state probability vector and the stability condition are obtained using matrix – geometric method.

T-Policy in Reliability and Inventory

In this thesis T-policy is implemented to the inventory system with random lead time and also repair in the reliability of k-out-of-n system. Inventory system may be considered as the system of keeping records of the amounts of commodities in stock. Reliability is defined as the ability of an entity to perform a required function under given conditions for a given time interval. It is measured by the probability that an entity E can perform a required function under given conditions for the time interval. In this thesis considered k-out-of-n system with repair and two modes of service under T-policy. In this case first server is available always and second server is activated on elapse of T time units. The lead time is exponentially distributed with parameter  and T is exponentially distributed with parameter  from the epoch at which it was inactivated after completion of repair of all failed units in the previous cycle, or the moment n-k failed units accumulate. The repaired units are assumed to be as good as new. In this study , three different situations, ie; cold system, warm system and hot system. A k-out-of-n system is called cold, warm or hot according as the functional units do not fail, fail at a lower rate or fail at the same rate when system is shown as that when it is up.

Retrial Queues with Orbital Search

Queueing system in which arriving customers who find all servers and waiting positions (if any) occupied many retry for service after a period of time are retrial queues or queues with repeated attempts. This study deals with two objectives one is to introduce orbital search in retrial queueing models which allows to minimize the idle time of the server. If the holding costs and cost of using the search of customers will be introduced, the results we obtained can be used for the optimal tuning of the parameters of the search mechanism. The second one is to provide insight of the link between the corresponding retrial queue and the classical queue. At the end we observe that when the search probability Pj = 1 for all j, the model reduces to the classical queue and when Pj = 0 for all j, the model becomes the retrial queue. It discusses the performance evaluation of single-server retrial queue. It was determined by using Poisson process. Then it discuss the structure of the busy period and its analysis interms of Laplace transforms and also provides a direct method of evaluation for the first and second moments of the busy period. Then it discusses the M/ PH/1 retrial queue with disaster to the unit in service and orbital search, and a multi-server retrial queueing model (MAP/M/c) with search of customers from the orbit. MAP is convenient tool to model both renewal and non-renewal arrivals. Finally the present model deals with back and forth movement between classical queue and retrial queue. In this model when orbit size increases, retrial rate also correspondingly increases thereby reducing the idle time of the server between services

Queues with retrial/self-generation of priorities /postponement of work and some related reliability problems

Application of Queueing theory in areas like Computer networking, ATM facilities, Telecommunications and to many other numerous situation made people study Queueing models extensively and it has become an ever expanding branch of applied probability. The thesis discusses Reliability of a ‘k-out-of-n system’ where the server also attends external customers when there are no failed components (main customers), under a retrial policy, which can be explained in detail. It explains the reliability of a ‘K-out-of-n-system’ where the server also attends external customers and studies a multi-server infinite capacity Queueing system where each customer arrives as ordinary but can generate into priority customer which waiting in the queue. The study gives details on a finite capacity multi-server queueing system with self-generation of priority customers and also on a single server infinite capacity retrial Queue where the customer in the orbit can generate into a priority customer and leaves the system if the server is already busy with a priority generated customer; else he is taken for service immediately. Arrival process is according to a MAP and service times follow MSP.