During recent years there has been a great focus on the climate changes within the media. More or less every day more newspaper articles are presented about the global warming issue and the effect on us human race. Climate models predict higher temperatures and more rain in the northern part of Europe. It is also predicted that the weather will become more extreme e.g. it will rain a lot during longer periods than has been the norm. If these predictions are correct, the amount of water that is going to be transported away in streams and rivers will increase and so also will the subsoil water level. The latter increases the risk for landslides in areas with fine grained soils. An early warning system that is able to alert people before a landslide take place would be of great interest. The purpose of this work is to develop a complete real-time displacement monitoring system based on observations from several GPS-receivers that could be used as an early warning system. Due to the complex correlation structure of the traditionally used double differences, an alternative method based on undifferenced observations is used. Theoretically this approach shows some advantages and simplifies the correlative structure of observables compared to the double differenced method. A complete model for the undifferenced approach is presented in this thesis including its software implementation. A displacement detection system includes not only the positioning algorithms, but also methods to detect if any displacement occurs. There are many methods available to discriminate displacements, which are used in the traditional control of manufacturing processes. Several of these methods are compared in this thesis, such as the Shewhart chart, different Weighted Moving Average (WMA) charts and the CUmulative SUMmation (CUSUM). Practical tests show that it is possible to detect an abrupt shift on sub centimetre level at the same epoch as the shift occurs. Smaller shifts are also detectable with the applied approach but with a slightly longer detection time. / QC 20100624

PCR is a rapid, reproducible method for nucleic acid detection. However, this technology displays significant deficiencies when applied in clinical microbiology. This work’s aim was to improve current diagnostics and provide sensitive and quantitative real-time PCRs. Paper I describes the development of a sensitive and specific quantitative real-time PCR for the detection of Streptococcus pneumoniae, based on the Spn9802 DNA fragment. Applied to nasopharyngeal aspirates from 166 pneumonia patients, Spn9802 PCR had a sensitivity of 94% and a specificity of 98%. In Paper II the performance of a ply gene PCR for identification of pneumococcal lower respiratory tract infection (LRTI) was evaluated on bronchoalveloar lavage fluids. At the detection limit 103 genome copies/mL, 89% sensitivity but only 43% specificity was achieved. Paper III shows that S. pneumoniae DNA is detectable in plasma from acutely febrile patients. Sensitivities were low (26-42%) for detection of pneumococcal pneumonia, for bacteraemic pneumococcal pneumonia they were 60-70%. Paper IV describes evaluation of four PCR targets for Haemophilus influenzae detection. A real-time PCR based on the P6 gene was developed and applied to 166 CAP patients, using cut-off of 104 genome copies/mL the assay had a sensitivity of 97% and a specificity of 96%. In paper V, the two real-time PCRs presented in papers I and IV were combined with a PCR for detection of Neisseriae meningitidis. The analytical sensitivity of this multiplex real-time PCR was not affected by using a mixture of reagents and a combined DNA standard (S. pneumoniae/H. influenzae) in single tubes. Applied to 156 LRTI patients, this PCR had sensitivities over 90% for S. pneumoniae and H. influenzae, and specificities of 89% and 96%, respectively. In conclusion, real-time PCR assays are useful for the diagnosis of S. pneumoniae and H. influenzae. They enable detection after antibiotic installation, and quantification increases the etiological specificity of pneumonia.

Reliable methods to analyze food for the presence of almond are important – not only for those allergic to almond, but also for monitoring the compliance with labelling regulations (EG directive 2003/89). Until now the Swedish National Food Administration has used methods like rocket immunoelectrophoresis and real-time PCR to detect almond in food. These methods are, however, not sensitive enough for protecting the most sensitive individuals. Therefore, the performance of a commercial ELISA kit was tested with regard to specificity/cross reactivity and limit of detection for almond both in solution and in different matrixes. The limit of quantitation was at least 3,1 ppm (mg/kg) in solution and similar concentrations were measured in bisquits and chocolate. The ELISA method was about 100-fold more sensitive than rocket immunoelectrophoresis and PCR. The specificity of the test kit was evaluated against a number of different nuts and seeds. No important cross reactivity was found. The antibodies against almond used in the kit can not differentiate between almond and apricot kernel. For such purposes the PCR method could be used.

Purpose: The aim of this thesis is to study the European (ESTRO/EAU/EORTC) and American (ABS) guidelines how to report the permanent seed implant and the most significant dosimetric parameters. It will also report on the permanent seed implant at Södersjukhuset, Karolinska University Hospital according to the guidelines. A large number of studies on pre- and post-implant dosimetry on permanent seed implants have recently been published but none is considered a standard. This makes it difficult, if not impossible, to compare data from different centres. The differences in reporting will also be discussed in this thesis. Another part of the study is to investigate how the morbidity correlates with the dose. The results in this report will give an overview of the experience at Södersjukhuset. Matherials and Methods: This study includes 198 patients who received implants between 2004-2007 with I-125 seeds under transperineal ultrasound at Södersjukhuset (to a prescribed dose of 145 Gy). The dose-planning system VariSeed 7.1 was used with an online connection to the ultrasound system with real-time verification. Dose constraints for the planning system are V(100)>99%, V(150)>60%, V(200)>25%, UrD(10)<130% and UrD(30)<125%. Outer and inner wall of rectum was outlined for 55 patients as recommended by ESTRO/EAU/EORTC and doses to rectum were also computed. Results: The median value for dosimetric parameters at Södersjukhuset, Karolinska University Hospital are for the prostate; D(90)=174Gy (153-194Gy), V(100)= 99% (93-100%), V(150)= 57% (40-74%), for the urethra; UrD(30) = 130% (112-147%), UrD(10) = 124% (107-142%) and for the rectum; RD2cc= 98Gy (73-128Gy), RD0.1cc=164Gy (119-240Gy), RV(100)=0.3cc (0.0-1.3cc), RV(150)=0.0cc (0.0-0.2cc). These values correspond to recommended data, except for the V(150) value. Regarding the clinically observed results, 3 patients had a relapse in their cancer, 2 patients had mild proctitis and 15 patients had urinary problems. Discussion and Conclusions: The significant dosimetric parameters for reporting according to ESTRO/EAU/EORTC and ABS for prostate are D90[Gy], V(100)[%] and V(150)[%], for urethra are D(30) and D(10), and for rectum RD2cc and RD0.1cc. These parameters consider as a minimum to use and they further recommend secondary parameters to report. Other authors have also recommended to report RV(100) and RV(150) for rectum. This study did not show any relationship between UrD(10), UrD(30) and urinary morbidity. According to the recommendations every patient should undergo a CT-based evaluation. Further investigations are needed on whether a post-implant CT-study is necessary for real-time implantation, as there is not enough published data on this aspect.

Picropodophyllin (PPP) is an analogue of the anti tumour lignan podophyllotoxin with the unique ability to selectively inhibit the receptor of Insulin like growth factor 1(IGF-1). IGF-1 is believed to play an important part in development of the endometrium facing implantation. With PPP treated mice, studies can be made to measure gene expression from tissue of both treated and untreated mice to compare the role of IGF-1 regarding ovulation, implantation and receptivity. The aim of this study was to analyze gene expression of some steroid hormone receptors and cytokines in ovaries from mice treated with PPP. In this study, seven mice were treated with PPP at different times and tissue was collected. PCR-primers for cDNA sequences of estrogene receptor α, estrogene receptor β, progesterone receptor A, progesterone receptor B, growth hormone receptor, interleukin 1 α, interleukin 1 β, tumour necrosis factor α and androgen receptor were used. Real Time PCR was run with the samples and gene expression was measured. The results of this study showed that the inhibition of IGF-1 receptor interacted with IGF-1 which lead to altered levels of estrogene receptor alpha, progesterone receptor, growth hormone receptor and androgen receptor that can decrease ovulation. The results also showed the differences in gene products between treated and untreated samples, suggesting that IGF-1 plays an important role regarding ovulation. / Studier med hjälp av den selektiva insulinlika tillväxtfaktor 1 receptorn (IGF-1R) antagonisten; picropodof?phyllin (PPP), hur samspelet mellan livmoderslemhinnan och implantationsprocessen, samt hur ovulationen påverkas av insulinlika tillväxtfaktorn 1 (IGF-1) kan nu utföras. IGF-1 tros ha en viktig roll för den reproduktiva processen, där den påverkar ovulation, implantation och embryoutveckling. IGF-familjen består av tre ligander; insulin, IGF-1 och IGF-2. IGF transporteras bundet till bindarprotein (IGFBP). Medlemmarna i IGF receptorfamiljen kan binda IGF-1, IGF-2 och insulin fast med olika affinitet. PPP som är en cykloligan, är en analog från podofyllotoxin och fungerar som en syntetisk IGF-1 receptorantagonist, som selektivt inhiberar receptorns aktivitet. PPP tros även kunna nedreglera genexpression av receptorn. Tre tidigare projektarbeten har utförts på vävnader från möss injicerade med PPP. Tyngdpunkterna i dessa arbeten har legat på immunhistokemiska studier av IGF-1 i reproduktionsorgan från möss, uttryck av IGF-1, dess receptor och bindarprotein 1 i ovarier och uterus efter behandling med PPP. I denna studie användes vävnad samt cDNA från sju möss behandlade med PPP, i olika stadier av reproduktionen samt även icke behandlade möss. Studiens syfte var att med sanntids-PCR jämföra genuttryck från östrogenreceptor α och β, progesteronreceptor A och B, tillväxthormonreceptor, Interleukin 1 α och β, ’tumor necrosis’ faktor α samt androgenreceptor i vävnad från PPP-behandlade och obehandlade möss och genom de erhållna resultaten från ovarievävnaden utläsa effekten på ovulationen och från uterusvävnaden effekten på implantation och receptivitet. Studieresultaten visade att IGF-1s frånvaro gav förändrade nivåer av genprodukter, som medförde minskad ovulationen. Studien visade att IGF-1s roll vid ovulationen var väsentlig.

The idea of automatic programming using the genetic programming paradigm is a concept that has been explored in the work of Koza and several works since. Most problems attempted using genetic programming are finite in size, meaning that the problem involved evolving a function that operates over a finite domain, or evolving a routine that will only run for a finite amount of time. For problems with a finite domain, the internal representation of each individual is typically a finite automaton that is unable to store an unbounded amount of data. This thesis will address the problem of applying genetic programming to problems that have a ``discrete unbounded domain", meaning the problem involves evolving a function that operates over an unbounded domain with discrete quantities. For problems with an discrete unbounded domain, the range of possible behaviors achievable by the evolved functions increases with more versatile internal memory schemes for each of the individuals. The specific problem that I will address in this thesis is the problem of evolving a real-time deciding program for a fixed language of strings. I will discuss two paradigms that I will use to attempt this problem. Each of the paradigms will allow each individual to store an unbounded amount of data, using an internal memory scheme with at least the capabilities of a Turing tape. As each character of an input string is being processed in real time, the individual will be able to imitate a single step of a Turing machine. While the real-time restriction will certainly limit the languages for which a decider may be evolved, the fact that the evolved deciding programs run in real-time yields possible applications for these paradigms in the discovery of new algorithms. The first paradigm that I will explore will take a naive approach that will ultimately prove to be unsuccessful. The second paradigm that I will explore will take a more careful approach that will have a much greater success, and will provide insight into the design of genetic programming paradigms for problems over a discrete unbounded domain.

Microblogging is an increasingly popular form of social media. One of the most popular microblogging services is Twitter. The number of messages posted to Twitter on a daily basis is extremely large. Accordingly, it becomes hard for users to sort through these messages and find ones that interest them. Twitter offers search mechanisms but they are relatively simple and accordingly the results can be lacklustre. Through participation in the 2011 Text Retrieval Conference's Microblog Track, this thesis examines real-time ad hoc search using standard information retrieval approaches without microblog or Twitter specific modifications. It was found that using pseudo-relevance feedback based upon a language model derived from Twitter posts, called tweets, in conjunction with standard ranking methods is able to perform competitively with advanced retrieval systems as well as microblog and Twitter specific retrieval systems. Furthermore, possible modifications both Twitter specific and otherwise are discussed that would potentially increase retrieval performance. Twitter has also spawned an interesting phenomenon called hashtags. Hashtags are used by Twitter users to denote that their message belongs to a particular topic or conversation. Unfortunately, tweets have a 140 characters limit and accordingly all relevant hashtags cannot always be present in tweet. Thus, Twitter users cannot easily find tweets that do not contain hashtags they are interested in but should contain them. This problem is investigated in this thesis in three ways using learning methods. First, learning methods are used to determine if it is possible to discriminate between two topically different sets of a tweets. This thesis then investigates whether or not it is possible for tweets without a particular hashtag, but discusses the same topic as the hashtag, to be separated from random tweets. This case mimics the real world scenario of users having to sift through random tweets to find tweets that are related to a topic they are interested in. This investigation is performed by removing hashtags from tweets and attempting to distinguish those tweets from random tweets. Finally, this thesis investigates whether or not topically similar tweets can also be distinguished based upon a sub-topic. This was investigated in almost an identical manner to the second case. This thesis finds that topically distinct tweets can be distinguished but more importantly that standard learning methods are able to determine that a tweet with a hashtag removed should have that hashtag. In addition, this hashtag reconstruction can be performed well with very few examples of what a tweet with and without the particular hashtag should look like. This provides evidence that it may be possible to separate tweets a user may be interested from random tweets only using hashtags they are interested in. Furthermore, the success of the hashtag reconstruction also provides evidence that users do not misuse or abuse hashtags since hashtag presence was taken to be the ground truth in all experiments. Finally, the applicability of the hashtag reconstruction results to the TREC Microblog Track and a mobile application is presented.

This thesis presents the framework of a complex business process driven event stream processing system to produce meaningful output with direct implications to the business objectives of an organization. This framework is demonstrated using a case study instantiating the management of a newborn infant with hypoglycaemia. Business processes defined within guidelines, are defined at build-time while critical knowledge found in the definition of business processes are used to support their enactment for stream analysis. Four major research contributions are delivered. The first contribution enables the definition and enactment of complex business processes in real-time. The second contribution supports the extraction of business process using knowledge found within the initial expression of the business process. The third contribution allows for the explicit use of temporal abstraction and stream analysis knowledge to support enactment in real-time. Finally, the last contribution is the real-time integration of heterogeneous streams based on Service-Oriented Architecture principles. / UOIT

With the advent of faster computer processors and better optimization algorithms, Model Predictive Control (MPC) systems are more readily used for real-time applications. This research focuses on the application of MPC to trajectory generation of autonomous vehicles in an online manner. The operating environment is assumed to be unknown with various different types of obstacles. Models of simplified 2-D dynamics of the vehicle are developed, discretized and validated against a nonlinear CarSim vehicle model. The developed model is then used to predict future states of the vehicle. The relationship of the weight transfer to the tire slip angle is investigated. The optimal trajectory tracking problem is formulated in terms of a cost function minimization with constraints. Initially, a gradient descent method is used to minimize the cost function. A MATLAB based MPC controller is developed and interfaced with CarSim in order to test the controller on a vehicle operating in a realistic environment. The effects of varying MPC look-ahead horizon lengths on the computation time, simulation cost and the tracking performance are also investigated. Simulation results show that the new MPC controller provides satisfactory online obstacle avoidance and tracking performance. Also, a trajectory tracking criterion with goal point information is found to be superior to traditional trajectory tracking methods since they avoid causing the vehicle to retreat once a large obstacle is detected on the desired path. It is further demonstrated that at a controller frequency of 20Hz, the implementation is real-time implementable only at shorter horizon lengths. / UOIT

Winter wheat (<i>Triticum aestivum</i> L.), seeded in the fall, cold acclimates when exposed to low fall temperatures. Growth resumes in spring, culminating in early summer harvest. Winter wheat yield is generally 20-25% higher than spring wheat. However, winter damage/kill can reduce its yield. A better understanding of the cold acclimation/tolerance process could help in the development of improved breeding strategies for winter wheat hardiness. Transcriptional activators and specific cold regulated (COR) genes are induced as a result of exposure to low temperatures. Thus, the objective of this study was to determine the quantitative expression of three COR genes (Wcs120, Wcor410 and Wcor14b) and one transcriptional activator (WCBF1) in field-grown wheat using real-time PCR and to establish any association with LT50 (temperature at which 50% of plants are killed). Winter Norstar (vrn-A1/vrn-A1), spring Manitou (Vrn-A1/Vrn-A1) and two near-isogenic lines (Spring Norstar (Vrn-A1/vrn-A1) and Winter Manitou (vrn-A1/vrn-A1), respectively) were used in these studies. Plants were sampled on three dates (Sept. 29, Oct. 12 and Oct. 26) in the fall of 2004. Accumulation of WCBF1 transcripts was highest in Norstar, but in all four genotypes there was an increase in transcripts by the second sampling date, followed by a decline on the third sampling date. Wcs120 transcripts increased from the first to the third sampling date in Norstar, Spring Norstar and Winter Manitou, but increased to the second sampling date and decreased by the third in Manitou. For Wcor14b, generally there was an increase to the second sampling date, followed by a decrease or steady levels on the third. Wcor410 showed a similar pattern, except for Spring Norstar wherein transcript levels increased by the third sampling date. With the exception of Wcor410 in Manitou, the Vrn-A1 locus affected gene expression in all genotypes. However, only Wcs120 expression followed the low-temperature tolerance pattern in these genotypes.