<p>Todays’ systems for telecommunication are getting more and more complex. Automatic testing is required to guarantee quality of the systems produced. An actual example is the introduction of GPRS traffic in the GSM network nodes. This thesis investigates the need and demands for such an automatic testing of the traffic channels in the GSM system. A solution intended to be a part of the Ericsson TSS is proposed. One problem to be solved is that today’s tools for testing do not support testing of speech channels with the speech transcoder unit installed. As part of the investigation, a speech codec is implemented for execution on current hardware used in the test platform. The selected speech codec is the enhanced full rate codec, generating a bitstream of 12.2 kbit/s, and gives a good trade-off between compression and speech quality. The report covers the design of the test tool and the implementation of speech codec. Particularly performance problems in the implementation of the encoder will be addressed.</p>

Philosophiae Doctor - PhD / Tsetse flies (Glossina spp) are the biological vectors for Trypanosomes, the causative magents of Human African Trypanosomiasis (HAT). HAT is a debilitating disease that continues to present a major public health problem and a key factor limiting rural development in vast regions of tropical Africa. To augment vector control efforts, the International Glossina Genome Initiative (IGGI) was established in 2004 with the ultimate goal of generating a fully annotated whole genome sequence for Glossina morsitans. A working draft genome of Glossina morsitans was availed in 2011. In this thesis, transcriptional regulatory features in Glossina morsitans were analysed using the draft genome. A method for TSS identification in the newly sequenced Glossina morsitans genome was developed using TSS-seq tags sampled from two developmental stages of Glossina morsitans. High throughput next generation sequencing reads obtained from Glossina morsitans larvae and pupae were used to locate transcription start sites (TSS) in the Glossina morsitans genome. TSS-seq tag clusters, defined as a minimum number of reads at the 5’ predicted UTR or first coding exon, were used to define transcription start sites. A total of 3134 tag clusters were identified on the Glossina genome. Approximately 45.4% (1424) of the tag clusters mapped to the first coding exons or their proximal predicted 5’UTR regions and include 31 tag clusters that mapped to transposons. A total of 1101 (35.1%) tag clusters mapped outside the genic region and/or scaffolds without gene predictions and may correspond to previously un-annotated transcripts or noncoding RNA TSS. The core promoter regions were classified as narrow or broad based on the number of TSS positions within a TSS-seq cluster. Majority (95%) of the core promoters analysed in this study were of the broad type while only 5% were of the narrow type. Comparison of canonical core promoter motif occurences between random and bona fide core promoters showed that, generally, the number of motifs in biologically functional genomic windows in the true dataset exceeded those in the random dataset (p <= 0.00164, 0.00135, 0.00185 for the narrow, broad with peak and broad without peak categories respectively). Frequency of motif co-occurrence in core promoter was found to be fundamentally different across various initiation patterns. Narrow core promoters recorded higher frequency of the TATA-box and INR motifs and two-way motif co-occurrence showed that the TATA-box-INR pair is over-represented in the narrow category. Broad core promoters showed higher frequency of the BREd and MTE motifs and two-way motif co-occurrence showed that the MTE-DPE pair is over-represented in broad core promoters. TATA-less promoters account for 77% of the core promoters in this analysis. TATA-less core promoters showed a higher frequency of the MTE and INR motifs in contrast to observations in Drosophila where the DPE motif has been reported to occur frequently in TATA-less promoters. These motif combinations suggest their equal importance to transcription in their corresponding promoter classes in Glossina morsitans.

This study is part of a project that was conducted by Florida International University (FIU), which designed, built, and characterized a constructed wetland (CW) wastewater treatment system in El Salvador, Central America. This study focuses on the detailed performance of a field-scale CW in the tropics, consisting of a subsurface flow wetland (SSF) and a surface flow wetland (SF). The SSF had a total area of 151.2 sq. m., filled with gravel and planted with Phragmites, Thalia, and Brachiaria, along three independent cells operating with a flow in parallel and receiving the influent domestic wastewater from a facultative lagoon and preceded the SF. The SF was a shallow open basin containing alternating regions of open water (195 sq. m. total) with submerged aquatic plants (Elodea) and regions of shallower water (605 sq. m. total) filled with emergent wetland vegetation (Typha, Thalia, and Cyperus). The design, construction, startup and operation phases of the field scale CW in that tropical setting are thus described with detail, including both SSF and SF characterization of influent and effluents. The SSF average hydraulic detention times during the wet and dry season were 2 days ± 0.9 days and 4 days ± 0.4 days, respectively; and the SF average hydraulic detention times during the wet and dry season were 20 days ± 11.1 days and 77 days ± 19.5 days, respectively. Brachiaria/Cyperus presented better results during the wet season with average BOD5 residuals of 36% ± 25%, and Thalia/Thalia during the dry season with average BOD5 residuals of 33% ± 22%. Phragmites/Typha presented better results during both seasons with average TSS residuals of 2% ± 3% (wet season), and 2% ± 2% (dry season). Residuals are also presented for COD, Oil & Grease, Total Fecal Coliform, Total Phosphorus, and Total Nitrogen. In addition, an assessment of the empirical models used in the design of the system is completed, having the EPA methodology as the preferred for BOD5 removal and three methodologies for TSS removal under tropical climate conditions. A comparison of the differences in treatment associated with each one of the selected plants and their combinations is also discussed. In summary, results strongly suggest that the CW system can effectively reduce contaminants in wastewater to levels that are comparable with the objective levels (i.e., secondary treatment levels).

Introduction: Eating disorders are serious psychiatric disorders that often require specialized care. Associated psychiatric comorbidity is frequent, with the most common comorbid conditions being anxiety and mood disorders. Eriksbergsgården in Örebro is one of Sweden’s specialized eating disorder treatment units.Aim: Primary aims were to describe clinical characteristics of the adult patient group at Eriksbergsgården and to evaluate treatment outcome and patient satisfaction at the one-year follow-up. An additional aim was to examine if factors such as psychiatric comorbidity affected treatment outcome.Methods: This study used data from Riksät and Stepwise, two large-scale Swedish registers for eating disorder treatment. Data for this study was registered into Stepwise and Riksät at Eriksbergsgården between August 2010 and December 2017 and 489 adult patients of both genders constituted the study group. Patient characteristics and DSM-IV axis I psychiatric comorbidity were assessed at the initial evaluation. At the one-year follow-up, treatment outcome and patient satisfaction were evaluated.Results: The most common diagnoses in this patient material were eating disorder not otherwise specified, 56.6 %, followed by bulimia nervosa, 26.4 %. At the initial evaluation, 62.0 % of the patients suffered from psychiatric comorbidity. Of the patients with initial comorbidity, 43.3 % were recovered at the one-year follow-up, compared to 62.8 % of the patients with no initial comorbidity, p=0.021.Conclusion: Our results confirm the previously known fact that psychiatric comorbidity among eating disorder patients is common. Also, the results identify psychiatric comorbidity as a possible factor to have negative effect on the treatment outcome.

Todays’ systems for telecommunication are getting more and more complex. Automatic testing is required to guarantee quality of the systems produced. An actual example is the introduction of GPRS traffic in the GSM network nodes. This thesis investigates the need and demands for such an automatic testing of the traffic channels in the GSM system. A solution intended to be a part of the Ericsson TSS is proposed. One problem to be solved is that today’s tools for testing do not support testing of speech channels with the speech transcoder unit installed. As part of the investigation, a speech codec is implemented for execution on current hardware used in the test platform. The selected speech codec is the enhanced full rate codec, generating a bitstream of 12.2 kbit/s, and gives a good trade-off between compression and speech quality. The report covers the design of the test tool and the implementation of speech codec. Particularly performance problems in the implementation of the encoder will be addressed.

Den tekniska utvecklingen har gjort att nya möjligheter har tillkommit för att säkra framförandet av fartyg och effektivisera ruttplaneringen. Ett av de effektiviseringssäten som för närvarande utvecklas är ruttutbyte. Syftet med studien är att med hjälp av ett simulerat scenario samt frågeformulär belysa eventuella risker förknippade med ruttutbyte till sjöss. Studien speglar deltagarnas upplevelse av den kritiska situationen som simuleringen återger och visar även skillnaden i beslutsfattandet mellan erfarna och oerfarna navigatörer. Tidigare forskning betonar till stor del fördelar med taktiskt ruttutbyte men mindre angående nackdelar med systemet. Med hjälp frågeformulär insamlades deltagarnas erfarenheter och upplevelser angående taktiskt ruttutbyte. Enligt scenariot var det planerat att ett av fartygen i trafikflödet skulle avvika från sin planerade rutt. Ruttutbyte har simulerats genom att visa fartygsrutter i ECDIS. Resultatet av studien visar att det finns ett klart mönster mellan olika gruppers beslutsfattande och graden av pålitlighet till de i ECDIS visade rutterna för andra fartyg. Studien visar även att det finns en påtaglig risk för kollision om navigatörer följer ruttutbytet utan vidare kritisk granskning på grund av falsk trygghet. / The technical advances in the maritime sector have led to new possibilities to secure the safe passage of the vessels and improve the process of route planning. One example of such advances is route exchange. The purpose of this study was by means of simulation to pinpoint whether there are any probable risks connected with the tactical route exchange. This study reflected the experience of the participants of the critical situation portrayed in the simulation. It also takes in to account the difference of the decision-making between the different groups. These groups are composed of experienced navigators and unexperienced navigators. The study also describes the simulation from a fact-based standpoint. Earlier research describes mostly advantages of the tactical route exchange and in less degree the disadvantages of the tactical route exchange. The study has been composed by means of simulation at several occasions. With the help of questionnaires, a general picture has been compiled of the participants’ background, experience and the general opinion about the tactical route exchange. According to the prepared scenario there was one vessel which was intended to deviate from its intended route. The route exchange was projected in the ECDIS console. The result shows that there is a pattern between the different groups´ decision-making and the degree of reliability of the projected routes. The study also points out the obvious risk of collision dependent on the incompleteness of the system and weaknesses for the worst-case scenario which should be taken into account in the future upgrades of the system.

Les bactéries sont en permanence confrontées à des changements d'environnements. La régulation transcriptionnelle joue alors un rôle majeur dans l'adaptation des bactéries. En particulier, la bactérie phytopathogène D. dadantii s'est récemment adaptée à l'hôte végétal. Elle produit en particulier des pectate lyases (Pel) qui dégradent la pectine, ciment des parois végétales, et jouent un rôle majeur dans le développement de la maladie. Les gènes pelD et pelE, malgré la forte divergence dans leur expression, sont issus d'un transfert horizontal suivi d'une duplication récente. La question de l'intégration de ces gènes avec les régulations préexistantes s'est alors posée.Dans un premier temps, les mécanismes moléculaires détaillés de la régulation de pelD ont été étudiés. Il a été montré que cette régulation s'appuie sur un promoteur divergent de forte affinité pour l'ARN polymérase mais de faible efficacité pour la transcription et sur un arrangement stratégique de quatre sites de fixation de répresseur FIS et deux sites de l'activateur CRP. Tous ces éléments interagissent entre eux pour produire une régulation fine de l'expression de pelD. L'origine de la divergence régulatrice entre les paralogues pelD et pelE a par la suite été explorée. De manière surprenante, la divergence entre ces deux gènes et leur sélection s'appuie presque exclusivement sur un décalage de la position du promoteur de pelE (« TSS turnover ») qui l'a transformé en initiateur de la dégradation de la pectine. Ce mécanisme très fréquent chez les eucaryotes pluricellulaires (homme, drosophile, souris…) n'avait jamais encore été décrit chez les bactéries.A travers l'étude des promoteurs pelD et pelE de D. dadantii, de nouveaux mécanismes renforçant l'importance de la régulation transcriptionnelle dans les processus adaptatifs ont ainsi été découverts / Bacteria face frequent environmental changes. Transcriptional regulation plays a major role in the adaptation to these changes. In particular, the phytopathogen bacteria Dickeya have recently adapted to vegetal hosts. They produce Pecate lyases (Pel), among others, to degrade pectin in plant cell walls, which is necessary for disease development. The pelD and pelE genes, despite the strong divergence in their expression, originate from a horizontal gene transfer followed by a recent duplication. This raises the question of their integration into the preexisting regulatory networks.Detailed molecular mechanisms of the transcriptional regulation of pelD were studied first. It was shown that this regulation relies on a high-affinity but low transcription efficiency divergent promoter and a strategic arrangement of four FIS repressor binding sites and two CRP activator binding sites. These elements interact together to fine-tune the expression of pelD. Next, the origin of the regulatory divergence between the paralogous genes pelD and pelE was explored. Surprisingly, their divergence and selection relies mostly on a TSS turnover which happened on the pelE regulatory region and transformed pelE into an initiator of pectin degradation. This widespread phenomenon in multicellular eukaryotes (human, fly, mouse…) had not yet been seen in bacteria. To conclude, through the study of D. dadantii pelD and pelE promoters, new mechanisms highlighting the relevance of transcriptional regulation in adaptation were discovered in this work

No description available.

Per- and polyfluoroalkyl substances (PFASs) are a group of artificial chemicals which have been used in a wide area of applications such as surface protection agents in cloths and different industrial applications. It has been found that PFASs are potentially toxic and are frequently found in the environment due to their persistent and mobile properties. Effluents from wastewater treatment plants (WWTPs) have been identified as an important point source of PFASs. Bark, by-product from the paper and wood industry, is a low-cost adsorbent and has the potential to be used as a filter material for PFASs in WWTPs. In this study, the removal of PFASs in wastewater has been investigated using granulated active carbon (GAC) (n = 2) and bark (n = 2) in a pilot scale experiment at Kungsängsverket, Uppsala over a period of five weeks. The specific objects included: i) investigate the influence of flow-rate (10, 30 40 and 60 Ld-1 ) on the removal efficiency of PFASs in the GAC and bark filters, ii) investigate the influence of particle size of bark on the removal efficiency of PFASs and iii) establish what circumstances that potentially promotes removal of PFASs in GAC and bark filters. The results showed that GAC was the most effective method compared to bark, with a reduction of 73-93%, with increasing efficiency under low flow (10-30 L d-1 ) conditions. The removal efficiency of bark was 45% with a particle size of 2-5 mm and under low flow conditions (10-30 L d-1 ), while under high flow conditions (60 L d-1 ) with the same particle size the removal of PFASs was not efficient, instead the total PFAS concentration increased with 40%. In contrast, bark with a particle size of 5-7 mm proved to be not efficient in removing PFASs (removal efficiency = 0%). In general, the removal efficiency increased with smaller particle size of the adsorbent and lower flow rate. The results indicate that bark may be a low-cost alternative in reducing PFASs from wastewater, under certain conditions. / Per- och polyfluroalkyla ämnen (PFAS) är en familj av artificiella fluorerade organiska föreningar som har använts sedan 1950-talet i en rad olika applikationer, såsom impregnering i kläder. Studier har visat att PFAS är potentiellt toxiska och att de förekommer globalt på grund av deras persistenta och mobila egenskaper. Spillvatten från avloppsreningsverk etablerats som en betydande källa för PFAS. Bark, vilket är en biprodukt från pappers- och träindustrin, är ett poröst material vilket möjligen kan användas som adsorbent av PFAS. Denna studie har jämfört effektiviteten hos granulerat aktivt kol (GAC) och bark för att minska PFAS i avloppsvatten. Experimentet var utformat som ett småskaligt kolonn-experiment vid Kungsängsängsverket, Uppsala, och pågick under en fem veckors period. Frågeställningen var att i) studera vilka effekter flödes-hastigheten (10, 30, 40 och 60 L d-1 ) har på reduktionen av PFAS hos GAC och barkfiltren, ii) studera vilka effekter partikelstorleken hos bark har på reduktion av PFAS och iii) redogöra vilka förhållanden som potentiellt gynnar reduktionen av PFAS i GAC och bark filtren. Resultaten visade att GAC var det mest effektiva av de två materialen, med en total reduktion på 73- 93% av PFAS, med ökande effektivitet under låga flödesförhållanden (10-30 L d-1 ). Bark minskade den totala mängden av PFAS med 45% då partikelstorleken var 2-5 mm och under låga flödesförhållanden (10-30 L d-1 ) medan bark med samma partikelstorlek under ökade flödesförhållanden (60 L d-1 ) visade en ökning på 40% av PFAS i det utgående vattnet. Bark med en partikelstorlek på 5-7 mm visade ingen reduktion av PFAS. Generellt visade resultaten att reduktionen av PFAS ökar under låga flödesförhållanden och minskad partikelstorlek. Resultaten visade att bark kan vara ett alternativt material för att minska PFAS i avloppsvatten förutsatt att gynnsamma förhållanden upprätthålls.

<p> </p><p>MTsim (Mobile Traffic Simulator) is an Ericsson AB internal software application that is part of 2Gsim. It is used to simulate elements of a GSM (Global System for Mobile communications) network for feature testing and automated testing. It is written in the programming language TSS Language, also known as SMILE which is a proprietary Ericsson programming language. SMILE is based on the principles of state matrix programming which in essence means that each program is on its own a finite state machine. The language is old and was originally intended as a macro language for smaller test programs, not for applications the size of MTsim.</p><p>It is of interest to evaluate the feasibility of performing an automatic conversion of applications written in SMILE, with special interest in converting MTsim, to a Java framework since Java has many advantages compared to SMILE. Java, as a language, is well suited for larger applications, there are numerous well supported tools and there is a much wider spread competence than there is for SMILE.</p><p>It is clear that in order to do a full conversion of a SMILE program to a Java framework two applications must be implemented. First a Java framework, which acts as a run time environment, must be designed which can host the translated programs. The other part is an actual translator which takes a SMILE program as input and ouputs a translated Java program. A more sophisticated framework is preferred since it makes the actual translated programs more light weight and easy to read which means higher degree of maintainability.</p><p>There are different ways to implement state machines in Java but the most flexible and versatile is to implement it as a black-box framework in an object oriented way where the framework has sophisticated mechanisms for message and event handling which is central to any state machine framework.</p><p>The translation for SMILE can easily be done by using a AST (abstract syntax tree) representation, which is a full representation of the SMILE program in tree-form. The AST is obtained from an intermediate state of the SMILE program compiler.</p><p> </p>