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Equine arteritis virus (EAV) establishes persistent infection in the stallion reproductive tract, and the carrier stallion continues to shed virus in semen for weeks to years or lifelong. The objective of this study was to elucidate the intra-host evolution of EAV during persistent infection in stallions. Seven EAV seronegative stallions were experimentally infected with EAV KY84 strain and followed for 726 days post-infection, and sequential clinical samples including semen were collected for virus isolation and next-generation sequencing (NGS). In addition, archived sequential semen samples from two stallions that were naturally infected with EAV KY84 for a long-period (up to 10 years) were also sequenced by NGS. The data demonstrated genetic bottleneck event and selection during acute infection followed by intra-host quasispecies diversification during persistent infection in the stallion reproductive tract. Also, the full-length genome of a novel EAV donkey strain from Chile and a noncytopathic bovine viral diarrhea virus-1 (ncpBVDV-1) strain contaminating rabbit kidney-13 cells were also sequenced by NGS. The EAV donkey strain was genetically distinct but antigenically cross-reacted with EAV antisera, and it was phylogenetically closely related to the South African donkey strain of EAV. Genetic and phylogenetic analyses demonstrated that ncpBVDV-1 belongs to BVDV-1b group.

La tesi que teniu a les mans recull quatre treballs amb un objectiu comú; determinar si els patògens (virus, bacteris, paràsits.) han exercit pressions selectives sobre els genomes dels seus hostes (com per exemple els humans).Sabent que la detecció de l'empremta de la selecció permet identificar aquelles regions del genoma que han estat rellevants al llarg de l'evolució d'una espècie, ja que a nivell local és la variació funcional qui acaba essent objecte de la selecció, ens hem disposat a estudiar els possibles senyals de selecció en gens relacionats amb la interacció hoste-patògen. En concret, hem analitzat gens que codifiquen per: a) components del sistema immunitari innat i, b) enzims de glicosilació, la majoria dels quals s'inclouen en quatre de les principals rutes biosintètiques de glicans, en diferents poblacions humanes.Com a conclusió principal; ambdós conjunts de gens mostren clars senyals de selecció. A més hem vist que segons el context biològic on és troben certs gens és veuen més afectats per l'acció de la selecció natural. / The present thesis includes four studies with a common objective: determining whether pathogens (virus, bacteria, parasites.) have exerted selective pressures on the genome of their hosts (for example, humans).Detecting signatures of positive selection is a useful tool to identify functionally relevant genomic regions since selection locally shapes the functional variation. Based on this premise, we have studied the possible signatures of selection in genes related to host-pathogen interactions. Specifically, we have analyzed those genes encoding: a) components of the innate immunity response; and ii) glycosylation enzymes most of them involved in four major glycan biosynthesis pathways, in different human populations.The main conclusion obtained from these studies is that both studied gene categories show clear signatures of selection. Moreover, we have determined that according to their biological context certain genes are more prone to the action of selection.

This report is commissioned by the Water and Sewage Agency in The City of Mariehamn, Åland. The basic aim is to investigate positive or negative effects of a relocation of the sewage pipe from a wastewater treatment plant, Lotsbroverket. The environmental licence of Lotsbroverket is to be revised and The Environmental Appeal Board at Åland’s Government and Administrative Board has made demands that several possible locations in an outer water area should be examined. The present location of the sewage pipe is in Svibyviken, which has been classified as an “inner water area”. The objective of this work is to study to which extent the nutrient loading from Lotsbroverket influence the environmental conditions in Svibyviken, and to investigate the suitability of different locations of the wastewater pipe from Lotsbroverket. The way a coastal area looks, i.e., its morphometry, determines to a large extent its ecological characteristics. The investigated coastal area was digitalized from a nautical chart. The software used for this was Roots 3.3 and the GIS-tool ArcGIS 8.3. The localization of the coastal boundaries for the entire coastal area and for investigated sub-areas was determined according to the topographical bottleneck method, i.e., the boundary lines were drawn where the exposure of the coast to the open sea is minimized. A process-based dynamic mass-balance model for total phosphorous has been used in this study. Using this model, one can estimate and quantify the effects of different nutrient sources in coastal areas. All the fluxes of phosphorous to, from and within the defined areas were studied and ranked. Model simulations have shown how changes in any of the phosphorous fluxes influence the mean monthly concentrations of total phosphorous. The situation for total nitrogen was determined with a statistical/empirical regression model between phosphorous and nitrogen concentrations. To estimate the expected ecological effects from a change in the nutrient loading from Lotsbroverket, statistical/empirical correlations between modelled nutrient concentrations and ecological effect variables have been used. Standard effect variables for the study of eutrophication effects in coastal areas are, e.g., the chlorophyll concentration, Secchi depth and oxygen saturation in deep water. These variables have also been used in this study. It has been shown that (1) the nutrient concentrations of the Baltic Sea controls the concentration of nutrients in the studied areas to a very large extent, (2) that the nutrient fluxes from Lotsbroverket are small compared to the nutrient fluxes from the Baltic Sea and hence also of minor importance for the nutrient state of the receiving water system, (3) that the influence of the nutrient emissions from Lotsbroverket are most noticeable in the present inner recipient, Svibyviken, and (4) that the impact logically decreases with distance between the location of the sewage pipe and boundary line to the open sea. The overall conclusion is that no major improvement of the conditions in Svibyviken can be expected by a reduction or a relocation of the nutrient emissions from Lotsbroverket. / Detta examensarbete är ett uppdrag av VA-verket vid Mariehamns stad, Åland, med syfte att utreda effekter av en eventuell flyttning av avloppsreningsverket Lotsbroverkets utloppsledning. Inför en revidering av Lotsbroverkets miljötillstånd har Miljöprövningsnämnden vid Ålands landskapsregering ställt villkor på att tillståndshavaren skall utreda möjligheter till att avleda det renade avloppsvattnet till ett yttre vattenområde. Utloppsledningen mynnar i dagsläget i Svibyviken, vilken har klassificerats som ett inre vattenområde. Målsättningen med detta arbete är att belysa vilka ekologiska effekter näringsämnesutsläppet från Lotsbroverket har på primärrecipienten Svibyviken samt att undersöka några andra områdens lämplighet som mottagare av avloppsvattnet. Ett kustområdes utseende och form, det vill säga dess morfometri, avgör i stor utsträckning dess ekologiska förhållanden. För att få en god bild av det undersökta områdets morfometri digitaliserades området utifrån ett sjökort i digitaliseringsprogrammet Roots 3.3, varefter data bearbetades med GIS-verktyget ArcGIS 8.3. Avgränsning av kustområdet som helhet och av undersökta delområden gjordes enligt den topografiska flaskhalsmetoden, det vill säga så att kustens öppenhet mot utanförliggande hav eller vattenområde minimeras (Håkanson et al., 1984; Pilesjö et al., 1991). För arbetet har en processbaserad, dynamisk massbalansmodell för totalfosfor använts. Modellen har tagits fram för att eutrofieringseffekter i kustområden skall kunna studeras (Håkanson & Karlsson, 2001). Vid användandet av modellen kan effekter av olika näringsämneskällor uppskattas och kvantifieras. Samtliga totalfosforflöden till, från och inom olika avgränsade områden har studerats och rangordnats. Modellsimuleringar har visat hur förändringar i något av fosfortillflödena inverkar på recipientens månadsmedelkoncentration av totalfosfor. Situationen för kväve har undersökts med hjälp av en statistisk/empirisk regressionsmodell mellan fosfor- och kvävehalt. För att belysa de ekologiska effekter som kan förväntas efter en förändring av Lotsbroverkets fosfor- och kväveutsläpp har statistiska/empiriska kopplingar gjorts mellan näringsämneskoncentrationer och ekologiska effektvariabler. Bra effektvariabler vid undersökning av eutrofieringseffekter är exempelvis klorofyllhalt, siktdjup samt syrgashalt i bottenvattnet. Dessa variabler har också använts i detta arbete. Resultaten visar att (1) närsaltskoncentrationerna i de studerade områdena i hög grad styrs av den allmänna eutrofieringsnivån i Östersjön, (2) att utsläppet av näringsämnen från Lotsbroverket inte inverkar på recipientens näringsstatus i någon stor utsträckning, (3) att Lotsbroverkets påverkan är störst på nuvarande recipient, Svibyviken, (4) och att påverkan sedan successivt minskar ju längre ut mot öppna havet utloppsledningen lokaliseras. Slutsatsen av utredningen är att en reduktion av Lotsbroverkets utsläpp eller nylokalisering av utloppsledningen inte kan förväntas ge någon omfattande förbättring av tillståndet i Svibyviken.

Diplomová práce se zabývá návrhem procesů oddělení System Activation & Deactivation společnosti IBM Česká Republika, s.r.o. s cílem zlepšení těchto procesů a navýšení efektivity těchto procesů v rámci firmy.

In low-income countries where maternal and child mortality remains high, there is limited use of context-specific evidence for decision making and prioritization of interventions in the planning process at the sub-national level, such as the district level. Knowledge on the utility of tools and interventions to promote use of district-specific evidence in the planning process is limited, yet it could contribute to the prioritization of high-impact interventions for women and children. This thesis aims to investigate, in the planning process, the use of district-specific evidence to identify gaps in service delivery in the district health system in Uganda in order to contribute to improving health services for women and children. Study I evaluated the use of the modified Tanahashi model to identify bottlenecks for service delivery of maternal and newborn interventions. Study II and III used qualitative methods to document the experiences of district managers in adopting tools to facilitate the utilization of district-specific evidence, and the barriers and enablers to the use of these tools in the planning process. Study IV used qualitative methods, and analysis of district annual health work plans and reports. District managers were able to adopt tools for the utilization of district-specific evidence in the planning process. Governance and leadership were a major influence on the use of district-specific evidence. Limited decision space and fiscal space, and limited financial resources, and inadequate routine health information systems were also barriers to the utilization of district-specific evidence. Use of district-specific evidence in the planning process is not an end in itself but part of a process to improve the prioritization of interventions for women and children. In order to prioritize high impact interventions at the district level, a multifaceted approach needs to be taken that not only focuses on use of evidence, but also focuses on broader health system aspects like governance and leadership, the decision and fiscal space available to the district managers, limited resources, and inadequate routine health information systems.

During the past century the Swedish otter (Lutra lutra) population showed a rapid decline in abundance and genetic diversity. Among the most affected areas was the southern province of Skåne. After prohibiting hunting of otters and banning harmful pollutants like PCB, Swedish populations slowly recovered. To some areas the otter returned late, like Kristianstad in north-eastern Skåne. Here, the River Helge å enters Kristianstad’s Vattenrike, Biosphere Reserve and forms a biodiverse wetland. By 2011, otters had established once more along the river. In recent years, a female otter with cubs have appeared outside Vattenriket visitor’s centre “naturum”, to the joy of inhabitants and visitors. In Kristianstad, otters have become a recurring winter attraction. However, not much is known about this new population. For assessment of abundance and genetic diversity, microsatellite variation was investigated among now-living individuals from eleven sites in the Biosphere reserve, and stored museum samples from ten otters with origins in North-eastern Skåne. Using a non-invasive methodology, investigated DNA was extracted from faeces and muscle tissue from dead individuals. Multiple replicate screening was performed to detect errors in genotyping procedures. Results show the presence of three now-living individuals (two males and one female). Now-living otters and museum specimens from north-eastern Skåne were not closely related. Sampled individuals show Hardy-Weinberg Equilibrium, but their heterozygosity is very low. Results suggest that, even though some individuals may remain undetected, low admixture of new genes may be a cause for concern. For long-term protection and management in Kristianstad’s Vattenrike, Biosphere Reserve, further knowledge is needed about our new and precious otter population. / Den svenska utterstammen (Lutra lutra) genomgick drastiska populationsminskningar under mitten av 1900-talet. Minskningen ledde till en förlust av genetisk diversitet i många områden, och bland de värst drabbade var Skåne. Uttern blev fredad från jakt och ett förbud mot det skadliga miljögiftet PCB infördes, vilket skapade förutsättningar för utterpopulationen i Sverige att långsamt återhämta sig i antal. Men uttern återvände sent till vissa områden, som Kristianstad i Nordöstra Skåne. Genom staden Kristianstad rinner Helge å, som formar vidsträckta, artrika våtmarker i Biosfärområde Kristianstads Vattenrike. Uttern visade inga tecken på återkomst till området förrän 2011. De senaste åren har en utterhona med ungar regelbundet visat sig vid besökscentret ”naturum”, till glädje för stadens invånare och besökare. Uttrarna har blivit en återkommande vinterattraktion i Kristianstad. Men kunskapen om den nya populationen är begränsad. För uppskattning av antal och genetisk diversitet, undersöktes mikrosatellitvariationer hos nu levande individer från elva lokaler i Vattenriket. För jämförelse inkluderades arkiverade prover från Naturhistoriska Riksmuseets ”Miljöprovbank”, från tio döda uttrar med ursprung i Nordöstra Skåne. Med icke-invasiva metoder undersöktes DNA som extraherats från avföring- och muskelvävnad. Multipel replikatanalys gjordes för detektering av eventuella fel i genotypningsproceduren. Resultaten visar förekomsten av tre nu levande individer i Vattenriket (två hanar och en hona). Det är dock troligt att en- eller flera nu levande individer kan ha undkommit identifiering. Individerna var inte nära släkt med museiexemplaren från Nordöstra Skåne. Studerade individer är i Hardy-Weinberg jämvikt, men heterozygositeten är låg. Låg heterozygositet kan bero på en låg genomblandning i populationen, vilket kan vara en anledning till oro och bör undersökas närmre. Det behövs ytterligare kunskap och studier för att långsiktigt skydda och förvalta den nya, värdefulla utterpopulationen i Kristianstads Vattenrike.

The thesis deals with production planning. It contains theoretical description of methods used for production planning and optimizing. Thesis describes bottleneck problems in production. It offers overview of ways to identify and analyze bottleneck influence to manufacturing process efficiency. Thesis proposes ways to eliminate bottlenecks using various algorithm types. It applies theoretical knowledges from optimization and graph theory to program creation that is focused on order delay and readjustment time minimizing. The program implements genetic algorithm.

The diploma thesis deals with the behaviour of traffic stream at work zones. It focuses primarily on alternating arranging just before funnelling of the traffic and creation of congestions. The study of parameters defined in the Aimsun program, that examines their effect on alternating arranging in micro-simulation, is a part of the thesis. The right setting of values is verified on traffic model formulated on the basis of video recording. The work aims to minimize effects of necessary repairs and reconstructions of roads by the telematic applications which dynamically affect the traffic stream by changing the maximum speed.

Die gängige Methodik zum Konzipieren automatisierter Montagesysteme umfasst die Planung der Montage und die physische Entwicklung der technischen Gesamtlösung. Zur Abbildung der konkreten Aufgabe werden standardisierte Symbole in einem Ablaufplan miteinander verknüpft. Die Hauptaufgabe des Konstrukteurs ist die Auswahl und die Zusammenstellung einer optimalen Konfiguration der Funktionsträger sowie deren Implementierung in einer Gesamtlösung unter Berücksichtigung der vorgegebenen Randbedingungen. Das Problem ist der fehlende Informationsgehalt der bisher eingesetzten Handhabungssymbole und Symbole zur Ermittlung der Funktionsträger zur Beschreibung der Montage- und Handhabungsplanung sowie die fehlende Vorgehensweise zur Auswahl der Funktionsträger aus den verschiedenen Varianten nach minimaler Taktzeit und Gesamtanschaffungskosten. Zur Realisierung eines effizienten Montageplanungssystems leitet sich daher die Zielstellung ab, den Informationsgehalt der standardisierten Symbole zu erweitern und mit logischen Schnittstellen für eine automatisierte Verknüpfung in der Funktionsfolge auszustatten. Diese neuen Symbole beinhalten die Definition der Funktionen sowie alle Randbedingungen und Parameter zur eindeutigen Beschreibung der Handhabungsaufgabe. Mithilfe dieser Parameter werden Anforderungslisten erstellt und nach passenden Anlagenkomponenten gesucht. Zur Auswahl der optimalen Komponenten des Montagesystems wird das lineare Optimierungsproblem hinsichtlich der Kombination aus Taktzeit und Gesamtanschaffungskosten gelöst. / The common methodology for designing automated assembly systems involves the assembly planning and the physical development of overall technical solution. To illustrate the concrete task, standardized symbols are connected together in a flowchart. The designer's main task is the selection and the composition of an optimal configuration of the functional carriers as well as their implementation in an overall solution in consideration of the predetermined boundary conditions. One problem is the lack of information content of the previously used handling symbols and the symbols for determining the functional carriers, which describe the assembly and handling planning. The other is the insufficient methods for selecting the functional carriers from the different variants based on minimum cycle time and total acquisition cost. In order to realize an efficient assembly planning system, the objective is therefore to expand the information content of the standardized symbols and equip them with logical interfaces for automated connection in the functional sequence. These new symbols contain the definition of the functions as well as all boundary conditions and parameters for the unambiguous description of the handling task. These parameters are utilised to create requirement lists and search for suitable plant components. In order to select the optimal components of the assembly system, the linear optimization problem regarding the combination of cycle time and total acquisition costs is solved.