Nontyphoidal Salmonella (NTS) causes invasive, and frequently fatal, disease in African children. The burden of disease secondary to NTS reflects inadequacy of Salmonella-control strategies in Africa, with expanding antibiotic resistance, and no licensed anti-NTS vaccine. The delivery of improved interventions to prevent, diagnose, and treat invasive NTS (iNTS) infection, will be facilitated by an improved understanding of the biological determinants of susceptibility to iNTS, including host genetic factors. To identify host genetic determinants of iNTS disease, we performed a GWAS and replication analysis of NTS bacteraemia in African children. This analysis identified and validated a common genetic variant in STAT4 associated with increased iNTS risk. To characterise the function of the NTS-associated STAT4 variant, we utilised a genotype-selectable bioresource of healthy European adults and samples from African children with iNTS disease. In these experiments, the risk genotype at STAT4 is associated with reduced STAT4 RNA expression in stimulated leukocytes, and reduced IFNγ production in both ex vivo stimulated natural killer cells and in the serum of African children with acute NTS bacteraemia. To validate genetic variation suggestively associated with NTS bacteraemia in the GWAS, NTS-associated loci with evidence of regulatory function were prioritised for functional characterisation. Using in vitro models of intracellular Salmonella infection and RNA interference, I characterise the role of a candidate NTS-susceptibility determinant, EVI5L, in Salmonella infections. Finally, applying a pathway enrichment analysis to the NTS bacteraemia GWAS demonstrated that NTS-associated genetic variation in African children is enriched for methionine salvage enzymes. I further investigate the potential for host-pathogen interaction in this pathway, generating and characterising Salmonella mutants deficient in methionine metabolism. Taken together, these data represent the first unbiased assessment of genetic susceptibility to iNTS disease in unselected populations. These results have important implications for the design of Salmonella-control strategies for use in Africa.

Anthropogenic climate change is one of the main challenges affecting the globe, with particular implications for the oceans. Marine climate change research has moved forward rapidly in recent years, and a range of physical model outputs are available that can be used by ecologists to help predict how species might be affected into the future. Policy makers require a level of understanding of how certain species and their ranges might change so that they can respond with sustainable management actions. This thesis aims to make use of a number of modelling techniques to explore implications of past and future conditions for marine species, and to appraise those tools that can be used under differing circumstances. Policy questions are answered relating to changes in the abundance and distribution of marine species. The links between historical climatic conditions and Barents Sea cod abundance are explored using Generalised Additive Models using data collected in the middle of the 20th century. This valuable historical data indicated that cod have temperature preferences and expand and shift their distributions based on environmental conditions. A simpler modelling technique is used to examine how oxygen conditions have changed in recent decades in the North Sea, how they might change in the future, and what implications this has for commercial fish species. The models show that oxygen conditions have improved recently and that they will not decrease to levels that result in large negative effects in the coming century. Species distribution modelling using a combination of global and downscaled model outputs shows that the UK will become more suitable for some non-native and harmful algal species in the 21st century, and less suitable for others. The model outputs contribute to the understanding of climate change effects and development of management tools to ensure the resilience of marine ecosystems into the future.

abstract: General ecological thought pertaining to plant biology, conservation, and urban areas has rested on two potentially contradictory underlying assumptions. The first is that non-native plants can spread easily from human developments to “pristine” areas. The second is that native plants cannot disperse through developed areas. Both assume anthropogenic changes to ecosystems create conditions that favor non-native plants and hinder native species. However, it is just as likely that anthropogenic alterations of habitats will favor certain groups of plant species with similar functional traits, whether native or not. Migration of plants can be divided into the following stages: dispersal, germination, establishment, reproduction and spread. Functional traits of species determine which are most successful at each of the stages of invasion or range enlargement. I studied the traits that allow both native and non-native plant species to disperse into freeway corridors, germinate, establish, reproduce, and then disperse along those corridors in Phoenix, Arizona. Field methods included seed bank sample collection and germination, vegetation surveys, and seed trapping. I also evaluated concentrations of plant-available nitrate as a result of localized nitrogen deposition. While many plant species found on the roadsides are either landscape varieties or typical weedy species, some uncommon native species and unexpected non-native species were also encountered. Maintenance regimes greatly influence the amount of vegetative cover and species composition along roadsides. Understanding which traits permit success at various stages of the invasion process indicates whether it is native, non-native, or species with particular traits that are likely to move through the city and establish in the desert. In a related case study conducted in Victoria, Australia, transportation professionals and ecologists were surveyed regarding preferences for roadside landscape design. Roadside design and maintenance projects are typically influenced by different groups of transportation professionals at various stages in a linear project cycle. Landscape architects and design professionals have distinct preferences and priorities compared to other transportation professionals and trained ecologists. The case study reveals the need for collaboration throughout the stages of design, construction and maintenance in order to efficiently manage roadsides for multiple priorities. / Dissertation/Thesis / Ph.D. Biology 2010

A técnica de videolaparoscopia exploratória da cavidade abdominal utilizada atualmente em equinos implica em uma série de dificuldades. Há necessidade do acesso cirúrgico bilateral da cavidade abdominal ou anestesia geral para acesso ventral com a finalidade de obter uma avaliação adequada das vísceras e, consequentemente, um diagnóstico mais preciso. Esse procedimento prolonga o tempo e aumenta os riscos de complicações transoperatórias e pós-cirúrgicas. Apesar de ser uma técnica bem estabelecida com situações em que as vantagens de sua utilização são evidentes, alguns fatores ainda limitam sua difusão, entre eles podemos destacar: o custo do equipamento que limita a utilização fora de Universidades, Centros de Pesquisas ou clínicas particulares especializadas em cirurgias veterinárias. Com o objetivo de minimizar os aspectos negativos dessa técnica e viabilizar seu uso na rotina clínica e cirúrgica de equinos, surgiu a ideia de buscar uma nova via de acesso à cavidade abdominal e utilizando o videocolonoscópio, equipamento de menor custo. No presente estudo, foi analisado o uso do endoscópio flexível na exploração abdominal de equinos machos castrados e fêmeas pelo acesso perianal. A técnica foi avaliada quanto à viabilidade de permitir ou não o acesso à cavidade e identificação das vísceras abdominais em equinos. Além disso, buscou-se verificar se o endoscópio flexível permite a obtenção de amostras de tecido hepático para avaliação histológica. Os animais foram, alimentados, desverminados e avaliados diariamente por meio de exame clínico geral durante o período do experimento. Colheitas de amostras de sangue para hemograma e dosagem de fibrinogênio foram realizadas antes e após o procedimento cirurgico para posterior analise. Todos os cuidados de rotina em relação à antissepsia cirúrgica foram devidamente tomados e os animais submetidos a protocolo de sedação e analgesia. Os procedimentos de pós-operatório como terapia analgésica, anti-inflamatória, inspeção e higienização diária do local de incisão foram prestados. O procedimento cirúrgico teve início com incisão na região perianal laterodorsal direita entre o ânus e o musculo semimembranoso utilizando bisturi e tesoura, seguida de divulsão romba com o dedo ao longo da parede retal até alcançar uma profundidade aproximada de 10 cm, momento no qual foi introduzida cânula metálica com 56 cm de comprimento e 16 mm de diâmetro (Ø). Por meio desta cânula foi introduzido o endoscópio flexível (videocolonoscópio), sendo o restante da introdução da cânula acompanhada por visualização indireta em monitor. A cânula foi forçada lentamente até atingir a cavidade peritoneal, momento a partir do qual foi realizada exploração da cavidade abdominal. As vísceras observadas foram anotadas em ficha especialmente desenvolvida para esta finalidade. Como parte da avaliação hepática foi realizada biópsia e o material obtido analisado no setor de patologia da Faculdade de Veterinária da UFRGS. Após dez dias de pós-operatório, quando em plenas condições de saúde, os equinos receberam alta. Os resultados permitem inferir que, o uso do endoscópio flexível na identificação das vísceras abdominais por meio de laparoscopia perianal é viável na rotina clínica e cirúrgica de equinos e possibilita obter amostras teciduais para avaliação histológica. No entanto, o emprego da técnica exige o treinamento da equipe cirúrgica, principalmente do cirurgião, bom planejamento e um diagnóstico pré-operatório incompleto que necessite complementação diagnóstica. / The technique of exploratory laparoscopy abdominal cavity used currently in horses involves a series of difficulties. There is need for bilateral abdominal cavity surgical access or general anesthesia for ventral access for the purpose of obtaining an adequate assessment of the viscera and, consequently, a more accurate diagnosis. This procedure extends and increases the risks of post-surgical complications and transoperatórias. Despite being a well-established technique in situations where the advantages of its use are evident, some factors still limit its spread, some of them are: the cost of equipment that limits the use out of universities, research centers or private clinics specialized in veterinary surgeries. In order to minimize the negative aspects of this technique and enable its use in routine clinical and surgical equine, the idea of seeking a new route to the abdominal cavity and using videocolonoscópio, lower equipment cost. In the present study, we analyzed the use of the flexible endoscope in the abdominal exploration equine barrows and gilts for access perianal. The technique was evaluated on the feasibility of allowing or not the access cavity and identification of the abdominal viscera in horses. In addition, sought to verify that the flexible endoscope allows obtaining liver tissue samples for histological evaluation. The animals were fed, wormed and evaluated daily by a general clinical examination during the period of the experiment. Sampling of blood for blood count and fibrinogen were measured before and after the surgical procedure for subsequent analysis. All routine care in relation to surgical antisepsis were duly taken and animals undergoing sedation and analgesia protocol. Procedures as postoperative analgesic therapy, anti-inflammatory, inspection and cleaning daily incision site were provided. The procedure began with surgical incision in the right laterodorsal perianal region between the anus and the semimembranosus muscle using a scalpel and scissors, then blunt dilatation of the finger along the rectal wall until it reaches an approximate depth of 10 cm, at which the metal cannula with 56 cm length and 16 mm in diameter (Ø) was introduced. Through this cannula was inserted flexible endoscope (videocolonoscópio), the remainder of the introduction of the cannula followed by indirect viewing monitor. The cannula was forced slowly to the peritoneal cavity, the time from which it was held exploration of the abdominal cavity. The cannula was forced slowly to the peritoneal cavity, the time from which it was held exploration of the abdominal cavity. The viscera were observed in annotated form specially developed for this purpose. As part of the evaluation of the liver, biopsy was performed and the obtained material analyzed at the pathology of the Veterinary School of UFRGS. After ten days postoperatively, when in full health, horses were discharged. The results allow us to conclude that the use of the flexible endoscope in the identification of abdominal viscera through perianal laparoscopy is feasible in routine clinical and surgical equine and enables to obtain tissue samples for histologic evaluation. However, the use of the technique requires training of the surgical team, especially the surgeon, good planning and a preoperative diagnosis requiring incomplete diagnostic workup.

Biomechanical imaging (BMI) is the process of non-invasively measuring the spatial distribution of mechanical properties of biological tissues. The most common approach uses ultrasound to non-invasively measure soft tissue deformations. The measured deformations are then used in an inverse problem to infer local tissue mechanical properties. Thus quantifying local tissue mechanical properties can enable better medical diagnosis, treatment, and understanding of various diseases. A major difficulty with ultrasound biomechanical imaging is getting accurate measurements of all components of the tissue displacement vector field. One component of the displacement field, that parallel to the direction of sound propagation, is typically measured accurately and precisely; the others are available at such low precision that they may be disregarded in the first instance. If all components were available at high precision, the inverse problem for mechanical properties could be solved directly, and very efficiently. When only one component is available, the inverse problem solution is necessarily iterative, and relatively speaking, computationally inefficient. The goal of this thesis, therefore, is to develop a processing method that can be used to recover the missing displacement data with sufficient precision to allow the direct reconstruction of the linear elastic modulus distribution in tissue. This goal was achieved by using a novel spatial regularization to adaptively enforce and locally relax a special form of momentum conservation on the measured deformation field. The new processing method was implemented with the Finite Element Method (FEM). The processing method was tested with simulated data, measured data from a tissue mimicking phantom, and in-vivo clinical data of breast masses, and in all cases it was able to recover precise estimates the full 2D displacement and strain fields. The recovered strains were then used to calculate the material property distribution directly.

Boston University. University Professors Program Senior theses. / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / 2031-01-02

Fungal infections are ignored by social and political communities. However, they are estimated to affect more than a billion people, resulting in approximately 11.5 million life-threatening infections in the 'at risk' population and more than 1.5 million deaths annually. Though there have been huge advances in diagnostics and antifungal drug development over the past two decades, however, resource limited settings have not benefited from these advances. The aim of this research was to determine the burden of serious fungal infections in Nigerians with the appropriate underlying diseases. This epidemiological research was conducted across four study populations. Study 1; HIV-infected patients with CD4+ counts < 250 cells/mm³, irrespective of their ART status, a CrAg lateral flow assay was used for detecting cryptococcal antigenaemia (n=214). Study 2; a cross-sectional multicentre survey of TB patients being managed for smear negative or treatment failure TB irrespective of their HIV status (n=208). Study 3; a multicentre histoplasmin skin sensitivity survey amongst healthy HIV-infected and non-HIV infected participants; intradermally; induration ≥ 5 mm was considered to be histoplasmin positive (n=750). Study 4; a prospective cohort study of critically ill patients in a Nigerian ICU (n=71). Two retrospective studies to analyse the clinical picture of serious fungal infections in two at risk populations (HIV/AIDS and neonatal intensive care babies) in Nigerians was also conducted (n=7034; n=2712 respectively). Results revealed an overall seroprevalence of cryptococcal antigenemia of 8.9% with 6 (9.8%) in those with CD4+ cell counts < 100cells/mm³, 4 (5.0%) in the 100-200 group and 9 (12.3%) in 200-250 cells/mm³ group; a CPA prevalence of 8.7% (6.5% had HIV infection and 14.5% were HIV-negative) and a prior subclinical histoplasmosis of 4.4%. The ICU study revealed a 45% healthcare associated infection rate representing an incidence rate of 79/1000 patient-days in the ICU. The retrospective studies revealed a 2.3% rate of neonatal ICI with a case fatality rate of 18.5%. In the 12 years retrospective study 18% had a fungal OI with 88% of patients having initiated ART. In conclusion, serious fungal infections do occur in the at risk population in Nigeria and they constitute a significant public health challenge. Our findings demonstrate that there has been an underestimation of the burden of the problem in Nigerians. There is a dire need to design guidelines for the management of fungal infections in at risk population.

Bakgrund:  Non-invasiv ventilering (NIV) är ett andningsstöd som med gott resultat kan behandla respiratorisk svikt vilket är vanligt förekommande på Intensivvårdsavdelningar (IVA). Med NIV minskar mortalitet, vårdtiden på IVA, behovet av invasiv ventilering samt förekomsten av ventilatorassocierad pneumoni. Behandlingen avslutas dock ofta i förtid på grund av att patienten inte accepterar den. Syfte: Syftet med studien var att belysa upplevelserna av NIV vid akut respiratorisk svikt och interaktionen mellan patient och sjuksköterska för att optimera behandlingen. Metod: Metoden för studien är en litteraturöversikt med beskrivande design baserad på kvalitativa studier Resultat: Patienten upplever sig som fånge bakom masken och lägger stor vikt på att lära sig hantera NIV och återfå kontroll. Behandlingen beskrivs som en nödvändig men obehaglig väg till överlevnad. Interaktionen mellan patient och sjuksköterska påverkas av hur sjuksköterskan kan tillgodose patientens behov av delaktighet, information och kontroll. Slutsats: Interaktionen mellan patient och sjuksköterska har stor betydelse för toleransen av behandlingen. Sjuksköterskans roll är att stötta patienten genom att skapa förståelse för behandlingen samt att göra patienten delaktig, på så vis kan patienten återvinna kontroll och behandlingen kan optimeras. / Background: Non-invasive ventilation (NIV) is a treatment that with good result can treat respiratory failure, a common syndrome in ICU units. NIV decrease mortality, invasive ventilation, time spent in ICU and ventilator- associated pneumonia. The treatment is often being terminated early due to that the patient does not accept it. Aim: The aim of the study was to illustrate the experience of NIV used during acute respiratory failure and the interaction between patient and nurse to optimize the treatment. Method: The study is a literature review with a descriptive design based on qualitative studies. Results: The patient experience a feeling of being trapped behind the mask and put a great effort in acceptance of NIV and to regain control. The treatment is described as a necessary but uncomfortable path to survival. The interaction between patient and nurse is affected by the way the nurses meet the patients need of participation, information and control.  Conclusion: For the tolerans of the treatment the interaction between patient and nurse have a great importance. The role of the nurse is to support the patient through create understanding and make the patient participate. Trough that the patient can regain control and the treatment can be optimized.

Magister Scientiae (Biodiversity and Conservation Biology) / The spread of invasive species is one of the greatest threats to global biodiversity. Alien plant invasions also have serious economic impact in terms of the delivery of ecosystem goods and services. Studies of biological invasions in southern Africa have tended to overlook grasses (family Poaceae), although there are many naturalised species in the region. Only a few of these, all perennials, have been officially categorised as invasive in South Africa, but in the winter rainfall region of the Western Cape, grass invasion especially by Mediterranean European annuals have also been noted. These grasses can be difficult to identify. DNA barcoding has been suggested as an alternative method of identifying grasses in the hope of facilitating identification of existing invaders and preventing future invasions. In this study a list of all known naturalised grasses in South Africa was compiled, and a DNA barcoding reference database was assembled for these naturalised grass species as well as for native southern African grass species. The two official markers for plant DNA barcoding (rbcLa + matK) were used in barcoding and phylogenetic analyses, both individually and in combination. The barcoding data was assessed for identification efficacy using three distance-based metrics and one tree-based metric in the R package SPIDER, both including and excluding singleton data. This study lists 128 naturalised grass species and subspecies found in South Africa. In the DNA barcoding analyses, matK was found to perform better as a single barcode than rbcLa, with identification success rates of up to 84% for matK and 76% for rbcLa, using the most successful metric which was the Nearest Neighbour criterion for both of these markers in the data sets without singletons. The combined rbcLa + matK data set performed better than either of the two individual markers, with identification success rates of up to 91% in the data without singletons, with the most successful metric again being the Nearest Neighbour criterion. The combined rbcLa + matK data would therefore be the recommended DNA barcode for southern African grasses of the three data sets tested, based on the results of this study. Phylogenetic trees were constructed with the DNA barcoding data using Bayesian Inference (BI) and Maximum Parsimony (MP) to assess the usefulness of the data in phylogenetic studies and to confirm the efficacy of this grass DNA barcoding data when using tree-based methods of identification. Both the matK and combined datasets resolved all of the grass tribes represented in this study as monophyletic, but the rbcLa data did not.

The purpose of this study was to investigate if botanical gardens in Stockholm, Uppsala and Gothenburg could be a source for spread of invasive species in Sweden. The method consisted of visits to each garden with inventory of the collections and interviews with the staff. The species included in the study were either on or suggested for the list in the EU regulation 1143/2014 or listed by the Swedish Environmental Protection Agency as invasive or potentially invasive species in Sweden. 16 of the 34 species included in the study were found within or around one or more gardens and of those are 8 already established in Sweden and 6 could establish and become invasive with climate change. The study showed that the invasive species could outcompete other organisms by being fast growing and persistent as well as highly reproductive and sometimes harmful to other plants, animals or humans. It also suggests that high seed production and vegetative reproduction from small plant fragments may facilitate spread from botanical gardens in general. By creating awareness of invasive species, the gardens could prevent spread from other sources. Whether or not the gardens’ management of their collections could lead to spread and introduction of invasive species in Sweden is still unexplored and suitable for further studies. The species’ traits however do pose a risk of spread from the botanical gardens in the study, as well as other gardens, and establishment in the Swedish nature.