Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial analysis of HIV infections in high burden sub-districts in KwaZulu-Natal, South Africa.

1 CHAPTER 1: INTRODUCTION . 3 1.1. Background . 4 1.2. Overview of the dissertation . 5 1.3. Literature review . 6 1.3. 1 The Epidemiology of HIV in sub-Saharan Africa and South Africa . 6 1.3. 2 Key populations to prioritize for HIV prevention . 8 1.3. 2.1. Adolescent girls and young women . 8 1.3. 2.2. Men who have sex with men (MSM) . 9 1.3. 2.3. Sex workers (SW) . 10 1.3. 2.4. People who inject drugs (PWID) . 11 1.3. 2.5. Transgender people . 12 1.3. 3. HIV Surveillance and monitoring of the HIV epidemic . 13 1.3. 4. Application of GIS and spatial analysis in health care . 14 1.3. 4.1. The use of GIS and spatial analysis in HIV prevention . 15 1.3. 4.2. Limitations and challenges of GIS application in health care . 21 1.3. 5. Targeting “Hot-spots” and key geographies for HIV transmission . 21 1.4. Rationale . 22
Cellular and molecular analysis of branching morphogenesis in "Drosophila melanogaster"

In the developing tracheal system of Drosophila melanogaster, six major branches arise by guided cell migration from a sac-like structure. The chemoattractant Branchless/FGF (Bnl) appears to guide cell migration and is essential for the formation of all tracheal branches, while Decapentaplegic (Dpp) signaling is strictly required for the formation of a subset of branches, the dorsal and ventral branches. The aim of this thesis was the analysis of the cellular mechanisms governing tracheal branching morphogenesis and the identification of new genes implicated in this process using large scale gene expression profiling. Using in vivo confocal video microscopy, we find that Bnl/FGF and Dpp signaling affect different cellular functions required for branching morphogenesis. Bnl/FGF signaling affects the formation of dynamic filopodia, possibly controlling cytoskeletal activity and motility as such, while Dpp controls cellular functions allowing branch morphogenesis and outgrowth. Further, we characterized the junctional remodeling events underlying cell intercalation in the dorsal branch and show that unicellularization is not induced by Dpp signaling. Dpp signaling is shown to be mainly required for the repression of sal in the dorsal branch. Therefore concomitant removal of Sal and Kni/Knrl leads to a rescue of dorsal branch formation. We also show that tracheal Sal controls cell-cell adhesion properties, leading to the formation of cell populations with different adhesive properties. These adhesive properties control cell rearrangements and branch formation. Based on these observations, we propose a model for tracheal morphogenesis, whose main features consist of Bnl/FGF induced cytoskeletal activity and motility, and Sal regulated cell adhesion modulation. We also performed an oligonucleotide array screen for Sal and Kni/Knrl targets in the tracheal system. Unfortunately, due to multiple reasons discussed in this thesis, this approach was not successful and had to be abandoned.
Crescimento de cultivares de arroz (Oryza sativa L.) influenciado pela inoculação com bactérias promotoras de crescimento de plantas = Growth of rice cultivars (Oryza sativa L.) as affected by inoculation with plant growth-promoting bacteria

Este trabalho objetivou avaliar o efeito da inoculacao de seis estirpes de bacterias promotoras de crescimento de plantas (BPCP), Burkholderia spp. (B7 e B16), Pseudomonas spp. (P18 e P21) e Rhizobium spp. (R65 e R82) e duas misturas contendo uma estirpe de cada genero no crescimento de seis cultivares de arroz (BRS Bonanca, BRS Aimore, BRS Talento, BRSMG Curinga, Japones e Bolinha). As caracteristicas fisiologicas das bacterias foram determinadas em ensaios in vitro. Foi conduzido um experimento sob condicoes de casa de vegetacao onde as BPCP foram inoculadas em cultivares de arroz, cultivados em vasos contendo 1 kg de solo, em delineamento de blocos casualizados com 4 repeticoes. Aos 60 dias apos a emergencia foram avaliados parâmetros de crescimentos relacionados a parte aerea e ao sistema radicular dos cultivares de arroz. Entre as bacterias, somente duas (B7 e R65) nao apresentaram capacidade de producao in vitro de auxina. Todas as estirpes apresentaram atividade de catalase e formacao de pelicula em meio NFb semi-solido sem N ou presenca de nodulo em feijoeiro, indicando capacidade de fixacao biologica de nitrogenio. A inoculacao das BPCP em arroz proporcionou aumentos medios de 10% em relacao ao controle para a area foliar e massa seca da parte aerea e de 9% para o comprimento e massa seca de raiz. Entre os cultivares, BRS Aimore apresentou maior interacao com as estirpes estudadas e a estirpe P21 de Pseudomonas spp. proporcionou diferenca significativa em relacao ao controle em parâmetros relacionados a parte aerea e ao sistema radicular.
n-FP-injective and n-flat complexes

In this paper, we extend the notions of n-FP-injective and n-flat modules to that of complexes which we call n-FP-injective and n-flat complexes, respectively and we show that the class of all n-FP-injective (resp., n-flat) complexes together with its left (resp., right) orthogonal class forms a complete cotorsion theory. Also we characterize n-coherent rings in terms of n-FP-injective and n-flat complexes.
Genetics of Soybean Agronomic Traits: II. Interactions between Yield Quantitative Trait Loci in Soybean

In order to breed efficiently, it is necessary to identify individual quantitative trait loci (QTLs) as well as interactions between these loci and to determine which QTLs produce phenotypes that are environment specific. This can be done by linking QTLs to molecular markers. The objective of this research was to carry out such an analysis for yield, one of the most complex agronomic traits. To do this, recombinant inbred lines of soybean [Glycine max (L.) Merrill] were characterized for molecular genetic markers and analyzed for yield in different environments, Interactions between QTLs were identified by subdividing the segregants into four sub-populations defined by molecular alleles at pairs of unlinked loci. Differences in the mean yields of these sub-populations defined interactions between QTLs. Measurements of yield in genotyped, recombinant inbred populations derived from crosses of Minsoy' with Archer' (MA population) and Noir 1' with Archer (NA population) have identified a pair of interacting yield QTLs whose effect was independent of environment as well as a pair of loci whose interaction was environment specific. Each example of epistasis, involved an allele specific interaction between the two QTLs. In the NA population, a pair of QTLs was identified in which Noir I alleles interact to specify a significant increase in yield that is not environment specific. These loci, located on linkage groups (LG) U3 and U9, do not affect either height or maturity. In all environments, the interaction between the QTLs was significant. In the MA population, a pair of QTLs was identified in which the Minsoy alleles interact to specify a significant increase in yield. However, this significant interaction is environment specifie. One of the loci (on LG U14) is also associated with effects on height, seed weight, and maturity that are found in other environments, but these latter effects do not appear to involve any interactions with other loci. The data from the MA population support the concept that interactions between QTLs also can result in location-specific effects on quantitative traits.
Mechanisms and Functions of Synaptic Plasticity in Mammalian Cortical Neurons

The memory system in the brain is conventionally divided into three categories: declarative memory, emotional memory, and procedural memory. We propose yet another type of memory that is one level higher than these normal memories, namely, memory of the“temporal organization of behavior”. This type of memory is thought to be formed and stored in the prefrontal cortex, taking at the cellular level the form of synaptic plasticity. Synaptic plasticity in rat prefrontal cortex is indeed powerfully modulated by dopamine, the critical neuromodulator for the function of this cortex, where abnormalities in the dopamine level lead to abnormalities in prefrontal synaptic plasticity. Abnormal synaptic plasticity is also seen in the prefrontal cortex after injection of the psychoactive drug MK801, which is known to cause schizophrenia-like cognitive dysfunction in humans. MK801 spontaneously induces in rats synaptic potentiation in hippocampus-prefrontal cortex projection, and this abnormal plasticity is indeed accompanied by deficits of hippocampus-prefrontal cortex projection-dependent cognition that involves memory of the temporal organization of behavior. These results show that synaptic plasticity in the prefrontal cortex correlates with cognitive processes that involve this cortex.
Influence of cobalt concentration on the growth and development of Dendrobium kingianum Bidwill orchid in an in vitro culture

The study investigated the influence of increased cobalt content in murashige and skoog (1962) solid medium on the growth and development of Dendrobium kingianum Bidwill orchid plants. Explants of shoots were used for micropropagation of the orchid plants on MS regeneration medium supplemented with 0.5 mg dm-3 NAA and 1.0 mg dm-3 kinetin. Cobalt (as CoCl2 · 6H2O) was added to all treatments in concentrations of 0.025 (control), 0.625, 1.25 and 2.5 mg dm-3. The results obtained after eight months showed that treatments with the cobalt chloride in concentrations 0.25-1.25 mg dm-3 did not influence the number of shoots and roots, and the length of shoots of the orchids. The treatment with the cobalt chloride in concentration 0.625 mg dm-3 positively influenced on the length of roots and increment of the fresh weight of plantlets. However, in media with the highest cobalt concentration (2.5 mg dm-3 CoCl2 · 6H2O), a negative influence of the metal on the number of shoots of the orchids was noted. Spectrophotometric analysis (ASA) showed that cobalt accumulation increased in both the shoots and the roots with the increase in the external Co level, whereas iron accumulation in these organs decreased. Cobalt and iron accumulation in the roots was 3-4 times higher than in the shoots.
Production of Tissue-Engineered Human 3D Bronchi In Vitro

Asthma is experienced during the life span in approximately 10% of the population [1]. Chronic obstructive pulmonary disease (COPD) is a complex inflammatory airway disease that results in airflow limitation that is not fully reversible. Many animal model systems have been developed that recapitulate various features of COPD but all present significant limitations [2-3]. The lack of understanding of the underlying mechanisms and mediators that drive the onset and progression of chronic inflammation, emphysema and changes in lung function have limited the development of useful models and subsequently effective treatments. Most of the normal human airway is lined by a pseudostratified epithelium of ciliated cells, secretory cells and 6–30% basal cells, the proportion of which varies along the proximal-distal axis [4]. Among several other bronchial cell types, goblet cells (GC) are important players in the development and maintenance of pulmonary disorders. Disturbance of their distribution and phenotypic features, hyperplasia, metaplasia, dysplasia and mucus hypersecretion are common patho‐ logical features of chronic respiratory diseases, including asthma, COPD, lung cancer, and cystic fibrosis. Despite numerous studies, the molecular basis for GC phenotypic changes remain elusive [5-6]. In asthmatic bronchi, the number of GCs is increased, due to the trans‐ differentiation of ciliated and club cells (Clara) to GCs, resulting in more abundant mucus production [7]. GCs secrete the mucins MUC5B and MUC5AC, which are responsible for the viscoelasticity and hydration of the mucus covering the ciliated escalator [7]. The sputum in
Towards a non-equilibrium ecology: perspectives from an arid land

'. the whole surrounding area has been overgrazed so thoroughly that only the large trees remain in a level plain of bare sand. There are no young trees nor can any raise its head owing to the intensive browsing of the numerous cattle, goats and donkeys . as the large trees die off one by one and no others take their place it seems that all vegetation must eventually disappear . (Van Warmelo, 1962, p. 39).
Robust portfolio selection for individuals: Minimizing the probability of lifetime ruin

Robust portfolio selection has become a popular problem in recent years. In this paper, we study the optimal investment problem for an individual who carries a constant consumption rate but worries about the model ambiguity of the financial market. Instead of using a conventional value function such as the utility of terminal wealth maximization, here, we focus on the purpose of risk control and seek to minimize the probability of lifetime ruin. This study is motivated by the work of [ 3 ], except that we use a standardized penalty for ambiguity aversion. The reason for taking a standardized penalty is to convert the penalty to units of the value function, which makes the difference meaningful in the definition of the value function. The advantage of taking a standardized penalty is that the closed-form solutions to both the robust investment policy and the value function can be obtained. More interestingly, we use the "Ambiguity Derived Ratio" to characterize the existence of model ambiguity which significantly affects the optimal investment policy. Finally, several numerical examples are given to illustrate our results.
Tumor antigens recognized by T cells and antibodies

Tumor Antigens Recognized by Antibodies. Human Tumor Antigens Recognized by Antibodies (SEREX). Antibodies to Tumor Oncoproteins in Cancer Patients. Antibody and CTL Responses to the NY-ESO Antigen. Tumor Antigens Recognized by CD4+ T Cells (predominantly TH1). Melanoma Antigens Recognized by CD4+ T Cells. Mouse Models in the Recognition of Tumor Antigens. Antigens of the MAGE Family Recognized by CD4+ T Cells. Tumor antigens Recognized by CD8 T Cells. Melanoma Antigens Recognized by CD8 T Cells. Squamous Cells and Adeno Cancer Antigens Recognized by T Cells. Heat/Shock Proteins and Tumor Antigens. The Wilms Tumor Antigens as CTL Target. Ex vivo and in situ Tetramer Analysis of CTL Responses to Tumors. Altered Peptide Ligands of Tumor T Cell Epitopes: Implications for More Effective Vaccine Therapy in Human Neoplasia.
Prize-winners to pariahs - a history of Japanese knotweed s.l. (Polygonaceae) in the British Isles.

93 The early history of the discovery and introduction to the British Isles of the alien invasive perennials belonging to Fallopia section Reynoutria (hereafter referred to as Japanese Knotweed s.l.) are described from a study of documentary evidence and herbarium material. The role of the various agencies involved in the dispersal of these plants is discussed, as is the influence that contemporaneous gardening trends had on the ornamental use of Japanese Knotweed s. I.
Eine evolutionsökologische Analyse des Aggregations-Koexistenz-Modells für Drosophila

Intraspezifische Aggregation ist als die wesentliche Steuergrose fur die lokale Artenvielfalt in vielen Insektengemeinschaften bekannt, in denen eine artspezifische Ressourcenaufteilung keine bedeutendende Rolle fur die Koexistenz mehrerer Arten spielt. Welche Faktoren jedoch eine Begunstigung von Eiaggregation durch Insektenweibchen auf nahrungslimitierten Ressourcen verursachen sind weitgehend unbekannt. In der vorliegenden Arbeit wurde mit der Taufliege Drosophila subobscura die Hypothese der Existenz von Allee-Effekten getestet, welche einen hoheren Entwicklungserfolg der Insektenlarven bei mittleren Larvaldichten ermoglichen. Durch den Einsatz einer Vielzahl von Entwicklungssubstraten der Fliegelarven (verfaulenden Fruchte) konnte die Existenz von bottom-up vermittelten Allee-Effekten bestatigt werden, wobei maternale Einflusse durch das Ubertragen von Hefen, als Nahrungsquelle fur die Larven, einen Uberlebensvorteil fur die Nachkommen bieten. Des weiteren konnten top-down Allee-Effekte herausgearbeitet werden, indem namlich die Fliegenlarven in groseren Gruppen in raumlichen Refugien gegenuber parasitoiden Wespen fressen konnen. Es wurde eine sehr starke interindividuelle Variabilitat in den Eiablageentscheidungen der Fliegenweibchen beobachtet, die als adaptive Verhaltensantwort auf unvorhersehbare Entwicklungsbedingungen fur die Larven diskutiert wird. Sie beinhaltet Elemente aus sowohl bet-hedging (kleine Eigelege) als auch gambling (grose Eigelege), wobei gambling von naturlicher Selektion favorisiert wird, wenn Allee-Effekte fur den Entwicklungserfolg der Nachkommen eine grose Rolle spielen. Die Ergebnisse dieser Arbeit werden als evolutionare Erklarung fur die Artenkoexistenz durch Aggregation diskutiert.
Development, Cytology, Topography and Connections

1 Introduction. - 2 Cytology of the STN. - 3 Ontogeny of the STN. - 4 Topography of the rat, cat, baboon, and human STN. - 5 Connections of the STN. - 6 Nigrosubthalamic connections in rat. - Subject index.
Ensuring the Safety of Classical Biological Control for Cabbage Seedpod Weevil in Canada: Assessment of the Ecological Host Range of Candidate Ectoparasitoids in Europe and Clarification of their Taxonomic Status

Classical biological control of insect pests and weeds can lead to potential conflicts, particularly if the insect pest and weed agents are closely related. Such a conflict may occur in biological control of the Cabbage Seedpod Weevil (CSPW), Ceutorhynchus obstrictus (Marsham) [=C. assimilis (Paykull); see Colonnelli (2004)] (Coleoptera: Curculionidae), which belongs to the same subfamily, Ceutorhynchinae, as a number of agents introduced or proposed for introduction against invasive alien weed species in North America. The CSPW is a serious pest of canola and rapeseed in North America. Some of the known European parasitoids such as Trichomalus perfectus Walker and Mesopolobus morys Walker (both Hym.; Pteromalidae) show the greatest potential for incorporation into an IPM programme in North America and are currently being considered for introduction. Prior to importation, several issues have to be assessed, and results are presented here: Taxonomy of the European species of the genus Trichomalus and Mesopolobus associated to Ceutorhynchinae hosts were revised and illustrated keys provided to ensure up to date information is available to biological control practitioners. A three years field survey has been carried out in five European countries to field collect Ceutorhynchinae hosts, rear their ectoparasitoids and identify them. Furthermore, implications of the host-parasitoid associations recovered by the surveys are discussed relative to introduction of species to North America for classical biological control of cabbage seedpod weevil.The host specificity of the candidate ectoparasitoids has to be determined in their native cultivated and non-cultivated habitats. A three year field survey has been carried out to document the European parasitoid assemblages associated with several Ceutorhynchinae species either already introduced in North America as classical weed biological control agents (Microplontus edentulus (Schultze) against scentless chamomile, Tripleurospermum perforatum (Merat) Lainz (=Matricaria perforata Merat) [Asteraceae]; Hadroplontus litura (Fabricuius) against Canada thistle, Cirsium arvense (L.) Scopoli [Asteraceae]), proposed for introduction (Ceutorhynchus turbatus Schultze against hoary cress, Lepidium draba L. (=Cardaria draba) [Asteraceae]) or of importance in term of conservation (Ceutorhynchus typhae (=C. floralis) (Paykull) on Shepherd s purse, Capsella bursa-pastoris (L.) Medicus [Brassicaceae]). These results are discussed to estimate potential non-target effects on other Ceutorhynchinae species and implications for classical biological control of cabbage seedpod weevil.
Epithelial cell rearrangements during tubular organ formation

The tracheal system of Drosophila is a simple branched tubular organ that consists of different branches with distinct cellular architectures. We have analyzed how these branches are formed during embryonic development and how this process is controlled genetically. In particular we focused our analysis on the intercalation process that underlies the transition from thick, multicellular branches to finer branches, in which single cells reach around the lumen and seal it with autocellular AJs. To study tracheal development at the cellular level, I developed a technique that allows for the visualization and manipulation of single tracheal cells in vivo. Using this technique we characterized the intercalation process during dorsal branch formation. Based on these findings we proposed a model of intercalation that involves four steps. We also found that intercalation is specifically blocked in the dorsal trunk by the expression of the transcription factor spalt (sal) and that sal is sufficient to block intercalation also in other branches. To mediate this function, sal expression is required in a group of cells. In the following I tried to identify genes that are involved in this process using different approaches. In a candidate approach I tested a variety of genes that have been implicated in cell rearrangement and intercalation in other systems. Furthermore I tested several candidates with potentially interesting domains that show a trachea-specific expression pattern. I also searched for phenotypes that resemble the gain or loss of function phenotype of sal in a genetic screen using molecularly mapped deficiencies. Finally I initiated a screen using gene chips to identify sal target genes. Using these different approaches I characterized the molecular basis of intercalation. On the one hand I ruled out that some obvious candidates contribute to the process. On the other hand I identified candidates that affect intercalation. In the deficiency screen I identified a deletion that shows ectopic intercalation. This deficiency also exhibits cargospecific secretion defects. I am currently mapping the gene responsible for these defects by generating new deficiencies. Finally I attempted to characterize the forces that drive intercalation. Investigating the role of the FGF pathway I identified a putative positive input of the FGF pathway on intercalation via the transcription factor pointed.
Effect of fertilization and variety on digestibility of phosphorus from plant feedstuffs in pigs

Three experiments were performed to determine the digestibility of phosphorus in plant feedstuffs for pigs. Pigs initially weighing 11 kg were kept in metabolism crates and fed twice daily at about 2 to 2.5-fold metabolizable energy requirement for maintenance. A semi-purified diet low in phosphorus and without intrinsic phytase activity was fed either alone or after blending into test diets containing 60% of barley or wheat or 40% of field bean or rye. Mixtures were calculated to contain not more than 2 g digestible P/kg DM and between 5.0 to 6.0 g Ca/kg DM. Faeces and urine were quantitatively collected for 7 days after 7 days of adaptation. Phosphorus digestibility for ingredients under test was calculated from differences of results on test and basal diet. Digestibility of phosphorus in three different batches of rye was 70% on average. In two batches of field bean the digestibility coefficient was 36 %. Phosphorus digestibility in 12 batches of wheat ranged from 43 to 59 %, with a mean of 56%, in six batches of barley the digestibility coefficient ranged from 42 to 52 % with a mean of 46%. There was no effect of fertilization with nitrogen or phosphorus on the digestibility of phosphorus in wheat, rye or barley. A variety effect on digestibility was indicated for barley and wheat. No clear relation was found between P digestibility on the one hand and portion of phytate-bound P or activity of intrinsic phytase activity on the other hand.