Automatic segmentation and 3D feature extraction of protein aggregates in Caenorhabditis Elegans

In the last years, it has become increasingly clear that neurodegenerative diseases involve protein aggregation, a process often used as disease progression readout and to develop therapeutic strategies. This work presents an image processing tool to automatic segment, classify and quantify these aggregates and the whole 3D body of the nematode Caenorhabditis Elegans. A total of 150 data set images, containing different slices, were captured with a confocal microscope from animals of distinct genetic conditions. Because of the animals’ transparency, most of the slices pixels appeared dark, hampering their body volume direct reconstruction. Therefore, for each data set, all slices were stacked in one single 2D image in order to determine a volume approximation. The gradient of this image was input to an anisotropic diffusion algorithm that uses the Tukey’s biweight as edge-stopping function. The image histogram median of this outcome was used to dynamically determine a thresholding level, which allows the determination of a smoothed exterior contour of the worm and the medial axis of the worm body from thinning its skeleton. Based on this exterior contour diameter and the medial animal axis, random 3D points were then calculated to produce a volume mesh approximation. The protein aggregations were subsequently segmented based on an iso-value and blended with the resulting volume mesh. The results obtained were consistent with qualitative observations in literature, allowing non-biased, reliable and high throughput protein aggregates quantification. This may lead to a significant improvement on neurodegenerative diseases treatment planning and interventions prevention

Distributed generation producers' reserve management

Sustainable development concerns are being addressed with increasing attention, in general, and in the scope of power industry, in particular. The use of distributed generation (DG), mainly based on renewable sources, has been seen as an interesting approach to this problem. However, the increasing of DG in power systems raises some complex technical and economic issues. This paper presents ViProd, a simulation tool that allows modeling and simulating DG operation and participation in electricity markets. This paper mainly focuses on the operation of Virtual Power Producers (VPP) which are producers’ aggregations, being these producers mainly of DG type. The paper presents several reserve management strategies implemented in the scope of ViProd and the results of a case study, based on real data.

Multi-agent negotiation for coalition formation and management in electricity markets

Negotiation is a fundamental tool for reaching understandings that allow each involved party to gain an advantage for themselves by the end of the process. In recent years, with the increasing of compe-titiveness in most sectors, negotiation procedures become present in practically all of them. One particular environment in which the competitiveness has been increasing exponentially is the electricity markets sector. This work is directed to the study of electricity markets’ partici-pating entities interaction, namely in what concerns the formation, management and operation of aggregating entities – Virtual Power Players (VPPs). VPPs are responsible for managing coalitions of market players with small market negotiating influence, which take strategic advantage in entering such aggregations, to increase their negotiating power. This chapter presents a negotiation methodology for the creation and management of coalitions in Electricity Markets. This approach is tested using MASCEM, taking advantage of its ability to provide the means to model and simulate VPPs. VPPs are represented as coalitions of agents, with the capability of negotiating both in the market, and internally, with their members, in order to combine and manage their individual specific characteristics and goals, with the strategy and objectives of the VPP itself.

Biology, ecology and conservation of mobulid rays in the Azores

Dissertação de Mestrado, Estudos Integrados dos Oceanos, 12 de Dezembro de 2013, Universidade dos Açores.

Experimental pulmonary schistosomiasis: lack of morphological evidence of modulation in schistosomal pulmonary granulomas

Numerous pulmonary schistosome egg granulomas were present in mice submitted to partial portal vein ligation (Warren's model). The granulomas were characterized by cellular aggregations formed within alveolar tissue. Main cellular types were macrophages (epithelioid cells), eosinophils, plasma cells and lymphocytes. These cells were supported by scanty fibrous stroma and exhibited close membrane contact points amongst themselves, but without forming specialized adhesion apparatus. When granulomas involved arterial structures, proliferation of cndothelial and smooth muscle cells occurred and fibrosis associated with angiogenesis became more evident. Granulomas formed around mature eggs in the pulmonary alveolar tissue presented approximately the same size and morphology regardless of the time of infection, the latter being 10, 18 and 25 weeks after cercarial exposure. This persistence of morphological appearance suggests that pulmonary granulomas do not undergo immunological modulation, as is the case with the granulomas in the liver and, to a lesser extent, in the intestines. Probably, besides general immunological factors, local (stromal) factors play an important role in schistosomal granuloma modulation.

BIOFILM FORMATION OF Vibrio cholerae ON STAINLESS STEEL USED IN FOOD PROCESSING

Vibrio cholerae represents a significant threat to human health in developing countries. This pathogen forms biofilms which favors its attachment to surfaces and its survival and transmission by water or food. This work evaluated the in vitro biofilm formation of V. cholerae isolated from clinical and environmental sources on stainless steel of the type used in food processing by using the environmental scanning electron microscopy (ESEM). Results showed no cell adhesion at 4 h and scarce surface colonization at 24 h. Biofilms from the environmental strain were observed at 48 h with high cellular aggregations embedded in Vibrio exopolysaccharide (VPS), while less confluence and VPS production with microcolonies of elongated cells were observed in biofilms produced by the clinical strain. At 96 h the biofilms of the environmental strain were released from the surface leaving coccoid cells and residual structures, whereas biofilms of the clinical strain formed highly organized structures such as channels, mushroom-like and pillars. This is the first study that has shown the in vitro ability of V. cholerae to colonize and form biofilms on stainless steel used in food processing.

Heliconia acuminata reproductive success is independent of local floral density

Reproductive plants in tropical forests are patchily distributed, with some in large aggregations of reproductive consepecifics while others are relatively isolated. This variation in floral density is hypothesized to have a major effect on plant reproductive success, since individuals in higher density neighborhoods can attract more or higher quality pollinators. We experimentally tested this hypothesis with populations of the understory herb Heliconia acuminata in central Amazonia. We created replicated plots in which reproductive plant density spanned the range of naturally occurring floral neighborhood size, then measured three surrogates of plant fitness in focal plants in each array. There was no significant difference between any of the three floral neighborhood treatments in total seed production, fruit set, or the number of seeds produced per fruit. Pollinator visitation rates to plants in all treatments were extremely low, with many plants not visited at all during the observation period. This could be because H. acuminata's hummingbird pollinators are unable to find the widely scattered reproductive plants, however this hypothesis appears unlikely. Instead, natural flowering plant densities may simply be below the threshold value at which neighborhood effects become important, even in "high-density" aggregations. Nutrient limitation, selective fruit abortion, and reproduction via male rather than female function may also be playing a role. We argue the absence of neighborhood effects may be a general phenomenon in central Amazonian forests, though additional experiments with other plant-pollinator systems are needed to determine the extent to which this hypothesis is supported.

Redes de inovação em pequenas e médias empresas: um estudo de caso no setor têxtil

Dissertação de mestrado em Engenharia Industrial

Population dynamics of 0-group flounder (Platichthys flesus L.) in Galway Bay, West of Ireland and the value of flounder from shore angling tourism in Ireland

The economic value of flounder from shore angling around Ireland was assessed. Flounder catches from shore angling tournaments around Ireland were related to domestic and overseas shore angling expenditure in order to determine an economic value for the species. Temporal trends in flounder angling catches, and specimen (trophy) flounder reports were also investigated. Flounder was found to be the most caught shore angling species in competitions around Ireland constituting roughly one third of the shore angling competition catch although this did vary by area. The total value of flounder from shore angling tourism was estimated to be of the order of €8.4 million. No significant temporal trends in flounder angling catches and specimen reports were found. Thus there is no evidence from the current study for any decline in flounder stocks. The population dynamics of 0-group flounder during the early benthic stage was investigated at estuarine sites in Galway Bay, west of Ireland. Information was analysed from the March to June sampling period over five years (2002 to 2006). Spatial and temporal variations in settlement and population length structure were analysed between beach and river habitats and sites. Settlement of flounder began from late March to early May of each year, most commonly in April. Peak settlement was usually in April or early May. Settlement was recorded earlier than elsewhere, although most commonly was similar to the southern part of the UK and northern France. Settlement was generally later in tidal rivers than on sandy beaches. Abundance of 0-group flounder in Galway Bay did not exhibit significant inter -annual variability. 0-group flounder were observed in dense aggregations of up to 105 m'2, which were patchy in distribution. Highest densities of 0-group flounder were recorded in limnetic and oligohaline areas as compared with the lower densities in polyhaline and to a lesser extent mesohaline areas. Measurements to of salinity allowed the classification of beaches, and tidal river sections near the mouth, into a salinity based scheme for length comparisons. Beaches were classified as polyhaline,the lower section of rivers as mesohaline, and the middle and upper sections as oligohaline. Over the March to June sampling period 0-group flounder utilised different sections at different length ranges and were significantly larger in more upstream sections. During initial settlement in April, 0-group flounder of 8-10 mm (standard length, SL) were present in abundance on polyhaline sandy beaches. By about 10mm (SL), flounder were present in all polyhaline, mesohaline and (oligohaline) sections. 0-group flounder became absent or in insignificant numbers in polyhaline and mesohaline sections in a matter of weeks after first appearance. From April to June, 0-group flounder of 12-30mm (SL) were found in more upstream locations in the oligohaline sections. About one month (May or June) after initial settlement, 0-group flounder became absent from the oligohaline sections. Concurrently, flounder start to reappear in mesohaline and polyhaline areas at approximately 30mm (SL) in June. The results indicate 0-group flounder in the early benthic stage are associated with low salinity areas, but as they grow, this association diminishes. Results strongly suggest that migration of 0-group flounder between habitats takes place during the early benthic phase.

Anurans of the Serra do Caraça, southeastern Brazil: species composition and phenological patterns of calling activity

Annual patterns of calling and breeding activity of 38 anuran species were studied at Serra do Caraça, an 11,233 ha reserve located in a contact zone between Cerrado and Atlantic forest at the southern Espinhaço range, southeastern Brazil. Five patterns were evident: (1) species that call year-round or nearly year-round with larger aggregations generally observed in the rainy months, (2) species with opportunistic calling activity associated with rainfall during the wettest months of the year, (3) winter species, (4) explosive breeders with intense calling activity triggered by heavy rains during the rainy season or only in the beginning of the rainy season, and (5) summer species with variable breeding seasons. Both the monthly number of species with calling males and the monthly number of species that showed the maximum class of calling males were positively correlated with both mean monthly temperature and monthly precipitation.

Habitat use by a tree frog species of Scinax (Amphibia, Hylidae) at an urban forest fragment from south-eastern Brazil

We studied the pattern of habitat use by the tree frog Scinax aff. perereca. Fieldworks were performed from August 1996 to August 1997 at Parque das Mangabeiras, Belo Horizonte, State of Minas Gerais, southeastern Brazil. Calling males were observed in September, October and December 1996, February to April and June 1997. Females were found only in October 1996. Specimens were found perched on vegetation, on the ground or on stones near waterfall. At Parque das Mangabeiras, S. aff. perereca occupied nine types of substrata. The most frequently used substrata were shrubs, stones at the stream edges, and fallen trunks. The pattern of spatial occupation varied among months. Males were found calling in aggregations on the vegetation and spatial niche breadth was related to species abundance.

Dial behavioral responses of Metamysidopsis elongata atlantica (Crustacea, Mysida) to gradients of salinity and temperature

Metamysidopsis atlantica elongata (Bascescu, 1968) is a common mysid in the surf zone of sandy beaches from the state of Rio Grande do Sul, Brazil, where it is frequently recorded forming dense aggregations. Trough laboratory trials, behavioral responses to salinity (10, 20, 25, 28, 30, 40 e 45), temperature (10, 15, 20, 30±1ºC) and light (yes/no) were tested using adult males, adult females and juveniles. Although there was no response to temperature, the species showed clear response to salinity and light. In the presence of light, organisms remained in the bottom of the aquaria, but moved to surface when bottom salinities were increased. In the absence of light, adults moved to the surface. However, juveniles moved down to or remained on the bottom, maybe as a response to avoid adult predation.

Morphological development of Corydoras aff. paleatus (Siluriformes, Callichthyidae) and correlation with the emergence of motor and social behaviors

Here we examine major anatomical characteristics of Corydoras aff. paleatus (Jenyns, 1842) post-hatching development, in parallel with its neurobehavioral evolution. Eleutheroembryonic phase, 4.3-8.8 days post-fertilization (dpf); 4.3-6.4 mm standard length (SL) encompasses from hatching to transition to exogenous feeding. Protopterygiolarval phase (8.9-10.9 dpf; 6.5-6.7 mm SL) goes from feeding transition to the commencement of unpaired fin differentiation, which marks the start of pterygiolarval phase (11-33 dpf; 6.8-10.7 mm SL) defined by appearance of lepidotrichia in the dorsal part of the median finfold. This phase ends with the full detachment and differentiation of unpaired fins, events signaling the commencement of the juvenile period (34-60 dpf; 10.8-18.0 mm SL). Eleutheroembryonic phase focuses on hiding and differentiation of mechanosensory, chemosensory and central neural systems, crucial for supplying the larval period with efficient escape and nutrient detection-capture neurocircuits. Protopterygiolarval priorities include visual development and respiratory, digestive and hydrodynamic efficiencies. Pterygiolarval priorities change towards higher swimming efficacy, including carangiform and vertical swimming, necessary for the high social interaction typical of this species. At the end of the protopterygiolarval phase, simple resting and foraging aggregations are seen. Resting and foraging shoals grow in complexity and participant number during pterygiolarval phase, but particularly during juvenile period.

Alterações cutâneas do cão no Kala-Azar sul-americano

According to E. Chagas (1938), South-American Kala Azar is a widespread disease from the jungle, several cases being reported from North Brazil (Estado do Pará: Marajó Island, Tocantins and Gurupi river valleys; Estados do Piauí and Ceará: coast and hinterland). Other cases were found in Northeast Brazil (Estados de Pernambuco, Alagôas and Sergipe: coast and hinterland; Estado da Bahia: hinterland). A few cases were described from Estado de Mato-Grosso (Brazil), Provincia de Salta and Território do Chaco (Argentine), and Zona contestada do Chaco (Paraguai-Bolívia). A well defined secondary anemia associated with enlargement of the liver and spleen are the chief symptoms. Death usually occurs in cachexia and with symptoms of heart failure. Half the patients were children aged less than ten years (CHAGAS, CASTRO & FERREIRA, 1937). Quite exhaustive epidemiological researches performed by CHAGAS, FERREIRA, DEANE, DEANE & GUIMARÃES (1938) in Municipio de Abaeté (Estado do Pará, Brazil) gave the incidence of 1.48% for the natural infection in human, 4.49% in dogs, and 2.63% in cats. The infection was arcribed (CUNHA & CHAGAS, 1937) to a new species of Leishmania (L. chagasi). Latter CUNHA (1938) state, that it is identical to L. infantum. ADLER (1940) found that so far it has been impossible to distinguish L. chagasi from L. infantum by any laboratory test but a final judgment must be reserved until further experiments with different species of sandflies have been carried out. Skin changes in canine Kala Azar were signaled by many workers, and their importance as regards the transmission of the disease is recognized by some of them (ADLER & THEODOR, 1931, 2. CUNHA, 1933). Cutaneous ulcers in naturally infected dogs are referred by CRITIEN (1911) in Malta, by CHODUKIN & SCHEVTSCHENKO (1928) in Taschkent, by DONATIEN & LESTOCQUARD (1929) and by LESTOCQUARD & PARROT (1929) in Algeria, and by BLANC & CAMINOPETROS (1931) in Greece. Depilation is signaled by YAKIMOFF & KOHL-YAKIMOFF (1911) in Tunis, by YAKIMOFF (1915) in Turkestan. Eczematous areas or a condition described as "eczema furfurace" is sometimes noted in the areas of depilation (DONATIEN & LESTOCQUARD). The skin changes noticed by ADLER & THEODOR (1932) in dogs naturally infected with Mediterranean Kala Azar can be briefly summarized as a selective infiltration of macrophages around hair follicles including the sebaceous glands and the presence of infected macrophages in normal dermis. The latter phenomenon in the complete absence of secondary infiltration of round cells and plasma cells is the most striking characteristic of canine Kala Azar and differentiates it from L. tropica. In the more advanced stages the dermis is more cellular than that of normal dogs and may even contain a few small dense areas of infiltration with macrophages and some round cells and polymorphs. The external changes, i. e., seborrhea and depilation are roughly proportional to the number of affected hair follicles. In dogs experimentally infected with South-American Kala Azar the parasites were regularly found in blocks of skin removed from the living animal every fortnight (CUNHA, 1938). The changes noticed by CUNHA, besides the presence of Leishmania, were perivascular and diffuse infiltration of the cutis with mononuclears sometimes more marked near hair follicles, as well as depilation, seborrhea and ulceration. The parasites were first discovered and very numerous in the paws. Our material was obtained from dogs experimentally infected by Dr. A. MARQUES DA CUNHA< and they were the subject of a previous paper by CUNHA (1938). In this study, however, several animals were discarded as it was found that they did develop a superimposed infection by Demodex canis. This paper deals with the changes found in 88 blocks of skin removed from five dogs, two infected with two different canine strains, and three with two distinct human strains of South-American Kala Azar. CUNHA'S valuable material affords serial observations of the cutaneous changes in Kala Azar as most of the blocks of skin were taken every fortnight. The following conclusions were drawn after a careful microscopic study. (1) Skin changes directly induced in the dog by the parasites of South-American Kala Azar may b described as an infiltration of the corium (pars papillaris and upper portion of the reticular layer) by histocytes. Parasites are scanty, at first, latter becoming very numerous in the cytoplasm of such cells. Sometimes the histocytes either embedding or not leishman bodies appear as distinct nodes of infiltration or cell aggregations (histocytic granuloma, Figs. 8 and 22) having a perivascular distribution. The capillary loops in the papillae, the vessels of the sweat glands, the subpapillary plexus, the vertical twigs connecting the superficial and deep plexuses are the ordinary seats of the histocytic Kala Azar granulomata. (2) Some of the cutaneous changes are transient, and show spontaneous tendency to heal. A gradual transformation of the histocytes either containing or not leishman bodies into fixed connective tissue cells or fibroblasts occut and accounts for the natural regression just mentioned. Figs. 3, 5, 18, 19 and 20 are good illustrations of such fibroblastic transformation of the histocytic Kala Azar granulomata. (3) Skin changes induced by the causative organism of South-American Kala Azar are neither uniform nor simultaneous. The same stage may be found in the same dog in different periods of the disease, and not the same changes take place when pieces from several regions are examined in the same moment. The fibroblastic transformation of the histocytic granulomata marking the beginning of the process of repair, e. g., was recognised in dog C, in the 196th as well as in the 213rd (Fig. 18) and 231st (Fig. 19) days after the inoculation. (4) The connective tissue of the skin in dogs experimentally infected with South-American Kala Azar is overflowed by blood cells (monocytes and lymphocytes) besides the proliferation in situ of undifferentiated mesenchymal cells. A marked increase in the number of cells specially the "ruhende Wanderzellen" (Figs. 4 and 15) is noticed even during the first weeks after inoculation (prodomal stage) when no leishman bodies are yet found in the skin. Latter a massive infiltration by amoeboid wandering cells similar to typical blood monocytes (Fig. 21) associated to a small number of lymphocytes and plasma cells (Figs. 9, 17, 21, and 24) indicates that the emigration of blood cells...

Synanthropic trends in urban andextraurban taxocenoses of Sarcophaginae (Diptera) in three central european cities

An attempt has been made to characterize the synanthropic trends in Sarcophaginae of three Central European cities, viz. Brno, Bratislava and Budapest. The polar ordination of both sarcophagine taxa and of their taxocenoses revealed clear-cut trends towards culturophily and synanthropy in the male preconnubial aggregations of Sarchophaginae evidencing that this group of high Diptera represent an excellent model for the study of this phenomenon.