Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni

The number of sequences generated by genome projects has increased exponentially, but gene characterization has not followed at the same rate. Sequencing and analysis of full-length cDNAs is an important step in gene characterization that has been used nowadays by several research groups. In this work, we have selected Schistosoma mansoni clones for full-length sequencing, using an algorithm that investigates the presence of the initial methionine in the parasite sequence based on the positions of alignment start between two sequences. BLAST searches to produce such alignments have been performed using parasite expressed sequence tags produced by Minas Gerais Genome Network against sequences from the database Eukaryotic Cluster of Orthologous Groups (KOG). This procedure has allowed the selection of clones representing 398 proteins which have not been deposited as S. mansoni complete CDS in any public database. Dedicated sequencing of 96 of such clones with reads from both 5' and 3' ends has been performed. These reads have been assembled using PHRAP, resulting in the production of 33 full-length sequences that represent novel S. mansoni proteins. These results shall contribute to construct a more complete view of the biology of this important parasite.

TFC J2EE : proyecto biblioteca virtual

Como Trabajo de Fin de Carrera (TFC) se ha realizado el análisis, diseño e implementación de una aplicación utilizando tecnología Java y una arquitectura J2EE. El proyecto Biblioteca Virtual consiste en una aplicación accesible a través de Internet, en la que los usuarios pueden consultar el catálogo de libros disponibles, solicitarlos, realizar búsquedas específicas, etc. Además, presenta opciones para administrar el stock de libros y los préstamos.

Measuring an effect size from dichotomized data : contrasted results whether using a correlation or an odds-ratio

It is well known that dichotomizing continuous data has the effect to decrease statistical power when the goal is to test for a statistical association between two variables. Modern researchers however are focusing not only on statistical significance but also on an estimation of the "effect size" (i.e., the strength of association between the variables) to judge whether a significant association is also clinically relevant. In this article, we are interested in the consequences of dichotomizing continuous data on the value of an effect size in some classical settings. It turns out that the conclusions will not be the same whether using a correlation or an odds ratio to summarize the strength of association between the variables: Whereas the value of a correlation is typically decreased by a factor pi/2 after each dichotomization, the value of an odds ratio is at the same time raised to the power 2. From a descriptive statistical point of view, it is thus not clear whether dichotomizing continuous data leads to a decrease or to an increase in the effect size, as illustrated using a data set to investigate the relationship between motor and intellectual functions in children and adolescents

Validation of Logistic Regression Models for Landslide Susceptibility Maps

A wide range of numerical models and tools have been developed over the last decades to support the decision making process in environmental applications, ranging from physical models to a variety of statistically-based methods. In this study, a landslide susceptibility map of a part of Three Gorges Reservoir region of China was produced, employing binary logistic regression analyses. The available information includes the digital elevation model of the region, geological map and different GIS layers including land cover data obtained from satellite imagery. The landslides were observed and documented during the field studies. The validation analysis is exploited to investigate the quality of mapping.

Asymptomatic Plasmodium spp. infection in Tierralta, Colombia

With the aim of determining the prevalence of asymptomatic Plasmodium spp. infection by thick smear and PCR and its association with demographic and epidemiological characteristics in the village of Nuevo Tay, Tierralta, Córdoba, Colombia, a cross-sectional population study was carried out, using random probabilistic sampling. Venous blood samples were taken from 212 people on day 0 for thick smear and PCR. Clinical follow-up and thick smears were carried out on days 14 and 28. The prevalence of Plasmodium spp. infection was 17.9% (38/212; 95% CI: 12.5-23.3%) and the prevalence of asymptomatic Plasmodiumspp. infection was 14.6% (31/212; 95% CI: 9.6-19.6%). Plasmodium vivax was found more frequently (20/31; 64.5%) than Plasmodium falciparum (9/31; 29%) and mixed infections (2/31; 6.5%). A significantly higher prevalence of asymptomatic infection was found in men (19.30%) than in women (9.18%) (prevalence ratio: 2.10; 95% CI: 1.01-4.34%; p = 0.02). People who developed symptoms had a significantly higher parasitemia on day 0 than those who remained asymptomatic, of 1,881.5 ± 3,759 versus 79 ± 106.9 (p = 0.008). PCR detected 50% more infections than the thick smears. The presence of asymptomatic Plasmodium spp. infection highlights the importance of carrying out active searches amongst asymptomatic populations residing in endemic areas.

Parts, places, and perspectives : a theory of spatial relations based an mereotopology and convexity

This thesis suggests to carry on the philosophical work begun in Casati's and Varzi's seminal book Parts and Places, by extending their general reflections on the basic formal structure of spatial representation beyond mereotopology and absolute location to the question of perspectives and perspective-dependent spatial relations. We show how, on the basis of a conceptual analysis of such notions as perspective and direction, a mereotopological theory with convexity can express perspectival spatial relations in a strictly qualitative framework. We start by introducing a particular mereotopological theory, AKGEMT, and argue that it constitutes an adequate core for a theory of spatial relations. Two features of AKGEMT are of particular importance: AKGEMT is an extensional mereotopology, implying that sameness of proper parts is a sufficient and necessary condition for identity, and it allows for (lower- dimensional) boundary elements in its domain of quantification. We then discuss an extension of AKGEMT, AKGEMTS, which results from the addition of a binary segment operator whose interpretation is that of a straight line segment between mereotopological points. Based on existing axiom systems in standard point-set topology, we propose an axiomatic characterisation of the segment operator and show that it is strong enough to sustain complex properties of a convexity predicate and a convex hull operator. We compare our segment-based characterisation of the convex hull to Cohn et al.'s axioms for the convex hull operator, arguing that our notion of convexity is significantly stronger. The discussion of AKGEMTS defines the background theory of spatial representation on which the developments in the second part of this thesis are built. The second part deals with perspectival spatial relations in two-dimensional space, i.e., such relations as those expressed by 'in front of, 'behind', 'to the left/right of, etc., and develops a qualitative formalism for perspectival relations within the framework of AKGEMTS. Two main claims are defended in part 2: That perspectival relations in two-dimensional space are four- place relations of the kind R(x, y, z, w), to be read as x is i?-related to y as z looks at w; and that these four-place structures can be satisfactorily expressed within the qualitative theory AKGEMTS. To defend these two claims, we start by arguing for a unified account of perspectival relations, thus rejecting the traditional distinction between 'relative' and 'intrinsic' perspectival relations. We present a formal theory of perspectival relations in the framework of AKGEMTS, deploying the idea that perspectival relations in two-dimensional space are four-place relations, having a locational and a perspectival part and show how this four-place structure leads to a unified framework of perspectival relations. Finally, we present a philosophical motivation to the idea that perspectival relations are four-place, cashing out the thesis that perspectives are vectorial properties and argue that vectorial properties are relations between spatial entities. Using Fine's notion of "qua objects" for an analysis of points of view, we show at last how our four-place approach to perspectival relations compares to more traditional understandings.

Compositional amalgamations and balances: a critical approach

The amalgamation operation is frequently used to reduce the number of parts of compositional data but it is a non-linear operation in the simplex with the usual geometry,the Aitchison geometry. The concept of balances between groups, a particular coordinate system designed over binary partitions of the parts, could be an alternative to theamalgamation in some cases. In this work we discuss the proper application of bothconcepts using a real data set corresponding to behavioral measures of pregnant sows

Genetic male infertility and mutation of CATSPER ion channels.

A clinically significant proportion of couples experience difficulty in conceiving a child. In about half of these cases male infertility is the cause and often genetic factors are involved. Despite advances in clinical diagnostics ∼50% of male infertility cases remain idiopathic. Based on this, further analysis of infertile males is required to identify new genetic factors involved in male infertility. This review focuses on cation channel of sperm (CATSPER)-related male infertility. It is based on PubMed literature searches using the keywords 'CATSPER', 'male infertility', 'male contraception', 'immunocontraception' and 'pharmacologic contraception' (publication dates from January 1979 to December 2009). Previously, contiguous gene deletions including the CATSPER2 gene implicated the sperm-specific CATSPER channel in syndromic male infertility (SMI). Recently, we identified insertion mutations of the CATSPER1 gene in families with recessively inherited nonsyndromic male infertility (NSMI). The CATSPER channel therefore represents a novel human male fertility factor. In this review we summarize the genetic and clinical data showing the role of CATSPER mutation in human forms of NSMI and SMI. In addition, we discuss clinical management and therapeutic options for these patients. Finally, we describe how the CATSPER channel could be used as a target for development of a male contraceptive.

Management of bleeding following major trauma: a European guideline

INTRODUCTION Evidence-based recommendations can be made with respect to many aspects of the acute management of the bleeding trauma patient, which when implemented may lead to improved patient outcomes. METHODS The multidisciplinary Task Force for Advanced Bleeding Care in Trauma was formed in 2005 with the aim of developing guidelines for the management of bleeding following severe injury. Recommendations were formulated using a nominal group process and the GRADE (Grading of Recommendations Assessment, Development, and Evaluation) hierarchy of evidence and were based on a systematic review of published literature. RESULTS Key recommendations include the following: The time elapsed between injury and operation should be minimised for patients in need of urgent surgical bleeding control, and patients presenting with haemorrhagic shock and an identified source of bleeding should undergo immediate surgical bleeding control unless initial resuscitation measures are successful. A damage control surgical approach is essential in the severely injured patient. Pelvic ring disruptions should be closed and stabilised, followed by appropriate angiographic embolisation or surgical bleeding control, including packing. Patients presenting with haemorrhagic shock and an unidentified source of bleeding should undergo immediate further assessment as appropriate using focused sonography, computed tomography, serum lactate, and/or base deficit measurements. This guideline also reviews appropriate physiological targets and suggested use and dosing of blood products, pharmacological agents, and coagulation factor replacement in the bleeding trauma patient. CONCLUSION A multidisciplinary approach to the management of the bleeding trauma patient will help create circumstances in which optimal care can be provided. By their very nature, these guidelines reflect the current state-of-the-art and will need to be updated and revised as important new evidence becomes available.

CoDa-dendrogram: A new exploratory too

The use of orthonormal coordinates in the simplex and, particularly, balance coordinates, has suggested the use of a dendrogram for the exploratory analysis of compositional data. The dendrogram is based on a sequential binary partition of a compositional vector into groups of parts. At each step of a partition, one group of parts isdivided into two new groups, and a balancing axis in the simplex between both groupsis defined. The set of balancing axes constitutes an orthonormal basis, and the projections of the sample on them are orthogonal coordinates. They can be represented in adendrogram-like graph showing: (a) the way of grouping parts of the compositional vector; (b) the explanatory role of each subcomposition generated in the partition process;(c) the decomposition of the total variance into balance components associated witheach binary partition; (d) a box-plot of each balance. This representation is useful tohelp the interpretation of balance coordinates; to identify which are the most explanatory coordinates; and to describe the whole sample in a single diagram independentlyof the number of parts of the sample

Vaporization behaviour and some thermodynamic properties of the Pd-In, Pd-Pb, Pd-Sn systems

In this study, the vaporization behaviour of solid Pd-rich phases in the Pd-Pb, Pd-In and Pd-Sn systems was investigated by Knudsen-effusion-cell coupled with mass-spectrometry. The Pb, Pd, In vapor pressures [no Sn(g) has been detected in the vapor of Pd-Sn system] were evaluated in the temperatures range 1190-1563 K from the ion intensities measured over two-phases regions. Thermodynamic quantities were derived from vapor pressure data. In particular, for the Pd-Sn binary, the intermediate phase Pd7Sn2, the existence of which has been recently proposed, has been studied here for the first time. Furthermore, preliminary thermochemical data are presented for the diatomic intermetallic molecules PdSn and PdPb, which have been for the first time identified in the vapors in equilibrium over liquid solutions of appropriate composition at higher temperatures (1935-2025 K). (C) 2000 Elsevier Science Ltd. All rights reserved.

Magma generation at the easternmost section of the Hellenic arc: Hf, Nd, Pb and Sr isotope geochemistry of Nisyros and Yali volcanoes (Greece)

Geochemical and petrographical studies of lavas and ignimbrites from the Quaternary Nisyros-Yali volcanic system in the easternmost part of the Hellenic arc (Greece) reveal insight into magma generating processes. A compositional gap between 61 and 68 wt.% SiO2 is recognized that coincides with the stratigraphic distinction between pre-caldera and postcaldera volcanic units. Trace element systematics support the subdivision of Nisyros and Yali volcanic units into two distinct suites of rocks. The variation of Nd and Hf present day isotope data and the fact that they are distinct from the isotope compositions of MORB rule out an origin by pure differentiation and require assimilation of a crustal component. Lead isotope ratios of Nisyros and Yali volcanic rocks support mixing of mantle material with a lower crust equivalent. However, Sr-87/Sr-86 ratios of 0.7036-0.7048 are incompatible with a simple binary mixing scenario and give low depleted mantle extraction ages (< 0.1 Ga), in contrast with Pb model ages of 0.3 Ga and Hf and Nd model ages of ca. 0.8 Ga. The budget of fluid-mobile elements Sr and Pb is likely to be dominated by abundant hydrous fluids characterised by mantle-like Sr isotope ratios. Late stage fluids probably were enriched in CO2, needed to explain the high Th concentrations. The occurrence of hydrated minerals (e.g., amphibole) in the first post-caldera unit with the lowermost Sr-87/Sr-86 ratio of 0.7036 +/- 2 can be interpreted as the result of the increased water activity in the source. The presence of two different plagioclase phenocryst generations in the first lava subsequent to the caldera-causing event is indicative for a longer storage time of this magma at a shallower level. A model capable of explaining these observations involves three evolutionary stages. First stage, assimilation of lower crustal material by a primitive magma of mantle origin (as modelled by Nd-Hf isotope systematics). This stage ended by an interruption in replenishment that led to an increase of crystallization and, hence, an increase in viscosity, suppressing eruption. During this time gap, differentiation by fractional crystallization led to enrichment of incompatible species, especially aqueous fluids, to silica depolymerisation and to a decrease in viscosity, finally enabling eruption again in the third stage. (c) 2005 Elsevier B.V. All rights reserved.

Absence of domestic triatomine colonies in an area of the coastal region of Ecuador where Chagas disease is endemic

Rhodnius ecuadoriensis is considered the second most important vector of Chagas disease in Ecuador. It is distributed across six of the 24 provinces and occupies intradomiciliary, peridomiciliary and sylvatic habitats. This study was conducted in six communities within the coastal province of Guayas. Triatomine searches were conducted in domestic and peridomestic habitats and bird nests using manual searches, live-bait traps and sensor boxes. Synantrhopic mammals were captured in the domestic and peridomestic habitats. Household searches (n = 429) and randomly placed sensor boxes (n = 360) produced no live triatomine adults or nymphs. In contrast, eight nymphs were found in two out of six searched Campylorhynchus fasciatus (Troglodytidae) nests. Finally, Trypanosoma cruzi DNA was amplified from the blood of 10% of the 115 examined mammals. Environmental changes in land use (intensive rice farming), mosquito control interventions and lack of intradomestic adaptation are suggested among the possible reasons for the lack of domestic triatomine colonies.

Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking approaches

Aim This study compares the direct, macroecological approach (MEM) for modelling species richness (SR) with the more recent approach of stacking predictions from individual species distributions (S-SDM). We implemented both approaches on the same dataset and discuss their respective theoretical assumptions, strengths and drawbacks. We also tested how both approaches performed in reproducing observed patterns of SR along an elevational gradient.Location Two study areas in the Alps of Switzerland.Methods We implemented MEM by relating the species counts to environmental predictors with statistical models, assuming a Poisson distribution. S-SDM was implemented by modelling each species distribution individually and then stacking the obtained prediction maps in three different ways - summing binary predictions, summing random draws of binomial trials and summing predicted probabilities - to obtain a final species count.Results The direct MEM approach yields nearly unbiased predictions centred around the observed mean values, but with a lower correlation between predictions and observations, than that achieved by the S-SDM approaches. This method also cannot provide any information on species identity and, thus, community composition. It does, however, accurately reproduce the hump-shaped pattern of SR observed along the elevational gradient. The S-SDM approach summing binary maps can predict individual species and thus communities, but tends to overpredict SR. The two other S-SDM approaches the summed binomial trials based on predicted probabilities and summed predicted probabilities - do not overpredict richness, but they predict many competing end points of assembly or they lose the individual species predictions, respectively. Furthermore, all S-SDM approaches fail to appropriately reproduce the observed hump-shaped patterns of SR along the elevational gradient.Main conclusions Macroecological approach and S-SDM have complementary strengths. We suggest that both could be used in combination to obtain better SR predictions by following the suggestion of constraining S-SDM by MEM predictions.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.