Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism

Lateral gene transfer (LGT) is considered as one of the drivers in bacterial genome evolution, usually associated with increased fitness and/or changes in behavior, especially if one considers pathogenic vs. non-pathogenic bacterial groups. The genomes of two phytopathogens, Xanthomonas campestris pv. campestris and Xanthomonas axonopodis pv. citri, were previously inspected for genome islands originating from LGT events, and, in this work, potentially early and late LGT events were identified according to their altered nucleotide composition. The biological role of the islands was also assessed, and pathogenicity, virulence and secondary metabolism pathways were functions highly represented, especially in islands that were found to be recently transferred. However, old islands are composed of a high proportion of genes related to cell primary metabolic functions. These old islands, normally undetected by traditional atypical composition analysis, but confirmed as product of LGT by atypical phylogenetic reconstruction, reveal the role of LGT events by replacing core metabolic genes normally inherited by vertical processes.

Image indexing and retrieval using an ART-2A neural network architecture

Traditional content-based image retrieval (CBIR) systems use low-level features such as colors, shapes, and textures of images. Although, users make queries based on semantics, which are not easily related to such low-level characteristics. Recent works on CBIR confirm that researchers have been trying to map visual low-level characteristics and high-level semantics. The relation between low-level characteristics and image textual information has motivated this article which proposes a model for automatic classification and categorization of words associated to images. This proposal considers a self-organizing neural network architecture, which classifies textual information without previous learning. Experimental results compare the performance results of the text-based approach to an image retrieval system based on low-level features. (c) 2008 Wiley Periodicals, Inc.

Regulation of Radial Glial Motility by Visual Experience

Radial glia in the developing optic tectum express the key guidance molecules responsible for topographic targeting of retinal axons. However, the extent to which the radial glia are themselves influenced by retinal inputs and visual experience remains unknown. Using multiphoton live imaging of radial glia in the optic tectum of intact Xenopus laevis tadpoles in conjunction with manipulations of neural activity and sensory stimuli, radial glia were observed to exhibit spontaneous calcium transients that were modulated by visual stimulation. Structurally, radial glia extended and retracted many filopodial processes within the tectal neuropil over minutes. These processes interacted with retinotectal synapses and their motility was modulated by nitric oxide (NO) signaling downstream of neuronal NMDA receptor (NMDAR) activation and visual stimulation. These findings provide the first in vivo demonstration that radial glia actively respond both structurally and functionally to neural activity, via NMDAR-dependent NO release during the period of retinal axon ingrowth.

Cross-situational learning of object-word mapping using Neural Modeling Fields

The issue of how children learn the meaning of words is fundamental to developmental psychology. The recent attempts to develop or evolve efficient communication protocols among interacting robots or Virtual agents have brought that issue to a central place in more applied research fields, such as computational linguistics and neural networks, as well. An attractive approach to learning an object-word mapping is the so-called cross-situational learning. This learning scenario is based on the intuitive notion that a learner can determine the meaning of a word by finding something in common across all observed uses of that word. Here we show how the deterministic Neural Modeling Fields (NMF) categorization mechanism can be used by the learner as an efficient algorithm to infer the correct object-word mapping. To achieve that we first reduce the original on-line learning problem to a batch learning problem where the inputs to the NMF mechanism are all possible object-word associations that Could be inferred from the cross-situational learning scenario. Since many of those associations are incorrect, they are considered as clutter or noise and discarded automatically by a clutter detector model included in our NMF implementation. With these two key ingredients - batch learning and clutter detection - the NMF mechanism was capable to infer perfectly the correct object-word mapping. (C) 2009 Elsevier Ltd. All rights reserved.

How language can help discrimination in the Neural Modelling Fields framework

The relationship between thought and language and, in particular, the issue of whether and how language influences thought is still a matter of fierce debate. Here we consider a discrimination task scenario to study language acquisition in which an agent receives linguistic input from an external teacher, in addition to sensory stimuli from the objects that exemplify the overlapping categories that make up the environment. Sensory and linguistic input signals are fused using the Neural Modelling Fields (NMF) categorization algorithm. We find that the agent with language is capable of differentiating object features that it could not distinguish without language. In this sense, the linguistic stimuli prompt the agent to redefine and refine the discrimination capacity of its sensory channels. (C) 2007 Elsevier Ltd. All rights reserved.

Rock magnetism in soils of the Pampean plain. Buenos Aires province, Argentina. Linking climate and magnetic behaviour

Results of the study of Argiudolls in two localities (Zarate and Veronica) of the Pampean plain, Argentina, are presented in this contribution. This is a typical area covered by loess. The magnetic studies carried out allowed to determine the presence of detrital magnetite and titanomagnetite, as well as maghemite, pedogenic goethite and superparamagnetic particles (SP). In Veronica soils, a depletion of ferromagnetic minerals is recorded The dominant process in these soils has been the reductive loss of detrital magnetite and titanomagnetite. This is associated with a greater degree of evolution of the soil, which is determined by the concentration and type of detected clays. The higher clay concentration in these soils facilitated reducing conditions and a greater loss of detrital magnetic particles. The loss is reinforced under poor drainage conditions. In the poorly drained soil of Zarate, a concentration of magnetic particles is observed in the Bt horizon, which is associated with an illuviation process. The well drained soil of the same locality shows neoformation of SP particles. These particles would have an ephemeral life until a new wet period in the annual cycle occurs. Although some characteristics of the magnetic signal appear reinforced by the conditions of drainage, this aspect does not seem to be too significant, at least in the Pampean region with low topographic gradients.

Denudation history of the Bocaina Plateau, Serra do Mar, southeastern Brazil: Relationships to Gondwana breakup and passive margin development

The Bocaina Plateau, which is situated on the eastern flank of the continental rift of southeastern Brazil, is the highest part of the Serra do Mar. Topographic relief in this area is suggested to be closely related to its complex tectono-magmatic evolution since the breakup of Western Gondwana and opening of the South Atlantic Ocean. Apatite fission track ages and track length distributions from 27 basement outcrops were determined to assess these hypotheses and reconstruct the denudation history of the Bocaina Plateau. The ages range between 303 +/- 32 and 46 +/- 5 Ma, and are significantly younger than the stratigraphic ages. Mean track lengths vary from 13.44 +/- 1.51 to 11.1 +/- 1.48 mu m, with standard deviations between 1.16 and 1.83 mu m. Contrasting ages within a single plateau and similar ages at different altitudes indicate a complex regional tectonothermal evolution. The thermal histories inferred from these data imply three periods of accelerated cooling related to the Early Cretaceous continental breakup, Early Cretaceous alkaline magmatism, and the Paleogene evolution of the continental rift of southeastern Brazil. The oldest fission track ages (>200 Ma) were obtained in the Serra do Mar region, suggesting that these areas were a long-lived source of sediments for the Parana, Bauru, and Santos basins. (C) 2010 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

SRTM resample with short distance-low nugget kriging

The shuttle radar topography mission (SRTM), was flow on the space shuttle Endeavour in February 2000, with the objective of acquiring a digital elevation model of all land between 60 degrees north latitude and 56 degrees south latitude, using interferometric synthetic aperture radar (InSAR) techniques. The SRTM data are distributed at horizontal resolution of 1 arc-second (similar to 30m) for areas within the USA and at 3 arc-second (similar to 90m) resolution for the rest of the world. A resolution of 90m can be considered suitable for the small or medium-scale analysis, but it is too coarse for more detailed purposes. One alternative is to interpolate the SRTM data at a finer resolution; it will not increase the level of detail of the original digital elevation model (DEM), but it will lead to a surface where there is the coherence of angular properties (i.e. slope, aspect) between neighbouring pixels, which is an important characteristic when dealing with terrain analysis. This work intents to show how the proper adjustment of variogram and kriging parameters, namely the nugget effect and the maximum distance within which values are used in interpolation, can be set to achieve quality results on resampling SRTM data from 3"" to 1"". We present for a test area in western USA, which includes different adjustment schemes (changes in nugget effect value and in the interpolation radius) and comparisons with the original 1"" model of the area, with the national elevation dataset (NED) DEMs, and with other interpolation methods (splines and inverse distance weighted (IDW)). The basic concepts for using kriging to resample terrain data are: (i) working only with the immediate neighbourhood of the predicted point, due to the high spatial correlation of the topographic surface and omnidirectional behaviour of variogram in short distances; (ii) adding a very small random variation to the coordinates of the points prior to interpolation, to avoid punctual artifacts generated by predicted points with the same location than original data points and; (iii) using a small value of nugget effect, to avoid smoothing that can obliterate terrain features. Drainages derived from the surfaces interpolated by kriging and by splines have a good agreement with streams derived from the 1"" NED, with correct identification of watersheds, even though a few differences occur in the positions of some rivers in flat areas. Although the 1"" surfaces resampled by kriging and splines are very similar, we consider the results produced by kriging as superior, since the spline-interpolated surface still presented some noise and linear artifacts, which were removed by kriging.

Screening the Schistosoma mansoni transcriptome for genes differentially expressed in the schistosomulum stage in search for vaccine candidates

Schistosomiasis affects more than 200 million people worldwide; another 600 million are at risk of infection. The schistosomulum stage is believed to be the target of protective immunity in the attenuated cercaria vaccine model. In an attempt to identify genes up-regulated in the schistosomulum stage in relation to cercaria, we explored the Schistosoma mansoni transcriptome by looking at the relative frequency of reads in EST libraries from both stages. The 400 genes potentially up-regulated in schistosomula were analyzed as to their Gene Ontology categorization, and we have focused on those encoding-predicted proteins with no similarity to proteins of other organisms, assuming they could be parasite-specific proteins important for survival in the host. Up-regulation in schistosomulum relative to cercaria was validated with real-time reverse transcription polymerase chain reaction (RT-PCR) for five out of nine selected genes (56%). We tested their protective potential in mice through immunization with DNA vaccines followed by a parasite challenge. Worm burden reductions of 16-17% were observed for one of them, indicating its protective potential. Our results demonstrate the value and caveats of using stage-associated frequency of ESTs as an indication of differential expression coupled to DNA vaccine screening in the identification of novel proteins to be further investigated as potential vaccine candidates.

För Sverige i framtiden : Bio-objektifiering av ny medicinsk teknologi

Taking Sweden into the future – Bio-objectification of new medical technology In this article, we analyze how contemporary discursive silences around new biotechnologies such as cybrids and induced pluripotent stem cells (iPSC), have been enabled by earlier policy processes in the area, e.g. boundary work around what is human and non-human, living and non-living, subject and object. The analysis of policy processes around xenotransplantations and the use of human embryonic stem cells, shows that the stem cells’ and xenografts’ “bio-identities” become stabilized through high expectations for the future, a lack of therapeutic possibilities and struggles over definitions of life. The policy processes around human embryonic stem cells and organs from other animals, are characterized by a normalization of certain understandings of ”life”, trust in scientific progress and it’s national financial potentials and a categorization of criticism as irrational. Through these “bio-objectification processes”, debate and decision making has been moved from a political and public context into ethical committees and research funding bodies. The article concludes by discussing consequences of this political non-handling of biomedical technologies and how these bioobjects could be re-politicized.

The priority of temporal aspects in L2-Swedish prosody : Studies in perception and production

Foreign accent can be everything from hardly detectable to rendering the second language speech unintelligible. It is assumed that certain aspects of a specific target language contribute more to making the foreign accented speech intelligible and listener friendly, than others. The present thesis examines a teaching strategy for Swedish pronunciation in second language education. The teaching strategy “Basic prosody” or BP, gives priority to temporal aspects of Swedish prosody, which means the temporal phonological contrasts word stress and quantity, as well as the durational realizations of these contrasts. BP does not prescribe any specific tonal realizations. This standpoint is based on the great regional variety in realization and distribution of Swedish word accents. The teaching strategy consists virtually of three directives: · Stress the proper word in the sentence. · Stress proper syllables in stressed words and make them longer. · Lengthen the proper segment – vowel or subsequent consonant – in the stressed syllable. These directives reflect the view that all phonological length is stress-induced, and that vowel length and consonant length are equally important as learning goals. BP is examined in the light of existing findings in the field of second language pronunciation and with respect to the phonetic correlates of Swedish stress and quantity. Five studies examine the relation between segment durations and the categorization made by native Swedish listeners. The results indicate that the postvocalic consonant duration contributes to quantity categorization as well as giving the proper duration to stressed syllables. Furthermore, native Swedish speakers are shown to apply the complementary /V: C/ - /VC:/ pattern also when speaking English and German, by lengthening postvocalic consonants. The correctness of the priority is not directly addressed but important aspects of BP are supported by earlier findings as well as the results from the present studies.

A framework for ICT-based knowledge sharing in sustainable rural development : the case of Gilgit-Baltistan, Pakistan

Some 50% of the people in the world live in rural areas, often under harsh conditions and in poverty. The need for knowledge of how to improve living conditions is well documented. In response to this need, new knowledge of how to improve living conditions in rural areas and elsewhere is continuously being developed by researchers and practitioners around the world. People in rural areas, in particular, would certainly benefit from being able to share relevant knowledge with each other, as well as with stakeholders (e.g. researchers) and other organizations (e.g. NGOs). Central to knowledge management is the idea of knowledge sharing. This study is based on the assumption that knowledge management can support sustainable development in rural and remote regions. It aims to present a framework for knowledge management in sustainable rural development, and an inventory of existing frameworks for that. The study is interpretive, with interviews as the primary source for the inventory of stakeholders, knowledge categories and Information and Communications Technology (ICT) infrastructure. For the inventory of frameworks, a literature study was carried out. The result is a categorization of the stakeholders who act as producers and beneficiaries of explicit and indigenous development knowledge. Stakeholders are local government, local population, academia, NGOs, civil society and donor agencies. Furthermore, the study presents a categorization of the development knowledge produced by the stakeholders together with specifications for the existing ICT infrastructure. Rural development categories found are research, funding, agriculture, ICT, gender, institutional development, local infrastructure development, and marketing & enterprise. Finally, a compiled framework is presented, and it is based on ten existing frameworks for rural development that were found in the literature study, and the empirical findings of the Gilgit-Baltistan case. Our proposed framework is divided in four levels where level one consists of the identified stakeholders, level two consists of rural development categories, level three of the knowledge management system and level four of sustainable rural development based on the levels below. In the proposed framework we claim that the sustainability of rural development can be achieved through a knowledge society in which knowledge of the rural development process is shared among all relevant stakeholders.

Tillhörighetens gränser : Internationell adoption och ursprungets betydelse i svensk utredningsretorik

Boundaries of belonging: transnational adoption and the significance of origin in Swedish official rhetoric This article explores how the category of ‘transnational adoptees’ in Sweden is constructed in two Official Government Reports (SOU). The article is inspired by poststructuralist perspectives on welfare and social categorization, and draws from a postcolonial and feminist theoretical framework. ‘Transnational adoptees’ as a category is understood as constituted through discourse, and given meaning in different contexts. In the reports, a fundamental importance is attached to the fact that individuals with a background as transnationally adopted have been separated from their birth family and country of birth. It is argued that mental problems and a split identity are consequences to be expected from the separation. (Re)connection to the origin is therefore considered to be crucial for the well-being of the group. The article concludes that this line of reasoning is based on a specific logic of blood and roots, in which ‘transnational adoptees’ are understood as belonging to their countries of birth, rather than Sweden. The logic of blood and roots can be read as a form of racialized othering, but also as a discursive exclusion of ‘transnational adoptees’ from Sweden as an imagined, national community.

Effect Of Different Hydrological Model Structures On The Assimilation Of Distributed Uncertain Observations

The reliable evaluation of the flood forecasting is a crucial problem for assessing flood risk and consequent damages. Different hydrological models (distributed, semi-distributed or lumped) have been proposed in order to deal with this issue. The choice of the proper model structure has been investigated by many authors and it is one of the main sources of uncertainty for a correct evaluation of the outflow hydrograph. In addition, the recent increasing of data availability makes possible to update hydrological models as response of real-time observations. For these reasons, the aim of this work it is to evaluate the effect of different structure of a semi-distributed hydrological model in the assimilation of distributed uncertain discharge observations. The study was applied to the Bacchiglione catchment, located in Italy. The first methodological step was to divide the basin in different sub-basins according to topographic characteristics. Secondly, two different structures of the semi-distributed hydrological model were implemented in order to estimate the outflow hydrograph. Then, synthetic observations of uncertain value of discharge were generated, as a function of the observed and simulated value of flow at the basin outlet, and assimilated in the semi-distributed models using a Kalman Filter. Finally, different spatial patterns of sensors location were assumed to update the model state as response of the uncertain discharge observations. The results of this work pointed out that, overall, the assimilation of uncertain observations can improve the hydrologic model performance. In particular, it was found that the model structure is an important factor, of difficult characterization, since can induce different forecasts in terms of outflow discharge. This study is partly supported by the FP7 EU Project WeSenseIt.

Meteomap: Generation Of Meteorological Variables For Distributed Physically-Based Hydrological Modeling

Distributed energy and water balance models require time-series surfaces of the meteorological variables involved in hydrological processes. Most of the hydrological GIS-based models apply simple interpolation techniques to extrapolate the point scale values registered at weather stations at a watershed scale. In mountainous areas, where the monitoring network ineffectively covers the complex terrain heterogeneity, simple geostatistical methods for spatial interpolation are not always representative enough, and algorithms that explicitly or implicitly account for the features creating strong local gradients in the meteorological variables must be applied. Originally developed as a meteorological pre-processing tool for a complete hydrological model (WiMMed), MeteoMap has become an independent software. The individual interpolation algorithms used to approximate the spatial distribution of each meteorological variable were carefully selected taking into account both, the specific variable being mapped, and the common lack of input data from Mediterranean mountainous areas. They include corrections with height for both rainfall and temperature (Herrero et al., 2007), and topographic corrections for solar radiation (Aguilar et al., 2010). MeteoMap is a GIS-based freeware upon registration. Input data include weather station records and topographic data and the output consists of tables and maps of the meteorological variables at hourly, daily, predefined rainfall event duration or annual scales. It offers its own pre and post-processing tools, including video outlook, map printing and the possibility of exporting the maps to images or ASCII ArcGIS formats. This study presents the friendly user interface of the software and shows some case studies with applications to hydrological modeling.