The International LAM Registry: A Component of an Innovative Web-Based Clinician, Researcher, and Patient-Driven Rare Disease Research Platform

Background: A relative friability to capture a sufficiently large patient population in any one geographic location has traditionally limited research into rare diseases. Methods and Results: Clinicians interested in the rare disease lymphangioleiomyomatosis (LAM) have worked with the LAM Treatment Alliance, the MIT Media Lab, and Clozure Associates to cooperate in the design of a state-of-the-art data coordination platform that can be used for clinical trials and other research focused on the global LAM patient population. This platform is a component of a set of web-based resources, including a patient self-report data portal, aimed at accelerating research in rare diseases in a rigorous fashion. Conclusions: Collaboration between clinicians, researchers, advocacy groups, and patients can create essential community resource infrastructure to accelerate rare disease research. The International LAM Registry is an example of such an effort.

Fossil groups in the Millennium simulation Their environment and its evolution

Context. Fossil systems are defined to be X- ray bright galaxy groups ( or clusters) with a two- magnitude difference between their two brightest galaxies within half the projected virial radius, and represent an interesting extreme of the population of galaxy agglomerations. However, the physical conditions and processes leading to their formation are still poorly constrained. Aims. We compare the outskirts of fossil systems with that of normal groups to understand whether environmental conditions play a significant role in their formation. We study the groups of galaxies in both, numerical simulations and observations. Methods. We use a variety of statistical tools including the spatial cross- correlation function and the local density parameter Delta(5) to probe differences in the density and structure of the environments of "" normal"" and "" fossil"" systems in the Millennium simulation. Results. We find that the number density of galaxies surrounding fossil systems evolves from greater than that observed around normal systems at z = 0.69, to lower than the normal systems by z = 0. Both fossil and normal systems exhibit an increment in their otherwise radially declining local density measure (Delta(5)) at distances of order 2.5 r(vir) from the system centre. We show that this increment is more noticeable for fossil systems than normal systems and demonstrate that this difference is linked to the earlier formation epoch of fossil groups. Despite the importance of the assembly time, we show that the environment is different for fossil and non- fossil systems with similar masses and formation times along their evolution. We also confirm that the physical characteristics identified in the Millennium simulation can also be detected in SDSS observations. Conclusions. Our results confirm the commonly held belief that fossil systems assembled earlier than normal systems but also show that the surroundings of fossil groups could be responsible for the formation of their large magnitude gap.

A binary engine fuelling HD 87643's complex circumstellar environment Determined using AMBER/VLTI imaging

Context. The star HD 87643, exhibiting the ""B[e] phenomenon"", has one of the most extreme infrared excesses for this object class. It harbours a large amount of both hot and cold dust, and is surrounded by an extended reflection nebula. Aims. One of our major goals was to investigate the presence of a companion in HD87643. In addition, the presence of close dusty material was tested through a combination of multi-wavelength high spatial resolution observations. Methods. We observed HD 87643 with high spatial resolution techniques, using the near-IR AMBER/VLTI interferometer with baselines ranging from 60 m to 130 m and the mid-IR MIDI/VLTI interferometer with baselines ranging from 25 m to 65 m. These observations are complemented by NACO/VLT adaptive-optics-corrected images in the K and L-bands, and ESO-2.2m optical Wide-Field Imager large-scale images in the B, V and R-bands. Results. We report the direct detection of a companion to HD 87643 by means of image synthesis using the AMBER/VLTI instrument. The presence of the companion is confirmed by the MIDI and NACO data, although with a lower confidence. The companion is separated by similar to 34 mas with a roughly north-south orientation. The period must be large (several tens of years) and hence the orbital parameters are not determined yet. Binarity with high eccentricity might be the key to interpreting the extreme characteristics of this system, namely a dusty circumstellar envelope around the primary, a compact dust nebulosity around the binary system and a complex extended nebula suggesting past violent ejections.

The close circumstellar environment of Betelgeuse II. Diffraction-limited spectro-imaging from 7.76 to 19.50 mu m with VLT/VISIR

Context. Mass-loss occurring in red supergiants (RSGs) is a major contributor to the enrichment of the interstellar medium in dust and molecules. The physical mechanism of this mass loss is however relatively poorly known. Betelgeuse is the nearest RSG, and as such a prime object for high angular resolution observations of its surface (by interferometry) and close circumstellar environment. Aims. The goal of our program is to understand how the material expelled from Betelgeuse is transported from its surface to the interstellar medium, and how it evolves chemically in this process. Methods. We obtained diffraction-limited images of Betelgeuse and a calibrator (Aldebaran) in six filters in the N band (7.76 to 12.81 mu m) and two filters in the Q band (17.65 and 19.50 mu m), using the VLT/VISIR instrument. Results. Our images show a bright, extended and complex circumstellar envelope at all wavelengths. It is particularly prominent longwards of approximate to 9-10 mu m, pointing at the presence of O-rich dust, such as silicates or alumina. A partial circular shell is observed between 0.5 and 1.0 '' from the star, and could correspond to the inner radius of the dust envelope. Several knots and filamentary structures are identified in the nebula. One of the knots, located at a distance of 0.9 '' west of the star, is particularly bright and compact. Conclusions. The circumstellar envelope around Betelgeuse extends at least up to several tens of stellar radii. Its relatively high degree of clumpiness indicates an inhomogeneous spatial distribution of the material lost by the star. Its extension corresponds to an important intermediate scale, where most of the dust is probably formed, between the hot and compact gaseous envelope observed previously in the near infrared and the interstellar medium.

Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Exceptional times for the dynamical discrete web

The dynamical discrete web (DyDW), introduced in the recent work of Howitt and Warren, is a system of coalescing simple symmetric one-dimensional random walks which evolve in an extra continuous dynamical time parameter tau. The evolution is by independent updating of the underlying Bernoulli variables indexed by discrete space-time that define the discrete web at any fixed tau. In this paper, we study the existence of exceptional (random) values of tau where the paths of the web do not behave like usual random walks and the Hausdorff dimension of the set of such exceptional tau. Our results are motivated by those about exceptional times for dynamical percolation in high dimension by Haggstrom, Peres and Steif, and in dimension two by Schramm and Steif. The exceptional behavior of the walks in the DyDW is rather different from the situation for the dynamical random walks of Benjamini, Haggstrom, Peres and Steif. For example, we prove that the walk from the origin S(0)(tau) violates the law of the iterated logarithm (LIL) on a set of tau of Hausdorff dimension one. We also discuss how these and other results should extend to the dynamical Brownian web, the natural scaling limit of the DyDW. (C) 2009 Elsevier B.V. All rights reserved.

Survival time of random walk in random environment among soft obstacles

We consider a Random Walk in Random Environment (RWRE) moving in an i.i.d. random field of obstacles. When the particle hits an obstacle, it disappears with a positive probability. We obtain quenched and annealed bounds on the tails of the survival time in the general d-dimensional case. We then consider a simplified one-dimensional model (where transition probabilities and obstacles are independent and the RWRE only moves to neighbour sites), and obtain finer results for the tail of the survival time. In addition, we study also the ""mixed"" probability measures (quenched with respect to the obstacles and annealed with respect to the transition probabilities and vice-versa) and give results for tails of the survival time with respect to these probability measures. Further, we apply the same methods to obtain bounds for the tails of hitting times of Branching Random Walks in Random Environment (BRWRE).

Use of Medical Subject Headings (MeSH) in Portuguese for categorizing web-based healthcare content

Introduction: Internet users are increasingly using the worldwide web to search for information relating to their health. This situation makes it necessary to create specialized tools capable of supporting users in their searches. Objective: To apply and compare strategies that were developed to investigate the use of the Portuguese version of Medical Subject Headings (MeSH) for constructing an automated classifier for Brazilian Portuguese-language web-based content within or outside of the field of healthcare, focusing on the lay public. Methods: 3658 Brazilian web pages were used to train the classifier and 606 Brazilian web pages were used to validate it. The strategies proposed were constructed using content-based vector methods for text classification, such that Naive Bayes was used for the task of classifying vector patterns with characteristics obtained through the proposed strategies. Results: A strategy named InDeCS was developed specifically to adapt MeSH for the problem that was put forward. This approach achieved better accuracy for this pattern classification task (0.94 sensitivity, specificity and area under the ROC curve). Conclusions: Because of the significant results achieved by InDeCS, this tool has been successfully applied to the Brazilian healthcare search portal known as Busca Saude. Furthermore, it could be shown that MeSH presents important results when used for the task of classifying web-based content focusing on the lay public. It was also possible to show from this study that MeSH was able to map out mutable non-deterministic characteristics of the web. (c) 2010 Elsevier Inc. All rights reserved.

E-contracting with price configuration for Web services and QoS

The large amount of information in electronic contracts hampers their establishment due to high complexity. An approach inspired in Software Product Line (PL) and based on feature modelling was proposed to make this process more systematic through information reuse and structuring. By assessing the feature-based approach in relation to a proposed set of requirements, it was showed that the approach does not allow the price of services and of Quality of Services (QoS) attributes to be considered in the negotiation and included in the electronic contract. Thus, this paper also presents an extension of such approach in which prices and price types associated to Web services and QoS levels are applied. An extended toolkit prototype is also presented as well as an experiment example of the proposed approach.

Analysis of foraminifera assemblages and sediment geochemical properties to characterise the environment near Araca and Saco da Cape la domestic sewage submarine outfalls of Sao Sebastiao Channel, Sao Paulo State, Brazil

Superficial bottom samples were collected near diffusers of domestic sewage submarine outfalls at Araca and Saco da Capela, Sao Sebastiao Channel, Brazil. The goal of this study was to investigate the distribution and composition of live benthic foraminifera assemblages and integrate the results obtained with geochemical analyses to assess human-induced changes. According to the results obtained no environmental stress was observed near the Saco da Capela submarine outfall diffusers. The foraminifera assemblage is characterised by species typical of highly hydrodynamic environments, with well-oxygenated bottom waters and low nutrient contents. In contrast, near Araca submarine outfall, organic enrichment was denoted by high phosphorus, sulphur and, to a lesser extent, total organic carbon content. Harmful influences on foraminifera could be identified by low richness and specific diversity, as well as the predominance of detritivore feeder species, which are associated with higher organic matter flux and low oxygen in the interstitial pore water. (C) 2009 Elsevier Ltd. All rights reserved.

Time Constraints in the School Environment: What Does a Sleepy Student Tell Us?

In this article, we discuss school schedules and their implications in the context of chronobiological contemporary knowledge, arguing for the need to reconsider time planning in the school setting. We present anecdotal observations regarding chronobiological challenges imposed by the school system throughout different ages and discuss the effects of these schedules in terms of sleepiness and its deleterious consequences on learning, memory, and attention. Different settings (including urban vs. rural habitats) influence timing, which also depends on self-selected sleep schedules. Finally, we criticize the traditional view of a necessary strict stability of sleep-wake habits.

New perspectives on the processing and release of public information

This article discusses issues related to the organization and reception of information in the context of services and public information systems driven by technology. It stems from the assumption that in a ""technologized"" society, the distance between users and information is almost always of cognitive and socio-cultural nature, a product of our effort to design communication. In this context, we favor the approach of the information sign, seeking to answer how a documentary message turns into information, i.e. a structure recognized as socially useful. Observing the structural, cognitive and communicative aspects of the documentary message, based on Documentary Linguistics, Terminology, as well as on Textual Linguistics, the policy of knowledge management and innovation of the Government of the State of Sao Paulo is analyzed, which authorizes the use of Web 2.0, also questioning to what extent this initiative represents innovation in the environment of libraries.

Environment-friendly soy flour-based resins without formaldehyde

Glyoxalated soy flour adhesives for wood particleboard added with a much smaller proportion of glyoxalated lignin or tannin and without any addition of either formaldehyde or formaldehyde-based resin are shown to yield results satisfying the relevant standard specifications for interior wood boards. Adhesive resin formulations in which the total content of natural material is either 70 or 80% of the total resin solids content gave good results. The resins comprising 70% by weight of natural material can be used in a much lower proportion on wood chips and can afford pressing times fast enough to be significant under industrial panel pressing conditions. The best formulation of all the ones tried was the one based on glyoxalated precooked soy flour (SG), to which a condensed tannin was added in water solution and a polymeric isocyanate (pMDI), where the proportions of the components SG/T/pMDI was 54/16/30 by weight. (C) 2008 Wiley Periodicals, Inc.

Surface treatment of reinforced concrete in marine environment: Influence on chloride diffusion coefficient and capillary water absorption

There are currently many types of protective materials for reinforced concrete structures and the influence of these materials in the chloride diffusion coefficient still needs more research. The aim of this paper is to study the efficacy of certain surface treatments (such as hydrophobic agents, acrylic coating, polyurethane coating and double systems) in inhibiting chloride penetration in concrete. The results indicated that all tested surface protection significantly reduced the sorptivity of concrete (reduction rate > 70%). However, only the polyurethane coating was highly effective in reducing the chloride diffusion coefficient (reduction rate of 86%). (C) 2008 Elsevier Ltd. All rights reserved.