A pointcut-based coverage analysis approach for aspect-oriented programs

Aspect-oriented programming (AOP) is a promising technology that supports separation of crosscutting concerns (i.e., functionality that tends to be tangled with, and scattered through the rest of the system). In AOP, a method-like construct named advice is applied to join points in the system through a special construct named pointcut. This mechanism supports the modularization of crosscutting behavior; however, since the added interactions are not explicit in the source code, it is hard to ensure their correctness. To tackle this problem, this paper presents a rigorous coverage analysis approach to ensure exercising the logic of each advice - statements, branches, and def-use pairs - at each affected join point. To make this analysis possible, a structural model based on Java bytecode - called PointCut-based Del-Use Graph (PCDU) - is proposed, along with three integration testing criteria. Theoretical, empirical, and exploratory studies involving 12 aspect-oriented programs and several fault examples present evidence of the feasibility and effectiveness of the proposed approach. (C) 2010 Elsevier Inc. All rights reserved.

Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory

The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs ""radio-hybrid"" measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request. (C) 2011 Elsevier B.V. All rights reserved.

ScriptLattes: an open-source knowledge extraction system from the Lattes platform

The Lattes platform is the major scientific information system maintained by the National Council for Scientific and Technological Development (CNPq). This platform allows to manage the curricular information of researchers and institutions working in Brazil based on the so called Lattes Curriculum. However, the public information is individually available for each researcher, not providing the automatic creation of reports of several scientific productions for research groups. It is thus difficult to extract and to summarize useful knowledge for medium to large size groups of researchers. This paper describes the design, implementation and experiences with scriptLattes: an open-source system to create academic reports of groups based on curricula of the Lattes Database. The scriptLattes system is composed by the following modules: (a) data selection, (b) data preprocessing, (c) redundancy treatment, (d) collaboration graph generation among group members, (e) research map generation based on geographical information, and (f) automatic report creation of bibliographical, technical and artistic production, and academic supervisions. The system has been extensively tested for a large variety of research groups of Brazilian institutions, and the generated reports have shown an alternative to easily extract knowledge from data in the context of Lattes platform. The source code, usage instructions and examples are available at http://scriptlattes.sourceforge.net/.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Background: High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results: This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion: These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at http://gdm.fmrp.usp.br/s3t/.S3T source code and datasets can also be downloaded from the aforementioned website.

Independent component analysis applied to raman spectra for classification of in vitro human coronary arteries

Optical diagnostic methods, such as near-infrared Raman spectroscopy allow quantification and evaluation of human affecting diseases, which could be useful in identifying and diagnosing atherosclerosis in coronary arteries. The goal of the present work is to apply Independent Component Analysis (ICA) for data reduction and feature extraction of Raman spectra and to perform the Mahalanobis distance for group classification according to histopathology, obtaining feasible diagnostic information to detect atheromatous plaque. An 830nm Ti:sapphire laser pumped by an argon laser provides near-infrared excitation. A spectrograph disperses light scattered from arterial tissues over a liquid-nitrogen cooled CCD to detect the Raman spectra. A total of 111 spectra from arterial fragments were utilized.

Desidratação e recomendações para a reposição hídrica em crianças fisicamente ativas

OBJETIVO: A prática de exercícios físicos, devido à produção inerente de calor, pode conduzir à desidratação. A maioria dos estudos que abordam os riscos da desidratação e fornecem recomendações de reposição hídrica é direcionada a indivíduos adultos residentes em regiões de clima temperado, porém, em regiões tropicais, pouco é conhecido sobre as necessidades de reposição hídrica em crianças fisicamente ativas. Esta revisão discute as recomendações para esta população e estabelece os riscos da prática esportiva em ambiente de clima tropical. FONTES DE DADOS: Análise sistemática com levantamento da literatura nacional (SciELO) e internacional (Medline) de artigos publicados entre 1972 e 2009, com os seguintes descritores isolados ou em combinação: hidratação, crianças, desidratação e reposição hídrica. Foram selecionados artigos publicados nas línguas portuguesa e inglesa. SÍNTESES DE DADOS: Observou-se que há riscos de desidratação e possível desenvolvimento de um quadro de hipertermia principalmente se as crianças são submetidas a condições climáticas desfavoráveis sem reposição hídrica adequada. O principal fator desencadeante da hipertermia é a menor adaptação das crianças aos extremos de temperatura, em comparação aos adultos, por possuírem área maior de superfície corporal e capacidade menor de termorregulação por evaporação. CONCLUSÕES: Conhecidos os fatores intervenientes da desidratação, a melhor recomendação, perante uma condição climática sabidamente desfavorável, é estabelecer um plano impositivo de hidratação com bebida com sabor e acréscimo de carboidratos e sódio, evitando-se uma perda hídrica significativa, diminuição da performance e, principalmente, com o objetivo de reduzir os riscos à saúde impostos pela hipertermia e desidratação a crianças fisicamente ativas.

A Mass-Conserving Algorithm for Dynamical Lubrication Problems With Cavitation

A numerical algorithm for fully dynamical lubrication problems based on the Elrod-Adams formulation of the Reynolds equation with mass-conserving boundary conditions is described. A simple but effective relaxation scheme is used to update the solution maintaining the complementarity conditions on the variables that represent the pressure and fluid fraction. The equations of motion are discretized in time using Newmark`s scheme, and the dynamical variables are updated within the same relaxation process just mentioned. The good behavior of the proposed algorithm is illustrated in two examples: an oscillatory squeeze flow (for which the exact solution is available) and a dynamically loaded journal bearing. This article is accompanied by the ready-to-compile source code with the implementation of the proposed algorithm. [DOI: 10.1115/1.3142903]

Analysis of source-follower buffers implemented with graded-channel SOI nMOSFETs operating at cryogenic temperatures

This work studies the operation of source-follower buffers implemented with standard and graded-channel (GC) fully depleted (FD) SCI nMOSFETs at low temperatures. The analysis is performed by comparing the voltage gain of buffers implemented with GC and standard SOI nMOS transistors considering devices with the same mask channel length and same effective channel length. It is shown that the use of GC devices allows for achieving improved gain in all inversion levels in a wide range of temperatures. In addition, this improvement increases as temperature is reduced. It is shown that GC transistors can provide virtually constant gain, while for standard devices, the gain departs from the maximum value depending on the temperature and inversion level imposed by the bias current and input voltage. Two-dimensional numerical simulations were performed in order to study the reasons for the enhanced gain of GC MOSFETs at low temperatures. (C) 2009 Elsevier Ltd. All rights reserved.

Numerical analysis of an incremented statistical sampling procedure in MCNP

MCNP has stood so far as one of the main Monte Carlo radiation transport codes. Its use, as any other Monte Carlo based code, has increased as computers perform calculations faster and become more affordable along time. However, the use of Monte Carlo method to tally events in volumes which represent a small fraction of the whole system may turn to be unfeasible, if a straight analogue transport procedure (no use of variance reduction techniques) is employed and precise results are demanded. Calculations of reaction rates in activation foils placed in critical systems turn to be one of the mentioned cases. The present work takes advantage of the fixed source representation from MCNP to perform the above mentioned task in a more effective sampling way (characterizing neutron population in the vicinity of the tallying region and using it in a geometric reduced coupled simulation). An extended analysis of source dependent parameters is studied in order to understand their influence on simulation performance and on validity of results. Although discrepant results have been observed for small enveloping regions, the procedure presents itself as very efficient, giving adequate and precise results in shorter times than the standard analogue procedure. (C) 2007 Elsevier Ltd. All rights reserved.

Porcine skin as a source of biodegradable matrices: alkaline treatment and glutaraldehyde crosslinking

In this work, the modifications promoted by alkaline hydrolysis and glutaraldehyde (GA) crosslinking on type I collagen found in porcine skin have been studied. Collagen matrices were obtained from the alkaline hydrolysis of porcine skin, with subsequent GA crosslinking in different concentrations and reaction times. The elastin content determination showed that independent of the treatment, elastin was present in the matrices. Results obtained from in vitro trypsin degradation indicated that with the increase of GA concentration and reaction time, the degradation rate decreased. From thermogravimetry and differential scanning calorimetry analysis it can be observed that the collagen in the matrices becomes more resistant to thermal degradation as a consequence of the increasing crosslink degree. Scanning electron microscopy analysis indicated that after the GA crosslinking, collagen fibers become more organized and well-defined. Therefore, the preparations of porcine skin matrices with different degradation rates, which can be used in soft tissue reconstruction, are viable.

Knoop microhardness and FT-Raman evaluation of composite resins: influence of opacity and photoactivation source

The aim of this study was to evaluate the degree of conversion by Knoop microhardness (KHN) and FT-Raman spectroscopy (FTIR) of one nanofilled (Filtek Supreme-3M-ESPE [FS]) and one microhybrid composite (Charisma-Heraeus-Kulzer [CH]), each with different opacities, namely enamel, dentin, and translucent, which were photo-activated by a quartz-tungsten-halogen lamp (QTH) and a light-emitting diode (LED). Resin was bulk inserted into a disc-shaped mold that was 2.0 mm thick and 4 mm in diameter, obtaining 10 samples per group. KHN and FTIR values were analyzed by two-way ANOVA and Tukey's tests (α = 0.05). Nanofilled resin activated by a LED presented higher microhardness values than samples activated by a QTH for dentin opacity (p < 0.05). The microhybrid resin showed no differences in KHN or FTIR values with different activation sources or opacity. The nanofilled dentin and enamel resins showed lower FTIR values than the translucent resin. The KHN values of the translucent resins were not influenced by the light source.

New Source of Muscle-Derived Stem Cells with Potential for Alveolar Bone Reconstruction in Cleft Lip and/or Palate Patients

Cleft lip and palate (CLP), one of the most frequent congenital malformations, affects the alveolar bone in the great majority of the cases, and the reconstruction of this defect still represents a challenge in the rehabilitation of these patients. One of the current most promising strategy to achieve this goal is the use of bone marrow stem cells (BMSC); however, isolation of BMSC or iliac bone, which is still the mostly used graft in the surgical repair of these patients, confers site morbidity to the donor. Therefore, in order to identify a new alternative source of stem cells with osteogenic potential without conferring morbidity to the donor, we have used orbicular oris muscle (OOM) fragments, which are regularly discarded during surgery repair (cheiloplasty) of CLP patients. We obtained cells from OOM fragments of four unrelated CLP patients (CLPMDSC) using previously described preplating technique. These cells, through flow cytometry analysis, were mainly positively marked for five mesenchymal stem cell antigens (CD29, CD90, CD105, SH3, and SH4), while negative for hematopoietic cell markers, CD14, CD34, CD45, and CD117, and for endothelial cell marker, CD31. After induction under appropriate cell culture conditions, these cells were capable to undergo chondrogenic, adipogenic, osteogenic, and skeletal muscle cell differentiation, as evidenced by immunohistochemistry. We also demonstrated that these cells together with a collagen membrane lead to bone tissue reconstruction in a critical-size cranial defects previously induced in non-immunocompromised rats. The presence of human DNA in the new bone was confirmed by PCR with human-specific primers and immunohistochemistry with human nuclei antibodies. In conclusion, we showed that cells from OOM have phenotypic and behavior characteristics similar to other adult stem cells, both in vitro and in vivo. Our findings suggest that these cells represent a promising source of stem cells for alveolar bone grafting treatment, particularly in young CLP patients.

Fast ray-tracing algorithm for circumstellar structures (FRACS) II. Disc parameters of the B[e] supergiant CPD-57 degrees 2874 from VLTI/MIDI data

Context. B[e] supergiants are luminous, massive post-main sequence stars exhibiting non-spherical winds, forbidden lines, and hot dust in a disc-like structure. The physical properties of their rich and complex circumstellar environment (CSE) are not well understood, partly because these CSE cannot be easily resolved at the large distances found for B[e] supergiants (typically greater than or similar to 1 kpc). Aims. From mid-IR spectro-interferometric observations obtained with VLTI/MIDI we seek to resolve and study the CSE of the Galactic B[e] supergiant CPD-57 degrees 2874. Methods. For a physical interpretation of the observables (visibilities and spectrum) we use our ray-tracing radiative transfer code (FRACS), which is optimised for thermal spectro-interferometric observations. Results. Thanks to the short computing time required by FRACS (<10 s per monochromatic model), best-fit parameters and uncertainties for several physical quantities of CPD-57 degrees 2874 were obtained, such as inner dust radius, relative flux contribution of the central source and of the dusty CSE, dust temperature profile, and disc inclination. Conclusions. The analysis of VLTI/MIDI data with FRACS allowed one of the first direct determinations of physical parameters of the dusty CSE of a B[e] supergiant based on interferometric data and using a full model-fitting approach. In a larger context, the study of B[e] supergiants is important for a deeper understanding of the complex structure and evolution of hot, massive stars.

ANALYSIS OF THE PICO DOS DIAS SURVEY HERBIG Ae/Be CANDIDATES

A large sample of Herbig Ae/Be (HAeBe) candidates, distributed in different Galactic regions south to declination +30 degrees, were identified by the Pico dos Dias Survey (a search for young stellar objects based on IRAS colors). Most of the candidates are nearby or associated with star-forming clouds, but several others are considered isolated objects. Aiming to verify the young nature of 93 HAeBe candidates, we searched for additional information that could be useful to confirm if they are pre-main-sequence (PMS) stars or evolved objects, which coincidentally show similar IRAS colors. By adopting a spectral index that is related to the amount of infrared excess and the shape of the spectral energy distribution, we have classified the sample according to three groups, which are analyzed on the basis of (1) circumstellar luminosity; (2) spatial distribution; (3) optical polarization; (4) near-infrared colors; (5) stellar parameters (mass, age, effective temperature); and (5) intensity of emission lines. Our analysis indicates that only 76% of the studied sample, mainly the group with intermediate to low levels of circumstellar emission, can be more confidently considered PMS stars. The nature of the remaining stars, which are in the other group that contains the highest levels of infrared excess, remains to be confirmed. They share the same characteristics of evolved objects, requiring complementary studies in order to correctly classify them. At least seven objects show characteristics typical of post-asymptotic giant branch or proto-planetary nebulae.

Human Dental Pulp Cells: A New Source of Cell Therapy in a Mouse Model of Compressive Spinal Cord Injury

Strategies aimed at improving spinal cord regeneration after trauma are still challenging neurologists and neuroscientists throughout the world. Many cell-based therapies have been tested, with limited success in terms of functional outcome. In this study, we investigated the effects of human dental pulp cells (HDPCs) in a mouse model of compressive spinal cord injury (SCI). These cells present some advantages, such as the ease of the extraction process, and expression of trophic factors and embryonic markers from both ecto-mesenchymal and mesenchymal components. Young adult female C57/BL6 mice were subjected to laminectomy at T9 and compression of the spinal cord with a vascular clip for 1 min. The cells were transplanted 7 days or 28 days after the lesion, in order to compare the recovery when treatment is applied in a subacute or chronic phase. We performed quantitative analyses of white-matter preservation, trophic-factor expression and quantification, and ultrastructural and functional analysis. Our results for the HDPC-transplanted animals showed better white-matter preservation than the DMEM groups, higher levels of trophic-factor expression in the tissue, better tissue organization, and the presence of many axons being myelinated by either Schwann cells or oligodendrocytes, in addition to the presence of some healthy-appearing intact neurons with synapse contacts on their cell bodies. We also demonstrated that HDPCs were able to express some glial markers such as GFAP and S-100. The functional analysis also showed locomotor improvement in these animals. Based on these findings, we propose that HDPCs may be feasible candidates for therapeutic intervention after SCI and central nervous system disorders in humans.