AcMus: an Open, Integrated Platform for Room Acoustics Research

This article describes the design, implementation, and experiences with AcMus, an open and integrated software platform for room acoustics research, which comprises tools for measurement, analysis, and simulation of rooms for music listening and production. Through use of affordable hardware, such as laptops, consumer audio interfaces and microphones, the software allows evaluation of relevant acoustical parameters with stable and consistent results, thus providing valuable information in the diagnosis of acoustical problems, as well as the possibility of simulating modifications in the room through analytical models. The system is open-source and based on a flexible and extensible Java plug-in framework, allowing for cross-platform portability, accessibility and experimentation, thus fostering collaboration of users, developers and researchers in the field of room acoustics.

REALISTIC IVUS IMAGE GENERATION IN DIFFERENT INTRALUMINAL PRESSURES

Intravascular ultrasound (IVUS) phantoms are important to calibrate and evaluate many IVUS imaging processing tasks. However, phantom generation is never the primary focus of related works; hence, it cannot be well covered, and is usually based on more than one platform, which may not be accessible to investigators. Therefore, we present a framework for creating representative IVUS phantoms, for different intraluminal pressures, based on the finite element method and Field II. First, a coronary cross-section model is selected. Second, the coronary regions are identified to apply the properties. Third, the corresponding mesh is generated. Fourth, the intraluminal force is applied and the deformation computed. Finally, the speckle noise is incorporated. The framework was tested taking into account IVUS contrast, noise and strains. The outcomes are in line with related studies and expected values. Moreover, the framework toolbox is freely accessible and fully implemented in a single platform. (E-mail: fernando.okara@gmail.com) (c) 2012 World Federation for Ultrasound in Medicine & Biology.

Experimental study on vortex-induced motions of a semi-submersible platform with four square columns, Part I: Effects of current incidence angle and hull appendages

An experimental study on Vortex-Induced Motion (VIM) of the semi-submersible platform concept with four square columns is presented. Model tests were carried out to check the influence of different headings and hull appendages (riser supports located at the pontoons; fairleads and the mooring stretches located vertically at the external column faces; and hard pipes located vertically at the internal column faces). The results comprise in-line, transverse and yaw motions, as well as combined motions in the XY plane, drag and lift forces and spectral analysis. The main results showed that VIM in the transverse direction occurred in a range of reduced velocity 4.0 up to 14.0 with amplitude peaks around reduced velocities around 7.0 and 8.0. The largest transverse amplitudes obtained were around 40% of the column width for 30 degrees and 45 degrees incidences. Another important result observed was a considerable yaw motion oscillation, in which a synchronization region could be identified as a resonance phenomenon. The largest yaw motions were verified for the 0 degrees incidence and the maxima amplitudes around 4.5 degrees. The hull appendages located at columns had the greatest influence on the VIM response of the semi-submersible. (C) 2012 Elsevier Ltd. All rights reserved.

Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli

To understand the regulatory dynamics of transcription factors (TFs) and their interplay with other cellular components we have integrated transcriptional, protein-protein and the allosteric or equivalent interactions which mediate the physiological activity of TFs in Escherichia coli. To study this integrated network we computed a set of network measurements followed by principal component analysis (PCA), investigated the correlations between network structure and dynamics, and carried out a procedure for motif detection. In particular, we show that outliers identified in the integrated network based on their network properties correspond to previously characterized global transcriptional regulators. Furthermore, outliers are highly and widely expressed across conditions, thus supporting their global nature in controlling many genes in the cell. Motifs revealed that TFs not only interact physically with each other but also obtain feedback from signals delivered by signaling proteins supporting the extensive cross-talk between different types of networks. Our analysis can lead to the development of a general framework for detecting and understanding global regulatory factors in regulatory networks and reinforces the importance of integrating multiple types of interactions in underpinning the interrelationships between them.

Three-dimensional solitons in cross-combined linear and nonlinear optical lattices

The existence and stability of three-dimensional (3D) solitons, in cross-combined linear and nonlinear optical lattices, are investigated. In particular, with a starting optical lattice (OL) configuration such that it is linear in the x-direction and nonlinear in the y-direction, we consider the z-direction either unconstrained (quasi-2D OL case) or with another linear OL (full 3D case). We perform this study both analytically and numerically: analytically by a variational approach based on a Gaussian ansatz for the soliton wavefunction and numerically by relaxation methods and direct integrations of the corresponding Gross-Pitaevskii equation. We conclude that, while 3D solitons in the quasi-2D OL case are always unstable, the addition of another linear OL in the z-direction allows us to stabilize 3D solitons both for attractive and repulsive mean interactions. From our results, we suggest the possible use of spatial modulations of the nonlinearity in one of the directions as a tool for the management of stable 3D solitons.

Running coupling and pomeron loop effects on inclusive and diffractive DIS cross sections

Within the framework of a (1 + 1)-dimensional model which mimics high-energy QCD, we study the behavior of the cross sections for inclusive and diffractive deep inelastic gamma*h scattering cross sections. We analyze the cases of both fixed and running coupling within the mean-field approximation, in which the evolution of the scattering amplitude is described by the Balitsky-Kovchegov equation, and also through the pomeron loop equations, which include in the evolution the gluon number fluctuations. In the diffractive case, similarly to the inclusive one, suppression of the diffusive scaling, as a consequence of the inclusion of the running of the coupling, is observed.

Measurement of the proton-air cross section at root s=57 TeV with the Pierre Auger Observatory

We report a measurement of the proton-air cross section for particle production at the center-of-mass energy per nucleon of 57 TeV. This is derived from the distribution of the depths of shower maxima observed with the Pierre Auger Observatory: systematic uncertainties are studied in detail. Analyzing the tail of the distribution of the shower maxima, a proton-air cross section of [505 +/- 22(stat)(-36)(+28)(syst)] mb is found.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Neoproterozoic evolution of the basement of the South-American platform

Neoproterozoic geologic and geotectonic processes were of utmost importance in forming and structuring the basement framework of the South-American platform. Two large domains with distinct evolutionary histories are identified with respect to the Neoproterozoic era: the northwest-west (Amazonian craton and surroundings) and the central-southeast (the extra-Amazonian domain). In the first domain, Neoproterozoic events occurred only locally and were of secondary significance, and the geologic events, processes, and structures of the pre-Neoproterozoic (and syn-Brasiliano) cratonic block were much more influential. In the second, the extra-Amazonian domain, the final evolution, structures and forms are assigned to events related to the development of a complex net of Neoproterozoic mobile belts. These in turn resulted in strong reworking of the older pre-Neoproterozoic basement. In this domain, four distinct structural provinces circumscribe or are separated by relatively small pre- Neoproterozoic cratonic nuclei, namely the Pampean, Tocantins, Borborema and Mantiqueira provinces. These extra-Amazonian provinces were formed by a complex framework of orogenic branching systems following a diversified post-Mesoproterozoic paleogeographic scenario. This scenario included many types of basement inliers as well as a diversified organization of accretionary and collisional orogens. The basement inliers date from the Archean toMesoproterozoic periods and are different in nature. The escape tectonics that operated during the final consolidation stages of the provinces were important to and responsible for the final forms currently observed. These latest events, which occurred from the Late Ediacaran to the Early Ordovician, present serious obstacles to paleogeographic reconstructions. Two groups of orogenic collage systems are identified. The older system from the Tonian (>850 Ma) period is of restricted occurrence and is not fully understood due to strong reworking subsequent to Tonian times. The second group of orogenies is more extensive and more important. Its development began with diachronic taphrogenic processes in the Early Cryogenian period (ca. 850e750 Ma) and preceded a complex scenario of continental, transitional and oceanic basins. Subsequent orogenies (post 800 Ma) were also created by diachronic processes that ended in the Early Ordovician. More than one orogeny (plate interaction) can be identified either in space or in time in every province. The orogenic processes were not necessarily synchronous in different parts of the orogenic system, even within the same province. This particular group of orogenic collage events is known as the “Brasiliano”. All of the structural provinces of the extra-Amazonian domain exhibit final events that are marked by extrusion processes, are represented by long lineaments, and are fundamental to unraveling the structural history of the Phanerozoic sedimentary basins.