Automatic selection of arterial input function on dynamic contrast-enhanced MR images

Dynamic susceptibility contrast-magnetic resonance imaging (DSC-MRI) data analysis requires the knowledge of the arterial input function (AIF) to quantify the cerebral blood flow (CBF), volume (CBV) and the mean transit time (MTT). AIF can be obtained either manually or using automatic algorithms. We present a method to derive the AIF on the middle cerebral artery (MCA). The algorithm draws a region of interest (ROI) where the MCA is located. Then, it uses a recursive cluster analysis on the ROI to select the arterial voxels. The algorithm had been compared on simulated data to literature state of art automatic algorithms and on clinical data to the manual procedure. On in silico data, our method allows to reconstruct the true AIF and it is less affected by partial volume effect bias than the other methods. In clinical data, automatic AIF provides CBF and MTT maps with a greater contrast level compared to manual AIF ones. Therefore, AIF obtained with the proposed method improves the estimate reliability and provides a quantitatively reliable physiological picture.     

Template-based quadrilateral mesh generation from imaging data

This paper describes a novel template-based meshing approach for generating good quality quadrilateral meshes from 2D digital images. This approach builds upon an existing image-based mesh generation technique called Imeshp, which enables us to create a segmented triangle mesh from an image without the need for an image segmentation step. Our approach generates a quadrilateral mesh using an indirect scheme, which converts the segmented triangle mesh created by the initial steps of the Imesh technique into a quadrilateral one. The triangle-to-quadrilateral conversion makes use of template meshes of triangles. To ensure good element quality, the conversion step is followed by a smoothing step, which is based on a new optimization-based procedure. We show several examples of meshes generated by our approach, and present a thorough experimental evaluation of the quality of the meshes given as examples.     

Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations

Treatment of prostate cancer patients with antiandrogens is initially successful, though the therapy often becomes refractory over the time. This mechanism is not fully understood, but the presence of androgen receptor (AR) mutant forms which are activated by antiandrogens and other endogenous ligands, and overexpression of the receptor have been suggested. In an attempt to explain the molecular basis for agonicity and antagonicity in the androgen receptor, and the changes on biological activity of subtle modifications at the ligand and receptor (mutations) level, molecular dynamics simulations were performed on the androgen receptor wild type (WT), and T877A and W741 mutant forms, complexed with several non-steroidal androgens. The stabilizing role of residues from helices 3, 5, 11 and 12 was observed in non-steroidal androgens R-3, S-1, and R-bicalutamide and hydroxyflutamide in resistant mutations. In the AR WT antiandrogen R-bicalutamide complex, destabilization of M895 by both W741 and the sulfonyl linkage of the ligand may be responsible for reported antagonism. Changes in the ligand or mutations alleviating this effect were observed to stabilize the receptor in the active conformation, thus developing resistance to R-bicalutamide. The results presented provide a plausible explanation for the molecular basis of agonicity and antagonicity in the androgen receptor, and complement previous studies using static crystal structures, incorporating for the first time protein dynamics into the analysis. Thus, our results provide a valuable framework for the structure-based design of improved antiandrogens.     

Shadow attacks on users’ anonymity in pervasive computing environments

Privacy preserving technologies are likely to become an essential component of adaptive services in pervasive and mobile computing. Although privacy issues have been studied for a long time in computer science as well as in other fields, most studies are focused on the release of data from large repositories. Mobile and pervasive computing pose new challenges, requiring specific formal models for attacks and new privacy preserving techniques. This paper considers a specific pervasive computing scenario, and shows that the application of state-of-the-art techniques for the anonymization of service requests is insufficient to protect the privacy of users. A specific class of attacks, called shadow attacks, is formally defined and a defense technique is proposed. This defense is formally proved to be correct, and its effectiveness is validated by extensive experiments in a simulated environment.     

A coarse-grain reconfigurable architecture for multimedia applications featuring subword computation capabilities

This paper presents the design and the implementation of a coarse-grain reconfigurable machine used as an accelerator for a programmable RISC core, to speed up the execution of computationally demanding tasks like multimedia applications. We created a VHDL model of the proposed architecture and implemented it on a FPGA board for prototyping purposes; then we mapped on our architecture some DSP and image processing algorithms as a benchmark. In particular, we provided the proposed architecture with subword computation capabilities, which turns out to be extremely effective especially when dealing with image processing algorithms, achieving significant benefits in terms of speed and efficiency in resource usage. To create the configuration bitstream (configware) we created a tool based on a graphical user interface (GUI) which provides a first step towards the automation of the programming flow of our design: the tool is meant to ease the life of the programmer, relieving him from the burden of calculating the configuration bits by hand. Synthesis results indicate that the area occupation and the operating frequency of our design are reasonable also when compared to other similar design. In addition to this, the amount of clock cycles taken by our machine to perform a given algorithm is orders of magnitude smaller than the one required by a corresponding software implementation on a RISC microprocessor.     

Atomic force microscopy of protein films and crystals

A customized atomic force microscopy (AFM) instrument optimized for imaging protein crystals in solution is described. The device was tested on crystals and Langmuir-Blodgett (LB) films of two proteins with quite different molecular weights. This approach enables the periodicity and morphology of crystals to be studied in their mother liquid, thereby preserving the native periodic protein crystal structure, which is typically destroyed by drying. Moreover, the instrument appears to distinguish protein crystals from salt crystals, which under the optical microscope are frequently quite similar, the difference between them often being revealed only during x-ray analysis. AFM estimates of the packing, order, and morphology of the given single proteins appear quite similar in the LB thin film and in the crystals, which means that routine crystal measurements can be performed at high resolution. The AFM consists of a custom-built measuring head and a homemade flexible SPM controller which can drive the head for contact, noncontact and spectroscopy modes, thus providing the user with a high degree of customization for crystal measurement.     

Querying and creating visualizations by analogy

While there have been advances in visualization systems, particularly in multi-view visualizations and visual exploration, the process of building visualizations remains a major bottleneck in data exploration. We show that provenance metadata collected during the creation of pipelines can be reused to suggest similar content in related visualizations and guide semi-automated changes. We introduce the idea of query-by-example in the context of an ensemble of visualizations, and the use of analogies as first-class operations in a system to guide scalable interactions. We describe an implementation of these techniques in VisTrails, a publicly-available, open-source system.     

Ambient occlusion and edge cueing to enhance real time molecular visualization

The paper presents a set of combined techniques to enhance the real-time visualization of simple or complex molecules (up to order of 106 atoms) space fill mode. The proposed approach includes an innovative technique for efficient computation and storage of ambient occlusion terms, a small set of GPU accelerated procedural impostors for space-fill and ball-and-stick rendering, and novel edge-cueing techniques. As a result, the user's understanding of the three-dimensional structure under inspection is strongly increased (even for still images), while the rendering still occurs in real time.     

Lower and upper bounds for the two-echelon capacitated location-routing problem

In this paper, we introduce two algorithms to address the two-echelon capacitated location-routing problem (2E-CLRP). We introduce a branch-and-cut algorithm based on the solution of a new two-index vehicle-flow formulation, which is strengthened with several families of valid inequalities. We also propose an adaptive large-neighbourhood search (ALNS) meta-heuristic with the objective of finding good-quality solutions quickly. The computational results on a large set of instances from the literature show that the ALNS outperforms existing heuristics. Furthermore, the branch-and-cut method provides tight lower bounds and is able to solve small- and medium-size instances to optimality within reasonable computing times.