Parallel Cyclostationarity-Exploiting Algorithm for Energy-Efficient Spectrum Sensing

The evolution of wireless communication systems leads to Dynamic Spectrum Allocation for Cognitive Radio, which requires reliable spectrum sensing techniques. Among the spectrum sensing methods proposed in the literature, those that exploit cyclostationary characteristics of radio signals are particularly suitable for communication environments with low signal-to-noise ratios, or with non-stationary noise. However, such methods have high computational complexity that directly raises the power consumption of devices which often have very stringent low-power requirements. We propose a strategy for cyclostationary spectrum sensing with reduced energy consumption. This strategy is based on the principle that p processors working at slower frequencies consume less power than a single processor for the same execution time. We devise a strict relation between the energy savings and common parallel system metrics. The results of simulations show that our strategy promises very significant savings in actual devices.

The RGBarrier assay: the parallel study of gene regulatory element performance at defined chromosomal locations

Vertebrate genomes are organised into a variety of nuclear environments and chromatin states that have profound effects on the regulation of gene transcription. This variation presents a major challenge to the expression of transgenes for experimental research, genetic therapies and the production of biopharmaceuticals. The majority of transgenes succumb to transcriptional silencing by their chromosomal environment when they are randomly integrated into the genome, a phenomenon known as chromosomal position effect (CPE). It is not always feasible to target transgene integration to transcriptionally permissive “safe harbour” loci that favour transgene expression, so there remains an unmet need to identify gene regulatory elements that can be added to transgenes which protect them against CPE. Dominant regulatory elements (DREs) with chromatin barrier (or boundary) activity have been shown to protect transgenes from CPE. The HS4 element from the chicken beta-globin locus and the A2UCOE element from a human housekeeping gene locus have been shown to function as DRE barriers in a wide variety of cell types and species. Despite rapid advances in the profiling of transcription factor binding, chromatin states and chromosomal looping interactions, progress towards functionally validating the many candidate barrier elements in vertebrates has been very slow. This is largely due to the lack of a tractable and efficient assay for chromatin barrier activity. In this study, I have developed the RGBarrier assay system to test the chromatin barrier activity of candidate DREs at pre-defined isogenic loci in human cells. The RGBarrier assay consists in a Flp-based RMCE reaction for the integration of an expression construct, carrying candidate DREs, in a pre-characterised chromosomal location. The RGBarrier system involves the tracking of red, green and blue fluorescent proteins by flow cytometry to monitor on-target versus off-target integration and transgene expression. The analysis of the reporter (GFP) expression for several weeks gives a measure of the protective ability of each candidate elements from chromosomal silencing. This assay can be scaled up to test tens of new putative barrier elements in the same chromosomal context in parallel. The defined chromosomal contexts of the RGBarrier assays will allow for detailed mechanistic studies of chromosomal silencing and DRE barrier element action. Understanding these mechanisms will be of paramount importance for the design of specific solutions for overcoming chromosomal silencing in specific transgenic applications.

Easy PRAM-based High-performance Parallel Programming with ICE

A poster of this paper will be presented at the 25th International Conference on Parallel Architecture and Compilation Technology (PACT ’16), September 11-15, 2016, Haifa, Israel.

Improving drug discovery using a neural networks based parallel scoring function

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface to find new hotspots, where ligands might potentially interact with, and which is implemented in massively parallel Graphics Processing Units, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to solve this problem, we propose a novel approach where neural networks are trained with databases of known active (drugs) and inactive compounds, and later used to improve VS predictions.

Wave impedance selection for passivity-based bilateral teleoperation

When a task must be executed in a remote or dangerous environment, teleoperation systems may be employed to extend the influence of the human operator. In the case of manipulation tasks, haptic feedback of the forces experienced by the remote (slave) system is often highly useful in improving an operator's ability to perform effectively. In many of these cases (especially teleoperation over the internet and ground-to-space teleoperation), substantial communication latency exists in the control loop and has the strong tendency to cause instability of the system. The first viable solution to this problem in the literature was based on a scattering/wave transformation from transmission line theory. This wave transformation requires the designer to select a wave impedance parameter appropriate to the teleoperation system. It is widely recognized that a small value of wave impedance is well suited to free motion and a large value is preferable for contact tasks. Beyond this basic observation, however, very little guidance exists in the literature regarding the selection of an appropriate value. Moreover, prior research on impedance selection generally fails to account for the fact that in any realistic contact task there will simultaneously exist contact considerations (perpendicular to the surface of contact) and quasi-free-motion considerations (parallel to the surface of contact). The primary contribution of the present work is to introduce an approximate linearized optimum for the choice of wave impedance and to apply this quasi-optimal choice to the Cartesian reality of such a contact task, in which it cannot be expected that a given joint will be either perfectly normal to or perfectly parallel to the motion constraint. The proposed scheme selects a wave impedance matrix that is appropriate to the conditions encountered by the manipulator. This choice may be implemented as a static wave impedance value or as a time-varying choice updated according to the instantaneous conditions encountered. A Lyapunov-like analysis is presented demonstrating that time variation in wave impedance will not violate the passivity of the system. Experimental trials, both in simulation and on a haptic feedback device, are presented validating the technique. Consideration is also given to the case of an uncertain environment, in which an a priori impedance choice may not be possible.

Sensitivity and specificity of parallel or serial serological testing for detection of canine Leishmania infection

In Brazil, human and canine visceral leishmaniasis (CVL) caused by Leishmania infantum has undergone urbanisation since 1980, constituting a public health problem, and serological tests are tools of choice for identifying infected dogs. Until recently, the Brazilian zoonoses control program recommended enzyme-linked immunosorbent assays (ELISA) and indirect immunofluorescence assays (IFA) as the screening and confirmatory methods, respectively, for the detection of canine infection. The purpose of this study was to estimate the accuracy of ELISA and IFA in parallel or serial combinations. The reference standard comprised the results of direct visualisation of parasites in histological sections, immunohistochemical test, or isolation of the parasite in culture. Samples from 98 cases and 1,327 noncases were included. Individually, both tests presented sensitivity of 91.8% and 90.8%, and specificity of 83.4 and 53.4%, for the ELISA and IFA, respectively. When tests were used in parallel combination, sensitivity attained 99.2%, while specificity dropped to 44.8%. When used in serial combination (ELISA followed by IFA), decreased sensitivity (83.3%) and increased specificity (92.5%) were observed. Serial testing approach improved specificity with moderate loss in sensitivity. This strategy could partially fulfill the needs of public health and dog owners for a more accurate diagnosis of CVL.

Drying of rye (Lolium miltiflorum l.) in fixed bed with parallel air flow.

This work aimed to study the drying of ryegrass seeds (Lolium multiflorum L.) in fixed bed dryer with parallel air flow.

Dynamics of undeactuated cable-driven parallel robots

This thesis focuses on the dynamics of underactuated cable-driven parallel robots (UACDPRs), including various aspects of robotic theory and practice, such as workspace computation, parameter identification, and trajectory planning. After a brief introduction to CDPRs, UACDPR kinematic and dynamic models are analyzed, under the relevant assumption of inextensible cables. The free oscillatory motion of the end-effector (EE), which is a unique feature of underactuated mechanisms, is studied in detail, from both a kinematic and a dynamic perspective. The free (small) oscillations of the EE around equilibria are proved to be harmonic and the corresponding natural oscillation frequencies are analytically computed. UACDPR workspace computation and analysis are then performed. A new performance index is proposed for the analysis of the influence of actuator errors on cable tensions around equilibrium configurations, and a new type of workspace, called tension-error-insensitive, is defined as the set of poses that a UACDPR EE can statically attain even in presence of actuation errors, while preserving tensions between assigned (positive) bounds. EE free oscillations are then employed to conceive a novel procedure aimed at identifying the EE inertial parameters. This approach does not require the use of force or torque measurements. Moreover, a self-calibration procedure for the experimental determination of UACDPR initial cable lengths is developed, which consequently enables the robot to automatically infer the EE initial pose at machine start-up. Lastly, trajectory planning of UACDPRs is investigated. Two alternative methods are proposed, which aim at (i) reducing EE oscillations even when model parameters are uncertain or (ii) eliminate EE oscillations in case model parameters are perfectly known. EE oscillations are reduced in real-time by dynamically scaling a nominal trajectory and filtering it with an input shaper, whereas they can be eliminated if an off-line trajectory is computed that accounts for the system internal dynamics.

Geometrico-static modelling of continuum parallel robots

In this thesis, we explore three methods for the geometrico-static modelling of continuum parallel robots. Inspired by biological trunks, tentacles and snakes, continuum robot designs can reach confined spaces, manipulate objects in complex environments and conform to curvilinear paths in space. In addition, parallel continuum manipulators have the potential to inherit some of the compactness and compliance of continuum robots while retaining some of the precision, stability and strength of rigid-links parallel robots. Subsequently, the foundation of our work is performed on slender beam by applying the Cosserat rod theory, appropriate to model continuum robots. After that, three different approaches are developed on a case study of a planar parallel continuum robot constituted of two connected flexible links. We solve the forward and inverse geometrico-static problem namely by using (a) shooting methods to obtain a numerical solution, (b) an elliptic method to find a quasi-analytical solution, and (c) the Corde model to perform further model analysis. The performances of each of the studied methods are evaluated and their limits are highlighted. This thesis is divided as follows. Chapter one gives the introduction on the field of the continuum robotics and introduce the parallel continuum robots that is studied in this work. Chapter two describe the geometrico-static problem and gives the mathematical description of this problem. Chapter three explains the numerical approach with the shooting method and chapter four introduce the quasi-analytical solution. Then, Chapter five introduce the analytic method inspired by the Corde model and chapter six gives the conclusions of this work.

Direct Kinematics of Underactuated Cable-Driven Parallel Robots: Sensitivity to Redundant Measurements

Underactuated cable-driven parallel robots (UACDPRs) shift a 6-degree-of-freedom end-effector (EE) with fewer than 6 cables. This thesis proposes a new automatic calibration technique that is applicable for under-actuated cable-driven parallel robots. The purpose of this work is to develop a method that uses free motion as an exciting trajectory for the acquisition of calibration data. The key point of this approach is to find a relationship between the unknown parameters to be calibrated (the lengths of the cables) and the parameters that could be measured by sensors (the swivel pulley angles measured by the encoders and roll-and-pitch angles measured by inclinometers on the platform). The equations involved are the geometrical-closure equations and the finite-difference velocity equations, solved using the least-squares algorithm. Simulations are performed on a parallel robot driven by 4 cables for validation. The final purpose of the calibration method is, still, the determination of the platform initial pose. As a consequence of underactuation, the EE is underconstrained and, for assigned cable lengths, the EE pose cannot be obtained by means of forward kinematics only. Hence, a direct-kinematics algorithm for a 4-cable UACDPR using redundant sensor measurements is proposed. The proposed method measures two orientation parameters of the EE besides cable lengths, in order to determine the other four pose variables, namely 3 position coordinates and one additional orientation parameter. Then, we study the performance of the direct-kinematics algorithm through the computation of the sensitivity of the direct-kinematics solution to measurement errors. Furthermore, position and orientation error upper limits are computed for bounded cable lengths errors resulting from the calibration procedure, and roll and pitch angles errors which are due to inclinometer inaccuracies.

Mechanical design and hybrid control strategies for overconstrained cable-driven parallel robots

Cable-driven parallel robots offer significant advantages in terms of workspace dimensions and payload capability. They are attractive for many industrial tasks to be performed on a large scale, such as handling and manufacturing, without a substantial increase in costs and mechanical complexity with respect to a small-scale application. However, since cables can only sustain tensile stresses, cable tensions must be kept within positive limits during the end-effector motion. This problem can be managed by overconstraining the end-effector and controlling cable tensions. Tension control is typically achieved by mounting a load sensor on all cables, and using specific control algorithms to avoid cable slackness or breakage while the end-effector is controlled in a desired position. These algorithms require multiple cascade control loops and they can be complex and computationally demanding. To simplify the control of overconstrained cable-driven parallel robots, this Thesis proposes suitable mechanical design and hybrid control strategies. It is shown how a convenient design of the cable guidance system allows kinematic modeling to be simplified, without introducing geometric approximations. This guidance system employs swiveling pulleys equipped with position and tension sensors and provides a parallelogram arrangement of cables. Furthermore, a hybrid force/position control in the robot joint space is adopted. According to this strategy, a particular set of cables is chosen to be tension-controlled, whereas the other cables are length-controlled. The force-controlled cables are selected based on the computation of a novel index called force-distribution sensitivity to cable-tension errors. This index aims to evaluate the maximum expected cable-tension error in the length-controlled cables if a unit tension error is committed in the force-controlled cables. In practice, the computation of the force-distribution sensitivity allows determining which cables are best to be force-controlled, to ensure the lowest error in the overall force distribution when a hybrid force/position joint-space strategy is used.

Contributions to the performance analysis of continuum parallel robots

Continuum parallel robots (CPRs) are manipulators employing multiple flexible beams arranged in parallel and connected to a rigid end-effector. CPRs promise higher payload and accuracy than serial CRs while keeping great flexibility. As the risk of injury during accidental contacts between a human and a CPR should be reduced, CPRs may be used in large-scale collaborative tasks or assisted robotic surgery. There exist various CPR designs, but the prototype conception is rarely based on performance considerations, and the CPRs realization in mainly based on intuitions or rigid-link parallel manipulators architectures. This thesis focuses on the performance analysis of CPRs, and the tools needed for such evaluation, such as workspace computation algorithms. In particular, workspace computation strategies for CPRs are essential for the performance assessment, since the CPRs workspace may be used as a performance index or it can serve for optimal-design tools. Two new workspace computation algorithms are proposed in this manuscript, the former focusing on the workspace volume computation and the certification of its numerical results, while the latter aims at computing the workspace boundary only. Due to the elastic nature of CPRs, a key performance indicator for these robots is the stability of their equilibrium configurations. This thesis proposes the experimental validation of the equilibrium stability assessment on a real prototype, demonstrating limitations of some commonly used assumptions. Additionally, a performance index measuring the distance to instability is originally proposed in this manuscript. Differently from the majority of the existing approaches, the clear advantage of the proposed index is a sound physical meaning; accordingly, the index can be used for a more straightforward performance quantification, and to derive robot specifications.

Energy consumption of parallel algorithms for solving linear systems on HPC architecture

Modern High-Performance Computing HPC systems are gradually increasing in size and complexity due to the correspondent demand of larger simulations requiring more complicated tasks and higher accuracy. However, as side effects of the Dennard’s scaling approaching its ultimate power limit, the efficiency of software plays also an important role in increasing the overall performance of a computation. Tools to measure application performance in these increasingly complex environments provide insights into the intricate ways in which software and hardware interact. The monitoring of the power consumption in order to save energy is possible through processors interfaces like Intel Running Average Power Limit RAPL. Given the low level of these interfaces, they are often paired with an application-level tool like Performance Application Programming Interface PAPI. Since several problems in many heterogeneous fields can be represented as a complex linear system, an optimized and scalable linear system solver algorithm can decrease significantly the time spent to compute its resolution. One of the most widely used algorithms deployed for the resolution of large simulation is the Gaussian Elimination, which has its most popular implementation for HPC systems in the Scalable Linear Algebra PACKage ScaLAPACK library. However, another relevant algorithm, which is increasing in popularity in the academic field, is the Inhibition Method. This thesis compares the energy consumption of the Inhibition Method and Gaussian Elimination from ScaLAPACK to profile their execution during the resolution of linear systems above the HPC architecture offered by CINECA. Moreover, it also collates the energy and power values for different ranks, nodes, and sockets configurations. The monitoring tools employed to track the energy consumption of these algorithms are PAPI and RAPL, that will be integrated with the parallel execution of the algorithms managed with the Message Passing Interface MPI.

Assessment Of The Fixation Of Mandibular Symphysis Fractures Using Conical Cannulated Screws: Mechanical And Photoelastic Tests.

The aim of this study was to use mechanical and photoelastic tests to compare the performance of cannulated screws with other fixation methods in mandibular symphysis fractures. Ten polyurethane mandibles were allocated to each group and fixed as follows: group PRP, 2 perpendicular miniplates; group PLL, 1 miniplate and 1 plate, parallel; and group CS, 2 cannulated screws. Vertical linear loading tests were performed. The differences between mean values were analyzed with the Tukey test. The photoelastic test was carried out using a polariscope. The results revealed differences between the CS and PRP groups at 1, 3, 5, and 10 millimeters of displacement. The photoelastic test confirmed higher stress concentration in all groups close to the mandibular base, whereas the CS group showed it throughout the region assessed. Conical cannulated screws performed well in mechanical and photoelastic tests.