User Full Control Research Articles

Protection and control of personal identifiable information: The PoSeID-on approach

Personal data is currently being used in countless applications in a vast number of areas. Despite national and international legislation, the fact is that users have little or no control over who uses their data and for what purposes, and data protection is still, in many cases, a theoretical possibility only. This paper presents an approach to solve the problem of user data protection and control, currently being developed in the scope of the Protection and control of Secured Information by means of a privacy enhanced Dashboard (PoSeID-on) H2020 European project. In addition to an overall view of the project goals, the paper provides information on the requirements, challenges, conceptual architecture and functional description of the main modules. The presented solution complies with the European Union’s General Data Protection Regulation and explores the use of the blockchain technology to provide data transactions protection and accountability as well as offer users full control over their personal information.

Time‐delayed photo‐induced depolymerization of poly(phthalaldehyde) self‐immolative polymer via in situ formation of weak conjugate acid

Poly(phthalaldehyde) (PPHA) can be used as a structural material in transient devices and photo‐catalytically depolymerized at the end of device life by the use of a photo‐acid generator (PAG). However, device degradation requires the presence of a radiation source at the end of device mission. It has been found that the onset of PPHA depolymerization after PAG photo‐exposure can be delayed by incorporation of a particular weak bases in the PPHA/PAG mixture. This method of delayed PPHA depolymerization allows for PAG activation prior to or during device deployment when the device is under full user control. The basicity of specific lactams and amides was found to slow the PPHA depolymerization, giving the transient device a longer but finite mission lifetime. The weak base reacts with the photo‐generated strong acid to form a weak conjugate acid, which reacts more slowly with PPHA to extend the onset of PPHA depolymerization. The addition of a molar excess of specific lactams or amides, with respect to PAG, maintains PPHA stability and mechanical properties for more than 80 minutes after photo‐exposure at room temperature. The amide or lactam mediated acid activation of PPHA follows first‐order kinetics. The time delay of PPHA depolymerization can allow for prelaunch photo‐exposure and eliminates the need for postmission photo‐exposure where reliable light‐sources may not be available.

RadFil: A Python Package for Building and Fitting Radial Profiles for Interstellar Filaments

Abstract We present RadFil, a publicly available Python package that gives users full control over how to build and fit radial profiles for interstellar filaments. RadFil builds filament profiles by taking radial cuts across the spine of a filament, thereby preserving the radial structure of the filament across its entire length. Pre-existing spines can be inputted directly into RadFil, or can be computed using the FilFinder package as part of the RadFil workflow. We provide Gaussian and Plummer built-in fitting functions, in addition to a background subtraction estimator, which can be fit to the entire ensemble of radial cuts or an average radial profile for the filament. Users can tweak parameters like the radial cut sampling interval, the background subtraction estimation radii, and the Gaussian/Plummer fitting radii. As a result, RadFil can provide treatment of how the resulting filament properties rely on systematics in the building and fitting process. We walk through the typical RadFil workflow and compare our results to those from an independent radial profile code obtained using the same data; we find that our results are entirely consistent. RadFil is open source and available on GitHub. We also provide a complete working tutorial of the code available as a Jupyter notebook, which users can download and run themselves.

MIDAS: A Modular DNA Assembly System for Synthetic Biology.

A modular and hierarchical DNA assembly platform for synthetic biology based on Golden Gate (Type IIS restriction enzyme) cloning is described. This enabling technology, termed MIDAS (for Modular Idempotent DNA Assembly System), can be used to precisely assemble multiple DNA fragments in a single reaction using a standardized assembly design. It can be used to build genes from libraries of sequence-verified, reusable parts and to assemble multiple genes in a single vector, with full user control over gene order and orientation, as well as control of the direction of growth (polarity) of the multigene assembly, a feature that allows genes to be nested between other genes or genetic elements. We describe the detailed design and use of MIDAS, exemplified by the reconstruction, in the filamentous fungus Penicillium paxilli, of the metabolic pathway for production of paspaline and paxilline, key intermediates in the biosynthesis of a range of indole diterpenes-a class of secondary metabolites produced by several species of filamentous fungi. MIDAS was used to efficiently assemble a 25.2 kb plasmid from 21 different modules (seven genes, each composed of three basic parts). By using a parts library-based system for construction of complex assemblies, and a unique set of vectors, MIDAS can provide a flexible route to assembling tailored combinations of genes and other genetic elements, thereby supporting synthetic biology applications in a wide range of expression hosts.

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data

Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches. Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic comparisons, all visualized in a graphic interface. CombiROC was designed without hard-coded thresholds, allowing a custom fit to each specific data: this dramatically reduces the computational burden and lowers the false negative rates given by fixed thresholds. The application was validated with published data, confirming the marker combination already originally described or even finding new ones. CombiROC is a novel tool for the scientific community freely available at http://CombiROC.eu.

Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software

Gentoo is a GNU/Linux metadistribution designed to maximize and simplify user control of the software environment. All determinants of a Gentoo environment are recorded in a small number of plain-text configuration files, from which the software make-up of the system can be reconstructed entirely. As such, Gentoo constitutes a replicable and transparent software infrastructure - as mandated by research valuing reproducibility. Of equal scientific interest is the flexibility of Gentoo's package management. All software is distributed in a rolling-release fashion, giving the user full control over which versions (including live versions and branches/tags from version control) of which programs to install, and with which compilation options. All of the above is accompanied by automatic, version-aware dependency resolution, which also tracks static library linking and prompts for rebuilds as necessary. We believe Gentoo is excellently suited to address many of the challenges in neuroscience software management; including: system replicability, system documentation, data analysis reproducibility, fine-grained dependency management, easy control over compilation options, and seamless access to cutting-edge software releases. We have made a substantial set of neuroimaging and data analysis packages - including their entire dependency stacks - available for any system using Gentoo's Package Management Standard. Neuroscientific software now usable under Gentoo includes but is not limited to: Dipy (Garyfallidis et al. 2014) FSL (Jenkinson et al. 2012) Nipype (Gorgolewski et al. 2016) Nilearn (Abraham et al. 2014) PsychoPy (Peirce 2008) Herein we describe the implementation and current capabilities of this environment, as well as its ability to accelerate and improve research.

What’s your anonymity worth? Establishing a marketplace for the valuation and control of individuals’ anonymity and personal data

PurposeThe viability of online anonymity is questioned in today’s online environment where many technologies enable tracking and identification of individuals. In light of the shortcomings of the government, industry and consumers in protecting anonymity, it is clear that a new perspective for ensuring anonymity is needed. Where current stakeholders have failed to protect anonymity, some proponents argue that economic models exist for valuation of anonymity. By placing a monetary value on anonymity through Rawls’ concept of primary goods, it is possible to create a marketplace for anonymity, therefore allowing users full control of how their personal data is used. This paper aims to explore the creation of a data marketplace, offering users the possibility of engaging with companies and other entities to sell and auction personal data. Importantly, participation in a marketplace does not sacrifice one’s anonymity, as there are different levels of anonymity in online systems.Design/methodology/approachThe paper uses a conceptual framework based on the abstractions of anonymity and data valuation.FindingsThe manuscript constructs a conceptual foundation for exploring the development and deployment of a personal data marketplace. By suggesting features allowing individuals’ control of their personal data, and properly establishing monetary valuation of one’s personal data, it is argued that individuals will undertake a more proactive management of personal data.Originality/valueAn overview of the available services and products offering increased anonymity is explored, in turn, illustrating the beginnings of a market response for anonymity as a valuable good. By placing a monetary value on individuals’ anonymity, it is reasoned that individuals will more consciously protect their anonymity in ways where legislation and other practices (i.e. privacy policies, marketing opt-out) have failed.

Area-preserving mesh parameterization for poly-annulus surfaces based on optimal mass transportation

This work proposes a novel method for computing area-preserving parameterization for genus zero surfaces with multiple boundaries (poly-annuli), which is based on discrete optimal mass transportation and surface Ricci Flow. We first begin with a conformal mapping (which may greatly distort area) by Ricci Flow and then correct the area distortion using the mass transport procedure via a convex optimization. The method is intrinsic and stable, and the resulting parameterization preserves area element and minimizes angle distortion. Comparing with existing algorithms, our method is more general and flexible. It can handle surfaces with more complicated topology, and gives users full control of the target measure, such as the areas of the holes. We have tested the method for applications in various fields. Our experimental results demonstrate the efficiency and efficacy of the proposed method.

ColorSketch: A Drawing Assistant for Generating Color Sketches from Photos.

A color sketch creates a vivid depiction of a scene using sparse pencil strokes and casual colored brush strokes. The interactive drawing system ColorSketch can help novice users generate color sketches from photos. To preserve artistic freedom and expressiveness, the proposed system gives users full control over pencil strokes, while automatically augmenting pencil sketches using color mapping, brush stroke rendering, and blank area creation. Experimental and user study results demonstrate that users, especially novices, can create better color sketches with our system than when using traditional manual tools.

Sensor fusion and computer vision for context-aware control of a multi degree-of-freedom prosthesis

Objective. Myoelectric activity volitionally generated by the user is often used for controlling hand prostheses in order to replicate the synergistic actions of muscles in healthy humans during grasping. Muscle synergies in healthy humans are based on the integration of visual perception, heuristics and proprioception. Here, we demonstrate how sensor fusion that combines artificial vision and proprioceptive information with the high-level processing characteristics of biological systems can be effectively used in transradial prosthesis control. Approach. We developed a novel context- and user-aware prosthesis (CASP) controller integrating computer vision and inertial sensing with myoelectric activity in order to achieve semi-autonomous and reactive control of a prosthetic hand. The presented method semi-automatically provides simultaneous and proportional control of multiple degrees-of-freedom (DOFs), thus decreasing overall physical effort while retaining full user control. The system was compared against the major commercial state-of-the art myoelectric control system in ten able-bodied and one amputee subject. All subjects used transradial prosthesis with an active wrist to grasp objects typically associated with activities of daily living. Main results. The CASP significantly outperformed the myoelectric interface when controlling all of the prosthesis DOF. However, when tested with less complex prosthetic system (smaller number of DOF), the CASP was slower but resulted with reaching motions that contained less compensatory movements. Another important finding is that the CASP system required minimal user adaptation and training. Significance. The CASP constitutes a substantial improvement for the control of multi-DOF prostheses. The application of the CASP will have a significant impact when translated to real-life scenarious, particularly with respect to improving the usability and acceptance of highly complex systems (e.g., full prosthetic arms) by amputees.

Using the Spatial Population Abundance Dynamics Engine for conservation management

Summary An explicit spatial understanding of population dynamics is often critical for effective management of wild populations. Sophisticated approaches are available to simulate these dynamics, but are largely either spatially homogeneous or agent based, and thus best suited to small spatial or temporal scales. These approaches also often ignore financial decisions crucial to choosing management approaches on the basis of cost‐effectiveness. We created a user‐friendly and flexible modelling framework for simulating these population issues at large spatial scales – the Spatial Population Abundance Dynamics Engine (SPADE). SPADE is based on the Spatio‐Temporal Animal Reduction (STAR) model (McMahon et al. 2010) and uses a reaction–diffusion approach to model population trajectories and a cost‐benefit analysis technique to calculate optimal management strategies over long periods and across broad spatial scales. It expands on STAR by incorporating species interactions and multiple concurrent management strategies, and by allowing full user control of functional forms and parameters. We used SPADE to simulate the eradication of feral domestic cats Felis catus on sub‐Antarctic Marion Island (Bester et al., South African Journal of Wildlife Research, 32, 2002, 65) and compared modelled outputs to observed data. The parameters of the best‐fitting model reflected the conditions of the management programme, and the model successfully simulated the observed movement of the cat population to the southern and eastern portion of the island under hunting pressure. We further demonstrated that none of the management strategies would likely have been successful within a reasonable time frame if performed in isolation. Spatial Population Abundance Dynamics Engine is applicable to a wide range of population management problems and allows easy generation, modification and analysis of management scenarios. It is a useful tool for the planning, evaluation and optimisation of the management of wild populations and can be used without specialised training.

MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

Quantitative Assessment of the Canine Pupillary Light Reflex

To develop instrumentation and methods for thorough quantitative assessment of the pupillary light reflex (PLR) in dogs under varying stimulus conditions. The PLR was recorded in normal Dachshunds using a custom system allowing full user control over stimulus intensity, color, and duration. Chemical restraint protocols were compared to determine which protocol provided for optimal baseline stability of pupil size and appropriate eye positioning. A series of white light stimuli of increasing intensity was used to elicit pupil constriction. Pupil images were concurrently recorded using continuous infrared illumination and an infrared-sensitive camera. The PLR was also recorded in response to blue and red stimuli. With injectable chemical restraint alone, spontaneous fluctuations in pupil size occurred independent of light stimulation, and spontaneous eye movements made it difficult to fully visualize the pupil. Combined injectable chemical and inhalation restraint provided a steady baseline pupil size throughout PLR assessment and allowed for stable positioning of the eye using a conjunctival stay suture. Robust PLRs were elicited with all light colors. PLR constriction amplitude increased with increasing flash intensity and ranged from 5% to 70%. A recording system and protocol have been developed to reliably quantify the canine PLR. The techniques and instrumentation will be useful for objective quantitative assessment of the PLR in dogs and other species in research applications and may be useful in clinical veterinary ophthalmology and neurology if PLR abnormalities detected with these procedures can be associated with specific diseases.

Spline-based framework for interactive segmentation in biomedical imaging

Active contours constitute a computationally attractive framework for image segmentation. In this paper, we describe a fully parametric design that relies on B-spline bases and is specified by control points on the image. Our technique yields successful segmentation results even for challenging datasets where object contours are not well-defined. We can achieve this because our parametric approach uses few parameters and allows us to constrain the topology of the curve. We provide the details for an efficient implementation and discuss different design alternatives. This work comes with a companion software that gives the end user full control over the snakes. We demonstrate the features of our software which includes an interactive interface where the user can manipulate the position of control points by simple mouse actions.

CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTION

Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined) characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG), an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA) for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors.

NUMERICAL MODELLING OF HUMAN BODY FOR BLUETOOTH BODY-WORN APPLICATIONS

The human body has got a pivotal role in portable devices operating in Body-centric Wireless Networks (BCWNs). Electromagnetic interaction between lossy human body tissues and wearable antennas degrades the system performance. E-cient deployment of such systems necessitates thorough understanding of these efiects. Numerical analysis is a powerful tool that provides useful information of such scenarios fairly quicker than the actual measurements giving the user full control of the design environment. This paper investigates usefulness of numerical analysis based on the comparison of three difierent homogeneous models of the human body. Efiectiveness of a numerical model is evaluated in terms of its resolution, computational e-ciency, time consumption and accuracy of the results in software followed by experimental veriflcations.

Digital planning of cranial implants

Computer-aided techniques can be used in the reconstruction of defects in the skull, although there are limitations for large defects. We describe a technique for the digital design of an implant for cranioplasty using one, easy-to-use, piece of generic industrial software that shows a curvature-based, hole-filling algorithm. This approach is suitable for all kinds of defects, including those that extend across the midline of the skull. The workflow gives the user full control over the design, production, and material used for the implant.

Empowering web portal users with personalized text mining services

Empowering web portal users with personalized text mining services

Informatics and Computing.

Informatics and Computing.

A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet–Neumann boundary conditions

A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Program summaryProgram title: FDMRP 1.0Catalogue identifier: AENQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License v3.0No. of lines in distributed program, including test data, etc.: 102793No. of bytes in distributed program, including test data, etc.: 369378Distribution format: tar.gzProgramming language: Matlab 2010a.Computer: PC, Macintosh.Operating system: Windows, OSX, Linux.RAM: 8GB (8,589,934,592 bytes)Classification: 4.3.Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions.Solution method: Finite difference with mesh refinement.Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D.Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement.Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.