Dwarna : a blockchain solution for dynamic consent in biobanking

Dynamic consent aims to empower research partners and facilitate active participation in the research process. Used within the context of biobanking, it gives individuals access to information and control to determine how and where their biospecimens and data should be used. We present Dwarna—a web portal for ‘dynamic consent’ that acts as a hub connecting the different stakeholders of the Malta Biobank: biobank managers, researchers, research partners, and the general public. The portal stores research partners’ consent in a blockchain to create an immutable audit trail of research partners’ consent changes. Dwarna’s structure also presents a solution to the European Union’s General Data Protection Regulation’s right to erasure—a right that is seemingly incompatible with the blockchain model. Dwarna’s transparent structure increases trustworthiness in the biobanking process by giving research partners more control over which research studies they participate in, by facilitating the withdrawal of consent and by making it possible to request that the biospecimen and associated data are destroyed.peer-reviewe

TextRWeb: Large-Scale Text Analytics with R on the Web

As digital data sources grow in number and size, they pose an opportunity for computational investigation by means of text mining, NLP, and other text analysis techniques. R is a popular and powerful text analytics tool; however, it needs to run in parallel and re- quires special handling to protect copyrighted content against full access (consumption). The HathiTrust Research Center (HTRC) currently has 11 million volumes (books) where 7 million volumes are copyrighted. In this paper we propose HTRC TextRWeb, an interactive R software environment which employs complexity hiding interfaces and automatic code generation to allow large-scale text analytics in a non-consumptive means. For our principal test case of copyrighted data in HathiTrust Digital Library, TextRWeb permits us to code, edit, and submit text analytics methods empowered by a family of interactive web user interfaces. All these methods combine to reveal a new interactive paradigm for large-scale text analytics on the web

A deep learning framework for quality assessment and restoration in video endoscopy

Endoscopy is a routine imaging technique used for both diagnosis and minimally invasive surgical treatment. Artifacts such as motion blur, bubbles, specular reflections, floating objects and pixel saturation impede the visual interpretation and the automated analysis of endoscopy videos. Given the widespread use of endoscopy in different clinical applications, we contend that the robust and reliable identification of such artifacts and the automated restoration of corrupted video frames is a fundamental medical imaging problem. Existing state-of-the-art methods only deal with the detection and restoration of selected artifacts. However, typically endoscopy videos contain numerous artifacts which motivates to establish a comprehensive solution. We propose a fully automatic framework that can: 1) detect and classify six different primary artifacts, 2) provide a quality score for each frame and 3) restore mildly corrupted frames. To detect different artifacts our framework exploits fast multi-scale, single stage convolutional neural network detector. We introduce a quality metric to assess frame quality and predict image restoration success. Generative adversarial networks with carefully chosen regularization are finally used to restore corrupted frames. Our detector yields the highest mean average precision (mAP at 5% threshold) of 49.0 and the lowest computational time of 88 ms allowing for accurate real-time processing. Our restoration models for blind deblurring, saturation correction and inpainting demonstrate significant improvements over previous methods. On a set of 10 test videos we show that our approach preserves an average of 68.7% which is 25% more frames than that retained from the raw videos.Comment: 14 page

Doctor of Philosophy

dissertationThe design of integrated circuit (IC) requires an exhaustive verification and a thorough test mechanism to ensure the functionality and robustness of the circuit. This dissertation employs the theory of relative timing that has the advantage of enabling designers to create designs that have significant power and performance over traditional clocked designs. Research has been carried out to enable the relative timing approach to be supported by commercial electronic design automation (EDA) tools. This allows asynchronous and sequential designs to be designed using commercial cad tools. However, two very significant holes in the flow exist: the lack of support for timing verification and manufacturing test. Relative timing (RT) utilizes circuit delay to enforce and measure event sequencing on circuit design. Asynchronous circuits can optimize power-performance product by adjusting the circuit timing. A thorough analysis on the timing characteristic of each and every timing path is required to ensure the robustness and correctness of RT designs. All timing paths have to conform to the circuit timing constraints. This dissertation addresses back-end design robustness by validating full cyclical path timing verification with static timing analysis and implementing design for testability (DFT). Circuit reliability and correctness are necessary aspects for the technology to become commercially ready. In this study, scan-chain, a commercial DFT implementation, is applied to burst-mode RT designs. In addition, a novel testing approach is developed along with scan-chain to over achieve 90% fault coverage on two fault models: stuck-at fault model and delay fault model. This work evaluates the cost of DFT and its coverage trade-off then determines the best implementation. Designs such as a 64-point fast Fourier transform (FFT) design, an I2C design, and a mixed-signal design are built to demonstrate power, area, performance advantages of the relative timing methodology and are used as a platform for developing the backend robustness. Results are verified by performing post-silicon timing validation and test. This work strengthens overall relative timed circuit flow, reliability, and testability

Physical design of USB1.1

In earlier days, interfacing peripheral devices to host computer has a big problematic. There existed so many different kinds’ ports like serial port, parallel port, PS/2 etc. And their use restricts many situations, Such as no hot-pluggability and involuntary configuration. There are very less number of methods to connect the peripheral devices to host computer. The main reason that Universal Serial Bus was implemented to provide an additional benefits compared to earlier interfacing ports. USB is designed to allow many peripheral be connecting using single standardize interface. It provides an expandable fast, cost effective, hot-pluggable plug and play serial hardware interface that makes life of computer user easier allowing them to plug different devices to into USB port and have them configured automatically. In this thesis demonstrated the USB v1.1 architecture part in briefly and generated gate level net list form RTL code by applying the different constraints like timing, area and power. By applying the various types design constraints so that the performance was improved by 30%. And then it implemented in physically by using SoC encounter EDI system, estimation of chip size, power analysis and routing the clock signal to all flip-flops presented in the design. To reduce the clock switching power implemented register clustering algorithm (DBSCAN). In this design implementation TSMC 180nm technology library is used

Observing the clouds : a survey and taxonomy of cloud monitoring

This research was supported by a Royal Society Industry Fellowship and an Amazon Web Services (AWS) grant. Date of Acceptance: 10/12/2014Monitoring is an important aspect of designing and maintaining large-scale systems. Cloud computing presents a unique set of challenges to monitoring including: on-demand infrastructure, unprecedented scalability, rapid elasticity and performance uncertainty. There are a wide range of monitoring tools originating from cluster and high-performance computing, grid computing and enterprise computing, as well as a series of newer bespoke tools, which have been designed exclusively for cloud monitoring. These tools express a number of common elements and designs, which address the demands of cloud monitoring to various degrees. This paper performs an exhaustive survey of contemporary monitoring tools from which we derive a taxonomy, which examines how effectively existing tools and designs meet the challenges of cloud monitoring. We conclude by examining the socio-technical aspects of monitoring, and investigate the engineering challenges and practices behind implementing monitoring strategies for cloud computing.Publisher PDFPeer reviewe