Automated DNA Fragments Recognition and Sizing through AFM Image Processing

This paper presents an automated algorithm to determine DNA fragment size from atomic force microscope images and to extract the molecular profiles. The sizing of DNA fragments is a widely used procedure for investigating the physical properties of individual or protein-bound DNA molecules. Several atomic force microscope (AFM) real and computer-generated images were tested for different pixel and fragment sizes and for different background noises. The automated approach minimizes processing time with respect to manual and semi-automated DNA sizing. Moreover, the DNA molecule profile recognition can be used to perform further structural analysis. For computer-generated images, the root mean square error incurred by the automated algorithm in the length estimation is 0.6% for a 7.8 nm image pixel size and 0.34% for a 3.9 nm image pixel size. For AFM real images we obtain a distribution of lengths with a standard deviation of 2.3% of mean and a measured average length very close to the real one, with an error around 0.33%

Power and timing modelling, optimisation and simulation

Editorial.Peer Reviewe

PVInGrid: A distributed infrastructure for evaluating the integration of photovoltaic systems in smart grid

© IFIP International Federation for Information Processing 2017 Published by Springer International Publishing AG 2017. All Rights Reserved. Planning and developing the future Smart City is becoming mandatory due to the need of moving forward to a more sustainable society. To foster this transition an accurate simulation of energy production from renewable sources, such as Photovoltaic Panels (PV), is necessary to evaluate the impact on the grid. In this paper, we present a distributed infrastructure that simulates the PV production and evaluates the integration of such systems in the grid considering data provided by smart-meters. The proposed solution is able to model the behaviour of PV systems solution exploiting GIS representation of rooftops and real meteorological data. Finally, such information is used to feed a real-time distribution network simulator

W2WNet: A two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality

Ideally, Convolutional Neural Networks (CNNs) should be trained with high quality images with minimum noise and correct ground truth labels. Nonetheless, in many real-world scenarios, such high quality is very hard to obtain, and datasets may be affected by any sort of image degradation and mislabelling issues. This negatively impacts the performance of standard CNNs, both during the training and the inference phase. To address this issue we propose Wise2WipedNet (W2WNet), a new two-module Convolutional Neural Network, where a Wise module exploits Bayesian inference to identify and discard spurious images during the training and a Wiped module takes care of the final classification, while broadcasting information on the prediction confidence at inference time. The goodness of our solution is demonstrated on a number of public benchmarks addressing different image classification tasks, as well as on a real-world case study on histological image analysis. Overall, our experiments demonstrate that W2WNet is able to identify image degradation and mislabelling issues both at training and at inference time, with positive impact on the final classification accuracy

A SGAM-based test platform to develop a scheme for wide area measurement-free monitoring of smart grids under high PV penetration

© 2019 by the authors. In order to systematically shift existing control and management paradigms in distribution systems to new interoperable communication supported schemes in smart grids, we need to map newly developed use cases to standard reference models like Smart Grid Architecture Model (SGAM). From the other side, any new use cases should be tested and validated ex-ante before being deployed in the real-world system. Considering various types of actors in smart grids, use cases are usually tested using co-simulation platforms. Currently, there is no efficient co-simulation platform which supports interoperability analysis based on SGAM. In this paper, we present our developed test platform which offers a support to design new use cases based on SGAM. We used this platform to develop a new scheme for wide area monitoring of existing distribution systems under growing penetration of Photovoltaic production. Off-the-shelf solutions of state estimation for wide area monitoring are either used for passive distribution grids or applied to the active networks with wide measurement of distributed generators. Our proposed distribution state estimation algorithm does not require wide area measurements and relies on the data provided by a PV simulator we developed. This practical scheme is tested experimentally on a realistic urban distribution grid. The monitoring results shows a very low error rate of about 1% by using our PV simulator under high penetration of PV with about 30% error of load forecast. Using our SGAM-based platform, we could propose and examine an Internet-of-Things-based infrastructure to deploy the use case

An online grey-box model based on unscented kalman filter to predict temperature profiles in smart buildings

Nearly 40% of primary energy consumption is related to the usage of energy in Buildings. Energy-related data such as indoor air temperature and power consumption of heating/cooling systems can be now collected due to the widespread diffusion of Internet-of-Things devices. Such energy data can be used (i) to train data-driven models than learn the thermal properties of buildings and (ii) to predict indoor temperature evolution. In this paper, we present a Grey-box model to estimate thermal dynamics in buildings based on Unscented Kalman Filter and thermal network representation. The proposed methodology has been applied in two different buildings with two different thermal network discretizations to test its accuracy in indoor air temperature prediction. Due to a lack of a real-world data sampled by Internet of Things (IoT) devices, a realistic data-set has been generated using the software Energy+, by referring to real industrial building models. Results on synthetic and realistic data show the accuracy of the proposed methodology in predicting indoor temperature trends up to the next 24 h with a maximum error lower than 2 °C, considering one year of data with different weather conditions

A Multi-modal Brain Image Registration Framework for US-guided Neuronavigation Systems - Integrating MR and US for Minimally Invasive Neuroimaging

US-guided neuronavigation exploits the simplicity of use and minimal invasiveness of Ultrasound (US) imaging and the high tissue resolution and signal-to-noise ratio of Magnetic Resonance Imaging (MRI) to guide brain surgeries. More specifically, the intra-operative 3D US images are combined with pre-operative MR images to accurately localise the course of instruments in the operative field with minimal invasiveness. Multi-modal image registration of 3D US and MR images is an essential part of such system. In this paper, we present a complete software framework that enables the registration US and MR brain scans based on a multi resolution deformable transform, tackling elastic deformations (i.e. brain shifts) possibly occurring during the surgical procedure. The framework supports also simpler and faster registration techniques, based on rigid or affine transforms, and enables the interactive visualisation and rendering of the overlaid US and MRI volumes. The registration was experimentally validated on a public dataset of realistic brain phantom images, at different levels of artificially induced deformations

Benchmarking a many-core neuromorphic platform with an MPI-based DNA sequence matching algorithm

SpiNNaker is a neuromorphic globally asynchronous locally synchronous (GALS)multi-core architecture designed for simulating a spiking neural network (SNN) in real-time. Several studies have shown that neuromorphic platforms allow flexible and efficient simulations of SNN by exploiting the efficient communication infrastructure optimised for transmitting small packets across the many cores of the platform. However, the effectiveness of neuromorphic platforms in executing massively parallel general-purpose algorithms, while promising, is still to be explored. In this paper, we present an implementation of a parallel DNA sequence matching algorithm implemented by using the MPI programming paradigm ported to the SpiNNaker platform. In our implementation, all cores available in the board are configured for executing in parallel an optimised version of the Boyer-Moore (BM) algorithm. Exploiting this application, we benchmarked the SpiNNaker platform in terms of scalability and synchronisation latency. Experimental results indicate that the SpiNNaker parallel architecture allows a linear performance increase with the number of used cores and shows better scalability compared to a general-purpose multi-core computing platform

miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction

The advent of Next Generation Sequencing (NGS) technology has enabled a new major approach for micro RNAs (miRNAs) expression profiling through the so called RNA-Sequencing (RNA-Seq). Different tools have been developed in the last years in order to detect and quantify miRNAs, especially in pathological samples, starting from the big amount of data deriving from RNA sequencing. These tools, usually relying on general purpose alignment algorithms, are however characterized by different sensitivity and accuracy levels and in the most of the cases provide not overlapping predictions. To overcome these limitations we propose a novel pipeline for miRNAs detection and quantification in RNA-Seq sample, miRNA Seed Extension Aligner (miR-SEA), based on an experimental evidence concerning miRNAs structure. The proposed pipeline was tested on three Colorectal Cancer (CRC) RNA-Seq samples and the obtained results compared with those provided by two well-known miRNAs detection tools showing good ability in performing detection and quantification more adherent to miRNAs structure