Automated Segmentation of Cells with IHC Membrane Staining

This study presents a fully automated membrane segmentation technique for immunohistochemical tissue images with membrane staining, which is a critical task in computerized immunohistochemistry (IHC). Membrane segmentation is particularly tricky in immunohistochemical tissue images because the cellular membranes are visible only in the stained tracts of the cell, while the unstained tracts are not visible. Our automated method provides accurate segmentation of the cellular membranes in the stained tracts and reconstructs the approximate location of the unstained tracts using nuclear membranes as a spatial reference. Accurate cell-by-cell membrane segmentation allows per cell morphological analysis and quantification of the target membrane proteins that is fundamental in several medical applications such as cancer characterization and classification, personalized therapy design, and for any other applications requiring cell morphology characterization. Experimental results on real datasets from different anatomical locations demonstrate the wide applicability and high accuracy of our approach in the context of IHC analysi

Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl

A Cloud Infrastructure for Optimization of a Massive Parallel Sequencing Workflow

Massive Parallel Sequencing is a term used to describe several revolutionary approaches to DNA sequencing, the so-called Next Generation Sequencing technologies. These technologies generate millions of short sequence fragments in a single run and can be used to measure levels of gene expression and to identify novel splice variants of genes allowing more accurate analysis. The proposed solution provides novelty on two fields, firstly an optimization of the read mapping algorithm has been designed, in order to parallelize processes, secondly an implementation of an architecture that consists of a Grid platform, composed of physical nodes, a Virtual platform, composed of virtual nodes set up on demand, and a scheduler that allows to integrate the two platform

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

Data Driven Patient-Specialized Neural Networks for Blood Glucose Prediction

Diabetes is an autoimmune disease characterized by glucose levels dysfunctions. It involves continuous monitoring combined with insulin treatment. Nowadays, continuous glucose monitoring systems (CGMs) have led to a greater availability of data. These can be effectively used by machine learning techniques to infer future values of the glycaemic concentration, allowing the early prevention of dangerous states and a better optimisation of the diabetic treatment. In this work, we investigate a patient-specialized prediction model. Thus, we designed a specialized solution based on Long Short-Term Memory (LSTM) neural network. Our solution was experimentally compared with two literature approaches, respectively based on Feed-Forward (FNN) and Recurrent (RNN) neural networks. The experimental results have highlighted that our LSTM solution obtained good performance both for short- and long-term glucose level inference (60 min.), overcoming the other methods both in terms of correlation between measured and predicted glucose signal and in terms of clinical outcome

MOCA: A Low-Power, Low-Cost Motion Capture System Based on Integrated Accelerometers

Human-computer interaction (HCI) and virtual reality applications pose the challenge of enabling real-time interfaces for natural interaction. Gesture recognition based on body-mounted accelerometers has been proposed as a viable solution to translate patterns of movements that are associated with user commands, thus substituting point-and-click methods or other cumbersome input devices. On the other hand, cost and power constraints make the implementation of a natural and efficient interface suitable for consumer applications a critical task. Even though several gesture recognition solutions exist, their use in HCI context has been poorly characterized. For this reason, in this paper, we consider a low-cost/low-power wearable motion tracking system based on integrated accelerometers called motion capture with accelerometers (MOCA) that we evaluated for navigation in virtual spaces. Recognition is based on a geometric algorithm that enables efficient and robust detection of rotational movements. Our objective is to demonstrate that such a low-cost and a low-power implementation is suitable for HCI applications. To this purpose, we characterized the system from both a quantitative point of view and a qualitative point of view. First, we performed static and dynamic assessment of movement recognition accuracy. Second, we evaluated the effectiveness of user experience using a 3D game application as a test bed

An Energy-autonomous Wireless Sensor Network Development Platform

Internet-of-things enabled applications are increasingly popular and are expected to spread even more in the next few years. Energy efficiency is fundamental to support the widespread use of such systems. This paper presents a practical framework for the development and the evaluation of low-power Wireless Sensor Networks equipped with energy harvesting, aiming at energy-autonomous applications. An experimental case study demonstrates the capabilities of the solution

IoT Software Infrastructure for Remote Monitoring of Patients with Chronic Metabolic Disorders

Novel Information and Communication Technologies, such as Internet-of-Things (IoT), middleware and cloud computing, are providing innovative solutions ranging in different contexts. Smart health is one of these scenarios. Indeed, there is a rising interest in developing new healthcare services for remote patient assistance and monitoring. Among all, the main promised benefits consist on improving the patients’ quality of life, speeding up therapeutic interventions and reducing hospitalizations’ costs. This is also known as Telemedicine. In this paper, we present a novel distributed software infrastructure for remote monitoring of patients with chronic metabolic disorders: i) it collects and and makes available information coming from IoT devices, ii) it performs analysis to help medical diagnosis and iii) it promotes a bidirectional communication among the end-users (i.e. medical personnel and patients). In this paper, we also present our experimental results performed in a laboratory test environment to validate the proposed solution

isomiR-SEA: An RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation

>Background: Massive parallel sequencing of transcriptomes, revealed the presence of many miRNAs and miRNAs variants named isomiRs with a potential role in several cellular processes through their interaction with a target mRNA. Many methods and tools have been recently devised to detect and quantify miRNAs from sequencing data. However, all of them are implemented on top of general purpose alignment methods, thus providing poorly accurate results and no information concerning isomiRs and conserved miRNA-mRNA interaction sites. >Results: To overcome these limitations we present a novel algorithm named isomiR-SEA, that is able to provide users with very accurate miRNAs expression levels and both isomiRs and miRNA-mRNA interaction sites precise classifications. Tags are mapped on the known miRNAs sequences thanks to a specialized alignment algorithm developed on top of biological evidence concerning miRNAs structure. Specifically, isomiR-SEA checks for miRNA seed presence in the input tags and evaluates, during all the alignment phases, the positions of the encountered mismatches, thus allowing to distinguish among the different isomiRs and conserved miRNA-mRNA interaction sites. >Conclusions: isomiR-SEA performances have been assessed on two public RNA-Seq datasets proving that the implemented algorithm is able to account for more reliable and accurate miRNAs expression levels with respect to those provided by two compared state of the art tools. Moreover, differently from the few methods currently available to perform isomiRs detection, the proposed algorithm implements the evaluation of isomiRs and conserved miRNA-mRNA interaction sites already in the first alignment phases, thus avoiding any additional filtering stages potentially responsible for the loss of useful information