Search results for "aRR"
showing 10 items of 10185 documents
HPG pore: an efficient and scalable framework for nanopore sequencing data.
2016
The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the MinION™ from Oxford Nanopore Technologies, is a USB-connected, portable device that allows real-time DNA analysis. In addition, other new instruments are expected to be released soon, which promise to outperform the current short-read technologies in terms of throughput. Despite the flood of data expected from this technology, the data analysis solutions currently available are only designed to manage small projects and are not scalable. Here we present HPG Pore, a toolkit for …
Deep learning architectures for prediction of nucleosome positioning from sequences data
2018
Abstract Background Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the primary functions of Chromatin i.e. packing the DNA into the nucleus of the Eukaryote cells. Several biological studies have shown that the nucleosome positioning influences the regulation of cell type-specific gene activities. Moreover, computational studies have shown evidence of sequence specificity concerning the DNA fragment wrapped into nucleosomes, clearly underlined by the organization of particular DNA substrings. As the main consequence, the identification of nucleosomes on a genomic scale has been successfully performed by com…
Quantitatively characterizing drug-induced arrhythmic contractile motions of human stem cell-derived cardiomyocytes.
2018
Quantification of abnormal contractile motions of cardiac tissue has been a noteworthy challenge and significant limitation in assessing and classifying the drug-induced arrhythmias (i.e. Torsades de pointes). To overcome these challenges, researchers have taken advantage of computational image processing tools to measure contractile motion from cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs). However, the amplitude and frequency analysis of contractile motion waveforms doesn't produce sufficient information to objectively classify the degree of variations between two or more sets of cardiac contractile motions. In this paper, we generated contractile motion dat…
Transcriptome Analysis of PA Gain and Loss of Function Mutants
2017
Functional genomics has become a forefront methodology for plant science thanks to the widespread development of microarray technology. While technical difficulties associated with the process of obtaining raw expression data have been diminishing, allowing the appearance of tremendous amounts of transcriptome data in different databases, a common problem using "omic" technologies remains: the interpretation of these data and the inference of its biological meaning. In order to assist to this complex task, a wide variety of software tools have been developed. In this chapter we describe our current workflow of the application of some of these analyses. We have used it to compare the transcr…
Network-Wide Adaptive Burst Detection Depicts Neuronal Activity with Improved Accuracy
2017
Neuronal networks are often characterized by their spiking and bursting statistics. Previously, we introducedan adaptive burst analysis methodwhich enhances the analysis power for neuronal networks with highly varying firing dynamics. The adaptation is based on single channels analyzing each element of a network separately. Such kind of analysis was adequate for the assessment of local behavior, where the analysis focuses on the neuronal activity in the vicinity of a single electrode. However, the assessment of the whole network may be hampered, if parts of the network are analyzed using different rules. Here, we test how using multiple channels and measurement time points affect adaptive b…
Spectral entropy based neuronal network synchronization analysis based on microelectrode array measurements
2016
Synchrony and asynchrony are essential aspects of the functioning of interconnected neuronal cells and networks. New information on neuronal synchronization can be expected to aid in understanding these systems. Synchronization provides insight in the functional connectivity and the spatial distribution of the information processing in the networks. Synchronization is generally studied with time domain analysis of neuronal events, or using direct frequency spectrum analysis, e.g., in specific frequency bands. However, these methods have their pitfalls. Thus, we have previously proposed a method to analyze temporal changes in the complexity of the frequency of signals originating from differ…
A new parallel pipeline for DNA methylation analysis of long reads datasets
2017
Background DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. Results In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while…
Vascular pathology: Cause or effect in Alzheimer disease?
2018
Introduction: Alzheimer disease (AD) is the main cortical neurodegenerative disease. The incidence of this disease increases with age, causing significant medical, social and economic problems, especially in countries with ageing populations. Objective: This review aims to highlight existing evidence of how vascular dysfunction may contribute to cognitive impairment in AD, as well as the therapeutic possibilities that might arise from this evidence. Development: The vascular hypothesis emerged as an alternative to the amyloid cascade hypothesis as an explanation for the pathophysiology of AD. This hypothesis locates blood vessels as the origin for a variety of pathogenic pathways that lead …
Solastalgia's mourning and the slowly evolving effect of asbestos pollution: A qualitative study in Italy
2019
In Italy, the problem of asbestos pollution is increasing in severity. In fact, in recent years, the number of people affected by asbestos-related illnesses has been growing because of the fibre's slowly evolving effects and its progressive pollution in the environment adjacent to the places where it is processed. Even though the physical consequences of asbestos are now quite clear, few studies have examined the psychological consequences of this kind of disaster. Since it is difficult to perceive its pathogenicity in daily life, this study was conducted in the affected areas of north-eastern Italy, using the qualitative research in psychology with 51 persons who experienced asbestos-relat…
BIOMARKERS OF CORONARY MICROVASCULAR DYSFUNCTION IN PATIENTS WITH MICROVASCULAR ANGINA: A NARRATIVE REVIEW
2021
The current gold standard for diagnosis of coronary microvascular dysfunction (CMD) in the absence of myocardial diseases, whose clinical manifestation is microvascular angina (MVA), is reactivity testing using adenosine or acetylcholine during coronary angiography. This invasive test can be difficult to perform, expensive, and harmful. The identification of easily obtainable blood biomarkers which reflect the pathophysiology of CMD, characterized by high reliability, precision, accuracy, and accessibility may reduce risks and costs related to invasive procedures and even facilitate the screening and diagnosis of CMD. In this review, we summarized the results of several studies that have i…