Search results for "processi"
showing 10 items of 9638 documents
Computational processing and quality control of Hi-C, capture Hi-C and capture-C data
2019
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish…
LRP1 Modulates APP Intraneuronal Transport and Processing in Its Monomeric and Dimeric State.
2017
The low-density lipoprotein receptor-related protein 1, LRP1, interacts with APP and affects its processing. This is assumed to be mostly caused by the impact of LRP1 on APP endocytosis. More recently, also an interaction of APP and LRP1 early in the secretory pathway was reported whereat retention of LRP1 in the ER leads to decreased APP cell surface levels and in turn, to reduced Aβ secretion. Here, we extended the biochemical and immunocytochemical analyses by showing via live cell imaging analyses in primary neurons that LRP1 and APP are transported only partly in common (one third) but to a higher degree in distinct fast axonal transport vesicles. Interestingly, co-expression of LRP1 a…
Assessment of tumor-infiltrating TCRV γ 9V δ 2 γδ lymphocyte abundance by deconvolution of human cancers microarrays
2017
Most human blood γδ cells are cytolytic TCRVγ9Vδ2+lymphocytes with antitumor activity. They are currently investigated in several clinical trials of cancer immunotherapy but so far, their tumor infiltration has not been systematically explored across human cancers. Novel algorithms allowing the deconvolution of bulk tumor transcriptomes to find the relative proportions of infiltrating leucocytes, such as CIBERSORT, should be appropriate for this aim but in practice they fail to accurately recognize γδ T lymphocytes. Here, by implementing machine learning from microarray data, we first improved the computational identification of blood-derived TCRVγ9Vδ2+γδ lymphocytes and then appl…
High-throughput sequencing for 1-methyladenosine (m1A) mapping in RNA
2016
Abstract Detection and mapping of modified nucleotides in RNAs is a difficult and laborious task. Several physico-chemical approaches based on differential properties of modified nucleotides can be used, however, most of these methods do not allow high-throughput analysis. Here we describe in details a method for mapping of rather common 1-methyladenosine (m1A) residues using high-throughput next generation sequencing (NGS). Since m1A residues block primer extension during reverse transcription (RT), the accumulation of abortive products as well as the nucleotide misincorporation can be detected in the sequencing data. The described library preparation protocol allows to capture both types …
Group analysis of ongoing EEG data based on fast double-coupled nonnegative tensor decomposition
2019
Abstract Background Ongoing EEG data are recorded as mixtures of stimulus-elicited EEG, spontaneous EEG and noises, which require advanced signal processing techniques for separation and analysis. Existing methods cannot simultaneously consider common and individual characteristics among/within subjects when extracting stimulus-elicited brain activities from ongoing EEG elicited by 512-s long modern tango music. New method Aiming to discover the commonly music-elicited brain activities among subjects, we provide a comprehensive framework based on fast double-coupled nonnegative tensor decomposition (FDC-NTD) algorithm. The proposed algorithm with a generalized model is capable of simultaneo…
Detecting differences with magnetoencephalography of somatosensory processing after tactile and electrical stimuli.
2018
Abstract Background Deviant stimuli within a standard, frequent stimulus train induce a cortical somatosensory mismatch response (SMMR). The SMMR reflects the brain’s automatic mechanism for the detection of change in a somatosensory domain. It is usually elicited by electrical stimulation, which activates nerve fibers and receptors in superficial and deep skin layers, whereas tactile stimulation is closer to natural stimulation and activates uniform fiber types. We recorded SMMRs after electrical and tactile stimuli. Method 306-channel magnetoencephalography recordings were made with 16 healthy adults under two conditions: electrical (eSMMR) and tactile (tSMMR) stimulations. The SMMR proto…
The Gut Metagenome Changes in Parallel to Waist Circumference, Brain Iron Deposition, and Cognitive Function.
2017
Context Microbiota perturbations seem to exert modulatory effects on emotional behavior, stress-, and pain-modulation systems in adult animals; however, limited information is available in humans. Objective To study potential relationships among the gut metagenome, brain microstructure, and cognitive performance in middle-aged, apparently healthy, obese and nonobese subjects after weight changes. Design This is a longitudinal study over a 2-year period. Setting A tertiary public hospital. Patients or other participants Thirty-five (18 obese) apparently healthy subjects. Intervention(s) Diet counseling was provided to all subjects. Obese subjects were followed every 6 months. Main outcome me…
Palmitoylation is a post-translational modification of Alix regulating the membrane organization of exosome-like small extracellular vesicles.
2018
Abstract Background Virtually all cell types have the capacity to secrete nanometer-sized extracellular vesicles, which have emerged in recent years as potent signal transducers and cell-cell communicators. The multifunctional protein Alix is a bona fide exosomal regulator and skeletal muscle cells can release Alix-positive nano-sized extracellular vesicles, offering a new paradigm for understanding how myofibers communicate within skeletal muscle and with other organs. S-palmitoylation is a reversible lipid post-translational modification, involved in different biological processes, such as the trafficking of membrane proteins, achievement of stable protein conformations, and stabilization…
Chemical–physical characteristics, polyphenolic content and total antioxidant activity of three Italian-grown pomegranate cultivars
2019
Background: In Mediterranean countries, there is an increasing demand for pomegranate fruits due to their antioxidant properties and nutritional values. The large diffusion of new genotypes and cultivars requires the knowledge of all fruit characteristics in connection with the cultivation area, to satisfy the market demand. This study seeks to determine the fruit quality attributes and nutraceutical values of three pomegranate cultivars (Wonderful, Acco and Kamel) grown in the Mediterranean climate. Methods: The fruits were evaluated for their main physico-chemical traits (weight, volume, height, width, thickness, total arils number, total arils weight, juiciness, fruit index, peel index a…
Exceptional Pattern Discovery
2017
This chapter is devoted to a discussion on exceptional pattern discovery, namely on scenarios, contexts, and techniques concerning the mining of patterns which are so rare or so frequent to be considered as exceptional and, then, of interest for an expert to shed lights on the domain. Frequent patterns have found broad applications in areas like association rule mining, indexing, and clustering [1, 20, 23]. The application of frequent patterns in classification also achieved some success in the classification of relational data [6, 13, 14, 19, 25], text [15], and graphs [7]. The part is organized as follows. First, the frequent pattern mining on classical datasets is presented. This is not …