Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons

In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, in situ hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of Hist1h1b was higher embryonically, while that of Hist1h1c was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as “replication-dependent. ” Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.
Genome Analysis Genome-Wide Annotation and Expression Profiling of Cell Cycle Regulatory Genes in Chlamydomonas reinhardtii 1 [ w ]

Eukaryotic cell cycles are driven by a set of regulators that have undergone lineage-specific gene loss, duplication, or divergence in different taxa. It is not known to what extent these genomic processes contribute to differences in cell cycle regulatory programs and cell division mechanisms among different taxonomic groups. We have undertaken a genome-wide characterization of the cell cycle genes encoded by Chlamydomonas reinhardtii, a unicellular eukaryote that is part of the green algal/land plant clade. Although Chlamydomonas cells divide by a noncanonical mechanism termed multiple fission, the cell cycle regulatory proteins from Chlamydomonas are remarkably similar to those found in higher plants and metazoans, including the proteins of the RB-E2F pathway that are absent in the fungal kingdom. Unlike in higher plants and vertebrates where cell cycle regulatory genes have undergone extensive duplication, most of the cell cycle regulators in Chlamydomonas have not. The relatively small number of cell cycle genes and growing molecular genetic toolkit position Chlamydomonas to become an important model for higher plant and metazoan cell cycles.
Accuracy of Gene Scores when Pruning Markers by Linkage Disequilibrium

Objective: Gene scores are often used to model the combined effects of genetic variants. When variants are in linkage disequilibrium, it is common to prune all variants except the most strongly associated. This avoids duplicating information but discards information when variants have independent effects. However, joint modelling of correlated variants increases the sampling error in the gene score. In recent applications, joint modelling has offered only small improvements in accuracy over pruning. We aimed to quantify the relationship between pruning and joint modelling in relation to sample size. Methods: We derived the coefficient of determination R2 for a gene score constructed from pruned markers, and for one constructed from correlated markers with jointly estimated effects. Results: Pruned scores tend to have slightly lower R2 than jointly modelled scores, but the differences are small at sample sizes up to 100,000. If the proportion of correlated variants is high, joint modelling can obtain modest improvements asymptotically. Conclusions: The small gains observed to date from joint modelling can be explained by sample size. As studies become larger, joint modelling will be useful for traits affected by many correlated variants, but the improvements may remain small. Pruning remains a useful heuristic for current studies.
Predicting EMG Based Elbow Joint Torque Model Using Multiple Input ANN Neurons for Arm Rehabilitation

This paper illustrates the Artificial Neural Network (ANN) technique to predict the joint torque estimation model for arm rehabilitation device in a clear manner. This device acts as an exoskeleton for people who had failure of their limb. Electromyography (EMG) is the techniques to analyze the presence of electrical activity in musculoskeletal systems. The electrical activity in muscles of disable person is failed to contract the muscle for movements. In order to prevent the muscles from paralysis becomes spasticity the force of movements should minimize the mental efforts. The objective of this work is to model the muscle EMG signal to torque using ANN technique. The EMG signal is collected from Biceps Brachii muscles to estimate the elbow joint torque. A two layer feed-forward network is trained using Back Propagation Neural Network (BPNN). The experimental results show that ANN can well represent EMG-torque relationship for arm rehabilitation device control.
Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin

Many long non-coding RNAs (lncRNAs) are expressed in cells but only a few have been well characterized. In these cases, lncRNAs have been shown to be key regulators of several cellular processes. Therefore, there is a great need to understand the function of more lncRNAs and their regulation in response to stimuli. Interferon (IFN) is a key molecule in the cellular antiviral response. IFN binding to its receptor activates transcription of several IFN-stimulated genes (ISGs) that function as potent antivirals. In addition, several ISGs are positive or negative regulators of the IFN pathway. This is essential to ensure a strong antiviral response and a later return of the cell to homeostasis. As the ISGs described to date are coding genes, we sought to determine whether IFN also regulates the expression of long non-coding ISGs. To this aim, we used RNA sequencing to analyze the transcriptome of control and HuH7 cells treated with IFNα2. The results show that IFN-treatment regulates the expression of several unknown non-coding transcripts. We have validated two lncRNAs upregulated after treatment with different doses of type I IFNα2 in different cells or with type III IFNλ. These lncRNAs were also induced by influenza and vesicular stomatitis virus mutants unable to block the IFN response, but not by several wild-type lytic viruses tested. These lncRNA genes were named lncISG15 and lncBST2 as they are located close to ISGs ISG15 and BST2, respectively. Interestingly, inhibition experiments showed that lncBST2 is a positive regulator of BST2. Therefore lncBST2 has been renamed BISPR, from BST2 IFN-stimulated positive regulator. Our results may have therapeutic implications as lncBST2/BISPR, but also lncISG15 and their coding neighbors, are increased in cells infected with hepatitis C virus and in the liver of infected patients. These results allow us to hypothesize that several lncRNAs could be activated by IFN to control the potency of the antiviral IFN response.
Clonal Diversification and Changes in Lipid Traits and Colony Morphology in Mycobacterium abscessus Clinical Isolates

ABSTRACT The smooth-to-rough colony morphology shift in Mycobacterium abscessus has been implicated in loss of glycopeptidolipid (GPL), increased pathogenicity, and clinical decline in cystic fibrosis (CF) patients. However, the evolutionary phenotypic and genetic changes remain obscure. Serial isolates from nine non-CF patients with persistent M. abscessus infection were characterized by colony morphology, lipid profile via thin-layer chromatography and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), sequencing of eight genes in the GPL locus, and expression level of fadD23, a key gene involved in the biosynthesis of complex lipids. All 50 isolates were typed as M. abscessus subspecies abscessus and were clonally related within each patient. Rough isolates, all lacking GPL, predominated at later disease stages, some showing variation within rough morphology. While most (77%) rough isolates harbored detrimental mutations in mps1 and mps2, 13% displayed previously unreported mutations in mmpL4a and mmpS4, the latter yielding a putative GPL precursor. Two isolates showed no deleterious mutations in any of the eight genes sequenced. Mixed populations harboring different GPL locus mutations were detected in 5 patients, demonstrating clonal diversification, which was likely overlooked by conventional acid-fast bacillus (AFB) culture methods. Our work highlights applications of MALDI-TOF MS beyond identification, focusing on mycobacterial lipids relevant in virulence and adaptation. Later isolates displayed accumulation of triacylglycerol and reduced expression of fadD23, sometimes preceding rough colony onset. Our results indicate that clonal diversification and a shift in lipid metabolism, including the loss of GPL, occur during chronic lung infection with M. abscessus. GPL loss alone may not account for all traits associated with rough morphology.
Spindles in Svarog: framework and software for parametrization of EEG transients

We present a complete framework for time-frequency parametrization of EEG transients, based upon matching pursuit (MP) decomposition, applied to the detection of sleep spindles. Ranges of spindles duration (>0.5 s) and frequency (11–16 Hz) are taken directly from their standard definitions. Minimal amplitude is computed from the distribution of the root mean square (RMS) amplitude of the signal within the frequency band of sleep spindles. Detection algorithm depends on the choice of just one free parameter, which is a percentile of this distribution. Performance of detection is assessed on the first cohort/second subset of the Montreal Archive of Sleep Studies (MASS-C1/SS2). Cross-validation performed on the 19 available overnight recordings returned the optimal percentile of the RMS distribution close to 97 in most cases, and the following overall performance measures: sensitivity 0.63 ± 0.06, positive predictive value 0.47 ± 0.08, and Matthews coefficient of correlation 0.51 ± 0.04. These concordances are similar to the results achieved on this database by other automatic methods. Proposed detailed parametrization of sleep spindles within a universal framework, encompassing also other EEG transients, opens new possibilities of high resolution investigation of their relations and detailed characteristics. MP decomposition, selection of relevant structures, and simple creation of EEG profiles used previously for assessment of brain activity of patients in disorders of consciousness are implemented in a freely available software package Svarog (Signal Viewer, Analyzer and Recorder On GPL) with user-friendly, mouse-driven interface for review and analysis of EEG. Svarog can be downloaded from http://braintech.pl/svarog.
Calcitonin gene-related peptide relates to cough sensitivity in children with chronic cough

Airway neuropeptides, in particular calcitonin gene-related peptide (CGRP), are likely to be important in the pathogenesis of chronic cough. The present authors evaluated the following: 1) the relationship between cough sensitivity and bronchoalveolar lavage (BAL) neuropeptides; and 2) the effect of reflux oesophagitis (RO) on cough, cough sensitivity and BAL neuropeptides in children not selected for cough. It was hypothesised that CGRP would be increased in children with chronic cough and would relate to cough sensitivity. Capsaicin cough sensitivity was performed in children undergoing gastro-duodenal endoscopy. CGRP, substance P and neurokinin A were measured in BAL obtained nonbronchoscopically. Children were defined as “coughers” if chronic cough was present. Coughers (n = 21) had significantly reduced cough sensitivity but were just as likely as noncoughers (n = 19) to have RO. The median CGRP was significantly higher in coughers with oesophagitis than in noncoughers with oesophagitis. CGRP significantly negatively correlated to cough sensitivity in coughers but not in noncoughers. Elevated calcitonin gene-related peptide, but not substance P or neurokinin A, is only associated with chronic cough in children when oesophagitis coexists. Calcitonin gene-related peptide in bronchoalveolar lavage relates to cough sensitivity and is likely to be important in the pathophysiology of chronic cough.
Learning Hierarchical Task Models by Demonstration (subsumed by TR2002-04)

Most previous work on learning task models, a special case of the well-known knowledge acquisition bottleneck, has dealt with non-hierarchical models. We present and analyze techniques for inferring a hierarchical task model from partially-annotated examples of task-solving behavior. We show our algorithm has desirable formal properties and that both restrictive and preference biases are useful for generating effective models. Finally, we describe experiments that explore the appropriate division of labor between the learning algorithm and the person who provides the
R5 Macrophage-Tropic HIV-1 in the Male Genital Tract

ABSTRACT The entry tropism of HIV-1 Env proteins from virus isolated from the blood and genital tract of five men with compartmentalized lineages was determined. The Env proteins isolated from the genital tract of subject C018 were macrophage-tropic proteins, while the remaining cloned env genes encoded R5 T cell-tropic proteins. The detection of a macrophage-tropic lineage of HIV-1 within the male genital tract strongly suggests that evolution of macrophage-tropic viruses can occur in anatomically isolated sites outside the central nervous system.
Fully Dynamic Betweenness Centrality Maintenance on Massive Networks

Measuring the relative importance of each vertex in a network is one of the most fundamental building blocks in network analysis. Among several importance measures, betweenness centrality, in particular, plays key roles in many real applications. Considerable effort has been made for developing algorithms for static settings. However, real networks today are highly dynamic and are evolving rapidly, and scalable dynamic methods that can instantly reflect graph changes into centrality values are required. In this paper, we present the first fully dynamic method for managing betweenness centrality of all vertices in a large dynamic network. Its main data structure is the weighted hyperedge representation of shortest paths called hypergraph sketch. We carefully design dynamic update procedure with theoretical accuracy guarantee. To accelerate updates, we further propose two auxiliary data structures called two-ball index and special-purpose reachability index. Experimental results using real networks demonstrate its high scalability and efficiency. In particular, it can reflect a graph change in less than a millisecond on average for a large-scale web graph with 106M vertices and 3.7B edges, which is several orders of magnitude larger than the limits of previous dynamic methods.
Active MAP Kinase in Mitosis: Localization at Kinetochores and Association with the Motor Protein CENP-E

To investigate possible involvement of the mitogen-activated protein (MAP) kinases ERK1 and ERK2 (extracellular signal-regulated kinases) in somatic cell mitosis, we have used indirect immunofluorescence with a highly specific phospho-MAP kinase antibody and found that a portion of the active MAP kinase is localized at kinetochores, asters, and the midbody during mitosis. Although the aster labeling was constant from the time of nuclear envelope breakdown, the kinetochore labeling first appeared at early prometaphase, started to fade during chromosome congression, and then disappeared at midanaphase. At telophase, active MAP kinase localized at the midbody. Based on colocalization and the presence of a MAP kinase consensus phosphorylation site, we identified the kinetochore motor protein CENP-E as a candidate mitotic substrate for MAP kinase. CENP-E was phosphorylated in vitro by MAP kinase on sites that are known to regulate its interactions with microtubules and was found to associate in vivo preferentially with the active MAP kinase during mitosis. Therefore, the presence of active MAP kinase at specific mitotic structures and its interaction with CENP-E suggest that MAP kinase could play a role in mitosis at least in part by altering the ability of CENP-E to mediate interactions between chromosomes and microtubules.
Genogeography and Immune Epitope Characteristics of Hepatitis B Virus Genotype C Reveals Two Distinct Types: Asian and Papua-Pacific

Distribution of hepatitis B virus (HBV) genotypes/subgenotypes is geographically and ethnologically specific. In the Indonesian archipelago, HBV genotype C (HBV/C) is prevalent with high genome variability, reflected by the presence of 13 of currently existing 16 subgenotypes. We investigated the association between HBV/C molecular characteristics with host ethnicity and geographical distribution by examining various subgenotypes of HBV/C isolates from the Asia and Pacific region, with further analysis on the immune epitope characteristics of the core and surface proteins. Phylogenetic tree was constructed based on complete HBV/C genome sequences from Asia and Pacific region, and genetic distance between isolates was also examined. HBV/C surface and core immune epitopes were analyzed and grouped by comparing the amino acid residue characteristics and geographical origins. Based on phylogenetic tree and geographical origins of isolates, two major groups of HBV/C isolates—East-Southeast Asia and Papua-Pacific—were identified. Analysis of core and surface immune epitopes supported these findings with several amino acid substitutions distinguishing the East-Southeast Asia isolates from the Papua-Pacific isolates. A west-to-east gradient of HBsAg subtype distribution was observed with adrq+ prominent in the East and Southeast Asia and adrq- in the Pacific, with several adrq-indeterminate subtypes observed in Papua and Papua New Guinea (PNG). This study indicates that HBV/C isolates can be classified into two types, the Asian and the Papua-Pacific, based on the virus genome diversity, immune epitope characteristics, and geographical distribution, with Papua and PNG as the molecular evolutionary admixture region in the switching from adrq+ to adrq-.
Privacy-Preserving Biometric Authentication: Challenges and Directions

An emerging direction for authenticating people is the adoption of biometric authentication systems. Biometric credentials are becoming increasingly popular as a means of authenticating people due to the wide range of advantages that they provide with respect to classical authentication methods (e.g., password-based authentication). The most characteristic feature of this authentication method is the naturally strong bond between a user and her biometric credentials. This very same advantageous property, however, raises serious security and privacy concerns in case the biometric trait gets compromised. In this article, we present the most challenging issues that need to be taken into consideration when designing secure and privacy-preserving biometric authentication protocols. More precisely, we describe the main threats against privacy-preserving biometric authentication systems and give directions on possible countermeasures in order to design secure and privacy-preserving biometric authentication protocols.
Involvement of IbeA in Meningitic Escherichia coli K1‐Induced Polymorphonuclear Leukocyte Transmigration Across Brain Endothelial Cells

Transmigration of neutrophil [polymorphonuclear neutrophil (PMN)] across the blood–brain barrier (BBB) is a critical event in the pathogenesis of bacterial meningitis. We have shown that IbeA is able to induce meningitic Escherichia coli invasion of brain microvascular endothelial cells (BMECs), which constitutes the BBB. In this report, we provide evidence that IbeA and its receptor, vimentin, play a key role in E. coli‐induced PMN transmigration across BMEC. In vitro and in vivo studies indicated that the ibeA‐deletion mutant ZD1 was significantly less active in stimulating PMN transmigration than the parent strain E44. ZD1 was fully complemented by the ibeA gene and its product. E. coli‐induced PMN transmigration was markedly inhibited by withaferin A, a dual inhibitor of vimentin and proteasome. These cellular effects were significantly stimulated and blocked by overexpression of vimentin and its head domain deletion mutant in human BMEC, respectively. Our studies further demonstrated that IbeA‐induced PMN migration was blocked by bortezomib, a proteasomal inhibitor and correlated with upregulation of endothelial ICAM‐1 and CD44 expression through proteasomal regulation of NFκB activity. Taken together, our data suggested that IbeA and vimentin contribute to E. coli K1‐stimulated PMN transendothelial migration that is correlated with upregulation of adhesion molecule expression at the BBB.
Oil spill detection based on a superpixel segmentation method for SAR image

In this paper, a rapid oil spill detection approach which still maintains high detection accuracy is presented. The major contribution of the approach is using a superpixel segmentation method to subdivide the target SAR image into many approximate uniform scale pieces and preserves the boundaries well. Furthermore, a novel approach combine space distance, intensity deviation and size information together (SIS) is presented to eliminate the potential false positive, which is convenient and effective meanwhile. The proposed approach performs well and fast in both the synthetic data and RAD ARS AT-1 ScanSAR data which contain verified oil spills. The processing time is about 6s for a 512×512 image.
Image intrinsic values from shading information

Since the pioneer work of Horn, a considerable amount of computer vision research has been done on shape from shading (SFS). The basic idea of SFS is to infer the shape of an object from its shading information in a single image. Since this problem is ill-posed, a number of assumptions have been used extensively in the computer vision community for the SFS problem, such as orthographic projection, Lambertian reflectance model, single light source, and constant surface albedo. In this paper, starting with this typical set of assumptions, we derive new image intrinsic values based on image shading information. We derive these values for a number of reflectance models such as the linear and quadratic models in addition to the popular Lambertian model. We validated the obtained intrinsic values on hundreds of real and synthetic images.
Analyzing the Structure of a Motion Capture Database under a Similarity Metric

The film and video game industries make use of large motion capture databases for creating realistic animations of human motion. Recently, significant research efforts have been devoted to data-driven animation techniques. These techniques allow new, realistic motion sequences to be automatically synthesized from existing motion capture sequences that are similar to the desired motion sequence. Unfortunately, identifying similar motion sequences is a challenging problem since logically similar motion sequences are often not numerically