Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons

Significance Retrotransposons constitute substantial proportions of mammalian genomes and can be harmful when activated ectopically. DNA methylation is the major mechanism for retrotransposon silencing, but we do not know how late preimplantation embryos, which are exceptionally hypomethylated, are protected from retrotransposons. Knockdown of the histone chaperone chromatin assembly factor 1 (CAF-1) resulted in significant up-regulation of retrotransposons (e.g., long interspersed element 1) and mouse embryonic death at morula stage. CAF-1 was responsible for deposition of histone variant H3.1/3.2 and repressive histone marks, including trimethylation of histone H4 on lysine 20 (H4K20me3) and H3K9me3, at retrotransposon regions. Depletion of H4K20me3 or H3K9me3 by knockdown of specific histone methyltransferases resulted in up-regulation of retrotransposons in morulae. Thus, hypomethylated preimplantation mouse embryos are protected by repressive histone modifications mediated by CAF-1. Substantial proportions of mammalian genomes comprise repetitive elements including endogenous retrotransposons. Although these play diverse roles during development, their appropriate silencing is critically important in maintaining genomic integrity in the host cells. The major mechanism for retrotransposon silencing is DNA methylation, but the wave of global DNA demethylation that occurs after fertilization renders preimplantation embryos exceptionally hypomethylated. Here, we show that hypomethylated preimplantation mouse embryos are protected from retrotransposons by repressive histone modifications mediated by the histone chaperone chromatin assembly factor 1 (CAF-1). We found that knockdown of CAF-1 with specific siRNA injections resulted in significant up-regulation of the retrotransposons long interspersed nuclear element 1, short interspersed nuclear element B2, and intracisternal A particle at the morula stage. Concomitantly, increased histone H2AX phosphorylation and developmental arrest of the majority (>95%) of embryos were observed. The latter was caused at least in part by derepression of retrotransposons, as treatment with reverse transcriptase inhibitors rescued some embryos. Importantly, ChIP analysis revealed that CAF-1 mediated the replacement of H3.3 with H3.1/3.2 at the retrotransposon regions. This replacement was associated with deposition of repressive histone marks, including trimethylation of histone H3 on lysine 9 (H3K9me3), H3K9me2, H3K27me3, and H4K20me3. Among them, H4K20me3 and H3K9me3 seemed to play predominant roles in retrotransposon silencing, as assessed by knockdown of specific histone methyltransferases and forced expression of unmethylatable mutants of H3.1K9 and H4K20. Our data thus indicate that CAF-1 is an essential guardian of the genome in preimplantation mouse embryos by deposition of repressive histone modifications via histone variant replacement.
A vibration-based electromagnetic energy harvester system with highly efficient interface electronics

This paper presents a vibration-based electromagnetic (EM) energy harvester system utilizing novel and highly efficient interface electronics. The energy harvesting module up-converts the environmental low frequency vibrations for increased AC power output. The interface circuit employs a boot-strap technique to reduce the threshold voltage of the rectifiers further increasing the power conversion efficiency of the overall system. The complete system, composed of an energy harvester module, and a compact 0.35 µm CMOS IC, was fully validated. It is capable of powering a 1.5V, 15µA load with 65% conversion efficiency, and 5% ripple, at an external vibration frequency of 10Hz. The recorded efficiency is the highest achieved value for vibration-based EM energy harvesters with passive rectification to the best of our knowledge.
The Factoid Queries Collection

We present a collection of over 15,000 queries, issued to commercial web search engines, whose answer is a single fact. The collection was produced based on queries landing on questions within a large community question answering website, each with a best answer no longer than 3 words and an explicit reference to a Wikipedia page. We describe the collection generation process and provide a variety of descriptive characteristics, demonstrating the collection? s uniqueness compared to existing datasets and its potential use for research of factoid question answering and retrieval.
Quality of life and measures of quality of life in patients with neuromuscular disorders

In this review we present an overview of quality of life (QOL) and QOL measures in neuromuscular disorders. We discuss the characteristics of QOL measures used in neuromuscular research, highlighting differences between generic versus disease‐specific and global versus health‐related QOL instruments. The phenomenon of response shift is reviewed. Commonly used QOL instruments are reviewed for amyotrophic lateral sclerosis, muscle diseases, myasthenia gravis, and polyneuropathy. We also review some of what is known about QOL for patients with these neuromuscular disorders. Muscle Nerve 46: 9–25, 2012
Hybrid Feature of Tamura Texture Based Image Retrieval System

Storage and retrieval of images in such libraries has become a real demand in industrial, medical, and other applications. Content-based image indexing and retrieval (CBIR) is considered as a solution. In such systems, in the indexing algorithm, some features are extracted from every picture and stored as an index vector. We apply tamura texture features on digital images and compute the low order statistics from the transformed images. Images are then represented using the extracted texture features. These feature combination integrate the pixels spatial distribution information into a numerical value. The experiment results show that this method is still effective when the data scale is very large, and it has superior scalability than traditional indexing methods. Keywords— CBIR, Image Retrieval, Image indexing
Computing utilization rate of Rate Monotonic scheduling mechanism in Controller Area Network

Utilization rate of hard real-time scheduling mechanism has an important effect on the schedulibility of real-time system like Controller Area Network. In this paper, based on the technique named bit-stuff and the maximum transmission time of frame we prove that if the priority of messages flow is allotted by Rate Monotonic (RM) policy and if requested capacity of CAN is not above 30% then time deadlines of all messages flow are met.
Facilitating interactive ADR signal detection and analysis with data cube technology

Adverse Drug Reaction (ADR) is one of the most important issues on drug safety assessment. In the past few years, many approaches that utilizes statistical and data mining methods for detecting ADRs has been proposed. However, most of these stand-alone methods are tedious and inconvenient to users and the processes of exploration are timeconsuming. In a previous work, we have proposed an interactive system platform for ADR detection, which by integrating the ADR data warehouse and innovative frequent pattern mining techniques, can support multidimensional analysis of ADRs. In this paper, we enhance the performance of the platform further. Specifically, a data cube-based method for facilitating interactive detection of suspected ADR signals is proposed.
Follow the information and you'll find a librarian

Librarians' career tracks are changing as the basic methods of storing and accessing information are changing. Les trajectoires professionnelles des bibliothecaires evoluent en meme temps que les methodes de stockage et d'acces a l'information, mais les principes de la bibliotheconomie restent les memes : la ou il y a de l'information, vous trouverez un bibliothecaire. Leur role dans l'utilisation et le developpement de l'internet, et en particulier du Web, comporte deux defis : bâtir une bibliotheque electronique de facon a guider les utilisateurs dans leur exploration du reseau, et s'impliquer dans l'etablissement de normes universelles pour le developpement a long terme du Web.
Stem Cell Therapy for Neurodegenerative Diseases

Aging-related neurodegenerative disorders mainly include Alzheimer’s disease (AD) and Parkinson’s disease (PD). AD is the most common form of dementia, which is one of the major causes of disability and dependency in the elderly. Since the pathologic characteristics of AD are beta-amyloid (Abeta) plaques and neurofibrillary tangles (NFT) [1], depleting Abeta should be a useful therapy for AD.
Direct measurement of CD8+ T cell responses in macaques infected with simian immunodeficiency virus.

The simian immunodeficiency virus (SIV) macaque model system has been used extensively to study AIDS pathogenesis and to test candidate vaccines for their ability to protect against homologous or heterologous challenge with pathogenic SIV or SHIV. Recent studies suggest that stimulation of HIV-1-specific CTL responses is important for effective vaccination against HIV-1. While quantitative measurements of SIV-specific cytotoxic T lymphocyte (CTL) responses have been facilitated by the use of tetrameric peptide complexes, this technique is currently limited to the study of Mamu-A*01-positive rhesus macaques. Furthermore, very few SIV-specific CTL epitopes have been identified, and there is limited identification of other MHC alleles in macaques. In this study, cytokine flow cytometry (CFC) was used to quantify SIV-specific CD8+ antigen-reactive T cells in macaques infected with SIV. We found a strong correlation (r = 0.96, P < 0.001) between CD8+ antigen-reactive T cells stained with the Mamu-A*01 p11C, C-M tetramer and production of intracellular TNF-alpha in the CFC assay. Furthermore, the CFC assay was used to identify a novel SIV-specific CTL epitope in Envelope (SIV Env, a.a. 486-494, sequence AEVAELYRL). The use of the CFC assay facilitates the study of antigen-reactive T cell responses in SIV infection and vaccination.
Increasing suppression of saccade-related transients along the human visual hierarchy

A key hallmark of visual perceptual awareness is robustness to instabilities arising from unnoticeable eye and eyelid movements. In previous human intracranial (iEEG) work (Golan et al., 2016) we found that excitatory broadband high-frequency activity transients, driven by eye blinks, are suppressed in higher-level but not early visual cortex. Here, we utilized the broad anatomical coverage of iEEG recordings in 12 eye-tracked neurosurgical patients to test whether a similar stabilizing mechanism operates following small saccades. We compared saccades (1.3°-3.7°) initiated during inspection of large individual visual objects with similarly-sized external stimulus displacements. Early visual cortex sites responded with positive transients to both conditions. In contrast, in both dorsal and ventral higher-level sites the response to saccades (but not to external displacements) was suppressed. These findings indicate that early visual cortex is highly unstable compared to higher-level visual regions which apparently constitute the main target of stabilizing extra-retinal oculomotor influences.
Peak-to-average power ratio reduction in alamouti multi-input??multi-output orthogonal frequency division multiplexing systems without side information using phase offset based-partial transmit sequence scheme

In this study, a novel phase offset-based partial transmit sequence (PTS) scheme is proposed to reduce the peak-to-average power ratio (PAPR) in Alamouti coded multi-input-multi-output orthogonal frequency division multiplexing systems, and its key idea is that different phase rotation sequences are multiplied by their corresponding phase offsets at the transmitter. Moreover, a minimum Euclidean distance decoder is proposed to recover the phase rotation sequences at the receiver. The theoretical analysis and simulation results show that the proposed PTS scheme could offer good performances of both the bit error rate and the PAPR reduction without transmitting the side information, resulting in the increase of the data rate.
An Investigation of Niche and Species Formation in Genetic Function Optimization

Niche formation allows evolutionary algorithms to be used when the location and maintenance of multiple solutions appertaining to diverse areas of the phenotypic space is required. Consequently the application field can be extended to multiobjective optimization, simulation of complex systems and multimodal function optimization. In this later case a conventional evolutionary algorithm tends to group the final population around the fittest individual. Thus, other areas of interest in the search process are lost. Niching methods permits the maintenance of solutions located around these areas of interest. This contribution briefly describe problems preventing niche formation in conventional genetic algorithms, a crowding method for niche formation and analysis of results when optimizing two multimodal functions.
Joint thresholding and quantizer selection for compression of medical ultrasound images in the wavelet domain

This paper introduces a simple and efficient technique for compression of medical ultrasound (US) images in the wavelet domain. The statistics of subband wavelet coefficients are modelled using the generalized Gaussian distribution (GGD). By exploiting these statistics, a uniform scalar quantizer is designed which adapts very well to the changing statistics of the signal across various subbands and scales. To increase the quantization performance, a threshold is chosen adaptively to zero-out the insignificant wavelet coefficients in the detail subbands before quantization. A distinctive feature of the proposed technique is that it unifies the two approaches to image adaptive coding: rate-distortion (R-D) optimized quantizer selection and R-D optimal thresholding, in order to increase the compression performance of the coder. The operational R-D criterion used for joint optimization is derived in the minimum description length (MDL) framework. The experimental results show that the joint R-D optimization leads to significant improvement in the compression performance of the proposed coder, named JTQ-WV, over the best state-of-the-art image coder, SPIHT. For example, the coding of US images at 0.25 bpp by JTQ-WV yields a PSNR gain of 1.0 dB over the benchmark SPIHT.
CSSWare: An Actor-Based Middleware for Mobile Crowd-Sourced Services

The growing ubiquity of personal connected devices -- each with a number of sensors -- has created the opportunity for a wide range of crowd-sourced services. Although the programming required for offering new services can be significant if done from scratch, we identify core communication mechanisms underlying such services, and implement them in a middleware, CSSWare. Service designers can then launch novel services over CSSWare by simply plugging in small pieces of service-specific code. This paper describes the key multi-origin communication mechanism underlying many crowd-sourced services, presents our design and implementation of CSSWare, an actor-based middleware, and evaluates it programmability benefits and scalability.
Miskito Slaving and Culture Contact: Ethnicity and Opportunity in an Expanding Population

During the colonial era the Miskito Indians of eastern Nicaragua established fruitful commercial ties with English colonists in eastern Central America and Jamaica. Among the diverse items they traded with the Europeans were captives obtained by slave raids into surrounding areas. For Miskito society slaving also coincided with demographic growth and ecological readaptation. For English settlers in Jamaica, indigenes from Central America provided a cheap source of labor early in the transition to a plantation economy. Comparable situations existed in the southeastern United States and the Orinoco region of South America, where native groups friendly with the British attacked other indigenous peoples with the intent to capture slaves for sale to foreign colonists.
Suppression of complex I gene expression induces optic neuropathy

Optic nerve degeneration is a feature common to diseases with mutations in genes that encode complex I of the respiratory chain. Vulnerability of this central nervous system tract is a mystery, because of the paucity of animal models used to investigate effects of the mutated DNA in tissues rather than isolated in cultured cells. Using a ribozyme designed to degrade the mRNA encoding a critical nuclear‐encoded subunit gene of complex I (NDUFA1), we tested whether oxidative phosphorylation deficiency can recapitulate the optic neuropathy of mitochondrial disease. Injection of adenoassociated virus expressing this ribozyme led to axonal destruction and demyelination, the hallmarks of Leber hereditary optic neuropathy. Ann Neurol 2003
Evidence Supporting a Zoonotic Origin of Human Coronavirus Strain NL63

ABSTRACT The relationship between bats and coronaviruses (CoVs) has received considerable attention since the severe acute respiratory syndrome (SARS)-like CoV was identified in the Chinese horseshoe bat (Rhinolophidae) in 2005. Since then, several bats throughout the world have been shown to shed CoV sequences, and presumably CoVs, in the feces; however, no bat CoVs have been isolated from nature. Moreover, there are very few bat cell lines or reagents available for investigating CoV replication in bat cells or for isolating bat CoVs adapted to specific bat species. Here, we show by molecular clock analysis that alphacoronavirus (α-CoV) sequences derived from the North American tricolored bat (Perimyotis subflavus) are predicted to share common ancestry with human CoV (HCoV)-NL63, with the most recent common ancestor between these viruses occurring approximately 563 to 822 years ago. Further, we developed immortalized bat cell lines from the lungs of this bat species to determine if these cells were capable of supporting infection with HCoVs. While SARS-CoV, mouse-adapted SARS-CoV (MA15), and chimeric SARS-CoVs bearing the spike genes of early human strains replicated inefficiently, HCoV-NL63 replicated for multiple passages in the immortalized lung cells from this bat species. These observations support the hypothesis that human CoVs are capable of establishing zoonotic-reverse zoonotic transmission cycles that may allow some CoVs to readily circulate and exchange genetic material between strains found in bats and other mammals, including humans.
Online movement prediction in a robotic application scenario

Current movement prediction systems based on electroencephalography were mainly developed and evaluated in highly controlled scenarios, in which subjects concentrate only on the desired task with as few as possible disturbing sources present. However, it has not been addressed sufficiently how the suggested methods perform in more complex and uncontrolled environments. In this work we predict arm movements online in a robotic teleoperation scenario and present a completely online running methodology. The system is evaluated on ten sessions from three subjects. Evaluation criteria are the overall classification performance and the success in predicting an upcoming movement in the application. Our results confirm that it is possible to predict movements in less restricted applications motivating the transfer of these methods to real world applications.
NCCAM-industry colloquium: exploring opportunities for collaboration.

On May 14, 2001, the National Center for Complementary and Alternative Medicine (NCCAM) convened a colloquium to begin a dialogue with two key groups: (1) industrial stakeholders that supply raw materials and manufacture and market complementary and alternative medicine (CAM) therapeutics (e.g., dietary supplements and other biologically based treatments)*; and (2) organizations that develop and apply standards to determine the identity, quality, and safety of these products. Chaired by Myron S. Weinberg, chairman of The Weinberg Group, Inc., the meeting was planned jointly with representatives of stakeholder groups and with Paul M. Coates, director of the Office of Dietary Supplements at the National Institutes of Health (NIH), Bethesda, Maryland. The NCCAM convened the colloquium because, as outlined in the NCCAM’s first 5-year strategic plan, “Expanding Horizons of Healthcare,” (see http://nccam.nih.gov/strategic) clinical research is the NCCAM’s highest research priority and because the Center seeks to leverage its intellectual and financial resources via collaborations. The goal of the meeting was to begin a dialogue regarding how the NCCAM and industry can work together to evaluate definitively CAM therapeutic products for composition, safety, and efficacy. More than 200 representatives of industry, members of the CAM and conventional research communities, third-party payers, consumers, organizations that produce and disseminate compendia of information; regulatory law personnel; representatives of government agencies; CAM and conventional practitioners; members of the media; and members of NCCAM advisory groups attended, thus ensuring input from the broad stakeholder community. In a series of sessions, speakers presented background material to contribute to the discussions of two panels charged with address-
Comments on "A New Product Growth for Model Consumer Durables The Bass Model"

The paper that I authored and that was published in Management Science in 1969 (Bass 1969) has become widely known as the "Bass Model" (see Morrison and Raju 2004). The model of the diffusion of new products and technologies developed in the paper is one of the most widely applied models in management science. It was especially gratifying for me to learn that INFORMS members have voted the "Bass Model" paper as one of the Top 10 Most Influential Papers published in the 50-year history of Management Science in connection with the 50th anniversary of the journal. In this commentary on the paper I shall discuss some background and history of the development of the paper, the reasons why the model has been influential, some important extensions of the model, some examples of applications, and some examples of the frontiers of research involving the Bass Model. In the current period, in which there is much discussion about the marketing of applications of management science methods and practice, I hope that this commentary will be useful in providing insights about some of the properties of models that will be applied.