Miracle-dz/UniFAR-FTUs huggingface dataset:
Explorer PRC 1 and PRC 2 Are Not Required for Targeting of H 2 A . Z to Developmental Genes in Embryonic Stem Cells

The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner. Citation: Illingworth RS, Botting CH, Grimes GR, Bickmore WA, Eskeland R (2012) PRC1 and PRC2 Are Not Required for Targeting of H2A.Z to Developmental Genes in Embryonic Stem Cells. PLoS ONE 7(4): e34848. doi:10.1371/journal.pone. 0034848 Editor: Robert Feil, CNRS, France Received October 8, 2011; Accepted March 9, 2012; Published April 9, 2012 Copyright: 2012 Illingworth et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Medical Research Council, UK and by grant BB/H008500/1 from the BBSRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: W.Bickmore@hgu.mrc. ac.uk (WB); Ragnhild.Eskeland@imbv.uio. no (RE) ¤ Current address: Department of Molecular Biosciences, University of Oslo, Oslo, Norway
Rate-based versus distortion-based optimal joint source-channel coding

We consider a joint source-channel coding system that protects an embedded wavelet bitstream against noise using a finite family of channel codes with error detection and error correction capability. The performance of this system may be measured by the expected distortion or by the expected number of correctly received source bits subject to a target total transmission rate. Whereas a rate-based optimal solution can be found in linear time, the computation of a distortion-based optimal solution is prohibitive. Under the assumption of the convexity of the operational distortion-rate function of the source coder, we give a lower bound on the expected distortion of a distortion-based optimal solution that depends only on a rate-based optimal solution. Then we show that a distortion-based optimal solution provides a stronger error protection than a rate-based optimal solution and exploit this result to reduce the time complexity of the distortion-based optimization. Finally, we propose a fast iterative improvement algorithm that starts from a rate-based optimal solution and converges to a local minimum of the expected distortion. Experimental results for a binary symmetric channel with the SPIHT coder and JPEG 2000 show that our lower bound is close to optimal. Moreover, the solution given by our local search algorithm has about the same quality as a distortion-based optimal solution, whereas its complexity is much lower than that of the previous best solution.
Emotion Detection from Text: Survey

: This paper discusses some relevant work of emotion detection from text which is a main field in affecting computing and artificial intelligence field. Artificial intelligence is not only the ability for a machine to think or interact with end user smartly but also to act humanly or rationally so emotion detection from text plays a key role in human-computer interaction. It has attracted the attention of many researchers due to the great revolution of emotional data available on social and web applications of computers and much more in mobile devices. This survey mainly collects history of unsupervised emotion detection from text.
Predicting Invariant Nodes in Large Scale Semantic Graphs

We are interested in understanding and predicting how large knowledge graphs change over time. An important subproblem is predicting which nodes within the graph won’t have any edges deleted or changed (what we call add-only nodes). Predicting add-only nodes correctly has practical importance, as such nodes can then be cached or represented using a more efficient data structure. This paper presents a logistic regression approach using attribute-values as features that achieves 95%+ precision on DBpedia yearly changes trained using Apache Spark. It concludes by outlining how we plan to use these models for Natural Language Generation.
Detailed Characterization of Al/Ice Propellants

Several experimental and theoretical studies over the last few decades have addressed the aluminum-water reaction. Practical applications making use of the heat generated and the products of the aluminum water reaction can be grouped into two main categories: power generation and propulsion. Power generation is typically achieved by feeding the hydrogen produced into a fuel cell. In propulsion applications, the products of the reaction burn at high pressure and are expelled at high velocity through a converging/diverging nozzle. With a focus on propulsion applications, we presented in a previous paper the results of nanoaluminum/ice (ALICE) small-scale static experiments. We showed that ALICE mixtures are stable, as well as insensitive to electrostatic discharge, impact and shock. Since then, a sounding rocket was successfully launched, powered by the ALICE propellant; the first time a propellant of this type has been flown. Although this formulation is not a practical formulation, the flight established a stepping stone for better performing propellant mixtures. Hydrogen peroxide and micron aluminum mixtures are under development and have shown promise to improve performance. Additional characterization with several nano energetic materials and bi-modal mixtures is also reported.
Concept-Map-Based Multi-Document Summarization using Concept Coreference Resolution and Global Importance Optimization

Concept-map-based multi-document summarization is a variant of traditional summarization that produces structured summaries in the form of concept maps. In this work, we propose a new model for the task that addresses several issues in previous methods. It learns to identify and merge coreferent concepts to reduce redundancy, determines their importance with a strong supervised model and finds an optimal summary concept map via integer linear programming. It is also computationally more efficient than previous methods, allowing us to summarize larger document sets. We evaluate the model on two datasets, finding that it outperforms several approaches from previous work.
PASSAGE OF PROPERTY ( gw ) FROM TWO OPERATORS TO THEIR TENSOR PRODUCT

A Banach space operator satisfies property (gw) if the complement of its B-Weyl essential approximate point spectrum in its approximate point spectrum is the set of isolated eigenvalues of the operator. We give necessary and/or sufficient conditions ensuring the passage of property (gw) from two Banach space operators A and B to their tensor product. In particular, we present a revised version of Theorem 2.3 in [20].
Light-induced atomic desorption for loading a sodium magneto-optical trap

We report studies of photon-stimulated desorption, also known as light-induced atomic desorption, of sodium atoms from a vacuum-cell glass surface used for loading a magneto-optical trap (MOT). Fluorescence detection was used to record the trapped atom number and the desorption rate. We observed a steep wavelength dependence of the desorption process above 2.6 eV photon energy, a result significant for estimations of sodium vapor density in the lunar atmosphere. Our data fit well to a simple model for the loading of the MOT dependent only on the sodium desorption rate and residual gas density. Up to 3.7x10{sup 7} Na atoms were confined under ultrahigh-vacuum conditions, creating promising loading conditions for a vapor-cell-based atomic Bose-Einstein condensate of sodium.
Privacy leakages in Smart Home wireless technologies

The concept of Smart Home where appliances, sensors, actuators, displays and computing resources are connected and interact to support the life of the citizen is being increasingly researched. In this context, the Wi-Fi communication technology has grown to become the de-facto standard for data communications in Smart Home environments, with cordless telephony being dominated by the DECT protocol. Even though both technologies incorporate sets of security features aimed at securing the confidentiality and integrity of the communications, the nature and the design of both radio-frequency protocols make them vulnerable, up to a certain extent, to privacy leakages through traffic analysis attacks. In this paper we explore the information leakage vulnerabilities inherent to these technologies and their potential impact on citizens' privacy in the context of the Smart Home. We demonstrate how the websites visited by a smart device can be inferred by applying machine learning and pattern matching techniques to eavesdropped encrypted traffic.
Association between polycystic ovary syndrome ( PCOS ) and CYP 11 A 1 polymorphism in Hainan , China : a case-control study

Polycystic ovary syndrome (PCOS) is one of the most common female endocrine disorders and a leading cause of female subfertility. The cytochrome P-450 11A1 (CYP11A1) gene encodes the key enzyme that catalyzes the initial and rate-limiting step in steroid hormone synthesis. In this study, the associations between seven single nucleotide polymorphisms (SNPs) in CYP11A1 and PCOS susceptibility were examined. Seven SNPs in CYP11A1 were genotyped using the MassARRAY iPLEX platform in 285 PCOS patients and 299 control individuals. Associations between the SNPs and the risk of PCOS were tested using various genetic models (co-dominant, dominant, recessive, and additive). Logistic regression models were used to derive odds ratios (ORs) and 95% confidence intervals. By χ2 test, the differences of genotype frequencies of rs4887139 (P = 0.035) and rs4886595 (P = 0.046) were significant statistically difference between PCOS patients and controls under recessive model. In the genetic model analyses, we also found that the genotype “GG” of rs4887139 (P = 0.035) and genotype “CC” of rs4886595 (P = 0.04) were significant associated with increased the risk of PCOS by recessive model. We found four SNPs (rs12917295, rs11632698, rs1484215, and rs6495096) constructed four haplotypes (“CACG”, “CATC”, “CACC”, and “GGCC”) in the CYP11A1 gene and none of the haplotype was significantly associated with risk of PCOS.
A multi-landing pad DNA integration platform for mammalian cell engineering

Abstract Engineering mammalian cell lines that stably express many transgenes requires the precise insertion of large amounts of heterologous DNA into well-characterized genomic loci, but current methods are limited. To facilitate reliable large-scale engineering of CHO cells, we identified 21 novel genomic sites that supported stable long-term expression of transgenes, and then constructed cell lines containing one, two or three ‘landing pad’ recombination sites at selected loci. By using a highly efficient BxB1 recombinase along with different selection markers at each site, we directed recombinase-mediated insertion of heterologous DNA to selected sites, including targeting all three with a single transfection. We used this method to controllably integrate up to nine copies of a monoclonal antibody, representing about 100 kb of heterologous DNA in 21 transcriptional units. Because the integration was targeted to pre-validated loci, recombinant protein expression remained stable for weeks and additional copies of the antibody cassette in the integrated payload resulted in a linear increase in antibody expression. Overall, this multi-copy site-specific integration platform allows for controllable and reproducible insertion of large amounts of DNA into stable genomic sites, which has broad applications for mammalian synthetic biology, recombinant protein production and biomanufacturing.
Symptoms of anxiety and depression among colorectal cancer survivors from the population‐based, longitudinal PROFILES Registry: Prevalence, predictors, and impact on quality of life

The aims of this study were to prospectively assess symptoms of anxiety and depression among survivors of colorectal cancer (CRC), to compare these survivors with a normative population, and to identify subgroups at risk for experiencing symptoms of anxiety and/or depression across a 4‐year time period. Also, the impact on health‐related quality of life (HRQOL) was studied.
Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment

ABSTRACT Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae. The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H2S, S0, and S2O32−) and electron acceptors (O2 and NO3−) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments.
High throughput metabolic screen of Physcomitrella transformants

Abstract A large-scale metabolic screen was performed for 51,180 targeted knockout mutants of the haploid moss Physcomitrella patens (Hedw.) Bruch & Schimp. The growth ability of each mutant was compared to the wild type. Plants were cultured on a minimal medium which contained only macroelements, as well as on a supplemented medium, additionally containing microelements, glucose, vitamins, ammonium tartrate, adenine, peptone and Na-palmitic acid. The screen resulted in the identification of 20 (0.04 %) auxotrophs. Medium supplementation tests were performed for five auxotrophs, which showed no growth on minimal medium, but were rescued on supplemented medium. One vitamin-deficient mutant was identified as p-aminobenzoic acid auxotroph, three plants were nitrate assimilation deficient mutants and one transformant showed undefined growth requirements. The screen resulted further in the identification of two physiological mutants, exhibiting an albino phenotype on minimal medium but a green wild type phenotype on the supplemented medium. The culture of both albinos under low light intensities could not prevent bleaching, revealing that the missing production of chlorophyll was not caused by light sensitivity. Astonishingly, the supplementation of the minimal medium with selected compounds of the supplemented medium did also not prevent bleaching. Moreover, both mutants produced green protonemata, even if single substances of the supplemented medium were lacking. It was concluded that a complex network of interactions related to photosynthesis in Physcomitrella was disturbed. This is the first detailed study of auxotrophic and albino Physcomitrella mutants produced by transformation-mediated gene disruption. The described physiological mutants provide valuable resources for the identification of essential gene functions of plant metabolism.
Guidelines to Optimize Survival and Migration Capacities of Equine Mesenchymal Stem Cells

Background: Although mesenchymal stem cell (MSC) therapy is commonly being used in veterinary medicine, no specific guidelines are described to guarantee an optimal cell survival and migration. However, this is indispensable in order to assure an optimal clinical use. Methods: In the present study, equine peripheral blood (PB)-derived MSCs were isolated and characterized. In order to determine the optimal parameters for long-term cryopreservation, the effects of different dimethyl sulfoxide (DMSO) concentrations (5-20%) and thawing methods (temperature-controlled or hand-thawed) on MSC viability were evaluated by means of trypan blue staining. Afterwards, MSC storage was evaluated for 12 months using only 10% of DMSO as a cryoprotectant without rate-controlled freezing. Then, the influence of frequently used anaesthetics and injectable gels on MSC viability was assessed. Finally, the migration capacity of MSCs through hyaluronic acid at different concentrations was assessed. Results: Firstly, we demonstrated that the DMSO concentration and the thawing method had no considerable influence on MSC viability within the 4 hour evaluation after thawing. Secondly, anaesthetics were highly cytotoxic and only 10% of the MSCs survived 3 hours of their presence. Hyaluronic acid- and glycosaminoglycan-based gels were compatible with MSCs and allowed a high cell survival (more than 90%) within 48 hours of follow-up. However, in a polyacrylamide gel, approximately 80% of the MSCs died within 48 hours. Finally, the concentration of the gel influenced the migration capacity of the MSCs. Indeed, only 60% of the MSCs in 20mg/ml of hyaluronic acid attached to the underlying surface within 48 hours, whereas almost 100% of the MSCs in 10mg/ml of the same substance were able to migrate through the gel. Conclusion: The present study reports practical guidelines for the clinical application of equine PB-derived MSCs.
Fighting a Losing Battle: Vigorous Immune Response Countered by Pathogen Suppression of Host Defenses in the Chytridiomycosis-Susceptible Frog Atelopus zeteki

The emergence of the disease chytridiomycosis caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) has been implicated in dramatic global amphibian declines. Although many species have undergone catastrophic declines and/or extinctions, others appear to be unaffected or persist at reduced frequencies after Bd outbreaks. The reasons behind this variance in disease outcomes are poorly understood: differences in host immune responses have been proposed, yet previous studies suggest a lack of robust immune responses to Bd in susceptible species. Here, we sequenced transcriptomes from clutch-mates of a highly susceptible amphibian, Atelopus zeteki, with different infection histories. We found significant changes in expression of numerous genes involved in innate and inflammatory responses in infected frogs despite high susceptibility to chytridiomycosis. We show evidence of acquired immune responses generated against Bd, including increased expression of immunoglobulins and major histocompatibility complex genes. In addition, fungal-killing genes had significantly greater expression in frogs previously exposed to Bd compared with Bd-naïve frogs, including chitinase and serine-type proteases. However, our results appear to confirm recent in vitro evidence of immune suppression by Bd, demonstrated by decreased expression of lymphocyte genes in the spleen of infected compared with control frogs. We propose susceptibility to chytridiomycosis is not due to lack of Bd-specific immune responses but instead is caused by failure of those responses to be effective. Ineffective immune pathway activation and timing of antibody production are discussed as potential mechanisms. However, in light of our findings, suppression of key immune responses by Bd is likely an important factor in the lethality of this fungus.
Stationary graph processes: Parametric power spectral estimation

Advancing a holistic theory of networks and network processes requires the extension of existing results in the processing of time-varying signals to signals supported on graphs. This paper focuses on the definition of stationarity and power spectral density for random graph signals, generalizes the concepts of autoregressive and moving average random processes to the graph domain, and investigates their parametric spectral estimation. Theoretical and algorithmic results are complemented with numerical tests on synthetic and real-world graphs.
From Talking and Listening Robots to Intelligent Communicative Machines

It is a popular view that the future will be inhabited by intelligent talking and listening robots with whom we shall converse using the full palette of linguistic expression available to us as human beings. Of course, recent technical and engineering developments such as Siri would appear to suggest that important steps are being made in that direction – and indeed they are. However, it is argued here that we need to go far beyond our current capabilities and understanding towards a more integrated perspective; simply interfacing state-of-the-art speech technology with a state-of-the-art robot is very unlikely to lead to effective human-robot interaction. We need to move from developing robots that simply talk and listen to evolving intelligent communicative machines that are capable of truly understanding human behavior, and this means that we need to look beyond speech, beyond words, beyond meaning, beyond communication, beyond dialog and beyond one-off interactions.