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Showing papers by "Russian Academy of Sciences published in 2017"


Proceedings ArticleDOI
21 Jul 2017
TL;DR: A unified implementation of the Faster R-CNN, R-FCN and SSD systems is presented and the speed/accuracy trade-off curve created by using alternative feature extractors and varying other critical parameters such as image size within each of these meta-architectures is traced out.
Abstract: The goal of this paper is to serve as a guide for selecting a detection architecture that achieves the right speed/memory/accuracy balance for a given application and platform. To this end, we investigate various ways to trade accuracy for speed and memory usage in modern convolutional object detection systems. A number of successful systems have been proposed in recent years, but apples-toapples comparisons are difficult due to different base feature extractors (e.g., VGG, Residual Networks), different default image resolutions, as well as different hardware and software platforms. We present a unified implementation of the Faster R-CNN [30], R-FCN [6] and SSD [25] systems, which we view as meta-architectures and trace out the speed/accuracy trade-off curve created by using alternative feature extractors and varying other critical parameters such as image size within each of these meta-architectures. On one extreme end of this spectrum where speed and memory are critical, we present a detector that achieves real time speeds and can be deployed on a mobile device. On the opposite end in which accuracy is critical, we present a detector that achieves state-of-the-art performance measured on the COCO detection task.

2,484 citations


Journal ArticleDOI
Bin Zhou1, James Bentham1, Mariachiara Di Cesare2, Honor Bixby1  +787 moreInstitutions (231)
TL;DR: The number of adults with raised blood pressure increased from 594 million in 1975 to 1·13 billion in 2015, with the increase largely in low-income and middle-income countries, and the contributions of changes in prevalence versus population growth and ageing to the increase.

1,573 citations


Journal ArticleDOI
TL;DR: The paper proposes to use the methods of cooperative game theory that highlight not only the link density but also the mechanisms of cluster formation, and suggests two approaches from Cooperative game theory based on the Myerson value and the hedonic games.
Abstract: The paper is devoted to game-theoretic methods for community detection in networks. The traditional methods for detecting community structure are based on selecting denser subgraphs inside the network. Here we propose to use the methods of cooperative game theory that highlight not only the link density but also the mechanisms of cluster formation. Specifically, we suggest two approaches from cooperative game theory: the first approach is based on the Myerson value, whereas the second approach is based on hedonic games. Both approaches allow to detect clusters with various resolution. However, the tuning of the resolution parameter in the hedonic games approach is particularly intuitive. Furthermore, the modularity based approach and its generalizations can be viewed as particular cases of the hedonic games.

1,191 citations


Journal ArticleDOI
TL;DR: Developments and improvements of the ATSAS software suite for analysis of small-angle scattering data of biological macromolecules or nanoparticles are described.
Abstract: ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8 ATSAS release series and highlights the latest developments. These include AMBIMETER, an assessment of the reconstruction ambiguity of experimental data; DATCLASS, a multiclass shape classification based on experimental data; SASRES, for estimating the resolution of ab initio model reconstructions; CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data; SHANUM, to evaluate the useful angular range in measured data; SREFLEX, to refine available high-resolution models using normal mode analysis; SUPALM for a rapid superposition of low- and high-resolution models; and SASPy, the ATSAS plugin for interactive modelling in PyMOL. All these features and other improvements are included in the ATSAS release 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.

1,135 citations


Journal ArticleDOI
TL;DR: The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems.
Abstract: Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in ...

1,065 citations


Journal ArticleDOI
02 Nov 2017-Nature
TL;DR: A genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry finds that heritability of Breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2–5-fold enriched relative to the genome- wide average.
Abstract: Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P < 5 × 10-8. The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.

1,014 citations


Journal ArticleDOI
B. P. Abbott1, Richard J. Abbott1, T. D. Abbott2, M. R. Abernathy3  +719 moreInstitutions (86)
Abstract: The second-generation of gravitational-wave detectors are just starting operation, and have already yielding their first detections. Research is now concentrated on how to maximize the scientific potential of gravitational-wave astronomy. To support this effort, we present here design targets for a new generation of detectors, which will be capable of observing compact binary sources with high signal-to-noise ratio throughout the Universe.

796 citations


Journal ArticleDOI
TL;DR: A comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes is presented, evolutionary scenarios for the independent origin of different class 2 CRISPR–Cas systems from mobile genetic elements are outlined, and an amended classification and nomenclature of CRISpr–Cas is proposed.
Abstract: Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.

740 citations


Journal ArticleDOI
TL;DR: The International Reference Ionosphere model (IRI-2016) as mentioned in this paper is the latest version of the IRI model and includes two new model options for the F2 peak height hmF2 and a better representation of topside ion densities at very low and high solar activities.
Abstract: The paper presents the latest version of the International Reference Ionosphere model (IRI-2016) describing the most important changes and improvements that were included with this version and discussing their impact on the IRI predictions of ionospheric parameters. IRI-2016 includes two new model options for the F2 peak height hmF2 and a better representation of topside ion densities at very low and high solar activities. In addition, a number of smaller changes were made concerning the use of solar indices and the speedup of the computer program. We also review the latest developments toward a Real-Time IRI. The goal is to progress from predicting climatology to describing the real-time weather conditions in the ionosphere.

735 citations


Journal ArticleDOI
TL;DR: In this article, the authors reported the INTernational Gamma-ray Astrophysics Laboratory (INTEGRAL) detection of the short gamma-ray burst GRB 170817A (discovered by Fermi-GBM) with a signal-to-noise ratio of 4.6, and, for the first time, its association with the gravitational waves from binary neutron star (BNS) merging event GW170817 detected by the LIGO and Virgo observatories.
Abstract: We report the INTernational Gamma-ray Astrophysics Laboratory (INTEGRAL) detection of the short gamma-ray burst GRB 170817A (discovered by Fermi-GBM) with a signal-to-noise ratio of 4.6, and, for the first time, its association with the gravitational waves (GWs) from binary neutron star (BNS) merging event GW170817 detected by the LIGO and Virgo observatories. The significance of association between the gamma-ray burst observed by INTEGRAL and GW170817 is 3.2σ, while the association between the Fermi-GBM and INTEGRAL detections is 4.2σ. GRB 170817A was detected by the SPI-ACS instrument about 2 s after the end of the GW event. We measure a fluence of (1.4 ± 0.4 ± 0.6) × 10(−)(7) erg cm(−)(2) (75–2000 keV), where, respectively, the statistical error is given at the 1σ confidence level, and the systematic error corresponds to the uncertainty in the spectral model and instrument response. We also report on the pointed follow-up observations carried out by INTEGRAL, starting 19.5 hr after the event, and lasting for 5.4 days. We provide a stringent upper limit on any electromagnetic signal in a very broad energy range, from 3 keV to 8 MeV, constraining the soft gamma-ray afterglow flux to <7.1 × 10(−)(11) erg cm(−)(2) s(−)(1) (80–300 keV). Exploiting the unique capabilities of INTEGRAL, we constrained the gamma-ray line emission from radioactive decays that are expected to be the principal source of the energy behind a kilonova event following a BNS coalescence. Finally, we put a stringent upper limit on any delayed bursting activity, for example, from a newly formed magnetar.

698 citations


Journal ArticleDOI
TL;DR: This review suggests that the focus of biostimulant research and validation should be upon proof of efficacy and safety and the determination of a broad mechanism of action, without a requirement for a specific mode of action.
Abstract: This review presents a comprehensive and systematic study of the field of plant biostimulants and considers the fundamental and innovative principles underlying this technology. The elucidation of the biological basis of biostimulant function is a prerequisite for the development of science-based biostimulant industry and sound regulations governing these compounds. The task of defining the biological basis of biostimulants as a class of compounds, however, is made more complex by the diverse sources of biostimulants present in the market, which include bacteria, fungi, seaweeds, higher plants, animals and humate-containing raw materials, and the wide diversity of industrial processes utilized in their preparation. To distinguish biostimulants from the existing legislative product categories we propose the following definition of a biostimulant as ‘a formulated product of biological origin that improves plant productivity as a consequence of the novel or emergent properties of the complex of constituents, and not as a sole consequence of the presence of known essential plant nutrients, plant growth regulators, or plant protective compounds’. The definition provided here is important as it emphasizes the principle that biological function can be positively modulated through application of molecules, or mixtures of molecules, for which an explicit mode of action has not been defined. Given the difficulty in determining a ‘mode of action’ for a biostimulant, and recognizing the need for the market in biostimulants to attain legitimacy, we suggest that the focus of biostimulant research and validation should be upon proof of efficacy and safety and the determination of a broad mechanism of action, without a requirement for the determination of a specific mode of action. While there is a clear commercial imperative to rationalize biostimulants as a discrete class of products, there is also a compelling biological case for the science-based development of, and experimentation with biostimulants in the expectation that this may lead to the identification of novel biological molecules and phenomenon, pathways and processes, that would not have been discovered if the category of biostimulants did not exist, or was not considered legitimate.

Journal ArticleDOI
TL;DR: It is shown that the ability of Cpf1 to process its own CRISPR RNA (crRNA) can be used to simplify multiplexed genome editing.
Abstract: Targeting of multiple genomic loci with Cas9 is limited by the need for multiple or large expression constructs. Here we show that the ability of Cpf1 to process its own CRISPR RNA (crRNA) can be used to simplify multiplexed genome editing. Using a single customized CRISPR array, we edit up to four genes in mammalian cells and three in the mouse brain, simultaneously.

Journal ArticleDOI
TL;DR: The Subseasonal to Seasonal (S2S) Prediction research project has been established by the World Weather Research Programme/World Climate Research Programme as discussed by the authors, which is the main deliverable of this project is the establishment of an extensive database containing sub-seasonal (up to 60 days) forecasts, 3 weeks behind real time, and reforecasts from 11 operational centers, modeled in part on the The Observing System Research and Predictability Experiment (THORPEX) Interactive Grand Global Ensemble (TIGGE) database for medium-range forecasts.
Abstract: Demands are growing rapidly in the operational prediction and applications communities for forecasts that fill the gap between medium-range weather and long-range or seasonal forecasts. Based on the potential for improved forecast skill at the subseasonal to seasonal time range, the Subseasonal to Seasonal (S2S) Prediction research project has been established by the World Weather Research Programme/World Climate Research Programme. A main deliverable of this project is the establishment of an extensive database containing subseasonal (up to 60 days) forecasts, 3 weeks behind real time, and reforecasts from 11 operational centers, modeled in part on the The Observing System Research and Predictability Experiment (THORPEX) Interactive Grand Global Ensemble (TIGGE) database for medium-range forecasts (up to 15 days).The S2S database, available to the research community since May 2015, represents an important tool to advance our understanding of the subseasonal to seasonal time range that has been co...

Journal ArticleDOI
Roel Aaij1, Bernardo Adeva2, Marco Adinolfi3, Ziad Ajaltouni4  +818 moreInstitutions (68)
TL;DR: In this article, a test of lepton universality is performed by measuring the ratio of the branching fractions of the B$0$ → K$*0}$ e$+}$ π$−}$ decays, and the ratio is measured in two regions of the dilepton invariant mass squared.
Abstract: A test of lepton universality, performed by measuring the ratio of the branching fractions of the B$^{0}$ → K$^{*0}$ μ$^{+}$ μ$^{−}$ and B$^{0}$ → K$^{*0}$ e$^{+}$ e$^{−}$ decays, $ {R}_{K^{*0}} $ , is presented. The K$^{*0}$ meson is reconstructed in the final state K$^{+}$ π$^{−}$, which is required to have an invariant mass within 100 MeV/c$^{2}$ of the known K$^{*}$(892)$^{0}$ mass. The analysis is performed using proton-proton collision data, corresponding to an integrated luminosity of about 3 fb$^{−1}$, collected by the LHCb experiment at centre-of-mass energies of 7 and 8 TeV. The ratio is measured in two regions of the dilepton invariant mass squared, q$^{2}$, to be $ {R}_{K^{*0}}=\left\{\begin{array}{l}{0.66_{-}^{+}}_{0.07}^{0.11}\left(\mathrm{stat}\right)\pm 0.03\left(\mathrm{syst}\right)\kern1em \mathrm{f}\mathrm{o}\mathrm{r}\kern1em 0.045<{q}^2<1.1\kern0.5em {\mathrm{GeV}}^2/{c}^4,\hfill \\ {}{0.69_{-}^{+}}_{0.07}^{0.11}\left(\mathrm{stat}\right)\pm 0.05\left(\mathrm{syst}\right)\kern1em \mathrm{f}\mathrm{o}\mathrm{r}\kern1em 1.1<{q}^2<6.0\kern0.5em {\mathrm{GeV}}^2/{c}^4.\hfill \end{array}\right. $

Journal ArticleDOI
06 Apr 2017-Nature
TL;DR: In this paper, a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol was developed to study three-dimensional chromatin organization in rare cell types.
Abstract: Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method. Here we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition in mice and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome, but the presence of each feature at a locus varies between cells. At the sub-megabase level, we observed stochastic clusters of contacts that can occur across TAD boundaries but average into TADs. Notably, we found that TADs and loops, but not compartments, are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from that of other interphase cells. An understanding of this zygotic chromatin 'ground state' could potentially provide insights into reprogramming cells to a state of totipotency.

Journal ArticleDOI
TL;DR: In this article, the authors describe the algorithms developed for the production of high-quality global VIIRS night-time lights, which can be used to generate monthly and annual science grade global radiance maps of human settlements with electric lighting.
Abstract: The Visible Infrared Imaging Radiometer Suite VIIRS Day/Night Band DNB collects global low-light imaging data that have significant improvements over comparable data collected for 40 years by the DMSP Operational Linescan System. One of the prominent features of DNB data is the detection of electric lighting present on the Earth’s surface. Most of these lights are from human settlements. VIIRS collects source data that could be used to generate monthly and annual science grade global radiance maps of human settlements with electric lighting. There are a substantial number of steps involved in producing a product that has been cleaned to exclude background noise, solar and lunar contamination, data degraded by cloud cover, and features unrelated to electric lighting e.g. fires, flares, volcanoes. This article describes the algorithms developed for the production of high-quality global VIIRS night-time lights. There is a broad base of science users for VIIRS night-time lights products, ranging from land-use scientists, urban geographers, ecologists, carbon modellers, astronomers, demographers, economists, and social scientists.

Journal ArticleDOI
23 Aug 2017-Nature
TL;DR: A pure culture of a comammox bacterium is isolated and it is shown that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms.
Abstract: A pure culture of the complete nitrifier Nitrospira inopinata shows a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers and genomic potential for alternative metabolisms, probably reflecting an important role in nitrification in oligotrophic environments. Nitrospira inopinata was the first bacterium identified that is capable of catalysing complete ammonia oxidization (referred to as comammox). Holger Daims and colleagues now report a pure culture of this organism, which enabled a characterization of its physiology. The authors find that N. inopinata has a high affinity for ammonia, a low maximum rate of ammonia oxidation, a high growth yield compared to canonical nitrifiers, and the genomic potential for alternative metabolisms. The team compare the nitrification kinetics of N. inopinata to that of four ammonia-oxidizing archaea. The results suggest that N. inopinata is likely to have an important role in nitrification, especially in oligotrophic environments. Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2−) to nitrate (NO3−), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira1,2, which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.

Journal ArticleDOI
Morad Aaboud, Georges Aad1, Brad Abbott2, Jalal Abdallah3  +2845 moreInstitutions (197)
TL;DR: This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton–proton collision data.
Abstract: During 2015 the ATLAS experiment recorded 3.8 fb(-1) of proton-proton collision data at a centre-of-mass energy of 13 TeV. The ATLAS trigger system is a crucial component of the experiment, respons ...

Journal ArticleDOI
TL;DR: The 5th edition of the General Catalogue of Variable Stars (GCVS 5.1) is freely accessible on the Internet as discussed by the authors and the current state of the catalog in its new version is described in detail.
Abstract: Work aimed at compiling detailed catalogs of variable stars in the Galaxy, which has been carried out continuously by Moscow variable-star researchers since 1946 on behalf of the International Astronomical Union, has entered the stage of the publication of the 5th, completely electronic edition of the General Catalogue of Variable Stars (GCVS). This paper describes the requirements for the contents of the 5th edition and the current state of the catalog in its new version, GCVS 5.1. The complete revision of information for variable stars in the constellation Carina and the compilation of the 81st Name-list of Variable Stars are considered as examples of work on the 5th edition. The GCVS 5.1 is freely accessible on the Internet. We recommend the present paper as a unified reference to the 5th edition of the GCVS.

Journal ArticleDOI
Georges Aad1, Alexander Kupco2, P. Davison3, Samuel Webb4  +2888 moreInstitutions (192)
TL;DR: Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS and is exploited to apply a local energy calibration and corrections depending on the nature of the cluster.
Abstract: The reconstruction of the signal from hadrons and jets emerging from the proton–proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.

Journal ArticleDOI
Ryan M Barber1, Nancy Fullman1, Reed J D Sorensen1, Thomas J. Bollyky  +757 moreInstitutions (314)
TL;DR: In this paper, the authors use the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) to improve and expand the quantification of personal health-care access and quality for 195 countries and territories from 1990 to 2015.

Journal ArticleDOI
TL;DR: Future research endeavors in biofuels production should be placed on the search of novel biofuel production species, optimization and improvement of culture conditions, genetic engineering of biofuel-producing species, and effective techniques for mass cultivation of microorganisms.

Journal ArticleDOI
TL;DR: An integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA libraries, with matching Cap Analysis Gene Expression (CAGE) data, is created, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
Abstract: MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

Journal ArticleDOI
TL;DR: In this paper, the authors discuss existing opinions concerning the possibilities of toxicity measurements, high toxicity of heavy-metal compounds, correlation between the structure of a metal compound and its toxicity, biological effect of direct/indirect contacts with metal compounds, and dangers of metal nanoparticles.

Journal ArticleDOI
Roel Aaij1, Bernardo Adeva2, Marco Adinolfi3, Ziad Ajaltouni4  +813 moreInstitutions (52)
TL;DR: In this article, a doubly charmed baryon Ξcc++ was observed in a sample of proton-proton collision data collected by the LHCb experiment at a center-of-mass energy of 13 TeV.
Abstract: A highly significant structure is observed in the Λc+K-π+π+ mass spectrum, where the Λc+ baryon is reconstructed in the decay mode pK-π+. The structure is consistent with originating from a weakly decaying particle, identified as the doubly charmed baryon Ξcc++. The difference between the masses of the Ξcc++ and Λc+ states is measured to be 1334.94±0.72(stat.)±0.27(syst.) MeV/c2, and the Ξcc++ mass is then determined to be 3621.40±0.72(stat.)±0.27(syst.)±0.14(Λc+) MeV/c2, where the last uncertainty is due to the limited knowledge of the Λc+ mass. The state is observed in a sample of proton-proton collision data collected by the LHCb experiment at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 1.7 fb-1, and confirmed in an additional sample of data collected at 8 TeV.

Journal ArticleDOI
TL;DR: A fully ranked, hierarchical classification summarizes recent advances in the phylogeny of the Gastropoda and Monoplacophora.
Abstract: 2,604 names at the rank of subtribe, tribe, subfamily, family and superfamily have been proposed for Recent and fossil gastropods, and another 35 for monoplacophorans. All names are listed in a nomenclator giving full bibliographical reference, date of publication, typification, and their nomenclatural availability and validity under the International Code of Zoological Nomenclature. Another 790 names, established for categories above the familygroup (infraorder to subclass) are listed separately. A fully ranked, hierarchical classification summarizes recent advances in the phylogeny of the Gastropoda and Monoplacophora. In all, the classification recognizes as valid a total of 721 gastropod families, of which 245 are known exclusively as fossils and 476 occur in the Recent with or without a fossil record; and 20 monoplacophoran families, of which 1 only occurs as Recent.Nomenclatural acts in this work: Amberleya bathonica Cox & Arkell, 1950, fixed as type species of Amberleya J. Morris & Lycett, 1851, under Art. 70.3; Ampezzopleura tenuis Nutzel, 1998, fixed as type species of Ampezzopleura Bandel, 1991, under Art. 70.3; Proserpina nitida G. B. Sowerby II, 1839, designated type species of Despoena Newton, 1891; Buccinum glabratum Linnaeus, 1758, designated type species of Dipsaccus H. Adams & A. Adams, 1853; Murex ficus Linnaeus, 1758, designated type species of Ficula Swainson, 1835; Oncomelania hupensis Gredler, 1881, designated type species of Hemibia Heude, 1890; Murex metaxa Delle Chiaje, 1828, fixed as type species of Metaxia Monterosato, 1884 under Art. 70.3; Neridomus anglicus Cox & Arkell, 1950, fixed as type species of Neridomus J. Morris & Lycett, 1851, under Art. 70.3; Navicella clypeolum Recluz, 1843, designated type species of Orthopoma Gray, 1868; Trochus viadrinus M. Schmidt, 1905, fixed as type species of Parataphrus Chavan, 1954 under Art. 70.3; Helix pomatia Linnaeus, 1758, designated type species of Pentataenia A. Schmidt, 1855; Flammulina ponsonbyi Suter, 1897, fixed as type species of Phenacohelix Suter, 1892, under Art. 70.3; Cyrtolites corniculum Eichwald, 1860, fixed as type species of Pollicina Koken, 1895, under Art. 70.3; Purpurina elegantula d'Orbigny, 1850, designated as type species of Purpurina d'Orbigny, 1850, and lectotype of Turbo bellona d'Orbigny, 1850, designated as neotype of Purpurina elegantula; Pyramidella minuscula Monterosato, 1880, fixed as type species of Tiberia Jeffreys, 1884, under Art. 70.3; Cyclostoma delicatum Philippi, 1844, fixed as type species of Trachysma G. O. Sars, 1878, under Art. 70.3; Helix elegans Gmelin, 1791, fixed as type species of Trochoidea T. Brown, 1827, under Art. 70.3; Turritellopsis stimpsoni Dall, 1919, fixed as type species of Turritellopsis G. O. Sars, 1878, under Art. 70.3; Fusus averillii Gabb, 1864, fixed as type species of Volutoderma Gabb, 1876, under Art. 70.3; Voluta pepo Lightfoot, 1786, fixed as type species of Yetus Bowdich, 1822. Curnonidae d'Udekem d'Acoz, nom. nov., and Curnon d'Udekem d'Acoz, nom. nov., are established for Charcotiidae Odhner, 1926, and Charcotia Vayssiere, 1906, (between 27 March and 1 May), non Charcotia Chevreux, 1906 (January) [Amphipoda]; Yuopisthonematidae Nutzel, nom. nov., and Yuopisthonema Nutzel, nom. nov., are established for Opisthonematidae Yu, 1976, and Opisthonema Yu, 1974, non Gill, 1862 [Pisces]. The new family-group name Burnupiidae Albrecht is established in this work; and the names Scolodontina and Orthalicoidei are first used here to denote, respectively, a suborder containing the family Scolodontidae, and an infraorder containing the superfamily Orthalicoidea.

Journal ArticleDOI
Rathin Adhikari1, Matteo Agostini, N. Anh Ky2, N. Anh Ky3, T. Araki4, Maria Archidiacono5, M. Bahr6, J. Baur7, J. Behrens8, Fedor Bezrukov9, P. S. Bhupal Dev10, Debasish Borah11, Alexey Boyarsky12, A. de Gouvea13, C. A. de S. Pires14, H. J. de Vega15, Alex G. Dias16, P. Di Bari17, Z. Djurcic18, Kai Dolde19, H. Dorrer20, M. Durero7, O. Dragoun, Marco Drewes21, Guido Drexlin19, Ch. E. Düllmann20, Klaus Eberhardt20, Sergey Eliseev22, Christian Enss23, Nick Evans, A. Faessler24, Pavel Filianin22, V. Fischer7, Andreas Fleischmann23, Joseph A. Formaggio25, Jeroen Franse12, F.M. Fraenkle19, Carlos S. Frenk26, George M. Fuller27, L. Gastaldo23, Antonella Garzilli12, Carlo Giunti, Ferenc Glück19, Maury Goodman18, M. C. Gonzalez-Garcia28, Dmitry Gorbunov29, Dmitry Gorbunov30, Jan Hamann31, Volker Hannen8, Steen Hannestad5, Steen Honoré Hansen32, C. Hassel23, Julian Heeck33, F. Hofmann22, T. Houdy7, T. Houdy34, A. Huber19, Dmytro Iakubovskyi35, Aldo Ianni36, Alejandro Ibarra21, Richard Jacobsson37, Tesla E. Jeltema38, Josef Jochum24, Sebastian Kempf23, T. Kieck20, M. Korzeczek7, M. Korzeczek19, V. N. Kornoukhov39, Tobias Lachenmaier24, Mikko Laine40, Paul Langacker41, Thierry Lasserre, J. Lesgourgues42, D. Lhuillier7, Yufeng Li43, W. Liao44, A.W. Long45, Michele Maltoni46, Gianpiero Mangano, Nick E. Mavromatos47, Nicola Menci48, Alexander Merle22, Susanne Mertens49, Susanne Mertens19, Alessandro Mirizzi50, Alessandro Mirizzi51, Benjamin Monreal6, A. A. Nozik29, A. A. Nozik30, Andrii Neronov52, V. Niro46, Yu. N. Novikov53, L. Oberauer21, Ernst W. Otten20, Nathalie Palanque-Delabrouille7, Marco Pallavicini54, V. S. Pantuev30, Emmanouil Papastergis55, Stephen J. Parke56, Silvia Pascoli26, Sergio Pastor57, Amol V. Patwardhan27, Apostolos Pilaftsis10, D. C. Radford58, P. C.-O. Ranitzsch8, O. Rest8, Dean J. Robinson59, P. S. Rodrigues da Silva14, Oleg Ruchayskiy60, Oleg Ruchayskiy35, Norma G. Sanchez61, Manami Sasaki24, Ninetta Saviano26, Ninetta Saviano20, Aurel Schneider62, F. Schneider20, T. Schwetz19, S. Schönert21, S. Scholl24, Francesco Shankar17, Robert Shrock28, N. Steinbrink8, Louis E. Strigari63, F. Suekane64, B. Suerfu65, R. Takahashi66, N. Thi Hong Van3, Igor Tkachev30, Maximilian Totzauer22, Y. Tsai67, Christopher George Tully65, Kathrin Valerius19, José W. F. Valle57, D. Vénos, Matteo Viel48, M. Vivier7, Mei-Yu Wang63, Ch. Weinheimer8, Klaus Wendt20, Lindley Winslow25, Joachim Wolf19, Michael Wurm20, Z. Xing43, Shun Zhou43, Kai Zuber68 
Jamia Millia Islamia1, Hanoi University of Science2, Vietnam Academy of Science and Technology3, Saitama University4, Aarhus University5, University of California, Santa Barbara6, Commissariat à l'énergie atomique et aux énergies alternatives7, University of Münster8, University of Connecticut9, University of Manchester10, Indian Institute of Technology Guwahati11, Leiden University12, Northwestern University13, Federal University of Paraíba14, Centre national de la recherche scientifique15, Universidade Federal do ABC16, University of Southampton17, Argonne National Laboratory18, Karlsruhe Institute of Technology19, University of Mainz20, Technische Universität München21, Max Planck Society22, Heidelberg University23, University of Tübingen24, Massachusetts Institute of Technology25, Durham University26, University of California, San Diego27, C. N. Yang Institute for Theoretical Physics28, Moscow Institute of Physics and Technology29, Russian Academy of Sciences30, University of Sydney31, University of Copenhagen32, Université libre de Bruxelles33, Paris Diderot University34, Niels Bohr Institute35, Estácio S.A.36, CERN37, University of California, Santa Cruz38, Institute on Taxation and Economic Policy39, University of Bern40, Institute for Advanced Study41, RWTH Aachen University42, Chinese Academy of Sciences43, East China University of Science and Technology44, University of Chicago45, Autonomous University of Madrid46, King's College London47, INAF48, Lawrence Berkeley National Laboratory49, University of Bari50, Istituto Nazionale di Fisica Nucleare51, University of Geneva52, Petersburg Nuclear Physics Institute53, University of Genoa54, Kapteyn Astronomical Institute55, Fermilab56, Spanish National Research Council57, Oak Ridge National Laboratory58, University of California, Berkeley59, École Polytechnique Fédérale de Lausanne60, University of Paris61, University of Zurich62, Mitchell Institute63, Tohoku University64, Princeton University65, Shimane University66, University of Maryland, College Park67, Dresden University of Technology68
TL;DR: A comprehensive review of keV-scale neutrino Dark Matter can be found in this paper, where the role of active neutrinos in particle physics, astrophysics, and cosmology is reviewed.
Abstract: We present a comprehensive review of keV-scale sterile neutrino Dark Matter, collecting views and insights from all disciplines involved—cosmology, astrophysics, nuclear, and particle physics—in each case viewed from both theoretical and experimental/observational perspectives. After reviewing the role of active neutrinos in particle physics, astrophysics, and cosmology, we focus on sterile neutrinos in the context of the Dark Matter puzzle. Here, we first review the physics motivation for sterile neutrino Dark Matter, based on challenges and tensions in purely cold Dark Matter scenarios. We then round out the discussion by critically summarizing all known constraints on sterile neutrino Dark Matter arising from astrophysical observations, laboratory experiments, and theoretical considerations. In this context, we provide a balanced discourse on the possibly positive signal from X-ray observations. Another focus of the paper concerns the construction of particle physics models, aiming to explain how sterile neutrinos of keV-scale masses could arise in concrete settings beyond the Standard Model of elementary particle physics. The paper ends with an extensive review of current and future astrophysical and laboratory searches, highlighting new ideas and their experimental challenges, as well as future perspectives for the discovery of sterile neutrinos.

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TL;DR: The aim of this tutorial is to highlight a novel chapter of control theory, dealing with applications to social systems, to the attention of the broad research community.

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TL;DR: It seems that CD68 is not involved in binding bacterial/viral pathogens, innate, inflammatory or humoral immune responses, although it may potentially be involved in antigen processing/presentation.

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TL;DR: Greater international cooperation using standardized protocols and methods to monitor and manage European freshwater mussel diversity will not only help conserve this vulnerable group but also, through the protection of these important organisms, will offer wider benefits to freshwater ecosystems.
Abstract: Freshwater mussels of the Order Unionida provide important ecosystem functions and services, yet many of their populations are in decline. We comprehensively review the status of the 16 currently recognized species in Europe, collating for the first time their life-history traits, distribution, conservation status, habitat preferences, and main threats in order to suggest future management actions. In northern, central, and eastern Europe, a relatively homogeneous species composition is found in most basins. In southern Europe, despite the lower species richness, spatially restricted species make these basins a high conservation priority. Information on freshwater mussels in Europe is unevenly distributed with considerable differences in data quality and quantity among countries and species. To make conservation more effective in the future, we suggest greater international cooperation using standardized protocols and methods to monitor and manage European freshwater mussel diversity. Such an approach will not only help conserve this vulnerable group but also, through the protection of these important organisms, will offer wider benefits to freshwater ecosystems.