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At least 1,351 records · Page 75

Evolving data standards for cryo-EM structures

Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microwave frequency standard on {sup 25}Mg{sup +} ions: expected characteristics and prospects

A scheme of the new frequency standard is reported based on a microwave transition between hyperfine components of the ground state in {sup 25}Mg{sup +} ions. It is proposed to capture ions into a linear quadrupole Paul trap and to perform the laser cooling, as well as to prepare the particle ensemble and to implement detection by using a single laser system based on a semiconductor laser. Characteristics of the suggested frequency standard are estimated. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Creation of the first Russian time and frequency standard on a fountain of ultracold rubidium atoms

Technical specific features of the first Russian rubidium frequency standard of a fountain type are described, which are distinct from those of abroad analogues. Test results of separate systems and the metrological characteristics of the standard are presented. The achievable output frequency instability is 4 × 10{sup −16} per measurement interval of 24 hours and 1 × 10{sup −16} per 16 days. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Acousto-optic modulators for a controlled frequency shift of light beams in optical and microwave cold-atom frequency standards

A series of specialised acousto-optic modulators/frequency shifters based on paratellurite (TeO{sub 2}) single crystals is developed for systems of laser cooling and frequency stabilisation of laser sources in optical and microwave frequency standards based on cold strontium, rubidium and caesium atoms. The methods of calculation and optimisation of the main parameters of acousto-optic modulators are considered; their basic technical characteristics are experimentally investigated in the spectral range of optical radiation 460 – 900 nm and in the frequency shift range of 5 – 400 MHz. The modulators have a high diffraction efficiency, low power consumption and the ability to work with linearly and randomly polarised optical radiation. (frequency standards)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Testing the Standard Model at the Precision Frontier with the Q weak Experiment

The standard model of particle physics (SM) has been wildly successful describing the strong, electromagnetic, and weak forces between visible matter. Despite this success, there is a host of phenomena it fails to describe, including neutrino oscillations, gravity, dark matter, and baryon asymmetry. Something is missing—the theory is not complete. This conviction has compelled physicists to develop ever-more-stringent tests in the hope of finding cracks in the SM that could point to where the beyond-the-standard-model (BSM) physics might lie. Direct searches at high-energy colliders have yielded no evidence for some of the most intriguing possibilities, like supersymmetry, and have not been able to shed much light on where to look next.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Performance based approaches in standards and regulations for smart ventilation in residential buildings: a summary review

As ventilation systems become more sophisticated (or ‘smart’) standards and regulations are changing to accommodate their use. A key smart ventilation concept is to use controls to ventilate more at times it provides either an energy or IAQ advantage (or both) and less when it provides a disadvantage. This paper discusses the favorable contexts that exist in many countries, with regulations and standards proposing ‘performance-based approaches’ that both enable and reward smart ventilation. The paper gives an overview of such approaches from five countries. The common thread in all these methods is the use of metrics for the exposure to an indoor generated parameter (usually CO 2 ), and condensation risk. As the result, demand-control ventilation strategies (DCV) are widely and easily available on the market, with more than 20–30 systems available in some countries.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Allan Franklin, Shifting Standards: Experiments in Particle Physics in the Twentieth Century . Book Review

The book Shifting Standards is a valuable contribution to the literature on the history and philosophy of science and specifically to the philosophy of scientific experimentation, the discipline of which Allan Franklin is one of the outstanding scholars and founders. Here, the central focus of the book is the contemporary shift in the norms of representation of experimental results in particle physics as well as the increasing role and drawbacks of statistical standards of acceptance for those results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hubble space telescope calspec flux standards: Sirius (and Vega)

The Space Telescope Imaging Spectrograph (STIS) has measured the flux for Sirius from 0.17 to 1.01 μm on the Hubble Space Telescope (HST) White Dwarf scale. Because of the cool debris disk around Vega, Sirius is commonly recommended as the primary IR flux standard. The measured STIS flux agrees well with predictions of a special Kurucz model atmosphere, adding confidence to the modeled IR flux predictions. The IR flux agrees to 2%-3% with respect to the standard template of Cohen and to 2% with the Midcourse Space Experiment absolute flux measurements in the mid-IR. A weighted average of the independent visible and mid-IR absolute flux measures implies that the monochromatic flux at 5557.5 Å (5556 Å in air) for Sirius and Vega, respectively, is 1.35 × 10{sup –8} and 3.44 × 10{sup –9} erg cm{sup –2} s{sup –1} Å{sup –1} with formal uncertainties of 0.5%. Contrary to previously published conclusions, the Hipparcos photometry offers no support for the variability of Vega. Pulse pileup severely affects the Hp photometry for the brightest stars.

79 ASTRONOMY AND ASTROPHYSICS↗

A new standard pulsar magnetosphere

In view of recent efforts to probe the physical conditions in the pulsar current sheet, we revisit the standard solution that describes the main elements of the ideal force-free pulsar magnetosphere. The simple physical requirement that the electric current contained in the current layer consists of the local electric charge moving outward at close to the speed of light yields a new solution for the pulsar magnetosphere everywhere that is ideal force-free except in the current layer. The main elements of the new solution are as follows: (1) the pulsar spindown rate of the aligned rotator is 23% larger than that of the orthogonal vacuum rotator; (2) only 60% of the magnetic flux that crosses the light cylinder opens up to infinity; (3) the electric current closes along the other 40%, which gradually converges to the equator; (4) this transfers 40% of the total pulsar spindown energy flux in the equatorial current sheet, which is then dissipated in the acceleration of particles and in high-energy electromagnetic radiation; and (5) there is no separatrix current layer. Our solution is a minimum free-parameter solution in that the equatorial current layer is electrostatically supported against collapse and thus does not require a thermal particle population. In this respect, it is one more step toward the development of a new standard solution. We discuss the implications for intermittent pulsars and long-duration gamma-ray bursts. We conclude that the physical conditions in the equatorial current layer determine the global structure of the pulsar magnetosphere.

79 ASTRONOMY AND ASTROPHYSICS↗

Study of VUV radiation of hybrid and standard X-pinches on KING electric discharge facility

The radiative characteristics of standard and hybrid X-pinches are studied in VUV range on the small-size KING electric discharge facility (200 kA, 190 ns, 45 kV) for the same initial conditions. In this work, studies were performed for different X-pinch materials. A comparative analysis of the VUV spectra was performed and the output energy of soft x-rays and VUV radiation was measured for standard and hybrid X-pinches.

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Updated constraints on non-standard neutrino interactions from Planck

We provide updated bounds on non-standard neutrino interactions based on data from the Planck satellite as well as auxiliary cosmological measurements. Two types of models are studied - A Fermi-like 4-point interaction and an interaction mediated by a light pseudoscalar - and we show that these two models are representative of models in which neutrinos either decouple or recouple in the early Universe. Current cosmological data constrain the effective 4-point coupling to be G{sub X} ≤ (0.06 GeV){sup -2}, corresponding to G{sub X} ≤ 2.5 × 10{sup 7} G{sub F}. For non-standard pseudoscalar interactions we set a limit on the diagonal elements of the dimensionless coupling matrix, g{sub ij}, of g{sub ii} ≤ 1.2 × 10{sup -7}. For the off-diagonal elements which induce neutrino decay the bound is significantly stronger, corresponding to g{sub ij} ≤ 2.3 × 10{sup -11}(m/0.05 eV){sup -2}, or a lifetime constraint of τ ≥ 1.2 × 10{sup 9} s (m/0.05 eV){sup 3} . This is currently the strongest known bound on this particular type of neutrino decay. We finally note that extremely strong neutrino self-interactions which completely suppress anisotropic stress over all of cosmic history are very highly disfavored by current data Δ χ{sup 2} ∼ 10{sup 4})

79 ASTRONOMY AND ASTROPHYSICS↗

Computation of the halo mass function using physical collapse parameters: application to non-standard cosmologies

In this article we compare the halo mass function predicted by the excursion set theory with a drifting diffusive barrier against the results of N-body simulations for several cosmological models. This includes the standard ΛCDM case for a large range of halo masses, models with different types of primordial non-Gaussianity, and the Ratra-Peebles quintessence model of Dark Energy. We show that in all those cosmological scenarios, the abundance of dark matter halos can be described by a drifting diffusive barrier, where the two parameters describing the barrier have physical content. In the case of the Gaussian ΛCDM, the statistics are precise enough to actually predict those parameters at different redshifts from the initial conditions. Furthermore, we found that the stochasticity in the barrier is non-negligible making the simple deterministic spherical collapse model a bad approximation even at very high halo masses. We also show that using the standard excursion set approach with a barrier inspired by peak patches leads to inconsistent predictions of the halo mass function.

79 ASTRONOMY AND ASTROPHYSICS↗

A NUMERICAL MODEL OF STANDARD TO BLOWOUT JETS

We report on three-dimensional (3D) MHD simulations of the formation of jets produced during the emergence and eruption of solar magnetic fields. The interaction between an emerging and an ambient magnetic field in the solar atmosphere leads to (external) reconnection and the formation of ''standard'' jets with an inverse Y-shaped configuration. Eventually, low-atmosphere (internal) reconnection of sheared fieldlines in the emerging flux region produces an erupting magnetic flux rope and a reconnection jet underneath it. The erupting plasma blows out the ambient field and, moreover, it unwinds as it is ejected into the outer solar atmosphere. The fast emission of the cool material that erupts together with the hot outflows due to external/internal reconnection form a wider ''blowout'' jet. We show the transition from ''standard'' to ''blowout'' jets and report on their 3D structure. The physical plasma properties of the jets are consistent with observational studies.

79 ASTRONOMY AND ASTROPHYSICS↗

ANTI-GLITCHES WITHIN THE STANDARD SCENARIO OF PULSAR GLITCHES

Recent observations of a sudden spin down of the magnetar 1E2259+586, occurring on a timescale not exceeding two weeks (an event that has been dubbed an {sup a}nti-glitch{sup )}, still has not received any interpretation in terms of the standard scenario of pulsar glitches. Motivated by this observation, here we present a toy model that allows for anti-glitches in neutron stars under certain conditions within the standard approach.

79 ASTRONOMY AND ASTROPHYSICS↗

Dispersive interactions between standard and Dirac materials and the role of dimensionality

The van der Waals (vdW) interaction plays a prominent role between neutral objects at separations where short ranged chemical forces are negligible. This type of dispersive coupling is determined by the interplay between geometry and response properties of the materials making up the objects. Here, we investigate the vdW interaction between 1D, 2D, and 3D standard and Dirac materials within the Random Phase Approximation, which takes into account collective excitations originating from the electronic Coulomb potential. A comprehensive understanding of characteristic functionalities and scaling laws are obtained for systems with parabolic energy dispersion (standard materials) and crossing linear bands (Dirac materials). By comparing the quantum mechanical and thermal limits the onset of thermal fluctuations in the vdW interaction is discussed showing that thermal effects are significantly pronounced at smaller scales in reduced dimensions.

36 MATERIALS SCIENCE↗

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗