bluuebunny/crossref_metadata_2025 huggingface dataset:
Channel branching ratios in CH2CN− photodetachment: Rotational structure and vibrational energy redistribution in autodetachment
Authors: Lyle Justin , Wedig Olivia , Gulania Sahil , Krylov Anna I. , Mabbs Richard
Published: December 2017

We report photoelectron spectra of CH2CN−, recorded at photon energies between 13 460 and 15 384 cm−1, which show rapid intensity variations in particular detachment channels. The branching ratios for various spectral features reveal rotational structure associated with autodetachment from an intermediate anion state. Calculations using equation-of-motion coupled-cluster method with single and double excitations reveal the presence of two dipole-bound excited anion states (a singlet and a triplet). The computed oscillator strength for the transition to the singlet dipole-bound state provides an estimate of the autodetachment channel contribution to the total photoelectron yield. Analysis of the different spectral features allows identification of the dipole-bound and neutral vibrational levels involved in the autodetachment processes. For the most part, the autodetachment channels are consistent with the vibrational propensity rule and normal mode expectation. However, examination of the rotational structure shows that autodetachment from the ν3 (v = 1 and v = 2) levels of the dipole-bound state displays behavior counter to the normal mode expectation with the final state vibrational level belonging to a different mode.
Fibrous structure in GaSb surfaces irradiated with fast Cu cluster ions
Authors: Tsuchida Hidetsugu , Nitta Noriko , Yanagida Yusuke , Okumura Yuya , Murase Ryu
Published: December 2017

The effect of fast cluster irradiation on the formation of fibrous structures is investigated for single crystal GaSb surfaces irradiated by Cun+ ions (n = 1–3) with an energy of 0.4 MeV/atom at ion fluences up to 5 × 1015 cm−2. We study the cluster size dependence on the growth of fibrous network structures. With increasing cluster size, the shape of the fiber changed from rod-like to spherical. To quantitatively evaluate this cluster effect, a fiber diameter d in rod or spherical portion is examined as a function of ion fluence Φ and cluster size n. We find that the fiber diameter nonlinearly increases and follows the relation d∝nα×Φ, with α≈2. This evidently implies that the amount of defects generated by n-sized cluster bombardments varies as n2 for n≤3. Cluster ion irradiation enhances the defect generation owing to the overlap between cascades of individual cluster constituents and is therefore effective for the growth of nanofibers.
First-principles investigation of elastic anomalies in niobium at high pressure and temperature
Authors: Wang Yi X. , Geng Hua Y. , Wu Q. , Chen Xiang R. , Sun Y.
Published: December 2017

Niobium does not show any structure transition up to very high pressures. Nonetheless, by using density functional theory, we demonstrate in this work that it exhibits striking softening in elastic moduli C44 and C′ at a pressure from 20 to 150 GPa. A novel anomaly softening in C44 from 275 to 400 GPa is also predicted. The physics behind these two anomalies is elaborated by electronic structure calculations, which revealed that they are actually different—first one directly relates to an underlying rhombohedral distortion whereas the latter originates in an electronic topological transition. The large magnitude of the softening leads to a remarkable elastic anisotropy in both the shear and the Young's moduli of Nb. Further investigation shows that thermo-electrons have an important role in these anomalies. This effect has not been noticed before. With increased electronic temperature, it is found that all anomalies (both the elastic softening and anisotropy) in Nb are gradually diminished, effectively giving rise to a temperature-induced hardening phenomenon.
Nanoparticle detection in an open-access silicon microcavity
Authors: Kuhn Stefan , Wachter Georg , Wieser Franz-Ferdinand , Millen James , Schneider Michael , Schalko Johannes , Schmid Ulrich , Trupke Michael , Arndt Markus
Published: December 2017

We report on the detection of free nanoparticles in a micromachined, open-access Fabry-Pérot microcavity. With a mirror separation of 130 μm, a radius of curvature of 1.3 mm, and a beam waist of 12 μm, the mode volume of our symmetric infrared cavity is smaller than 15 pL. The small beam waist, together with a finesse exceeding 34 000, enables the detection of nanoscale dielectric particles in high vacuum. This device allows monitoring of the motion of individual 150 nm radius silica nanospheres in real time. We observe strong coupling between the particles and the cavity field, a precondition for optomechanical control. We discuss the prospects for optical cooling and detection of dielectric particles smaller than 10 nm in radius and 1 × 107 amu in mass.
Impact of neutron irradiation on the structural and optical properties of PVP/gelatin blends doped with dysprosium (III) chloride
Authors: Basha Ahmad Fouad , Basha Mohammad Ahmad-Fouad
Published: December 2017

Polymer composites of a system of Polyvinylpyrrolidone (PVP)/gelatin/DyCl3·6H2O were prepared in three groups that have different concentrations of PVP/gelatin contents to study the effect of neutron irradiation on their structural and optical properties. Results showed that the interaction of neutrons led to various complex phenomena, mainly bond breaking, main chain scission and intermolecular cross-linking. These processes introduced defects inside the material that were responsible for the changes in their optical and structural properties. All the calculated parameters were found to be dependent on the irradiation fluence in a uniform manner that makes these materials excellent candidates in the applications of dosimetry and radiology. Moreover, the sensitivity of the three groups of composites to the irradiation doses was found to be different. The variation in the structure of the composite group that contains the least PVP content was found to be less significant; hence, these materials were more stable against high doses that make them suitable for high radiation dose applications.
Molecular geometries and other properties of H2O⋯AgI and H3N⋯AgI as characterised by rotational spectroscopy and ab initio calculations
Authors: Medcraft Chris , Gougoula Eva , Bittner Dror M. , Mullaney John C. , Blanco Susana , Tew David P. , Walker Nicholas R. , Legon Anthony C.
Published: December 2017

The rotational spectra of H3N⋯AgI and H2O⋯AgI have been recorded between 6.5 and 18.5 GHz by chirped-pulse Fourier-transform microwave spectroscopy. The complexes were generated through laser vaporisation of a solid target of silver or silver iodide in the presence of an argon gas pulse containing a low concentration of the Lewis base. The gaseous sample subsequently undergoes supersonic expansion which results in cooling of rotational and vibrational motions such that weakly bound complexes can form within the expanding gas jet. Spectroscopic parameters have been determined for eight isotopologues of H3N⋯AgI and six isotopologues of H2O⋯AgI. Rotational constants, B0; centrifugal distortion constants, DJ, DJK or ΔJ, ΔJK; and the nuclear quadrupole coupling constants, χaa(I) and χbb(I) − χcc(I) are reported. H3N⋯AgI is shown to adopt a geometry that has C3v symmetry. The geometry of H2O⋯AgI is Cs at equilibrium but with a low barrier to inversion such that the vibrational wavefunction for the v = 0 state has C2v symmetry. Trends in the nuclear quadrupole coupling constant of the iodine nucleus, χaa(I), of L⋯AgI complexes are examined, where L is varied across the series (L = Ar, H3N, H2O, H2S, H3P, or CO). The results of experiments are reported alongside those of ab initio calculations at the CCSD(T)(F12*)/AVXZ level (X = T, Q).
Threshold switching in SiGeAsTeN chalcogenide glass prepared by As ion implantation into sputtered SiGeTeN film
Authors: Liu Guangyu , Wu Liangcai , Song Zhitang , Liu Yan , Li Tao , Zhang Sifan , Song Sannian , Feng Songlin
Published: December 2017

A memory cell composed of a selector device and a storage device is the basic unit of phase change memory. The threshold switching effect, main principle of selectors, is a universal phenomenon in chalcogenide glasses. In this work, we put forward a safe and controllable method to prepare a SiGeAsTeN chalcogenide film by implanting As ions into sputtered SiGeTeN films. For the SiGeAsTeN material, the phase structure maintains the amorphous state, even at high temperature, indicating that no phase transition occurs for this chalcogenide-based material. The electrical test results show that the SiGeAsTeN-based devices exhibit good threshold switching characteristics and the switching voltage decreases with the increasing As content. The decrease in valence alternation pairs, reducing trap state density, may be the physical mechanism for lower switch-on voltage, which makes the SiGeAsTeN material more applicable in selector devices through component optimization.
Pulse splitting of stimulated Raman backscattering with a chirped pump
Authors: Chen Q. , Wu Z. , Johnson L. , Gordon D. , Sprangle P. , Suckewer S.
Published: December 2017

Raman amplified seed splitting was demonstrated in the backscattering scheme in a plasma, when a significant chirp was introduced into the pump. Particle-in-cell simulations have shown that a single seed laser pulse gradually splits into two, self-compressed pulses in the nonlinear amplification regime. This is in difference to previous studies of the pump chirp, which mainly have focused on its compensation for the plasma density gradient, in order to maximize the resonant amplification. The splitting, as revealed by the spectral evolution of the amplified seed, is attributed to resonance slipping, which is the result of the spatio-temporal distribution of the gain of the chirped pump.
Broadband low-frequency sound isolation by lightweight adaptive metamaterials
Authors: Liao Yunhong , Chen Yangyang , Huang Guoliang , Zhou Xiaoming
Published: December 2017

Blocking broadband low-frequency airborne noises is highly desirable in lots of engineering applications, while it is extremely difficult to be realized with lightweight materials and/or structures. Recently, a new class of lightweight adaptive metamaterials with hybrid shunting circuits has been proposed, demonstrating super broadband structure-borne bandgaps. In this study, we aim at examining their potentials in broadband sound isolation by establishing an analytical model that rigorously combines the piezoelectric dynamic couplings between adaptive metamaterials and acoustics. Sound transmission loss of the adaptive metamaterial is investigated with respect to both the frequency and angular spectrum to demonstrate their sound-insulation effects. We find that efficient sound isolation can indeed be pursued in the broadband bi-spectrum for not only the case of the small resonator's periodicity where only one mode relevant to the mass-spring resonance exists, but also for the large-periodicity scenario, so that the total weight can be even lighter, in which the multiple plate-resonator coupling modes appear. In the latter case, the negative spring stiffness provided by the piezoelectric stack has been utilized to suppress the resonance-induced high acoustic transmission. Such kinds of adaptive metamaterials could open a new approach for broadband noise isolation with extremely lightweight structures.
Superconducting micro-resonator arrays with ideal frequency spacing
Authors: Liu X. , Guo W. , Wang Y. , Dai M. , Wei L. F. , Dober B. , McKenney C. M. , Hilton G. C. , Hubmayr J. , Austermann J. E. , Ullom J. N. , Gao J. , Vissers M. R.
Published: December 2017

We present a wafer trimming technique for producing superconducting micro-resonator arrays with highly uniform frequency spacing. With the light-emitting diode mapper technique demonstrated previously, we first map the measured resonance frequencies to the physical resonators. Then, we fine-tune each resonator's frequency by lithographically trimming a small length, calculated from the deviation of the measured frequency from its design value, from the interdigitated capacitor. We demonstrate this technique on a 127-resonator array made from titanium-nitride and show that the uniformity of frequency spacing is greatly improved. The array yield in terms of frequency collisions improves from 84% to 97%, while the quality factors and noise properties are unaffected. The wafer trimming technique provides an easy-to-implement tool to improve the yield and multiplexing density of large resonator arrays, which is important for various applications in photon detection and quantum computing.
An R-matrix study of electron induced processes in BF3 plasma
Authors: Gupta Dhanoj , Chakrabarti Kalyan , Yoon Jung-Sik , Song Mi-Young
Published: December 2017

An R-matrix formalism is used to study electron collision with the BF3 molecule using Quantemol-N, a computational system for electron molecule collisions which uses the molecular R-matrix method. Several target models are tested for BF3 in its equilibrium geometry, and the results are presented for the best model. Scattering calculations are then performed to yield resonance parameters, elastic, differential, excitation, and momentum transfer cross sections. The results for all the cross sections are compared with the experimental and theoretical data, and a good agreement is obtained. The resonances have been detected at 3.79 and 13.58 eV, with the ionization threshold being 15.7 eV. We have also estimated the absolute dissociative electron attachment (DEA) cross section for the F− ion production from BF3, which is a maiden attempt. The peak of the DEA is at around 13.5 eV, which is well supported by the resonance detected at 13.58 eV. The cross sections reported here find a variety of applications in the plasma technology.
Direct evaluation of boson dynamics via finite-temperature time-dependent variation with multiple Davydov states
Authors: Fujihashi Yuta , Wang Lu , Zhao Yang
Published: December 2017

Recent advances in quantum optics allow for exploration of boson dynamics in dissipative many-body systems. However, the traditional descriptions of quantum dissipation using reduced density matrices are unable to capture explicit information of bath dynamics. In this work, efficient evaluation of boson dynamics is demonstrated by combining the multiple Davydov Ansatz with finite-temperature time-dependent variation, going beyond what state-of-the-art density matrix approaches are capable to offer for coupled electron-boson systems. To this end, applications are made to excitation energy transfer in photosynthetic systems, singlet fission in organic thin films, and circuit quantum electrodynamics in superconducting devices. Thanks to the multiple Davydov Ansatz, our analysis of boson dynamics leads to clear revelation of boson modes strongly coupled to electronic states, as well as in-depth description of polaron creation and destruction in the presence of thermal fluctuations.
Frameworks with metal nodes improve organic solar cell power conversion efficiency
Authors: Cockbill Louisa
Published: December 2017

First principle calculations assess and optimize the physical and optoelectronic properties of a 2-D metal organic network.
Structure and biological activity of endogenous and synthetic agonists of GPR119
Authors: Tyurenkov Ivan N. , Ozerov Alexander A. , Kurkin Denis V. , Logvinova Ekaterina O. , Bakulin Dmitry A. , Volotova Elena V. , Borodin Dmitry D.
Published: December 2017

A G-protein-coupled receptor, GPR119, is a promising pharmacological target for a new class of hypoglycaemic drugs with an original mechanism of action, namely, increase in the glucose-dependent incretin and insulin secretion. In 2005, the first ligands were found and in the subsequent years, a large number of GPR119 agonists were synthesized in laboratories in various countries; the safest and most promising agonists have entered phase I and II clinical trials as agents for the treatment of type 2 diabetes mellitus and obesity. The review describes the major endogenous GPR119 agonists and the main trends in the design and modification of synthetic structures for increasing the hypoglycaemic activity. The data on synthetic agonists are arranged according to the type of the central core of the molecules.

The bibliography includes 104 references.
18F-Labelled catecholamine type radiopharmaceuticals in the diagnosis of neurodegenerative diseases and neuroendocrine tumours: approaches to synthesis and development prospects
Authors: Vatsadze Sergey Z. , Eremina Olga E. , Veselova Irina A. , Kalmykov Stepan N. , Nenajdenko Valentin G.
Published: December 2017

The pathogenesis of many socially significant diseases such as neurodegenerative dementias and neuroendocrine tumours involves imbalance of neurotransmitters. Among the known neuroimaging methods, positron emission tomography (PET) is the most perfect and informative technique for diagnosing these diseases. The potential of PET is largely determined by the inventory of available radiopharmaceuticals, that is, biologically active molecules containing short-lived nuclides with positron decay. This review gives a systematic account of the application of fluorine-18-labelled catecholamine type radiopharmaceuticals in clinical investigations of the sympathetic and central nervous systems. The methods for the synthesis of these agents and existing problems are considered. The material is arranged according to the mechanisms of reactions that underlie the synthetic approaches: electrophilic, nucleophilic and metal-catalyzed reactions.

The bibliography includes 198 references.
Imidazoline and imidazolidine nitroxides as controlling agents in nitroxide-mediated pseudoliving radical polymerization
Authors: Edeleva Mariya V. , Marque Sylvain R. A. , Bagryanskaya Elena G.
Published: December 2017

Controlled, or pseudoliving, radical polymerization provides unique opportunities for the synthesis of structurally diverse polymers with a narrow molecular-weight distribution. These reactions occur under relatively mild conditions with broad tolerance to functional groups in the monomers. The nitroxide-mediated pseudoliving radical polymerization is of particular interest for the synthesis of polymers for biomedical applications. This review briefly describes one of the mechanisms of controlled radical polymerization. The studies dealing with the use of imidazoline and imidazolidine nitroxides as controlling agents for nitroxide-mediated pseudoliving radical polymerization of various monomers are summarized and analyzed. The publications addressing the key steps of the controlled radical polymerization in the presence of imidazoline and imidazolidine nitroxides and new approaches to nitroxide-mediated polymerization based on protonation of both nitroxides and monomers are considered.

The bibliography includes 154 references.
Salicylaldehydes as privileged synthons in multicomponent reactions
Authors: Heravi Majid Momahed , Zadsirjan Vahideh , Mollaiye Malihe , Heydari Masumeh , Koshvandi Afsaneh Taheri Kal
Published: December 2017

Salicylaldehyde (2-hydroxybenzaldehyde) bearing two different active functional groups, namely, a hydroxy group and an aldehyde group, finds wide application as a key chemical in a variety of industrial processes, especially in the large-scale production of pharmaceuticals. Salicylaldehyde and most of its derivatives are commercially available or readily accessible, and hence are ideal starting materials for multicomponent reactions (MCRs), mostly in pseudo-three and four-component ones, giving rise to a plethora of heterocyclic systems. The importance of salicylaldehyde and an impressive amount of studies concerning its applications in MCRs prompted us to highlight in this review the important role of this compound as a privileged synthon in the synthesis of heterocycles.

The bibliography includes 276 references.
Arbidol: a quarter-century after. Past, present and future of the original Russian antiviral
Authors: Balakin Konstantin V. , Filosa Rosanna , Lavrenov Sergey N. , Mkrtchyan Arthur S. , Nawrozkij Maxim B. , Novakov Ivan A.
Published: December 2017

The present review is concerned with the synthesis and structure–activity relationship studies of Arbidol and its structural analogues. The latter are roughly divided into several unequal parts: indole- and benzofuran-based compounds, benzimidazole and imidazopyridine bioisosteres and ring-expanded quinoline derivatives. Much attention is focused on various types of antiviral activity of the above-mentioned Arbidol congeners, as well as of the parent compound itself. Features of Arbidol synthesis and metabolic changes are also discussed.

The bibliography includes 166 references.
Evaluating the progress and needs of taxonomy since the Convention on Biological Diversity: going beyond the rate of species description
Authors: Tancoigne Elise , Ollivier Guillaume
Published: December 2017

There is a long tradition of assessing the activity and progress of taxonomy with quantitative indicators, such as, for example, number of taxonomists, species described and species collected. These evaluations play a key role in the context of a worldwide concern over biodiversity and its governance. We have described and analysed these evaluations since 1992, the year in which the Convention on Biological Diversity (CBD) was adopted. We showed that despite the establishment of a dedicated body inside the CBD (the Global Taxonomy Initiative), these quantitative evaluations are mostly sporadic and independent initiatives, performed by non-taxonomists. They do not map the places where most of the taxonomic activities take place, and they are performed on small scales, with scarce and heterogeneous sources of data, making comparisons almost impossible. Most of the indicators they use refer to the activity of species description. We argue that there is a need to rethink the way we evaluate taxonomy today and we discuss why it is urgent to move beyond indicators of species description. We suggest the use of a new set of indicators that would focus on taxonomic resources and dynamics, instead of taxonomic outputs.
Histone demethylase LSD1 regulates hematopoietic stem cells homeostasis and protects from death by endotoxic shock
Authors: Wang Jianxun , Saijo Kaoru , Skola Dylan , Jin Chunyu , Ma Qi , Merkurjev Daria , Glass Christopher K. , Rosenfeld Michael G.
Published: December 2017

Significance

The histone demethylase LSD1, a critical regulator of mammalian hematopoiesis, serves as an important suppressor of endotoxic shock. Inflammation-induced deletion of LSD1 results in failure to generate all mature hematopoietic cells, and induces acute expansion of a pathological population of hyperproliferative and hyperinflammatory myeloid progenitors that cause “cytokine storm” and acute lethality. LSD1 proves to be a downstream target of Toll-like/cytokine receptors in HSCs during endotoxic shock, with its down-regulation caused by a cohort of inflammation-induced microRNAs. The resultant acute expansion of a population of pathological myeloid progenitors in bone marrow causes a septic shock phenotype. Inhibitors of these inflammation-induced microRNAs block the down-regulation of LSD1 and prevent LPS-induced mortality, suggesting a potential therapeutic approach for treatment of septic shock.
Effect of vanadium on microstructure and mechanical properties of Fe–1.8Ni–0.5Mo–2Cu–0.45C PM steel
Authors: Tang Zhihao , Liu Zili , Liu Xiqin , Huang Xin , Li Haohao , Li Dong , Zou Yuwen
Published: December 2017

In this research, the microstructure and mechanical properties of Fe–1.8Ni–0.5Mo–2Cu–0.45C powder metallurgy (PM) steels with 0–0.3% vanadium were investigated by optical microscopy, scanning electron microscopy, transverse rupture, hardness and tribological tests. It is revealed that the volume fraction of polygonal ferrite in the sintered PM steels increased with the increasing of V addition, and more fine V(C,N) particles were formed during the sintering process. The enhancement of transverse rupture strength of the sintered and heat-treated PM steels with V addition was due to the grain refinement and precipitation strengthening effect. The friction coefficient the heat-treated steels decreased with an increase in V addition, whereas the wear loss increased.
Laser additive manufacturing foam aluminium-12 wt-% silicon with different addition TiH2 foaming agent
Authors: Zhang Min , Chen Changjun , Huang Yong
Published: December 2017

The aim of this work is to study the effects of laser additive manufacturing on microstructure and mechanical properties of foam Al–12 wt-%Si aluminium alloy with/without TiH2 foaming agent. The results showed that low porosity closed foam Al–12Si was successfully obtained. The effect of processing parameters on the porosity is discussed. The porosity was changed from initial 20.9% without foaming agent to 32.3 and 45.9% with 5 and 10% addition of foaming agent, respectively. Average micro-hardness values of the obtain foam Al–Si alloy is varied from 100 to 130 HV and the shape of compressive stress–strain curve is as the same as foam aluminium made by powder metallurgy and casting methods.
Realising equal strength welding to parent metal in precipitation-hardened Al–Mg–Si alloy via low heat input friction stir welding
Authors: Zeng X. H. , Xue P. , Wang D. , Ni D. R. , Xiao B. L. , Ma Z. Y.
Published: December 2017

Two millimetres thick Al–Mg–Si (6061Al-T6) alloy plates were friction stir welded at various welding conditions. Under a low rotation rate of 400 rev min–1 with rapid water cooling, the softening zone in the joint disappeared and a nanostructure with an average grain size of 80 nm was obtained in the stir zone (SZ). Therefore, a weld with equal strength to the parent metal (PM) was successfully achieved with the fracture occurring in the PM. Further, the average microhardness and ultimate tensile strength (UTS) of the SZs increased with the decreasing rotation rate and increasing cooling speed. The average microhardness and UTS of the SZ with nanostructure reached up to 134 HV and 505 MPa, respectively; though the initial strengthened precipitates disappeared. This work provides an effective strategy of achieving high property joints and enhancing the mechanical properties of precipitation-hardened Al alloys.
Opportunities for organoids as new models of aging
Authors: Hu Jennifer L. , Todhunter Michael E. , LaBarge Mark A. , Gartner Zev J.
Published: December 2017

The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research.
A toolbox of anti–mouse and anti–rabbit IgG secondary nanobodies
Authors: Pleiner Tino , Bates Mark , Görlich Dirk
Published: December 2017

Polyclonal anti–immunoglobulin G (anti-IgG) secondary antibodies are essential tools for many molecular biology techniques and diagnostic tests. Their animal-based production is, however, a major ethical problem. Here, we introduce a sustainable alternative, namely nanobodies against all mouse IgG subclasses and rabbit IgG. They can be produced at large scale in Escherichia coli and could thus make secondary antibody production in animals obsolete. Their recombinant nature allows fusion with affinity tags or reporter enzymes as well as efficient maleimide chemistry for fluorophore coupling. We demonstrate their superior performance in Western blotting, in both peroxidase- and fluorophore-linked form. Their site-specific labeling with multiple fluorophores creates bright imaging reagents for confocal and superresolution microscopy with much smaller label displacement than traditional secondary antibodies. They also enable simpler and faster immunostaining protocols, and allow multitarget localization with primary IgGs from the same species and of the same class.
RAF/MEK/extracellular signal–related kinase pathway suppresses dendritic cell migration and traps dendritic cells in Langerhans cell histiocytosis lesions
Authors: Hogstad Brandon , Berres Marie-Luise , Chakraborty Rikhia , Tang Jun , Bigenwald Camille , Serasinghe Madhavika , Lim Karen Phaik Har , Lin Howard , Man Tsz-Kwong , Remark Romain , Baxter Samantha , Kana Veronika , Jordan Stefan , Karoulia Zoi , Kwan Wing-hong , Leboeuf Marylene , Brandt Elisa , Salmon Helene , McClain Kenneth , Poulikakos Poulikos , Chipuk Jerry , Mulder Willem J.M. , Allen Carl E. , Merad Miriam
Published: December 2017

Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by granulomatous lesions containing pathological CD207+ dendritic cells (DCs) with constitutively activated mitogen-activated protein kinase (MAPK) pathway signaling. Approximately 60% of LCH patients harbor somatic BRAFV600E mutations localizing to CD207+ DCs within lesions. However, the mechanisms driving BRAFV600E+ LCH cell accumulation in lesions remain unknown. Here we show that sustained extracellular signal–related kinase activity induced by BRAFV600E inhibits C-C motif chemokine receptor 7 (CCR7)–mediated DC migration, trapping DCs in tissue lesions. Additionally, BRAFV600E increases expression of BCL2-like protein 1 (BCL2L1) in DCs, resulting in resistance to apoptosis. Pharmacological MAPK inhibition restores migration and apoptosis potential in a mouse LCH model, as well as in primary human LCH cells. We also demonstrate that MEK inhibitor-loaded nanoparticles have the capacity to concentrate drug delivery to phagocytic cells, significantly reducing off-target toxicity. Collectively, our results indicate that MAPK tightly suppresses DC migration and augments DC survival, rendering DCs in LCH lesions trapped and resistant to cell death.
APMP comparison on luminous flux units (APMP.PR-K4)
Authors: Liu H , Lin Y D , Yang C Z , Yu J
Published: December 2017

During the 18th APMP meeting in 2004, TCPR agreed that the luminous flux should be one of the several regional comparisons to be conducted in the field of photometry and radiometry, and the project was named as APMP.PR-K4. Nine laboratories took part in this comparison. A group of LF 200W lamps (no less than three) was used as transfer artifacts by each participant. The National Institute of Metrology (NIM, China) acted as the pilot laboratory. Presented in this report are the detailed procedures and results of the work.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCPR, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report of AFRIMETS.M.M-S6: supplementary comparison of 100 mg, 100 g 500 g, 1 kg and 5 kg stainless steel mass standards
Authors: Mautjana R T , Molefe P T , Mayindu N F , Armah M N , Ramasawmy V , Albasini G L , Matali S , Richmond H , Rusimbi V , Kiwanuka J , Mutale D M , Mutsimba F
Published: December 2017

This report summarizes the results of AFRIMETS.M.M-S6 mass standards comparison conducted between eleven participating laboratories/countries. Two sets of five weights with nominal values 100 mg, 100 g, 500 g, 1 kg and 5 kg were used as the traveling standards. These nominal values were decided from the needs of participating laboratories submitted to the pilot laboratory through a questionnaire and agreed upon by all participants. The traveling standards were hand carried between laboratories starting from February 2014 and were received from the last participants in October 2014. The programme was coordinated by National Metrology Institute of South Africa (NMISA), who provided the travelling standards and reference values for the comparison. The corrections to the BIPM as-maintained mass unit [5] have insignificant influence on the results of this comparison.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Final report of the SIM.QM-S7 supplementary comparison, trace metals in drinking water
Authors: Yang Lu , Nadeau Kenny , Pihillagawa Indu Gedara , Meija Juris , Grinberg Patricia , Mester Zoltan , Moya Edith Valle , Solís González Faviola Alejandra , Torres María del Rocio Arvizu , Yañez Muñoz Oscar , Lara-Manzano Judith Velina , Mazzitello Gisela , Prina Pedro , Acosta Osvaldo , Napoli Romina , Pérez Zambra Ramiro , Ferreira Elizabeth , Dobrovolskiy Vladimir , Aprelev Aleksei , Stakheev Aleksei , Frolov Dmitriy , Gusev Leonid , Ivanova Veronika , Näykki Teemu , Sara-Aho Timo , Padilla Jimmy Venegas , Acuña Cubillo Carlos , Bremmer Dwyte , Freemantle Ruel , Taebunpakul Sutthinun , Tangpaisarnkul Nongluck , Rodruangthum Patumporn , Kaewkhomdee Nattikarn , Thiengmanee Usana , Tangjit Tararat , Buzoianu Mirella , Forigua Diego Alejandro Ahumada , Gamba Johanna Paola Abella , Medina Luis Alfredo Chavarro , Sobina Egor , Tabatchikova Tatyana , Alexopoulos Charalambos , Kakoulides Elias , Delgado Mabel , Flores Liliana , Knox Saira , Siewlal Kester , Maharaj Avinash
Published: December 2017

SIM.QM-S7 was performed to assess the analytical capabilities of National Metrology Institutes (NMIs) and Designated Institutes (DIs) of SIM members (or other regions) for the accurate determination of trace metals in drinking water. The study was proposed by the coordinating laboratories National Research Council Canada (NRC) and Centro Nacional de Metrologia (CENAM) as an activity of Inorganic Analysis Working Group (IAWG) of Consultative Committee for Amount of Substance - Metrology in Chemistry and Biology (CCQM). Participants included 16 NMIs/DIs from 15 countries. No measurement method was prescribed by the coordinating laboratories. Therefore, NMIs used measurement methods of their choice. However, the majority of NMIs/DIs used ICP-MS.

This SIM.QM-S7 Supplementary Comparison provides NMIs/DIs with the needed evidence for CMC claims for trace elements in fresh waters and similar matrices.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
From Page to Stage to Screen: The Live Theatre Broadcast as a New Medium
Authors: Hitchman Lauren
Published: December 2017

The live theatre broadcast has witnessed a phenomenal rise in both popularity and profile over the past decade. This article considers the live theatre broadcast as both a new medium and a form of adaptation. It examines how the medium is ontologically, economically, and culturally positioned between theatre and film, and the extent to which it is, as John Wyver puts it, a ‘hybrid form’. Analyzing the medium in terms of Walter Benjamin’s ‘The Work of Art in the Age of Mechanical Reproduction’, I question how the live theatre broadcast challenges the ‘here’ and the ‘now’ that Benjamin sees as vital to the ‘aura’ of the work of art. I investigate how the live theatre broadcast’s lack of ‘here’ affects audience perception, and how liveness might be seen as a condition of perception rather than of transmission. Exploring Benjamin’s suggestion that film’s celebrization of the actor acts as compensation for the actor’s lack of physical presence, I ask how this concept might inform our understanding of actors in the live theatre broadcast. Finally, the article assesses the extent to which the live theatre broadcast directs the perception of the viewer, and how this direction removes the autonomy of viewing that theatre affords.
Examining Household Food Waste Decisions: A Vignette Approach
Authors: Ellison Brenna , Lusk Jayson L
Published: December 2017

Although food waste is increasingly recognized as an environmental and food security problem, there remains uncertainty over its primary contributors. Some food waste analyses seem to treat household food waste as a “mistake” or careless decision; however, consumer decisions to waste also likely reflect trade‐offs and economic incentives. These issues were explored in large surveys of U.S. food consumers using both within‐ and between‐subject designs, where we study consumers’ decisions to discard food in different scenarios that vary safety, price, and opportunity costs. We find that food waste is a function of consumers’ demographic characteristics, and that decisions to discard food vary with contextual factors.
The Economic Status of Rural America in the President Trump Era and beyond
Authors: Goetz Stephan J , Partridge Mark D , Stephens Heather M
Published: December 2017

To set the stage for future research aimed at developing public policies that support economic prosperity in rural areas, we review the current economic conditions of rural America and the current literature. Rural America is often characterized as a uniform, distressed place where agriculture dominates. In fact, rural America is diverse, with many regions doing well economically. In some areas, labor‐saving technologies have reduced the workforce in manufacturing and resource‐dependent industries. However, integration with urban areas has weakened the economic divide between urban and some rural areas, while natural amenities have boosted the fortunes of others. There is also evidence that homegrown enterprises can support growth even in the most remote, distressed regions. To support economic growth, policies should recognize the unique features of each place or region and balance the farm sector with the larger nonfarm rural economy. Economists are well‐positioned to provide research‐based evidence of what works, as well as rigorous evaluation of new polices.
Real World Home Blood Pressure Variability in Over 56,000 Individuals With Nearly 17 Million Measurements
Authors: Kim Kwang-il , Nikzad Nima , Quer Giorgio , Wineinger Nathan E , Vegreville Matthieu , Normand Alexis , Schmidt Nicolas , Topol Eric J , Steinhubl Steven
Published: December 2017

BACKGROUND

Using the data from 56,365 individuals, from 185 countries, and a Nokia Health Wireless blood pressure (BP) monitor, we investigated real-world characteristics of BP variability (BPV).

METHODS

All included individuals self-measured and uploaded their BP using Bluetooth at least 20 times over a period of ≥1 month at a frequency and duration of their choosing. In total, 16,904,844 BP measurements were analyzed, with a median of 146 measurements per person (interquartile range [IQR] 73–321) over a median of 14 months (IQR 7–31). SD, coefficient of variation, maximum BP, and maximum minus minimum BP difference were all calculated as measures of BPV.

RESULTS

BPV showed a distinct pattern, influenced by season of year, day of week, and time of day. BPV index was higher in females compared with males (P < 0.001) and increased with age (P < 0.001). Compared to the weekend, the weekday BPV index was significantly higher, and this finding was more prominent in females (P = 0.001). In multivariate analysis, BPV index were significantly associated with age, gender, geographic location, and mean BP values.

CONCLUSION

Using the largest BP data set we are aware of, with the benefits and limitations of real-world measurement, we could show the pattern of BPV and provide reference values that may be helpful in understanding the nature of BPV as self-measurement at home becomes more common, and help guide individualized management.
PINE-SPARKY.2 for automated NMR-based protein structure research
Authors: Lee Woonghee , Markley John L
Published: December 2017

Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein–ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models.

Availability and implementation

PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). For a detailed description of the program, see http://www.nmrfam.wisc.edu/pine-sparky2.htm.

Supplementary information

Supplementary data are available at Bioinformatics online.
A high-resolution map of the human small non-coding transcriptome
Authors: Fehlmann Tobias , Backes Christina , Alles Julia , Fischer Ulrike , Hart Martin , Kern Fabian , Langseth Hilde , Rounge Trine , Umu Sinan Ugur , Kahraman Mustafa , Laufer Thomas , Haas Jan , Staehler Cord , Ludwig Nicole , Hübenthal Matthias , Meder Benjamin , Franke Andre , Lenhof Hans-Peter , Meese Eckart , Keller Andreas
Published: December 2017

Motivation

Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome.

Results

In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.8% of the human genome are reliably covered by 874 123 regions with an average length of 31 nt. On the basis of these regions, we found that among the known small non-coding RNA classes, microRNAs were the most prevalent. In subsequent steps, we characterized variations of miRNAs and performed a staged validation of 11 877 candidate miRNAs. Of these, many were actually expressed and significantly dysregulated in lung cancer. Selected candidates were finally validated by northern blots. Although isolated miRNAs could still be present in the human genome, our presented set likely contains the largest fraction of human miRNAs.

Supplementary information

Supplementary data are available at Bioinformatics online.
Computational identification of binding energy hot spots in protein–RNA complexes using an ensemble approach
Authors: Pan Yuliang , Wang Zixiang , Zhan Weihua , Deng Lei
Published: December 2017

Motivation

Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein–RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein–RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage.

Results

Here, we describe a computational method, PrabHot (Prediction of protein–RNA binding hot spots), that can effectively detect hot spot residues on protein–RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein–RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result.

Availability and implementation

The PrabHot webserver is freely available at http://denglab.org/PrabHot/.

Supplementary information

Supplementary data are available at Bioinformatics online.
DPMIND: degradome-based plant miRNA–target interaction and network database
Authors: Fei Yuhan , Wang Rui , Li Haoyuan , Liu Shu , Zhang Hongsheng , Huang Ji
Published: December 2017

Motivation

MicroRNAs (miRNAs) play essential roles in plant growth, development and stress responses through post-transcriptionally regulating the expression levels of their target mRNAs. Although some tools and databases were developed for predicting the relationships between miRNAs and their targets (miR-Tar), most of them were dependent on computational methods without experimental validations. With the development of degradome sequencing techniques, researchers can identify potential interactions based on degradome sequencing data. The validations with specific degradome data are useful to identify the miR-Tar interactions (MTIs) occurring in/under some specific tissues or treatments. Degradome-based plant miRNA–target interaction and network database (DPMIND) collected almost all available plant degradome data and built a retrieval and analysis platform of miRNA–target interactions and miRNA regulatory networks (MRNs).

Results

DPMIND contains the recently updated 3794 miRNAs and 28 666 verified MTIs with 69 degradomes from 10 plant species. Not only the verified MTIs but also the degradome-based MRNs can be retrieved from DPMIND. Users can search for the verified MTIs and build degradome-based MRNs for the specific miRNAs or targets. DPMIND can build the MRNs based on all degradomes or specific degradomes, which helps to identify all possible connections among specific miR-Tar and compare the miRNA-mediated networks among various tissues or treatments. It can also build the networks mediated by all known miRNAs based on specific degradomes. Furthermore, DPMIND can be used to study the conservation and specificity of MTIs and sub-networks across different plant tissues or species.

Availability and implementation

http://202.195.246.60/DPMIND/.

Supplementary information

Supplementary data are available at Bioinformatics online.