bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructural, Mineralogical and Petrographical Characteristics of the Medieval Ceramics from the Studenica Monastery (UNESCO World Heritage Site): Implications on the Pottery Technology and Provenance of The Raw Material
Authors: Šarić Kristina , Bikić Vesna , Erić Suzana
Published: December 2018

On the basis of optical microscopy, scanning electron microscopy with energy-dispersive spectrometry and X-ray powder diffraction analyses, we present detailed mineralogical and petrographical characteristics of 63 samples of cooking and tablewares, which originate from two Medieval horizons (S1 and S2) in the Studenica Monastery, as well as of three samples of clays regarded as possible pottery raw material. The composition of the ceramic matrix is compatible with the composition of local clay and clasts that reflect the geology of the Studenica’s surroundings. This indicates that almost all studied vessels are unequivocally made locally. However, four wares may represent imports because they show similarities with Byzantine sgraffito wares, and ceramics from the Peloponnese (13th century). In terms of technological and morphological characteristics, the studied pottery collection represents a standardized production. Firing temperatures, estimated according to the level of matrix crystallinity, mineral reactions, and the mode of the appearance of fracture surfaces, indicate that most of cooking wares were fired at 600–700°C. All glazed wares, including tablewares and cooking pots from both S1 and S2, were fired at minimum 800–900°C. Along with technological and morphological standardization the characteristics of the studied collection show knowledge of traditional skills as well as trends within the Byzantine artistic craft circle.
INEFFABILITY AND REVENGE
Authors: SCAMBLER CHRIS
Published: December 2018

In recent work Philip Welch has proven the existence of ‘ineffable liars’ for Hartry Field’s theory of truth. These are offered as liar-like sentences that escape classification in Field’s transfinite hierarchy of determinateness operators. In this article I present a slightly more general characterization of the ineffability phenomenon, and discuss its philosophical significance. I show the ineffable sentences to be less ‘liar-like’ than they appear in Welch’s presentation. I also point to some open technical problems whose resolution would greatly clarify the philosophical issues raised by the ineffability phenomenon.
Dennis P. Lettenmaier Receives 2018 Robert E. Horton Medal
Authors:   AGU
Published: December 2018

Dennis P. Lettenmaier was awarded the 2018 Robert E. Horton Medal at the AGU Fall Meeting Honors Ceremony, held on 12 December 2018 in Washington, D. C. The medal is for “outstanding contributions to hydrology.”
Sensitivity Kernels of PP Precursor Traveltimes and Their Limitations for Imaging Topography of Discontinuities
Authors: Koroni Maria , Paulssen Hanneke , Trampert Jeannot
Published: December 2018

We analyze the sensitivity of PP precursor traveltimes that are often used to infer lateral variation in the depths of the 410‐ and 660‐km discontinuities in the mantle. Previous results were inconclusive due to complex wave phenomena, such as multiple energy conversions and focusing/defocusing, that hamper their interpretation. Using spectral‐element synthetics and Fréchet derivatives calculated with adjoint methods, we compute sensitivity kernels for volumetric and boundary parameters in a 1‐D model for representative epicentral distances of past studies, and a dominant period of 11–25 s. Our results indicate that the boundary sensitivity of PP precursors is low and that these phases are not coherently seen in exact synthetics. Our most important finding is the strong sensitivity to both shear and compressional wave speeds, indicating that wave interference and wave conversions are dominant. The PP precursor traveltimes appear more sensitive to structural parameters, that is, compressional and shear wave speed, than to the boundaries; therefore, they are unlikely sources for valuable insight into discontinuity topography.
An Examination of Several Discrete Lunar Nearside Photometric Anomalies Observed in Lyman‐α Maps
Authors: Cahill Joshua T. S. , Wirth Anna A. , Hendrix Amanda R. , Retherford Kurt D. , Greathouse Thomas K. , Mandt Kathleen E. , Liu Yang , Greenhagen Benjamin T. , Denevi Brett W. , Stickle Angela M. , Hurley Dana M.
Published: December 2018

The Lyman Alpha Mapping Project has detected five discrete low‐albedo anomalies in Lyman‐α (Ly‐α; 121.6 nm) nighttime reflectance maps. These anomalies reside on the nearside of the Moon within the southeastern Oceanus Procellarum and northwestern Mare Nubium, coincident with regions that have been observed to be photometrically anomalous at visible wavelengths. Some of the spectral properties of these regions within near ultraviolet (NUV) to visible (VIS) wavelengths are consistent with lunar swirls, and they have been reported as “probable swirls” in at least one of these studies. However, while these regions have low Ly‐α normal albedo values relative to nearby highlands regions and are consistent with Ly‐α albedo observations of other swirls, they do not spectrally redden at wavelengths >160 nm as other swirls have been shown to do and they are not associated with regions of higher magnetic intensity. Interestingly, while these anomalies are not easily discerned in NUV single‐band images, the anomalies can be discerned in NUV color ratio composites of the Lunar Reconnaissance Orbiter Camera Wide‐Angle Camera. At least one anomaly observed in the far ultraviolet is not easily observed in the NUV. Additional analyses of their thermal emission Christiansen Feature values, empirically corrected for maturity, suggest that regolith maturity is what differentiates them from their surroundings. While these anomalies may not be swirls, they may represent an “endmember” to swirls minus the influence magnetic materials, which have been hypothesized to provide solar wind shielding. If true, they may provide additional insight into the generation of lunar swirls.
High‐Resolution Modeling of Reservoir Release and Storage Dynamics at the Continental Scale
Authors: Shin Sanghoon , Pokhrel Yadu , Miguez‐Macho Gonzalo
Published: December 2018

Manmade reservoirs are important components of the terrestrial water balance. Thus, considering the hydro‐climatic effects of reservoirs is important in water cycle studies at a river basin to global scales; yet, reservoirs are represented poorly in large‐scale hydrological and climate models. Here we present a high‐resolution (5 km) continental‐scale reservoir storage dynamics and release scheme by enhancing existing schemes and adding critical novel parameterizations to improve reservoir storage and release simulations. The new scheme simulates river‐floodplain‐reservoir storages in an integrated manner considering their spatial and temporal variations. A new calibration scheme is also incorporated to better simulate reservoir dynamics considering cascade‐reservoir effects. Further, since no reservoir bathymetry data are available over large domains, we use a state‐of‐the‐art digital elevation model and reservoir extent data to derive reservoir bed elevation. The new scheme is integrated within the river‐floodplain routing scheme of a continental hydrological model LEAF‐Hydro‐Flood. Results from the simulation of ~1,900 reservoirs within the contiguous United States suggest that the model well captures the observed reservoir storage‐release dynamics. Comparison of our results with those from the existing schemes suggest a significant improvement; importantly, the new scheme reduces the excessive and frequent reservoir overfilling and underfilling. Comparison of results with satellite‐based surface water data shows that the model accurately reproduces the large‐scale patterns of reservoir‐floodplain inundation extents. It is expected that the results of this study will inform the incorporation of reservoirs in hyper‐resolution models to improve simulations of terrestrial water storage and flow and examine reservoir‐atmosphere interactions over large domains.
Three‐Dimensional Modeling of the Coevolution of Landscape and Soil Organic Carbon
Authors: Yan Qina , Le Phong V. V. , Woo Dong K. , Hou Tingyu , Filley Timothy , Kumar Praveen
Published: December 2018

Soil organic carbon (SOC) is going through rapid reorganization due to anthropogenic influences. Understanding how biogeochemical transformation and erosion‐induced SOC redistribution influence SOC profiles and stocks is critical to our food security and adaptation to climate change. The important roles of erosion and deposition on SOC dynamics have drawn increasing attention in the past decades, but quantifying such dynamics is still challenging. Here we develop a process‐based quasi 3‐D model that couples surface runoff, soil moisture dynamics, biogeochemical transformation, and landscape evolution. We apply this model to a subcatchment in Iowa to understand how natural forcing and farming practices affect the SOC dynamics in the critical zone. The net soil thickness and SOC stock change rates are −0.336 (mm/yr) and −1.9 (g C/m2/year), respectively. Our model shows that in a fast transport landscape, SOC transport is the dominant control on SOC dynamics compared to biogeochemical transformation. The SOC profiles have “noses” below the surface at depositional sites, which are consistent with cores sampled at the same site. Generally, erosional sites are local net atmospheric carbon sinks and vice versa for depositional sites, but exceptions exist as seen in the simulation results. Furthermore, the mechanical soil mixing arising from tillage enhances SOC stock at erosional sites and reduces it at depositional ones. This study not only helps us understand the evolution of SOC stock and profiles in a watershed but can also serve as an instrument to develop practical means for protecting carbon loss due to human activities.
Compounding tropical and stratospheric forcing of the record low Antarctic sea-ice in 2016
Authors: Wang Guomin , Hendon Harry H. , Arblaster Julie M. , Lim Eun-Pa , Abhik S. , van Rensch Peter
Published: December 2018

After exhibiting an upward trend since 1979, Antarctic sea ice extent (SIE) declined dramatically during austral spring 2016, reaching a record low by December 2016. Here we show that a combination of atmospheric and oceanic phenomena played primary roles for this decline. The anomalous atmospheric circulation was initially driven by record strength tropical convection over the Indian and western Pacific Oceans, which resulted in a wave-3 circulation pattern around Antarctica that acted to reduce SIE in the Indian Ocean, Ross and Bellingshausen Sea sectors. Subsequently, the polar stratospheric vortex weakened significantly, resulting in record weakening of the circumpolar surface westerlies that acted to decrease SIE in the Indian Ocean and Pacific Ocean sectors. These processes appear to reflect unusual internal atmosphere-ocean variability. However, the warming trend of the tropical Indian Ocean, which may partly stem from anthropogenic forcing, may have contributed to the severity of the 2016 SIE decline.
Selective single molecule sequencing and assembly of a human Y chromosome of African origin
Authors: Kuderna Lukas F. K. , Lizano Esther , Julià Eva , Gomez-Garrido Jessica , Serres-Armero Aitor , Kuhlwilm Martin , Alandes Regina Antoni , Alvarez-Estape Marina , Juan David , Simon Heath , Alioto Tyler , Gut Marta , Gut Ivo , Schierup Mikkel Heide , Fornas Oscar , Marques-Bonet Tomas
Published: December 2018

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.
Compound climate events transform electrical power shortfall risk in the Pacific Northwest
Authors: Turner S. W. D. , Voisin N. , Fazio J. , Hua D. , Jourabchi M.
Published: December 2018

Power system reliability is sensitive to climate-driven variations in both energy demand and water availability, yet the combined effect of these impacts is rarely evaluated. Here we show that combined climate change impacts on loads and hydropower generation may have a transformative effect on the nature and seasonality of power shortfall risk in the U.S. Pacific Northwest. Under climate change, potential shortfall events occur more readily, but are significantly less severe in nature. A seasonal reversal in shortfall risk occurs: winter shortfalls are eradicated due to reduced building heating demands, while summer shortfalls multiply as increased peak loads for day-time cooling coincide with impaired hydropower generation. Many of these summer shortfalls go unregistered when climate change impacts on loads and hydropower dispatch are analyzed in isolation—highlighting an important role of compound events.
Quantum transport characteristics of heavily doped bismuth selenide nanoribbons
Authors: Tang Hao , Yan Xuejun , Xiong Yucheng , Dou Kunpeng , Zhao Yang , Jie Jiansheng , Wang Xiaomeng , Fu Qiang , Yang Juekuan , Lu Minghui , Xu Dongyan
Published: December 2018

This work experimentally investigated quantum transport characteristics of heavily doped bismuth selenide topological insulator nanoribbons to understand their physical origins. Transport properties of nanoribbons were measured via a suspended micro-device for eliminating the substrate effect. A series of quantum transport behaviors such as weak antilocalization, Shubnikov-de Haas oscillations, universal conductance fluctuation, and linear perpendicular-field magnetoresistance have been systematically studied to achieve a coherent understanding on their origins in topologically protected surface states, band bending, or bulk states. The parallel-field magnetoresistance, however, is found to be diverse, which can exhibit negative or positive values for the whole measurement range of the magnetic field strength or change from positive to negative values with the increase of the magnetic field strength. The tunable behavior of the parallel-field magnetoresistance is suggested to be the collective effects of the positive magnetoresistance from surface transport and the negative magnetoresistance possibly owing to the axial anomaly, resulting from long-range ionic impurity-scattering processes in bulk carriers.
Effect of the Wnt signal-RANKL/OPG axis on the enhanced osteogenic integration of a lithium incorporated surface
Authors: Huang Ting-ben , Li Yong-zheng , Yu Ke , Yu Zhou , Wang Ying , Jiang Zhi-wei , Wang Hui-ming , Yang Guo-li
Published: December 2018

Bone remolding involves the formation of new bone by osteoblasts and the absorption of old bones by osteoclasts.
Three layer-structured cadmium coordination polymers based on flexible 5-(4-pyridyl)-methoxylisophthalic acid: rapid synthesis and luminescence sensing
Authors: Guo Xiuli , Xu Jianing , Sun Jing , Chen Xiaodong , Wang Li , Fan Yong
Published: December 2018

Three layered Cd-CPs, synthesized by a MW-assisted solvothermal method within two or three minutes, serve as fluorescent sensors for Fe3+ ions.
Intramolecular geometry and intermolecular interactions of the CNO group of crystalline benzonitrile oxides: a comparison with phenyl cyanates, phenyl isocyanates, and phenyl azides
Authors: Dhami Jaya K. , Idzorek Kiersten M. , Johnson Ryan B. , Van Auken Kaitlyn S. , Ojala William H.
Published: December 2018

Crystal structures of four halogenated benzonitrile oxides allow intramolecular geometry and packing motif comparison with phenyl cyanates, isocyanates, and azides.
Self-emitting blue and red EuOX (X = F, Cl, Br, I) materials: band structure, charge transfer energy, and emission energy
Authors: Kim Donghyeon , Jeong Jae Ryeol , Jang Yujin , Bae Jong-Seong , Chung In , Liang Runli , Seo Dong-Kyun , Kim Seung-Joo , Park Jung-Chul
Published: December 2018

Novel self-emitting blue and red EuOX (X = F, Cl, Br, I) phosphors were successfully synthesized and characterized.
Mono-oxo molybdenum(vi) and tungsten(vi) complexes bearing chelating aryloxides: synthesis, structure and ring opening polymerization of cyclic esters
Authors: Sun Ziyue , Zhao Yanxia , Prior Timothy J. , Elsegood Mark R. J. , Wang Kuiyuan , Xing Tian , Redshaw Carl
Published: December 2018

Mono-oxo Mo and W complexes bearing di- or tetra-phenolates were active for the ROP of small cyclic esters, albeit with poor control. Related metallocalix[4]arenes were less active.
Synthesis of stable and phase-adjustable CsPbBr3@Cs4PbBr6 nanocrystals via novel anion–cation reactions
Authors: Xu Leimeng , Li Jianhai , Fang Tao , Zhao Yongli , Yuan Shichen , Dong Yuhui , Song Jizhong
Published: December 2018

In this study, a novel anion–cation method to synthesize highly emissive and stable diphase CsPbBr3@Cs4PbBr6 composite NCs has been developed.
Powder exfoliated MoS2 nanosheets with highly monolayer-rich structures as high-performance lithium-/sodium-ion-battery electrodes
Authors: Li Yihui , Chang Kun , Shangguan Enbo , Guo Donglei , Zhou Wei , Hou Yan , Tang Hongwei , Li Bao , Chang Zhaorong
Published: December 2018

The proposed powder exfoliated monolayer-rich MoS2 electrode exhibits remarkable specific capacities and stable cyclic performance.
Tailoring pore structures with optimal mesopores to remarkably promote DNA adsorption guiding the growth of active Mn3(PO4)2toward sensitive superoxide biomimetic enzyme sensors
Authors: Zou Zhuo , Ma Xiao Qing , Zou Long , Shi Zhuan Zhuan , Sun Qiang Qiang , Liu Qian , Liang Tao Tao , Li Chang Ming
Published: December 2018

Optimizing the structure of mesopores to greatly boost Mn3(PO4)2–DNA adsorption for a highly sensitive and selective biomimetic enzyme O2˙−sensor.
Short peptide-regulated aggregation of porphyrins for photoelectric conversion
Authors: Wang Shengjie , Zhang Dongxiu , Zhang Xiao , Yu Daoyong , Jiang Xiaofeng , Wang Zhenyang , Cao Meiwen , Xia Yongqing , Liu Heyuan
Published: December 2018

A facile method was developed to construct ordered porphyrin J-aggregates with high light-to-electron conversion efficiency through the regulation of cationic short-peptide assemblies.
LaGOON : a simple energy‐aware routing protocol for wireless nano‐sensor networks
Authors: Al‐Turjman Fadi , Kilic Kemal Ihsan
Published: December 2018

Although nanoscale sensors provide valuable data at finer levels, their size limitations impose difficulties in designing nanoscale systems. The limitations in the hardware part of such systems consequentially affect the software part too. Routing, being one of the main functions of the communication software of nano‐sensors, it requires customised design, where constraints such as the energy efficiency have to be considered. Knowing that communication is the most energy consuming operation for the sensor networks, in general, the importance of routing protocol becomes clear. With this motivation, the existing routing protocols for the wireless nano‐sensor networks are reviewed. The presentation of the classification and comparison of the existing protocols, followed by the discussion on the proposed simple energy‐aware routing protocol based on the ‘backward‐learning’ paradigm. Simulations are carried out in ns‐3 by using Nano‐Sim package. Results are listed to show the efficiency of the proposed method in terms of energy use and the packet statistics.
The Fornax 3D project: dust mix and gas properties in the centre of early-type galaxy FCC 167
Authors: Viaene S. , Sarzi M. , Zabel N. , Coccato L. , Corsini E. M. , Davis T. A. , De Vis P. , de Zeeuw P. T. , Falcón-Barroso J. , Gadotti D. A. , Iodice E. , Lyubenova M. , McDermid R. , Morelli L. , Nedelchev B. , Pinna F. , Spriggs T. W. , van de Ven G.
Published: December 2018

Galaxies continuously reprocess their interstellar material. We can therefore expect changing dust grain properties in galaxies that have followed different evolutionary pathways. Determining the intrinsic dust grain mix of a galaxy helps in reconstructing its evolutionary history. Early-type galaxies occasionally display regular dust lanes in their central regions. Owing to the relatively simple geometry and composition of their stellar bodies, these galaxies are ideal to disentangle dust mix variations from geometric effects. We therefore modelled the various components of such a galaxy (FCC 167). We reconstructed its recent history and investigated the possible fate of the dust lane. Observations from MUSE and the Atacama Large Millimeter/submillimeter Array (ALMA) reveal a nested interstellar medium structure. An ionised-gas disc pervades the central regions of FCC 167, including those occupied by the main dust lane. Inward of the dust lane, we also find a disc/ring of cold molecular gas where stars are forming and HII regions contribute to the ionised-gas emission. Further in, the gas ionisation points towards an active galactic nucleus and the fuelling of a central supermassive black hole from its surrounding ionised and molecular reservoir. Observational constraints and radiative transfer models suggest the dust and gas are distributed in a ring-like geometry and the dust mix lacks small grains. The derived dust destruction timescales from sputtering in hot gas are short, and we conclude that the dust must be strongly self-shielding and clumpy or will quickly be eroded and disappear. Our findings show how detailed analyses of individual systems can complement statistical studies of dust-lane ETGs.
The effect of film/electrode interfaces on the dielectric responses of highly (000l)-oriented M-type BaFe12O19 thin films synthesized using chemical solution deposition
Authors: Dong Wenxia , Zhang Yuanyuan , Yang Jing , Song Haili , Bai Wei , Tang Xiaodong
Published: December 2018

Highly (000l)-oriented, M-type, hexaferrite BaFe12O19 (BaM) thin films were fabricated on La0.7Sr0.3MnO3/(111)SrTiO3(LSMO/STO) and (111)Pt using chemical solution deposition. The temperature dependent dielectric properties and ac conductivity of the BaM films with different film/electrode interfaces were investigated. The results show that the chemical interfaces rather than the contact interfaces in the film/electrode played a significant role in the resulting electrical properties. For both BaM films, hopping conduction accompanied by dielectric relaxation at low frequencies was observed, which can be explained by the localized hopping of electrons through energy barriers separating different Anderson localized states, i.e., multivalent Fe sites. The X-ray photoelectron spectroscopy data confirm that the Fe2+/Fe3+ ratio of the BaM/LSMO was less than that of the BaM/Pt, which might lead to more difficult hopping processes and better electrical properties.
Cu diffusion in CdTe detected by nano-metal-plasmonic enhanced resonant Raman scattering
Authors: Shao Yanjie , Li Xun , Wu Lingling , Wang Deliang
Published: December 2018

Copper is widely used as a p-dopant in CdTe thin film solar cells. However, Cu is not stable in CdTe and its diffusion is a big concern regarding the device stability when the CdTe solar cell is applied for long-term deployment. In this work, a new technique of nano-metal-plasmonic enhanced resonant Raman scattering (RRS) was demonstrated for quantitative study of Cu diffusion in CdTe along grain boundaries. The experimental setup was designed to directly detect Cu diffusion in CdTe. The experimental results showed that Cu diffusion in CdTe can be well described by the classical diffusion mechanism. The activation energy of Cu thermal diffusion was found to be 0.40 eV, which explains the easy diffusion of Cu in CdTe.
O2 reduction on a Au film electrode in an ionic liquid in the absence and presence of Mg2+ ions: Product formation and adlayer dynamics
Authors: Jusys Zenonas , Schnaidt Johannes , Behm R. Jürgen
Published: December 2018

Aiming at a detailed understanding of the interaction between an ionic liquid, O2, and electrodes in Mg-air batteries, we performed a combined differential electrochemical mass spectrometry and in situ infrared spectroscopy model study on the interaction between the ionic liquid (IL) 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl) imide (BMP-TFSI) and a gold film electrode in the presence and absence of O2 and Mg2+ ions in the potential range relevant for the oxygen reduction reaction (ORR) and evolution reaction. Detailed information on the dynamic exchange of adsorbed ions, on the stability/decomposition of the ionic liquid, and on the activity/selectivity/reversibility of the ORR is derived from measurements performed under potentiodynamic and potentiostatic conditions. In neat BMP-TFSI, we find the dynamics of the potential induced exchange of adsorbed ions to depend significantly on the exchange direction. In the presence of O2, the anions formed in the ORR distinctly affect the adsorption characteristics of the IL ions and the exchange dynamics. Furthermore, the ORR changes from reduction to superoxide anions at moderate potentials to reduction to peroxide anion at more negative potentials. In the additional presence of Mg2+ ions, dominant magnesium peroxide and oxide formation result in an irreversible ORR, in contrast to the requirements of an efficient re-chargeable Mg-air battery. In addition, these ions result in the increasing formation of a blocking adlayer, reducing the coverage of adsorbed IL species.
Low-scaling analytical gradients for the direct random phase approximation using an atomic orbital formalism
Authors: Beuerle Matthias , Ochsenfeld Christian
Published: December 2018

We present an atomic orbital formalism to obtain analytical gradients within the random phase approximation for calculating first-order properties. Our approach allows exploiting sparsity in the electronic structure in order to reduce the computational complexity. Furthermore, we introduce Cholesky decomposed densities to remove the redundancies present in atomic orbital basis sets, making our method a competitive alternative to canonical theories also for small molecules. The approach is presented in a general framework that allows extending the methodology to other correlation methods. Beyond showing the validity and accuracy of our approach and the approximations used in this work, we demonstrate the efficiency of our method by computing nuclear gradients for systems with up to 600 atoms and 5000 basis functions.
Water fluctuation in methanol, ethanol, and 1-propanol aqueous-mixture probed by Brownian motion
Authors: Furukawa Kazuki , Kuronuma Sumito , Judai Ken
Published: December 2018

The origin of the driving force in Brownian motion is the collision between the colloidal particle and the molecules of the surrounding fluid. Therefore, Brownian motion contains information on the local solvent structures of the surrounding colloid. The mean square displacement in a water-ethanol mixture is greater than that anticipated from the macroscopic shear viscosity, indicating that the microscopic movement of Brownian motion involves the local information on the water-ethanol mixture on a molecular level, i.e., an inhomogeneity in the Brownian particle size (∼1 μm). Here, the Brownian motion of mixtures of water and methanol, ethanol, and 1-propanol are systematically investigated. Similar discrepancies between the microscopic and macroscopic viscosities are observed at low alcohol molar concentrations, for all the alcohol mixtures. This means that inhomogeneity with water fluctuation is important in explanation of the unusual Brownian diffusions of alcohol aqueous solutions. The Brownian motion also reveals a thermal energy conversion mechanism between translation and rotation.
Jellium and cell model for titratable colloids with continuous size distribution
Authors: Bareigts Guillaume , Labbez Christophe
Published: December 2018

A good understanding and determination of colloidal interactions is paramount to comprehend and model the thermodynamic and structural properties of colloidal suspensions. In concentrated aqueous suspensions of colloids with a titratable surface charge, this determination is, however, complicated by the density dependence of the effective pair potential due to both the many-body interactions and the charge regulation of the colloids. In addition, colloids generally present a size distribution which results in a virtually infinite combination of colloid pairs. In this paper, we develop two methods and describe the corresponding algorithms to solve this problem for arbitrary size distributions. An implementation in Nim is also provided. The methods, inspired by the seminal work of Torres et al., [J. Chem. Phys. 128, 154906 (2008)] are based on a generalization of the cell and renormalized jellium models to polydisperse suspensions of spherical colloids with a charge regulating boundary condition. The latter is described by the one-pK-Stern model. The predictions of the models are confronted to the equations of state of various commercially available silica dispersions. The renormalized Yukawa parameters (effective charges and screening lengths) are also calculated. The importance of size and charge polydispersity as well as the validity of these two models is discussed in light of the results.
Arithmetic of arithmetic Coxeter groups
Authors: Milea Suzana , Shelley Christopher D. , Weissman Martin H.
Published: December 2018

Significance

Conway’s topograph provided a combinatorial-geometric perspective on integer binary quadratic forms—quadratic functions of two variables with integer coefficients. This perspective is practical for solving equations and easily bounds the minima of binary quadratic forms. It appears that Conway’s topograph is just the first in a series of applications of arithmetic Coxeter groups to arithmetic. Four other applications are described in this article, and dozens more may be possible.
Clocked atom delivery to a photonic crystal waveguide
Authors: Burgers A. P. , Peng L. S. , Muniz J. A. , McClung A. C. , Martin M. J. , Kimble H. J.
Published: December 2018

Significance

Traditional atom–light coupling techniques have propelled the field of quantum optics and atomic physics. Now, by drawing on spectacular improvements in nanofabrication and nanophotonics, we advance a different platform for studying atom–light interactions. The data and simulations presented here are a first step in understanding how cold atoms are delivered to these nanophotonic structures.
Imperfect language learning vs. dynamic sound change
Authors: Reshef Yael , Gonen Einat
Published: December 2018

Modern Hebrew provides an idiosyncratic case for historical linguistic study: due to the discontinuity of its use as a spoken
language, differences between contemporary structures and classical ones do not necessarily reflect change processes, but may
instead result from imperfect language learning by the original L2 speakers of Modern Hebrew at the initial stages of speech
revival. This article offers a new research direction for delineating the boundaries between the two types of phenomena based on
the recent discovery of two collections of recordings of spontaneous Hebrew speech made in the 1960s. Focusing on one conspicuous
sound change in contemporary Modern Hebrew, namely the transition from [i] to [e] in the prefix of the verbal pattern
hif’il, we show that the variability in contemporary language between hif’il and
hef’il has two distinct sources: (i) an initial state of variability between [i] and [e] in forms derived
from weak root verbs (initial-[n] and middle-[w/y] roots, e.g. higi’a-hegi’a ‘arrived’) due to imperfect language
learning in the initial phases of the formation of Modern Hebrew; and (ii) a recent change from [i] to [e] in forms derived from
regular roots (e.g. hitxil-hetxil ‘started’). In this category, the 1960s recordings attest to a stable
realization of [i] amongst all age groups, with deviations from the rules of traditional Hebrew grammar occurring only marginally.
Based on this data, the measure of synchronic variation documented in the 1960s recordings is analyzed as a precursor of the sound
change that developed in the language at a later stage.
Nivel de competencia fonológica y edad de inicio de adquisición de español L2 en inmigrantes francófonos residentes en España
Authors: Planelles Almeida Margarita , de Saint Preux Anna Doquin
Published: December 2018

El presente estudio investiga la posibilidad de que exista relación entre la edad de inicio de adquisición de una L2 y el nivel de competencia fonológica alcanzado en inmigrantes francófonos residentes en España que aprenden español como L2. Los participantes fueron 20 aprendices francófonos de español con diferentes edades de inicio de adquisición y 6 nativos como grupo de control. Se evaluó el grado de acento extranjero en la pronunciación de los informantes a través de un panel de jueces nativos. Para el análisis de los resultados, los informantes fueron clasificados en dos grupos en función de su edad de inicio de adquisición. El análisis de los datos obtenidos muestra la existencia de una relación entre la edad de inicio de adquisición de la L2 y el nivel de competencia fonológica alcanzado. Sin embargo, el análisis de los resultados revela también la existencia de un aprendiz tardío que presentó un nivel de competencia fonológica similar al nativo, sugiriendo que es posible para los aprendices francófonos tardíos alcanzar un nivel de dominio de la pronunciación del español similar al nativo. Los resultados del estudio no son consistentes con la hipótesis de que las diferencias entre niños y adultos en la adquisición de la pronunciación de la L2 se deben a la superación de un periodo crítico (Abrahamsson, 2012;Asher y García, 1969;Granena y Long, 2012;Oyama, 1976).
Physical demands and power profile of different stage types within a cycling grand tour
Authors: Sanders Dajo , Heijboer Mathieu
Published: December 2018

This study aims to describe the intensity and load demands of different stage types within a cycling Grand Tour. Nine professional cyclists, whom are all part of the same World‐Tour professional cycling team, participated in this investigation. Competition data were collected during the 2016 Giro d'Italia. Stages within the Grand Tour were classified into four categories: flat stages (FLAT), semi‐mountainous stages (SMT), mountain stages (MT) and individual time trials (TT). Exercise intensity, measured with different heart rate and power output based variables, was highest in the TT compared to other stage types. During TT's the main proportion of time was spent at the high‐intensity zone, whilst the main proportion of time was spent at low intensity for the mass start stage types (FLAT, SMT, MT). Exercise load, quantified using Training Stress Score and Training Impulse, was highest in the mass start stage types with exercise load being highest in MT (329, 359 AU) followed by SMT (280, 311 AU) and FLAT (217, 298 AU). Substantial between‐stage type differences were observed in maximal mean power outputs over different durations. FLAT and SMT were characterised by higher short‐duration maximal power outputs (5–30 s for FLAT, 30 s–2 min for SMT) whilst TT and MT are characterised by high longer duration maximal power outputs (>10 min). The results of this study contribute to the growing body of evidence on the physical demands of stage types within a cycling Grand Tour.
Packing the Courts
Authors: Menounou Elli , Feldman Adam , Giallouri Thora , Peterson Jordan Carr
Published: December 2018

What explains expansions to the federal judiciary? Whereas existing research focuses on unified government as an explanation, we argue ideological proximity between institutions involved in the expansion process more accurately predicts judicial expansions. We examine whether Congress chose to add seats to each federal district or circuit court annually from 1937 to 2012 and find expansions are more likely when (1) the ideological distance between chambers of Congress is smaller and (2) the ideological distance between Congress and individual district or circuit courts is greater. These findings suggest the administration of federal courts is influenced by the political concerns in another branch of government, raising important questions about judicial independence.
Generation of antibody-based therapeutics targeting the idiotype of B-cell malignancies
Authors: Weiss Emily , Sarnovsky Robert , Ho Mitchell , Arons Evgeny , Kreitman Robert , Angelus Evan , Antignani Antonella , FitzGerald David
Published: December 2018

Background

A feature of many B-cell tumors is a surface-expressed immunoglobulin (sIg). The complementarity-determining regions (CDRs) of the sIg, termed the ‘idiotype’, are unique to each tumor. We report on a phage selection strategy to generate anti-idiotype therapeutics that reacts with sIg CDR3 sequences; the MEC1 B-cell tumor line was used as proof of concept.

Methods

To create a mimetic of the MEC1 idiotype, CDR3 sequences from heavy and light chains of the sIg were grafted into a single chain variable fragment (scFv) framework scaffold. Using the Tomlinson I phage library of human scFvs, we enriched for binders to MEC1 CDR3 sequences over unrelated CDR3 sequences.

Results

By ELISA we identified 10 binder phages. Of these, five were sequenced, found to be unique and characterized further. By flow cytometry each of the five phages bound to MEC1 cells, albeit with different patterns of reactivity. To establish specificity of binding and utility, the scFv sequences from two of these binders (phages 1 and 7) were converted into antibody-toxin fusion proteins (immunotoxins) and also cloned into a human IgG1 expression vector. Binders 1 and 7 immunotoxins exhibited specific killing of MEC1 cells with little toxicity for non-target B-cell lines. The full-length antibody recreated from the binder-1 scFv also exhibited specific binding.

Conclusion

Our results establish the utility of using engrafted CDR3 sequences for selecting phage that recognize the idiotype of B-cell tumors.
Surgical Management of Cosmetic Surgery Tourism-Related Complications: Current Trends and Cost Analysis Study of the Financial Impact on the UK National Health Service (NHS)
Authors: Thacoor Amitabh , van den Bosch Peter , Akhavani Mohammed Ali
Published: December 2018

Background

Cosmetic surgery tourism is thriving. Lower costs and all-inclusive cosmetic surgery holiday packages have led to more patients seeking cheaper aesthetic surgery abroad. However, limited postoperative care results in patients frequently presenting to UK National Health Service hospitals with postoperative complications requiring surgery.

Objectives

The authors sought to identify current trends and the financial impact of surgically managed complications from cosmetic surgery tourism.

Methods

A retrospective review of consecutive surgically managed patients attending a London Teaching Hospital between 2006 and 2018 with complications following cosmetic surgery abroad was performed. Patient demographics, procedure characteristics, and length of stay were determined and a comprehensive cost analysis was performed.

Results

Twenty-four patients presented with complications. Twenty-two were females aged a mean of 36 years (range, 25-58 years). Gluteal enhancement was the most common procedure (38%) and infection (92%) was the primary complication. Most procedures were undertaken in Turkey (29%) and performed in the last 5 years (63%). Twenty-one patients were inpatients and mean length of stay was 8 days (range, 1-49 days); abdominoplasty patients stayed the longest. The total cost to the hospital was $406,233, leading to an average cost per patient of $16,296 (range, $817-$41,778). Complications from abdominoplasty resulted in the highest cost per patient of $20,404.

Conclusions

Cosmetic surgery tourism is on the rise as patients travel for cheaper aesthetic surgery. There is urgent need to better address this issue to help reduce the growing financial strain on the National Health Service, safeguard patients, and optimize the use of valuable resources.
DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences
Authors: Ludwiczak Jan , Winski Aleksander , Szczepaniak Krzysztof , Alva Vikram , Dunin-Horkawicz Stanislaw
Published: December 2018

Motivation

Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function.

Results

Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains.

Availability and implementation

DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil.

Supplementary information

Supplementary data are available at Bioinformatics online.
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model
Authors: Yang Yang , Zhou Mingyu , Fang Qingwei , Shen Hong-Bin
Published: December 2018

Motivation

In the post-genomic era, image-based transcriptomics have received huge attention, because the visualization of gene expression distribution is able to reveal spatial and temporal expression pattern, which is significantly important for understanding biological mechanisms. The Berkeley Drosophila Genome Project has collected a large-scale spatial gene expression database for studying Drosophila embryogenesis. Given the expression images, how to annotate them for the study of Drosophila embryonic development is the next urgent task. In order to speed up the labor-intensive labeling work, automatic tools are highly desired. However, conventional image annotation tools are not applicable here, because the labeling is at the gene-level rather than the image-level, where each gene is represented by a bag of multiple related images, showing a multi-instance phenomenon, and the image quality varies by image orientations and experiment batches. Moreover, different local regions of an image correspond to different CV annotation terms, i.e. an image has multiple labels. Designing an accurate annotation tool in such a multi-instance multi-label scenario is a very challenging task.

Results

To address these challenges, we develop a new annotator for the fruit fly embryonic images, called AnnoFly. Driven by an attention-enhanced RNN model, it can weight images of different qualities, so as to focus on the most informative image patterns. We assess the new model on three standard datasets. The experimental results reveal that the attention-based model provides a transparent approach for identifying the important images for labeling, and it substantially enhances the accuracy compared with the existing annotation methods, including both single-instance and multi-instance learning methods.

Availability and implementation

http://www.csbio.sjtu.edu.cn/bioinf/annofly/

Supplementary information

Supplementary data are available at Bioinformatics online.
Promoter analysis and prediction in the human genome using sequence-based deep learning models
Authors: Umarov Ramzan , Kuwahara Hiroyuki , Li Yu , Gao Xin , Solovyev Victor
Published: December 2018

Motivation

Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many attempts to develop computational promoter identification methods, we have no reliable tool to analyze long genomic sequences.

Results

In this work, we further develop our deep learning approach that was relatively successful to discriminate short promoter and non-promoter sequences. Instead of focusing on the classification accuracy, in this work we predict the exact positions of the transcription start site inside the genomic sequences testing every possible location. We studied human promoters to find effective regions for discrimination and built corresponding deep learning models. These models use adaptively constructed negative set, which iteratively improves the model’s discriminative ability. Our method significantly outperforms the previously developed promoter prediction programs by considerably reducing the number of false-positive predictions. We have achieved error-per-1000-bp rate of 0.02 and have 0.31 errors per correct prediction, which is significantly better than the results of other human promoter predictors.

Availability and implementation

The developed method is available as a web server at http://www.cbrc.kaust.edu.sa/PromID/.
Skeletal and soft tissue injuries after manual and mechanical chest compressions
Authors: Friberg Niklas , Schmidbauer Simon , Walther Charles , Englund Elisabet
Published: December 2018

Aims

To determine the rate of injuries related to cardiopulmonary resuscitation (CPR) in cardiac arrest non-survivors, comparing manual CPR with CPR performed using the Lund University Cardiac Assist System (LUCAS).

Methods and results

We prospectively evaluated 414 deceased adult patients using focused, standardized post-mortem investigation in years 2005 through 2013. Skeletal and soft tissue injuries were noted, and soft tissue injuries were evaluated with respect to degree of severity. We found sternal fracture in 38%, rib fracture in 77%, and severe soft tissue injury in 1.9% of cases treated with CPR with manual chest compressions (n = 52). Treatment with LUCAS CPR (n = 362) was associated with significantly higher rates of sternal fracture (80% of cases), rib fracture (96%), and severe soft tissue injury (10%), including several cases of potentially life-threatening injuries.

Conclusion

LUCAS CPR causes significantly more CPR-related injuries than manual CPR, while providing no proven survival benefit on a population basis. We suggest judicious use of the LUCAS device for cardiac arrest.
Performance Characteristics and Clinical Value of the Lipoprotein-Associated Phospholipase A2 by an Enzymatic Kinetic Method
Authors: Lu Mengli , Lv Liying
Published: December 2018

Objective

To analyze the performance characteristics, stability, and clinical value of lipoprotein-associated phospholipase A2 (Lp-PLA2) using an enzymatic kinetic method.

Methods

The performance characteristics included reference intervals, precision, and accuracy. We assessed Lp-PLA2 stability by comparing Lp-PLA2 changes under different conditions. Lp-PLA2 was determined in the following groups: control individuals, patients with coronary heart disease (CHD), patients of different lipid subgroups within CHD, and patients with high total cholesterol (TC). Also, correlations between Lp-PLA2 and traditional cardiovascular risk factors were assessed.

Results

The mean (SD) reference interval of serum Lp-PLA2 activity was 451 (113) U per L with sex differences. Inter- and intra-assay precision revealed coefficients of variance (CVs) of 1.81% to 2.63% and 1.43% to 1.77%. The average bias was 0.33%. Lp-PLA2 activity was stable. In the CHD group, high-lipid subgroups, and high-TC group, Lp-PLA2 was elevated, and correlation was observed between Lp-PLA2 and traditional risk factors.

Conclusion

Lp-PLA2 activity has important clinical value in CHD.