bluuebunny/crossref_metadata_2025 huggingface dataset:
Validating fatty acid intake as estimated by an FFQ: how does the 24 h recall perform as reference method compared with the duplicate portion?
Authors: Trijsburg Laura , de Vries Jeanne HM , Hollman Peter CH , Hulshof Paul JM , van ’t Veer Pieter , Boshuizen Hendriek C , Geelen Anouk
Published: May 2018

Objective

To compare the performance of the commonly used 24 h recall (24hR) with the more distinct duplicate portion (DP) as reference method for validation of fatty acid intake estimated with an FFQ.

Design

Intakes of SFA, MUFA, n-3 fatty acids and linoleic acid (LA) were estimated by chemical analysis of two DP and by on average five 24hR and two FFQ. Plasma n-3 fatty acids and LA were used to objectively compare ranking of individuals based on DP and 24hR. Multivariate measurement error models were used to estimate validity coefficients and attenuation factors for the FFQ with the DP and 24hR as reference methods.

Setting

Wageningen, the Netherlands.

Subjects

Ninety-two men and 106 women (aged 20–70 years).

Results

Validity coefficients for the fatty acid estimates by the FFQ tended to be lower when using the DP as reference method compared with the 24hR. Attenuation factors for the FFQ tended to be slightly higher based on the DP than those based on the 24hR as reference method. Furthermore, when using plasma fatty acids as reference, the DP showed comparable to slightly better ranking of participants according to their intake of n-3 fatty acids (0·33) and n-3:LA (0·34) than the 24hR (0·22 and 0·24, respectively).

Conclusions

The 24hR gives only slightly different results compared with the distinctive but less feasible DP, therefore use of the 24hR seems appropriate as the reference method for FFQ validation of fatty acid intake.
Neural Network Emulation of Reionization Simulations
Authors: Schmit Claude J. , Pritchard Jonathan R.
Published: May 2018

Next generation radio experiments such as LOFAR, HERA and SKA are expected to probe the Epoch of Reionization and claim a first direct detection of the cosmic 21cm signal within the next decade. One of the major challenges for these experiments will be dealing with enormous incoming data volumes. Machine learning is key to increasing our data analysis efficiency. We consider the use of an artificial neural network to emulate 21cmFAST simulations and use it in a Bayesian parameter inference study. We then compare the network predictions to a direct evaluation of the EoR simulations and analyse the dependence of the results on the training set size. We find that the use of a training set of size 100 samples can recover the error contours of a full scale MCMC analysis which evaluates the model at each step.
The Square Kilometre Array Epoch of Reionisation and Cosmic Dawn Experiment
Authors: Trott Cathryn M.
Published: May 2018

The Square Kilometre Array (SKA) Epoch of Reionisation and Cosmic Dawn (EoR/CD) experiments aim to explore the growth of structure and production of ionising radiation in the first billion years of the Universe. Here I describe the experiments planned for the future low-frequency components of the Observatory, and work underway to define, design and execute these programs.
Status of Foreground and Instrument Challenges for 21cm EoR experiments – Design Strategies for SKA and HERA
Authors: Thyagarajan Nithyanandan
Published: May 2018

Direct detection of the Epoch of Reionization (EoR) via redshifted 21 cm line of H i will reveal the nature of the first stars and galaxies as well as revolutionize our understanding of a poorly explored evolutionary phase of the Universe. Projects such as the MWA, LOFAR, and PAPER commenced in the last decade with the promise of high significance statistical detection of the EoR, but have so far only weakly constrained models owing to unforeseen challenges from bright foreground sources and instrument systematics. It is essential for next generation instruments like the HERA and SKA to have these challenges addressed. I present an analysis of these challenges – wide-field measurements, antenna beam chromaticity, reflections in the instrument, and antenna position errors – along with performance specifications and design solutions that will be critical to designing successful next-generation instruments in enabling the first detection and also in placing meaningful constraints on reionization models.
Spatial distribution of the gamma-ray bursts at very high redshift
Authors: Mészáros Attila
Published: May 2018

The author - with his collaborators - already in years 1995-96 have shown - purely from the analyses of the observations - that the gamma-ray bursts (GRBs) can be till redshift 20. Since that time several other statistical studies of the spatial distribution of GRBs were provided. Remarkable conclusions concerning the star-formation rate and the validity of the cosmological principle were obtained about the regions of the cosmic dawn. In this contribution these efforts are surveyed.
Results From PAPER/HERA
Authors: Pober Jonathan C.
Published: May 2018

The Precision Array for Probing the Epoch of Reionization (PAPER) was a first-generation 21 cm cosmology experiment with the specific goal of detecting the power spectrum of the 21 cm emission from the Epoch of Reionization. Analysis of PAPER data is still ongoing, but lessons learned from PAPER to date have played a critical role in designing the next-generation Hydrogen Epoch of Reionization Array (HERA) experiment. This article reviews five key design choices made by PAPER: use of a non-imaging configuration, redundancy, short baselines, small antenna elements, and a large instantaneous bandwidth. We describe the impact of these choices and the role they played in designing HERA.
Formation of the First Stars and Blackholes
Authors: Yoshida Naoki
Published: May 2018

Cosmic reionization is thought to be initiated by the first generation of stars and blackholes. We review recent progress in theoretical studies of early structure formation. Cosmic structure formation is driven by gravitational instability of primeval density fluctuations left over from Big Bang. At early epochs, there are baryonic streaming motions with significant relative velocity with respect to dark matter. The formation of primordial gas clouds is typically delayed by the streaming motions, but then physical conditions for the so-called direct collapse blackhole formation are realized in proto-galactic halos. We present a promising model in which intermediate mass blackholes are formed as early as z = 30.
Quasars at the Cosmic Dawn: effects on Reionization properties in cosmological simulations
Authors: Garaldi Enrico , Compostella Michele , Porciani Cristiano
Published: May 2018

We study a model of cosmic reionization where quasars (QSOs) are the dominant source of ionizing photons at all relevant epochs. We employ a suite of adaptive hydrodynamical simulations post-processed with a multi-wavelength Monte Carlo radiative-transfer code and calibrate them in order to accurately reproduce the observed quasar luminosity function and emissivity evolution. Our results show that the QSO-only model fails in reproducing key observables linked to the Helium reionization, as the temperature evolution of the inter-galactic medium (IGM) and the HeII effective optical depth in synthetic Lyα spectra. Nevertheless, we find hints that an increased quasar contribution can explain recent measurements of a large inhomogeneity in the IGM at redshift z ≈ 5. Finally, we devise a method capable of constraining the QSOs contribution to the reionization from the properties of the HeII Lyα forest at z ≈ 3.5.
Galactic neutral hydrogen and the magnetic ISM foreground
Authors: Clark S.E.
Published: May 2018

The interstellar medium is suffused with magnetic fields, which inform the shape of structures in the diffuse gas. Recent high-dynamic range observations of Galactic neutral hydrogen, combined with novel data analysis techniques, have revealed a deep link between the morphology of neutral gas and the ambient magnetic field. At the same time, an observational revolution is underway in low-frequency radio polarimetry, driven in part by the need to characterize foregrounds to the cosmological 21-cm signal. A new generation of experiments, capable of high angular and Faraday depth resolution, are revealing complex filamentary structures in diffuse polarization. The relationship between filamentary structures observed in radio-polarimetric data and those observed in atomic hydrogen is not yet well understood. Multiwavelength observations will enable new insights into the magnetic interstellar medium across phases.
The structure of the ISM in the Zone of Avoidance by high-resolution multi-wavelength observations
Authors: Tóth L. V. , Doi Y. , Pinter S. , Kovács T. , Zahorecz S. , Bagoly Z. , Balázs L. G. , Horvath I. , Racz I. I. , Onishi T.
Published: May 2018

We estimate the column density of the Galactic foreground interstellar medium (GFISM) in the direction of extragalactic sources. All-sky AKARI FIS infrared sky survey data might be used to trace the GFISM with a resolution of 2 arcminutes. The AKARI based GFISM hydrogen column density estimates are compared with similar quantities based on HI 21cm measurements of various resolution and of Planck results. High spatial resolution observations of the GFISM may be important recalculating the physical parameters of gamma-ray burst (GRB) host galaxies using the updated foreground parameters.
Foreground Subtraction and Signal reconstruction in redshifted 21cm Global Signal Experiments using Artificial Neural Networks
Authors: Choudhury Madhurima , Datta Abhirup
Published: May 2018

Observations of HI 21cm transition line is a promising probe into the Dark Ages and Epoch-of-Reionization. Detection of this redshifted 21cm signal is one of the key science goal for several upcoming low-frequency radio telescopes like HERA, SKA and DARE. Other global signal experiments include EDGES, LEDA, BIGHORNS, SCI-HI, SARAS. One of the major challenges for the detection of this signal is the accuracy of the foreground source removal. Several novel techniques have been explored already to remove bright foregrounds from both interferometric as well as total power experiments. Here, we present preliminary results from our investigation on application of ANN to detect 21cm global signal amidst bright galactic foreground. Following the formalism of representing the global 21cm signal by ’tanh’ model, this study finds that the global 21cm signal parameters can be accurately determined even in the presence of bright foregrounds represented by 3rd order log-polynomial or higher.
Robust Foregrounds Removal for 21-cm Experiments
Authors: Mertens F. , Ghosh A. , Koopmans L. V. E.
Published: May 2018

Direct detection of the Epoch of Reionization via the redshifted 21-cm line will have unprecedented implications on the study of structure formation in the early Universe. To fulfill this promise current and future 21-cm experiments will need to detect the weak 21-cm signal over foregrounds several order of magnitude greater. This requires accurate modeling of the galactic and extragalactic emission and of its contaminants due to instrument chromaticity, ionosphere and imperfect calibration. To solve for this complex modeling, we propose a new method based on Gaussian Process Regression (GPR) which is able to cleanly separate the cosmological signal from most of the foregrounds contaminants. We also propose a new imaging method based on a maximum likelihood framework which solves for the interferometric equation directly on the sphere. Using this method, chromatic effects causing the so-called “wedge” are effectively eliminated (i.e. deconvolved) in the cylindrical (k⊥, k∥) power spectrum.
The Galactic interstellar medium: foregrounds and star formation
Authors: Miville-Deschênes Marc-Antoine
Published: May 2018

This review presents briefly two aspects of Galactic interstellar medium science that seem relevant for studying EoR. First, we give some statistical properties of the Galactic foreground emission in the diffuse regions of the sky. The properties of the emission observed in projection on the plane of the sky are then related to how matter is organised along the line of sight. The diffuse atomic gas is multi-phase, with dense filamentary structures occupying only about 1% of the volume but contributing to about 50% of the emission. The second part of the review presents aspect of structure formation in the Galactic interstellar medium that could be relevant for the subgrid physics used to model the formation of the first stars.
Measurements of the global 21-cm signal from the Cosmic Dawn
Authors: Bernardi Gianni
Published: May 2018

The sky-averaged (global) 21-cm signal is a very promising probe of the Cosmic Dawn, when the first luminous sources were formed and started to shine in a substantially neutral intergalactic medium. I here report on the status and early result of the Large-Aperture Experiment to Detect the Dark Age that focuses on observations of the global 21-cm signal in the 16 ≲ z ≲ 30 range.
Analysis of 21-cm tomographic data
Authors: Mellema Garrelt , Giri Sambit , Ghara Raghunath
Published: May 2018

The future SKA1-Low radio telescope will be powerful enough to produce tomographic images of the 21-cm signal from the Epoch of Reionization. Here we address how to identify ionized regions in such data sets, taking into account the resolution and noise levels associated with SKA1-Low. We describe three methods of which one, superpixel oversegmentation, consistently performs best.
Can Rates of Ocean Primary Production and Biological Carbon Export Be Related Through Their Probability Distributions?
Authors: Cael B. B. , Bisson Kelsey , Follett Christopher L.
Published: May 2018

We describe the basis of a theory for interpreting measurements of two key biogeochemical fluxes—primary production by phytoplankton (p, μg C · L−1 · day−1) and biological carbon export from the surface ocean by sinking particles (f, mg C · m−2 · day−1)—in terms of their probability distributions. Given that p and f are mechanistically linked but variable and effectively measured on different scales, we hypothesize that a quantitative relationship emerges between collections of the two measurements. Motivated by the many subprocesses driving production and export, we take as a null model that large‐scale distributions of p and f are lognormal. We then show that compilations of p and f measurements are consistent with this hypothesis. The compilation of p measurements is extensive enough to subregion by biome, basin, depth, or season; these subsets are also well described by lognormals, whose log‐moments sort predictably. Informed by the lognormality of both p and f we infer a statistical scaling relationship between the two quantities and derive a linear relationship between the log‐moments of their distributions. We find agreement between two independent estimates of the slope and intercept of this line and show that the distribution of f measurements is consistent with predictions made from the moments of the p distribution. These results illustrate the utility of a distributional approach to biogeochemical fluxes. We close by describing potential uses and challenges for the further development of such an approach.
Van Allen Probes Observation of a Fundamental Poloidal Standing Alfvén Wave Event Related to Giant Pulsations
Authors: Takahashi Kazue , Claudepierre Seth G. , Rankin Robert , Mann Ian R. , Smith Charles W.
Published: May 2018

The Van Allen Probes‐A spacecraft observed an ∼9‐mHz ultralow‐frequency wave on 6 October 2012, at L ∼ 5.7, in the dawn sector, and very near the magnetic equator. The wave had a strong electric field that was initially stronger in the azimuthal component and later in the radial component, exhibited properties of a fundamental standing Alfvén wave, and was associated with giant pulsations observed on the ground near the magnetic field footprint of the spacecraft. The wave was accompanied by oscillations of the flux of energetic protons (jH+). The amplitude of
oscillations was large at equatorial pitch angles away from 90°, and the energy dependence of the phase and amplitude of the oscillations exhibited features consistent with drift resonance of ∼140‐keV protons with a westward‐propagating wave having an azimuthal wave number of ∼−40. The wave was detected when the spacecraft entered a region of an earthward gradient of the proton phase space density, in support of a theoretical prediction that such a gradient can drive fundamental poloidal waves.
A Statistical Model for Earthquake Recurrence Based on the Assimilation of Paleoseismicity, Historic Seismicity, and Instrumental Seismicity
Authors: Zöller Gert
Published: May 2018

Paleoearthquakes and historic earthquakes are the most important source of information for the estimation of long‐term earthquake recurrence intervals in fault zones, because corresponding sequences cover more than one seismic cycle. However, these events are often rare, dating uncertainties are enormous, and missing or misinterpreted events lead to additional problems. In the present study, I assume that the time to the next major earthquake depends on the rate of small and intermediate events between the large ones in terms of a “clock change” model. Mathematically, this leads to a Brownian passage time distribution for recurrence intervals. I take advantage of an earlier finding that under certain assumptions the aperiodicity of this distribution can be related to the Gutenberg‐Richter b value, which can be estimated easily from instrumental seismicity in the region under consideration. In this way, both parameters of the Brownian passage time distribution can be attributed with accessible seismological quantities. This allows to reduce the uncertainties in the estimation of the mean recurrence interval, especially for short paleoearthquake sequences and high dating errors. Using a Bayesian framework for parameter estimation results in a statistical model for earthquake recurrence intervals that assimilates in a simple way paleoearthquake sequences and instrumental data. I present illustrative case studies from Southern California and compare the method with the commonly used approach of exponentially distributed recurrence times based on a stationary Poisson process.
Origin of Abyssal NW Atlantic Water Masses Since the Last Glacial Maximum
Authors: Pöppelmeier F. , Gutjahr M. , Blaser P. , Keigwin L. D. , Lippold J.
Published: May 2018

The notion of a shallow northern sourced intermediate water mass is a well evidenced feature of the Atlantic circulation scheme of the Last Glacial Maximum (LGM). However, recent observations from stable carbon isotopes (δ13C) at the Corner Rise in the deep northwest Atlantic suggested a significant contribution of a Northern Component Water mass to the abyssal northwest Atlantic basin that has not been described before. Here we test the hypothesis of this northern sourced water mass underlying the southern sourced glacial Antarctic Bottom Water by measuring the authigenic neodymium (Nd) isotopic composition from the same sediments from 5,010‐m water depth. Neodymium isotopes act as a semiconservative water mass tracer capable of distinguishing between Northern and Southern Component Waters at the northwest Atlantic. Our new Nd isotopic record resolves various water mass changes from the LGM to the early Holocene in agreement with existing Nd‐based reconstructions from across the west Atlantic Ocean. Especially pronounced are the Younger Dryas and Bølling‐Allerød with unprecedented changes in the Nd isotopic composition. For the LGM we found Nd isotopic evidence for a northern sourced water mass contributing to abyssal depths, thus being in agreement with previous δ13C data from Corner Rise. Overall, however, the deep northwest Atlantic was still dominated by southern sourced water, since we found signatures that are intermediate between northern and southern end member compositions. Furthermore, this new record indicates that C and Nd isotopes were partly decoupled, pointing to nonconservative behavior of one or more likely of both water mass proxies during the LGM.
Predicting Spatial Patterns in Precipitation Isotope (δ2H and δ18O) Seasonality Using Sinusoidal Isoscapes
Authors: Allen Scott T. , Kirchner James W. , Goldsmith Gregory R.
Published: May 2018

Understanding how precipitation isotopes vary spatially and temporally is important for tracer applications. We tested how well month‐to‐month variations in precipitation δ18O and δ2H were captured by sinusoidal cycles, and how well spatial variations in these seasonal cycles could be predicted, across Switzerland. Sine functions representing seasonal cycles in precipitation isotopes explained between 47% and 94% of the variance in monthly δ18O and δ2H values at each monitoring site. A significant sinusoidal cycle was also observed in line‐conditioned excess. We interpolated the amplitudes, phases, and offsets of these sine functions across the landscape, using multiple linear regression models based on site characteristics. These interpolated maps, here referred to as a sinusoidal isoscape, reproduced monthly observations with prediction errors that were smaller than or similar to those of other isoscapes. Sinusoidal isoscapes are likely broadly useful because they concisely describe seasonal isotopic behavior and can be estimated efficiently from sparse or irregular data.
Transient Reactivation of a Deep‐Seated Landslide by Undrained Loading Captured With Repeat Airborne and Terrestrial Lidar
Authors: Booth Adam M. , McCarley Justin , Hinkle Jason , Shaw Susan , Ampuero Jean‐Paul , Lamb Michael P.
Published: May 2018

Landslides reactivate due to external environmental forcing or internal mass redistribution, but the process is rarely documented quantitatively. We capture the three‐dimensional, 1‐m resolution surface deformation field of a transiently reactivated landslide with image correlation of repeat airborne lidar. Undrained loading by two debris flows in the landslide's head, rather than external forcing, triggered reactivation. After that loading, the lower 2 km of the landslide advanced by up to 14 m in 2 years before completely stopping. The displacement field over those 2 years implies that the slip surface gained 1 kPa of shear strength, which was likely accomplished by a negative dilatancy‐pore pressure feedback as material deformed around basal roughness elements. Thus, landslide motion can be decoupled from external environmental forcing in cases, motivating the need to better understand internal perturbations to the stress field to predict hazards and sediment fluxes as landscapes evolve.
The Effect of the Madden‐Julian Oscillation on the Mesospheric Migrating Diurnal Tide: A Study Using SD‐WACCM
Authors: Yang Chengyun , Smith Anne K. , Li Tao , Dou Xiankang
Published: May 2018

The response of the mesospheric migrating diurnal (DW1) tide to the Madden‐Julian oscillation (MJO) is investigated for the first time using a simulation from the Specified‐Dynamic Whole Atmosphere Community Climate Model (SD‐WACCM), which is driven by reanalysis data. Analysis shows that a significant connection exists between the MJO and the mesospheric DW1 tidal amplitude. During MJO phases 2 and 3, the convection anomalies are associated with enhancement in both the solar insolation absorption and latent heat release in the equatorial troposphere; these in turn lead to stronger DW1 forcing. Conversely, the forcing of DW1 by solar and latent heating in the troposphere is weaker during MJO phase 8. The difference of the tidal amplitude during the opposite MJO phases from the boreal winter mean state is ~15–20%. The parameterized gravity wave variations are found to have a significant impact on the DW1 tidal response in some phases of the MJO.
Strike‐Slip Motion Within the Yalu River Fault Zone, NE Asia: The Development of a Shear Continental Margin
Authors: Zhang Shuai , Zhu Guang , Liu Cheng , Li Yunjian , Su Nan , Xiao Shiye , Gu Chengchuan
Published: May 2018

The ca. 700‐km long Yalu River Fault Zone (YRFZ) is a major component of the NE striking strike‐slip fault system of the East Asia continental margin, which was active during the late Mesozoic. Despite its importance, the origin and timing of activity along the fault zone remain unclear. We present structural data that indicate that the NE striking YRFZ was initiated as a sinistral strike‐slip fault zone. Ductile, brittle‐ductile, and brittle structures are exposed along its length, with more ductile structures in the southwest. The shear belts and faults predominantly dip steeply to the southeast and have a minor reverse component of motion. Microstructures indicate deformation temperatures of ~300°C–500°C for the ductile region and ~200°C–300°C for the brittle‐ductile region. Inversion of fault slip data measured from brittle faults indicates that the sinistral motion was a result of N‐S compression. We present in situ zircon U‐Pb dating results for deformed and undeformed igneous rocks sampled from the ductile shear belts, indicating that sinistral faulting occurred between 146 and 131 Ma. This result correlates with the timing of a regional N‐S shortening event during the earliest Early Cretaceous. Our data, together with other published studies of this strike‐slip fault system, suggest that the East Asia shear margin was initiated at the beginning of the Early Cretaceous with the synchronous formation of a series of NE to NNE striking sinistral faults. This brief transpressive event along the shear margin was a result of the rapid, oblique subduction of the Izanagi Plate along a NNE trending trench.
A Comprehensive Analysis on the Stress Field and Seismic Anisotropy in Eastern Tibet
Authors: Yang Yihai , Liang Chuntao , Fang Lihua , Su Jinrong , Hua Qian
Published: May 2018

Widespread rotations of maximum compressive stress in the upper crust are revealed in eastern Tibet by the focal mechanism stress inversion technique. Because of the good correlation with locations of folds, anticlines, and mountains in the region, the upper crustal stress variation is related to the lateral displacement of upper crust. To compare deformations in upper crust and upper mantle, we use SKS/SKKS splitting measurements to investigate the seismic anisotropy in eastern Tibet. The fast polarization directions subparallel to the strikes of faults in Chuandian fragment and southern boundary tectonic belt. This may indicate that the induced anisotropy mainly resulted from alignment of fault fabrics by strong shearing along strike‐slip faults, while the widespread stress rotations and systemic angular difference between upper crustal stress field and seismic anisotropy suggest that the decoupling of upper crustal deformation from middle‐lower crust by a series of detachments in the process of the crust thickening resulted from the obstruction of eastward expansion by Sichuan Basin.
Engineering modular intracellular protein sensor-actuator devices
Authors: Siciliano Velia , DiAndreth Breanna , Monel Blandine , Beal Jacob , Huh Jin , Clayton Kiera L , Wroblewska Liliana , McKeon AnneMarie , Walker Bruce D. , Weiss Ron
Published: May 2018

Understanding and reshaping cellular behaviors with synthetic gene networks requires the ability to sense and respond to changes in the intracellular environment. Intracellular proteins are involved in almost all cellular processes, and thus can provide important information about changes in cellular conditions such as infections, mutations, or disease states. Here we report the design of a modular platform for intrabody-based protein sensing-actuation devices with transcriptional output triggered by detection of intracellular proteins in mammalian cells. We demonstrate reporter activation response (fluorescence, apoptotic gene) to proteins involved in hepatitis C virus (HCV) infection, human immunodeficiency virus (HIV) infection, and Huntington’s disease, and show sensor-based interference with HIV-1 downregulation of HLA-I in infected T cells. Our method provides a means to link varying cellular conditions with robust control of cellular behavior for scientific and therapeutic applications.
Neural encoding and production of functional morphemes in the posterior temporal lobe
Authors: Lee Daniel K. , Fedorenko Evelina , Simon Mirela V. , Curry William T. , Nahed Brian V. , Cahill Dan P. , Williams Ziv M.
Published: May 2018

Morphemes are the smallest meaning-carrying units in human language, and are among the most basic building blocks through which humans express specific ideas and concepts. By using time-resolved cortical stimulations, neural recordings, and focal lesion evaluations, we show that inhibition of a small cortical area within the left dominant posterior–superior temporal lobe selectively impairs the ability to produce appropriate functional morphemes but does not distinctly affect semantic and lexical retrieval, comprehension, or articulation. Additionally, neural recordings within this area reveal the localized encoding of morphological properties and their planned production prior to speech onset. Finally, small lesions localized to the gray matter in this area result in a selective functional morpheme-production deficit. Collectively, these findings reveal a detailed division of linguistic labor within the posterior–superior temporal lobe and suggest that functional morpheme processing constitutes an operationally discrete step in the series of computations essential to language production.
Quantifying compressive forces between living cell layers and within tissues using elastic round microgels
Authors: Mohagheghian Erfan , Luo Junyu , Chen Junjian , Chaudhary Gaurav , Chen Junwei , Sun Jian , Ewoldt Randy H. , Wang Ning
Published: May 2018

Increasing evidence shows that mechanical stresses are critical in regulating cell functions, fate, and diseases. However, no methods exist that can quantify isotropic compressive stresses. Here we describe fluorescent nanoparticle-labeled, monodisperse elastic microspheres made of Arg-Gly-Asp-conjugated alginate hydrogels (elastic round microgels, ERMGs). We generate 3D displacements and calculate strains and tractions exerted on an ERMG. Average compressive tractions on an ERMG are 570 Pa within cell layers and 360 Pa in tumor-repopulating cell (TRC) colonies grown in 400-Pa matrices. 3D compressive tractions on a 1.4-kPa ERMG are applied by surrounding cells via endogenous actomyosin forces but not via mature focal adhesions. Compressive stresses are substantially heterogeneous on ERMGs within a uniform cell colony and do not increase with TRC colony sizes. Early-stage zebrafish embryos generate spatial and temporal differences in local normal and shear stresses. This ERMG method could be useful for quantifying stresses in vitro and in vivo.
CO2-sensitive tRNA modification associated with human mitochondrial disease
Authors: Lin Huan , Miyauchi Kenjyo , Harada Tai , Okita Ryo , Takeshita Eri , Komaki Hirofumi , Fujioka Kaoru , Yagasaki Hideki , Goto Yu-ichi , Yanaka Kaori , Nakagawa Shinichi , Sakaguchi Yuriko , Suzuki Tsutomu
Published: May 2018

It has been generally thought that tRNA modifications are stable and static, and their frequencies are rarely regulated. N6-threonylcarbamoyladenosine (t6A) occurs at position 37 of five mitochondrial (mt-)tRNA species. We show that YRDC and OSGEPL1 are responsible for t6A37 formation, utilizing L-threonine, ATP, and CO2/bicarbonate as substrates. OSGEPL1-knockout cells exhibit respiratory defects and reduced mitochondrial translation. We find low level of t6A37 in mutant mt-tRNA isolated from the MERRF-like patient’s cells, indicating that lack of t6A37 results in pathological consequences. Kinetic measurements of t6A37 formation reveal that the Km value of CO2/bicarbonate is extremely high (31 mM), suggesting that CO2/bicarbonate is a rate-limiting factor for t6A37 formation. Consistent with this, we observe a low frequency of t6A37 in mt-tRNAs isolated from human cells cultured without bicarbonate. These findings indicate that t6A37 is regulated by sensing intracellular CO2/bicarbonate concentration, implying that mitochondrial translation is modulated in a codon-specific manner under physiological conditions.
Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs
Authors: O’Connor Rebecca E. , Romanov Michael N. , Kiazim Lucas G. , Barrett Paul M. , Farré Marta , Damas Joana , Ferguson-Smith Malcolm , Valenzuela Nicole , Larkin Denis M. , Griffin Darren K.
Published: May 2018

Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical ‘avian-like’ karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya. This genome organisation therefore predates the emergence of early dinosaurs and pterosaurs and the evolution of flight. Remaining largely unchanged interchromosomally through the dinosaur–theropod route that led to modern birds, intrachromosomal changes nonetheless reveal evolutionary breakpoint regions enriched for genes with ontology terms related to chromatin organisation and transcription. This genomic structure therefore appears highly stable yet contributes to a large degree of phenotypic diversity, as well as underpinning adaptive responses to major environmental disruptions via intrachromosomal repatterning.
Controlling evanescent waves using silicon photonic all-dielectric metamaterials for dense integration
Authors: Jahani Saman , Kim Sangsik , Atkinson Jonathan , Wirth Justin C. , Kalhor Farid , Noman Abdullah Al , Newman Ward D. , Shekhar Prashant , Han Kyunghun , Van Vien , DeCorby Raymond G. , Chrostowski Lukas , Qi Minghao , Jacob Zubin
Published: May 2018

Ultra-compact, densely integrated optical components manufactured on a CMOS-foundry platform are highly desirable for optical information processing and electronic-photonic co-integration. However, the large spatial extent of evanescent waves arising from nanoscale confinement, ubiquitous in silicon photonic devices, causes significant cross-talk and scattering loss. Here, we demonstrate that anisotropic all-dielectric metamaterials open a new degree of freedom in total internal reflection to shorten the decay length of evanescent waves. We experimentally show the reduction of cross-talk by greater than 30 times and the bending loss by greater than 3 times in densely integrated, ultra-compact photonic circuit blocks. Our prototype all-dielectric metamaterial-waveguide achieves a low propagation loss of approximately 3.7±1.0 dB/cm, comparable to those of silicon strip waveguides. Our approach marks a departure from interference-based confinement as in photonic crystals or slot waveguides, which utilize nanoscale field enhancement. Its ability to suppress evanescent waves without substantially increasing the propagation loss shall pave the way for all-dielectric metamaterial-based dense integration.
Sculpting and fusing biomimetic vesicle networks using optical tweezers
Authors: Bolognesi Guido , Friddin Mark S. , Salehi-Reyhani Ali , Barlow Nathan E. , Brooks Nicholas J. , Ces Oscar , Elani Yuval
Published: May 2018

Constructing higher-order vesicle assemblies has discipline-spanning potential from responsive soft-matter materials to artificial cell networks in synthetic biology. This potential is ultimately derived from the ability to compartmentalise and order chemical species in space. To unlock such applications, spatial organisation of vesicles in relation to one another must be controlled, and techniques to deliver cargo to compartments developed. Herein, we use optical tweezers to assemble, reconfigure and dismantle networks of cell-sized vesicles that, in different experimental scenarios, we engineer to exhibit several interesting properties. Vesicles are connected through double-bilayer junctions formed via electrostatically controlled adhesion. Chemically distinct vesicles are linked across length scales, from several nanometres to hundreds of micrometres, by axon-like tethers. In the former regime, patterning membranes with proteins and nanoparticles facilitates material exchange between compartments and enables laser-triggered vesicle merging. This allows us to mix and dilute content, and to initiate protein expression by delivering biomolecular reaction components.
Top-down descending facilitation of spinal sensory excitatory transmission from the anterior cingulate cortex
Authors: Chen Tao , Taniguchi Wataru , Chen Qi-Yu , Tozaki-Saitoh Hidetoshi , Song Qian , Liu Ren-Hao , Koga Kohei , Matsuda Tsuyoshi , Kaito-Sugimura Yae , Wang Jian , Li Zhi-Hua , Lu Ya-Cheng , Inoue Kazuhide , Tsuda Makoto , Li Yun-Qing , Nakatsuka Terumasa , Zhuo Min
Published: May 2018

Spinal sensory transmission is under descending biphasic modulation, and descending facilitation is believed to contribute to chronic pain. Descending modulation from the brainstem rostral ventromedial medulla (RVM) has been the most studied, whereas little is known about direct corticospinal modulation. Here, we found that stimulation in the anterior cingulate cortex (ACC) potentiated spinal excitatory synaptic transmission and this modulation is independent of the RVM. Peripheral nerve injury enhanced the spinal synaptic transmission and occluded the ACC-spinal cord facilitation. Inhibition of ACC reduced the enhanced spinal synaptic transmission caused by nerve injury. Finally, using optogenetics, we showed that selective activation of ACC-spinal cord projecting neurons caused behavioral pain sensitization, while inhibiting the projection induced analgesic effects. Our results provide strong evidence that ACC stimulation facilitates spinal sensory excitatory transmission by a RVM-independent manner, and that such top-down facilitation may contribute to the process of chronic neuropathic pain.
The rise of South–South trade and its effect on global CO2 emissions
Authors: Meng Jing , Mi Zhifu , Guan Dabo , Li Jiashuo , Tao Shu , Li Yuan , Feng Kuishuang , Liu Junfeng , Liu Zhu , Wang Xuejun , Zhang Qiang , Davis Steven J.
Published: May 2018

Economic globalization and concomitant growth in international trade since the late 1990s have profoundly reorganized global production activities and related CO2 emissions. Here we show trade among developing nations (i.e., South–South trade) has more than doubled between 2004 and 2011, which reflects a new phase of globalization. Some production activities are relocating from China and India to other developing countries, particularly raw materials and intermediate goods production in energy-intensive sectors. In turn, the growth of CO2 emissions embodied in Chinese exports has slowed or reversed, while the emissions embodied in exports from less-developed regions such as Vietnam and Bangladesh have surged. Although China’s emissions may be peaking, ever more complex supply chains are distributing energy-intensive industries and their CO2 emissions throughout the global South. This trend may seriously undermine international efforts to reduce global emissions that increasingly rely on rallying voluntary contributions of more, smaller, and less-developed nations.
Silicon-chip-based mid-infrared dual-comb spectroscopy
Authors: Yu Mengjie , Okawachi Yoshitomo , Griffith Austin G. , Picqué Nathalie , Lipson Michal , Gaeta Alexander L.
Published: May 2018

The development of a spectroscopy device on a chip that could realize real-time fingerprinting with label-free and high-throughput detection of trace molecules represents one of the big challenges in sensing. Dual-comb spectroscopy (DCS) in the mid-infrared is a powerful technique offering high acquisition rates and signal-to-noise ratios through use of only a single detector with no moving parts. Here, we present a nanophotonic silicon-on-insulator platform designed for mid-infrared (mid-IR) DCS. A single continuous-wave low-power pump source generates two mutually coherent mode-locked frequency combs spanning from 2.6 to 4.1 μm in two silicon microresonators. A proof-of-principle experiment of vibrational absorption DCS in the liquid phase is achieved acquiring spectra of acetone spanning from 2900 to 3100 nm at 127-GHz (4.2-cm−1) resolution. These results represent a significant step towards a broadband, mid-IR spectroscopy instrument on a chip for liquid/condensed matter phase studies.
Olfactory bulb acetylcholine release dishabituates odor responses and reinstates odor investigation
Authors: Ogg M. Cameron , Ross Jordan M. , Bendahmane Mounir , Fletcher Max L.
Published: May 2018

Habituation and dishabituation modulate the neural resources and behavioral significance allocated to incoming stimuli across the sensory systems. We characterize these processes in the mouse olfactory bulb (OB) and uncover a role for OB acetylcholine (ACh) in physiological and behavioral olfactory dishabituation. We use calcium imaging in both awake and anesthetized mice to determine the time course and magnitude of OB glomerular habituation during a prolonged odor presentation. In addition, we develop a novel behavioral investigation paradigm to determine how prolonged odor input affects odor salience. We find that manipulating OB ACh release during prolonged odor presentations using electrical or optogenetic stimulation rapidly modulates habituated glomerular odor responses and odor salience, causing mice to suddenly investigate a previously ignored odor. To demonstrate the ethological validity of this effect, we show that changing the visual context can lead to dishabituation of odor investigation behavior, which is blocked by cholinergic antagonists in the OB.
Low energy cost for cultured pearl formation in grafted chimeric Pinctada margaritifera
Authors: Le Moullac Gilles , Soyez Claude , Ky Chin-Long
Published: May 2018

The pearl oyster is one of the rare animal models that support two distinct genomes, through the surgical graft process operated for culture pearl production. This grafted organism is assimilated to a chimera whose physiological functioning remains poorly known. The question of the energy expenditure comparison between chimera and non-chimera animals arises. To answer this question, grafted and non-grafted pearl oysters were evaluated for their energetic needs by the indirect calorimetry method. This method made it possible to measure the energy expenditure based on the respiration rate (RR) measurement, reflecting the basal metabolism. The results showed that the RR values for grafted and non-grafted pearl oysters were not significantly different (p < 0.05). The estimated cost of pearl calcification including CaCO3 and proteins synthesis was 0.237 ± 0.064 J h−1, representing 0.64% of the total energy expenditure of grafted pearl oysters. This study made it possible, for the first time, to see the energy cost of cultured pearl formation in P. margaritifera and the little impact in the energetic metabolism of the chimera organism.
Simultaneous Amelioratation of Colitis and Liver Injury in Mice by Bifidobacterium longum LC67 and Lactobacillus plantarum LC27
Authors: Jang Se-Eun , Jeong Jin-Ju , Kim Jeon-Kyung , Han Myung Joo , Kim Dong-Hyun
Published: May 2018

Disturbances in the gut microbiota composition are associated with chronic inflammatory diseases of the intestine and the liver. In a preliminary study, Lactobacillus plantarum LC27 and Bifidobacterium longum LC67 could inhibit Escherichia coli growth and lipopolysaccharide-induced NF-κB activation linked to gut inflammation. Here, we investigated their effects on 2,4,6-trinitrobenzesulfonic acid (TNBS)-induced colitis and liver damage in mice. First, oral administration of LC27 or LC67 (1 × 109 CFU/mouse) inhibited TNBS-induced colon shortening [F(5,30) = 100.66, P < 0.05] and myeloperoxidase activity [F(5,30) = 56.48, P < 0.05]. These probiotics restored TNBS-induced disturbance of gut microbiota, leading to the suppression of Proteobacteria to Bacteroidetes ratio and fecal and blood lipopolysaccharide levels. Second, LC27 and LC67 inhibited TNBS-induced NF-κB activation, reversed TNBS-suppressed tight junction protein expression, and restored Th17/Treg balance. Also, treatment with LC27 or LC67 significantly decreased TNBS-induced alanine transaminase [ALT, F(5,30) = 3.50, P < 0.05] and aspartate transaminase [AST, F(5,30) = 12.81, P < 0.05] levels in the blood, as well as t-butylhydroperoxide-induced ALT and AST levels. Finally, the mixture of LC27 and LC67 (0.5 × 109 CFU/mouse, respectively) synergistically attenuated TNBS- or t-butylhydroperoxide-induced colitis and liver damage. The capability of LC27 and LC67 to reverse TNBS-mediated microbiota shift and damage signals suggests that these probiotics may synergistically attenuate colitis and liver injury by alleviating gut microbiota imbalance.
Tuning of the Hanle effect from EIT to EIA using spatially separated probe and control beams
Authors: Bhattarai Mangesh , Bharti Vineet , Natarajan Vasant
Published: May 2018

We demonstrate a technique for continuous tuning of the Hanle effect from electromagnetically induced transparency (EIT) to electromagnetically induced absorption (EIA) by changing the polarization ellipticity of a control beam. In contrast to previous work in this field, we use spatially separated probe and control beams. The experiments are done using magnetic sublevels of the Fg = 4 → Fe = 5 closed hyperfine transition in the 852 nm D2 line of 133Cs. The atoms are contained in a room temperature vapor cell with anti-relaxation (paraffin) coating on the walls. The paraffin coating is necessary for the atomic coherence to be transported between the beams. The experimental results are supported by a density-matrix analysis of the system, which also explains the observed amplitude and zero-crossing of the resonances. Such continuous tuning of the sign of a resonance has important applications in quantum memory and other precision measurements.
Urban sparrows respond to a sexually selected trait with increased aggression in noise
Authors: Phillips Jennifer N. , Derryberry Elizabeth P.
Published: May 2018

Animals modify acoustic communication signals in response to noise pollution, but consequences of these modifications are unknown. Vocalizations that transmit best in noise may not be those that best signal male quality, leading to potential conflict between selection pressures. For example, slow paced, narrow bandwidth songs transmit better in noise but are less effective in mate choice and competition than fast paced, wide bandwidth songs. We test the hypothesis that noise affects response to song pace and bandwidth in the context of competition using white-crowned sparrows (Zonotrichia leucophrys). We measure male response to song variation along a gradient of ambient noise levels in San Francisco, CA. We find that males discriminate between wide and narrow bandwidth songs but not between slow and fast paced songs. These findings are biologically relevant because songs in noisy areas tend to have narrow bandwidths. Therefore, this song phenotype potentially increases transmission distance in noise, but elicits weaker responses from competitors. Further, we find that males respond more strongly to stimuli in noisier conditions, supporting the ‘urban anger’ hypothesis. We suggest that noise affects male responsiveness to song, possibly leading to more territorial conflict in urban areas.