bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of Synoptic Weather Patterns and their Persistency on Free Tropospheric Carbon Monoxide Concentrations and Outflow in Eastern China
Authors: Han Han , Liu Jane , Yuan Huiling , Jiang Fei , Zhu Ye , Wu Yue , Wang Tijian , Zhuang Bingliang
Published: June 2018

The relationship between synoptic weather patterns (SWPs) and variability of air pollution has not been fully understood. In this study, we assess the sensitivity of carbon monoxide (CO) concentrations and outflow in the free troposphere over eastern China to SWPs and their persistency, using daily CO data from the spaceborne Atmospheric Infrared Sounder (AIRS) instrument from 2003 to 2015. The SWPs over eastern China are classified into eight patterns following the Kirchhofer approach. On a regional average over the 13 years, distinct differences are observed in CO distributions and outflows among the eight SWPs. CO concentrations tend to increase under three SWPs that are characterized with anticyclonic circulations and downdrafts in all or part of eastern China. In contrast, three SWPs related to the East Asian summer monsoon (EASM) tend to reduce CO concentrations. The remaining two SWPs, dominant in winter and autumn, respectively, tend to bring more clean episodes. CO outflow from eastern China is sensitive to the influence of the SWPs on zonal winds. CO outflow is enhanced under two SWPs that prevail in winter and spring. Under the other SWPs, CO outflow decreases or changes only slightly. CO concentrations either increase or decrease by 5–15% under the persistent control of a SWP for two to seven days. In most cases, the anomalies of CO concentrations and CO outflow tend to be amplified if a SWP persists for several days. This study statistically illustrates the synoptic influences on the regional distribution and transport of air pollutants.
Crevasses as Indicators of Surge Dynamics in the Bering Bagley Glacier System, Alaska: Numerical Experiments and Comparison to Image Data Analysis
Authors: Trantow Thomas , Herzfeld Ute C.
Published: June 2018

One of the largest sources of uncertainty in sea level rise prediction is glacial acceleration, of which the surge phenomenon is the least understood type. The surge of the Bering Bagley Glacier System (BBGS), Alaska, in 2011–2013 has provided a rare opportunity to study the surge phenomenon in a large and complex glacier system. A surge results in widespread crevassing throughout the glacier system complicating many traditional techniques used to study glacier dynamics. In this paper, we utilize crevassing as a means to investigate the recent BBGS surge through numerical modeling and geostatistical data analysis. Following the principles of structural glaciology, image‐based crevasse characterizations are obtained through geostatistical methods applied to Landsat‐7 data, supplemented by airborne field observations. On the modeling side, a 3‐D full‐Stokes finite element model of the BBGS is developed and applied to investigate ice dynamics and surface structures during the recent surge. A von Mises criterion is adopted to simulate crevassing at the glacier surface, oriented along the axes of maximum principal tensile stress. To facilitate evaluation of model‐ and data‐derived crevasse characteristics, three different comparison methods are introduced. General agreement in the model‐data comparisons indicates that the model has the ability to represent the BBGS system during peak acceleration. The crevasse‐based approach is also employed to optimize the basal sliding parameter and the von Mises stress threshold in the model. Results further indicate that bed topography is an important constraint in modeling the surge process.
Geometric Controls on Tidewater Glacier Retreat in Central Western Greenland
Authors: Catania G. A. , Stearns L. A. , Sutherland D. A. , Fried M. J. , Bartholomaus T. C. , Morlighem M. , Shroyer E. , Nash J.
Published: June 2018

Glacier terminus changes are one of the hallmarks of worldwide glacier change, and thus, there is significant focus on the controls and limits to retreat in the literature. Here we use the observational record of glacier terminus change from satellite remote sensing data to characterize glacier retreat in central West Greenland with a focus on the last 30 years. We compare terminus observations of retreat to glacier/fjord geometry from available bed and bathymetry data and find that glacier retreat accelerates through wide, overdeepened parts of the bed characterized by retrograde bed slopes. We find that the morphology of the overdeepening can be used as a predictive measure for the length of retreat and that short regions (less than twice the seasonal change in terminus position) of the bed with prograde bed slopes are not sufficient to stop a retreating terminus. Even narrow overdeepenings can control glacier retreat, likely because they focus subglacial runoff, which entrains warm water in the fjords when it emerges at the grounding line and melts the terminus, creating enhanced local retreat. Future retreat of these glaciers is assessed given upstream fjord geometry.
Long‐Term Evolution of Sand Transport Through a River Network: Relative Influences of a Dam Versus Natural Changes in Grain Size From Sand Waves
Authors: Topping David J. , Mueller Erich R. , Schmidt John C. , Griffiths Ronald E. , Dean David J. , Grams Paul E.
Published: June 2018

Temporal and spatial nonuniformity in supplies of water and sand in a river network leads to sand transport that is in local disequilibrium with the upstream sand supply. In such river networks, sand is transported downstream as elongating waves in which coupled changes in grain size and transport occur. Depending on the magnitude of each sand‐supplying event and the interval between such events, changes in bed‐sand grain size associated with sand‐wave passage may more strongly regulate sand transport than do changes in water discharge. When sand transport is controlled more by episodic resupply of sand than by discharge, upstream dam construction may exacerbate or mitigate sand‐transport disequilibria, thus leading to complicated and difficult‐to‐predict patterns of deposition and erosion. We analyzed all historical sediment‐transport data and embarked on a 4‐year program of continuous sediment‐transport measurements to describe disequilibrium sand transport in a river network. Results indicate that sand transport in long river segments can evolve over ≥50‐year timescales following rare large sand‐supplying events. These natural changes in sand transport in distal downstream river segments can be larger than those caused by an upstream dam. Because there is no way to know a priori whether sand transport in a river has changed in response to changes in the upstream sand supply, contemporary continuous measurements of sand transport are required for accurate sand loads and budgeting. Analysis of only historical sediment‐transport measurements, as is common in the literature, may lead to incorrect conclusions with respect to current or future sediment‐transport conditions.
Turbulent Flow Structure Associated With Collision Between Laterally Offset, Fixed‐Bed Barchan Dunes
Authors: Bristow N. R. , Blois G. , Best J. L. , Christensen K. T.
Published: June 2018

Barchan dunes are three‐dimensional, crescent‐shaped bedforms found in regions of unidirectional flow and limited sediment supply, and while most commonly associated with aeolian environments, they have recently been observed in subaqueous domains and on the surfaces of Mars and Titan. As barchans migrate in the direction of the flow, they interact with their neighbors, typically by way of collision. The morphodynamics of such collision processes are complex, where the role of the turbulent flow structure is strongly coupled to that of sediment transport and morphological change. Here we study the flow structure in a decoupled manner through measurements of turbulent flow over fixed‐bed barchan models in a series of configurations mimicking the early stages of a laterally offset collision between two dunes. Particle image velocimetry is used to measure the flow in a refractive‐index matched flume that enables uninhibited access to the flow field to study the role that the upstream barchan plays in modifying the turbulent structure over the downstream one. Flow sheltering by the upstream barchan results in a momentum deficit in its wake that is also marked by heightened levels of turbulence over the downstream barchan. Additionally, flow asymmetry induced by the lateral offset between barchans drives a flow channeling effect around the horn of the downstream barchan. Decomposition of Reynolds shear stresses in the interdune space via quadrant analysis reveals that near‐bed turbulent fluctuations capable of mobilizing sediment are particularly enhanced at mean flow reattachment where vortices within the shear layer impact the bed.
The Cessation Threshold of Nonsuspended Sediment Transport Across Aeolian and Fluvial Environments
Authors: Pähtz Thomas , Durán Orencio
Published: June 2018

Using particle‐scale simulations of nonsuspended sediment transport for a large range of Newtonian fluids driving transport, including air and water, we determine the bulk transport cessation threshold
by extrapolating the transport load as a function of the dimensionless fluid shear stress (Shields number) Θ to the vanishing transport limit. In this limit, the simulated steady states of continuous transport can be described by simple analytical model equations relating the average transport layer properties to the law of the wall flow velocity profile. We use this model to calculate
for arbitrary environments and derive a general Shields‐like threshold diagram in which a Stokes‐like number replaces the particle Reynolds number. Despite the simplicity of our hydrodynamic description, the predicted cessation threshold, both from the simulations and analytical model, quantitatively agrees with measurements for transport in air and viscous and turbulent liquids despite not being fitted to these measurements. We interpret the analytical model as a description of a continuous rebound motion of transported particles and thus
as the minimal fluid shear stress needed to compensate the average energy loss of transported particles during an average rebound at the bed surface. This interpretation, supported by simulations near
, implies that entrainment mechanisms are needed to sustain transport above
. While entrainment by turbulent events sustains intermittent transport, entrainment by particle‐bed impacts sustains continuous transport. Combining our interpretations with the critical energy criterion for incipient motion by Valyrakis and coworkers, we put forward a new conceptual picture of sediment transport intermittency.
Studying Soil from a New Perspective
Authors: Witman Sarah
Published: June 2018

Cosmic ray neutrons probe soil moisture in the Great Plains.
In situ Raman Quantitative Detection of the Cold Seep Vents and Fluids in the Chemosynthetic Communities in the South China Sea
Authors: Du Zengfeng , Zhang Xin , Luan Zhendong , Wang Minxiao , Xi Shichuan , Li Lianfu , Wang Bing , Cao Lei , Lian Chao , Li Chaolun , Yan Jun
Published: June 2018

Based on the previously developed deep‐sea hybrid Raman insertion probe for cold seeps, the in situ detection of a cold seep vent and geochemistry analysis of fluids in chemosynthetic communities were conducted at the Formosa Ridge in the northern South China Sea. Three different methods were used to measure the components of the fluids erupting from the cold seep vent. The in situ Raman spectra of the cold seep fluids indicated the presence of gaseous CH4, C3H8, and H2S. The results indicate that the gases at this site are of biogenic origin; however, the presence of C3H8 suggests that thermogenic methane should not be excluded. The conclusion is also supported by the results of gas chromatography and stable carbon isotope analysis. More significantly, we found that the concentration of SO42− decreases with increasing depth, while the concentrations of CH4 and S8 increase in fluids in chemosynthetic communities, but without H2S. This finding indicates that the methane is oxidized by sulfate and that elemental sulfur is formed. This process usually occurs in marine sediments as the anaerobic oxidation of methane. Overall, the findings in this work provide a new insight into the geochemical analysis of cold seep fluids and in situ evidence of the oxidation of methane in the chemosynthetic communities near cold seeps.
Interdecadal Sea Level Variations in the Pacific: Distinctions Between the Tropics and Extratropics
Authors: Merrifield M. A. , Thompson P. R.
Published: June 2018

Long tide gauge records from Fremantle and San Diego are used to examine interdecadal sea level fluctuations and their relationship to Pacific climate variability. The sea level difference between the tide gauges and the Southern Oscillation Index (SOI) provide a consistent depiction of trade wind variations along the equator over the past century. The sea level difference and SOI exhibit weak interdecadal variability prior to the late 1970s, followed by an extended 40‐year period of high levels at San Diego and low at Fremantle, and low SOI levels signifying weakened equatorial trade winds. By referencing the tide gauge records to global mean sea level, we infer that Pacific trade winds exhibited weak departures from mean conditions on interdecadal time scales prior to the late 1970s and that a prolonged El Niño‐like lull dominated the tropics at the end of the century. A recent shift suggests that the trades are reverting back to the El Niño‐like state. These tropical interdecadal variations have counterparts in the extratropical North Pacific after the 1970s, as captured by the Pacific Decadal Oscillation, but the early twentieth century quiescent phase in the tropical Pacific is not reflected in the extratropics, which exhibits more energetic oscillatory behavior over the same time span.
Ion Trapping and Acceleration at Dipolarization Fronts: High‐Resolution MHD and Test‐Particle Simulations
Authors: Ukhorskiy A. Y. , Sorathia K. A. , Merkin V. G. , Sitnov M. I. , Mitchell D. G. , Gkioulidou M.
Published: June 2018

Much of plasma heating and transport from the magnetotail into the inner magnetosphere occurs in the form of mesoscale discrete injections associated with sharp dipolarizations of magnetic field (dipolarization fronts). In this paper we investigate the role of magnetic trapping in acceleration and transport of the plasma sheet ions into the ring current. For this purpose we use high‐resolution global magnetohydrodynamic (MHD) and three‐dimensional test‐particle simulations. It is shown that trapping, produced by sharp magnetic field gradients at the interface between dipolarizations and the ambient plasma, affects plasma sheet protons with energies above approximately 10 keV, enabling their transport across more than 10 Earth radii and acceleration by a factor of 10. Our estimates show that trapping is important to the buildup of the ring current plasma pressure of injected particles; depending on the plasma sheet temperature and energy spectrum, trapped protons can contribute between 20% and 60% of the plasma pressure. It is also shown that the acceleration process does not conserve the particle first invariant; on average protons are accelerated to higher energies compared to a purely adiabatic process. We also investigate how trapping and energization vary for deferent ions species and show that in accordance with recent observations, ion acceleration is proportional to the ion charge and is independent of its mass.
X‐ray Emissions in a Multiscale Fluid Model of a Streamer Discharge
Authors: Lehtinen Nikolai G. , Østgaard Nikolai
Published: June 2018

We use a three‐specie fluid model of electric discharge in air to simulate streamer evolution from the avalanche‐to‐streamer transition to the collision of opposite‐polarity streamers. We estimate the upper limit on the production of thermal runaway electrons, which is dominant during the second of these processes. More thermal runaways are produced if the ionization due to natural background and photoionization is reduced, due to possibility of creation of higher electric fields at streamer tips. The test‐particle simulation shows, however, that these thermal runaway electrons have insufficient energies to become relativistic runaways. The simulations are done in constant uniform background fields of E0=4 and 6 MV/m. A simulation was also performed in E0=2 MV/m after formation of streamers in 4‐MV/m field, in order to approximate the average background field created by ∼1‐MV voltage over a ∼1‐m electrode gap used in laboratory spark experiments. We conclude that the used fluid model is insufficient to explain X‐ray observations during such experiments. We discuss the possible role of mechanisms which were not included in this or previous modeling but may play the deciding role in the electron acceleration and X‐ray production during a streamer collision.
Identification of Extreme Ultraviolet Emission Lines of the Io Plasma Torus Observed by Hisaki/EXCEED
Authors: Hikida R. , Yoshioka K. , Murakami G. , Kimura T. , Tsuchiya F. , Yamazaki A. , Yoshikawa I. , Iwagami N.
Published: June 2018

The sulfur and oxygen ions in the Io plasma torus (IPT), which is located at a distance of ~6 RJ from Jupiter, emit light in various wavelength regions. In particular, radiative cooling in the ultraviolet wavelength range plays an important role in the energy balance of the Io torus, and it is important to explore the detailed spectral structure in the ultraviolet region. The ultraviolet spectrum of the IPT in the wavelength range 52.0–148.0 nm with a resolution of 0.3–0.4 nm was obtained by Extreme Ultraviolet Spectroscope for Exospheric Dynamics on the Hisaki satellite. Owing to its instrument performance and long integration time, 10 emission lines from the IPT were detected for the first time. By summarizing previous observations and using the results obtained by Extreme Ultraviolet Spectroscope for Exospheric Dynamics, we updated the term diagrams for S II, S III, and S IV emissions from the IPT. Four excited levels in the IPT were detected for the first time. Detection of the emission lines may improve the estimation accuracy of the fraction of hot electron density using the atomic data.
Reply to Comment by Sookhak Lari, K. and Davis, G. B. on “ ‘Large Eddy Simulation of Turbulence and Solute Transport in a Forested Headwater Stream’: Invalid Representation of Scalar Transport by the Act of Diffusion”
Authors: Khosronejad A. , Sotiropoulos F.
Published: June 2018

Based on the molecular diffusion coefficient used in the large eddy simulation (LES) (equation (3) of the article), one can easily infer that a molecular Schmidt number of 700 was adopted for the solute. It should be acknowledged that in the published article we omitted to include the value used for the molecular diffusion and did not mention that is the reciprocal of the turbulent Schmidt number. Although these details should have been included, these omissions do not change well‐established facts that in turbulent flows the mixing of the solute by the molecular diffusion is many orders of magnitude less important than that induced by the turbulence. As we mentioned in our article, the viscous sublayer in the Eagle Creek stream was not resolved in our simulations as the first node off the solid boundaries in wall units was (on average) equal to 45 (see Table 3 of the article). This implies that all of the computational nodes are located well outside of the viscous sublayer, where molecular diffusion becomes dominant. Moreover, since we carry out LES, we do not resolve the Kolmogorov scales in the flow the rate of dissipation of which is governed by molecular viscosity. Rather, the subgrid scale eddy viscosity of the LES acts as the model for the effect of the unresolved scales of motion. Even though all these are well‐known facts from fundamental theory of turbulent mixing, we include in this response additional simulations to address the concerns raised in this commentary.
Environmental Controls, Emergent Scaling, and Predictions of Greenhouse Gas (GHG) Fluxes in Coastal Salt Marshes
Authors: Abdul‐Aziz Omar I. , Ishtiaq Khandker S. , Tang Jianwu , Moseman‐Valtierra Serena , Kroeger Kevin D. , Gonneea Meagan Eagle , Mora Jordan , Morkeski Kate
Published: June 2018

Coastal salt marshes play an important role in mitigating global warming by removing atmospheric carbon at a high rate. We investigated the environmental controls and emergent scaling of major greenhouse gas (GHG) fluxes such as carbon dioxide (CO2) and methane (CH4) in coastal salt marshes by conducting data analytics and empirical modeling. The underlying hypothesis is that the salt marsh GHG fluxes follow emergent scaling relationships with their environmental drivers, leading to parsimonious predictive models. CO2 and CH4 fluxes, photosynthetically active radiation (PAR), air and soil temperatures, well water level, soil moisture, and porewater pH and salinity were measured during May–October 2013 from four marshes in Waquoit Bay and adjacent estuaries, MA, USA. The salt marshes exhibited high CO2 uptake and low CH4 emission, which did not significantly vary with the nitrogen loading gradient (5–126 kg · ha−1 · year−1) among the salt marshes. Soil temperature was the strongest driver of both fluxes, representing 2 and 4–5 times higher influence than PAR and salinity, respectively. Well water level, soil moisture, and pH did not have a predictive control on the GHG fluxes, although both fluxes were significantly higher during high tides than low tides. The results were leveraged to develop emergent power law‐based parsimonious scaling models to accurately predict the salt marsh GHG fluxes from PAR, soil temperature, and salinity (Nash‐Sutcliffe Efficiency = 0.80–0.91). The scaling models are available as a user‐friendly Excel spreadsheet named Coastal Wetland GHG Model to explore scenarios of GHG fluxes in tidal marshes under a changing climate and environment.
Structure and Evolution of Mesoscale Convective Systems: Sensitivity to Cloud Microphysics in Convection‐Permitting Simulations Over the United States
Authors: Feng Zhe , Leung L. Ruby , Houze Robert A. , Hagos Samson , Hardin Joseph , Yang Qing , Han Bin , Fan Jiwen
Published: June 2018

Regional climate simulations over the continental United States were conducted for the 2011 warm season using the Weather Research and Forecasting model at convection‐permitting resolution (4 km) with two commonly used microphysics parameterizations (Thompson and Morrison). Sensitivities of the simulated mesoscale convective system (MCS) properties and feedbacks to large‐scale environments are systematically examined against high‐resolution geostationary satellite and 3‐D mosaic radar observations. MCS precipitation including precipitation amount, diurnal cycle, and distribution of hourly precipitation intensity are reasonably captured by the two simulations despite significant differences in their simulated MCS properties. In general, the Thompson simulation produces better agreement with observations for MCS upper level cloud shield and precipitation area, convective feature horizontal and vertical extents, and partitioning between convective and stratiform precipitation. More importantly, Thompson simulates more stratiform rainfall, which agrees better with observations and results in top‐heavier heating profiles from robust MCSs compared to Morrison. A stronger dynamical feedback to the large‐scale environment is therefore seen in Thompson, wherein an enhanced mesoscale vortex behind the MCS strengthens the synoptic‐scale trough and promotes advection of cool and dry air into the rear of the MCS region. The latter prolongs the MCS lifetimes in the Thompson relative to the Morrison simulations. Hence, different treatment of cloud microphysics not only alters MCS convective‐scale dynamics but also has significant impacts on their macrophysical properties such as lifetime and precipitation. As long‐lived MCSs produced 2–3 times the amount of rainfall compared to short‐lived ones, cloud microphysics parameterizations have profound impact in simulating extreme precipitation and the hydrologic cycle.
Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects
Authors: Shaani Yoav , Zehavi Tamar , Eyal Stav , Miron Joshuah , Mizrahi Itzhak
Published: June 2018

Niche modification is a process whereby the activity of organisms modifies their local environment creating new niches for other organisms. This process can have a substantial role in community assembly of gut microbial ecosystems due to their vast and complex metabolic activities. We studied the postprandial diurnal community oscillatory patterns of the rumen microbiome and showed that metabolites produced by the rumen microbiome condition its environment and lead to dramatic diurnal changes in community composition and function. After feeding, microbiome composition undergoes considerable change in its phylogenetic breadth manifested as a significant 3–5-fold change in the relative abundance of methanogenic archaea and main bacterial taxa such as Prevotella, in a manner that was independent of individual host variation and diet. These changes in community composition were accompanied by changes in pH and methane partial pressure, suggesting a strong functional connection. Notably, cross-incubation experiments combining metabolites and organisms from different diurnal time points showed that the metabolites released by microbes are sufficient to reproduce changes in community function comparable to those observed in vivo. These findings highlight microbiome niche modification as a deterministic process that drives diurnal community assembly via environmental filtering.
Neuroimaging-informed phenotypes of suicidal behavior: a family history of suicide and the use of a violent suicidal means
Authors: Jollant Fabrice , Wagner Gerd , Richard-Devantoy Stéphane , Köhler Stefanie , Bär Karl-Jürgen , Turecki Gustavo , Pereira Fabricio
Published: June 2018

The identification of brain markers of suicidal risk is highly expected. However, neuroimaging studies have yielded mixed results, possibly due to phenotypic heterogeneity. In the present study, we addressed this issue using structural brain imaging. First, two independent samples of suicide attempters (n = 17 in Montreal, 32 in Jena), patient controls (n = 26/34), and healthy controls (n = 66/34) were scanned with magnetic resonance imaging. Groups were compared with FSL. We then reviewed the literature and run a GingerALE meta-analysis of 12 structural imaging studies comparing suicide attempters and patient controls with whole-brain analyses (n = 693). Finally, we explored the potential contribution of two variables previously associated with biological/cognitive deficits: a family history of suicide (FHoS), and the use of a violent suicidal means (VSM). Here, we added two groups of healthy first-degree biological relatives of suicide victims and depressed patients (n = 32). When comparing all suicide attempters and controls, very limited between-group differences were found in the two samples, and none in the meta-analysis. In contrast, a FHoS was associated with reduced volumes in bilateral temporal regions, right dorsolateral prefrontal cortex, and left putamen, several of these differences being observed across groups. VSM was associated with increased bilateral caudate (and left putamen) volumes. Some morphometric variations in cortico-subcortical networks may therefore be endophenotypes increasing the suicidal vulnerability, while others (notably in striatum) may modulate action selection. These results therefore confirm at the neural level two phenotypes at high lethal risk with a strong biological background, and uncover motives of heterogeneous findings in neuroimaging studies of suicidal behavior.
Arousal dependent modulation of thalamo-cortical functional interaction
Authors: Stitt Iain , Zhou Zhe Charles , Radtke-Schuller Susanne , Fröhlich Flavio
Published: June 2018

Ongoing changes in arousal influence sensory processing and behavioral performance. Yet the circuit-level correlates for this influence remain poorly understood. Here, we investigate how functional interaction between posterior parietal cortex (PPC) and lateral posterior (LP)/Pulvinar is influenced by ongoing fluctuations in pupil-linked arousal, which is a non-invasive measure of neuromodulatory tone in the brain. We find that fluctuations in pupil-linked arousal correlate with changes to PPC to LP/Pulvinar oscillatory interaction, with cortical alpha oscillations driving activity during low arousal states, and LP/Pulvinar driving PPC in the theta frequency band during higher arousal states. Active visual exploration by saccadic eye movements elicits similar transitions in thalamo-cortical interaction. Furthermore, the presentation of naturalistic video stimuli induces thalamo-cortical network states closely resembling epochs of high arousal in the absence of visual input. Thus, neuromodulators may play a role in dynamically sculpting the patterns of thalamo-cortical functional interaction that underlie visual processing.
Glycolytic metabolism is essential for CCR7 oligomerization and dendritic cell migration
Authors: Guak Hannah , Al Habyan Sara , Ma Eric H. , Aldossary Haya , Al-Masri Maia , Won So Yoon , Ying Thomas , Fixman Elizabeth D. , Jones Russell G. , McCaffrey Luke M. , Krawczyk Connie. M.
Published: June 2018

Dendritic cells (DCs) are first responders of the innate immune system that integrate signals from external stimuli to direct context-specific immune responses. Current models suggest that an active switch from mitochondrial metabolism to glycolysis accompanies DC activation to support the anabolic requirements of DC function. We show that early glycolytic activation is a common program for both strong and weak stimuli, but that weakly activated DCs lack long-term HIF-1α-dependent glycolytic reprogramming and retain mitochondrial oxidative metabolism. Early induction of glycolysis is associated with activation of AKT, TBK, and mTOR, and sustained activation of these pathways is associated with long-term glycolytic reprogramming. We show that inhibition of glycolysis impaired maintenance of elongated cell shape, DC motility, CCR7 oligomerization, and DC migration to draining lymph nodes. Together, our results indicate that early induction of glycolysis occurs independent of pro-inflammatory phenotype, and that glycolysis supports DC migratory ability regardless of mitochondrial bioenergetics.
Topological light-trapping on a dislocation
Authors: Li Fei-Fei , Wang Hai-Xiao , Xiong Zhan , Lou Qun , Chen Ping , Wu Rui-Xin , Poo Yin , Jiang Jian-Hua , John Sajeev
Published: June 2018

Topological insulators have unconventional gapless edge states where disorder-induced back-scattering is suppressed. In photonics, such edge states lead to unidirectional waveguides which are useful for integrated photonic circuitry. Cavity modes, another type of fundamental component in photonic chips, however, are not protected by band topology because of their lower dimensions. Here we demonstrate that concurrent wavevector space and real-space topology, dubbed as dual-topology, can lead to light-trapping in lower dimensions. The resultant photonic-bound state emerges as a Jackiw–Rebbi soliton mode localized on a dislocation in a two-dimensional photonic crystal, as proposed theoretically and discovered experimentally. Such a strongly confined cavity mode is found to be robust against perturbations. Our study unveils a mechanism for topological light-trapping in lower dimensions, which is invaluable for fundamental physics and various applications in photonics.
Simultaneous and stoichiometric purification of hundreds of oligonucleotides
Authors: Pinto Alessandro , Chen Sherry X. , Zhang David Yu
Published: June 2018

Purification of oligonucleotides has traditionally relied on mobility-based separation methods. However, these are imperfect, biased, and difficult to scale high multiplex. Here, we present a method for simultaneous purification of many oligonucleotides that also normalizes concentrations. The method uses a rationally designed randomer capture probe to enrich for oligos with perfect 5′ sequences, based on the observation that synthesis errors are correlated: product molecules with one or more deletions in one region are also more likely to have deletions in other regions. Next-generation sequencing analysis of 64-plex 70 nt purification products show a median 78% purity, a significant improvement over polyacrylamide gel electrophoresis and high pressure liquid chromatography (60% median purity). Additionally, 89% of the oligo products are within a factor of 2 of the median concentration.
Translational control of depression-like behavior via phosphorylation of eukaryotic translation initiation factor 4E
Authors: Aguilar-Valles Argel , Haji Nabila , De Gregorio Danilo , Matta-Camacho Edna , Eslamizade Mohammad J. , Popic Jelena , Sharma Vijendra , Cao Ruifeng , Rummel Christoph , Tanti Arnaud , Wiebe Shane , Nuñez Nicolas , Comai Stefano , Nadon Robert , Luheshi Giamal , Mechawar Naguib , Turecki Gustavo , Lacaille Jean-Claude , Gobbi Gabriella , Sonenberg Nahum
Published: June 2018

Translation of mRNA into protein has a fundamental role in neurodevelopment, plasticity, and memory formation; however, its contribution in the pathophysiology of depressive disorders is not fully understood. We investigated the involvement of MNK1/2 (MAPK-interacting serine/threonine-protein kinase 1 and 2) and their target, eIF4E (eukaryotic initiation factor 4E), in depression-like behavior in mice. Mice carrying a mutation in eIF4E for the MNK1/2 phosphorylation site (Ser209Ala, Eif4e ki/ki), the Mnk1/2 double knockout mice (Mnk1/2−/−), or mice treated with the MNK1/2 inhibitor, cercosporamide, displayed anxiety- and depression-like behaviors, impaired serotonin-induced excitatory synaptic activity in the prefrontal cortex, and diminished firing of the dorsal raphe neurons. In Eif4e ki/ki mice, brain IκBα, was decreased, while the NF-κB target, TNFα was elevated. TNFα inhibition in Eif4e ki/ki mice rescued, whereas TNFα administration to wild-type mice mimicked the depression-like behaviors and 5-HT synaptic deficits. We conclude that eIF4E phosphorylation modulates depression-like behavior through regulation of inflammatory responses.
Antifungal tolerance is a subpopulation effect distinct from resistance and is associated with persistent candidemia
Authors: Rosenberg Alexander , Ene Iuliana V. , Bibi Maayan , Zakin Shiri , Segal Ella Shtifman , Ziv Naomi , Dahan Alon M. , Colombo Arnaldo Lopes , Bennett Richard J. , Berman Judith
Published: June 2018

Tolerance to antifungal drug concentrations above the minimal inhibitory concentration (MIC) is rarely quantified, and current clinical recommendations suggest it should be ignored. Here, we quantify antifungal tolerance in Candida albicans isolates as the fraction of growth above the MIC, and find that it is distinct from susceptibility/resistance. Instead, tolerance is due to the slow growth of subpopulations of cells that overcome drug stress more efficiently than the rest of the population, and correlates inversely with intracellular drug accumulation. Many adjuvant drugs used in combination with fluconazole, a widely used fungistatic drug, reduce tolerance without affecting resistance. Accordingly, in an invertebrate infection model, adjuvant combination therapy is more effective than fluconazole in treating infections with highly tolerant isolates and does not affect infections with low tolerance isolates. Furthermore, isolates recovered from immunocompetent patients with persistent candidemia display higher tolerance than isolates readily cleared by fluconazole. Thus, tolerance correlates with, and may help predict, patient responses to fluconazole therapy.
Elucidating the genetic basis of social interaction and isolation
Authors: Day Felix R. , Ong Ken K. , Perry John R. B.
Published: June 2018

The negative impacts of social isolation and loneliness on health are well documented. However, little is known about their possible biological determinants. In up to 452,302 UK Biobank study participants, we perform genome-wide association study analyses for loneliness and regular participation in social activities. We identify 15 genomic loci (P < 5 × 10−8) for loneliness, and demonstrate a likely causal association between adiposity and increased susceptibility to loneliness and depressive symptoms. Further loci were identified for regular attendance at a sports club or gym (N = 6 loci), pub or social club (N = 13) or religious group (N = 18). Across these traits there was strong enrichment for genes expressed in brain regions that control emotional expression and behaviour. We demonstrate aetiological mechanisms specific to each trait, in addition to identifying loci that are pleiotropic across multiple complex traits. Further study of these traits may identify novel modifiable risk factors associated with social withdrawal and isolation.
Materials informatics for self-assembly of functionalized organic precursors on metal surfaces
Authors: Packwood Daniel M. , Hitosugi Taro
Published: June 2018

Bottom-up fabrication via on-surface molecular self-assembly is a way to create defect-free, low-dimensional nanomaterials. For bottom-up fabrication to succeed, precursor molecules which correctly assemble into the target structure must be first identified. Here we present an informatics technique which connects self-assembled structures with particular chemical properties of the precursor molecules. Application of this method produces a visual output (a dendrogram) that functions much like the periodic table, but whereas the periodic table puts atoms into categories according to the way in which they bond to each other, the dendrogram put molecules into categories according to the way in which they arrange in a self-assembled structure. By applying this method to the case of functionalized bianthracene precursors adsorbed to copper(111), we identify the functional groups needed to assemble one-dimensional chains, two-dimensional tilings, and other shapes. This methodology can therefore help to identify appropriate precursor molecules for forming target nanomaterials via bottom-up fabrication.
Integrating educational knowledge: reactivation of prior knowledge during educational learning enhances memory integration
Authors: van Kesteren Marlieke Tina Renée , Krabbendam Lydia , Meeter Martijn
Published: June 2018

In everyday life and in education, we continuously build and structure our knowledge. Successful knowledge construction is suggested to happen through reactivation of previously learned information during new learning. This reactivation is presumed to lead to integration of old and new memories and strengthen long-term retention. Additionally, congruency with prior knowledge is shown to enhance subsequent memory. However, it is unknown how subjective reactivation and congruency jointly influence learning in an educational context. In two experiments, we investigated this question using an AB-AC inference paradigm where students were asked to first study an AB (word-picture) and then an AC-association (word-description). BC-associations were either congruent or incongruent and were linked by a common, unknown word (A). During AC-learning, participants were instructed to actively reactivate B (the picture) and report their subjective reactivation strength. Participants were first-year university students studying either psychology or family studies and the stimuli consisted of new information from their curricula. We expected that both reactivation and congruency would enhance subsequent associative memory for the inferred BC-association. This was assessed by cueing participants with C (the description) and asking to freely describe the associated picture. Results show a significant enhancement of both B-reactivation and congruency on associative memory scores in both experiments. Additionally, subjective meta-memory measures exhibited the same effect. These outcomes, showing beneficial effects of both reactivation and congruency on memory formation, can be of interest to educational practice, where effectively building knowledge through reactivation is imperative for success.
Microstructure and mechanical properties of hard Acrocomia mexicana fruit shell
Authors: Flores-Johnson E. A. , Carrillo J. G. , Zhai C. , Gamboa R. A. , Gan Y. , Shen L.
Published: June 2018

Fruit and nut shells can exhibit high hardness and toughness. In the peninsula of Yucatan, Mexico, the fruit of the Cocoyol palm tree (Acrocomia mexicana) is well known to be very difficult to break. Its hardness has been documented since the 1500 s, and is even mentioned in the popular Maya legend The Dwarf of Uxmal. However, until now, no scientific studies quantifying the mechanical performance of the Cocoyol endocarp has been found in the literature to prove or disprove that this fruit shell is indeed “very hard”. Here we report the mechanical properties, microstructure and hardness of this material. The mechanical measurements showed compressive strength values of up to ~150 and ~250 MPa under quasi-static and high strain rate loading conditions, respectively, and microhardness of up to ~0.36 GPa. Our findings reveal a complex hierarchical structure showing that the Cocoyol shell is a functionally graded material with distinctive layers along the radial directions. These findings demonstrate that structure-property relationships make this material hard and tough. The mechanical results and the microstructure presented herein encourage designing new types of bioinspired superior synthetic materials.
High fidelity visualization of multiscale dynamics of laser-induced bubbles in liquids containing gold nanoparticles
Authors: Bhuyan Manoj K. , Soleilhac Antonin , Somayaji Madhura , Itina Tatiana E. , Antoine Rodolphe , Stoian Razvan
Published: June 2018

Cavitation in pure liquids and in liquids containing nanoparticles enables applications in mechanics, bio-medicine, and energy. Its evolution carries a significant interest. We describe the multiscale dynamic evolution of ultrafast-laser-induced cavitation in pure and gold-nanoparticles-doped liquids in one-dimensional geometries induced by non-diffractive ultrashort Bessel-Gauss laser beams. Covering the complete electronic and thermomechanical cycle, from the early plasma phase to bubble cavitation and collapse on ms timescales, we reconstitute, using time-resolved imaging with amplitude and phase sensitivity, the hydrodynamic phenomena concurring to bubble evolution. We indicate geometry-specific instabilities accompanying the collapse. The insertion of gold nanoparticles of 200 nm size has subtle effects in the process energetics. Albeit a moderate field enhancement minimizing the contribution to breakdown, the nanoparticles play a role in the overall relaxation dynamics of bubbles. The evolving bubble border in nanoparticles-containing liquids create a snow-plough effect that sweeps the nanoparticles at the gas liquid interface. This indicates that during the macroscopic cavity development, the nanoparticles were removed from the interaction region and dragged by the hydrodynamic movement. We thus shed light on the evolution of cavitation bubbles not triggered but perturbed by the presence of nanoparticles.
A comparison of the effects of agricultural pesticide uses on peripheral nerve conduction in China
Authors: Zhang Chao , Sun Yiduo , Hu Ruifa , Huang Jikun , Huang Xusheng , Li Yifan , Yin Yanhong , Chen Zhaohui
Published: June 2018

Evidence on the adverse effects of agricultural pesticide use by farmers under the actual field conditions on their peripheral nerve conduction in China is limited. This study was to investigate the association of agricultural pesticide use with the abnormalities of farmers’ peripheral nerve conduction based on two rounds of conventional nerve conduction studies. The level of pesticide exposure was assessed by measuring total amount of pesticides used by farmers in 2012. The logistic and negative binomial regression analyses were performed on a cohort study of 218 farmers. Results show that agricultural use of neither glyphosate nor non-glyphosate herbicides was not found to induce the abnormalities of farmers’ peripheral nerve conduction. However, agricultural use of organophosphorus compounds was significantly associated with increased risk of demylination disease of peripheral nerve conduction described by the reduced velocity. Moreover, the use of organonitrogen compounds by farmers would not only increase risk of demylination disease but axonal damages described by the reduced amplitude. By contrast, agricultural uses of organosulfur and pyrethroid compounds would not induce the abnormalities of farmers’ peripheral nerve conduction. The findings demonstrated the importance of developing health-friendly pesticides to replace organophosphorus and organonitrogen insecticides and fungicides in China.
Temperature-dependent virus lifecycle choices may reveal and predict facets of the biology of opportunistic pathogenic bacteria
Authors: Egilmez Halil I. , Morozov Andrew Yu. , Clokie Martha R. J. , Shan Jinyu , Letarov Andrey , Galyov Edouard E.
Published: June 2018

Melioidosis, a serious illness caused by Burkholderia pseudomallei, results in up to 40% fatality in infected patients. The pathogen is found in tropical water and soil. Recent findings demonstrated that bacterial numbers can be regulated by a novel clade of phages that are abundant in soil and water. These phages differentially infect their bacterial hosts causing lysis at high temperatures and lysogeny at lower temperatures. Thus seasonal and daily temperature variations would cause switches in phage-bacteria interactions. We developed mathematical models using realistic parameters to explore the impact of phages on B. pseudomallei populations in the surface water of rice fields over time and under seasonally changing environmental conditions. Historical records were used to provide UV radiation levels and temperature for two Thailand provinces. The models predict seasonal variation of phage-free bacterial numbers correlates with the higher risk of melioidosis acquisition during the “warm and wet” season. We find that enrichment of the environment may lead to irregular large amplitude pulses of bacterial numbers that could significantly increase the probability of disease acquisition. Our results suggest that the phages may regulate B. pseudomallei populations throughout the seasons, and these data can potentially help improve the melioidosis prevention efforts in Southeast Asia.
Comparison of multi-lineage differentiation of hiPSCs reveals novel miRNAs that regulate lineage specification
Authors: Li Lu , Miu Kai-Kei , Gu Shen , Cheung Hoi-Hung , Chan Wai-Yee
Published: June 2018

MicroRNAs (miRNAs) are known to be crucial players in governing the differentiation of human induced pluripotent stem cells (hiPSCs). Despite their utter importance, identifying key lineage specifiers among the myriads of expressed miRNAs remains challenging. We believe that the current practice in mining miRNA specifiers via delineating dynamic fold-changes only is inadequate. Our study, therefore, provides evidence to pronounce “lineage specificity” as another important attribute to qualify for these lineage specifiers. Adopted hiPSCs were differentiated into representative lineages (hepatic, nephric and neuronal) over all three germ layers whilst the depicted miRNA expression changes compiled into an integrated atlas. We demonstrated inter-lineage analysis shall aid in the identification of key miRNAs with lineage-specificity, while these shortlisted candidates were collectively known as “lineage-specific miRNAs”. Subsequently, we followed through the fold-changes along differentiation via computational analysis to identify miR-192 and miR-372-3p, respectively, as representative candidate key miRNAs for the hepatic and nephric lineages. Indeed, functional characterization validated that miR-192 and miR-372-3p regulate lineage differentiation via modulation of the expressions of lineage-specific genes. In summary, our presented miRNA atlas is a resourceful ore for the mining of key miRNAs responsible for lineage specification.