bluuebunny/crossref_metadata_2025 huggingface dataset:
Observations of Low‐Latitude Red Aurora in Mexico During the 1859 Carrington Geomagnetic Storm
Authors: González‐Esparza J. A. , Cuevas‐Cardona M. C.
Published: May 2018

One of the most intense geomagnetic storm that has been documented in recent history occurred on 1 September 1859. This storm is known as the Carrington Event. In the morning of 1 September at around 11:15 UT, Richard Carrington and Richard Hodgson observed in England, independently and for the first time, an intense white light solar flare. About 17 hr after this solar event, there occurred the strongest geomagnetic perturbation ever recorded as well as a greatly extended red aurora, which covered unusually at low latitudes. The red auroral display on 2 September was reported in regions where this kind of phenomena is very rare, like in Cuba and Hawaii. Until now however, it was not known to scientists that the low‐latitude red aurora is also registered in Mexico. At that time, Mexico was in a civil war, and there were very difficult conditions in where to establish astronomical and magnetic observatories. Nevertheless, the geomagnetic storm was observed with a maximum intensity between 7:00 and 8:00 UTC and was reported to a Mexican newspaper from five different locations (Mexico City, Querétaro, Guadalajara, Hidalgo, and Guanajuato) and registered also from at least in two additional sites (Michoacán and San Luis Potosí) in other historical documents. These records confirm that the Carrington geomagnetic storm was a global event with planetary repercussions, and that the Mexican low‐latitude region is susceptible to significant effects associated with intense space weather events.
Mechanisms of Earthquake‐Induced Chemical and Fluid Transport to Carbonate Groundwater Springs After Earthquakes
Authors: Rosen Michael R. , Binda Gilberto , Archer Claire , Pozzi Andrea , Michetti Alessandro M. , Noble Paula J.
Published: May 2018

Mechanisms by which hydrochemical changes occur after earthquakes are not well documented. We use the 2016–2017 central Italy seismic sequence, which caused notable hydrochemical transient variations in groundwater springs to address this topic, with special reference to effects on fractured carbonate aquifers. Hydrochemistry measured before and after the earthquakes at four springs at varying distances from the epicenters all showed immediate postmainshock peaks in trace element concentrations but little change in major elements. Most parameters returned to preearthquake values before the last events of the seismic sequence. The source of solutes, particularly trace elements, is longer residence time pore water stored in slow‐moving fractures or abandoned karstic flow paths. These fluids were expelled into the main flow paths after an increase in pore pressure, hydraulic conductivity, and shaking from coseismic aquifer stress. The weak response to the later earthquakes is explained by progressive depletion of high solute fluids as earlier shocks flushed out the stored fluids in the fractures. Spring δ13CDIC values closest to a deep magma source to the west became enriched relative to preearthquake values following the 24 August event. This enrichment indicates input from deeply sourced dissolved CO2 gas after dilation of specific fault conduits. Differences in carbon isotopic responses between springs are attributed to proximity to the deep gaseous CO2 source. Most of the transient chemical changes seen in the three fractured carbonate aquifers are attributed to local shaking and emptying of isolated pores and fractures and are not from rapid upward movement of deep fluids.
Estimating Seasonally Frozen Ground Depth From Historical Climate Data and Site Measurements Using a Bayesian Model
Authors: Qin Yue , Chen Jinsong , Yang Dawen , Wang Taihua
Published: May 2018

We develop a Bayesian model to predict the maximum thickness of seasonally frozen ground (MTSFG) using historical air temperature and precipitation observations. We use the Stefan solution and meteorological data from 11 stations to estimate the MTSFG changes from 1961 to 2016 in the Yellow River source region of northwestern China. We employ an antecedent precipitation index model to estimate changes in the liquid soil water content. The marginal posterior probability distributions of the antecedent precipitation index parameters are estimated using Markov chain Monte Carlo sampling methods. We compare the results of our stochastic method with those obtained from the traditional deterministic method and find that they are consistent in general. The stochastic approach is effective for estimating the historical changes in the frozen ground depth (root‐mean‐square errors = 0.13–0.35 m), and it provides more information on model uncertainty regarding soil moisture variations. Additionally, simulation shows that the MTSFG has decreased by 0.31 cm per year over the last 56 years on the northeastern Qinghai‐Tibet Plateau. This decrease in frost depth accelerated in the 1990s and 2000s. Considering the lack of data on seasonally frozen soil monitoring, the Bayesian method provides a pragmatic approach to statistically model frozen ground changes using available meteorological data.
Coastal Ocean Warming Adds to CO2 Burden
Authors: Brewer Peter
Published: May 2018

With coastal oceans around the world changing from the effects of urbanization, rising carbon dioxide levels, and climate warming, recent work begins to find new land-sea linkages.
Sea Ice Versus Storms: What Controls Sea Salt in Arctic Ice Cores?
Authors: Rhodes Rachael H. , Yang Xin , Wolff Eric W.
Published: May 2018

The sea ice surface is thought to be a major source of sea salt aerosol, suggesting that sodium records of polar ice cores may trace past sea ice extent. Here we test this possibility for the Arctic, using a chemical transport model to simulate aerosol emission, transport, and deposition in the satellite era. Our simulations suggest that sodium records from inland Greenland ice cores are strongly influenced by the impact of meteorology on aerosol transport and deposition. In contrast, sodium in coastal Arctic cores is predominantly sourced from the sea ice surface and the strength of these aerosol emissions controls the ice core sodium variability. Such ice cores may therefore record decadal to centennial scale Holocene sea ice changes. However, any relationship between ice core sodium and sea ice change may depend on how sea ice seasonality impacts sea salt emissions. Field‐based observations are urgently required to constrain this.
The Seismic Signature of Debris Flows: Flow Mechanics and Early Warning at Montecito, California
Authors: Lai Voon Hui , Tsai Victor C. , Lamb Michael P. , Ulizio Thomas P. , Beer Alexander R.
Published: May 2018

Debris flows are concentrated slurries of water and sediment that shape the landscape and pose a major hazard to human life and infrastructure. Seismic ground motion‐based observations promise to provide new, remote constraints on debris flow physics, but the lack of data and a theoretical basis for interpreting them hinders progress. Here we present a new mechanistic physical model for the seismic ground motion of debris flows and apply this to the devastating debris flows in Montecito, California on 9 January 2018. The amplitude and frequency characteristics of the seismic data can distinguish debris flows from other seismic sources and enable the estimation of debris‐flow speed, width, boulder sizes, and location. Results suggest that present instrumentation could have provided 5 min of early warning over limited areas, whereas a seismic array designed for debris flows would have provided 10 min of warning for most of the city.
Local Radiative Feedbacks Over the Arctic Based on Observed Short‐Term Climate Variations
Authors: Zhang Rudong , Wang Hailong , Fu Qiang , Pendergrass Angeline G. , Wang Minghuai , Yang Yang , Ma Po‐Lun , Rasch Philip J.
Published: May 2018

We compare various radiative feedbacks over the Arctic (60–90°N) estimated from short‐term climate variations occurring in reanalysis, satellite, and global climate model data sets using the combined Kernel‐Gregory approach. The lapse rate and surface albedo feedbacks are positive, and their magnitudes are comparable. Relative to the tropics (30°S–30°N), the lapse rate feedback is the largest contributor to Arctic amplification among all feedbacks, followed by surface albedo feedback and Planck feedback deviation from its global mean. Both shortwave and longwave water vapor feedbacks are positive, leading to a significant positive net water vapor feedback over the Arctic. The net cloud feedback has large uncertainties including its sign, which strongly depends on the data used for all‐sky and clear‐sky radiative fluxes at the top of the atmosphere, the time periods considered, and the methods used to estimate the cloud feedback.
GPS Interferometric Reflectometry Reveals Cyclic Elevation Changes in Thaw and Freezing Seasons in a Permafrost Area (Barrow, Alaska)
Authors: Hu Yufeng , Liu Lin , Larson Kristine M. , Schaefer Kevin M. , Zhang Jiahua , Yao Yibin
Published: May 2018

Ground surface over permafrost area undergoes seasonal subsidence and uplift caused by the annual thawing and freezing of the active layer. Applying the Global Positioning System (GPS) interferometric reflectometry technique to the signal‐to‐noise ratio data collected by a continuously operating GPS station in a permafrost area in Barrow, we retrieve the daily surface elevation changes on snow‐free days over a decade (2007–2016). Among these years, 2016 had the longest snow‐free season, offering the longest and most complete records of elevation changes. Use this year as an example, we show that the ground subsided in thaw season and then uplifted from September to early November (freezing season) with an amplitude of 5.1 ± 0.2 cm. We also develop a composite model that includes both thaw and freeze indices to characterize the cyclic movements. Our composite model effectively explains the observed cyclic elevation changes and could be used in other permafrost studies.
Evaluation of Triple‐Frequency Radar Retrieval of Snowfall Properties Using Coincident Airborne In Situ Observations During OLYMPEX
Authors: Chase Randy J. , Finlon Joseph A. , Borque Paloma , McFarquhar Greg M. , Nesbitt Stephen W. , Tanelli Simone , Sy Ousmane O. , Durden Stephen L. , Poellot Michael R.
Published: May 2018

Scattering models of precipitation‐size ice particles have shown that aggregates and spheroidal particles occupy distinct regions of the Ku‐Ka‐W‐band dual‐frequency ratio (DFR) plane. Furthermore, past ground‐based observations suggest that particle bulk density and characteristic size can be retrieved from the DFR plane. This study, for the first time, evaluates airborne DFR observations with coincident airborne microphysical measurements. Over 2 hr of microphysical data collected aboard the University of North Dakota Citation from the Olympic Mountains Experiment are matched with Airborne Precipitation and cloud Radar Third Generation triple‐frequency radar observations. Across all flights, 31% (63%) of collocated data points show nonspheroidal (spheroidal) particle scattering characteristics. DFR observations compared with in situ observations of effective density and particle characteristic size reveal relationships that could potentially be used to develop quantitative dual‐ and triple‐frequency DFR ice property retrievals.
First Simultaneous Rocket and Radar Detections of Rare Low Summer Mesospheric Clouds
Authors: Havnes O. , Latteck R. , Hartquist T. W. , Antonsen T.
Published: May 2018

On 30 June 2016 a layer of dust, possibly meteoric smoke particles (MSPs), was observed with a rocket borne probe at 69.29°N, 16.02°E and altitudes of ~74 km where patchy thin cloud layers, detected with the Middle Atmosphere Alomar Radar System, were present. The rocket traversed a layer with a net positive dust charge density of ~107 unit charges per cubic meters and a number density of neutral dust particles with sizes ≥4 nm of ~108 m−3. The positive charge density may require that elements that lower the photoelectric work function coat MSPs. The presence of this relatively large dust is consistent with smaller MSPs being swept out of the low mesospheric cloud region during the summer, while larger MSPs remain where their fall velocities equals the circulation updraught velocities. Large MSPs initially embedded in icy particles that subsequently sublimate may also fall until their fall velocities match the updraught velocities.
Advanced Molecular Techniques Provide New Rigorous Tools for Characterizing Organic Matter Quality in Complex Systems
Authors: Wilson Rachel M. , Tfaily Malak M.
Published: May 2018

Carbon flux rates are widely understood to be substrate controlled; however, characterizing substrate quality continues to be a challenge. We suggest that, while optical measurements have their place, they are not the only, or the best, tool for characterizing organic matter quality. Nominal oxidation state of the carbon provides a thermodynamically relevant measure, which could be used as a metric of organic matter quality. Calculating nominal oxidation state of the carbon requires a suite of advanced complementary analysis but is then trivial to calculate from the resulting data sets.
High-resolution multimodal flexible coherent Raman endoscope
Authors: Lombardini Alberto , Mytskaniuk Vasyl , Sivankutty Siddharth , Andresen Esben Ravn , Chen Xueqin , Wenger Jérôme , Fabert Marc , Joly Nicolas , Louradour Frédéric , Kudlinski Alexandre , Rigneault Hervé
Published: May 2018

Coherent Raman scattering microscopy is a fast, label-free, and chemically specific imaging technique that shows high potential for future in vivo optical histology. However, the imaging depth in tissues is limited to the sub-millimeter range because of absorption and scattering. Realization of coherent Raman imaging using a fiber endoscope system is a crucial step towards imaging deep inside living tissues and providing information that is inaccessible with current microscopy tools. Until now, the development of coherent Raman endoscopy has been hampered by several issues, mainly related to the fiber delivery of the excitation pulses and signal collection. Here, we present a flexible, compact, coherent Raman, and multimodal nonlinear endoscope (4.2 mm outer diameter, 71 mm rigid length) based on a resonantly scanned hollow-core Kagomé-lattice double-clad fiber. The fiber design enables distortion-less, background-free delivery of femtosecond excitation pulses and back-collection of nonlinear signals through the same fiber. Sub-micrometer spatial resolution over a large field of view is obtained by combination of a miniature objective lens with a silica microsphere lens inserted into the fiber core. We demonstrate high-resolution, high-contrast coherent anti-Stokes Raman scattering, and second harmonic generation endoscopic imaging of biological tissues over a field of view of 320 µm at a rate of 0.8 frames per second. These results pave the way for intraoperative label-free imaging applied to real-time histopathology diagnosis and surgery guidance.
Weight loss and mortality risk in patients with different adiposity at diagnosis of type 2 diabetes: a longitudinal cohort study
Authors: Owusu Ebenezer S. Adjah , Samanta Mayukh , Shaw Jonathan E. , Majeed Azeem , Khunti Kamlesh , Paul Sanjoy K.
Published: May 2018

Background

Undiagnosed comorbid diseases that independently lead to weight loss before type 2 diabetes mellitus (T2DM) diagnosis could explain the observed increased mortality risk in T2DM patients with normal weight.

Objectives

To evaluate the impact of weight change patterns before the diagnosis of T2DM on the association between body mass index (BMI) at diagnosis and mortality risk.

Methods

This was a longitudinal cohort study using 145,058 patients from UK primary care, with newly diagnosed T2DM from January 2000. Patients aged 18–70, without established disease history at diagnosis (defined as the presence of cardiovascular diseases, cancer, and renal diseases on or before diagnosis) were followed up to 2014. Longitudinal 6-monthly measures of bodyweight three years before (used to define groups of patients who lost bodyweight or not before diagnosis) and 2 years after diagnosis were obtained. The main outcome was all-cause mortality.

Results

At diagnosis, mean (SD) age was 52 (12) years, 56% were male, 52% were current or ex-smokers, mean BMI was 33 kg/m2, and 66% were obese. Normal weight and overweight patients experienced a small but significant reduction in body weight 6 months before diagnosis. Among all categories of obese patients, consistently increasing body weight was observed within the same time window.

Among patients who did not lose body weight pre-diagnosis (n = 117,469), compared with the grade 1 obese, normal weight patients had 35% (95% CI of HR: 1.17, 1.55) significantly higher adjusted mortality risk. However, among patients experiencing weight loss before diagnosis (n = 27,589), BMI at diagnosis was not associated with mortality risk (all p > 0.05).

Conclusions

Weight loss before the diagnosis of T2DM was not associated with the observed increased mortality risk in normal weight patients with T2DM. This emphasises the importance of addressing risk factors post diagnosis for excess mortality in this group.
Bdellovibrio bacteriovorus HD100, a predator of Gram-negative bacteria, benefits energetically from Staphylococcus aureus biofilms without predation
Authors: Im Hansol , Dwidar Mohammed , Mitchell Robert J
Published: May 2018

Bdellovibrio bacteriovorus HD100 is a predatory bacterium which lives by invading the periplasm of Gram-negative bacteria and consuming them from within. Although B. bacteriovorus HD100 attacks only Gram-negative bacterial strains, our work here shows attack-phase predatory cells also benefit from interacting with Gram-positive biofilms. Using Staphylococcus aureus biofilms, we show this predator degrades the biofilm matrix, obtains nutrients and uses these to produce and secrete proteolytic enzymes to continue this process. When exposed to S. aureus biofilms, the transcriptome of B. bacteriovorus HD100 was analogous to that seen when present intraperiplasmically, suggesting it is responding similarly as when in a prey. Moreover, two of the induced proteases (Bd2269 and Bd2692) were purified and their activities against S. aureus biofilms verified. In addition, B. bacteriovorus HD100 gained several clear benefits from its interactions with S. aureus biofilms, including increased ATP pools and improved downstream predatory activities when provided prey.
Author Correction: High-performance, polymer-based direct cellular interfaces for electrical stimulation and recording
Authors: Kim Seong-Min , Kim Nara , Kim Youngseok , Baek Min-Seo , Yoo Minsu , Kim Dongyoon , Lee Won-June , Kang Dong-Hee , Kim Sohee , Lee Kwanghee , Yoon Myung-Han
Published: May 2018

Correction to:NPG Asia Materials (2018) 10.1038/s41427-018-0014-9 published online on 16 April 2018
The homeobox protein VentX reverts immune suppression in the tumor microenvironment
Authors: Le Yi , Gao Hong , Bleday Ronald , Zhu Zhenglun
Published: May 2018

Immune suppression in the tumor microenvironment (TME) is a central obstacle to effective immunotherapy. Tumor-associated macrophages (TAMs) are key components of the TME. Although TAMs have been viewed as an ideal target of intervention to steer immunity in cancer treatment, the approach has been hampered by the lack of knowledge of how TAM plasticity is controlled by cell intrinsic factors. VentX is a homeobox protein implicated in proliferation and differentiation of human hematopoietic and immune cells. Using clinical samples obtained from cancer patients, we find that VentX expression is drastically reduced in TAMs. We show here that VentX promotes M1 differentiation of TAMs, and that VentX-regulated TAMs, in turn, revert immune suppression at the TME. Using a NSG mouse model of human colon cancers, we demonstrate that VentX regulates TAM function in tumorigenesis in vivo. Our findings suggest a mechanism underlying immune suppression at TME and potential applications of VentX-regulated TAMs in cancer immunotherapy.
The global flood protection savings provided by coral reefs
Authors: Beck Michael W. , Losada Iñigo J. , Menéndez Pelayo , Reguero Borja G. , Díaz-Simal Pedro , Fernández Felipe
Published: May 2018

Coral reefs can provide significant coastal protection benefits to people and property. Here we show that the annual expected damages from flooding would double, and costs from frequent storms would triple without reefs. For 100-year storm events, flood damages would increase by 91% to $US 272 billion without reefs. The countries with the most to gain from reef management are Indonesia, Philippines, Malaysia, Mexico, and Cuba; annual expected flood savings exceed $400 M for each of these nations. Sea-level rise will increase flood risk, but substantial impacts could happen from reef loss alone without better near-term management. We provide a global, process-based valuation of an ecosystem service across an entire marine biome at (sub)national levels. These spatially explicit benefits inform critical risk and environmental management decisions, and the expected benefits can be directly considered by governments (e.g., national accounts, recovery plans) and businesses (e.g., insurance).
In vivo base editing of post-mitotic sensory cells
Authors: Yeh Wei-Hsi , Chiang Hao , Rees Holly A. , Edge Albert S. B. , Liu David R.
Published: May 2018

Programmable nucleases can introduce precise changes to genomic DNA through homology-directed repair (HDR). Unfortunately, HDR is largely restricted to mitotic cells, and is typically accompanied by an excess of stochastic insertions and deletions (indels). Here we present an in vivo base editing strategy that addresses these limitations. We use nuclease-free base editing to install a S33F mutation in β-catenin that blocks β-catenin phosphorylation, impedes β-catenin degradation, and upregulates Wnt signaling. In vitro, base editing installs the S33F mutation with a 200-fold higher editing:indel ratio than HDR. In post-mitotic cells in mouse inner ear, injection of base editor protein:RNA:lipid installs this mutation, resulting in Wnt activation that induces mitosis of cochlear supporting cells and cellular reprogramming. In contrast, injection of HDR agents does not induce Wnt upregulation. These results establish a strategy for modifying posttranslational states in signaling pathways, and an approach to precision editing in post-mitotic tissues.
Amplitude mode in the planar triangular antiferromagnet Na0.9MnO2
Authors: Dally Rebecca L. , Zhao Yang , Xu Zhijun , Chisnell Robin , Stone M. B. , Lynn Jeffrey W. , Balents Leon , Wilson Stephen D.
Published: May 2018

Amplitude modes arising from symmetry breaking in materials are of broad interest in condensed matter physics. These modes reflect an oscillation in the amplitude of a complex order parameter, yet are typically unstable and decay into oscillations of the order parameter’s phase. This renders stable amplitude modes rare, and exotic effects in quantum antiferromagnets have historically provided a realm for their detection. Here we report an alternate route to realizing amplitude modes in magnetic materials by demonstrating that an antiferromagnet on a two-dimensional anisotropic triangular lattice (α-Na0.9MnO2) exhibits a long-lived, coherent oscillation of its staggered magnetization field. Our results show that geometric frustration of Heisenberg spins with uniaxial single-ion anisotropy can renormalize the interactions of a dense two-dimensional network of moments into largely decoupled, one-dimensional chains that manifest a longitudinally polarized-bound state. This bound state is driven by the Ising-like anisotropy inherent to the Mn3+ ions of this compound.
Mapping uncharted territory in ice from zeolite networks to ice structures
Authors: Engel Edgar A. , Anelli Andrea , Ceriotti Michele , Pickard Chris J. , Needs Richard J.
Published: May 2018

Ice is one of the most extensively studied condensed matter systems. Yet, both experimentally and theoretically several new phases have been discovered over the last years. Here we report a large-scale density-functional-theory study of the configuration space of water ice. We geometry optimise 74,963 ice structures, which are selected and constructed from over five million tetrahedral networks listed in the databases of Treacy, Deem, and the International Zeolite Association. All prior knowledge of ice is set aside and we introduce “generalised convex hulls” to identify configurations stabilised by appropriate thermodynamic constraints. We thereby rediscover all known phases (I–XVII, i, 0 and the quartz phase) except the metastable ice IV. Crucially, we also find promising candidates for ices XVIII through LI. Using the “sketch-map” dimensionality-reduction algorithm we construct an a priori, navigable map of configuration space, which reproduces similarity relations between structures and highlights the novel candidates. By relating the known phases to the tractably small, yet structurally diverse set of synthesisable candidate structures, we provide an excellent starting point for identifying formation pathways.
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms
Authors: Mazein Alexander , Ostaszewski Marek , Kuperstein Inna , Watterson Steven , Le Novère Nicolas , Lefaudeux Diane , De Meulder Bertrand , Pellet Johann , Balaur Irina , Saqi Mansoor , Nogueira Maria Manuela , He Feng , Parton Andrew , Lemonnier Nathanaël , Gawron Piotr , Gebel Stephan , Hainaut Pierre , Ollert Markus , Dogrusoz Ugur , Barillot Emmanuel , Zinovyev Andrei , Schneider Reinhard , Balling Rudi , Auffray Charles
Published: May 2018

The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes.
Author Correction: Evaluation of three methods for biomass estimation in small invertebrates, using three large disparate parasite species as model organisms
Authors: Llopis-Belenguer Cristina , Blasco-Costa Isabel , Balbuena Juan Antonio
Published: May 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Lateral intraparietal area (LIP) is largely effector-specific in free-choice decisions
Authors: Christopoulos Vassilios N. , Kagan Igor , Andersen Richard A.
Published: May 2018

Despite many years of intense research, there is no strong consensus about the role of the lateral intraparietal area (LIP) in decision making. One view of LIP function is that it guides spatial attention, providing a “saliency map” of the external world. If this were the case, it would contribute to target selection regardless of which action would be performed to implement the choice. On the other hand, LIP inactivation has been shown to influence spatial selection and oculomotor metrics in free-choice decisions, which are made using eye movements, arguing that it contributes to saccade decisions. To dissociate between a more general attention role and a more effector specific saccade role, we reversibly inactivated LIP while non-human primates freely selected between two targets, presented in the two hemifields, with either saccades or reaches. Unilateral LIP inactivation induced a strong choice bias to ipsilesional targets when decisions were made with saccades. Interestingly, the inactivation also caused a reduction of contralesional choices when decisions were made with reaches, albeit the effect was less pronounced. These findings suggest that LIP is part of a network for making oculomotor decisions and is largely effector-specific in free-choice decisions.
Field Effect Transistor Based on Layered NiPS
3
Authors: Jenjeti Ramesh Naidu , Kumar Rajat , Austeria Muthu P. , Sampath S.
Published: May 2018

Layered metal phosphochalcogenides of molecular formula, MPX3 (M = Mn, Fe, Co, Ni, etc and X = S, Se) have been emerging as new class of semiconductors towards various catalytic and optoelectronic applications. The low cleavage energy associated with these layered chalcogenides may lead to devices with very thin semiconductor channels. Herein, we report the first successful fabrication of field effect transistor (FET) using layered NiPS3 that reveals n-type semiconducting behavior. Devices using bulk and few-layer NiPS3 with gold contacts show on/off ratios of ~103–105 at 25 °C. The device characteristics reveal an increase in on-state current with decrease in threshold voltage and the Schottky barrier height is extracted to be 112 meV. Density functional theory calculations reveal various parameters that affect electron/hole doping in the layered phosphochalcogenide material.
The structural and proteomic analysis of Spiroplasma eriocheiris in response to colchicine
Authors: Liu Peng , Du Jie , Zhang Jia , Wang Jian , Gu Wei , Wang Wen , Meng Qingguo
Published: May 2018

Spiroplasma eriocheiris, a pathogen that causes mass mortality of Chinese mitten crab Eriocheir sinensis, is a wall less bacteria and belongs to the Mollicutes. This study was designed to investigate the effects of colchicine on S. eriocheiris growth, cell morphology, and proteins expression. We found that in the presence of colchicine, the spiroplasma cells lost their helicity, and the length of the cells in the experimental group was longer than that of the control. With varying concentrations of the colchicine treatment, the total time to achieve a stationary phase of the spiroplasma was increased, and the cell population was decreased. The virulence ability of S. eriocheiris to E. sinensis was effectively reduced in the presence of colchicine. To expound the toxical mechanism of colchicine on S. eriocheiris, 208 differentially expressed proteins of S. eriocheiris were reliably quantified by iTRAQ analysis, including 77 up-regulated proteins and 131 down-regulated proteins. Especially, FtsY, putative Spiralin, and NADH oxidase were down-regulated. F0F1 ATP synthase subunit delta, ParB, DNABs, and NAD(FAD)-dependent dehydrogenase were up-regulated. A qRT-PCR was conducted to detect 7 expressed genes from the iTRAQ results during the incubation. The qRT-PCR results were consistent with the iTRAQ results. All of our results indicate that colchicine have a strong impact on the cell morphology and cellular metabolism of S. eriocheiris.
RNA Sequencing Reveals Novel Transcripts from Sympathetic Stellate Ganglia During Cardiac Sympathetic Hyperactivity
Authors: Bardsley Emma N. , Davis Harvey , Ajijola Olujimi A. , Buckler Keith J. , Ardell Jeffrey L. , Shivkumar Kalyanam , Paterson David J.
Published: May 2018

Cardiovascular disease is the most prevalent age-related illness worldwide, causing approximately 15 million deaths every year. Hypertension is central in determining cardiovascular risk and is a strong predictive indicator of morbidity and mortality; however, there remains an unmet clinical need for disease-modifying and prophylactic interventions. Enhanced sympathetic activity is a well-established contributor to the pathophysiology of hypertension, however the cellular and molecular changes that increase sympathetic neurotransmission are not known. The aim of this study was to identify key changes in the transcriptome in normotensive and spontaneously hypertensive rats. We validated 15 of our top-scoring genes using qRT-PCR, and network and enrichment analyses suggest that glutamatergic signalling plays a key role in modulating Ca2+ balance within these ganglia. Additionally, phosphodiesterase activity was found to be altered in stellates obtained from the hypertensive rat, suggesting that impaired cyclic nucleotide signalling may contribute to disturbed Ca2+ homeostasis and sympathetic hyperactivity in hypertension. We have also confirmed the presence of these transcripts in human donor stellate samples, suggesting that key genes coupled to neurotransmission are conserved. The data described here may provide novel targets for future interventions aimed at treating sympathetic hyperactivity associated with cardiovascular disease and other dysautonomias.
Author Correction: Overcoming Bias: Cognitive Control Reduces Susceptibility to Framing Effects in Evaluating Musical Performance
Authors: Aydogan Gökhan , Flaig Nicole , Ravi Srekar N. , Large Edward W. , McClure Samuel M. , Margulis Elizabeth Hellmuth
Published: May 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Regulation of CD4+CD8−CD25+ and CD4+CD8+CD25+ T cells by gut microbiota in chicken
Authors: Lee In Kyu , Gu Min Jeong , Ko Kwang Hyun , Bae Suhan , Kim Girak , Jin Gwi-Deuk , Kim Eun Bae , Kong Young-Yun , Park Tae Sub , Park Byung-Chul , Jung Hyun Jung , Han Seung Hyun , Yun Cheol-Heui
Published: May 2018

The gut microbiota in chicken has long been studied, mostly from the perspective of growth performance. However, there are some immunological studies regarding gut homeostasis in chicken. Although CD4+CD25+T cells are reported to act as regulatory T cells (Tregs) in chicken, there have been no studies showing the relationship between gut microbiota and Tregs. Therefore, we established a model for ‘antibiotics (ABX)-treated chickens’ through administration of an antibiotic cocktail consisting of ampicillin, gentamycin, neomycin, metronidazole, and vancomycin in water for 7 days. CD4+CD8−CD25+and CD4+CD8+CD25+T cells in cecal tonsils were significantly decreased in this model. Gram-positive bacteria, especially Clostridia, was responsible for the changes in CD4+CD8−CD25+or CD4+CD8+CD25+T cells in cecal tonsils. Feeding ABX-treated chickens with acetate recovered CD4+CD8−CD25+and CD4+CD8+CD25+T cells in cecal tonsils. GPR43, a receptor for acetate, was highly expressed in CD4+CD8−CD25+T cells. In conclusion, our study demonstrated that the gut microbiota can regulate the population of CD4+CD8−CD25+and CD4+CD8+CD25+T cells, and that acetate is responsible for the induction of CD4+CD8−CD25+T cells in cecal tonsils via GPR43.
Are Systemic Manifestations Ascribable to COPD in Smokers? A Structural Equation Modeling Approach
Authors: Boyer Laurent , Bastuji-Garin Sylvie , Chouaid Christos , Housset Bruno , Le Corvoisier Philippe , Derumeaux Geneviève , Boczkowski Jorge , Maitre Bernard , Adnot Serge , Audureau Etienne
Published: May 2018

Whether the systemic manifestations observed in Chronic Obstructive Pulmonary Disease (COPD) are ascribable to lung dysfunction or direct effects of smoking is in debate. Structural Equations Modeling (SEM), a causal-oriented statistical approach, could help unraveling the pathways involved, by enabling estimation of direct and indirect associations between variables. The objectives of the study was to investigate the relative impact of smoking and COPD on systemic manifestations, inflammation and telomere length. In 292 individuals (103 women; 97 smokers with COPD, 96 smokers without COPD, 99 non-smokers), we used SEM to explore the pathways between smoking (pack-years), lung disease (FEV1, KCO), and the following parameters: arterial stiffness (aortic pulse wave velocity, PWV), bone mineral density (BMD), appendicular skeletal muscle mass (ASMM), grip strength, insulin resistance (HOMA-IR), creatinine clearance (eGFR), blood leukocyte telomere length and inflammatory markers (Luminex assay). All models were adjusted on age and gender. Latent variables were created for systemic inflammation (inflammatory markers) and musculoskeletal parameters (ASMM, grip strength, BMD). SEM showed that most effects of smoking were indirectly mediated by lung dysfunction: e.g. via FEV1 on musculoskeletal factor, eGFR, HOMA-IR, PWV, telomere length, CRP, white blood cells count (WBC) and inflammation factor, and via KCO on musculoskeletal factor, eGFR and PWV. Direct effects of smoking were limited to CRP and WBC. Models had excellent fit. In conclusion, SEM highlighted the major role of COPD in the occurrence of systemic manifestations while smoking effects were mostly mediated by lung function.
Particle Shape Influences Settling and Sorting Behavior in Microfluidic Domains
Authors: Başağaoğlu Hakan , Succi Sauro , Wyrick Danielle , Blount Justin
Published: May 2018

We present a new numerical model to simulate settling trajectories of discretized individual or a mixture of particles of different geometrical shapes in a quiescent fluid and their flow trajectories in a flowing fluid. Simulations unveiled diverse particle settling trajectories as a function of their geometrical shape and density. The effects of the surface concavity of a boomerang particle and aspect ratio of a rectangular particle on the periodicity and amplitude of oscillations in their settling trajectories were numerically captured. Use of surrogate circular particles for settling or flowing of a mixture of non-circular particles were shown to miscalculate particle velocities by a factor of 0.9–2.2 and inaccurately determine the particles’ trajectories. In a microfluidic chamber with particles of different shapes and sizes, simulations showed that steady vortices do not necessarily always control particle entrapments, nor do larger particles get selectively and consistently entrapped in steady vortices. Strikingly, a change in the shape of large particles from circular to elliptical resulted in stronger entrapments of smaller circular particles, but enhanced outflows of larger particles, which could be an alternative microfluidics-based method for sorting and separation of particles of different sizes and shapes.
Dynamic microbial succession of Shanxi aged vinegar and its correlation with flavor metabolites during different stages of acetic acid fermentation
Authors: Zhu Yunping , Zhang Feifei , Zhang Chengnan , Yang Li , Fan Guangsen , Xu Youqiang , Sun Baoguo , Li Xiuting
Published: May 2018

Shanxi aged vinegar (SAV), one of the famous Chinese vinegars, is produced by multispecies solid-state fermentation in which the acetic acid fermentation stage (AAF) is especially important. However, how bacterial succession and their metabolites change along with the different stages of AAF is still poorly understood. In this study, we investigated the dynamic bacterial succession and flavor formation in three batches of SAV using high-throughput sequencing and metabolomics approaches. It is interesting to find that AAF can be divided into three stages based on its bacterial community succession (early stage, days 0–4; medium stage, days 5–21; and later stage, days 22–26). Pantoea, Pediococcus, Lactococcus and Rhizobium played an important role in the early stage; Lactobacillus was dominant in the medium stage (67.72%); and Acetobacter, Komagataeibacter and Kroppenstedtia were the key bacteria in the later stage. A total of seven organic acids and 42 volatile constituents (esters, alcohol, ketones and aldehydes) were detected during the AAF. Spearman correlation analysis showed a significant correlation between the bacterial community and these flavor metabolites during the AAF of the SAV. This is the first report to explore the relationships between volatile flavor metabolites and bacterial community succession by a three-staged method and provide theoretical support for a flavor formation mechanism in traditional SAV.
Intermittent strong transport of the quasi-adiabatic plasma state
Authors: Kim Chang-Bae , An Chan-Yong , Min Byunghoon
Published: May 2018

The dynamics of the fluctuating electrostatic potential and the plasma density couched in the resistive-drift model at nearly adiabatic state are simulated. The linear modes are unstable if the phase difference between the potential and the density are positive. Exponential growth of the random small perturbations slows down due to the nonlinear E × B flows that work in two ways. They regulate the strength of the fluctuations by transferring the energy from the energy-producing scale to neighboring scales and reduce the cross phase at the same time. During quasi-steady relaxation sporadic appearance of very strong turbulent particle flux is observed that is characterized by the flat energy spectrum and the broad secondary peak in the mesoscale of the order of the gyro-radius. Such boost of the transport is found to be caused by presence of relatively large cross phase as the E × B flows are not effective in cancelling out the cross phase.
Prestressed cells are prone to cytoskeleton failures under localized shear strain: an experimental demonstration on muscle precursor cells
Authors: Streppa Laura , Ratti Francesca , Goillot Evelyne , Devin Anne , Schaeffer Laurent , Arneodo Alain , Argoul Françoise
Published: May 2018

We report on a wavelet based space-scale decomposition method for analyzing the response of living muscle precursor cells (C2C12 myoblasts and myotubes) upon sharp indentation with an AFM cantilever and quantifying their aptitude to sustain such a local shear strain. Beyond global mechanical parameters which are currently used as markers of cell contractility, we emphasize the necessity of characterizing more closely the local fluctuations of the shear relaxation modulus as they carry important clues about the mechanisms of cytoskeleton strain release. Rupture events encountered during fixed velocity shear strain are interpreted as local disruptions of the actin cytoskeleton structures, the strongest (brittle) ones being produced by the tighter and stiffer stress fibers or actin agglomerates. These local strain induced failures are important characteristics of the resilience of these cells, and their aptitude to maintain their shape via a quick recovery from local strains. This study focuses on the perinuclear region because it can be considered as a master mechanical organizing center of these muscle precursor cells. Using this wavelet-based method, we combine the global and local approaches for a comparative analysis of the mechanical parameters of normal myoblasts, myotubes and myoblasts treated with actomyosin cytoskeleton disruptive agents (ATP depletion, blebbistatin).
Plasma N-glycans in colorectal cancer risk
Authors: Doherty Margaret , Theodoratou Evropi , Walsh Ian , Adamczyk Barbara , Stöckmann Henning , Agakov Felix , Timofeeva Maria , Trbojević-Akmačić Irena , Vučković Frano , Duffy Fergal , McManus Ciara A. , Farrington Susan M. , Dunlop Malcolm G. , Perola Markus , Lauc Gordan , Campbell Harry , Rudd Pauline M.
Published: May 2018

Aberrant glycosylation has been associated with a number of diseases including cancer. Our aim was to elucidate changes in whole plasmaN-glycosylation between colorectal cancer (CRC) cases and controls in one of the largest cohorts of its kind. A set of 633 CRC patients and 478 age and gender matched controls was analysed. Additionally, patients were stratified into four CRC stages. Moreover,N-glycan analysis was carried out in plasma of 40 patients collected prior to the initial diagnosis of CRC. Statistically significant differences were observed in the plasmaN-glycome at all stages of CRC, this included a highly significant decrease in relation to the core fucosylated bi-antennary glycans F(6)A2G2 and F(6)A2G2S(6)1 (P < 0.0009). Stage 1 showed a unique biomarker signature compared to stages 2, 3 and 4. There were indications that at risk groups could be identified from the glycome (retrospective AUC = 0.77 and prospective AUC = 0.65).N-glycome biomarkers related to the pathogenic progress of the disease would be a considerable asset in a clinical setting and it could enable novel therapeutics to be developed to target the disease in patients at risk of progression.
Semi-Supervised Maximum Discriminative Local Margin for Gene Selection
Authors: Li Zejun , Liao Bo , Cai Lijun , Chen Min , Liu Wenhua
Published: May 2018

In the present study, we introduce a novel semi-supervised method called the semi-supervised maximum discriminative local margin (semiMM) for gene selection in expression data. The semiMM is a “filter” approach that exploits local structure, variance, and mutual information. We first constructed a local nearest neighbour graph and divided this information into within-class and between-class local nearest neighbour graphs by weighing the edge between the two data points. The semiMM aims to discover the most discriminative features for classification via maximizing the local margin between the within-class and between-class data, the variance of all data, and the mutual information of features with class labels. Experiments on five publicly available gene expression datasets revealed the effectiveness of the proposed method compared to three state-of-the-art feature selection algorithms.
High Throughput Discovery and Design of Strong Multicomponent Metallic Solid Solutions
Authors: Coury Francisco G. , Clarke Kester D. , Kiminami Claudio S. , Kaufman Michael J. , Clarke Amy J.
Published: May 2018

High Entropy Alloys (HEAs) are new classes of structural metallic materials that show remarkable property combinations. Yet, often times interesting compositions are still found by trial and error. Here we show an “Effective Atomic Radii for Strength” (EARS) methodology, together with different semi-empirical and first-principle models, can be used to predict the extent of solid solution strengthening to discover and design new HEAs with unprecedented properties. We have designed a Cr45Ni27.5Co27.5 alloy with a yield strength over 50% greater with equivalent ductility than the strongest HEA (Cr33.3Ni33.3Co33.3) from the CrMnFeNiCo family reported to date. We show that values determined by the EARS methodology are more physically representative of multicomponent concentrated solid solutions. Our methodology permits high throughput, property-driven discovery and design of HEAs, enabling the development of future high-performance advanced materials for extreme environments.
Identifying conserved UV exposure genes and mechanisms
Authors: Gomes Susana I. L. , Roca Carlos P. , Scott-Fordsmand Janeck J. , Amorim Mónica J. B.
Published: May 2018

Studies have been showing how changes in ultraviolet (UV) affect the terrestrial system, mostly focusing on higher plants and indirect effects, e.g. UV changed food quality/decomposition. Much less attention has been given to direct effect on terrestrial species, although the negative effects have been recognized for some earthworms. Further, the actual mechanisms of UV toxicity to soil invertebrates are even less understood. We here studied the effect of UV on the soil oligochaeteEnchytraeus crypticus, and attempted to identify the possible mechanisms of toxicity using high-throughput gene expression. Applying a UV dose equivalent to UV during the winter months in northern Europe we observed an 80% decrease in reproduction. For these organisms, approximately 5% of the genes were differentially expressed. Among the observations was an activation of the DNA repair mechanisms, nucleotide excision repair, which correlated with survival of the organisms. An observed repressing of apoptosis seems to have deleterious effects (e.g. because it may lead to the accumulation of aberrant cells) leading to a decline in reproduction. The mechanisms activated by UV were similar to those mechanisms activated in humans, showing conservation across species.