bluuebunny/crossref_metadata_2025 huggingface dataset:
Small‐Scale Flux Transfer Events Formed in the Reconnection Exhaust Region Between Two X Lines
Authors: Hwang K.‐J. , Sibeck D. G. , Burch J. L. , Choi E. , Fear R. C. , Lavraud B. , Giles B. L. , Gershman D. , Pollock C. J. , Eastwood J. P. , Khotyaintsev Y. , Escoubet Philippe , Fu H. , Toledo‐Redondo S. , Torbert R. B. , Ergun R. E. , Paterson W. R. , Dorelli J. C. , Avanov L. , Russell C. T. , Strangeway R. J.
Published: October 2018

We report MMS observations of the ion‐scale flux transfer events (FTEs) that may involve two main X lines and tearing instability between the two X lines. The four spacecraft detected multiple isolated regions with enhanced magnetic field strength and bipolar Bn signatures normal to the nominal magnetopause, indicating FTEs. The currents within the FTEs flow mostly parallel to B, and the magnetic tension force is balanced by the total pressure gradient force. During these events, the plasma bulk flow velocity was directed southward. Detailed analysis of the magnetic and electric field and plasma moments variations suggests that the FTEs were initially embedded within the exhaust region north of an X line but were later located southward/downstream of a subsequent X line. The cross sections of the individual FTEs are in the range of ~2.5–6.8 ion inertial lengths. The observations suggest the formation of multiple secondary FTEs. The presence of an X line in the exhaust region southward of a second X line results from the southward drift of an old X line and the reformation of a new X line. The current layer between the two X lines is unstable to the tearing instability, generating multiple ion‐scale flux‐rope‐type secondary islands.
Ionospheric and Thermospheric Responses to the Recent Strong Solar Flares on 6 September 2017
Authors: Li Wang , Yue Jianping , Yang Yang , He Changyong , Hu Andong , Zhang Kefei
Published: October 2018

Two solar flares X2.2 and X9.3 erupted over the active region 2673 on 6 September 2017, and the second flare is the strongest since 2005. In order to investigate the ionospheric and thermospheric responses to the two solar flares, the global total electron content and the critical frequency of F2 layer obtained from GPS stations and ionosondes are used. The results indicate that the ionosphere in the sunlit hemisphere increased significantly with magnitudes of 0.1 and 0.5 total electron content units for the X2.2 and X9.3 solar flares, respectively. The electron density, thermospheric neutral density, and neutral temperature simulated by the Thermosphere‐Ionosphere Electrodynamics Global Circulation Model show that the behavior of ionospheric and thermospheric responses is different. The ionospheric disturbances occurred at the altitude ranges of 150−300 km, and the thermospheric responses occurred at the altitudes of 250−400 km are caused by solar extreme ultraviolet and ultraviolet photons, respectively. Both ionospheric and thermospheric responses are proportional to the height within their corresponding altitude ranges. Observations and simulations reveal that the ionospheric and thermospheric responses are nonlinearly dependent on the solar zenith angle. The disturbances caused by the X2.2 solar flare are symmetric, but the X9.3 solar flare are not. The O/N2 density ratio simulated by Thermosphere‐Ionosphere Electrodynamics Global Circulation Model increases from lev0 to lev5.0 pressure surface with a magnitude of 0.1–1.8, while the ratio decreases in the American sector with a magnitude of −0.6 to −0.3. The longitudinal asymmetry of O/N2 density ratio is a major contributor to the longitudinal asymmetry of ionospheric and thermospheric responses.
Diagnostics of Closed Magnetic Flux Depletion in the Near‐Earth Magnetotail During the Substorm Growth Phase
Authors: Shukhtina M. A. , Gordeev E. I. , Sergeev V. A. , Shinohara I.
Published: October 2018

Based on magnetohydrodynamics simulations, it was recently suggested that magnetotail reconfiguration during the substorm growth phase results from combined action of two large‐scale processes: (1) open magnetic flux accumulation (OMFA) in the tail lobes and (2) closed magnetic flux depletion (CMFD) in the near‐Earth tail, caused by flux evacuation to the dayside magnetopause. Simultaneous action of uniform along the tail OMFA and strongly nonuniform CMFD leads to different rates of magnetic flux growth in different tail cross sections. According to Global magnetohydrodynamics simulations CMFD is about 35% of OMFA, the corresponding differences of magnetic flux increase in two‐tail cross sections at −7RE and −20RE being as large as 0.1–0.2 GWb. To study this effect on real data, we applied the recent method of magnetotail flux estimation (Shukhtina et al., ) to simultaneous Cluster and Geotail observations in the tail lobes. By finding such rare observations in the inner and middle magnetotail (at −10 RE and − 21RE) we confirm a larger magnetic flux increase in the midtail, with the ratio between OMFA and CMFD comparable to that obtained in magnetohydrodynamics, although with a large scatter. These results confirm the scenario of two decoupled magnetotail regions with different convection regimes during the growth phase. Convection is depressed in the midtail plasma sheet, showing the pressure crisis in action inherent to tail‐like 2‐D magnetic configuration. At the same time convection is substantially enhanced in the inner magnetosphere, where the pressure crisis is solved due to azimuthal flux transport around the Earth, essentially a 3‐D effect.
Using Fast Marching Eikonal Solver to Compute 3‐D Pds Traveltime for Deep Receiver‐Function Imaging
Authors: Guan Zhe , Niu Fenglin
Published: October 2018

In common‐conversion‐point stacking of receiver functions, most current studies compute 3‐D relative Pds traveltime corrections by integrating traveltime anomalies along 1‐D raypaths. This ray tracing approach is generally time‐consuming and less accurate when prominent velocity anomalies exist and effects of 3‐D raypaths become significant. In this study we introduce a new scheme that utilizes a fast‐marching method eikonal solver to improve both the efficiency and accuracy of 3‐D Pds traveltime computation. We first employ a 1‐D raytracing method and the iasp91 model to calibrate the accuracy of the new scheme and optimize the parameters of the numerical solver. We then apply the new scheme to compute a massive number of Pds traveltimes using two sets of 3‐D synthetic models, one set with a high‐velocity slab and another set with a low‐velocity plume, and compare these 3‐D traveltimes with those computed with the raypath integrating approach. We find 2.7% and 11.8% raypaths in the two slab models and 7.8% and 12.0% raypaths in the two plume models show a 3‐D traveltime difference of ≥0.5 s. We apply the proposed scheme to a subset of transportable array receiver functions that sample the transition zone beneath the Yellowstone hotspot and find that a common‐conversion‐point stack using 3‐D Pds traveltimes computed by the eikonal solver method has the best focused P660s. Finally, we illustrate that computational times can be reduced by 1 to 2 orders of magnitude with the new scheme to compute 3‐D Pds traveltimes of 20,000–200,000 receiver functions.
Last Glacial Maximum and Mid‐Holocene Thermal Growing Season Simulations
Authors: Jiang Dabang , Sui Yue , Lang Xianmei , Tian Zhiping
Published: October 2018

The growing season—the number of days per year during which the climate favors plant growth—is an important factor for describing climate. Based on daily data of all available numerical experiments from the Paleoclimate Modeling Intercomparison Project phases two and three, we examine the growing season over global ice‐free land for the last glacial maximum and mid‐Holocene to improve our understanding of glacial and interglacial climates. Compared to the preindustrial period, the last glacial maximum growing season was shortened at midlatitude and high latitude and by 26.1 days globally in terms of nine climate models due to a later start and an earlier end. Growing degree days above 5 °C (GDD5) decreased by 24% due to both cooling and shortening of the growing season, agreeing with pollen‐based reconstructions of globally decreased signal and spatial pattern of GDD5 changes at 88 grid cells. Twenty‐four models indicate that the mid‐Holocene growing season start and end dates and length were similar to preindustrial states globally but featured a latitude‐varying difference. The length increased north of ~50°N and decreased in much of the area from 20–50°N owing to variations in both the start and end dates. In response to orbital forcing, both the growing season temperature and GDD5 increased at northern midlatitude and high latitude but decreased elsewhere. The GDD5 simulations agreed in sign with the reconstructions at 516 grid cells more often than not, though their spatial patterns were different to some extent.
Large Increases in Primary Trimethylaminium and Secondary Dimethylaminium in Atmospheric Particles Associated With Cyclonic Eddies in the Northwest Pacific Ocean
Authors: Hu Qingjing , Qu Keming , Gao Huiwang , Cui Zhengguo , Gao Yang , Yao Xiaohong
Published: October 2018

Dimethylaminium (DMA+) and trimethylaminium (TMA+) ions in size‐segregated atmospheric particles are measured across the marginal seas of China and the northwest Pacific Ocean (NWPO) in March–May 2014. The concentrations of DMA+ and TMA+ in particles with diameters of 0.056–10 μm (PM0.056–10) collected from the eutrophic seas are 0.22 ± 0.38 nmol/m3 and 0.11 ± 0.23 nmol/m3, respectively. Surprisingly, an average TMA+ concentration that is 1 order of magnitude higher and a slightly higher average DMA+ concentration are observed across the oligotrophic NWPO. However, the concentrations of chlorophyll‐a in the NWPO are approximately 5 times lower than those in the marginal seas. The maximum concentrations of TMA+ (4.39 nmol/m3) and DMA+ (0.92 nmol/m3) in PM0.056–10 are observed close to the largest cyclonic eddy in the NWPO under an average wind speed of 14 m/s. The concentrations of TMA+ increase with decreasing particle size in the sample, whereas those of DMA+ exhibit a condensation mode at 0.2 μm and a droplet mode at 1–2 μm. The bimodal size distribution of DMA+ is conventionally interpreted in terms of secondary reactions in the atmosphere. The unique size distribution of TMA+ suggests that it very likely originates from sea‐spray aerosols. Based on their size distributions in other samples collected over the NWPO, these conclusions may generally apply for TMA+ and DMA+. Moreover, we propose a novel conceptual model to explain how the largely increased primary TMA+ and secondary DMA+ are linked to emissions of sea‐spray aerosols and gaseous precursors from various cyclonic eddies.
Model Intercomparison of Atmospheric 137Cs From the Fukushima Daiichi Nuclear Power Plant Accident: Simulations Based on Identical Input Data
Authors: Sato Yousuke , Takigawa Masayuki , Sekiyama Tsuyoshi Thomas , Kajino Mizuo , Terada Hiroaki , Nagai Haruyasu , Kondo Hiroaki , Uchida Junya , Goto Daisuke , Quélo Denis , Mathieu Anne , Quérel Arnaud , Fang Sheng , Morino Yu , von Schoenberg Pontus , Grahn Håkan , Brännström Niklas , Hirao Shigekazu , Tsuruta Haruo , Yamazawa Hiromi , Nakajima Teruyuki
Published: October 2018

A model intercomparison of the atmospheric dispersion of cesium‐137 (137Cs) emitted after the Fukushima Daiichi Nuclear Power Plant accident in Japan was conducted to understand the behavior of atmospheric 137Cs in greater detail. The same meteorological data with a fine spatiotemporal resolution and an emission inventory were applied to all models to exclude the differences among the models originating from differences in meteorological and emission data. The meteorological data were used for initial, boundary, and nudging data or offline meteorological field. Furthermore, a horizontal grid with the same resolution as that of the meteorological data was adopted for all models. This setup enabled us to focus on model variability originating from the processes included in each model, for example, physical processes. The multimodel ensemble captured 40% of the atmospheric 137Cs events observed by measurements, and the figure of merit in space for the total deposition of 137Cs exceeded 80. The lower score of the atmospheric 137Cs than that of the deposition originated from the difference in timing between observed and simulated atmospheric 137Cs. Our analyses indicated that meteorological data were most critical for reproducing the atmospheric 137Cs events. The results further revealed that differences in 137Cs concentrations among the models originated from deposition and diffusion processes when the meteorological field was simulated reasonably well. The models with small deposition fluxes produced higher scores for atmospheric 137Cs, and those with strong diffusion succeeded in capturing the high 137Cs concentrations observed; however, they also tended to overestimate the concentrations.
A Systematic Method for Classifying and Grouping Late Noachian and Early Hesperian Rock Targets Analyzed by the Mars Exploration Rover Opportunity at Endeavour Crater, Mars
Authors: Bouchard Michael C. , Jolliff Bradley L.
Published: October 2018

The Mars rover Opportunity has collected in situ compositional data with the Alpha Particle X‐ray Spectrometer at almost 500 sites. To analyze these data, hierarchical clustering analysis and an error‐weighted similarity index are applied to a subset of 57 APXS target compositions and selected Martian meteorites. Hierarchical clustering provides a rapid first approximation of compositional relationships, whereas the error‐weighted similarity index provides an in‐depth and quantifiable comparison of individual composition pairs. These analyses are combined into a statistical grouping model that provides insight into lithologic relationships and is critically informed by examination of Panoramic Camera and Microscopic Imager images. Major lithologies are (1) the Burns formation sulfate sandstones; (2) Shoemaker impact breccias (Endeavour crater ejecta/rim deposits); (3) the morphologically distinct Grasberg formation, associated with Endeavour crater rim deposits; (4) the Matijevic formation, an exposure interpreted to be Endeavour crater target rocks; and (5) erratics or other rocks that do not cluster with groups 1–4. The Grasberg formation is more similar to the Shoemaker formation than any other formation, and thus likely incorporated eroded Shoemaker material. The lowest Shoemaker member (Copper Cliff breccia) may contain material from the preimpact Matijevic formation. The Matijevic formation is the most chemically distinct formation and is most similar to the volcanic erratic rock “Marquette Island.” Clustering and similarity index values also show that regolith breccia Martian meteorites (represented by the NWA 7475/7034 paired meteorites) are similar in bulk composition to Mars surface materials at Meridiani, especially the Matijevic formation.
Survivability of 1‐Chloronapthalene During Simulated Early Diagenesis: Implications for Chlorinated Hydrocarbon Detection on Mars
Authors: Royle Samuel H. , Tan Jonathan , Kounaves Samuel P. , Sephton Mark A.
Published: October 2018

All missions to Mars which have attempted to detect organic molecules have detected simple chlorohydrocarbons, the source of which has yet to be firmly established. This study assessed the likelihood of these chlorinated molecules being indigenous to the sedimentary units in which they were detected or if they were chlorinated during analysis. The survivability of 1‐chloronapthalene was examined via hydrous pyrolysis experiments and its dechlorination kinetics were determined. The results of these experiments were used to model the survivability of this simple chlorohydrocarbon under Mars‐relevant diagenetic conditions using the Sheepbed mudstone unit as a case study. It was found that 1‐chloronapthalene was rapidly dechlorinated under Noachian conditions, and thus, the detected Martian chlorohydrocarbons are unlikely to be ancient and probably formed within the rover's sample handling chain during analysis.
Using Persistent Scatterer Interferometry to Map and Quantify Permafrost Thaw Subsidence: A Case Study of Eboling Mountain on the Qinghai‐Tibet Plateau
Authors: Chen Jie , Liu Lin , Zhang Tingjun , Cao Bin , Lin Hui
Published: October 2018

Permafrost thaw subsidence, a key indicator of permafrost degradation, remains poorly quantified or understood. It is particularly challenging to detect and measure surface subsidence due to the loss of subsurface ice over a large area because it usually develops gradually, over several years or decades. Here we utilize the persistent scatterer interferometric synthetic aperture radar (PSI) approach to remotely measure gradual surface subsidence on Eboling Mountain in the northeastern region of the Qinghai‐Tibet Plateau, where thermal erosion gullies are well developed. Most of the previous multitemporal interferometric synthetic aperture radar studies on permafrost used the small baseline subset method. By contrast, the PSI approach benefits from the full spatial resolution and is less affected by temporal or geometric decorrelation. In the PSI analysis, we incorporate a piecewise elevation change model that includes periodic subsidence/uplift because of its seasonally varying components as well as its linear subsidence trends. Applying this permafrost‐designated PSI algorithm to 17‐L band ALOS‐1 PALSAR images taken between 2006 and 2011, we find that both the thermal erosion gullies and the surrounding regions (within about 300 m) subside gradually. The subsidence trends range from 0.3 to 3 cm/yr. This suggests that permafrost areas near the gullies are more vulnerable to gradual thawing and degradation. This study demonstrates the potential of using PSI to study permafrost thaw processes and of assessing its impacts over vast areas on the Qinghai‐Tibet Plateau and in the Arctic.
Weathering of Reactive Mineral Phases in Landslides Acts as a Source of Carbon Dioxide in Mountain Belts
Authors: Emberson R. , Galy A. , Hovius N.
Published: October 2018

Bedrock landsliding in mountain belts can elevate overall chemical weathering rates through rapid dissolution of exhumed reactive mineral phases in transiently stored deposits. This link between a key process of erosion and the resultant weathering affects the sequestering of carbon dioxide through weathering of silicate minerals and broader links between erosion in active orogens and climate change. Here we address the effect on the carbon cycle of weathering induced by bedrock landsliding in Taiwan and the Western Southern Alps of New Zealand. Using solute chemistry data from samples of seepage from landslide deposits and river discharge from catchments with variable proportions of landsliding, we model the proportion of silicate and carbonate weathering and the balance of sulfuric and carbonic acids that act as weathering agents. We correct for secondary precipitation, geothermal, and cyclic input, to find a closer approximation of the weathering explicitly occurring within landslide deposits. We find highly variable proportions of sulfuric and carbonic acids driving weathering in landslides and stable hillslopes. Despite this variability, the predominance of rapid carbonate weathering within landslides and catchments where mass wasting is prevalent results at best in limited sequestration of carbon dioxide by this process of rapid erosion. In many cases where sulfuric acid is a key weathering agent, a net release of CO2 to the atmosphere occurs. This suggests that a causal link between erosion in mountain belts and climate change through the sequestration of CO2, if it exists, must operate through a process other than chemical weathering driven by landsliding.
Ventilation of Northern and Southern Sources of Aged Carbon in the Eastern Equatorial Pacific During the Younger Dryas Rise in Atmospheric CO2
Authors: Bova Samantha C. , Herbert Timothy D. , Altabet Mark A.
Published: October 2018

Atmospheric carbon dioxide (CO2) levels rose by ~90 ppmv during the last deglaciation, but the source of this carbon remains unknown. One popular hypothesis suggests carbon accumulated in the deep Southern Ocean, becoming increasingly radiocarbon (14C) depleted during the last glacial period, and was released into Antarctic Intermediate Water (AAIW) and, subsequently, the atmosphere during deglaciation. Detection of extremely 14C depleted carbon in the intermediate‐depth tropical oceans during periods of atmospheric CO2 rise was initially considered the smoking gun for the hypothesis, but attempts to reproduce the anomalies closer to the Southern Ocean source have largely failed. Here we present new 14C records from four cores recovered at intermediate depths in the eastern equatorial Pacific (EEP). In the context of additional geochemical records, including benthic foraminiferal stable isotopes and sedimentary nitrogen isotopes, we demonstrate that the extreme 14C anomalies observed during the last deglaciation do not reflect the radiocarbon content of AAIW. We show that although AAIW likely transported modestly 14C depleted carbon to the EEP subsurface, the extreme 14C signatures might reflect a distinct source of aged carbon arriving from the north, suggesting the North Pacific helped transport deep ocean carbon to the atmosphere during the last deglaciation. In the EEP, additional local hydrothermal inputs of 14C‐free carbon near the Galapagos Islands magnified the already low‐14C signatures. Finally, regardless of arrival route (North/South Pacific or hydrothermal), 14C‐depleted carbon was released from the EEP subsurface during a late deglacial pulse of renewed upwelling, likely contributing to the Younger Dryas rise in atmospheric CO2.
ERCP in Patients With Cirrhosis: “Risky Business” Or “Just Do it”?
Authors: Shah Tilak , Tapper Elliot B.
Published: October 2018

Acute-on-chronic-liver-failure (ACLF) describes acute deterioration of liver function in patients with decompensated cirrhosis resulting in organ failure, and can occur as a procedural complication. In the current issue, Leal et al found that, compared to in-patients with cirrhosis who did not undergo interventions, ACLF was significantly more common among undergoing ERCP, but not more so than other non-ERCP interventions. ACLF risk increased significantly, however, if an ERCP-related AE occurred. ACLF can be a consequence of both the indication for and a complication of ERCP. When the indication is strong, the benefit of ERCP still outweighs risk among patients with cirrhosis.
To Scope or Not to Scope? The Safety of Upper Endoscopy in the Setting of Pulmonary Embolism
Authors: Cohen-Mekelburg Shirley , Rosenblatt Russell , Mathews Steven , Namn Yunseok , Tafesh Zaid , Wan David , Crawford Carl
Published: October 2018

OBJECTIVES:

We aimed to describe the frequency of upper endoscopy and associated outcomes in subjects hospitalized with upper GI bleeding (UGIB) and pulmonary embolism (PE).

METHODS:

We performed a cross-sectional study using the Nationwide Inpatient Sample from 2007 to 2014. The association between upper endoscopy and in-hospital mortality was evaluated using propensity score matching.

RESULTS:

A total of 44,412 subjects had a coexistent PE and UGIB. 63.5% had an inpatient upper endoscopy with a lower likelihood of in-hospital death and a shorter length of stay.

CONCLUSIONS:

A substantial proportion of inpatients with PE and UGIB undergo endoscopy with a relatively lowmortality rate.
Space-time-coding digital metasurfaces
Authors: Zhang Lei , Chen Xiao Qing , Liu Shuo , Zhang Qian , Zhao Jie , Dai Jun Yan , Bai Guo Dong , Wan Xiang , Cheng Qiang , Castaldi Giuseppe , Galdi Vincenzo , Cui Tie Jun
Published: October 2018

The recently proposed digital coding metasurfaces make it possible to control electromagnetic (EM) waves in real time, and allow the implementation of many different functionalities in a programmable way. However, current configurations are only space-encoded, and do not exploit the temporal dimension. Here, we propose a general theory of space-time modulated digital coding metasurfaces to obtain simultaneous manipulations of EM waves in both space and frequency domains, i.e., to control the propagation direction and harmonic power distribution simultaneously. As proof-of-principle application examples, we consider harmonic beam steering, beam shaping, and scattering-signature control. For validation, we realize a prototype controlled by a field-programmable gate array, which implements the harmonic beam steering via an optimized space-time coding sequence. Numerical and experimental results, in good agreement, demonstrate good performance of the proposed approach, with potential applications to diverse fields such as wireless communications, cognitive radars, adaptive beamforming, holographic imaging.
Lewis basicity generated by localised charge imbalance in noble metal nanoparticle-embedded defective metal–organic frameworks
Authors: Tan Ying Chuan , Zeng Hua Chun
Published: October 2018

Interactions between metal nanoparticles (NPs) and metal–organic frameworks (MOFs) in their composite forms have proven to exhibit beneficial properties, such as enhanced catalytic performance through synergistic effects. Herein, we show that Lewis basic sites can be created within an anionic defective MOF by engineering the electronic state of the pendant carboxylate groups situated at the defect sites. This is achieved from the concerted interactions between the pendant carboxylate groups, embedded Pd NPs and charge-balancing cations (Mn+ = Ce3+, Co2+, Ni2+, Cu2+, Mg2+, Li+, Na+ or K+). This work is the first example of generating a new collective property, i.e. Lewis basicity, in metal-carboxylate MOFs. Importantly, the choice of Mn+, used during cation exchange, acts as a convenient parameter to tune the Lewis basicity of the MOF-based nanocomposites. It also provides a facile way to incorporate active metal sites and basic sites within carboxylate-based MOFs to engineer multifunctional nanocatalysts.
Design of 2D massless Dirac fermion systems and quantum spin Hall insulators based on sp–sp2 carbon sheets
Authors: Park Minwoo , Kim Youngkuk , Lee Hoonkyung
Published: October 2018

Grapheneis a massless Dirac fermion system, featuring Dirac points in momentum space. It was also first identified as a quantum spin Hall (QSH) insulator when considering spin–orbit coupling (SOC), which opens a band gap at the Dirac points. This discovery has initiated new research efforts to study the QSH effect, towards its application for quantum computing and spintronics. Although the QSH effect has been observed in HgTe quantum wells, the SOC strength of graphene is too small (~1 µeV) to induce the topological insulator phase in an experimentally achievable temperature regime. Here, we perform a systematic atomistic simulation to design two-dimensional sp–sp2 hybrid carbon sheets to discover new Dirac systems, hosting the QSH phase. 21 out of 31 newly discovered carbon sheets are identified as Dirac fermion systems without SOC, distinct from graphene in the number, shape, and position of the Dirac cones occurring in the Brillouin zone. Moreover, we find 19 out of the 21 new Dirac fermion systems become QSH insulators with a sizable SOC gap enhanced up to an order of meV, thus allowing for the QSH effect at experimentally accessible temperatures. In addition, based on the 26 Dirac fermion systems, we make a connection between the number of Dirac points without SOC and the resultant QSH phase in the presence of SOC. Our findings present new prospects for the design of topological materials with desired properties.
Gal epitope expression and immunological properties in iGb3S deficient mice
Authors: Shao Anliang , Xu Liming , Wu Xi , Liu Susu , Lu Yan , Fan Changfa
Published: October 2018

The Gal antigen is synthesized by glycoprotein galactosyltransferase alpha 1, 3 (GGTA1) or (and) isoglobotrihexosylceramide 3 synthase (iGb3S). However, whetheriGb3Sdeletion changes Gal epitope expression and immunological properties in animals is still not clear. The objective of this study was to developiGb3Sdeficient mice, and characterize their Gal epitope expression and Gal epitope-related immunological properties.iGb3Sgene knockout mice were generated on the C57BL/6 background using the bacterial artificial chromosome homology region recombination technique. Gal epitope expression in theiGb3Sdeficient mice was determined by using a monoclonal anti-Gal antibody. Immunological properties were analyzed by enzyme linked immune sorbent assay. It was found that Gal epitope expression was decreased from 5.19% to 21.74% in the main organs ofiGb3Sdeficient mice, compared with that of C57BL/6 wild type mice, suggesting that theiGb3Sgene participated to Gal epitope expression. However,iGb3Sdeletion alone did not cause significant changes in the immunological properties ofiGb3Sdeficient mice with or without exogenous Gal antigen (Rabbit Red Blood Cell) stimulation. The data from this study suggest that theiGb3Sgene likely contributes to Gal epitope expression, but may have a very weak effect on immunological properties of theiGb3Sdeficient mice.
A novel diagnostic algorithm to predict significant liver inflammation in chronic hepatitis B virus infection patients with detectable HBV DNA and persistently normal alanine transaminase
Authors: Li Qiang , Zhou Yu , Huang Chenlu , Li Weixia , Chen Liang
Published: October 2018

Significant liver inflammation might be found in 20–34% of chronic hepatitis B virus (HBV) infection patients with detectable HBV DNA and persistently normal alanine transaminase (ALT) (PNALT). We aimed to develop a diagnostic algorithm to predict significant liver inflammation in these specific patients. Using liver biopsy as the gold standard, we developed a novel, simple diagnostic algorithm to predict significant liver inflammation in a training set of 365 chronic HBV infection patients with detectable HBV DNA and PNALT, and validated the diagnostic accuracy in a validation set of 164 similar patients. The novel algorithm (AAGP) attributed to age, ALT, gamma-glutamyl transpeptidase (GGT), and platelet count was developed. In the training set, the area under the receiver operating characteristic curve (AUROC) of AAGP was higher than that of ALT and aspartate transaminase (AST), to diagnose significant liver inflammation (0.77, 0.67, and 0.59, respectively, p < 0.001). In the validation set, the AUROC of AAGP was also higher than ALT and AST (0.75, 0.61, and 0.54, respectively, p < 0.001). Using AAGP ≥2, the sensitivity and negative predictive value (NPV) was 91% and 93%, respectively, to diagnose significant liver inflammation. Using AAGP ≥8, the specificity and NPV was 91% and 86%, respectively, for significant liver inflammation. In conclusion, the AAGP algorithm is a novel, simple, user-friendly algorithm for the diagnosis of significant liver inflammation in chronic HBV infection patients with detectable HBV DNA and PNALT.
Persistent mRNA and miRNA expression changes in irradiated baboons
Authors: Port Matthias , Hérodin Francis , Valente Marco , Drouet Michel , Ostheim Patrick , Majewski Matthäus , Abend Michael
Published: October 2018

We examined the transcriptome/post-transcriptome for persistent gene expression changes after radiation exposure in a baboon model. Eighteen baboons were irradiated with a whole body equivalent dose of 2.5 or 5 Gy. Blood samples were taken before, 7, 28 and 75–106 days after radiation exposure. Stage I was a whole genome screening for mRNA combined with a qRT-PCR platform for detection of 667 miRNAs. Candidate mRNAs and miRNAs differentially up- or down-regulated in stage I were chosen for validation in stage II using the remaining samples. Only 12 of 32 candidate genes provided analyzable results with two mRNAs showing significant 3–5-fold differences in gene expression over the reference (p < 0.0001). From 667 candidate miRNAs, 290 miRNA were eligible for analysis with 21 miRNAs independently validated using qRT-PCR. These miRNAs showed persistent expression changes on each day and over days 7–106 days after exposure (n = 7). In particular miR-212 involved in radiosensitivity and immune modulation appeared persistently and 48–77-fold up-regulated over the entire time period. We are finally trying to put our results into a context of clinical implications and provide possible hints on underlying molecular mechanisms to be examined in future studies.
Mitochondrial chaotic dynamics: Redox-energetic behavior at the edge of stability
Authors: Kembro Jackelyn M. , Cortassa Sonia , Lloyd David , Sollott Steven J. , Aon Miguel A.
Published: October 2018

Mitochondria serve multiple key cellular functions, including energy generation, redox balance, and regulation of apoptotic cell death, thus making a major impact on healthy and diseased states. Increasingly recognized is that biological network stability/instability can play critical roles in determining health and disease. We report for the first-time mitochondrial chaotic dynamics, characterizing the conditions leading from stability to chaos in this organelle. Using an experimentally validated computational model of mitochondrial function, we show that complex oscillatory dynamics in key metabolic variables, arising at the “edge” between fully functional and pathological behavior, sets the stage for chaos. Under these conditions, a mild, regular sinusoidal redox forcing perturbation triggers chaotic dynamics with main signature traits such as sensitivity to initial conditions, positive Lyapunov exponents, and strange attractors. At the “edge” mitochondrial chaos is exquisitely sensitive to the antioxidant capacity of matrix Mn superoxide dismutase as well as to the amplitude and frequency of the redox perturbation. These results have potential implications both for mitochondrial signaling determining health maintenance, and pathological transformation, including abnormal cardiac rhythms.
Genomics of experimental adaptation of Staphylococcus aureus to a natural combination of insect antimicrobial peptides
Authors: Makarova Olga , Johnston Paul , Rodriguez-Rojas Alexandro , El Shazely Baydaa , Morales Javier Moreno , Rolff Jens
Published: October 2018

Antimicrobial peptides (AMP) are highly conserved immune effectors across the tree of life and are employed as combinations. In the beetle Tenebrio molitor, a defensin and a coleoptericin are highly expressed in vivo after inoculation with S. aureus. The defensin displays strong in vitro activity but no survival benefit in vivo. The coleoptericin provides a survival benefit in vivo, but no activity in vitro. This suggests a potentiating effect in vivo, and here we wanted to investigate the effects of this combination on resistance evolution using a bottom-approach in vitro starting with a combination of two abundant AMPs only. We experimentally evolved S. aureus in the presence of the defensin and a combination of the defensin and coleoptericin. Genome re-sequencing showed that resistance was associated with mutations in either the pmt or nsa operons. Strains with these mutations show longer lag phases, slower Vmax, and nsa mutants reach lower final population sizes. Mutations in the rpo operon showed a further increase in the lag phase in nsa mutants but not in pmt mutants. In contrast, final MICs (minimum inhibitory concentrations) do not differ according to mutation. All resistant lines display AMP but not antibiotic cross-resistance. Costly resistance against AMPs readily evolves for an individual AMP as well as a naturally occurring combination in vitro and provides broad protection against AMPs. Such non-specific resistance could result in strong selection on host immune systems that rely on cocktails of AMPs.
Impulsive UV-pump/X-ray probe study of vibrational dynamics in glycine
Authors: Mincigrucci Riccardo , Kowalewski Markus , Rouxel Jérémy R. , Bencivenga Filippo , Mukamel Shaul , Masciovecchio Claudio
Published: October 2018

We report an ab-initio study of a pump-probe experiment on the amino-acid glycine. We consider an UV pump followed by an X-ray probe tuned to carbon K-edge and study the vibronic structure of the core transition. The simulated experiment is feasible using existing free electron laser or high harmonic generation sources and thanks to the localization of the core orbitals posseses chemical selectivity. The present theory applies to other experimental schemes, including the use of a THz probe, available with present soft X-ray free electron lasers and/or high harmonic generation sources.
Common Functional Brain States Encode both Perceived Emotion and the Psychophysiological Response to Affective Stimuli
Authors: Bush Keith A. , Privratsky Anthony , Gardner Jonathan , Zielinski Melissa J. , Kilts Clinton D.
Published: October 2018

Multivariate pattern analysis (MVPA) of functional magnetic resonance imaging (fMRI) data has critically advanced the neuroanatomical understanding of affect processing in the human brain. Central to these advancements is the brain state, a temporally-succinct fMRI-derived pattern of neural activation, which serves as a processing unit. Establishing the brain state’s central role in affect processing, however, requires that it predicts multiple independent measures of affect. We employed MVPA-based regression to predict the valence and arousal properties of visual stimuli sampled from the International Affective Picture System (IAPS) along with the corollary skin conductance response (SCR) for demographically diverse healthy human participants (n = 19). We found that brain states significantly predicted the normative valence and arousal scores of the stimuli as well as the attendant individual SCRs. In contrast, SCRs significantly predicted arousal only. The prediction effect size of the brain state was more than three times greater than that of SCR. Moreover, neuroanatomical analysis of the regression parameters found remarkable agreement with regions long-established by fMRI univariate analyses in the emotion processing literature. Finally, geometric analysis of these parameters also found that the neuroanatomical encodings of valence and arousal are orthogonal as originally posited by the circumplex model of dimensional emotion.
Effect of superamphiphobic macrotextures on dynamics of viscous liquid droplets
Authors: Raiyan Asif , Mclaughlin Tabor Scott , Annavarapu Rama Kishore , Sojoudi Hossein
Published: October 2018

The ability of hydrophobic surfaces to repel impinging liquid droplets is important in applications ranging from self-cleaning of solar panels to avoiding ice formation in freezing rain environments. In quest of maximizing water repellency, modification of droplet dynamics and subsequent reduction of contact time have been achieved by incorporating macrotexture on the superhydrophobic surfaces. However, the dynamics of low temperature water, and other viscous liquid droplets impacting anti-wetting surfaces with macrotextures is not well explored. Here, we investigate the effect of viscosity on the bouncing dynamics of liquid droplets impacting macrotextured superamphiphobic surfaces using various glycerol-water mixtures as model liquids at different impacting conditions. We demonstrate that the changes of reduction in contact times by macrotextures due to the increasing viscosity are in opposite trends at low and at high impact velocities. Since macrotexture executes substantial contact time reduction for the droplets which exhibit splitting after the impact, a preliminary model for predicting the minimum impact velocity to observe droplet splitting by macrotexture is proposed considering the important parameters of an impinging droplet along with the surface characteristics and the macrotexture size. This work aims to provide an insight on several possible outcomes of viscous droplets impacting on the macrotextured surfaces and a model that will help to design the desired superamphiphobic surfaces capable of exhibiting reduced contact time and enhanced repellency of low-temperature water droplets (such as freezing rain) and other viscous liquids (such as oils) under different impacting conditions.
A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations
Authors: Singh Mugdha , Sarkar Anujit , Nandineni Madhusudan R.
Published: October 2018

India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.
A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Authors: Li Yongpeng , Fu Xing , Zhao Meicheng , Zhang Wei , Li Bo , An Diaoguo , Li Junming , Zhang Aimin , Liu Renyi , Liu Xigang
Published: October 2018

Wheat spike development is a coordinated process of cell proliferation and differentiation with distinctive phases and architecture changes. However, the dynamic alteration of gene expression in this process remains enigmatic. Here, we characterized and dissected bread wheat spike into six developmental stages, and used genome-wide gene expression profiling, to investigate the underlying regulatory mechanisms. High gene expression correlations between any two given stages indicated that wheat early spike development is controlled by a small subset of genes. Throughout, auxin signaling increased, while cytokinin signaling decreased. Besides, many genes associated with stress responses highly expressed during the double ridge stage. Among the differentially expressed genes (DEGs), were identified 375 transcription factor (TF) genes, of which some homologs in rice or Arabidopsis are proposed to function in meristem maintenance, flowering time, meristem initiation or transition, floral organ development or response to stress. Gene expression profiling demonstrated that these genes had either similar or distinct expression pattern in wheat. Several genes regulating spike development were expressed in the early spike, of which Earliness per se 3 (Eps-3) was found might function in the initiation of spikelet meristem. Our study helps uncover important genes associated with apical meristem morphology and development in wheat.
Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis
Authors: Štefanić Zoran , Narczyk Marta , Mikleušević Goran , Kazazić Saša , Bzowska Agnieszka , Luić Marija
Published: October 2018

Purine nucleoside phosphorylase (PNP) catalyses the cleavage of the glycosidic bond of purine nucleosides using phosphate instead of water as a second substrate. PNP from Escherichia coli is a homohexamer, build as a trimer of dimers, and each subunit can be in two conformations, open or closed. This conformational change is induced by the presence of phosphate substrate, and very likely a required step for the catalysis. Closing one active site strongly affects the others, by a yet unclear mechanism and order of events. Kinetic and ligand binding studies show strong negative cooperativity between subunits. Here, for the first time, we managed to monitor the sequence of nucleoside binding to individual subunits in the crystal structures of the wild-type enzyme, showing that first the closed sites, not the open ones, are occupied by the nucleoside. However, two mutations within the active site, Asp204Ala/Arg217Ala, are enough not only to significantly reduce the effectiveness of the enzyme, but also reverse the sequence of the nucleoside binding. In the mutant the open sites, neighbours in a dimer of those in the closed conformation, are occupied as first. This demonstrates how important for the effective catalysis of Escherichia coli PNP is proper subunit cooperation.
Outpacing the pneumococcus: Antibody dynamics in the first few days following pneumococcal capsular antigen stimulation
Authors: Kimaro Mlacha Sheila Z. , Warira Anne , Gatakaa Hellen , Goldblatt David , Scott J. Anthony G.
Published: October 2018

Children in developing countries are frequently exposed to the pneumococcus, but few develop invasive pneumococcal disease (IPD). We test the hypothesis that natural variation exists in the rapidity of IgG responses following exposure to pneumococcal polysaccharides, and that these differences are sufficiently great to affect susceptibility to and outcome of IPD. We recruited children aged 24–36 months, who had recovered from IPD, and age-matched healthy controls and vaccinated them with 1 dose of the 23-valent PPV to mimic natural exposure. We collected serum samples after vaccination and analysed the dynamics of anti-polysaccharide antibody responses to several capsular antigens. Mean IgG response times to different serotypes were 6.4–7.3 days, with standard deviations of 0.9–1.85 days, suggesting a natural range in response times of up to 7 days. Serotype 1 elicited the largest fold-rise, serotype 23F the smallest. The proportion of responses achieved by day 7 was similar in children with a history of IPD and healthy children. There was considerable natural variation in the rapidity of anti-capsular IgG responses extending over 4–7 days. There was no evidence to suggest that children who have experienced IPD respond more slowly to heterologous pneumococcal capsular antigens than do healthy children.
The dynamic transcriptome and metabolomics profiling in Verticillium dahliae inoculated Arabidopsis thaliana
Authors: Su Xiaofeng , Lu Guoqing , Guo Huiming , Zhang Kaixuan , Li Xiaokang , Cheng Hongmei
Published: October 2018

Verticillium wilt caused by the soil-borne fungus Verticillium dahliae is a common, devastating plant vascular disease notorious for causing economic losses. Despite considerable research on plant resistance genes, there has been little progress in modeling the effects of this fungus owing to its complicated pathogenesis. Here, we analyzed the transcriptional and metabolic responses of Arabidopsis thaliana to V. dahliae inoculation by Illumina-based RNA sequencing (RNA-seq) and nuclear magnetic resonance (NMR) spectroscopy. We identified 13,916 differentially expressed genes (DEGs) in infected compared with mock-treated plants. Gene ontology analysis yielded 11,055 annotated DEGs, including 2,308 for response to stress and 2,234 for response to abiotic or biotic stimulus. Pathway classification revealed involvement of the metabolic, biosynthesis of secondary metabolites, plant–pathogen interaction, and plant hormone signal transduction pathways. In addition, 401 transcription factors, mainly in the MYB, bHLH, AP2-EREBP, NAC, and WRKY families, were up- or downregulated. NMR analysis found decreased tyrosine, asparagine, glutamate, glutamine, and arginine and increased alanine and threonine levels following inoculation, along with a significant increase in the glucosinolate sinigrin and a decrease in the flavonoid quercetin glycoside. Our data reveal corresponding changes in the global transcriptomic and metabolic profiles that provide insights into the complex gene-regulatory networks mediating the plant’s response to V. dahliae infection.