bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonhysteretic Capillary Pressure in Two‐Fluid Porous Medium Systems: Definition, Evaluation, Validation, and Dynamics
Authors: Miller C. T. , Bruning K. , Talbot C. L. , McClure J. E. , Gray W. G. 
Published: July 2019

AbstractA closure relation for capillary pressure plays an important role in the formulation of both traditional and evolving models of two‐fluid‐phase flow in porous medium systems. We review the traditional approaches to define capillary pressure, to describe it mathematically, to determine parameters for this relation, and to constrain the domain of applicability of this relation. In contrast to the traditional approach, we provide a rigorous, multiscale definition of capillary pressure, define the state domain of interest in practice, summarize computational and experimental approaches to investigate the system state, and apply the methods for two‐fluid states in a model ink bottle system, the classical Finney pack of spheres, and a synthetic sphere pack system. The results of these applications show that a state equation exists that describes capillary pressure without hysteresis. This state equation parameterizes a function that describes the nonwetting phase volume fraction in terms of the capillary pressure, the interfacial area, and the specific Euler characteristic of the nonwetting phase. Furthermore, this state equation applies over the complete range of conditions encountered in practice, and it applies under both equilibrium and dynamic conditions. This state equation involving capillary pressure forms an important foundation for the development of the next generation of macroscale two‐fluid‐phase flow models in porous medium systems.
Initial 40Ar‐39Ar Ages of the Paleocene‐Eocene Boundary Impact Spherules
Authors: Schaller Morgan F. , Turrin Brent D. , Fung Megan K. , Katz Miriam E. , Swisher Carl C. 
Published: July 2019

AbstractWe report 40Ar‐39Ar step‐heating ages of Paleocene‐Eocene (P‐E) boundary impact spherules from Atlantic Margin coastal plain and open ocean sites. We test the hypothesis that the P‐E spherules are reworked from an earlier event (e.g., K‐Pg impact at ~66 Ma), which predicts a cooling age discordant from their depositional age of 55.93 ± 0.05 Ma at the P‐E boundary. Isochrons from the step‐heating analysis yield 40Ar‐36Ar intercepts in excess of the modern in most cases, indicating that the spherules have excess radiogenic Ar (40Ar*), typical of impact glasses incompletely degassed before solidification. The weighted mean of the isochron‐corrected plateau age is 54.2 ± 2.5 Ma (1σ), and their isochron age is 55.4 ± 4.0 Ma, both indistinguishable from their P‐E depositional age, not supporting the K‐Pg reworking hypothesis. This is consistent with all other stratigraphic and geochemical evidence for an impact at the P‐E boundary and ejecta distribution by air fall.
Why Do Antarctic Ozone Recovery Trends Vary?
Authors: Strahan Susan E. , Douglass Anne R. , Damon Megan R. 
Published: July 2019

AbstractWe use satellite ozone records and Global Modeling Initiative chemistry transport model simulations integrated with Modern Era Retrospective for Research and Analysis 2 meteorology to identify a metric that accurately captures the trend in Antarctic ozone attributable to the decline in ozone depleting substances (ODSs). The GMI CTM Baseline simulation with realistically varying ODS levels closely matches observed interannual to decadal scale variations in Antarctic September ozone over the past four decades. The expected increase or recovery trend is obtained from the differences between the Baseline simulation and one with identical meteorology and fixed 1995 ODS levels. The differences show that vortex‐averaged column O3 has the greatest sensitivity to ODS change from 1 to 20 September. The observed vortex‐averaged column O3 during this period produces a trend consistent with the expected recovery attributable to ODS decline. Trends from dates after 20 September have smaller sensitivity to ODS decline and are more uncertain due to transport variability. Simulations show that the greatest decrease in O3 loss (i.e., recovery) occurs inside the vortex near the edge. The polar cap metrics have vortex size‐dependent bias and do not consistently sample this region. Because the 60–90°S 220 Dobson unit O3 mass deficit metric does not sample the edge region, its trend is lower than the expected trend; this is improved by area weighting. The 250‐Dobson unit O3 mass deficit metric samples more of the edge region, which increases its trend. Approximately 25% of the September Antarctic O3 increase is due to higher O3 levels in June prior to winter depletion.
Bayesian Calibration and Sensitivity Analysis for a Karst Aquifer Model Using Active Subspaces
Authors: Teixeira Parente Mario , Bittner Daniel , Mattis Steven A. , Chiogna Gabriele , Wohlmuth Barbara 
Published: July 2019

AbstractIn this article, we perform a parameter study for a recently developed karst hydrological model. The study consists of a high‐dimensional Bayesian inverse problem and a global sensitivity analysis. For the first time in karst hydrology, we use the active subspace method to find directions in the parameter space that dominate the Bayesian update from the prior to the posterior distribution in order to effectively reduce the dimension of the problem and for computational efficiency. Additionally, the calculated active subspace can be exploited to construct sensitivity metrics on each of the individual parameters and be used to construct a natural model surrogate. The model consists of 21 parameters to reproduce the hydrological behavior of spring discharge in a karst aquifer located in the Kerschbaum spring recharge area at Waidhofen a.d. Ybbs in Austria. The experimental spatial and time series data for the inference process were collected by the water works in Waidhofen. We show that this case study has implicit low dimensionality, and we run an adjusted Markov chain Monte Carlo algorithm in a low‐dimensional subspace to construct samples of the posterior distribution. The results are visualized and verified by plots of the posterior's push‐forward distribution displaying the uncertainty in predicting discharge values due to the experimental noise in the data. Finally, a discussion provides hydrological interpretation of these results for the Kerschbaum area.
A brain somatic RHEB doublet mutation causes focal cortical dysplasia type II
Authors: Zhao Shanshan , Li Zhenghui , Zhang Muxian , Zhang Lingliang , Zheng Honghua , Ning Jinhuan , Wang Yanyan , Wang Fengpeng , Zhang Xiaobin , Gan Hexia , Wang Yuanqing , Zhang Xian , Luo Hong , Bu Guojun , Xu Huaxi , Yao Yi , Zhang Yun-wu 
Published: July 2019

AbstractFocal cortical dysplasia type II (FCDII) is a cerebral cortex malformation characterized by local cortical structure disorganization, neuronal dysmorphology, and refractory epilepsy. Brain somatic mutations in several genes involved in the PI3K/AKT/mTOR pathway are associated with FCDII, but they are only found in a proportion of patients with FCDII. The genetic causes underlying the development FCDII in other patients remain unclear. Here, we carried out whole exome sequencing and targeted sequencing in paired brain–blood DNA from patients with FCDII and identified a brain somatic doublet mutation c.(A104T, C105A) in the Ras homolog, mTORC1 binding (RHEB) gene, which led to the RHEB p.Y35L mutation in one patient with FCDII. This RHEB mutation carrier had a dramatic increase of ribosomal protein S6 phosphorylation, indicating mTOR activation in the region of the brain lesion. The RHEB p.Y35L mutant protein had increased GTPλS-binding activity compared with wild-type RHEB. Overexpression of the RHEB p.Y35L variant in cultured cells also resulted in elevated S6 phosphorylation compared to wild-type RHEB. Importantly, in utero electroporation of the RHEB p.Y35L variant in mice induced S6 phosphorylation, cytomegalic neurons, dysregulated neuron migration, abnormal electroencephalogram, and seizures, all of which are found in patients with FCDII. Rapamycin treatment rescued abnormal electroencephalograms and alleviated seizures in these mice. These results demonstrate that brain somatic mutations in RHEB are also responsible for the pathogenesis of FCDII, indicating that aberrant activation of mTOR signaling is a primary driver and potential drug target for FCDII.
Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein Rbm14
Authors: Xiao Yue , Chen Jiehui , Wan Yihan , Gao Qi , Jing Naihe , Zheng Yixian , Zhu Xueliang 
Published: July 2019

AbstractRNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish Rbm14 regulates embryonic dorsoventral patterning through phase separation. Zebrafish rbm14 morphants displayed dorsalized phenotypes associated with attenuated BMP signaling. Consistently, depletion of mammalian Rbm14 downregulated BMP regulators and effectors Nanog, Smad4/5, and Id1/2, whereas overexpression of the BMP-related proteins in the morphants significantly restored the developmental defects. Importantly, the IDR of zebrafish Rbm14 demixed into liquid droplets in vitro despite poor sequence conservation with its mammalian counterpart. While its phase separation mutants or IDR failed to rescue the morphants, its chimeric proteins containing an IDR from divergent phase separation proteins were effective. Rbm14 complexed with proteins involved in RNA metabolism and phase separated into cellular ribonucleoprotein compartments. Consistently, RNA deep sequencing analysis on the morphant embryos revealed increased alternative splicing events as well as large-scale transcriptomic downregulations. Our results suggest that Rbm14 functions in ribonucleoprotein compartments through phase separation to modulate multiple aspects of RNA metabolism. Furthermore, IDRs conserve in phase separation ability but not primary sequence and can be functionally interchangeable.
Room-temperature superionic-phase nanocrystals synthesized with a twinned lattice
Authors: Gong Jianxiao , Jain Prashant K. 
Published: July 2019

AbstractThe engineering of nanoscale features enables the properties of solid-state materials to be tuned. Here, we show the tunable preparation of cuprous sulfide nanocrystals ranging in internal structures from single-domain to multi-domain. The synthetic method utilizes in-situ oxidation to grow nanocrystals with a controlled degree of copper deficiency. Copper-deficient nanocrystals spontaneously undergo twinning to a multi-domain structure. Nanocrystals with twinned domains exhibit markedly altered crystallographic phase and phase transition characteristics as compared to single-domain nanocrystals. In the presence of twin boundaries, the temperature for transition from the ordered phase to the high-copper-mobility superionic phase is depressed. Whereas the superionic phase is stable in the bulk only above ca. 100 °C, cuprous sulfide nanocrystals of ca. 7 nm diameter and a twinned structure are stable in the superionic phase well below ambient temperature. These findings demonstrate twinning to be a structural handle for nanoscale materials design and enable applications for an earth-abundant mineral in solid electrolytes for Li-S batteries.
Conditional expression explains molecular evolution of social genes in a microbe
Authors: de Oliveira Janaina Lima , Morales Atahualpa Castillo , Stewart Balint , Gruenheit Nicole , Engelmoer Jennifer , Brown Suzanne Battom , de Brito Reinaldo A. , Hurst Laurence D. , Urrutia Araxi O. , Thompson Christopher R. L. , Wolf Jason B. 
Published: July 2019

AbstractConflict is thought to play a critical role in the evolution of social interactions by promoting diversity or driving accelerated evolution. However, despite our sophisticated understanding of how conflict shapes social traits, we have limited knowledge of how it impacts molecular evolution across the underlying social genes. Here we address this problem by analyzing the genome-wide impact of social interactions using genome sequences from 67Dictyostelium discoideumstrains. We find that social genes tend to exhibit enhanced polymorphism and accelerated evolution. However, these patterns are not consistent with conflict driven processes, but instead reflect relaxed purifying selection. This pattern is most likely explained by the conditional nature of social interactions, whereby selection on genes expressed only in social interactions is diluted by generations of inactivity. This dilution of selection by inactivity enhances the role of drift, leading to increased polymorphism and accelerated evolution, which we call the Red King process.
Acoustic radiation pressure for nonreciprocal transmission and switch effects
Authors: Devaux Thibaut , Cebrecos Alejandro , Richoux Olivier , Pagneux Vincent , Tournat Vincent 
Published: July 2019

AbstractSystems capable of breaking wave transmission reciprocity have recently led to tremendous developments in wave physics. We report herein on a concept that enables one-way transmission of ultrasounds, an acoustic diode, by relying on the radiation pressure effect. This effect makes it possible to reconfigure a multilayer system by significantly deforming a water-air interface. Such a reconfiguration is then used to achieve an efficient acoustic transmission in a specified direction of propagation but not in the opposite, hence resulting in a highly nonreciprocal transmission. The corresponding concept is experimentally demonstrated using an aluminum-water-air-aluminum multilayer system, providing the means to overcome key limitations of current nonreciprocal acoustic devices. We also demonstrate that this diode functionality can even be extended to the design and operations of an acoustic switch, thus paving the way for new wave control possibilities, such as those based on acoustic transistors, phonon computing and amplitude-dependent filters.
Pathogen transmission risk by opportunistic gulls moving across human landscapes
Authors: Navarro Joan , Grémillet David , Afán Isabel , Miranda Francisco , Bouten Willem , Forero Manuela G. , Figuerola Jordi 
Published: July 2019

AbstractWildlife that exploit human-made habitats hosts and spreads bacterial pathogens. This shapes the epidemiology of infectious diseases and facilitates pathogen spill-over between wildlife and humans. This is a global problem, yet little is known about the dissemination potential of pathogen-infected animals. By combining molecular pathogen diagnosis with GPS tracking of pathogen-infected gulls, we show how this knowledge gap could be filled at regional scales. Specifically, we generated pathogen risk maps of Salmonella, Campylobacter and Chlamydia based on the spatial movements of pathogen-infected yellow-legged gulls (Larus michahellis) equipped with GPS recorders. Also, crossing this spatial information with habitat information, we identified critical habitats for the potential transmission of these bacteria in southern Europe. The use of human-made habitats by infected-gulls could potentially increase the potential risk of direct and indirect bidirectional transmission of pathogens between humans and wildlife. Our findings show that pathogen-infected wildlife equipped with GPS recorders can provide accurate information on the spatial spread risk for zoonotic bacteria. Integration of GPS-tracking with classical epidemiological approaches may help to improve zoonosis surveillance and control programs.
The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities
Authors: Vimercati Lara , Darcy John L. , Schmidt Steve K. 
Published: July 2019

AbstractMicrobial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genusPolaromonasemphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation “island of the cryosphere” before the glaciers of Kilimanjaro disappear forever.
Mapping the conductivity of graphene with Electrical Resistance Tomography
Authors: Cultrera Alessandro , Serazio Danilo , Zurutuza Amaia , Centeno Alba , Txoperena Oihana , Etayo David , Cordon Alvaro , Redo-Sanchez Albert , Arnedo Israel , Ortolano Massimo , Callegaro Luca 
Published: July 2019

AbstractElectronic applications of large-area graphene films require rapid and accurate methods to map their electrical properties. Here we present the first electrical resistance tomography (ERT) measurements on large-area graphene samples, obtained with a dedicated measurement setup and reconstruction software. The outcome of an ERT measurement is a map of the graphene electrical conductivity. The same setup allows to perform van der Pauw (vdP) measurements of the average conductivity. We characterised the electrical conductivity of chemical-vapour deposited graphene samples by performing ERT, vdP and scanning terahertz time-domain spectroscopy (TDS), the last one by means of a commercial instrument. The measurement results are compared and discussed, showing the potential of ERT as an accurate and reliable technique for the electrical characterization of graphene samples.
C70 Fullerene Cage as a Novel Catalyst for Efficient Proton Transfer Reactions between Small Molecules: A Theoretical study
Authors: Varadwaj Pradeep R. , Varadwaj Arpita , Marques Helder M. 
Published: July 2019

AbstractWhen acids are supplied with an excess electron (or placed in an Ar or the more polarizable N2 matrix) in the presence of species such as NH3, the formation of ion-pairs is a likely outcome. Using density functional theory and first-principles calculations, however, we show that, without supplying an external electron or an electric field, or introducing photo-excitation and -ionization, a single molecule of HCl or HBr in the presence of a single molecule of water inside a C70 fullerene cage is susceptible to cleavage of the σ-bond of the Brønsted-Lowry acid into X− and H+ ions, with concomitant transfer of the proton along the reaction coordinate. This leads to the formation of an X−···+HOH2 (X = Cl, Br) conjugate acid-base ion-pair, similar to the structure in water of a Zundel ion. This process is unlikely to occur in other fullerene derivatives in the presence of H2O without significantly affecting the geometry of the carbon cage, suggesting that the interior of C70 is an ideal catalytic platform for proton transfer reactions and the design of related novel materials. By contrast, when a single molecule of HF is reacted with a single molecule of H2O inside the C70 cage, partial proton transfers from HF to H2O is an immediate consequence, as recently observed experimentally. The geometrical, energetic, electron density, orbital, optoelectronic and vibrational characteristics supporting these observations are presented. In contrast with the views that have been advanced in several recent studies, we show that the encaged species experiences significant non-covalent interaction with the interior of the cage. We also show that the inability of current experiments to detect many infrared active vibrational bands of the endo species in these systems is likely to be a consequence of the substantial electrostatic screening effect of the cage.
Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen
Authors: Liu Sha , Feng Jie , Pu Ji , Xu Xuefang , Lu Shan , Yang Jing , Wang Yiting , Jin Dong , Du Xiaochen , Meng Xiangli , Luo Xia , Sun Hui , Xiong Yanwen , Ye Changyun , Lan Ruiting , Xu Jianguo 
Published: July 2019

AbstractWildlife is a reservoir of emerging infectious diseases of humans and domestic animals. Marmota himalayana mainly resides 2800–4000 m above sea level in the Qinghai-Tibetan Plateau, and is the primary animal reservoir of plague pathogen Yersinia pestis. Recently we isolated a new species, Escherichia marmotae from the faeces of M. himalayana. In this study we characterised E. marmotae by genomic analysis and in vitro virulence testing to determine its potential as a human pathogen. We sequenced the genomes of the seven E. marmotae strains and found that they contained a plasmid that carried a Shigella-like type III secretion system (T3SS) and their effectors, and shared the same O antigen gene cluster as Shigella dysenterae 8 and E. coli O38. We also showed that E. marmotae was invasive to HEp-2 cells although it was much less invasive than Shigella. Thus E. marmotae is likely to be an invasive pathogen. However, E. marmotae has a truncated IpaA invasin, and lacks the environmental response regulator VirF and the IcsA-actin based intracellular motility, rendering it far less invasive in comparison to Shigella. E. marmotae also carried a diverse set of virulence factors in addition to the T3SS, including an IS1414 encoded enterotoxin gene astA with 37 copies, E. coli virulence genes lifA/efa, cif, and epeA, and the sfp gene cluster, Yersinia T3SS effector yopJ, one Type II secretion system and two Type VI secretion systems. Therefore, E. marmotae is a potential invasive pathogen.