bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Immiscible Two‐Phase Flow in Rough Fractures From Capillary to Viscous Fingering
Authors: Yang Zhibing , Méheust Yves , Neuweiler Insa , Hu Ran , Niemi Auli , Chen Yi‐Feng 
Published: February 2019

AbstractWe develop an efficient computational model for simulating fluid invasion patterns emerging in variable aperture fractures. This two‐dimensional model takes into account the effect of capillary force on the fluid‐fluid interfaces and viscous pressure drop in both fluid phases. The pressure distribution is solved at each time step based on mass balance and local cubic law, considering an imposed pressure jump condition at the fluid‐fluid interface. This pressure jump corresponds to the Laplace pressure which includes both terms related to the out‐of‐plane (aperture‐spanning) curvature and to the in‐plane curvature. Simulating a configuration that emulates viscous fingering in two‐dimensional random porous media confirms that the model accounts properly for the role of viscous forces. Furthermore, direct comparison with previously obtained experimental results shows that the model reproduces the observed drainage patterns in a rough fracture reasonably well. The evolutions of tip location, the inlet pressures, and the invading phase fractal dimensions are analyzed to characterize the transition from capillary fingering to viscous fingering regimes. A radial injection scenario of immiscible invasion is also studied with varying modified capillary number and viscosity ratio, showing displacement patterns ranging from capillary fingering to viscous fingering to stable displacement. Such simulations using two contact angles show that the invading phase becomes more compact when the wetting condition changes from strong to weak drainage, as already observed in 2‐D porous media. The model can be used to bridge the gap in spatial scales of two‐phase flow between pore‐scale modeling approaches and the continuum Darcy‐scale models.
Numerical Modeling of Hyperconcentrated Confluent Floods From the Middle Yellow and Lower Weihe Rivers
Authors: Wang Zenghui , Xia Junqiang , Zhou Meirong , Li Tao 
Published: February 2019

AbstractHyperconcentrated confluent floods in the Middle Yellow River and its tributaries are characterized by the phenomena of extremely high backwater stage, flood water intrusion, and local channel blockage in confluence areas. In order to study the propagation process of hyperconcentrated confluent floods, most existing channel network models need reinforcement in the computation of sediment transport and improvement in the treatment of interior boundary at channel junctions. A river network model for hyperconcentrated confluent floods is proposed based on the finite volume method scheme, in which the study domain is represented by ordinary 1‐D cells and junction cells. As a preprocess step, a bathymetry interpolation algorithm is developed to generate topography data and to extract the stage‐volume relationship for the junction cell. The storage change and sediment transport in the junction cell are calculated in each time step with no need to distinguish convergent or divergent flow pattern, and the solution in each reach can be executed simultaneously. The model was validated by simulating the hyperconcentrated confluent flood events in 1977 and 1966, with the maximum backwater stage and the occurrence time of flood water intrusion in the Lower Weihe River being well predicted. The response was investigated of the Middle Yellow River and Lower Weihe River to the arrangement of peak times of confluent floods, with the critical condition for flood water intrusion and the scenario that achieves the most effective scouring in the downstream channel being identified.
Decadal‐Scale Climate Forcing of Alpine Glacial Hydrological Systems
Authors: Lane S. N. , Nienow P. W. 
Published: February 2019

AbstractQuantification of climate forcing of glacial hydrological systems at the decadal scale is rare because most measurement stations are too far downstream for glacier impacts to be clearly detected. Here we apply a measure of daily hydrograph entropy to a unique set of reliable, high‐altitude gauging stations, dating from the late 1960s. We find a progressive shift to a greater number of days with diurnal discharge variation as well as more pronounced diurnal discharge amplitude. These changes were associated with the onset of rapid warming in the 1980s as well as declining end of winter snow depths as inferred from climate data. In glaciated catchments, lower winter snow depths reduce the magnitude and duration of snowpack buffering and encourage the earlier onset of glacier ice exposure, with associated lower surface albedo and more rapid melt. Together, these processes explain the increase in the observed intensity of diurnal discharge fluctuations.
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network
Authors: Bouma-Gregson Keith , Olm Matthew R , Probst Alexander J , Anantharaman Karthik , Power Mary E , Banfield Jillian F 
Published: February 2019

Abstract
Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared &lt;96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.
Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes
Authors: Jones Daniel S , Walker Gabriel M , Johnson Nathan W , Mitchell Carl P J , Coleman Wasik Jill K , Bailey Jake V 
Published: February 2019

Abstract
Methylmercury (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota’s Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.
Planar cell polarity protein Dishevelled 3 (Dvl3) regulates ectoplasmic specialization (ES) dynamics in the testis through changes in cytoskeletal organization
Authors: Li Linxi , Mao Baiping , Yan Ming , Wu Siwen , Ge Renshan , Lian Qingquan , Cheng C. Yan 
Published: February 2019

AbstractIn the mammalian testes, such as in rats, the directional alignment of polarized elongating/elongated spermatids, in particular step 17–19 spermatids, across the plane of seminiferous epithelium resembles planar cell polarity (PCP) found in hair cells of the cochlea. It is obvious that spermatid PCP is necessary to support the simultaneous development of maximal number of elongating/elongated spermatids to sustain the daily production of > 50 million sperm per adult rat. Studies have shown that the testis indeed expresses multiple PCP proteins necessary to support spermatid PCP. Herein, using physiological and biochemical assays, and morphological analysis, and with the technique of RNA interference (RNAi) to knockdown PCP protein Dishevelled (Dvl) 1 (Dvl1), Dvl2, Dvl3, or Dvl1/2/3, Dvl proteins, in particular Dvl3, it was shown that Dvl3 played a crucial role of support Sertoli cell tight junction (TJ)-permeability barrier function through changes in the organization of actin- and microtubule (MT)-based cytoskeletons. More important, an in vivo knockdown of Dvl1/2/3 in the testis, defects of spermatid polarity were remarkably noted across the seminiferous epithelium, concomitant with defects of spermatid adhesion and spermatid transport, leading to considerably defects in spermatogenesis. More important, Dvl1/2/3 triple knockdown in the testis also impeded the organization of actin- and MT-based cytoskeletons owing to disruptive spatial expression of actin- and MT-regulatory proteins. In summary, PCP Dishevelled proteins, in particular, Dvl3 is a regulator of Sertoli cell blood–testis barrier (BTB) and also spermatid PCP function through its effects on the actin- and MT-based cytoskeletons in Sertoli cells.
Modified carbon nitride nanozyme as bifunctional glucose oxidase-peroxidase for metal-free bioinspired cascade photocatalysis
Authors: Zhang Peng , Sun Dengrong , Cho Ara , Weon Seunghyun , Lee Seonggyu , Lee Jinwoo , Han Jeong Woo , Kim Dong-Pyo , Choi Wonyong 
Published: February 2019

AbstractNanomaterials-based biomimetic catalysts with multiple functions are necessary to address challenges in artificial enzymes mimicking physiological processes. Here we report a metal-free nanozyme of modified graphitic carbon nitride and demonstrate its bifunctional enzyme-mimicking roles. With oxidase mimicking, hydrogen peroxide is generated from the coupled photocatalysis of glucose oxidation and dioxygen reduction under visible-light irradiation with a near 100% apparent quantum efficiency. Then, the in situ generated hydrogen peroxide serves for the subsequent peroxidase-mimicking reaction that oxidises a chromogenic substrate on the same catalysts in dark to complete the bifunctional oxidase-peroxidase for biomimetic detection of glucose. The bifunctional cascade catalysis is successfully demonstrated in microfluidics for the real-time colorimetric detection of glucose with a low detection limit of 0.8 μM within 30 s. The artificial nanozymes with physiological functions provide the feasible strategies for mimicking the natural enzymes and realizing the biomedical diagnostics with a smart and miniature device.
Ti and its alloys as examples of cryogenic focused ion beam milling of environmentally-sensitive materials
Authors: Chang Yanhong , Lu Wenjun , Guénolé Julien , Stephenson Leigh T. , Szczpaniak Agnieszka , Kontis Paraskevas , Ackerman Abigail K. , Dear Felicity F. , Mouton Isabelle , Zhong Xiankang , Zhang Siyuan , Dye David , Liebscher Christian H. , Ponge Dirk , Korte-Kerzel Sandra , Raabe Dierk , Gault Baptiste 
Published: February 2019

AbstractHydrogen pick-up leading to hydride formation is often observed in commercially pure Ti (CP-Ti) and Ti-based alloys prepared for microscopic observation by conventional methods, such as electro-polishing and room temperature focused ion beam (FIB) milling. Here, we demonstrate that cryogenic FIB milling can effectively prevent undesired hydrogen pick-up. Specimens of CP-Ti and a Ti dual-phase alloy (Ti-6Al-2Sn-4Zr-6Mo, Ti6246, in wt.%) were prepared using a xenon-plasma FIB microscope equipped with a cryogenic stage reaching −135 °C. Transmission electron microscopy (TEM), selected area electron diffraction, and scanning TEM indicated no hydride formation in cryo-milled CP-Ti lamellae. Atom probe tomography further demonstrated that cryo-FIB significantly reduces hydrogen levels within the Ti6246 matrix compared with conventional methods. Supported by molecular dynamics simulations, we show that significantly lowering the thermal activation for H diffusion inhibits undesired environmental hydrogen pick-up during preparation and prevents pre-charged hydrogen from diffusing out of the sample, allowing for hydrogen embrittlement mechanisms of Ti-based alloys to be investigated at the nanoscale.
A network-centric approach to drugging TNF-induced NF-κB signaling
Authors: Pabon Nicolas A. , Zhang Qiuhong , Cruz J. Agustin , Schipper David L. , Camacho Carlos J. , Lee Robin E. C. 
Published: February 2019

AbstractTarget-centric drug development strategies prioritize single-target potency in vitro and do not account for connectivity and multi-target effects within a signal transduction network. Here, we present a systems biology approach that combines transcriptomic and structural analyses with live-cell imaging to predict small molecule inhibitors of TNF-induced NF-κB signaling and elucidate the network response. We identify two first-in-class small molecules that inhibit the NF-κB signaling pathway by preventing the maturation of a rate-limiting multiprotein complex necessary for IKK activation. Our findings suggest that a network-centric drug discovery approach is a promising strategy to evaluate the impact of pharmacologic intervention in signaling.
Quantitative sensing and signalling of single-stranded DNA during the DNA damage response
Authors: Bantele Susanne C. S. , Lisby Michael , Pfander Boris 
Published: February 2019

AbstractThe DNA damage checkpoint senses the presence of DNA lesions and controls the cellular response thereto. A crucial DNA damage signal is single-stranded DNA (ssDNA), which is frequently found at sites of DNA damage and recruits the sensor checkpoint kinase Mec1-Ddc2. However, how this signal – and therefore the cell's DNA damage load – is quantified, is poorly understood. Here, we use genetic manipulation of DNA end resection to induce quantitatively different ssDNA signals at a site-specific double strand break in budding yeast and identify two distinct signalling circuits within the checkpoint. The local checkpoint signalling circuit leading to γH2A phosphorylation is unresponsive to increased amounts of ssDNA, while the global checkpoint signalling circuit, which triggers Rad53 activation, integrates the ssDNA signal quantitatively. The global checkpoint signal critically depends on the 9-1-1 and its downstream acting signalling axis, suggesting that ssDNA quantification depends on at least two sensor complexes.
Stokes flow analogous to viscous electron current in graphene
Authors: Mayzel Jonathan , Steinberg Victor , Varshney Atul 
Published: February 2019

AbstractElectron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments.
Dimerization energetics of curli fiber subunits CsgA and CsgB
Authors: Dunbar Martha , DeBenedictis Elizabeth , Keten Sinan 
Published: February 2019

AbstractCurli fibers are functional amyloids that exhibit strong adhesion and robust self-assembly as biofilm structural components; however, the binding energetics and mechanical properties of wild-type curli are not well understood. To address this, we present dimer structures made up of the major and minor curli subunits (CsgA and CsgB), perform free energy calculations to obtain absolute binding energies, and estimate the Young’s modulus and persistence length of curli fibers. Equilibrium molecular dynamics simulations are used to evaluate nonbonded interactions. Binding energies are most favorable for CsgB–CsgA, while CsgA–CsgA dimers have a higher binding energy than CsgB–CsgB despite possessing less favorable nonbonded interaction energies. Decomposing each potential of mean force of separation indicated that solvent effects positively impact CsgA–CsgA binding but not CsgB–CsgB and CsgB–CsgA. Charged residues and conserved polar residues were also notable contributors to attractive nonbonded interactions, underlining their importance in dimer assembly. Our findings elucidate sequence effects on binding energy contributions and establish theoretical limits for the elasticity, persistence length, and strength of curli fibers.
Mechanism of surface uranium hydride formation during corrosion of uranium
Authors: Ji Hefei , Wu Haoxi , Pan Qifa , Cai Dingzhou , Meng Xiandong , Chen Xianglin , Shi Peng , Wang Xiaolin 
Published: February 2019

AbstractUranium is widely used in the nuclear industry and it is well known that uranium hydride, UH3, forms when uranium is exposed to air. The associated volume change during this transition can cause the surface region to crack, compromising structural integrity. Here, hydriding regions beneath hydride surface craters are studied by secondary ion mass spectroscopy (SIMS) and X-ray photoelectron spectroscopy (XPS). Our results indicate that strain transition regions exist, which are induced by hydrogen with a certain thickness between hydride craters and the uranium bulk. The SIMS and XPS results suggest that hydrogen exists covalently with uranium and oxygen in these transition regions. A micro-scale induction period model based on the transition region and previous hydriding models is developed. Within the so-called micro-scale induction period, hydrogen diffuses and accumulates at particular sites before reaching the critical concentration required to form stoichiometric UH3 in the transition regions.
Lateral parabrachial neurons innervate orexin neurons projecting to brainstem arousal areas in the rat
Authors: Arima Yosuke , Yokota Shigefumi , Fujitani Masashi 
Published: February 2019

AbstractOrexin (ORX) neurons in the hypothalamus send their axons to arousal-promoting areas. We have previously shown that glutamatergic neurons in the lateral parabrachial nucleus (LPB) innervate ORX neurons. In this study, we examined potential pathways from the LPB to ORX neurons projecting to arousal-promoting areas in the brainstem by a combination of tract-tracing techniques in male Wistar rats. We injected the anterograde tracer biotinylated dextranamine (BDA) into the LPB and the retrograde tracer cholera toxin B subunit (CTb) into the ventral tegmental area, dorsal raphe nucleus, pedunculopontine tegmental nucleus, laterodorsal tegmental area, or locus coeruleus (LC). We then analyzed the BDA-labeled fibers and ORX-immunoreactive neurons in the hypothalamus. We found that double-labeled ORX and CTb neurons were the most abundant after CTb was injected into the LC. We also observed prominently overlapping distribution of BDA-labeled fibers, arising from neurons located in the lateral-most part of the dorsomedial nucleus and adjacent dorsal perifornical area. In these areas, we confirmed by confocal microscopy that BDA-labeled synaptophysin-immunoreactive axon terminals were in contiguity with cell bodies and dendrites of CTb-labeled ORX-immunoreactive neurons. These results suggest that the LPB innervates arousal-promoting areas via ORX neurons and is likely to promote arousal responses to stimuli.
Retrospective analysis of the association between intraoperative magnesium sulfate infusion and postoperative acute kidney injury after major laparoscopic abdominal surgery
Authors: Oh Tak Kyu , Oh Ah-Young , Ryu Jung-Hee , Koo Bon-Wook , Lee Yea Ji , Do Sang-Hwan 
Published: February 2019

AbstractMagnesium sulfate can be used as a co-adjuvant drug during the perioperative period and has multiple benefits. Recent evidence suggested that perioperative magnesium sulfate infusion may lower the risk of postoperative acute kidney injury (AKI). We investigated the association between intraoperative magnesium sulfate infusion and incidence of AKI after major laparoscopic abdominal surgery. We retrospectively analyzed the medical records of adult patients 20 years or older who underwent elective major laparoscopic abdominal surgery (>2 hours) between 2010 and 2016. We investigated the association between intraoperative magnesium sulfate infusion and the incidence of postoperative AKI until postoperative day (POD) 3 using a multivariable logistic regression analysis. We included 3,828 patients in this analysis; 357 patients (9.3%) received an intraoperative magnesium sulfate infusion and 186 patients (4.9%) developed postoperative AKI by POD 3. A multivariable logistic regression analysis showed that magnesium infusion was associated with a significant decrease (63%) in postoperative AKI (odds ratio, 0.37; 95% confidence interval, 0.14–0.94; P = 0.037). Our study suggested that intraoperative magnesium sulfate infusion is associated with a reduced risk of postoperative AKI until POD 3 for patients who underwent laparoscopic major abdominal surgery. Well-designed, prospective studies should be conducted to further substantiate these findings.