bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing a common ice‐ocean parameterization with laboratory experiments
Authors: McConnochie C. D. , Kerr R. C. 
Published: July 2017

AbstractNumerical models of ice‐ocean interactions typically rely upon a parameterization for the transport of heat and salt to the ice face that has not been satisfactorily validated by observational or experimental data. We compare laboratory experiments of ice‐saltwater interactions to a common numerical parameterization and find a significant disagreement in the dependence of the melt rate on the fluid velocity. We suggest a resolution to this disagreement based on a theoretical analysis of the boundary layer next to a vertical heated plate, which results in a threshold fluid velocity of approximately 4 cm/s at driving temperatures between 0.5 and C, above which the form of the parameterization should be valid.
Three‐dimensional transient rip currents: Bathymetric excitation of low‐frequency intrinsic variability
Authors: Uchiyama Yusuke , McWilliams James C. , Akan Cigdem 
Published: July 2017

AbstractThe ROMS‐WEC model [Uchiyama et al., 2010] based on an Eulerian wave‐averaged vortex‐force asymptotic theory of McWilliams et al. (2004) is applied to analyze 3‐D transient wave‐driven rip currents and associated intrinsic very low‐frequency (VLF) variability in the surf zone on a surveyed bathymetry under spatiotemporally uniform offshore incident waves. The 3‐D rip currents are substantially depth‐dependent due to the vertical recirculation, composed of pairs of counter‐rotating longitudinal overturning roll cells that promote surface convergence. The vortex force plays an important role in vorticity budget, preconditioning overall vorticity reduction. These rip currents are intrinsically unstable and contribute about 70% to kinetic energy (KE) as eddy kinetic energy (EKE), consistent with observations. The dominant fluctuation period fits the VLF band, at about 18 min. The current effect on waves (CEW) alters not only the mean rip structure, but also the associated turbulence as the modified cross‐shore EKE profile with considerable accentuation in the inner surf zone. Increased alongshore bathymetric variability proportionally intensifies KE and intrinsic EKE, whereas it reduces the VLF period. With a guide of a pseudo 2D model, we reveal that vortex tilting effect due to the horizontal vorticity inherent in the 3‐D rip currents promotes collapse of the 3‐D eddies through an enhanced forward kinetic energy cascade, leading to short‐lived, laterally‐stretched 3‐D eddies resulting in elongated filaments that decay more quickly than coherent, long‐lived, circular 2‐D eddies.
Sedimentary processes of the Bagnold Dunes: Implications for the eolian rock record of Mars
Authors: Ewing R. C. , Lapotre M. G. A. , Lewis K. W. , Day M. , Stein N. , Rubin D. M. , Sullivan R. , Banham S. , Lamb M. P. , Bridges N. T. , Gupta S. , Fischer W. W. 
Published: July 2017

AbstractThe Mars Science Laboratory rover Curiosity visited two active wind‐blown sand dunes within Gale crater, Mars, which provided the first ground‐based opportunity to compare Martian and terrestrial eolian dune sedimentary processes and study a modern analog for the Martian eolian rock record. Orbital and rover images of these dunes reveal terrestrial‐like and uniquely Martian processes. The presence of grainfall, grainflow, and impact ripples resembled terrestrial dunes. Impact ripples were present on all dune slopes and had a size and shape similar to their terrestrial counterpart. Grainfall and grainflow occurred on dune and large‐ripple lee slopes. Lee slopes were ~29° where grainflows were present and ~33° where grainfall was present. These slopes are interpreted as the dynamic and static angles of repose, respectively. Grain size measured on an undisturbed impact ripple ranges between 50 μm and 350 μm with an intermediate axis mean size of 113 μm (median: 103 μm). Dissimilar to dune eolian processes on Earth, large, meter‐scale ripples were present on all dune slopes. Large ripples had nearly symmetric to strongly asymmetric topographic profiles and heights ranging between 12 cm and 28 cm. The composite observations of the modern sedimentary processes highlight that the Martian eolian rock record is likely different from its terrestrial counterpart because of the large ripples, which are expected to engender a unique scale of cross stratification. More broadly, however, in the Bagnold Dune Field as on Earth, dune‐field pattern dynamics and basin‐scale boundary conditions will dictate the style and distribution of sedimentary processes.
Quantifying the impacts of vegetation changes on catchment storage‐discharge dynamics using paired‐catchment data
Authors: Cheng Lei , Zhang Lu , Chiew Francis H. S. , Canadell Josep G. , Zhao Fangfang , Wang Ying‐Ping , Hu Xianqun , Lin Kairong 
Published: July 2017

AbstractIt is widely recognized that vegetation changes can significantly affect the local water availability. Methods have been developed to predict the effects of vegetation change on water yield or total streamflow. However, it is still a challenge to predict changes in base flow following vegetation change due to limited understanding of catchment storage‐discharge dynamics. In this study, the power law relationship for describing catchment storage‐discharge dynamics is reformulated to quantify the changes in storage‐discharge relationship resulting from vegetation changes using streamflow data from six paired‐catchment experiments, of which two are deforestation catchments and four are afforestation catchments. Streamflow observations from the paired‐catchment experiments clearly demonstrate that vegetation changes have led to significant changes in catchment storage‐discharge relationships, accounting for about 83–128% of the changes in groundwater discharge in the treated catchments. Deforestation has led to increases in groundwater discharge (or base flow) but afforestation has resulted in decreases in groundwater discharge. Further analysis shows that the contribution of changes in groundwater discharge to the total changes in streamflow varies greatly among experimental catchments ranging from 12% to 80% with a mean of 38 ± 22% (μ ± σ). This study proposed a new method to quantify the effects of vegetation changes on groundwater discharge from catchment storage and will improve our predictability about the impacts of vegetation changes on catchment water yields.
HYPPS: A hybrid geostatistical modeling algorithm for subsurface modeling
Authors: Tahmasebi Pejman 
Published: July 2017

AbstractDealing with complex and geologically realistic modeling of subsurface systems requires detailed spatial data sets. Such a big data can be usually provided through an image. Despite various developments, the training image‐based techniques are still not well‐designed for modeling multiscale and complex structures. Pixel‐based methods honor the conditioning point data with poor reproduction of large‐scale features, while some other techniques, termed pattern‐based, represent a superior reproduction of long‐range and complex structures and being biased around the conditioning data. In this paper, a new look at the geostatistical modeling using a hybrid pattern‐pixel‐based simulation (HYPPS) is proposed, wherein the pixel and pattern‐based techniques are used simultaneously. A perfect reproduction of the conditioning point data is achieved using the proposed HYPPS method. The algorithm is developed for single and multivariate simulations. This method is applied on different 2‐D/3‐D categorical data and the results show significant improvement over the previous techniques.
Trace‐Element Incorporation into Intracellular Pools Uncovers Calcium‐Pathways in a Coccolithophore
Authors: Gal Assaf , Sviben Sanja , Wirth Richard , Schreiber Anja , Lassalle‐Kaiser Benedikt , Faivre Damien , Scheffel André 
Published: July 2017

AbstractMany organisms form minerals from precursor phases that crystallize under strict biological control. The dynamic intracellular processes of formation, transport, and deposition of these precursor phases are challenging to identify. An unusual situation is recently revealed for the calcifying alga Emiliania huxleyi, as the cells contain a compartment filled with a concentrated Ca and P phase but the final calcite crystals, which are nucleated in a different compartment, are P‐free. Thus, the connection of the Ca–P‐rich pool to the mineralization process remains unclear. Here, pulse‐chase experiments are used with Sr to label the Ca–P‐rich phase in E. huxleyi cells, and cryo X‐ray absorption spectroscopy and analytical transmission electron microscopy to follow the Sr within cells. It is found that Sr is first found in the Ca–P‐rich phase and then becomes incorporated into the calcite. This demonstrates that the calcium used by the cells to build calcite originates from the Ca–P‐rich pool.
An Important Function of Petrosiol E in Inducing the Differentiation of Neuronal Progenitors and in Protecting Them against Oxidative Stress
Authors: Liu Jing , Wang Linlin , Du Yuguo , Liu Sijin 
Published: July 2017

AbstractInsufficient endogenous neurotrophin supply contributes to neurodegeneration. Meanwhile, neuronal injuries are also attributed to oxidative stress upon toxin exposure. Thus, reconstruction neurite extension and antioxidative stress are the potential strategies for ameliorating neuronal injuries. However, there is no well‐defined therapeutic developed in this regard. In search of such therapeutics, Petrosiol E is identified here as a potent inducer to guide the differentiation of neuronal progenitor cells. Petrosiol E also considerably promotes embryonic stem cell differentiation into neural ectoderm features. Moreover, Petrosiol E reveals an antioxidant function to protect cells from oxidative stress induced by arsenic. Moreover, the molecular mechanism underlying Petrosiol E‐induced neuronal differentiation is uncovered: (a) enhancement of NF‐E2‐related factor 2 (Nrf 2) activity in driving neuronal differentiation; (b) diminishment of oxidative stress. Petrosiol E activates the mitogen‐activated protein kinase and serine/threonine kinase signaling to enhance the activity of Nrf 2. As a result of enhanced Nrf 2 activity, neuronal differentiation is accelerated, and the cellular antioxidation responses are also enforced, even under arsenic‐induced neurotoxicity. Together, the combined results unveil a desirable role of Petrosiol E in driving neuronal differentiation and in combating oxidative stress. This study would open an avenue to develop new therapeutics based on Petrosiol compounds to treat neurodegenerative diseases.
Delineating the Mechanism of Ionic Liquids in the Synthesis of Quinazoline‐2,4(1H,3H)‐dione from 2‐Aminobenzonitrile and CO2
Authors: Hulla Martin , Chamam Sami M. A. , Laurenczy Gabor , Das Shoubhik , Dyson Paul J. 
Published: July 2017

AbstractIonic liquids (ILs) are versatile solvents and catalysts for the synthesis of quinazoline‐2,4‐dione from 2‐aminobenzonitrile and CO2. However, the role of the IL in this reaction is poorly understood. Consequently, we investigated this reaction and showed that the IL cation does not play a significant role in the activation of the substrates, and instead plays a secondary role in controlling the physical properties of the IL. A linear relationship between the pKa of the IL anion (conjugate acid) and the reaction rate was identified with maximum catalyst efficiency observed at a pKa of >14.7 in DMSO. The base‐catalyzed reaction is limited by the acidity of the quinazoline‐2,4‐dione product, which is deprotonated by more basic catalysts, leading to the formation of the quinazolide anion (conjugate acid pKa 14.7). Neutralization of the original catalyst and formation of the quinazolide anion catalyst leads to the observed reaction limit.
Sulfur‐33 Isotope Tracing of the Hydrodesulfurization Process: Insights into the Reaction Mechanism, Catalyst Characterization and Improvement
Authors: Sushkevich Vitaly L. , Popov Andrey G. , Ivanova Irina I. 
Published: July 2017

AbstractThe novel approach based on 33S isotope tracing is proposed for the elucidation of hydrodesulfurization (HDS) mechanisms and characterization of molybdenum sulfide catalysts. The technique involves sulfidation of the catalyst with 33S‐isotope‐labeled dihydrogen sulfide, followed by monitoring the fate of the 33S isotope in the course of the hydrodesulfurization reaction by online mass spectrometry and characterization of the catalyst after the reaction by temperature‐programmed oxidation with mass spectrometry (TPO‐MS). The results point to different pathways of thiophene transformation over Co or Ni‐promoted and unpromoted molybdenum sulfide catalysts, provide information on the role of promoter and give a key for the design of new efficient HDS catalysts.
The Limits of Social Protection: The Case of Hydropower Dams and Indigenous Peoples' Land
Authors: Cooke Fadzilah Majid , Nordensvard Johan , Saat Gusni Bin , Urban Frauke , Siciliano Giuseppina 
Published: July 2017

AbstractHydropower dams have been criticised for their social and environmental implications. There have been attempts to create international social standards for hydropower dam projects, but these standards have had limited impact. This article uses an extended environmental justice framework to make sense of the resettlement and compensation schemes for Indigenous peoples who were resettled for the construction of the Bakun dam in Borneo, East Malaysia. The article therefore analyses the social protection measures designed for the protection of Indigenous peoples and their livelihoods. The case study is based on in‐depth interviews and focus group discussions with local communities, institutional actors in Malaysia, Chinese actors and dam builders. The article concludes that the social protection policies did not protect Indigenous people and their land sufficiently, but it facilitated a commodification process of both land and people. This should also be understood as a colonisation of their land and their cultures.
Optimal Control Problem for Risk‐Sensitive Mean‐Field Stochastic Delay Differential Equation with Partial Information
Authors: Ma Heping , Liu Bin 
Published: July 2017

AbstractThis paper deals with the risk‐sensitive control problem for mean‐field stochastic delay differential equations (MF‐SDDEs) with partial information. Firstly, under the assumptions that the control domain is not convex and the value function is non‐smooth, we establish a stochastic maximum principle (SMP). Then, by means of Itô's formula and some continuous dependence, we prove the existence and uniqueness results for another type of MF‐SDDEs. Meanwhile, the verification theorem for the MF‐SDDEs is obtained by using a clever construction of the Hamiltonian function. Finally, based on our verification theorem, a linear‐quadratic system is investigated and the optimal control is also derived by the stochastic filtering technique.
Increasing the Cleaning Efficiency of the Cleaning‐in‐Place Method by Applying Discontinuous Liquid Jets
Authors: Fuchs Enrico , Helbig Manuel , Pfister Marius , Majschak Jens‐Peter 
Published: July 2017

AbstractHohe Kosten für die Reinigung von Maschinen und Anlagen führen zu Bestrebungen, diese hinsichtlich Reinigungszeit und ‐flüssigkeitseinsatz zu optimieren. Ein Ansatz ist die Anwendung diskontinuierlicher Flüssigkeitsstrahlen. Hierfür wurden zwei Strömungsarten hinsichtlich ihrer effizienzsteigernden Wirkung für zwei Lebensmittelbestandteile Xanthan und Stärke untersucht. Im Ergebnis konnte der Reinigungsflüssigkeitsverbrauch für einzelne Betriebspunkte um die Hälfte gesenkt werden. Die Reinigungszeit sank bei der Xanthanverschmutzung ebenfalls, wohingegen sie bei Stärke gleich oder höher war.
Efficient Discrete Element Method Simulation Strategy for Analyzing Large‐Scale Agitated Powder Mixers
Authors: Siegmann Eva , Jajcevic Dalibor , Radeke Charles , Strube Dieter , Friedrich Karsten , Khinast Johannes G. 
Published: July 2017

AbstractPowder mixing is one of the most important pharmaceutical manufacturing operations. Computation methods are required to transform mixer design and scale‐up from art to science. Due to an increase in the computational power and the development of graphics cards, the discrete element method is becoming a widely‐used technique. For an industrial granular mixer, it is demonstrated that a smart simulation strategy together with a highly efficient code can reduce the simulation time. The good agreement between simulation and measurement data confirms that the simulation strategy can be applied to the product development.
Exploring the Influence of Shapes and Heterogeneity of Glyco‐Gold Nanoparticles on Bacterial Binding for Preventing Infections
Authors: Toraskar Suraj , Gade Madhuri , Sangabathuni Sivakoti , Thulasiram Hirekodathakallu V. , Kikkeri Raghavendra 
Published: July 2017

AbstractTo investigate the effects of the heterogeneity and shape of glyco‐nanoprobes on carbohydrate–protein interactions (CPIs), α‐d‐mannose‐ and β‐d‐galactose‐linked homo‐ and heterogeneous glycodendrons were synthesized and immobilized on spherical and rod‐shaped gold nanoparticles (AuNPs). Lectin and bacterial binding studies of these glyco‐AuNPs clearly illustrate that multivalency and shape of AuNPs contribute significantly to CPIs than the heterogeneity of glycodendrons. Finally, bacterial infection of HeLa cells was effectively inhibited by the homogeneous glycodendron‐conjugated rod‐shaped AuNPs relative to their heterogeneous counterparts. Overall, these results provide insight into the role of AuNP shape and multivalency as potential factors to regulate CPIs.
The role of early magnetic resonance imaging in predicting survival on bevacizumab for recurrent glioblastoma: Results from a prospective clinical trial (CABARET)
Authors: Field Kathryn M. , Phal Pramit M. , Fitt Greg , Goh Christine , Nowak Anna K. , Rosenthal Mark A. , Simes John , Barnes Elizabeth H. , Sawkins Kate , Cher Lawrence M. , Hovey Elizabeth J. , Wheeler Helen 
Published: July 2017

BACKGROUNDBevacizumab has been associated with prolonged progression‐free survival for patients with recurrent glioblastoma; however, not all derive a benefit. An early indicator of efficacy or futility may allow early discontinuation for nonresponders. This study prospectively assessed the role of early magnetic resonance imaging (eMRI) and its correlation with subsequent routine magnetic resonance imaging (MRI) results and survival.METHODSPatients were part of a randomized phase 2 clinical trial (CABARET) comparing bevacizumab with bevacizumab plus carboplatin for recurrent glioblastoma. eMRI was conducted after 4 weeks in the trial (after 2 treatments with bevacizumab [10 mg/kg every 2 weeks]). The results were compared with the results of the subsequent 8‐week MRI standard.RESULTSFor 119 of 122 patients, eMRI was available, and 111 had subsequent MRI for comparison. Thirty‐six (30%) had an early radiological response, and 17 (14%) had progressive disease. The concordance between eMRI and 8‐week MRI was moderate (κ = 0.56), with most providing the same result (n = 79 [71%]). There was strong evidence that progression‐free survival and overall survival were predicted by the eMRI response (both P values < .001). The median survival was 8.6 months for an eMRI response, 6.6 months for stable disease, and 3.7 months for progressive disease; the hazard ratio (progressive disease vs stable disease) was 3.4 (95% confidence interval, 1.9‐6.0). Landmark analyses showed that eMRI progression was a strong predictor of mortality independent of other potential baseline predictors.CONCLUSIONSIn this study, early progression on MRI appears to be a robust marker of a poor prognosis for patients on bevacizumab. Cancer 2017;123:3576‐82. © 2017 American Cancer Society.
Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction
Authors: Cang Zixuan , Wei Guo‐Wei 
Published: July 2017

AbstractProtein‐ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein‐ligand binding affinities is vital to rational drug design and the understanding of protein‐ligand binding and binding induced function. Existing binding affinity prediction methods are inundated with geometric detail and involve excessively high dimensions, which undermines their predictive power for massive binding data. Topology provides the ultimate level of abstraction and thus incurs too much reduction in geometric information. Persistent homology embeds geometric information into topological invariants and bridges the gap between complex geometry and abstract topology. However, it oversimplifies biological information. This work introduces element specific persistent homology (ESPH) or multicomponent persistent homology to retain crucial biological information during topological simplification. The combination of ESPH and machine learning gives rise to a powerful paradigm for macromolecular analysis. Tests on 2 large data sets indicate that the proposed topology‐based machine‐learning paradigm outperforms other existing methods in protein‐ligand binding affinity predictions. ESPH reveals protein‐ligand binding mechanism that can not be attained from other conventional techniques. The present approach reveals that protein‐ligand hydrophobic interactions are extended to 40Å away from the binding site, which has a significant ramification to drug and protein design.
Stochastic Optical Reconstruction Microscopy (STORM)
Authors: Xu Jianquan , Ma Hongqiang , Liu Yang 
Published: July 2017

AbstractSuper‐resolution (SR) fluorescence microscopy, a class of optical microscopy techniques at a spatial resolution below the diffraction limit, has revolutionized the way we study biology, as recognized by the Nobel Prize in Chemistry in 2014. Stochastic optical reconstruction microscopy (STORM), a widely used SR technique, is based on the principle of single molecule localization. STORM routinely achieves a spatial resolution of 20 to 30 nm, a ten‐fold improvement compared to conventional optical microscopy. Among all SR techniques, STORM offers a high spatial resolution with simple optical instrumentation and standard organic fluorescent dyes, but it is also prone to image artifacts and degraded image resolution due to improper sample preparation or imaging conditions. It requires careful optimization of all three aspects—sample preparation, image acquisition, and image reconstruction—to ensure a high‐quality STORM image, which will be extensively discussed in this unit. © 2017 by John Wiley & Sons, Inc.
Cannabinoid‐Induced Tetrad in Mice
Authors: Metna‐Laurent Mathilde , Mondésir Miguel , Grel Agnès , Vallée Monique , Piazza Pier‐Vincenzo 
Published: July 2017

AbstractCannabinoid‐induced tetrad is a preclinical model commonly used to evaluate if a pharmacological compound is an agonist of the central type‐1 cannabinoid (CB1) receptor in rodents. The tetrad is characterized by hypolocomotion, hypothermia, catalepsy, and analgesia, four phenotypes that are induced by acute administration of CB1 agonists exemplified by the prototypic cannabinoid delta‐9‐tetrahydrocannabinol (THC). This unit describes a standard protocol in mice to induce tetrad phenotypes with THC as reference cannabinoid. We provide typical results obtained with this procedure showing a dose effect of THC in different mouse strains. The effect of the CB1 antagonist rimonabant is also shown. This tetrad protocol is well adapted to reveal new compounds acting on CB1 receptors in vivo. © 2017 by John Wiley & Sons, Inc.