bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observational Relationship Between Entrainment Rate and Environmental Relative Humidity and Implications for Convection Parameterization
Authors: Lu Chunsong , Sun Cheng , Liu Yangang , Zhang Guang J. , Lin Yanluan , Gao Wenhua , Niu Shengjie , Yin Yan , Qiu Yujun , Jin Lianji 
Published: November 2018

AbstractEntrainment rate is a critical but highly uncertain quantity in convective parameterizations; especially, the effects of environmental relative humidity on entrainment rate are controversial, or even opposite, in different studies. Analysis of aircraft observations of cumuli from the Routine AAF (Atmospheric Radiation Measurement [ARM] Aerial Facility) Clouds with Low Optical Water Depths (CLOWD) Optical Radiative Observations (RACORO) and Rain in Cumulus over the Ocean (RICO) field campaigns shows that entrainment rate is positively correlated with relative humidity. Physical analysis shows that higher relative humidity promotes entrainment by reducing buoyancy in the cloud cores and by weakening downdrafts near the cloud cores. The reduced buoyancy in the cloud cores and weakened downdrafts surrounding the cores further reduce updrafts in the cloud cores; the cloud cores with smaller updrafts are more significantly affected by their environment, resulting in larger entrainment rate. The relationship between entrainment rate and relative humidity is consistent with the buoyancy sorting concept widely used in convection parameterizations. The results provide reliable in situ observations to improve parameterizations of entrainment rate.
Downscaling of Rainfall Extremes From Satellite Observations
Authors: Zorzetto Enrico , Marani Marco 
Published: November 2018

AbstractThe estimation of the frequency of intense rainfall events is a crucial step for quantifying their impact on human societies and on the environment. This process is hindered by large gaps in ground observational networks at the global scale, such that extensive areas remain ungauged. The increasing availability of satellite‐based rainfall estimates, while providing data with unprecedented resolution and global coverage, also introduces new challenges: the scale disparity between gridded and rain‐gauge precipitation products on the one hand, and the short length of the available satellite records on the other. Here we propose a statistical framework for the estimation of rainfall extremes that is specifically designed to simultaneously address these two key issues, providing a new way of estimating extreme rainfall magnitudes from space. A downscaling procedure is here introduced to recover the spatial correlation and the probability density function of daily rainfall at the point (gauge) scale from coarse‐scale satellite estimates. The results are then combined with a recent statistical model of extremes (the Metastatistical Extreme Value distribution), which optimizes the use of the information obtained from relatively short satellite observational time series. The methodology is tested using data from the Tropical Rainfall Measuring Mission Multisatellite Precipitation Analysis over the Little Washita River, Oklahoma. We find that our approach satisfactorily reproduces downscaled daily rainfall probability density functions and can significantly improve the Tropical Rainfall Measuring Mission Multisatellite Precipitation Analysis‐based estimation of quantiles with return times larger than the length of the available data set (19 years here), which are especially important for several water‐related applications.
Evaluating Soil Resistance Formulations in Thermal‐Based Two‐Source Energy Balance (TSEB) Model: Implications for Heterogeneous Semiarid and Arid Regions
Authors: Li Yan , Kustas William P. , Huang Chunlin , Nieto Hector , Haghighi Erfan , Anderson Martha C. , Domingo Francisco , Garcia Monica , Scott Russell L. 
Published: November 2018

AbstractRelatively small fluctuations in the surface energy balance and evapotranspiration in semiarid and arid regions can be indicative of significant changes to ecosystem health. Therefore, it is imperative to have approaches for monitoring surface fluxes in these regions. The remote sensing‐based two‐source energy balance (TSEB) model is a suitable method for flux estimation over sparsely vegetated semiarid and arid landscapes since it explicitly considers surface energy flux contributions from soil and vegetation. However, previous studies indicate that TSEB generally underestimates sensible heat flux (H) and hence overestimates latent heat flux (LE) or evapotranspiration for these regions unless soil resistance coefficients are modified based on additional ground information. In this study, TSEB is applied over semiarid and arid regions on three continents using the original soil resistance formulation with modified coefficients and a recently developed physically based soil resistance formulation. Model sensitivity analysis demonstrates the high sensitivity of TSEB with original soil resistance formulation to soil resistance coefficients, while TSEB with the new soil resistance formulation has relatively low sensitivity to uncertainties in all coefficients. The performance of TSEB using different soil resistance formulations is evaluated by comparing modeled H against eddy covariance measurements in six semiarid and arid study sites and ranking the error statistics. Our results indicate that incorporating the new soil resistance formulation into TSEB would enhance its utility in flux estimation over heterogeneous landscapes by obviating its reliance on semiempirical coefficients and thus provide more robust fluxes over sparsely vegetated regions without model calibration and/or parameter tuning.
Impact of Dynamically Changing Discharge on Hyporheic Exchange Processes Under Gaining and Losing Groundwater Conditions
Authors: Wu Liwen , Singh Tanu , Gomez‐Velez Jesus , Nützmann Gunnar , Wörman Anders , Krause Stefan , Lewandowski Jörg 
Published: November 2018

AbstractChannel discharge, geomorphological setting, and regional groundwater flow determine the spatiotemporal variability of bedform‐induced hyporheic exchange and the emergence of biogeochemical hot spots and hot moments that it drives. Of particular interest, and significantly understudied, is the role that dynamically changing discharge has on the hyporheic exchange process and how regional groundwater flow modulates the effects of transience. In this study, we use a reduced‐complexity model to systematically explore the bedform‐induced hyporheic responses to dynamically changing discharge events in systems with different bedform geometries exposed to varying degrees of groundwater flow (under both upwelling and downwelling conditions). With this in mind, we define metrics to quantify the effects of transience: spatial extent of the hyporheic zone, net hyporheic flux, mean residence time, and denitrification efficiency. We find that regional groundwater flow and geomorphological settings greatly modulate the temporal evolution of bedform‐induced hyporheic responses driven by a single‐peak discharge event. Effects of transience diminish with increasing groundwater upwelling or downwelling fluxes, decreasing bedform aspect ratios, and decreasing channel slopes. Additionally, we notice that increasing discharge intensities can reduce the modulating impacts of regional groundwater flow on the effects of transience but hardly overcomes the geomorphological controls. These findings highlight the necessities of evaluating hyporheic exchange processes in a more comprehensive framework.
Calcimimetic restores diabetic peripheral neuropathy by ameliorating apoptosis and improving autophagy
Authors: Chung You Chul , Lim Ji Hee , Oh Hyun Mi , Kim Hyung Wook , Kim Min Young , Kim Eun Nim , Kim Yaeni , Chang Yoon Sik , Kim Hye Won , Park Cheol Whee 
Published: November 2018

AbstractDecreased AMPK-eNOS bioavailability mediates the development of diabetic peripheral neuropathy (DPN) through increased apoptosis and decreased autophagy activity in relation to oxidative stress. Schwann cells are responsible for maintaining structural and functional integrity of neurons and for repairing damaged nerves. We evaluated the neuro-protective effect of cinacalcet on DPN by activating the AMPK-eNOS pathway using db/db mice and human Schwann cells (HSCs). Sciatic nerve of db/db mice was characterized by disorganized myelin, axonal shrinkage, and degeneration that were accompanied by marked fibrosis, inflammation, and apoptosis. These phenotypical alterations were significantly improved by cinacalcet treatment along with improvement in sensorimotor functional parameters. Cinacalcet demonstrated favorable effects through increased expression and activation of calcium-sensing receptor (CaSR)-CaMKKβ and phosphorylation of AMPK-eNOS signaling in diabetic sciatic nerve. Cinacalcet decreased apoptosis and increased autophagy activity in relation to decreased oxidative stress in HSCs cultured in high-glucose medium as well. This was accompanied by increased expression of the CaSR, intracellular Ca++ ([Ca++]i) levels, and CaMKKβ-LKB1-AMPK signaling pathway, resulting in the net effect of increased eNOS phosphorylation, NOx concentration, Bcl-2/Bax ratio, beclin 1, and LC3-II/LC3-I ratio. These results demonstrated that cinacalcet treatment ameliorates inflammation, apoptosis, and autophagy through increased expression of the CaSR, [Ca++]i levels and subsequent activation of CaMKKβ-LKB-1-AMPK-eNOS pathway in the sciatic nerve and HSCs under diabetic condition. Therefore, cinacalcet may play an important role in the restoration and amelioration of DPN by ameliorating apoptosis and improving autophagy.
Reply to ‘Dissimilarity measures affected by richness differences yield biased delimitations of biogeographic realms’
Authors: Costello Mark J. , Tsai Peter , Cheung Alan Kwok Lun , Basher Zeenatul , Chaudhary Chhaya 
Published: November 2018

AbstractRecently, we classified the oceans into 30 biogeographic realms based on species’ endemicity. Castro-Insua et al. criticize the choices of dissimilarity coefficients and clustering approaches used in our paper, and reanalyse the data using alternative techniques. Here, we explain how the approaches used in our original paper yield results in line with existing biogeographical knowledge and are robust to alternative methods of analysis. We also repeat the analysis using several similarity coefficients and clustering algorithms, and a neural network theory method. Although each combination of methods produces outputs differing in detail, the overall pattern of realms is similar. The coarse nature of the present boundaries of the realms reflects the limited field data but may be improved with additional data and mapping to environmental variables.
Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts
Authors: Duss Olivier , Stepanyuk Galina A. , Grot Annette , O’Leary Seán E. , Puglisi Joseph D. , Williamson James R. 
Published: November 2018

AbstractCellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation.
Degassing-induced fractionation of multiple sulphur isotopes unveils post-Archaean recycled oceanic crust signal in hotspot lava
Authors: Beaudry Patrick , Longpré Marc-Antoine , Economos Rita , Wing Boswell A. , Bui Thi Hao , Stix John 
Published: November 2018

AbstractMantle source regions feeding hotspot volcanoes likely contain recycled subducted material. Anomalous sulphur (S) isotope signatures in hotspot lavas have tied ancient surface S to this deep geological cycle, but their potential modification by shallow magmatic processes has generally been overlooked. Here we present S isotope measurements in magmatic sulphides, silicate melt inclusions and matrix glasses from the recent eruption of a hotspot volcano at El Hierro, Canary Islands, which show that degassing induces strongly negative δ34S fractionation in both silicate and sulphide melts. Our results reflect the complex interplay among redox conditions, S speciation and degassing. The isotopic fractionation is mass dependent (Δ33S = 0‰), thus lacking evidence for the recycled Archaean crust signal recently identified at other hotspot volcanoes. However, the source has an enriched signature (δ34S ~ + 3‰), which supports the presence of younger 34S-rich recycled oceanic material in the Canary Island mantle plume.
Bioreactor-based mass production of human iPSC-derived macrophages enables immunotherapies against bacterial airway infections
Authors: Ackermann Mania , Kempf Henning , Hetzel Miriam , Hesse Christina , Hashtchin Anna Rafiei , Brinkert Kerstin , Schott Juliane Wilhelmine , Haake Kathrin , Kühnel Mark Philipp , Glage Silke , Figueiredo Constanca , Jonigk Danny , Sewald Katherina , Schambach Axel , Wronski Sabine , Moritz Thomas , Martin Ulrich , Zweigerdt Robert , Munder Antje , Lachmann Nico 
Published: November 2018

AbstractThe increasing number of severe infections with multi-drug-resistant pathogens worldwide highlights the need for alternative treatment options. Given the pivotal role of phagocytes and especially alveolar macrophages in pulmonary immunity, we introduce a new, cell-based treatment strategy to target bacterial airway infections. Here we show that the mass production of therapeutic phagocytes from induced pluripotent stem cells (iPSC) in industry-compatible, stirred-tank bioreactors is feasible. Bioreactor-derived iPSC-macrophages (iPSC-Mac) represent a highly pure population of CD45+CD11b+CD14+CD163+ cells, and share important phenotypic, functional and transcriptional hallmarks with professional phagocytes, however with a distinct transcriptome signature similar to primitive macrophages. Most importantly, bioreactor-derived iPSC-Mac rescue mice from Pseudomonas aeruginosa-mediated acute infections of the lower respiratory tract within 4-8 h post intra-pulmonary transplantation and reduce bacterial load. Generation of specific immune-cells from iPSC-sources in scalable stirred-tank bioreactors can extend the field of immunotherapy towards bacterial infections, and may allow for further innovative cell-based treatment strategies.
Coincident molecular auxeticity and negative order parameter in a liquid crystal elastomer
Authors: Mistry D. , Connell S. D. , Mickthwaite S. L. , Morgan P. B. , Clamp J. H. , Gleeson H. F. 
Published: November 2018

AbstractAuxetic materials have negative Poisson’s ratios and so expand rather than contract in one or several direction(s) perpendicular to applied extensions. The auxetics community has long sought synthetic molecular auxetics – non-porous, inherently auxetic materials which are simple to fabricate and avoid porosity-related weakening. Here, we report, synthetic molecular auxeticity for a non-porous liquid crystal elastomer. For strains above ~0.8 applied perpendicular to the liquid crystal director, the liquid crystal elastomer becomes auxetic with the maximum negative Poisson’s ratio measured to date being -0.74 ± 0.03 – larger than most values seen in naturally occurring molecular auxetics. The emergence of auxeticity coincides with the liquid crystal elastomer backbone adopting a negative order parameter, QB = -0.41 ± 0.01 – further implying negative liquid crystal ordering. The reported behaviours consistently agree with theoretical predictions from Warner and Terentjev liquid crystal elastomer theory. Our results open the door for the design of synthetic molecular auxetics.
X-ray rheography uncovers planar granular flows despite non-planar walls
Authors: Baker James , Guillard François , Marks Benjy , Einav Itai 
Published: November 2018

AbstractExtremely useful techniques exist to observe the interior of deforming opaque materials, but these methods either require that the sample is replaced with a model material or that the motion is stopped intermittently. For example, X-ray computed tomography cannot measure the continuous flow of materials due to the significant scanning time required for density reconstruction. Here we resolve this technological gap with an alternative X-ray method that does not require such tomographs. Instead our approach uses correlation analysis of successive high-speed radiographs from just three directions to directly reconstruct three-dimensional velocities. When demonstrated on a steady granular system, we discover a compressible flow field that has planar streamlines despite curved confining boundaries, in surprising contrast to Newtonian fluids. More generally, our new X-ray technique can be applied using synchronous source/detector pairs to investigate transient phenomena in various soft matter such as biological tissues, geomaterials and foams.
Observation of non-locality sharing among three observers with one entangled pair via optimal weak measurement
Authors: Hu Meng-Jun , Zhou Zhi-Yuan , Hu Xiao-Min , Li Chuan-Feng , Guo Guang-Can , Zhang Yong-Sheng 
Published: November 2018

AbstractBell non-locality plays a fundamental role in quantum theory. Numerous tests of the Bell inequality have been reported as the ground-breaking discovery of the Bell theorem. Up to now, however, most discussions of the Bell scenario have focused on a single pair of entangled particles distributed to only two separated observers. Recently, it has been shown surprisingly that multiple observers can share the non-locality from an entangled pair using the method of weak measurement without post-selection [Phys. Rev. Lett. 114, 250401 (2015)]. Here we report an observation of double CHSH-Bell inequality violations for a single pair of entangled photons with strength continuous-tunable optimal weak measurement in a photonic system. Our results shed new light on the interplay between non-locality and quantum measurements and our design of weak measurement protocol may also be significant for important applications such as unbounded randomness certification and quantum steering.
High density Huh7.5 cell hollow fiber bioreactor culture for high-yield production of hepatitis C virus and studies of antivirals
Authors: Pihl Anne F. , Offersgaard Anna F. , Mathiesen Christian K. , Prentoe Jannick , Fahnøe Ulrik , Krarup Henrik , Bukh Jens , Gottwein Judith M. 
Published: November 2018

AbstractChronic hepatitis C virus (HCV) infection poses a serious global public health burden. Despite the recent development of effective treatments there is a large unmet need for a prophylactic vaccine. Further, antiviral resistance might compromise treatment efficiency in the future. HCV cell culture systems are typically based on Huh7 and derived hepatoma cell lines cultured in monolayers. However, efficient high cell density culture systems for high-yield HCV production and studies of antivirals are lacking. We established a system based on Huh7.5 cells cultured in a hollow fiber bioreactor in the presence or absence of bovine serum. Using an adapted chimeric genotype 5a virus, we achieved peak HCV infectivity and RNA titers of 7.6 log10FFU/mL and 10.4 log10IU/mL, respectively. Bioreactor derived HCV showed high genetic stability, as well as buoyant density, sensitivity to neutralizing antibodies AR3A and AR4A, and dependency on HCV co-receptors CD81 and SR-BI comparable to that of HCV produced in monolayer cell cultures. Using the bioreactor platform, treatment with the NS5A inhibitor daclatasvir resulted in HCV escape mediated by the NS5A resistance substitution Y93H. In conclusion, we established an efficient high cell density HCV culture system with implications for studies of antivirals and vaccine development.
Electrophysiological measurement of ion channels on plasma/organelle membranes using an on-chip lipid bilayer system
Authors: Kamiya Koki , Osaki Toshihisa , Nakao Kenji , Kawano Ryuji , Fujii Satoshi , Misawa Nobuo , Hayakawa Masatoshi , Takeuchi Shoji 
Published: November 2018

AbstractIon channels are located in plasma membranes as well as on mitochondrial, lysosomal, and endoplasmic reticulum membranes. They play a critical role in physiology and drug targeting. It is particularly challenging to measure the current mediated by ion channels in the lysosomal and the endoplasmic reticulum membranes using the conventional patch clamp method. In this study, we show that our proposed device is applicable for an electrophysiological measurement of various types of ion channel in plasma and organelle membranes. We designed an on-chip device that can form multiple electrical contacts with a measurement system when placed on a mount system. Using crude cell membranes containing ion channels extracted from cultured cells without detergents, we detected open/close signals of the hERG, TRPV1, and NMDA channels on plasma membranes, those of the TRPML1 channels on lysosomal membranes, and open/close signals of the RyR channels on SR membranes. This method will provide a highly versatile drug screening system for ion channels expressed by various cell membranes, including plasma, SR, mitochondrial, Golgi, and lysosomal membranes.
Identification of Immune Signatures of Novel Adjuvant Formulations Using Machine Learning
Authors: Chaudhury Sidhartha , Duncan Elizabeth H. , Atre Tanmaya , Storme Casey K. , Beck Kevin , Kaba Stephen A. , Lanar David E. , Bergmann-Leitner Elke S. 
Published: November 2018

AbstractAdjuvants have long been critical components of vaccines, but the exact mechanisms of their action and precisely how they alter or enhance vaccine-induced immune responses are often unclear. In this study, we used broad immunoprofiling of antibody, cellular, and cytokine responses, combined with data integration and machine learning to gain insight into the impact of different adjuvant formulations on vaccine-induced immune responses. A Self-Assembling Protein Nanoparticles (SAPN) presenting the malarial circumsporozoite protein (CSP) was used as a model vaccine, adjuvanted with three different liposomal formulations: liposome plus Alum (ALFA), liposome plus QS21 (ALFQ), and both (ALFQA). Using a computational approach to integrate the immunoprofiling data, we identified distinct vaccine-induced immune responses and developed a multivariate model that could predict the adjuvant condition from immune response data alone with 92% accuracy (p = 0.003). The data integration also revealed that commonly used readouts (i.e. serology, frequency of T cells producing IFN-γ, IL2, TNFα) missed important differences between adjuvants. In summary, broad immune-profiling in combination with machine learning methods enabled the reliable and clear definition of immune signatures for different adjuvant formulations, providing a means for quantitatively characterizing the complex roles that adjuvants can play in vaccine-induced immunity. The approach described here provides a powerful tool for identifying potential immune correlates of protection, a prerequisite for the rational pairing of vaccines candidates and adjuvants.