bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Assimilation and Online Parameter Optimization in Groundwater Modeling Using Nested Particle Filters
Authors: Ramgraber M. , Albert C. , Schirmer M. 
Published: October 2019

AbstractOver the past decades, advances in data collection and machine learning have paved the way for the development of autonomous simulation frameworks. Among these, many are capable not only of assimilating real‐time data to correct their predictive shortcomings but also of improving their future performance through self‐optimization. In hydrogeology, such techniques harbor great potential for informing sustainable management practices. Simulating the intricacies of groundwater flow requires an adequate representation of unknown, often highly heterogeneous geology. Unfortunately, it is difficult to reconcile the structural complexity demanded by realistic geology with the simplifying assumptions introduced in many calibration methods. The particle filter framework would provide the necessary versatility to retain such complex information but suffers from the curse of dimensionality, a fundamental limitation discouraging its use in systems with many unknowns. Due to the prevalence of such systems in hydrogeology, the particle filter has received little attention in groundwater modeling so far. In this study, we explore the combined use of dimension‐reducing techniques and artificial parameter dynamics to enable a particle filter framework for a groundwater model. Exploiting freedom in the design of the dimension‐reduction approach, we ensure consistency with a predefined geological pattern. The performance of the resulting optimizer is demonstrated in a synthetic test case for three such geological configurations and compared to two Ensemble Kalman Filter setups. Favorable results even for deliberately misspecified settings make us hopeful that nested particle filters may constitute a useful tool for geologically consistent real‐time parameter optimization.
Dynamically Triggered Changes of Plate Interface Coupling in Southern Cascadia
Authors: Materna Kathryn , Bartlow Noel , Wech Aaron , Williams Charles , Bürgmann Roland 
Published: October 2019

AbstractIn Southern Cascadia, precise Global Navigation Satellite System (GNSS) measurements spanning about 15 years reveal steady deformation due to locking on the Cascadia megathrust punctuated by transient deformation from large earthquakes and episodic tremor and slip events. Near the Mendocino Triple Junction, however, we recognize several abrupt GNSS velocity changes that reflect a different process. After correcting for earthquakes and seasonal loading, we find that several dozen GNSS time series show spatially coherent east‐west velocity changes of ~2 mm/yr and that these changes coincide in time with regional M > 6.5 earthquakes. We consider several hypotheses and propose that dynamically triggered changes in megathrust coupling best explain the data. Our inversions locate the coupling changes slightly updip of the tremor‐producing zone. We speculate that fluid exchange surrounding the tremor region may be important. Such observations of transient coupling changes are rare and challenging to explain mechanistically but have important implications for earthquake processes on faults.
Equatorial Pacific 1,000‐dbar Velocity and Isotherm Displacements From Argo Data: Beyond the Mean and Seasonal Cycle
Authors: Zanowski Hannah , Johnson Gregory C. , Lyman John M. 
Published: October 2019

AbstractEquatorial Pacific zonal velocity at 1,000 dbar and vertical isotherm displacements from 0–2,000 dbar are analyzed using Argo data through February 2018. In agreement with previous studies, the mean 1,000‐dbar zonal velocity is characterized by alternating eastward and westward jets of amplitude 5–10 cm/s. Similarly, the seasonal cycle is dominated by an annual Rossby wave that is apparent in annual harmonic fits to both the isotherm displacement and velocity fields. Residual (mean, annual, and semiannual harmonics removed) zonal velocity and isotherm displacements are analyzed using Complex Empirical Orthogonal Functions (CEOFs) and their Principal Components. For the analysis at 1,000 dbar, the first velocity CEOF accounts for 28% of the variance and the first isotherm displacement CEOF 24%. Spatial patterns of the lead CEOFs are broadly consistent with Rossby waves, but only isotherm displacement CEOF1 can be clearly linked to known physical processes in the equatorial Pacific. This is true of the isotherm displacement CEOF1s across pressure surfaces, despite being estimated independently on each one. The Principal Component of isotherm displacement CEOF1 at 1,000 dbar is well correlated (r = –0.65) with the Niño3.4 index at a 12‐month lag, suggesting that El Niño signals propagate deep into the equatorial Pacific Ocean. The 3‐D structure of the isotherm displacement CEOF1s suggests that the deep isotherm displacement signals are consistent with a vertically propagating Rossby wave of vertical mode 3–4.
Analysis of Suspended Sediment Variability in a Large Highly Turbid Estuary Using a 5‐Year‐Long Remotely Sensed Data Archive at High Resolution
Authors: Normandin C. , Lubac B. , Sottolichio A. , Frappart F. , Ygorra B. , Marieu V. 
Published: October 2019

AbstractSpatial variability of surface suspended particulate matter (SPM) concentration in the Gironde estuary and their relationships with environmental forcing are investigated through high spatial resolution multispectral data collected from July 2013 to August 2018 by the Operational Land Imager (Landsat‐8/OLI) and MultiSpectral Instrument (Sentinel‐2/MSI). A principal component analysis using the T‐mode orientation is applied to the discontinuous multiannual time series composed of 41 remotely sensed images. The three first principal components (PC1, PC2, and PC3) explain 65.7% of the total variance. The SPM distribution associated with PC1 and PC2 exhibits a privileged along‐estuary direction of the oscillation modes, while the spatial patterns of PC3 are clearly dominated by lateral oscillations opposing channels and shoals. The main environmental factors affecting the SPM distribution are identified by the analysis of their temporal patterns. The tidal range and the daily river discharge control the spatial patterns of PC1 and PC2, while the tidal cycles and the wind speed are significantly correlated with PC3. Furthermore, the analysis in the along‐estuary and lateral directions shows marked longitudinal and transverse SPM gradients and a strong control of bathymetry on the SPM spatial distribution. For the first time, we highlight that the maxima of surface residual turbidity are located on the shoals regardless of the environmental (tidal and hydrological) conditions. Compared to previous studies, usually based on single‐point in‐water column measurements, these results provide a novel and complementary description of the spatial variability of SPM. They are useful to validate sediment transport numerical models, but also may improve our understanding of suspended sediment dynamics in estuarine systems governed by an estuarine turbidity maximum.
Impact of Future Warming and Enhanced [CO2] on the Vegetation‐Cloud Interaction
Authors: Sikma M. , Vilà‐Guerau de Arellano J. , Pedruzo‐Bagazgoitia X. , Voskamp T. , Heusinkveld B.G. , Anten N.P.R. , Evers J.B. 
Published: October 2019

AbstractThe effects of increases in carbon dioxide and temperature on the vegetation‐atmosphere‐cloud interaction are studied with a bottom‐up approach. Using the 3‐D large‐eddy simulation technique coupled with a CO2‐sensitive dynamic plant physiological submodel, we aimed to spatially and temporally understand the surface and vegetation forcing on the coupled land‐atmosphere interactions in future scenarios. Four simulations were designed: a control simulation for current conditions, an enhanced carbon dioxide simulation (current +200 ppm), an elevated temperature simulation (current +2 K), and a simulation covering the combination of both elevations in temperature and CO2. With elevations in carbon dioxide, plant transpiration is reduced due to stomatal closure, resulting in reduced latent‐ and increased sensible heat fluxes. Although no effects on cloud cover were found in this simulation, the in‐cloud moisture flux was enhanced. Elevations in temperature yielded opposite results with reduced sensible and increased latent heat fluxes, which reduced the turbulent kinetic energy and buoyancy rates, thereby negatively impacting cloud formation. Our future climate mimicking simulation shows minimal changes in the regional energy balance due to offsetting effects between increased temperature and [CO2], while plant photosynthesis increased and transpiration decreased. The atmospheric boundary layer was drier, even though surface fluxes were very similar current conditions, thereby hampering cloud formation and development. Our results highlight the necessity of small scales and interactions, which require a bottom‐up approach to be able to accurately capture the nonlinear plant‐atmosphere interactions.
The Correlation of Mesoscale Humidity Anomalies With Mesoscale Organization of Marine Stratocumulus From Observations Over the ARM Eastern North Atlantic Site
Authors: Zhou Xiaoli , Bretherton Christopher S. 
Published: October 2019

AbstractThe structure of mesoscale cellular organization in marine cloud‐topped boundary layers is found to be well characterized by using a novel compositing approach based on mesoscale variations in the column water vapor path (WVP). The approach is applied to ground‐based observations from the Atmospheric Radiation Measurement (ARM) Eastern North Atlantic site. Based on a set of satellite and ground‐based observational criteria, 381 hr of closed‐cell and 227 hr of open‐cell cases were selected from late 2015 to early 2018. Strong correlations are found between mesoscale‐filtered cloud properties and WVP for both closed‐cell and open‐cell regimes. In the moist atmospheric columns, the clouds are thicker with higher tops and lower bases, and stronger precipitation compared to that in the dry columns. Overall, cloud properties of open and closed cells covary similarly with mesoscale moisture perturbations, except that the correlation of liquid water path with WVP is much weaker for open cells. The relations of subcloud properties with WVP are also examined. In the moist columns, surface equivalent potential temperature and relative humidity are higher than in the dry columns. A marginally negative correlation between mesoscale‐filtered subcloud turbulence eddy dissipation rate and WVP is found for closed cells. These results are consistent with the conceptual model of closed cellular mesoscale circulations of Zhou and Bretherton (2019).
Signature of a Quasi 30‐Day Oscillation at Midlatitude Based on Wind Observations From MST Radar and Meteor Radar
Authors: Huang Kai Ming , Xi Yu , Wang Rui , Zhang Shao Dong , Huang Chun Ming , Gong Yun , Cheng Hao 
Published: October 2019

AbstractLots of works make contributions to revealing propagation features and excitation mechanisms of intraseasonal oscillations (ISOs) in the tropics; however, there are few reports on ISOs at higher latitudes. By using measurements of mesosphere‐stratosphere‐troposphere radar at Xianghe (39.8°N, 116.5°E) and meteor radar at Beijing (40.3°N, 116.2°E) and reanalysis data for 105 days from 16 November 2013 to 28 February 2014, we study an ISO with about 30‐day period at midlatitude and high latitude. Radar observations indicate that in the troposphere, the oscillation attains an amplitude peak in zonal wind at about 9 km and propagates downward below 9 km. At about 9–16 km, the oscillation gradually decays with height and then strengthens again as it propagates upward in the stratosphere. In the mesosphere, the oscillation obviously appears at 78–86 km with a maximum amplitude at 80 km. Reanalysis data show that in the troposphere, the oscillation propagates southward. At about 100 (~16 km)‐ to 10 (~32 km)‐hPa levels, the oscillation is gradually reflected back to propagate northward, and then propagates poleward at higher altitude. Refractive index can explain its complex propagation characteristics very well. Consistence and coherence of its phase progression indicate that in the lower atmosphere, the oscillation comes from the polar region. Hence, ISOs can not only originate from but also propagate in the atmosphere at mid and high latitudes.
Multisite Daily Streamflow Simulation With Time Irreversibility
Authors: Mathai Jeenu , Mujumdar P. P. 
Published: October 2019

AbstractSynthetic daily streamflow generation requires a critical understanding of the underlying dynamics resulting from the inherent temporal asymmetry (time irreversibility) in the rising and falling limbs of the hydrograph. Most models considering the time irreversibility deal with single‐site streamflow simulation. Addressing intersite dependencies is, however, crucial for interconnected stream networks. This study presents a time irreversibility dynamics‐based multisite streamflow generating framework to simulate concurrent streamflow sequences at multiple sites in a basin. This framework explicitly takes into account the spatial correlation and time irreversible dynamics of streamflow. To demonstrate the utility and applicability, a few selected streamflow gauging stations in the Godavari River Basin, located in southern India, are considered. The proposed framework shows the ability to adequately generate multisite simulations capturing at‐site statistics as well as intersite correlations for the case study. Furthermore, the approach ensures that the simulated flow values are not merely resampled from the historical data, uses the physical features of the hydrograph, and shows variability beyond that observed in the historical sequence. Such a rich variety of streamflow sequences can help water managers to investigate how existing water resources systems on interconnected stream networks will operate in scenarios which have not been observed in the historical record.
Experimental quantum network coding
Authors: Lu He , Li Zheng-Da , Yin Xu-Fei , Zhang Rui , Fang Xiao-Xu , Li Li , Liu Nai-Le , Xu Feihu , Chen Yu-Ao , Pan Jian-Wei 
Published: October 2019

AbstractDistributing quantum state and entanglement between distant nodes is a crucial task in distributed quantum information processing on large-scale quantum networks. Quantum network coding provides an alternative solution for quantum-state distribution, especially when the bottleneck problems must be considered and high communication speed is required. Here, we report the first experimental realization of quantum network coding on the butterfly network. With the help of prior entanglements shared between senders, two quantum states can be transmitted perfectly through the butterfly network. We demonstrate this protocol by employing eight photons generated via spontaneous parametric downconversion. We observe cross-transmission of single-photon states with an average fidelity of 0.9685 ± 0.0013, and that of two-photon entanglement with an average fidelity of 0.9611 ± 0.0061, both of which are greater than the theoretical upper bounds without prior entanglement.
On the importance of field driven single particle processes in short pulse absorption of clusters
Authors: Sarkar Soubhik , Gopal R. , Anand M. , Kumar M. Praveen , Krishnamurthy M. 
Published: October 2019

AbstractNano-clusters are acclaimed to be very efficient absorbers of intense femto second light due to dominant collective mechanisms. Enhanced near 100% absorption due to collective linear plasma resonance compared to a small fraction of absorption by unclustered gas was an important drive in nano-plasma studies. Contrary to such perception, we show that if the pulse duration is (<100 fs), absorption is same irrespective of whether the systems are condensed to large clusters or not. So long as there are same number of similar ionizable systems in the focal volume, absorption is the same and such absorption can be accounted for by single particle response to the field and collisional ionization of atoms. Short pulse absorption by the single particle response can be comparable to the linear plasma resonance absorption for smaller clusters.
eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA
Authors: Mizuno Kei , Akamatsu Shusuke , Sumiyoshi Takayuki , Wong Jing Hao , Fujita Masashi , Maejima Kazuaki , Nakano Kaoru , Ono Atushi , Aikata Hiroshi , Ueno Masaki , Hayami Shinya , Yamaue Hiroki , Chayama Kazuaki , Inoue Takahiro , Ogawa Osamu , Nakagawa Hidewaki , Fujimoto Akihiro 
Published: October 2019

AbstractPlasma cell-free DNA (cfDNA) testing plays an increasingly important role in precision medicine for cancer. However, circulating cell-free tumor DNA (ctDNA) is highly diluted by cfDNA from non-cancer cells, complicating ctDNA detection and analysis. To identify low-frequency variants, we developed a program, eVIDENCE, which is a workflow for filtering candidate variants detected by using the ThruPLEX tag-seq (Takara Bio), a commercially-available molecular barcoding kit. We analyzed 27 cfDNA samples from hepatocellular carcinoma patients. Sequencing libraries were constructed and hybridized to our custom panel targeting about 80 genes. An initial variant calling identified 36,500 single nucleotide variants (SNVs) and 9,300 insertions and deletions (indels) across the 27 samples, but the number was much greater than expected when compared with previous cancer genome studies. eVIDENCE was applied to the candidate variants and finally 70 SNVs and 7 indels remained. Of the 77 variants, 49 (63.6%) showed VAF of < 1% (0.20–0.98%). Twenty-five variants were selected in an unbiased manner and all were successfully validated, suggesting that eVIDENCE can identify variants with VAF of ≥ 0.2%. Additionally, this study is the first to detect hepatitis B virus integration sites and genomic rearrangements in the TERT region from cfDNA of HCC patients. We consider that our method can be applied in the examination of cfDNA from other types of malignancies using specific custom gene panels and will contribute to comprehensive ctDNA analysis.
Bioimaging structural signatures of the oomycete pathogen Sclerospora graminicola in pearl millet using different microscopic techniques
Authors: Shetty Hunthrike Shekar , Suryanarayan Sharada Mysore , Jogaiah Sudisha , Janakirama Aditya Rao Shimoga , Hansen Michael , Jørgensen Hans Jørgen Lyngs , Tran Lam-Son Phan 
Published: October 2019

AbstractIn this case study, the mycelium growth of Sclerospora graminicola in the infected tissues of pearl millet and the process of sporulation and liberation of sporangia and zoospores were observed using four different microscopic techniques. The cotton blue-stained samples observed under light microscope revealed the formation of zoospores with germ tubes, appressoria and initiation of haustorium into the host cells, while the environmental scanning electron microscopy showed the rapid emergence of sporangiophores with dispersed sporangia around the stomata. For fluorescence microscopy, the infected leaf samples were stained with Fluorescent Brightener 28 and Calcofluor White, which react with β-glucans present in the mycelial walls, sporangiophores and sporangia. Calcoflour White was found to be the most suitable for studying the structural morphology of the pathogen. Therefore, samples observed by confocal laser scanning microscopy (CLSM) were pre-treated with Calcofluor White, as well as with Syto-13 that can stain the cell nuclei. Among the four microscopic techniques, CLSM is ideal for observing live host-pathogen interaction and studying the developmental processes of the pathogen in the host tissues. The use of different microscopic bioimaging techniques to study pathogenesis will enhance our understanding of the morphological features and development of the infectious propagules in the host.
Mitotic granule cell precursors undergo highly dynamic morphological transitions throughout the external germinal layer of the chick cerebellum
Authors: Hanzel Michalina , Rook Victoria , Wingate Richard J. T. 
Published: October 2019

AbstractThe developing cerebellum of amniotes is characterised by a unique, transient, secondary proliferation zone: the external germinal layer (EGL). The EGL is comprised solely of granule cell precursors, whose progeny migrate inwardly to form the internal granule cell layer. While a range of cell morphologies in the EGL has long been known, how they reflect the cells’ differentiation status has previously only been inferred. Observations have suggested a deterministic maturation from outer to inner EGL that we wished to test experimentally. To do this, we electroporated granule cell precursors in chick with plasmids encoding fluorescent proteins and probed labelled cells with markers of both proliferation (phosphohistone H3) and differentiation (Axonin1/TAG1 and NeuroD1). We show that granule cell precursors can display a range of complex forms throughout the EGL while mitotically active. Overexpression of full length NeuroD1 within granule cell precursors does not abolish proliferation, but biases granule cells towards precocious differentiation, alters their migration path and results in a smaller and less foliated cerebellum. Our results show that granule cells show a greater flexibility in differentiation than previously assumed. We speculate that this allows the EGL to regulate its proliferative activity in response to overall patterns of cerebellar growth.
Eating Style and the Frequency, Size and Timing of Eating Occasions: A cross-sectional analysis using 7-day weighed dietary records
Authors: Magklis Emmanouil , Howe Laura Diane , Johnson Laura 
Published: October 2019

AbstractThe tendencies to overeat in response to negative emotions (emotional eating) and environmental cues (external eating) have both been associated with BMI. However, it is unclear how they are expressed at the eating architecture level, for example, respecting frequency, timing and size of eating occasions, which could comprise ‘downstream’ specific behavioural intervention targets. In our analyses of the UK National Diet and Nutrition Survey 2000–2001, a 1-unit higher emotional eating score was associated with meals containing approximately 15 (3, 26) fewer kcals per occasion, consuming 1.4 (0.5, 2.3) more snacks per week and snacking over a 35- (16, 53) minute longer period a day. A 1-unit higher external eating score was associated with snacking over a 24- (1, 46) minute shorter period a day. Associations were independent of BMI and other potential confounders. The distinct pattern of eating architecture associated with emotional eating, suggests specific approaches to intervention, such as the number, timing and caloric content of snacks, could be considered further in experimental studies for their potential to prevent weight gain in people with a higher emotional eating tendency. Longitudinal studies and better measurement are also needed to strengthen causal inference in terms of the downstream effects of eating styles.