bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen Budget and Topographic Controls on Nitrous Oxide in a Shale‐Based Watershed
Authors: Weitzman Julie N. , Kaye Jason P. 
Published: May 2018

AbstractThe high spatial and temporal variabilities of nitrous oxide (N2O) emissions from the soil surface have made it difficult to predict flux patterns at the ecosystem scale, leading to imbalances in nitrogen (N) budgets at all scales. Our research sought to quantify topographic controls on the sources or sinks of N2O in the soil profile to improve our ability to predict soil‐atmosphere N2O fluxes and their contribution to watershed N budgets. We monitored surface‐to‐atmosphere N2O fluxes for 2 years in the Susquehanna Shale Hills Critical Zone Observatory in central Pennsylvania. Topographically convergent flow path locations had significantly higher surface N2O flux rates than nonconvergent flow path locations in the summer, but not other seasons. Overall, N2O fluxes were a large percentage (~19%) of total ecosystem N losses, and nearly twice as large as stream N export. Surface N2O fluxes were better correlated with concentrations of O2, N2O, and NO3−in shallow soil layers (<30 cm) than deeper soils. Following decades of anthropogenic atmospheric deposition and additional N from shale weathering, watershed N inputs (~8 kgN ha−1 yr−1) are greater than outputs (~3.7 kgN ha−1 yr−1). Our research revealed patterns of N cycling that are distinct from many other watersheds that have been extensively studied to understand N saturation; despite showing no other symptoms of N saturation, the watershed had high upland N2O losses, especially in convergent flow paths during summer. High upland N gas losses may be a mechanism that maintains N limitation to biota in the Shale Hills catchment.
Stratification Effects on Flow Hydrodynamics and Mixing at a Confluence With a Highly Discordant Bed and a Relatively Low Velocity Ratio
Authors: Cheng Zhengyang , Constantinescu George 
Published: May 2018

AbstractThe effects of temperature induced stratification on flow hydrodynamics, thermal mixing, and the capacity of the flow to entrain sediment at a medium‐size stream confluence with a highly discordant bed are investigated. To isolate the effects due to differences in the temperature/density of the incoming streams, two simulations were conducted with identical flow conditions (mean velocity ratio = 0.41 and temperature difference between the two streams ΔT = 4.7°C). In the first case the Richardson number was Ri = 0 (no coupling between the temperature and the momentum equations via the Boussinesq approximation), while in the second simulation Ri = 0.67. Even in the Ri = 0 case the structure of the mixing interface (MI) was different from the one expected for concordant bed confluences with a similar confluence angle and velocity ratio. The MI contained only corotating eddies shed in the shear layer forming on the fast‐speed side of the confluence apex. In the Ri = 0.67 case no wake region was present but a large recirculation eddy formed not far from the confluence apex. In both cases, the flow near the upstream part of the MI was found to be highly 3‐D and to allow the passage of particles from one side of the confluence to the other. While in the Ri = 0 case mixing was driven by the MI eddies, in the Ri = 0.67 case mixing was controlled by large near‐bed intrusions of heavier fluid from the tributary containing colder water and also by the fluid advected in and out of the recirculation eddy.
An Adaptive Multiphysics Model Coupling Vertical Equilibrium and Full Multidimensions for Multiphase Flow in Porous Media
Authors: Becker Beatrix , Guo Bo , Bandilla Karl , Celia Michael A. , Flemisch Bernd , Helmig Rainer 
Published: May 2018

AbstractEfficient multiphysics (or hybrid) models that can adapt to the varying complexity of physical processes in space and time are desirable for modeling fluid migration in the subsurface. Vertical equilibrium (VE) models are simplified mathematical models that are computationally efficient but rely on the assumption of instant gravity segregation of the two phases, which may not be valid at all times or at all locations in the domain. Here we present a multiphysics model that couples a VE model to a full multidimensional model that has no reduction in dimensionality. We develop a criterion that determines subdomains where the VE assumption is valid during simulation. The VE model is then adaptively applied in those subdomains, reducing the number of computational cells due to the reduction in dimensionality, while the rest of the domain is solved by the full multidimensional model. We analyze how the threshold parameter of the criterion influences accuracy and computational cost of the new multiphysics model and give recommendations for the choice of optimal threshold parameters. Finally, we use a test case of gas injection to show that the adaptive multiphysics model is much more computationally efficient than using the full multidimensional model in the entire domain, while maintaining much of the accuracy.
Seismic and Geologic Evidence of Water‐Induced Earthquakes in the Three Gorges Reservoir Region of China
Authors: Huang Rong , Zhu Lupei , Encarnacion John , Xu Yixian , Tang Chi‐Chia , Luo Song , Jiang Xiaohuan 
Published: May 2018

AbstractEarthquakes induced by reservoir impoundment pose great risk to property and lives worldwide, but studies demonstrating relationships between reservoir water levels, specific faults, and the local geology are rare. Here we show that the 2013M 5.1 Badong Earthquake, the largest earthquake so far in the Three Gorges Reservoir (TGR) region of China, occurred at a shallow depth on a right‐lateral south‐dipping strike‐slip fault. The fault is at least 15 km long and intercepts the TGR at the NS‐running Shennongxi River. We find that the earthquake and its foreshocks and aftershocks are confined to a fractured Triassic carbonate formation that crops out in the reservoir. The precise locations of earthquakes coupled with the local geology suggest that the sequence was induced by high pore pressure due to reservoir water infiltration in a specific rock type. The newly identified fault has the potential to generate earthquakes of magnitude approaching the designed seismic intensity limit of the Three Gorges Dam.
Reconciling Atmospheric and Oceanic Views of the Transient Climate Response to Emissions
Authors: Katavouta Anna , Williams Richard G. , Goodwin Philip , Roussenov Vassil 
Published: May 2018

AbstractThe Transient Climate Response to Emissions (TCRE), the ratio of surface warming and cumulative carbon emissions, is controlled by a product of thermal and carbon contributions. The carbon contribution involves the airborne fraction and the ratio of ocean saturated and atmospheric carbon inventories, with this ratio controlled by ocean carbonate chemistry. The evolution of the carbon contribution to the TCRE is illustrated in a hierarchy of models: a box model of the atmosphere‐ocean and an Earth system model, both integrated for 1,000 years, and a suite of Earth system models integrated for 140 years. For all models, there is the same generic carbonate chemistry response: An acidifying ocean during emissions leads to a decrease in the ratio of the ocean saturated and atmospheric carbon inventories and the carbon contribution to the TCRE. Hence, ocean carbonate chemistry is important in controlling the magnitude of the TCRE and its evolution in time.
On the Cause of Recent Variations in Lower Stratospheric Ozone
Authors: Chipperfield Martyn P. , Dhomse Sandip , Hossaini Ryan , Feng Wuhu , Santee Michelle L. , Weber Mark , Burrows John P. , Wild Jeanette D. , Loyola Diego , Coldewey‐Egbers Melanie 
Published: May 2018

AbstractWe use height‐resolved and total column satellite observations and 3‐D chemical transport model simulations to study stratospheric ozone variations during 1998–2017 as ozone‐depleting substances decline. In 2017 extrapolar lower stratospheric ozone displayed a strong positive anomaly following much lower values in 2016. This points to large interannual variability rather than an ongoing downward trend, as reported recently by Ball et al. (2018, https://doi.org/10.5194/acp‐18‐1379‐2018). The observed ozone variations are well captured by the chemical transport model throughout the stratosphere and are largely driven by meteorology. Model sensitivity experiments show that the contribution of past trends in short‐lived chlorine species to the ozone changes is small. Similarly, the potential impact of modest trends in natural brominated short‐lived species is small. These results confirm the important role that atmospheric dynamics plays in controlling ozone in the extrapolar lower stratosphere on multiannual time scales and the continued importance of monitoring ozone profiles as the stratosphere changes.
A 500‐Year Tree Ring‐Based Reconstruction of Extreme Cold‐Season Precipitation and Number of Atmospheric River Landfalls Across the Southwestern United States
Authors: Steinschneider Scott , Ho Michelle , Williams A. Park , Cook Edward R. , Lall Upmanu 
Published: May 2018

AbstractThis study develops a reconstruction of the frequency of extreme cold‐season precipitation and the occurrence of landfalling atmospheric river (AR) storm tracks across the southwestern Unites States using a network of tree ring chronologies and the Living Blended Drought Atlas (LBDA), a 500‐year tree ring based reconstruction of the summer Palmer Drought Severity Index. The first two rotated empirical orthogonal functions of the LBDA across the Southwest are shown to relate well to previously identified patterns of regional AR activity. Accordingly, the rotated empirical orthogonal functions also record patterns of extreme precipitation associated with those ARs, albeit with some uncertainty introduced by nonextreme precipitation. A network of chronologies sensitive to cold‐season precipitation is then used to reconstruct the occurrence of landfalling ARs and extreme precipitation along the southern Californian coast, demonstrating for the first time the feasibility of reconstructing AR landfalls and extreme events in the Southwest based on spatial patterns in a network of dendroclimatic proxies.
Composite regulation of ERK activity dynamics underlying tumour-specific traits in the intestine
Authors: Muta Yu , Fujita Yoshihisa , Sumiyama Kenta , Sakurai Atsuro , Taketo M. Mark , Chiba Tsutomu , Seno Hiroshi , Aoki Kazuhiro , Matsuda Michiyuki , Imajo Masamichi 
Published: May 2018

AbstractActing downstream of many growth factors, extracellular signal-regulated kinase (ERK) plays a pivotal role in regulating cell proliferation and tumorigenesis, where its spatiotemporal dynamics, as well as its strength, determine cellular responses. Here, we uncover the ERK activity dynamics in intestinal epithelial cells (IECs) and their association with tumour characteristics. Intravital imaging identifies two distinct modes of ERK activity, sustained and pulse-like activity, in IECs. The sustained and pulse-like activities depend on ErbB2 and EGFR, respectively. Notably, activation of Wnt signalling, the earliest event in intestinal tumorigenesis, augments EGFR signalling and increases the frequency of ERK activity pulses through controlling the expression of EGFR and its regulators, rendering IECs sensitive to EGFR inhibition. Furthermore, the increased pulse frequency is correlated with increased cell proliferation. Thus, ERK activity dynamics are defined by composite inputs from EGFR and ErbB2 signalling in IECs and their alterations might underlie tumour-specific sensitivity to pharmacological EGFR inhibition.
A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis
Authors: Vafaee Fatemeh , Diakos Connie , Kirschner Michaela B. , Reid Glen , Michael Michael Z. , Horvath Lisa G. , Alinejad-Rokny Hamid , Cheng Zhangkai Jason , Kuncic Zdenka , Clarke Stephen 
Published: May 2018

AbstractRecent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex-omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed a multi-objective optimisation method that effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. The proposed multi-objective framework has the capacity to adjust for conflicting biomarker objectives and to incorporate heterogeneous information facilitating systems approaches to biomarker discovery. We have found a prognostic signature of colorectal cancer comprising 11 circulating microRNAs. The identified signature predicts the patients’ survival outcome and targets pathways underlying colorectal cancer progression. The altered expression of the identified microRNAs was confirmed in an independent public data set of plasma samples of patients in early stage vs advanced colorectal cancer. Furthermore, the generality of the proposed method was demonstrated across three publicly available miRNA data sets associated with biomarker studies in other diseases.
Rapid Crop Cover Mapping for the Conterminous United States
Authors: Dahal Devendra , Wylie Bruce , Howard Danny 
Published: May 2018

AbstractTimely crop cover maps with sufficient resolution are important components to various environmental planning and research applications. Through the modification and use of a previously developed crop classification model (CCM), which was originally developed to generate historical annual crop cover maps, we hypothesized that such crop cover maps could be generated rapidly during the growing season. Through a process of incrementally removing weekly and monthly independent variables from the CCM and implementing a ‘two model mapping’ approach, we found it viable to generate conterminous United States-wide rapid crop cover maps at a resolution of 250 m for the current year by the month of September. In this approach, we divided the CCM model into one ‘crop type model’ to handle the classification of nine specific crops and a second, binary model to classify the presence or absence of ‘other’ crops. Under the two model mapping approach, the training errors were 0.8% and 1.5% for the crop type and binary model, respectively, while test errors were 5.5% and 6.4%, respectively. With spatial mapping accuracies for annual maps reaching upwards of 70%, this approach demonstrated a strong potential for generating rapid crop cover maps by the 1st of September.
Reducing sitting time versus adding exercise: differential effects on biomarkers of endothelial dysfunction and metabolic risk
Authors: Duvivier Bernard M. F. M. , Bolijn Johanne E. , Koster Annemarie , Schalkwijk Casper G. , Savelberg Hans H. C. M. , Schaper Nicolaas C. 
Published: May 2018

AbstractRecent studies suggest that substituting sitting with light physical activity has beneficial metabolic effects, but it is unclear if this is associated with parallel changes in endothelial function. Data from three randomized cross-over studies were analyzed, in which 61 subjects (with normal weight, overweight and type 2 diabetes) followed different activity regimens (Sit, SitLess and/or Exercise) of four days each. Subjects were instructed to sit 14 h/day (‘Sit’), to substitute 1 h/day of sitting with moderate-to-vigorous cycling (‘Exercise’) or to substitute 5–6 h/day sitting with light-intensity walking and standing (‘SitLess’). Physical activity was assessed 24 h/day by accelerometry (ActivPAL) and diet was standardized. Fasted circulating biomarkers of endothelial dysfunction, lipids and insulin sensitivity were assessed the morning after each activity regimen. The endothelial dysfunction score (ED-score) was computed by averaging the Z-scores of the circulating biomarkers of endothelial dysfunction. Compared to Sit, Exercise resulted in lower ED-score, sICAM1 and sE-selectin (p < 0.05), while no significant changes were observed after SitLess. The ED-score, sVCAM1 and sE-selectin were lower after Exercise compared to SitLess (p < 0.05). In contrast, compared to Sit, insulin sensitivity (HOMA2-IR) and plasma lipids (HDL-cholesterol, non-HDL-cholesterol, total cholesterol and Apo B) did not change significantly after Exercise but were improved after SitLess (p < 0.05). In conclusion, light physical activity and moderate-to-vigorous physical activity had a differential effect on risk markers of cardio-metabolic health and suggest the need of both performing structured exercise as well as reducing sitting time on a daily basis.
Prediction of sarcopenia using a combination of multiple serum biomarkers
Authors: Kwak Ju Yeon , Hwang Hyeoncheol , Kim Seon-Kyu , Choi Jeong Yi , Lee Seung-Min , Bang Hyun , Kwon Eun-Soo , Lee Kwang-Pyo , Chung Sun Gun , Kwon Ki-Sun 
Published: May 2018

AbstractSarcopenia is a gradual loss of skeletal muscle mass and function with aging. Given that sarcopenia has been recognized as a disease entity, effective molecular biomarkers for early diagnosis are required. We recruited 46 normal subjects and 50 patients with moderate sarcopenia aged 60 years and older. Sarcopenia was clinically identified on the basis of the appendicular skeletal muscle index by applying cutoff values derived from the Asian Working Group for Sarcopenia. The serum levels of 21 potential biomarkers were analyzed and statistically examined. Interleukin 6, secreted protein acidic and rich in cysteine, macrophage migration inhibitory factor, and insulin-like growth factor 1 levels differed significantly between the normal and sarcopenia groups. However, in each case, the area under the receiver operating characteristics curve (AUC) was <0.7. Subsequent combination of the measurements of these biomarkers into a single risk score based on logistic regression coefficients enhanced the accuracy of diagnosis, yielding an AUC value of 0.763. The best cutoff value of 1.529 had 70.0% sensitivity and 78.3% specificity (95% CI = 2.80–21.69, p < 0.0001). Combined use of the selected biomarkers provides higher diagnostic accuracy than individual biomarkers, and may be effectively utilized for early diagnosis and prognosis of sarcopenia.
Molecular basis of resistance to the microtubule-depolymerizing antitumor compound plocabulin
Authors: Pantazopoulou Areti , Galmarini Carlos María , Peñalva Miguel A. 
Published: May 2018

AbstractPlocabulin (PM060184) is a microtubule depolymerizing agent with potent antiproliferative activity undergoing phase II clinical trials for the treatment of solid tumors. Plocabulin shows antifungal activity virtually abolishing growth of the filamentous fungus Aspergillus nidulans. A. nidulans hyphae depend both on mitotic and interphase microtubules, as human cells. Here, we exploited the A. nidulans genetic amenability to gain insight into the mechanism of action of plocabulin. By combining mutations in the two A. nidulans β-tubulin isotypes we obtained a plocabulin-insensitive strain, showing that β-tubulin is the only molecular target of plocabulin in fungal cells. From a genetic screen, we recovered five mutants that show plocabulin resistance but do not carry mutations in β-tubulin. Resistance mutations resulted in amino acid substitutions in (1) two subunits of the eukaryotic translation initiation factor eIF2B activating the General Amino Acid Control, (2) TIM44, an essential component of the inner mitochondrial membrane translocase, (3) two transcription factors of the binuclear zinc cluster family potentially interfering with the uptake or efflux of plocabulin. Given the conservation of some of the identified proteins and their respective cellular functions in the tumor environment, our results pinpoint candidates to be tested as potential biomarkers for determination of drug efficiency.
Accelerating polygon beam with peculiar features
Authors: Fang Zhao-Xiang , Zhao Hong-Ze , Chen Yue , Lu Rong-De , He Li-Qun , Wang Pei 
Published: May 2018

AbstractWe report on a novel kind of accelerating beams that follow parabolic paths in free space. In fact, this accelerating peculiar polygon beam (APPB) is induced by the spectral phase symmetrization of the regular polygon beam (RPB) with five intensity peaks, and it preserves a peculiar symmetric structure during propagation. Specially, such beam not only exhibits autofocusing property, but also possesses two types of accelerating intensity maxima, i.e., the cusp and spot-like structure, which does not exist in the previously reported accelerating beams with a single kind of lobes. We also provide a detailed insight into the theoretical origin and characteristics of this spatially accelerating beam through catastrophe theory. Moreover, an experimental scheme based on a digital micromirror device (DMD) with the binary spectral hologram is proposed to generate the target beam by precise modulation, and a longitudinal needle-like focus is observed around the focal region. The experimental results confirm the peculiar features presented in the theoretical findings. Further, the APPB is verified to exhibit self-healing property during propagation with either obstructed cusp or spot reconstructing after a certain distance. Hence, we believe that the APPB will facilitate the applications in the areas of particle manipulation, material processing and optofludics.
Localization and Speciation of Chromium in Coptis chinensis Franch. using Synchrotron Radiation X-ray Technology and Laser Ablation ICP-MS
Authors: Huang Wenli , Jiao Jie , Ru Mei , Bai Zhenqing , Yuan Honglin , Bao Zhian , Liang Zongsuo 
Published: May 2018

AbstractCoptis chinensis Franch. is one of the most important medicinal plants globally. However, this species contains relatively high concentrations of chromium (Cr) which potentially detrimental to human health. It is important to understand Cr localization and speciation in order to evaluate its accumulation and transportation mechanisms and minimize Cr transfer to humans. As little previous work in this area has been carried out, we utilized synchrotron radiation microscopic X-ray fluorescence (SR-μXRF) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to spatially locate Cr, X-ray absorption near-edge spectroscopy (XANES) to analyze Cr speciation, and inductively coupled plasma mass spectrometry (ICP-MS) to detect Cr subcellular concentration. Micromapping results showed that Cr was distributed predominantly within the vascular cylinder, the periderm and some outer cortex, and the cortex and some vascular bundles in root, rhizome, and petiole, respectively. XANES data showed that Cr(VI) can be reduced to Cr(III) when grown with Cr(VI), and yielded a novel conclusion that this plant contain elemental chromium. ICP-MS data showed that Cr was primarily compartmentalized in cell walls in all tissues. The new insights on Cr accumulation in C. chinensis Franch. provide a theoretical basis for the evaluation of Cr in other medicinal plants.