bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnitudes and Drivers of Greenhouse Gas Fluxes in Floodplain Ponds During Drawdown and Inundation by the Three Gorges Reservoir
Authors: Miller B. L. , Chen H. , He Y. , Yuan X. , Holtgrieve G. W. 
Published: July 2019

AbstractHydropower reservoirs are well‐known emitters of greenhouse gases to the atmosphere. This is due in part to seasonal water level fluctuations that transfer terrestrial C and N from floodplains to reservoirs. Partial pressures and fluxes of the greenhouse gases CH4, CO2, and N2O are also a function of in situ biological C and N cycling and overall ecosystem metabolism, which varies on a diel basis within inland waters. Thus, greenhouse gas emissions in hydropower reservoirs likely vary over seasonal and diel time scales with local hydrology and ecosystem metabolism. China's Three Gorges Reservoir is among the largest and newest in the world, with a floodplain that encompasses approximately one third of the reservoir area. We measured diel partial pressures and fluxes of greenhouse gases in ponds on the Three Gorges Floodplain. We repeated these measurements on the submerged floodplain following inundation by the Three Gorges Reservoir. During reservoir drawdown, CH4 ebullition comprised 60–68% of emissions from floodplain ponds to the atmosphere. Using linear mixed effects modeling, we show that partial pressures of CH4 and CO2 and diffusive CO2 fluxes in floodplain ponds varied on a diel basis with in situ respiration. Floodplain inundation by the Three Gorges Reservoir significantly moderated areal CH4 diffusion and ebullition. Diel pCO2, pCH4, pN2O, and diffusive fluxes of CO2 on the submerged floodplain were also driven by in situ respiration. The drawdown/inundation cycle of the Three Gorges Reservoir therefore changes the magnitudes of aquatic greenhouse gas fluxes on its floodplain.
Spatiotemporal Variations of Riverine Discharge Within the Amazon Basin During the Late Holocene Coincide With Extratropical Temperature Anomalies
Authors: Bertassoli D. J. , Sawakuchi A. O. , Chiessi C. M. , Schefuß E. , Hartmann G. A. , Häggi C. , Cruz F. W. , Zabel M. , McGlue M. M. , Santos R. A. , Pupim F. N. 
Published: July 2019

AbstractLate Holocene hydroclimate variations have been extensively recognized in Amazonia, but the effects of such changes on riverine discharge within the Amazon lowlands are still poorly understood. We investigated a sediment core covering circa 4,000 to 300 cal yr BP collected in the lower valley of the Xingu River (Xingu Ria) in an area under the influence of the Amazon River. Our results indicate a decrease in precipitation in the Amazon lowlands throughout the studied period and reduced input of coarser and potassium‐rich Amazon River sediments to the confluence from about 2,600 to 1,400 cal yr BP. We suggest that lower temperatures in the extratropical Southern Hemisphere weakened the South American Summer Monsoon and led to a decrease in the water discharge of the Amazon River during this period.
Along‐Slope Variability of Cross‐Slope Eddy Transport in East Antarctica
Authors: Foppert Annie , Rintoul Stephen R. , England Matthew H. 
Published: July 2019

AbstractCircumpolar Deep Water (CDW) transport across the Antarctic continental slope regulates the delivery of heat to the shelf and its availability to melt floating ice shelves. The cross‐slope density field, calculated from profiles collected by conductivity‐temperature‐depth‐tagged marine mammals on the East Antarctic slope (0–160°E, above 1,000‐ to 3,000‐m isobaths), indicates eddy‐driven overturning: onshore transport of CDW and offshore transport of shallower Antarctic Surface Water. Enhanced eddy activity, determined by a spice standard deviation threshold in the CDW layer, is present over about a third of the East Antarctic slope analyzed. Significantly stronger CDW transport in regions of elevated spice variability produces subsurface temperature anomalies of 0.2–0.25 °C relative to the East Antarctic average. Estimating eddy diffusivity from the hydrography yields about 0.8 m2/s of warm CDW transport to the shelf break in high‐variability regions. Variability of eddy‐induced CDW transport influences the reservoir of heat available for transport across the shelf break.
Glacially Induced Hydromechanical Coupling in Shale May Have Caused Underpressured Water in the Eastern Michigan Basin Despite the Possible Presence of Gas Phase Methane
Authors: Plampin Michelle R. 
Published: July 2019

AbstractWhen glacial cycles occur above low‐permeability geologic formations, such as the shale and limestone units being considered for nuclear waste disposal in Canada, pressures may differ greatly from normal hydrostatic conditions. Although shale also often has the propensity to generate separate phase fluids like natural gas, it is largely uncertain how the processes that control this behavior might affect water pressure evolution during glacial loading cycles. Therefore, this study investigates the relationships among these system components via an example site that exhibits both a dramatic underpressure and potential evidence for gas phase methane in situ. A simple 1‐D representation of the site was constructed, and hydromechanical coupling during a glacial cycle was simulated with and without gas phase methane present. Results indicate that, while the presence of gas phase dampened the effects of the loading cycle due to its higher compressibility compared to water, it did not preclude underpressure development.
The Role of Intense Upper Hybrid Resonance Emissions in the Generation of Saturn Narrowband Emission
Authors: Menietti J. D. , Yoon P. H. , Pisa D. , Averkamp T. F. , Sulaiman A. H. , Kurth W. S. , Santolík O. , Arridge C. S. 
Published: July 2019

AbstractTwenty high‐inclination ring‐grazing orbits occurred in the final period of the Cassini mission. These orbits intercepted a region of intense Z‐mode and narrowband (NB) emission (Ye et al., 2010, https://doi.org/10.1029/2009JA015167) along with isolated, intense upper hybrid resonance (UHR) emissions that are often associated with NB source regions. We have singled out such UHR emission seen on earlier Cassini orbits that also lie near the region crossed by the ring‐grazing orbits. These previous orbits are important because Cassini electron phase‐space distributions are available and dispersion analysis can be performed to better understand the free energy source and instability of the UHR emission. We present an example of UHR emission on a previous orbit that is similar to that observed during the ring‐grazing orbits. Analysis of the observed plasma distribution of the previous orbit leads us to conclude that episodes of UHR emission and NB radiation observed during the ring‐grazing orbits are likely due to plasma distributions containing loss cones, temperature anisotropies, and strong density gradients near the ring plane. Z‐mode emissions associated with UHR and NB emission can be in Landau resonance with electrons to produce scattering or acceleration (Woodfield et al., 2018, https://doi.org/10.1038/s41467‐018‐07549‐4).
Subseismic to Seismic Slip in Smectite Clay Nanofoliation
Authors: Aretusini S. , Plümper O. , Spagnuolo E. , Di Toro G. 
Published: July 2019

AbstractSmectite clays are the main constituent of slipping zones found in subduction zone faults at shallow depth (e.g., <1‐km depth in the Japan Trench) and in the decollements of large landslides (e.g., 1963 landslide, Vajont, Italy). Therefore, deformation processes in smectite clays may control the mechanical behavior from slow creep to fast accelerations and slip during earthquakes and landslides. Here, we use (1) laboratory experiments to investigate the mechanical behavior of partly water‐saturated smectite‐rich gouges sheared from subseismic to seismic slip rates V and (2) nanoscale microscopy to study the gouge fabric. At all slip rates, deformation localizes in volumes of the gouge layer that contain a “nanofoliation” consisting of anastomosing smectite crystals. “Seismic” nanofoliations produced at V = 0.01, 0.1, and 1.3 m/s are similar to “subseismic” nanofoliations obtained at V = 10−5 m/s. This similarity suggests that frictional slip along water‐lubricated smectite grain boundaries and basal planes may occur from subseismic to seismic slip rates in natural smectite‐rich faults. Thus, if water is available along smectite grain boundaries and basal planes, nanofoliations can develop from slow to fast slip rates. Still, when nanofoliations are found highly localized in a volume, they can be diagnostic of slip that occurred at rates equal or larger than 0.01 m/s. In such a case, they could be markers of past seismic events when found in natural fault rocks.
Understanding Intermodel Diversity of CMIP5 Climate Models in Simulating East Asian Marginal Sea Surface Temperature in the Near Future (2020–2049)
Authors: Yi Dong‐Won , Yeh Sang‐Wook 
Published: July 2019

AbstractUsing 14 Coupled Model Intercomparison Projections Phase 5 (CMIP5) climate models, we examined the intermodel diversity when simulating East Asian Marginal Seas (EAMSs) sea surface temperature (SST) in the near future period (2020–2049) under four different Representative Concentration Pathway runs. We classified two groups for the CMIP5 climate models: for models that simulate SSTs in the EAMS that are higher (H_EAMS) and lower (L_EAMS) than the ensemble mean, respectively. Results show that compared to L_EAMS, H_EAMS tends to simulate weaker westerlies in the western‐to‐central North Pacific, together with a weaker Aleutian Low intensity, which causes higher EAMS SSTs through a reduction in latent heat flux. Furthermore, H_EAMS is characterized by cooler SST, less precipitation, and stronger trade winds in the central‐to‐eastern tropical Pacific than in L_EAMS. We argued that the intermodel diversity of simulated tropical Pacific SST is associated with the diversity of EAMS SST, which is related to atmospheric teleconnections from the tropics to the western‐to‐central North Pacific. It is also found that the bifurcation latitude of the North Equatorial Current is lower in H_EAMS than in L_EAMS, which is associated with the difference of tropical Pacific mean state between H_EAMS and L_EAMS. A lower bifurcation latitude transports more warm water into the EAMS, resulting in warmer SSTs in the H_EAMS than in the L_EAMS. These results show the importance of correctly simulating the tropical Pacific mean state to reduce the uncertainty in EAMS SST during the near‐future period.
Habitable Snowballs: Temperate Land Conditions, Liquid Water, and Implications for CO2 Weathering
Authors: Paradise Adiv , Menou Kristen , Valencia Diana , Lee Christopher 
Published: July 2019

AbstractHabitable planets are commonly imagined to be temperate planets like Earth, with areas of open ocean and warm land. In contrast, planets in snowball states, where oceans are entirely ice covered, are believed to be inhospitable. However, we show using a general circulation model that terrestrial planets in the inner habitable zone are able to support large unfrozen areas of land while in a snowball state. Due to their lower albedo, these unfrozen regions reach summer temperatures in excess of 10 °C. Such conditions permit CO2 weathering, suggesting that continental weathering can provide a mechanism for trapping planets in stable snowball states. The presence of land areas with warm temperatures and liquid surface water motivates a more‐nuanced understanding of habitability during these snowball events.
Toward a Stochastic Relaxation for the Quasi‐Equilibrium Theory of Cumulus Parameterization: Multicloud Instability, Multiple Equilibria, and Chaotic Dynamics
Authors: Khouider Boualem , Leclerc Etienne 
Published: July 2019

AbstractThe representation of clouds and organized tropical convection remains one of the biggest sources of uncertainties in climate and long‐term weather prediction models. Some of the most common cumulus parameterization schemes, namely, mass‐flux schemes, rely on the quasi‐equilibrium (QE) closure, which assumes that convection consumes the large‐scale instability and restores large‐scale equilibrium instantaneously. However, the QE hypothesis has been challenged both conceptually and in practice. Subsequently, the QE assumption was relaxed, and instead, prognostic equations for the cloud work function (CWF) and the cumulus kinetic energy (CKE) were derived and used. It was shown that even if the CWF kernel serves to damp the CWF, the prognostic system exhibits damped oscillations on a timescale of a few hours, giving parameterized‐cumulus‐clouds enough memory to interact with each other, with the environment, and with stratiform anvils in particular. Herein, we show that when cloud‐cloud interactions are reintroduced into the CWF‐CKE equations, the coupled system becomes unstable. Moreover, we couple the CWF‐CKE prognostic equations to dynamical equations for the cloud area fractions, based on the mean field limit of a stochastic multicloud model. Qualitative analysis and numerical simulations show that the CKE‐CWF‐cloud area fraction equations exhibit interesting dynamics including multiple equilibria, limit cycles, and chaotic behavior both when the large‐scale forcing is held fixed and when it oscillates with various frequencies. This is representative of cumulus convection variability, and its capability to transition between various regimes of organization at multiple scales and regimes of scattered convection, in an intermittent and chaotic fashion.
A Latent Variable Approach to Multivariate Quantitative Trait Loci
Authors: O'Hara Bob , Komulainen Päivi , Savolainen Outi , Sillanpää Mikko 
Published: July 2019

AbstractA novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits (including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as functions of latent variables, which are then affected by quantitative trait loci. Separating the analysis in this way means that measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine.
Fluorescence Correlation Spectroscopy as a Quantitative Tool Applied to Drug Delivery Model Systems
Authors: Jung Christoph , Polier Sigrun , Schoeffel Markus , Drechsler M , Jerome Valerie , Freitag Ruth 
Published: July 2019

AbstractThe delivery of drugs to cells is a very active area of research. Drugs are commonly believed to ameliorate illnesses. The targeted, controlled and/or enhanced uptake of the drug into cells is facilitated by loading the drug into carrier vehicles (nanoparticles, e.g.. micelles).The distribution of a drug over the nanoparticles used to deliver the drug to the targeted cells is of vital importance. It makes a difference, whether all nanoparticles carry the same amount of drug or whether a little amount of the nanoparticles carries a high proportion of the drug material and most nanoparticles carry no material. This depends on the method used to load the drugs into the carriers. Furthermore, the absolute amount of drug present in the nanoparticles and the absolute number of nanoparticles loaded with drug molecules is very important, because &quot;dosis venum facit&quot; [Paracelsus]. We present an approach to resolve these issues by optical means.If the drug is fluorescent or labeled with a fluorescent label, fluorescence correlation spectroscopy (FCS) can be used to determine quantitative size distributions with a (confocal) microscope. In order to determine absolute concentrations the spatial dimensions of the confocal observation volume have to be known. These can be obtained from numerical simulations using vectorial diffraction theory. The theoretical results have been compared with experimental results from FCS using the calibration dye Rhodamine 6G. In a straightforward procedure the results were corrected for adsorption effects and excellent agreement to the theory was found
Pepper yellow leaf curl Indonesia virus, a new bipartite begomovirus species that belongs to distinct clade of Old World geminiviruses
Authors: Sharma Pradeep , Sakata J. , Shibuya Y. , Ikegami Masato 
Published: July 2019

AbstractBegomoviruses are currently emerging as a major threat to vegetable production in many tropical and subtropical regions worldwide. Pepper yellow leaf curl disease (PepYLCD) has been noticed in many Capsicum annum L. producing regions from East Asia especially from Indonesia and causes devastating damage to pepper crop production since 2000. In this study we have cloned and sequenced complete nucleotide of begomoviruses from pepper exhibiting leaf curling and bright yellowing symptoms. Besides, we also determined the occurrence of disease on tomato evoking leaf curl symptoms and ageratum with yellow vein type of symptoms. On the basis of genome organization and sequence homology, these viruses were designated as Pepper yellow leaf curl Indonesia virus (PeYLCIV)- new species followed by its two new starins i.e. PeYLCIV-Tomato and PeYLCIV-Ageratum. These viruses have bipartite genomes. Pepper virus DNAs from Indonesia (PepYLCIV, PepYLCIV-Tomato and PepYLCIV-Ageratum DNA-As) were noticeably distinct, forming a separate branch from the other viruses infecting pepper. A considerable divergence is observed in the common region (CR) of the genomic components of PeYLCIV (77%), PeYLCIV-Tomato (82%) and PeYLCIV-Ageratum (75%). A stem-loop forming region and Rep-binding motif are identical in CRs of three viruses. CR of PepYLCIV-Ageratum DNA-A is approximately 10 nucleotides longer than those of PepYLCIV DNA-A and PepYLCIV-Tomato DNA-A. Similar insertion is also found in the common region of PepYLCIV-Ageratum DNA-B. PeYLCIV DNA-A alone is infectious in pepper and N. benthamiana plants and association with DNA-B increases symptom severity.
Chronic hyperplastic anemia as an independent risk factor for atherosclerotic lesions: a lesson from thalassemia intermedia
Authors: Lai Maria Eliana , Vacquer Stefania , Carta Maria Paola , Spiga Alessandra , Cocco Pier Luigi , Angius Fabrizio , Mandas Antonella , Dessi Sandra 
Published: July 2019

AbstractIntroduction. Cardiovascular involvement represents a well-known complication and the primary cause of mortality, both in transfusion-dependent beta thalassemia major (β-TM) and in transfusion-independent beta thalassemia intermedia (β-TI). In β-TM, heart iron overload is considered the main cause of this complication. This is likely due to poor adherence to iron-chelating therapy, resulting in the inability of the body to efficiently remove iron excess derived from transfused red blood cell breakdown. Different clinical pictures may instead be evoked in cardiovascular involvement occurring in β-TI; however, until now, no factor has emerged as the major one responsible for these complications. Design and Methods. In the present study, iron status, and lipid profiles in serum, as well as lipid content in peripheral blood mononuclear cells (PBMCs) were evaluated in 70 adult β-TM and in 22 adult β-TI patients. Ninety-two age-matched blood donors, free from any form of thalassemia, were utilized as controls. The mRNA levels of genes involved in the regulation of iron metabolism, such as interleukine 1 alfa (IL1α), tumor necrosis factor alfa (TNFα), as well as those involved in cholesterol homeostasis, such as acetyl-coenzymeA: cholesterol acyltransferase (ACAT-1), neutral cholesterol ester hydrolase (nCEH), and ATP binding cassette-A (ABCA1), were also evaluated in PBMCs from the above subjects.
Results.
In β-TI patients, serum iron, transferrin saturation and erythropoietin levels were higher, while transferrin and hepcidin were lower, compared to both β-TM and controls. Hepcidin and ILα mRNA levels were found to be reduced in β-TI-PBMCs, while those of TNFα were increased. A reduction in total and high density lipoprotein cholesterol (TC and HDL-C) in serum, and an accumulation of neutral lipids (NL), coupled with increased mRNA levels of ACAT-1 and decreased nCEH in PBMCs were also observed in β-TI.

Conclusions.
Since most of the parameters found to be altered in β-TI patients have a key role in the initiation and progression of atherosclerosis, we suggest that cardiovascular complications in these patients may be, at least partially, dependent on the occurrence of premature atherosclerotic lesions.
A Universal Carrier Test for the Long Tail of Mendelian Disease
Authors: Srinivasan Balaji , Flannick Jason , Patterson A. Scott , Chang Christopher , Pham Tuan , Young Sharon , Kaushal Amit , Lee James , Patrizio Pasquale , Evans Eric 
Published: July 2019

Abstract
Background:
Mendelian disorders are individually rare but collectively common, forming a "long tail" of genetic disease. More than 20 million people worldwide suffer from a disease in this long tail before the age of 25, with minorities and developing countries at highest risk and with the number of carriers far in excess of this figure. Importantly, the Jewish community’s campaign for universal Tay-Sachs screening shows that these incurable diseases can nevertheless be prevented if carrier status is known before conception. A single highly-accurate assay for the long tail of Mendelian disease would allow us to scale this successful campaign up to the general population, thereby improving millions of lives, greatly benefiting minority health, and saving billions of dollars.*Methods and Findings:*We have addressed the need for such an assay by designing the Universal Genetic Test (UNIT), a non-invasive, saliva-based carrier test for more than 100 Mendelian diseases across all major population groups. We exhaustively validated the test with a median of 147 positive and 525 negative samples per variant. By combining probes for risk alleles with family history information, we show that we can achieve extremely high levels of accuracy (median 95% CI [0.99988, 0.999999]), precision (median 95% CI [0.99993, 0.99999]), sensitivity (median 95% CI [0.99988, 0.999999]), and specificity (median 95% CI [0.99643, 1]) at the level of individual mutations. In particular, through a combination of replicated probes and confirmatory testing, we are able to reliably detect rare alleles at q ≈ 1/1000 with positive predictive values above 0.995. To put this in context, this performance for a multiplex assay compares favorably with FDA-approved single-gene carrier tests.

Conclusions:
The UNIT represents a dramatic reduction in the cost and complexity of large scale population screening. With a single inexpensive assay for a substantial fraction of the global Mendelian disease burden, an end to many preventable genetic diseases is now in sight. Moreover, given that the assay requires only a saliva sample, it is for the first time feasible to contemplate an "at-home carrier test" as a successor to the at-home pregnancy test.*Authors' note:*_Nature Precedings is a preprint server used by scientists to communicate results in advance of the often lengthy publication process. This manuscript is a preprint and has not yet been accepted for publication by a peer-reviewed journal. It is currently undergoing expedited review at a peer-reviewed journal and is posted publicly to allow collegial feedback in advance of publication. Please address technical comments to balajis@stanford.edu_