ALBERT

Description: Bone remodeling is a natural process that enables growth and maintenance of the skeleton. It involves the deposition of mineralized matrix by osteoblasts and resorption by osteoclasts. Several cancers that metastasize to bone negatively perturb the remodeling process through a series of interactions with osteoclasts, and osteoblasts. These interactions have been described as the “vicious cycle” of cancer metastasis in bone. Due to the inaccessibility of the skeletal tissue it is difficult to study this system in vivo . In contrast, standard tissue culture lacks sufficient complexity. We have developed a specialized three-dimensional culture system that permits growth of a non-vascularized, multiple-cell-layer of mineralized osteoblastic tissue from pre-osteoblasts. In this study, the essential properties of bone remodeling were created in vitro by co-culturing the mineralized collagenous osteoblastic tissue with actively resorbing osteoclasts followed by reinfusion with proliferating pre-osteoblasts. Cell-cell and cell-matrix interactions were determined by confocal microscopy as well as by assays for cell specific cytokines and growth factors. Osteoclasts, differentiated in the presence of osteoblasts, led to degradation of the collagen-rich extracellular matrix. Further addition of metastatic breast cancer cells to the co-culture mimicked the vicious cycle; i.e. there was a further reduction in osteoblastic tissue thickness, an increase in osteoclastogenesis, chemotaxis of cancer cells to osteoclasts and formation of cancer cells into large colonies. The resulting model system permits detailed study of fundamental osteobiological and osteopathological processes in a manner that will enhance development of therapeutic interventions to skeletal diseases. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: This paper proposes a method to identify blocking onset and decay by means of two stability indicators: enstrophy advection and its integral. The key to this technique is the use of local Lyapunov exponents for the barotropic vorticity equation which can be approximated by the integral of enstrophy (IRE) over a fixed, finite, region. The IRE can then be viewed as a measure of stability. However, by differentiating the IRE with respect to time, two measures of stability can be derived to assess blocking onset and decay: (i) the integral of enstrophy advection (DIRE), for which a time series is used to assess stability; and (ii) enstrophy advection, for which contours are plotted in conjunction with 500 hPa heights to locate blocking. One year of Northern Hemisphere blocking events from July 2011-July 2012 are studied to demonstrate that the integral of enstrophy advection is a useful diagnostic. In particular, time series of IRE and DIRE for four of the blocking cases are presented, while contour plots of enstrophy advection for one case are presented. In all cases studied, the diagnostics were seen to detect the instability in an incipient blocking event and in its decay.

Description: Cervical carcinoma represents the paradigm of virus-induced cancers, where virtually all cervical cancers come from previous “high-risk” HPV infection. The persistent expression of the HPV viral oncoproteins E6 and E7 is responsible for the reprogramming of fundamental cellular functions in the host cell, thus generating a noticeable, yet only partially explored, imbalance in protein molecular networks and cell signaling pathways. Eighty-eight cellular factors, identified as HPV direct or surrogate targets, were chosen and monitored in a retrospective analysis for their mRNA expression in HPV-induced cervical lesions, from dysplasia to cancer. Real-time quantitative PCR (qPCR) was performed by using formalin-fixed, paraffin embedded archival samples. Gene expression analysis identified 40 genes significantly modulated in LSIL, HSIL and squamous cervical carcinoma. Interestingly, among these, the expression level of a panel of four genes, TOP2A, CTNNB1, PFKM and GSN, was able to distinguish between normal tissues and cervical carcinomas. Immunohistochemistry was also done to assess protein expression of two genes among those up-regulated during the transition between dysplasia and carcinoma, namely E2F1 and CDC25A, and their correlation with clinical parameters. Besides the possibility of significantly enhancing the use of some of these factors in diagnostic or prognostic procedures, these data clearly outline specific pathways, and thus key biological processes, altered in cervical dysplasia and carcinoma. Deeper insight on how these molecular mechanisms work may help widen the spectrum of novel innovative approaches to these virus-induced cell pathologies. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Cellular pathways are numerous and are highly integrated in function in the control of cellular systems. They collectively regulate cell division, proliferation, survival and apoptosis of cells and mutagenesis of key genes that control these pathways can initiate neoplastic transformations. Understanding these pathways is crucial to future therapeutic and preventive strategies of the disease. Ovarian cancers are of three major types; epithelial, germ-cell and stromal. However, ovarian cancers of epithelial origin, arising from the mesothelium, are the predominant form. Of the subtypes of ovarian cancer, the high-grade serous tumors are fatal, with low survival rate due to late detection and poor response to treatments. Close examination of preserved ovarian tissues and in vitro studies have provided insights into the mechanistic changes occurring in cells mediated by a few key genes. This review will focus on pathways and key genes of the pathways that are mutated or have aberrant functions in the pathology of ovarian cancer. Non-genetic mechanisms that are gaining prominence in the pathology of ovarian cancer, miRNAs and epigenetics, will also be discussed in the review. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Normal pregnancy is associated with systemic vasodilation and decreased vascular contraction, partly due to increased release of endothelium-derived vasodilator substances. Endothelin-1 (ET-1) is an endothelium-derived vasoconstrictor acting via endothelin receptor type A (ET A R) and possibly type B (ET B R) in vascular smooth muscle cells (VSMCs), with additional vasodilator effects via endothelial ET B R. However, the role of ET-1 receptor subtypes in the regulation of vascular function during pregnancy is unclear. We investigated whether the decreased vascular contraction during pregnancy reflects changes in the expression/activity of ET A R and ET B R. Contraction was measured in single aortic VSMCs isolated from virgin, mid-pregnant (mid-Preg, day 12) and late-Preg (day 19) Sprague-Dawley rats, and the mRNA expression, protein amount, tissue and cellular distribution of ET A R and ET B R were examined using RT-PCR, Western blots, immunohistochemistry and immunofluorescence. Phenylephrine (Phe, 10 −5  M), KCl (51 mM) and ET-1 (10 −6  M) caused VSMC contraction that was in late-Preg 〈 mid-Preg and virgin rats. In VSMCs treated with ET B R antagonist BQ788, ET-1 caused significant contraction that was still in late-Preg 〈 mid-Preg and virgin rats. In VSMCs treated with the ET A R antagonist BQ123, ET-1 caused a small contraction; and the ET B R agonists IRL-1620 and sarafotoxin 6c (S6c) caused similar contraction that was in late-Preg 〈 mid-Preg and virgin rats. RT-PCR revealed similar ET A R, but greater ET B R mRNA expression in pregnant vs. virgin rats. Western blots revealed similar ET A R, and greater protein amount of ET B R in endothelium-intact vessels, but reduced ET B R in endothelium-denuded vessels of pregnant vs. virgin rats. Immunohistochemistry revealed prominent ET B R staining in the intima, but reduced ET A R and ET B R in the aortic media of pregnant rats. Immunofluorescence signal for ET A R and ET B R was less in VSMCs of pregnant vs. virgin rats. The pregnancy-associated decrease in ET A R- and ET B R-mediated VSMC contraction appears to involve downregulation of ET A R and ET B R expression/activity in VSM, and may play a role in the adaptive vasodilation during pregnancy. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Neuroregenerative medicine is an ever-growing field in which regeneration of lost cells/tissues due to a neurodegenerative disease is the ultimate goal. With the scarcity of available replacement alternatives, stem cells provide an attractive source for regenerating neural tissue. While many stem cell sources exist, including: mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs), the limited cellular potency, technical difficulties, and ethical considerations associated with these make finding alternate sources a desirable goal. Periodontal ligament stem cells (PDLSCs) derived from the neural crest were induced into neural-like cells using a combination of epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). Morphological changes were evident in our treated group, seen under both light microscopy and scanning electron microscopy (SEM). A statistically significant increase in the expression of neuron-specific β-tubulin III and the neural stem/progenitor cell marker nestin, along with positive immunohistochemical staining for glial fibrillary acidic protein (GFAP), demonstrated the success of our treatment in inducing both neuronal and glial phenotypes. Positive staining for synaptophysin demonstrated neural connections and electrophysiological recordings indicated that when subjected to whole cell patch clamping, our treated cells displayed inward currents conducted through voltage-gated sodium (Na + ) channels. Taken together, our results indicate the success of our treatment in inducing PDLSCs to neural-like cells. The ease of sourcing and expansion, their embryologic neural crest origin, and the lack of ethical implications in their use make PDLSCs an attractive source for use in neuroregenerative medicine. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Urotensin II (UII), a vasoactive peptide modulates renal hemodynamics. However, the physiological functions of UII in glomerular cells are unclear. In particular, whether UII alters mesangial tone remains largely unknown. The present study investigates the physiological effects of UII on intracellular Ca 2+ ([Ca 2+ ] i ) and contraction in glomerular mesangial cells (GMCs). This study also tested the hypothesis that the regulator of G-protein signaling (RGS) controls UII receptor (UTR) activity in GMCs. RT-PCR, Western immunoblotting, and immunofluorescence revealed UTR expression and localization in cultured murine GMCs. Mouse UII (mUII) stimulated [Ca 2+ ] i elevation in GMCs in the absence and presence of extracellular Ca 2+ . mUII also caused a reduction in planar GMC surface area. mUII-induced [Ca 2+ ] i elevation and contraction in GMCs were attenuated by SB 657510, a UTR antagonist, araguspongin B, an inositol 1,4,5-trisphosphate receptor antagonist, thapsigargin, a sarco/endoplasmic reticulum Ca 2+ -ATPase inhibitor, and La 3+ , a store-operated Ca 2+ channel blocker, but not nimodipine, an L-type Ca 2+ channel blocker. In situ proximity ligation assay indicated molecular proximity between endogenous RGS2 and UTR in the cells. Treatment of GMCs with mUII increased plasma membrane association of RGS2 by ∼ 2-fold. mUII also increased the interaction between RGS2 and UTR in the cells. siRNA-mediated knockdown of RGS2 in murine GMCs increased mUII-induced [Ca 2+ ] i elevation and contraction by ∼ 35 and 31%, respectively. These findings indicate that mUII induces [Ca 2+ ] i elevation and contraction in murine GMCs. Data also suggest that UTR activation stimulates RGS2 recruitment to GMC plasma membrane as a negative feedback mechanism to regulate UTR signaling. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Poly-N-acetyllactosamine (PLN) is a unique glycan composed of repeating units of the common disaccharide (Galβ1,4-GlcNAcβ1,3) n . The expression of PLN on glycoprotein core structures minimally requires enzyme activities for β1,4-galactosyltransferase (β4GalT) and β1,3-N-acetylglucosminyltransferase (β3GnT). Because β4GalTs are ubiquitous in most cells, PLN expression is generally ascribed to the tissue-specific transcription of 8 known β3GnT genes in mice. In the olfactory epithelium (OE), β3GnT2 regulates expression of extended PLN chains that are essential for axon guidance and neuronal survival. N-glycan branching and core composition, however, can also modulate the extent of PLN modification. Here we show for the first time that the β1,6-branching glycosyltransferase GCNT2 (formerly known as IGnT) is expressed at high levels specifically in the OE and other sensory ganglia. Postnatally, GCNT2 is maintained in mature olfactory neurons that coexpress β3GnT2 and PLN. This highly specific coexpression suggests that GCNT2 and β3GnT2 function cooperatively in PLN synthesis. In support of this, β3GnT2 and GCNT2 cotransfection in HEK293T cells results in high levels of PLN expression on the cell surface and on adenylyl cyclase 3, a major carrier of PLN glycans in the OE. These data clearly suggest that GCNT2 functions in vivo together with β3GnT2 to determine PLN levels in olfactory neurons by regulating β1,6-branches that promote PLN extension. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: The Weather Research and Forecasting (WRF) model was used to simulate the evolution of Tropical Storm Ivan (2004) in the southeast (SE) US using both the Yonsei University (YSU) and Mellor-Yamada-Janjić (MYJ) boundary layer parameterizations. In contrast with tropical cyclone (TC) simulations over the ocean, the effect of surface layer becomes secondary for a dissipating hurricane along its terrestrial track. Although these two schemes can reproduce Ivan reasonably well, our results suggest that the mixing properties for damped mechanical turbulent conditions (weakly stable) are strongly underestimated by both parameterizations. This underestimation impacts the thermodynamic properties of the storm, leading to significant differences in the storm areal extent and the simulated precipitation fields. Suggestions for further improvements are provided. An evaluation of the impact of using or not using a convective parameterization, specifically the Kain-Fritsch (KF) scheme, at 3 km grid spacing shows marginal impact on storm coverage, intensity and precipitation, except for the presence of widespread light rainfall in the Piedmont east of the mountains when the KF is employed. Analysis of the thermal structure of the simulated storm indicates that, in the inner-storm region, the KF is either not activated or primarily produces ( parameterized ) shallow convection. As a result, the net heating tendency associated with adiabatic and diabatic processes is almost unaltered inside the storm, together with a nearly equivalent surface momentum sink, leading to similar storm areal extent and intensity. Light rainfall to the east of the mountains can be due to the trigger mechanism of KF, which depends on boundary layer convergence, forcing parameterized deep convection near the coast, where surface roughness changes enhance convergence.

Description: Heavy precipitation events (HPEs) affect the south-eastern area of France frequently during the months of September to November. Very high amounts of rain can fall during these events, with the ensuing flash-floods causing widespread damage. The cases of the 6th of September 2010 and the 1st to the 4th of November 2011 represent the different large-scale conditions in which these episodes can occur. These HPEs are forecast with differing levels of skill by the Méso-NH model at a 2.5 km resolution. The case of the 6th of September is used to test different methods of addressing cloud physics parameterisation uncertainties. Three ensembles are constructed, where the warm process microphysical time tendencies are perturbed by different methods. Results are compared by examining the spatio-temporal distribution of the precipitation field as well as looking at ensemble statistics. The ensemble methodology which induces the most dispersion in the rainfall field is deemed the most suitable. This method is then used to examine the sensitivity of four cases from November 2011 to errors in the microphysical and turbulent parameterisations. It appears that according to the model skill for the HPE, the sensitivity to microphysical perturbations varies. Events where the model skill is high (low) show low (moderate) sensitivity. These cases show a stronger sensitivity to perturbations performed upon the turbulent tendencies, while perturbing the microphysical and turbulent tendencies together produces even further dispersion. The results show the importance and the usefulness of ensembles with perturbed physical parameterisations in the forecasting of HPEs.

Description: This paper analyses the annual mean vertical and latitudinal structure of the Brewer-Dobson circulation in the CMIP5 models. The strength of the tropical mass upwelling is found to increase at all altitudes throughout the stratosphere due to climate change. However, the width of the tropical upwelling region narrows below about 20hPa, and widens above 20hPa, suggesting different physical mechanisms may play a role in this change above and below 20hPa. In the lower stratosphere, an equatorward shift in the stationary wave critical line allows waves to propagate further into the tropics. However, in the upper stratosphere, where the behaviour is dominated by what happens during the winter, an increase in the extratropical zonal mean westerly jet leads to a reduced equatorward refraction of planetary waves. The seasonal cycle of the change in the Brewer-Dobson circulation is also considered, and differences are found in the latitudinal structure of the increased extratropical downwelling between the Northern and Southern Hemispheres in winter.

Description: Sub-seasonal forecasts have been routinely produced at ECMWF since 2002 with re-forecasts produced "on the fly" to calibrate the real-time sub-seasonal forecasts. In this study, the skill of the re-forecasts from April 2002 to March 2012 and covering a common set of years (1995 to 2001) has been evaluated. Results indicate that the skill of the ECMWF re-forecasts to predict the Madden Julian Oscillation has improved significantly since 2002, with an average gain of about 1 day of prediction skill per year. The amplitude of the MJO has also become more realistic, although the model still tends to produce MJOs which are weaker than in the ECMWF re-analysis. As a consequence, the ability of the ECMWF model to simulate realistic MJO teleconnections over the northern and southern Extratropics has improved dramatically over the 10-year period. Forecast skill scores have also improved in the Extratropics. For instance, weekly mean forecasts of the North Atlantic Oscillation Index are more skillful in recent years than ten years ago. A large part of this improvement seems to be linked to the improvements in the representation of the Madden Julian Oscillation. Skill to predict 2-metre temperature anomalies over the northern Extratropics has also improved almost continuously since 2002. Changes in the horizontal and vertical resolutions of the atmospheric model had only a small impact on the skill scores, suggesting that most of the improvements in the ECMWF sub-seasonal forecasts were due to changes in model physics which were primarily designed to improve the model climate and medium-range forecasts. The impact of changes in the data assimilation system and in the observing data has not been considered in this study, since all the re-forecasts used for this study were initialized from the same re-analysis over a common set of years.

Description: At present continental to global scale flood forecasting predicts at a point discharge, with little attention to detail and accuracy of local scale inundation predictions. Yet, inundation variables are of interest and all flood impacts are inherently local in nature. This paper proposes a large scale flood inundation ensemble forecasting model that uses best available data and modeling approaches in data scarce areas. The model was built for the Lower Zambezi River to demonstrate current flood inundation forecasting capabilities in large data-scarce regions. ECMWF ensemble forecast (ENS) data were used to force the VIC (Variable Infiltration Capacity) hydrological model, which simulated and routed daily flows to the input boundary locations of a 2-D hydrodynamic model. Efficient hydrodynamic modeling over large areas still requires model grid resolutions that are typically larger than the width of channels that play a key a role in flood wave propagation. We therefore employed a novel sub-grid channel scheme to describe the river network in detail whilst representing the floodplain at an appropriate scale. The modeling system was calibrated using channel water levels from satellite laser altimetry and then applied to predict the February 2007 Mozambique floods. Model evaluation showed that simulated flood edge cells were within a distance of between one and two model resolutions compared to an observed flood edge and inundation area agreement was on average 86%. Our study highlights that physically plausible parameter values and satisfactory performance can be achieved at spatial scales ranging from tens to several hundreds of thousands of km 2 and at model grid resolutions up to several km 2 .

Description: A class of capillary flows in unsaturated porous media is characterized by quasi-steady viscous flow confined behind curved air-water interfaces and within liquid bodies held by capillary forces along crevices and grain contacts. The geometry of the connected capillary liquid network within the pore space resembles channels that form between adjacent bubbles in foam (Plateau borders) with solid grains representing gas bubbles in foam. For simplified channel geometry we combine expressions for viscous flow with continuity considerations to describe the evolution of the channels cross-sectional area during gravity drainage. This formulation enables modeling of unsaturated flow without invoking the Richards equation and associated hydraulic functions. We adapt a formalism originally developed for foam “free drainage” (drainage under gravity) or “forced drainage” (infiltration front motion) to a class of unsaturated flows in porous media that require a few input parameters only (mean channel corner angle, air entry value and porosity) for certain initial and boundary conditions. We demonstrate that the reduction in capillary channel cross section yields a consistent description of self-regulating internal fluxes towards attainment of the so-called “field capacity” in soil and provides an alternative method for interpretation of outflow experiments for prescribed pressure boundary conditions. Additionally, the geometrically-explicit formulation provides a more intuitive picture of capillary flows across textural boundaries (changes in channel cross-section and number of channels). The foam drainage methodology expands the range of tools available for analyses of unsaturated flow processes and offers more realistic links between liquid configuration and flow dynamics in unsaturated porous media.

Description: Synthetic streamflows at different sites in a river basin are needed for planning, operation and management of water resources projects. Modeling the temporal and spatial dependence structure of monthly streamflow at different sites is generally required. In this study, the maximum entropy copula method is proposed for multisite monthly streamflow simulation, in which the temporal and spatial dependence structure is imposed as constraints to derive the maximum entropy copula. The monthly streamflows at different sites are then generated by sampling from the conditional distribution. A case study for the generation of monthly streamflow at three sites in the Colorado River basin illustrates the application of the proposed method. Simulated streamflow from the maximum entropy copula is in satisfactory agreement with observed streamflow.

Description: The Krycklan Catchment Study (KCS) provides a unique field infrastructure for hillslope to landscape-scale research on short and long-term ecosystem dynamics in boreal landscapes. The site is designed for process-based research assessing the role of external drivers including forest management, climate change, and long-range pollutant transport on forests, mires, soils, streams, lakes and groundwater. The over-arching objectives of KCS are to (1) provide a state-of-the-art infrastructure for experimental and hypothesis driven research, (2) maintain a collection of high quality, long-term climatic, biogeochemical, hydrological and environmental data, and (3) support the development of models and guidelines for research, policy and management.

Description: 3-D Hydraulic Tomography (3-D HT) is a method for aquifer characterization whereby the 3-D spatial distribution of aquifer flow parameters (primarily hydraulic conductivity, K) is estimated by joint inversion of head change data from multiple partially-penetrating pumping tests. While performance of 3-D HT has been studied extensively in numerical experiments, few field studies have demonstrated the real-world performance of 3-D HT. Here we report on a 3-D transient hydraulic tomography (3-D THT) field experiment at the Boise Hydrogeophysical Research Site which is different from prior approaches in that it represents a “baseline” analysis of 3-D THT performance using only a single arrangement of a central pumping well and 5 observation wells with nearly complete pumping and observation coverage at 1m intervals. We jointly analyze all pumping tests using a geostatistical approach based on the quasi-linear estimator of kitanidis [1995]. We reanalyze the system after progressively removing pumping and/or observation intervals; significant progressive loss of information about heterogeneity is quantified as reduced variance of the K field overall, reduced correlation with slug test K estimates at wells, and reduced ability to accurately predict independent pumping tests. We verify that imaging accuracy is strongly improved by pumping and observational densities comparable to the aquifer heterogeneity geostatistical correlation lengths. Discrepancies between K profiles at wells, as obtained from HT and slug tests, are greatest at the tops and bottoms of wells where HT observation coverage was lacking.

Description: Spermatogenesis is a special process by which spermatogonial stem cells (SSCs) divide and differentiate to male gametes called mature spermatozoa. SSCs are the unique cells because they are adult stem cells that transmit genetic information to subsequent generations. Accumulating evidence has demonstrated that SSCs can be reprogrammed to acquire pluripotency to become embryonic stem-like cells that differentiate into all cell lineages of the three germ layers, highlighting potential important applications of SSCs for regenerative medicine. Recent studies from peers and us have made great achievements on the characterization, isolation and culture of mouse and human SSCs, which could lead to better understanding the biology of SSCs and the applications of SSCs in both reproductive and regenerative medicine. In this review, we first compared the cell identity and biochemical phenotypes between mouse SSCs and human SSCs. Notably, the cell types of mouse and human SSCs are distinct, and human SSCs share some but not all phenotypes with mouse SSCs. The approaches for isolating SSCs as well as short- and long- term culture of mouse SSCs and short-period culture of human SSCs were also discussed. We further addressed the new advances on the self-renewal of SSCs with an aim to establish the long-term culture of human SSCs which has not yet been achieved. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Dual-polarisation radar measurements provide valuable information about the shapes and orientations of atmospheric ice particles. For quantitative interpretation of these data in the Rayleigh regime, common practice is to approximate the true ice crystal shape with that of a spheroid. Calculations using the discrete dipole approximation for a wide range of crystal aspect ratios demonstrate that approximating hexagonal plates as spheroids leads to significant errors in the predicted differential reflectivity, by as much as 1.5dB. An empirical modification of the shape factors in Gans's spheroid theory was made using the numerical data. The resulting simple expressions, like Gans's theory, can be applied to crystals in any desired orientation, illuminated by an arbitrarily polarised wave, but are much more accurate for hexagonal particles. Calculations of the scattering from more complex branched and dendritic crystals indicate that these may be accurately modelled using the new expression, but with a reduced permittivity dependent on the volume of ice relative to an enclosing hexagonal prism.

Description: The parameterisation of diabatic processes in numerical models is critical for the accuracy of weather forecasts and for climate projections. A novel approach to the evaluation of these processes in models is introduced in this contribution. The approach combines a suite of on-line tracer diagnostics with off-line trajectory calculations. Each tracer tracks accumulative changes in potential temperature associated with a particular parameterised diabatic process in the model. A comparison of tracers therefore allows the identification of the most active diabatic processes and their downstream impacts. The tracers are combined with trajectories computed using model-resolved winds, allowing the various diabatic contributions to be tracked back to their time and location of occurrence. We have used this approach to investigate diabatic processes within a simulated extratropical cyclone. We focus on the warm conveyor belt, in which the dominant diabatic contributions come from large-scale latent heating and parameterised convection. By contrasting two simulations, one with standard convection parameterisation settings and another with reduced parameterised convection, the effects of parameterised convection on the structure of the cyclone have been determined. Under reduced parameterised convection conditions, the large-scale latent heating is forced to release convective instability that would otherwise have been released by the convection parameterisation. Although the spatial distribution of precipitation depends on the details of the split between parameterised convection and large-scale latent heating, the total precipitation amount associated with the cyclone remains largely unchanged. For reduced parameterised convection, a more rapid and stronger latent heating episode takes place as air ascends within the warm conveyor belt.

Description: Probabilistic estimates of future water levels and river discharge are usually simulated with hydrologic models using ensemble weather forecasts as main inputs. As hydrologic models are imperfect and the meteorological ensembles tend to be biased and underdispersed, the ensemble forecasts for river runoff typically are biased and underdispersed, too. Thus, in order to achieve both reliable and sharp predictions statistical post-processing is required. In this work Bayesian model averaging (BMA) is applied to statistically post-process ensemble runoff raw forecasts for a catchment in Switzerland, at lead-times ranging from 1 to 240 hours. The raw forecasts have been obtained using deterministic and ensemble forcing meteorological models with different forecast lead-time ranges. First, BMA is applied based on mixtures of univariate normal distributions, subject to the assumption of independence between distinct lead-times. Then, the independence assumption is relaxed in order to estimate multivariate runoff forecasts over the entire range of lead-times simultaneously, based on a BMA version that uses multivariate normal distributions. Since river runoff is a highly skewed variable, Box-Cox transformations are applied in order to achieve approximate normality. Both univariate and multivariate BMA approaches are able to generate well calibrated probabilistic forecasts that are considerably sharper than climatological forecasts. Additionally, multivariate BMA provides a promising approach for incorporating temporal dependencies into the post-processed forecasts. Its major advantage against univariate BMA is an increase in reliability when the forecast system is changing due to model availability.

Description: We derive a series solution for the nonlinear Boussinesq equation in terms of the similarity variable of the Boltzmann transformation in a semi-infinite domain. The first few coefficients of the series have been known for a long time, having been obtained by a truncated inversion of the series solution of the Blasius equation, but no direct recurrence relation was known for the complete series representing the solution of the Boussinesq equation. The series turns out to have a finite radius of convergence, which we estimate with a numerical complex-plane integration method that identifies the singularities of the solution when the equation is extended to the complex plane. The homogeneous condition at the origin produces a singularity which complicates numerical solutions with Runge-Kutta methods. We present two variable transformations that circumvent the problem and that are best suited to the complex-variable and the real-variable versions of the equation, respectively. Using those tools, an approximate solution accurate to 1.75 × 10 -10 and valid for the entire positive real axis is then developed by matching a Padé approximant of the exact series and an asymptotic solution (to overcome the restriction imposed by the finite radius of convergence of the series), along the same lines of the expression proposed by Hogarth and Parlange [1999]. The accuracies of all of the existing and the newly proposed solutions are obtained.

Description: Field sampling in unwadeable and flashy flood events encounters the problem that lateral variability of flow hydraulics and sediment transport cannot be captured adequately, and there is also an accuracy problem because parameters change while being measured. Moreover, event based gravel-sand mixed transport data in rapidly changing conditions are largely missing, in particular for gravel-bed rivers in small catchments. In this study, field measurements of bed load, suspended load, flow velocities, water depths and cross section geometry were collected during flood events at a monitoring station near the mouth of the Versilia river, Italy. Since the observed hydrographs are characterized by short durations, to the order of a few hours, an analysis of the lateral and temporal flow variability was carried out to enable the design of a sampling strategy and to minimize the errors created by the time variations of discharge associated with unsteady flow conditions. The measurements were interpreted using a 1D hydro-morphodynamic numerical model simulating the dynamics of flow and sediment discharges during a flood event for a given return period. The flow and sediment rating curves were then developed through an integrated approach combining different methodologies: field measurements, laboratory analyses and mathematical modeling. The developed approach allows one to capture the main physical mechanisms associated to the transport of sand–gravel mixtures, such as selective transport, and the hysteretic behaviour of sediment transport produced by rapid and intense flood events.

Description: Motivated by observations of the mean state of tropical precipitable water (PW), a moist, first baroclinic mode, shallow water system on an equatorial β -plane with a background saturation profile that depends on latitude and longitude is studied. In the presence of a latitudinal moisture gradient, linear analysis of the non-rotating problem reveals large-scale, symmetric, eastward and westward propagating unstable modes. The introduction of a zonal moisture gradient breaks the east–west symmetry of the unstable modes. The effects of rotation are then included by numerically solving the resulting eigenvalue problem on an equatorial β -plane. With a purely meridional moisture gradient, the system supports large-scale, low-frequency, eastward and westward moving neutral modes. Some of the similarities, and some of the discrepancies of these modes with intraseasonal tropical waves are pointed out. Finally, a zonal moisture gradient in the presence of rotation renders some of the aforementioned neutral modes unstable. In particular, as per observations of large-scale, low-frequency tropical variability, it is seen that regions where the background saturation profile increases (decreases) to the east favour eastward (westward) moving moist modes.

Description: In this study changes in the Northern Hemisphere winter storm tracks during the 20th century are investigated based on the individual 56 ensemble-members of the 20th Century Reanalysis dataset. It is found that the 20th century trends in storm track activities exhibit large discrepancies between the upper and lower troposphere. In the upper troposphere, a substantial intensification is identified at the poleward and downstream regions of the North Pacific and North Atlantic storm track activities, indicating a large northeastward expansion of storm tracks in the late 20th century. However, in the lower troposphere the synoptic eddy activities, especially in terms of the eddy kinetic energy (EKE) and meridional eddy heat flux, tend to be significantly weakened over the high-latitudes of central-western North Pacific and the upstream regions of the North Atlantic storm tracks. Further inspections find that such strengthening (weakening) of storm tracks in the upper (lower) troposphere are mainly attributed to the increase (decrease) of the baroclinic instability, which is predominantly determined by the meridional temperature gradient changes. Moreover, from a local energetic perspective, the baroclinic generation and barotropic damping of the synoptic eddies are found to be substantially enhanced at the upstream and downstream regions of the two storm tracks in the upper troposphere, respectively, while in the lower troposphere the baroclinic energy conversion to eddies are generally decreased.

Description: We derive a family of ideal (nondissipative) 3D sound-proof fluid models that includes both the Lipps-Hemler anelastic approximation (AA) and the Durran pseudo-incompressible approximation (PIA). This family of models arises in the Euler-Poincaré framework involving a constrained Hamilton's principle expressed in the Eulerian fluid description. The derivation in this framework establishes the following properties of each member of the entire family: the Kelvin-Noether circulation theorem, conservation of potential vorticity on fluid parcels, a Lie-Poisson Hamiltonian formulation possessing conserved Casimirs, a conserved domain integrated energy and an associated variational principle satisfied by the equilibrium solutions. Having set the stage with the derivations of 3D models using the constrained Hamilton's principle, we then derive the corresponding 2D vertical slice models for these sound-proof theories.

Description: ABSTRACT A study was performed to characterize over land precipitation associated with tropical cyclones (TCs) for basins around the world based upon the International Best Track Archive for Climate Stewardship (IBTrACS). From 1998 to 2009, data from the Tropical Rainfall Measuring Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA) product 3B42, showed that TCs accounted for 5.5%, 7.5%, 6%, 9.5%, and 8.9% of the annual precipitation for impacted over land areas of the Americas, East Asia, South and West Asia, Oceania, and East Africa respectively, and that TC contribution decreased significantly within the first 150-km from the coast. Locally, TCs contributed on average to more than 25% and up to 61% of the annual precipitation budget over very different climatic areas with arid or tropical characteristics. East Asia represented the higher and most constant TC rain (118±19% mm y -1 ) normalized over the area impacted, while East Africa presented the highest variability (108±60% mm y -1 ), and the Americas displayed the lowest average TC rain (65±24% mm y -1 ) despite a higher TC activity. Furthermore, the maximum monthly TC contribution (8-11%) was found later in the TC season and depended on the peak of TC activity, TC rainfall, and the domain transition between dry and wet regimes if any. Finally, because of their importance in terms of rainfall amount, the contribution of TCs was provided for a selection of 50 urban areas experiencing cyclonic activity. Results showed that for particularly intense years, urban areas prone to cyclonic activity received more than half of their annual rainfall from TCs.

Description: A multivariate, multi-site daily weather generator is presented for use in decision-centric vulnerability assessments under climate change. The tool is envisioned useful for a wide range of socioeconomic and biophysical systems sensitive to different aspects of climate variability and change. The proposed stochastic model has several components, including 1) a wavelet decomposition coupled to an autoregressive model to account for structured, low-frequency climate oscillations, 2) a Markov Chain and k-nearest-neighbor (KNN) resampling scheme to simulate spatially-distributed, multivariate weather variables over a region, and 3) a quantile mapping procedure to enforce long-term distributional shifts in weather variables that result from prescribed climate changes. The Markov Chain is used to better represent wet and dry spell statistics while the KNN bootstrap resampler preserves the covariance structure between the weather variables and across space. The wavelet-based autoregressive model is applied to annual climate over the region and used to modulate the Markov Chain and KNN resampling, embedding appropriate low-frequency structure within the daily weather generation process. Parameters can be altered in any of the components of the proposed model to enable the generation of realistic time series of climate variables that exhibit changes to both lower-order and higher-order statistics at long-term (inter-annual), mid-term (seasonal), and short-term (daily) timescales. The tool can be coupled with impact models in a bottom-up risk assessment to efficiently and exhaustively explore the potential climate changes under which a system is most vulnerable. An application of the weather generator is presented for the Connecticut River basin to demonstrate the tool's ability to generate a wide range of possible climate sequences over an extensive spatial domain.

Description: The objective of the least cost design problem of a water distribution system is to find its minimum cost with discrete diameters as decision variables and hydraulic controls as constraints. The goal of a robust least cost design is to find solutions which guarantee its feasibility independent of the data (i.e., under model uncertainty). A robust counterpart approach for linear uncertain problems is adopted in this study, which represents the uncertain stochastic problem as its deterministic equivalent. Robustness is controlled by a single parameter providing a trade-off between the probability of constraint violation and the objective cost. Two principal models are developed-uncorrelated uncertainty model with implicit design reliability, and correlated uncertainty model with explicit design reliability. The models are tested on three example applications and compared for uncertainty in consumers’ demands. The main contribution of this study is the inclusion of the ability to explicitly account for different correlations between water distribution systems demand nodes. In particular it is shown that including correlation information in the design phase has a substantial advantage in seeking more efficient robust solutions.

Description: Moving from univariate to multivariate frequency analysis, this study extends the Klemeš' critique of the widespread belief that the increasingly refined mathematical structures of probability functions increase the accuracy and credibility of the extrapolated upper tails of the fitted distribution models. In particular, we discuss key aspects of multivariate frequency analysis applied to hydrological data such as the selection of multivariate design events (i.e., appropriate subsets or scenarios of multiplets that exhibit the same joint probability to be used in design applications) and the assessment of the corresponding uncertainty. Since these problems are often overlooked or treated separately, and sometimes confused, we attempt to clarify properties, advantages, shortcomings and reliability of results of frequency analysis. We suggest a selection method of multivariate design events with prescribed joint probability based on simple Monte Carlo simulations that accounts for the uncertainty affecting the inference results and the multivariate extreme quantiles. It is also shown that the exploration of the p -level probability regions of a joint distribution returns a set of events that is a subset of the p -level scenarios resulting from an appropriate assessment of the sampling uncertainty, thus tending to overlook more extreme and potentially dangerous events with the same (uncertain) joint probability. Moreover, a quantitative assessment of the uncertainty of multivariate quantiles is provided by introducing the concept of joint confidence intervals. From an operational point of view, the simulated event sets describing the distribution of the multivariate p -level quantiles can be used to perform multivariate risk analysis under sampling uncertainty. As an example of the practical implications of this study, we analyse two case studies already presented in the literature.

Description: Angiogenin (ANG) undergoes nuclear translocation and promotes ribosomal RNA (rRNA) transcription thereby enhancing cell growth and proliferation. However, the mode of action of ANG in stimulating rRNA transcription is unclear. Here, we show that ANG enhances the formation of RNA polymerase I (Pol I) pre-initiation complex at the ribosomal DNA (rDNA) promoter. ANG binds at the upstream control element (UCE) of the promoter and enhances promoter occupancy of RNA Pol I as well as the selectivity factor SL1 components TAF I 48 and TAF I 110. We also show that ANG increases the number of actively transcribing rDNA by epigenetic activation through promoter methylation and histone modification. ANG binds to histone H3, inhibits H3K9 methylation, and activates H3K4 methylation as well as H4 acetylation at the rDNA promoter. These data suggest that one of the mechanisms by which ANG stimulates rRNA transcription is through an epigenetic activation of rDNA promoter. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Sparse geologic dictionaries provide a novel approach for subsurface flow model representation and calibration. Learning sparse dictionaries from prior training datasets is an effective approach to describe complex geologic connectivity patterns in subsurface imaging applications. However, the computational cost of sparse learning algorithms becomes prohibitive for large models. Performing the sparse dictionary learning process on smaller image patches (segments) provides a simple approach to address this problem in image processing applications. However, in underdetermined subsurface flow model calibration inverse problems, reconstruction of a segmented image can introduce significant structural distortion and discontinuity at the boundaries of the segments. This paper proposes an alternative sparse learning approach where the sparse dictionaries are learned from low-rank representations of the large-scale training dataset in spectral domains (e.g., frequency domain). The objective is to develop a computationally efficient dictionary learning approach that emphasizes large-scale spatial connectivity patterns. This is achieved by removing the strong spatial correlations in the training data, thereby eliminating a large number of insignificant components from the sparse learning computation. In addition to improving the computational complexity, sparse learning from low-rank training datasets suppresses the small-scale details from entering the reconstruction of large-scale connectivity patterns, and providing a regularization effect in solving the resulting ill-posed inverse problems. We apply the proposed approach to travel-time tomography inversion and nonlinear subsurface flow model calibration inverse problems to demonstrate its effectiveness and practicality.

Description: The surface wind response to SST and SST meridional gradient is investigated in the Gulf of Guinea by using daily observations and reanalyses in the 2000–2009 decade, with a focus on boreal spring and summer months (May to August), where quasi-biweekly fluctuations in the position of the northern front of the equatorial cold tongue induce quasi-biweekly equatorial sea surface temperature (SST) anomalies. Following a large-scale wind acceleration (deceleration), an equatorial SST cold (warm) anomaly is created within a few days. In order to explain the local atmospheric response to this SST anomaly, the two following mechanisms are invoked: first, a colder (warmer) ocean decreases (increases) the vertical stability in the marine atmospheric boundary layer, which favors a weaker (stronger) surface wind; and second, a negative (positive) anomaly of SST meridional gradient induces a positive (negative) anomaly of sea level pressure meridional gradient, which decelerate (accelerate) the surface wind. The first mechanism has an immediate effect in the equatorial belt between 1°S-1°N (and to a lesser extent between 3°S and 1°S), while the second takes one or two days to adjust and damps anomalous southeasterlies up to 800 hPa in the low troposphere between 7°S and 1°N, through reversed anomalies of meridional SST and pressure gradient. This negative feedback leads to weaker (stronger) winds in the southeastern Tropical Atlantic, which forces the opposite phase of the oscillation within about a week. Around the equator, where the amplitude of the oscillation is found maximal, both mechanisms combine to maximize the wind response to the front fluctuations. Between the equator and the coast, a low-level secondary atmospheric circulation takes control of the surface wind acceleration or deceleration around 3°N, which reduces the influence of the SST front fluctuations.

Description: The purpose of the operational-oriented system COALITION ( C ontext and Scale Oriented Thunderstorm Satellite Predictors Development) is to automatically detect severe thunderstorms early in their development and consequently help weather forecasters to increase lead time when issuing severe weather warnings. This new object-oriented system integrates data provided by different sources. Data from Meteosat Second Generation Rapid Scan Service, weather radar and numerical weather prediction, as well as climatology are utilized by the system. One of its primary purposes is to use all the best operationally available information about convective processes and to integrate it into a heuristic model. Furthermore the orographic forcing, which is often neglected in heuristic nowcasting models, is taken into account and included in the system as an additional convective triggering mechanism. This is particularly important for areas characterized by complex orography like the Alpine region. The COALITION algorithm merges evolving thunderstorm properties with selected predictors. The forecasted evolution of the storm is the result of the interaction between convective signatures and surrounding storm environment. Eight different "object-environment" interactions are analysed in eight modules, providing ensemble nowcasts of thunderstorm attributes (satellite- and radar-based) for the following 60 minutes. All ensemble nowcasts are then combined through a weighting and thresholding scheme and the results are summarized into a single graphical map in order to facilitate user interpretation. The COALITION nowcast system has an update frequency of 5 minutes. The output highlights the cells having a high probability of severe thunderstorm development within the next 30 minutes. Verification statistics confirm that COALITION is able to nowcast the intensity of developing convective cells with sufficient skill up to a lead time of about 20 minutes.

Description: In late February 2010 the extraordinary windstorm Xynthia crossed over Southwestern and Central Europe and caused severe damage, affecting particularly the Spanish and French Atlantic coasts. The storm was embedded in uncommon large-scale atmospheric and boundary conditions prior to and during its development, namely enhanced sea surface temperatures (SST) within the low-level entrainment zone of air masses, an unusual southerly position of the polar jet stream, and a remarkable split jet structure in the upper troposphere. To analyse the processes that led to the rapid intensification of this exceptional storm originating close to the subtropics (30°N), the sensitivity of the cyclone intensification to latent heat release is determined using the regional climate model COSMO-CLM forced with ERA-Interim data. A control simulation with observed SST shows that moist and warm air masses originating from the subtropical North Atlantic were involved in the cyclogenesis process and led to the formation of a vertical tower with high values of potential vorticity (PV). Sensitivity studies with reduced SST or increased laminar boundary roughness for heat led to reduced surface latent heat fluxes. This induced both a weaker and partly retarded development of the cyclone and a weakening of the PV-tower together with reduced diabatic heating rates, particularly at lower and mid levels. We infer that diabatic processes played a crucial role during the phase of rapid deepening of Xynthia and thus to its intensity over the Southeastern North Atlantic. We suggest that windstorms like Xynthia may occur more frequently under future climate conditions due to the warming SSTs and potentially enhanced latent heat release, thus increasing the windstorm risk for Southwestern Europe.

Description: A new hybrid wavelet–bootstrap–neural network (WBNN) model is proposed in this study for short term (1, 3 and 5 day; 1 and 2 week; and 1 and 2 month) urban water demand forecasting. The new method was tested using data from the city of Montreal in Canada. The performance of the WBNN method was compared with the autoregressive integrated moving average (ARIMA) and autoregressive integrated moving average model with exogenous input variables (ARIMAX), traditional NNs, wavelet analysis based NNs (WNN), bootstrap based NNs (BNN), and a simple naïve persistence index model. The WBNN model was developed as an ensemble of several NNs built using bootstrap resamples of wavelet sub-time series instead of raw datasets. The results demonstrated that the hybrid WBNN and WNN models produced significantly more accurate forecasting results than the traditional NN, BNN, ARIMA and ARIMAX models. It was also found that the WBNN model reduces the uncertainty associated with the forecasts, and the performance of WBNN forecasted confidence bands were found to be more accurate and reliable than BNN forecasted confidence bands. It was found in this study that maximum temperature and total precipitation improved the accuracy of water demand forecasts using wavelet analysis. The performance of WBNN models was also compared for different numbers of bootstrap resamples (i.e., 25, 50, 100, 200, and 500) and it was found that WBNN models produced optimum results with different numbers of bootstrap resamples for different lead time forecasts with considerable variability.

Description: ABSTRACT Although mechanistic reaction networks have been developed to quantify the biogeochemical evolution of subsurface systems associated with bioremediation, it is difficult in practice to quantify the onset and distribution of these transitions at the field scale using commonly collected wellbore datasets. As an alternative approach to the mechanistic methods, we develop a data-driven, statistical model to identify biogeochemical transitions using various time-lapse aqueous geochemical data (e.g., Fe(II), sulfate, sulfide, acetate, and uranium concentrations) and induced polarization (IP) data. We assume that the biogeochemical transitions can be classified as several dominant states that correspond to redox transitions and test the method at a uranium-contaminated site. The relationships between the geophysical observations and geochemical time-series vary depending upon the unknown underlying redox status, which is modeled as a hidden Markov random field. We estimate unknown parameters by maximizing the joint likelihood function using the maximization-expectation algorithm. The case study results show that when considered together aqueous geochemical data and IP imaginary conductivity provide a key diagnostic signature of biogeochemical stages. The developed method provides useful information for evaluating the effectiveness of bioremediation, such as the probability of being in specific redox stages following biostimulation where desirable pathways (e.g., uranium removal) are more highly favored. The use of geophysical data in the approach advances the possibility of using non-invasive methods to monitor critical biogeochemical system stages and transitions remotely and over field relevant scales (e.g., from square meters to several hectares).

Description: In recent years, a number of numerical modelling studies of transient sea-level rise (SLR) and seawater intrusion (SWI) in flux-controlled systems have reported an overshoot phenomenon, whereby the freshwater-saltwater interface temporarily extends further inland than the eventual steady-state position. In this study, we have carried out physical sand tank modelling of SLR-SWI in a flux-controlled unconfined aquifer setting to test if SWI overshoot is a measurable physical process. Photographs of the physical SLR experiments show, for the first time, that an overshoot occurs under controlled laboratory conditions. A sea-level drop (SLD) experiment was also carried out, and overshoot was again observed, whereby the interface was temporarily closer to the coast than the eventual steady-state position. This shows that an overshoot can occur for the case of a retreating interface. Numerical modelling corroborated the physical SLR and SLD experiments. The magnitude of the overshoot for SLR and SLD in the physical experiments was 24% of the change in steady-state interface position, albeit the laboratory setting is designed to maximise overshoot extent by adopting high groundwater flow gradients and large and rapid sea-level changes. While the likelihood of overshoot at the field scale appears to be low, this work has shown that it can be observed under controlled laboratory conditions.

Description: A new analytical solution of the flow equation has been developed to estimate the time to reach a near-equilibrium state in mixed aquifers, i.e. having unconfined and confined portions, following a large hydraulic perturbation. Near-equilibrium is defined as the time for an initial aquifer perturbation to dissipate by an average 95% across the aquifer.The new solution has been obtained by solving the flow system of a simplified conceptual model of a mixed aquifer using Laplace transforms. The conceptual model is based on two assumptions: 1) the groundwater flow can be reduced to a horizontal 1D problem; and 2) the transmissivity, a function of the saturated thickness, is assumed constant on the unconfined portion. This new solution depends on the storativity of the unconfined portion, the lengths of the unconfined and confined portions and the transmissivity, assumed to be constant and equal in both portions of the mixed aquifer. This solution was then tested and validated against a numerical flow model, where the variations of the saturated thickness and therefore variations of the transmissivity were either ignored, or properly modeled. The agreement between the results from the new solution and those from the numerical model is good, validating the use of this new solution to estimate the time to reach near-equilibrium in mixed aquifers. This solution for mixed aquifers, as well as the solutions for a fully confined or fully unconfined aquifer, have been used to estimate the time to reach near-equilibrium in thirteen large aquifers in the world. For those different aquifers, the time to reach near-equilibrium ranges between 0.7 ky to 2.4x10 7 ky. These results suggest that the present hydraulic heads in these aquifers are typically a mixture of responses induced from current and past hydrologic conditions and thus climate conditions. For some aquifers, the modern hydraulic heads may in fact depend upon hydrologic conditions resulting from several past climate cycles.

Description: The impact of contact angle on 2D spatial and temporal water content distribution during infiltration and drainage was experimentally studied. The 0.3-0.5 mm fraction of a quartz dune sand was treated and turned sub-critically repellent (contact angle of 33 0 , 48 0 , 56 0 , and 75 0 for S33, S48, S56, and S75, respectively). The media were packed uniformly in transparent flow chambers and water was supplied to the surface as a point source at different rates (1 to 20 ml/min). A sequence of grey-value images was taken by CCD camera during infiltration and subsequent drainage; grey values were converted to volumetric water content by water volume balance. Narrow and long plumes with water accumulation behind the downward moving wetting front (tip) and negative water gradient above it (tail) developed in the S56 and S75 media during infiltration at lower water application rates. The plumes became bulbous with spatially uniform water content distribution as water application rates increased. All plumes in these media propagated downward at a constant rate during infiltration and were frozen during drainage. In contrast, regular plume shapes were observed in the S33 and S48 media at all flow rates, and drainage profiles were non-monotonic with a transition plane at the depth that water reached during infiltration. Given that the studied media have similar pore-size distributions, the conclusion is that imbibition hindered by the non-zero contact angle induced pressure buildup at the wetting front (dynamic water entry value) that controlled the plume shape and internal water-content distribution during infiltration and drainage.

Description: We present a series of idealized numerical model experiments to investigate aspects of deep convection in tropical depressions, including the effects of a boundary layer wind structure on storm structure, especially on vertical vorticity production and updraught splitting, and the combined effects of horizontal and vertical shear on vertical vorticity production, with and without background rotation. In warm-cored disturbances such as tropical depressions, the vertical shear and horizontal vorticity change sign at some level near the top of the boundary layer so that, unlike in the typical middle-latitude ‘supercell’ storm, the tilting of horizontal vorticity by a convective updraught leads not only to dipole patterns of vertical vorticity, but also to a reversal in sign of the updraught rotation with height. This finding has implications for understanding the merger of convectively-induced vorticity anomalies during vortex evolution. Ambient cyclonic horizontal shear and/or cyclonic vertical vorticity favour amplification of the cyclonically-rotating gyre of the dipole. Consistent with an earlier study, storm splitting occurs in environments with pure horizontal shear as well as pure vertical shear, but the morphology of splitting is different. In both situations, splitting is found to require a relatively unstable sounding and relatively strong wind shear.

Description: Estimation of design quantiles of hydro-meteorological variables at critical locations in river basins is necessary for hydrological applications. To arrive at reliable estimates for locations (sites) where no or limited records are available, various regional frequency analysis (RFA) procedures have been developed over the past five decades. The most widely used procedure is based on Index-flood approach and L -moments. It assumes that values of scale and shape parameters of frequency distribution are identical across all the sites in a homogeneous region. In real world scenario, this assumption may not be valid even if a region is statistically homogeneous. To address this issue, a novel mathematical approach is proposed. It involves (i) identification of an appropriate frequency distribution to fit the random variable being analyzed for homogeneous region, (ii) use of a proposed transformation mechanism to map observations of the variable from original space to a dimensionless space where the form of distribution does not change, and variation in values of its parameters is minimal across sites, (iii) construction of a growth curve in the dimensionless space, and (iv) mapping the curve to the original space for the target site by applying inverse transformation to arrive at required quantile(s) for the site. Effectiveness of the proposed approach in predicting quantiles for ungauged sites is demonstrated through Monte-Carlo simulation experiments considering five frequency distributions that are widely used in RFA, and by case study on watersheds in conterminous United States. Results indicate that the proposed approach outperforms methods based on index-flood approach.

Description: Prediction of microbial surface water contamination is a formidable task because of the inherent randomness of environmental processes driving microbial fate and transport. In this article we develop a theoretical framework of a fully stochastic model of microbial transport in watersheds, and apply the theory to a simple flow network to demonstrate its use. The framework bridges the gap between microscopic behavior of individual microorganisms and macroscopic ensemble dynamics. This scaling is accomplished within a single mathematical framework, where each microorganism behaves according to a continuous-time discrete-space Markov process, and the Markov behavior of individual microbes gives rise to a non-homogeneous Poisson random field that describes microbial population dynamics. Mean value functions are derived, and the spatial and temporal distribution of water contamination risk is computed in a straightforward manner.

Description: Constitutive androstane receptor (CAR) was originally identified as xenobiotic sensor that regulates the expression of cytochrome P450 genes. However, recent studies suggest that this nuclear receptor is also involved in the regulation of energy metabolism including glucose and lipid homeostasis. This study investigated the role of CAR in the regulation of bone mass in vivo using CAR -/- mice. Endogenous mRNA expression of CAR was observed in both primary osteoblasts and osteoclast precursors. CAR -/- mice have exhibited significant increase in whole body bone mineral density (BMD) by 9.5% ( p  〈 0.01) and 5.5% (p 〈 0.05) at 10 and 15 weeks of age, respectively, compared with WT mice in males. Microcomputed tomography analysis of proximal tibia demonstrated a significant increase in trabecular bone volume (62.7%), trabecular number (54.1%) in male CAR -/- mice compared with WT mice. However, primary culture of calvarial cells exhibited no significant changes in osteogenic differentiation potential between CAR -/- and WT. In addition, the number of tartrate-resistant acid-phosphatase positive osteoclasts in the femur and serum level of CTx was not different between CAR -/- and WT mice. The higher BMD and microstructural parameters were not observed in female mice. Interestingly, serum level of testosterone in male CAR -/- mice was 2.5-fold higher compared with WT mice and the mRNA expressions of Cyp2b9 and 2b10 in the liver, which regulate testosterone metabolism, were significantly down-regulated in male CAR -/- mice. Furthermore, the difference in BMD between CAR -/- and WT mice disappeared at 8 weeks after performing orchiectomy. CAR -/- mice also exhibited significant increase in serum1,25(OH) 2 D 3 levels but Cyp 27B1 which converts 25(OH)D 3 to 1,25(OH) 2 D 3 was significantly down-regulated compared to WT mice. These results suggest that in vivo deletion of CAR resulted in higher bone mass, which appears to be a result from reduced metabolism of testosterone due to down-regulation of Cyp2b. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: The anomalously snowy winter season of 2010/11 in the Sierra Nevada is analyzed in terms of snow water equivalent (SWE) anomalies and the role of atmospheric rivers (ARs)―narrow channels of enhanced meridional water vapor transport between the tropics and extratropics. Mean April 1 SWE was 0.44 m (56%) above normal averaged over 100 snow sensors. AR occurrence was anomalously high during the period, with 20 AR dates during the season and 14 in the month of December 2010, compared to the mean occurrence of 9 dates per season. Fifteen out of the 20 AR dates were associated with the negative phases of the Arctic Oscillation (AO) and the Pacific-North American (PNA) teleconnection pattern. Analysis of all winter ARs in California during water years 1998–2011 indicates more ARs occur during the negative phase of AO and PNA, with the increase between positive and negative phases being ˜90% for AO, and ˜50% for PNA. The circulation pattern associated with concurrent negative phases of AO and PNA, characterized by cyclonic anomalies centered northwest of California, provides a favorable dynamical condition for ARs. The analysis suggests that the massive Sierra Nevada snowpack during the 2010/11 winter season is primarily related to anomalously high frequency of ARs favored by the joint phasing of −AO and −PNA, and that a secondary contribution is from increased snow accumulation during these ARs favored by colder air temperatures associated with −AO, −PNA and La Niña.

Description: The baseflow recession constant, K b , is used to characterize the interaction of groundwater and surface water systems. Estimation of K b is critical in many studies including rainfall-runoff modeling, estimation of low flow statistics at ungaged locations and baseflow separation methods. The performance of several estimators of K b are compared, including several new approaches which account for the impact of human withdrawals. A traditional semi-log estimation approach adapted to incorporate the influence of human withdrawals was preferred over other derivative-based estimators. Human withdrawals are shown to have a significant impact on the estimation of baseflow recessions, even when withdrawals are relatively small. Regional regression models are developed to relate seasonal estimates of K b to physical, climatic, and anthropogenic characteristics of stream-aquifer systems. Among the factors considered for explaining the behavior of K b , both drainage density and human withdrawals have significant and similar explanatory power. We document the importance of incorporating human withdrawals into models of the baseflow recession response of a watershed and the systemic downward bias associated with estimates of K b obtained without consideration of human withdrawals.

Description: There are significant uncertainties inherent in precipitation forecasts and these uncertainties can be communicated to users via large ensembles that are generated using stochastic models of forecast error. The Met Office and the Australian Bureau of Meteorology developed the Short Term Ensemble Prediction System (STEPS) which has been operational for a number of years. The initial formulation of Bowler et al. [2006] has been revised and extended to improve the performance over large domains, to include radar observation errors, and to facilitate the combination of forecasts from a number of sources. This paper reviews the formulation of STEPS, discusses those aspects of the formulation that have proved most problematic and presents some solutions. The performance of STEPS nowcasts is evaluated using a combination of case study examples and statistical verification from the UK. Routine forecast verification demonstrates that STEPS is capable of producing near optimal blends of a rainfall nowcast and high resolution NWP forecast. It also shows that the spread of STEPS nowcast ensembles are a good predictor of the error in the control member (unperturbed) nowcast.

Description: In this study seasonal and interannual variability of the main atmospheric moisture sources over eight regions in the Mediterranean basin were investigated along a twenty one year period. The Lagrangian dispersion model FLEXPART, developed by Stohl and James [2004, 2005], was applied to identify the contribution of humidity to the moisture budget of each region. This methodology is used to compute budgets of evaporation minus precipitation (E-P) by calculating changes in the specific humidity along backward trajectories, for the preceding ten-day periods. The results show clear seasonal differences in the moisture sources between wet and dry seasons. The Western Mediterranean Sea is the dominant moisture source for almost all the regions in the Mediterranean basin during the wet season, while the local net evaporation dominates during the dry season. The highest interannual variability is found in contributions to the Iberian Peninsula, Italy and the Eastern Mediterranean. It is seen that the role of teleconnections is more limited than for the precipitation recorded in the region.

Description: We present a new hydrologic model based on the frequency distribution of hillslope landscape elements along the stream network as a basis for simulating landscape-scale hydrologic connectivity and catchment runoff. Hydrologic connectivity describes shallow water table continuity between upland and stream elements of the catchment and is important for the movement of water and solutes to streams. This concept has gained traction in physical hydrology but has received less attention in rainfall-runoff modeling. Our model is based on the empirical studies of Jencso et al. [2009; 2010], who found a strong correlation between the duration of shallow groundwater connectivity across hillslope, riparian, and stream zones and upslope accumulated area. We explored the relationship between catchment form and function by testing the extent to which streamflow generation could be predicted by a model based on the topographic form (distribution of landscape elements) of the catchment. We applied the model to the Stringer Creek catchment of the Tenderfoot Creek Experimental Forest, located in Montana, USA. Detailed field observations collected by Jencso et al. [2009] were used to inform the underpinnings of the model and to corroborate internal consistency of the model simulations. The model demonstrated good agreement between the observed and predicted streamflow and connectivity duration curves. The ability of this model to simulate internal dynamics without conditioning the parameters on these data suggests that it has the potential to be more confidently extrapolated to other shallow, topographically driven catchments than hydrologic models that fail to consistently reproduce internal variables.

Description: Knowledge of hydrological model complexity can aid selection of an optimal prediction model out of a set of available models. Optimal model selection is formalized as selection of the least complex model out of a subset of models that have lower empirical risk. This may be considered equivalent to minimizing an upper bound on prediction error, defined here as the mathematical expectation of empirical risk. In this paper we derive an upper bound that is free from assumptions on data and underlying process distribution as well as on independence of model predictions over time. We demonstrate that hydrological model complexity, as defined in the presented theoretical framework, plays an important role in determining the upper bound. The model complexity also acts as a stabilizer to a hydrological model selection problem if it is deemed ill-posed. We provide an algorithm for computing complexity of any arbitrary hydrological model. We also demonstrate that hydrological model complexity has a geometric interpretation as the size of model output space. The presented theory is applied to quantify complexities of two hydrological model structures: SAC-SMA and SIXPAR. It detects that SAC-SMA is indeed more complex than SIXPAR. We also develop an algorithm to estimate the upper bound on prediction error, which is applied on 5 different rainfall-runoff model structures that vary in complexity. We show that a model selection problem is stabilized by regularizing it with model complexity. Complexity regularized model selection yields models that are robust in predicting future but yet unseen data.

Description: The temporal dynamics and spatial distribution of the concentrations of dissolved gases (He, Ar, Kr, N 2 , O 2 and CO 2 ) in an infiltrating groundwater system fed by the peri-alpine River Thur (Switzerland) were analysed before, during and after a single, well-defined flood event. The analysis was based on measurements taken in five different groundwater observation wells that were located approximately 10 m apart and tapped the same groundwater body, but were situated in three different riparian zones. The input of O 2 into the groundwater as a result of the formation of excess air was found to be of the same order of magnitude as that resulting from the advection of river water, although the amount of excess air formed and the amount of O 2 delivered varied significantly among the riparian zones. The results suggest that the input of O 2 into groundwater as a result of excess air formation is controlled not only by the hydraulic conditions prevailing in the river and the groundwater, but also by the thickness of the confining bed at the top of the aquifer. The sandy gravel aquifer itself is too coarse to trap a significant amount of air during the water level rise. The clay layer confining the aquifer, however, acts as a barrier hindering the escape of air from the subsoil to the surface, and hence is likely to be a key factor controlling the trapping and dissolution of air in groundwater.

Description: Estimation of parameter values in hydrological models has gradually moved from subjective, trial-and-error methods into objective estimation methods. Translation of nature's complexity to bit operations is an uncertain process as a result of data errors, epistemic gaps, computational deficiencies, and other limitations, and relies on calibration to fit model output to observed data. The robustness of the calibrated parameter values to these types of uncertainties is therefore an important concern. In this study, we investigated how the hydrological robustness of the model-parameter values varied within the geometric structure of the behavioral (well-performing) parameter space with a depth function based on α shapes and an in-depth posterior performance analysis of the simulations in relation to the observed discharge uncertainty. The α shape depth is a non-convex measure that may provide an accurate and tight delimitation of the geometric structure of the behavioral space for both uni- and multimodal parameter-value distributions. WASMOD, a parsimonious rainfall-runoff model, was applied to six Honduran and one UK catchment, with differing data quality and hydrological characteristics. Model evaluation was done with two performance measures, the Nash-Sutcliffe efficiency and one based on flow-duration curves. Deep parameter vectors were in general found to be more hydrologically robust than shallow ones in the analyses we performed; model-performance values increased with depth, deviations to the observed data for the high-flow aspects of the hydrograph generally decreased with increasing depth, deep parameter vectors generally transferred in time with maintained high performance values, and the model had a low sensitivity to small changes in the parameter values. The tight delimitation of the behavioral space provided by the α shapes depth function showed a potential to improve the efficiency of calibration techniques that require further exploration. For computational reasons only a three-parameter model could be used, which limited the applicability of this depth measure and the conclusions drawn in this paper, especially concerning hydrological robustness at low flows.

Description: The cosmic-ray neutron probe measures soil moisture over tens of hectares, thus averaging spatially variable soil moisture fields. A previous paper described how variable soil moisture profiles affect the integrated cosmic-ray neutron signal from which depth-average soil moisture is computed. Here, we investigate the effect of horizontal heterogeneity on the relationship between neutron counts and average soil moisture. Observations from a distributed sensor network at a site in southern Arizona indicate that the horizontal component of the total variance of the soil moisture field is less variably in time than the vertical component. Using results from neutron particle transport simulations we show that 1-D binary distributions of soil moisture may affect both the mean and variance of neutron counts of a cosmic-ray neutron detector placed arbitrarily in a soil moisture field, potentially giving rise to an underestimate of the footprint average soil moisture. Similar simulations that used 1 and 2-D Gaussian soil moisture fields indicate consistent mean and variances of a randomly placed detector if the correlation length scales are short (〈˜30 m) and/or the soil moisture field variance is small (〈0.032 m 6 m -6 ). Taken together, these soil moisture observations and neutron transport simulations show that horizontal heterogeneity likely has a small effect on the relationship between mean neutron counts and average soil moisture for soils under natural conditions.

Description: Observations have been obtained within an intense (precipitation rates 〉 50 mm hour -1 ) narrow cold-frontal rainband (NCFR) embedded within a broader region of stratiform precipitation. In-situ data were obtained from an aircraft which flew near a steerable dual-polarisation Doppler radar. The observations were obtained to characterise the microphysical properties of cold frontal clouds, with an emphasis on ice and precipitation formation and development. Primary ice nucleation near cloud top (−55°C) appeared to be enhanced by convective features. However, ice multiplication led to the largest ice particle number concentrations being observed at relatively high temperatures (〉 −10°C). The multiplication process (most likely rime-splintering) occurs when stratiform precipitation interacts with supercooled water generated in the NCFR. Graupel was notably absent in the data obtained. Ice multiplication processes are known to have a strong impact in glaciating isolated convective clouds, but have rarely been studied within larger organised convective systems such as NCFRs. Secondary ice particles will impact on precipitation formation and cloud dynamics due to their relatively small size and high number density. Further modelling studies are required to quantify the effects of rime splintering on precipitation and dynamics in frontal rainbands. Available parameterizations used to diagnose the particle size distributions do not account for the influence of ice multiplication. This deficiency in parameterizations is likely to be important in some cases for modelling the evolution of cloud systems and the precipitation formation. Ice multiplication has significant impact on artefact removal from in-situ particle imaging probes.

Description: This paper proposes a selective ensemble mean technique for tropical cyclone (TC) track forecast based on the errors of ensemble prediction system (EPS) members at short lead times (SLTs, 12 h in this study). The means (SEAV) and weighted means (SEWE) of selected EPS members are applied to EPS products from the European Centre for Medium-Range Weather Forecasts (ECMWF), Japan Meteorological Agency (JMA), National Centers for Environmental Prediction (NCEP), and China Meteorological Administration for 35 TCs in the Western North Pacific in 2010 and 2011. Verification results show that SEAV behaves better than SEWE, with a skill of 5% to 30% over relevant ensemble means of EPS within 72 h. The SEAV method is the most effective for the JMA EPS, with a skill of 10% even at 96 h. SEAV predictions are compared with the high-resolution deterministic model predictions of ECMWF and several official forecasts, with special consideration given to the time delay associated with numerical model products in operation. The SEAV for the ECMWF EPS can overcome the high-resolution ECMWF deterministic model at 24 h. Case analyses and sensitivity tests on the error thresholds of member selection and SLT lead times are also presented in this paper.

Description: The predictive quality of an ensemble model of cirrus ice crystals to model passive and active measurements of ice cloud, from the ultraviolet (UV) to the microwave, is tested. The ensemble model predicts ice mass ∝ D 2 (m-D), where D is the maximum dimension of the ice crystal, and m is the mass. This predicted m-D relationship is applied to a moment estimation parametrization of the particle size distribution (PSD), to estimate the PSD shape, given ice water content (IWC) and in-cloud temperature. The same microphysics is applied across the electromagnetic spectrum to model UV, infrared, microwave and radar observations. The short-wave measurements consist of airborne UV backscatter lidar estimates of the volume extinction coefficient, total solar optical depth, and space-based multi-directional spherical albedo measurements, at 0.865 µm, between the scattering angles 85 o and 125 o . The airborne long-wave measurements consist of high-resolution interferometer upwelling brightness temperatures, obtained between the wavelengths of about 3.45 µm and 4.1 µm, and 8.0 µm to 12.0 µm. The low frequency measurements consist of ground-based Chilbolton 35 GHz radar reflectivity measurements and space-based upwelling 190 GHz brightness temperature measurements. The predictive quality of the ensemble model is demonstrated to be generally within the experimental uncertainty of the lidar backscatter estimates of the volume extinction coefficient and total solar optical depth. The ensemble model prediction of the high-resolution brightness temperature measurements is generally within ±2 K and ±1K, at solar and infrared wavelengths, respectively. The 35 GHz radar reflectivity and 190 GHz brightness temperatures are generally simulated to within ±2 dBZ e , and ±2 K, respectively. The directional spherical albedo observations suggest that the scattering phase function of the most randomized ensemble model gives the best fit to the measurements (generally within ±3%). This paper demonstrates that the ensemble model, assuming the same microphysics , is physically consistent across the electromagnetic spectrum.

Description: This paper investigates two schemes that perturb sea-surface temperatures (SSTs) and soil moisture content (SMC) in the Met Office Global and Regional Ensemble Prediction System (MOGREPS), to address a known deficiency of a lack of ensemble spread near the surface. Results from a two-month long trial during the northern hemisphere summer show positive benefits from these schemes. These include a decrease in the spread deficit of surface temperature and improved probabilistic verification scores. SST perturbations exhibit a stronger impact than SMC perturbations, but when combined the increased spread from the two schemes is cumulative. A regional ensemble system driven by the global ensemble members largely reflects the same changes seen in the global ensemble but cycling fields, like SMC, between successive regional forecasts does show some benefit.

Description: Widespread disturbance within forested catchments typically increases runoff. However, following widespread fire in 1939 throughout south-east Australia Kuczera [1987] reported persistent reductions in runoff that were attributed to increased evapotranspiration from regenerating ‘ash’ forests. Kuczera projected ongoing reductions of water yield for ~150 years. In 2003 widespread fire in the headwaters of the Murray-Darling Basin (MDB) again stimulated extensive regeneration of ash forests, raising the prospect of subsequent water yield reductions. To understand the potential impact of the 2003 bushfires we re-evaluated yield reductions from three of the catchments originally studied by Kuczera using the same calibration period. We also used an expanded pre-fire calibration period (1908-1938) based on data not originally available to Kuczera. The trend of post-fire water yield that we observed in 1939-affected catchments is qualitatively consistent with Kuczera's projections, but the quantitative details were, as expected, sensitive to the pre-fire calibration period used. We then used a simplified method to examine a further five ash-dominated catchments affected by the 2003 fires. We report relative reductions in mean annual stream flow in all five catchments and a statistically significant (α=0.05) post-fire reduction in one of five catchments. Post-fire yield reductions during the austral summer (October-April) were greater in relative magnitude in all five catchments and were statistically significant (α=0.05) in three of five catchments. We conclude that a post-bushfire Kuczera-type response may be widespread in regenerating ash forests. On that basis we anticipate post-fire yield reductions in ash forests elsewhere and conclude that further reductions in stream flow are likely in the MDB for at least another decade.

Description: Testosterone exerts important effects in the heart. Cardiomyocytes are target cells for androgens, and testosterone induces rapid effects via Ca 2+ release and protein kinase activation and long-term effects via cardiomyocyte differentiation and hypertrophy. Furthermore, it stimulates metabolic effects such as increasing glucose uptake in different tissues. Cardiomyocytes preferentially consume fatty acids for ATP production, but under particular circumstances, glucose uptake is increased to optimize energy production. We studied the effects of testosterone on glucose uptake in cardiomyocytes. We found that testosterone increased uptake of the fluorescent glucose analog 2-(N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl)amino)-2-deoxyglucose and [ 3 H]2-deoxyglucose, which was blocked by the glucose transporter 4 (GLUT4) inhibitor indinavir. Testosterone stimulation in the presence of cyproterone or albumin-bound testosterone induced glucose uptake, which suggests an effect that is independent of the intracellular androgen receptor. To determine the degree of GLUT4 cell surface exposure, cardiomyocytes were transfected with the plasmid GLUT4 myc -eGFP. Subsequently, testosterone increased GLUT4 myc- GFP exposure at the plasma membrane. Inhibition of Akt by the Akt-inhibitor-VIII had no effect. However, inhibition of Ca 2+ /calmodulin protein kinase (CaMKII) (KN-93 and autocamtide-2 related inhibitory peptide II) and AMP-activated protein kinase (AMPK) (compound C and siRNA for AMPK) prevented glucose uptake induced by testosterone. Moreover, GLUT4 myc- eGFP exposure at the cell surface caused by testosterone was also abolished after CaMKII and AMPK inhibition. These results suggest that testosterone increases GLUT4-dependent glucose uptake, which is mediated by CaMKII and AMPK in cultured cardiomyocytes. Glucose uptake could represent a mechanism by which testosterone increases energy production and protein synthesis in cardiomyocytes. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Although the role of Cbl-family proteins as key cellular regulators has been established, phenomena regulated in a Cbl-dependent fashion are multiple and the mechanisms mediating the effects of Cbl proteins are diverse. This finding makes it important to consider different phenomena affected by functions of Cbl proteins individually. Among effects of Cbl on various biological functions there are many cases of regulation of cellular phenomena related to cytoskeletal rearrangements, such as cell adhesion, motility and invasion. Some of these regulatory functions are mediated by adaptor-type interactions of Cbl, especially by Cbl-dependent modulation of phosphatidyl-inositol-3' kinase (PI3K), while others are caused by Cbl-dependent ubiquitylation of various cytoskeletal and regulatory proteins, identified and unidentified. The role of Cbl in regulation of cytoskeleton-dependent cellular functions is discussed in this review. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Two statistical downscaling models were developed for downscaling monthly GCM outputs to precipitation at a site in north-western Victoria, Australia. The first downscaling model was calibrated and validated with the NCEP/NCAR reanalysis outputs over the periods of 1950–1989 and 1990–2010 respectively. The projections of precipitation into future were produced by introducing the outputs of HadCM3, ECHAM5, GFDL2.0 and GFDL2.1, pertaining to A2 and B1 greenhouse gas emission scenarios to this downscaling model. In this model, the input data used in the development and future projections are not homogeneous, as they originate from two different sources. As a solution to this issue, the second downscaling model was developed and precipitation projections into future were produced with a homogeneous set of inputs. To produce a homogeneous set of inputs to this model, regression relationships were formulated between the NCEP/NCAR reanalysis outputs and the 20 th century climate experiment outputs corresponding to the variables used in the first downscaling model obtained from the ensemble consisted of HadCM3, ECHAM5 and GFDL2.0. The outputs of these relationships pertaining to the periods of 1950–1989 and 1990–1999, were used for the calibration and validation of this downscaling model respectively. Using the outputs of HadCM3, ECHAM5 and GFDL2.0 pertaining to A2 and B1 emission scenarios on these relationships, inputs for the second downscaling model pertaining to the period of 2000–2099 were generated. The first downscaling model with NCEP/NCAR reanalysis outputs, showed a high Nash-Sutcliffe Efficiency (NSE) of 0.75 over the period 1950–1999. When this downscaling model was run with the 20 th century climate experiment outputs of HadCM3, ECHAM5, GFDL2.0 and GFDL2.1, it exhibited limited performances over the period 1950–1999, which was indicated by relatively low NSEs of −0.62, -2.54, -0.40 and −0.48 respectively. The second downscaling model displayed a NSE of 0.35 over the period 1950–1999.

Description: The U.S. Navy's relocatable (RELO) ensemble prediction system is fully described and is examined in the Gulf of Mexico for 2010. After briefly describing the Ensemble Transfer (ET) method for the initial perturbation generation, we introduce a new time-deformation technique to generate the surface forcing perturbations from the atmospheric model fields. The extended forecast time (EFT) is introduced to quantify the advantages of the ensemble mean forecasts over a single deterministic forecast. The ensemble spread and its growth are investigated together with their relations with the ensemble forecast accuracy, reliability and skill. Similar to many other operational ensemble forecast systems at Numerical Weather Prediction (NWP) centers, the initial analysis error is underestimated by the technique used in the data-assimilation (DA) system. Growth of the ocean ensemble spread is also found to lag the growth of the ensemble mean error, a tendency attributed to insufficiently accounting for model-related uncertainties. As an initial step, we randomly perturb the two most important parameters in the ocean model mixing parameterizations, namely the Smagorinsky horizontal and Mellor-Yamada vertical mixing schemes. We examine three different parameter perturbation schemes based on both uniform and Gaussian distributions. It is found that all three schemes improve the ensemble spread to a certain extent, particularly the scheme with Gaussian distribution of perturbations imposed on both the horizontal and vertical mixing parameters. The findings in this paper indicate that the RELO ensemble forecast demonstrates superior accuracy and skill relative to a single deterministic forecast for all the variables and over all the domains considered in this paper. The ensemble spread provides valuable estimate of forecast uncertainty. However, the RELO uncertainty forecast capability could be further improved by accounting for more model-related uncertainties, for example, by the development of an error parameterization that imposes stochastic forcing at each model grid point.

Description: The gamma family of probability densities has recently been used to model raindrop size. The traditional approach of using method of moments to estimate the gamma distribution parameters, however, is known to be biased and can have substantial errors. A recently-developed approach combining moment information and a weighted least squares analysis generally produces substantially better results. Other procedures superior to the method of moments approach include maximum likelihood. In particular, maximum likelihood estimates have been shown to outperform method of moments estimators both in the case in which the full range of drop sizes are observed as well as the case in which small drop sizes fail to be observed because of the inability of disdrometers to record observations below a threshold. The foregoing comments on maximum likelihood concern the situation in which drop sizes are measured on a continuous scale. In this work we consider drop sizes from gamma distributions which are classified into broad size bins, as would be the case with data obtained from many disdrometers; this requires some modification of the maximum likelihood procedure. We do also allow for the possibility of drop sizes below a threshold or above another threshold not being observed. Maximum likelihood performance in this case is investigated through simulation of volume sampling from gamma distributions with known parameters. We compare the performance of the maximum likelihood estimates with those of method of moments (only a truncated-data version is viable) and the recently developed weighted least squares procedure, and also apply the three estimation procedures to some experimental data. Since the experimental data are surface data we indicate how drop fall velocity may be incorporated to obtain parameters for the volume distributions from the surface data.

Description: Despite the availability of several atmospheric reanalyses (e.g. ERA-Interim) there exists both considerable uncertainty in surface forcing fields for ice/ocean modelling and sensitivity to the choice of product used. Here we introduce a relatively high-resolution alternative forcing data set for ice-ocean models derived from the Canadian Meteorological Centre's (CMC) Global Deterministic Prediction System (GDPS). A set of daily 30 hr reforecasts is produced using the GDPS 33 km resolution model providing hourly atmospheric forcing fields for the period 2002–2011. The CMC GDPS Reforecasts (CGRF) are compared to ERA-Interim and several observational datasets to evaluate their suitability for forcing ocean models. In particular, the CGRF surface temperature, humidity and winds show equivalent biases to those found in ERA-interim. Moreover, the higher resolution of the CGRFs permit a more detailed representation of atmospheric structures and topographic steering resulting in finer-scale coastal features and wind stress curl. While the CGRF dataset is not a reanalysis and thus is expected to be less well constrained by available observations, its higher resolution and small bias make it an attractive alternative for forcing ice/ocean models.

Description: Drought triggers are patterns in hydro-climatic variables that herald upcoming droughts and form the basis for mitigation plans. This study develops a new method for identification of triggers for hydrologic droughts by examining the association between the various hydro-climatic variables and streamflows. Since numerous variables influence streamflows to varying degrees, Principal Component Analysis (PCA) is utilized for dimensionality reduction in predictor hydro-climatic variables. The joint dependence between the first two principal components, that explain over 98% of the variability in the predictor set, and streamflows is computed by a scale-free measure of association using asymmetric Archimedean copulas over two study watersheds in Indiana, USA, with unregulated streamflows. The M6 copula model is found to be suitable for the data and is utilized to find expected values and ranges of predictor hydro-climatic variables for different streamflow quantiles. This information is utilized to develop drought triggers for one-month lead time over the study areas. For the two study watersheds, soil moisture, precipitation and runoff are found to provide the fidelity to resolve amongst different drought classes. Combining the strengths of PCA for dimensionality reduction and copulas for building joint dependence allows the development of hydrologic drought triggers in an efficient manner.

Description: We present a unified asymptotic theory of rainfall extremes including annual maxima, excesses above high thresholds, and intensity-duration-frequency (IDF) curves that builds on previous findings and derive new non-asymptotic results. The analysis is based on stationary multifractal representations of rainfall and produces extensions of the familiar results from extreme value (EV) and extreme excess (EE) theories. The latter results apply to the T -yr maximum as and the excess above z as . By exploiting the scaling relationship among the distributions of rainfall intensity for different averaging durations d , the multifractal asymptotics include, in addition, results in the small-scale limits and with α 〉 0. In all cases the maximum distributions are of the generalized extreme value (GEV) type, but the index k depends on the limit considered. Multifractal models produce also asymptotic scaling results for the IDF curves. For the non-asymptotic case ( d and T finite), we obtain accurate approximations of the IDF curves and derive a semi-theoretical formula for the index k of the GEV model that best approximates the distribution of the annual maximum over a finite range of return-period intensities. The non-asymptotic analysis explains several observed deviations of rainfall extremes from the asymptotic predictions, such as the tendency of k to decrease as the averaging duration d increases and the tendency of the IDF curves to converge as d or the return period T increase.

Description: Remaining oil saturation established by waterflooding was measured in Indiana limestone in its original, water-wet state and under mixed-wet conditions established by adding organic acid to the oil phase. The porous plate technique was used to establish initial oil saturations ranging from S nwi = 0.23 to 0.93 under capillary-dominated conditions. For water-wet conditions, the residual oil saturation increased linearly with its initial saturation. In contrast, the remaining oil saturation under mixed-wet conditions, S nw , displayed three distinct regimes. First, S nw increased with its initial saturation up to S nwi = 0.58. Next, S nw decreased from S nwi = 0.58 to 0.76. Finally, S nw increased again as S nwi approached one. The non-monotonic dependence of S nw on S nwi at S nwi 〉 0.5 is well described by a concave-up quadratic function, and may be a salient feature of mixed-wet rocks.

Description: We present a general phenomenological formalism for the modeling of hydraulic head behaviour in naturally fractured aquifers. A non local in time version of the double porosity model is developed for Euclidean and fractal reservoirs. In the fractal case, time non-locality allows to find the geometric and topological factors responsible for subdiffusive behaviour in such heterogeneous environments. Opposite to other fractal models presented in the literature Chang and Yortsos [1990], our model include dead-ends-backbone interactions instead of matrix-fracture interactions with clear and well defined scaling exponents, thus giving a better characterization of the reservoir after such parameters are estimated. Applications to field tests are discussed. In particular, a distinctive short time head behaviour during well tests is found.

Description: The publicly available global discharge database is limited in spatial and temporal coverage. Although regional exceptions exist, the population of the database has declined over the past several years. As discharge is one of the most important parameters for modeling hydrological interactions, alternative measuring techniques must be sought. In the recent past, satellite altimetry has been investigated as an alternative for monitoring inland water level. In the present study, altimetry footprints in the vicinity of river gauging stations for the Amazon, Amur, Brahmaputra, Danube, Don, Mekong, Niger, Ob and Vistula rivers are analyzed for a functional relationship between the water level measurements from altimetry and discharge from the gauging stations. Such a functional relationship is conventionally established via a rating curve computed using simultaneous data. This study proposes a statistical approach based on quantile functions to infer this functional relation without the need for having synchronous datasets. The statistical approach provides the opportunity of extracting discharge values from altimetry data for rivers like the Mekong, Brahmaputra, Don and Vistula for which the discharge measurements at the selected gauges were made before the age of satellites. The algorithm is then validated over those rivers which do have discharge measurements available within periods of altimetry. Our validation shows that our algorithm is in the same quality range as the conventional approach. We are thus able to salvage pre-satellite altimetry discharge data and turn them into active use for the satellite altimetry time frame.

Description: While satellite based remote-sensing has provided hydrologists with valuable new datasets, integration of such datasets in operational modeling systems is usually not straightforward due to spatial or temporal resolution issues or because remote sensing does not directly measure the hydrological quantities of interest. This is the case for satellite based radar-altimetry. River level variations can be tracked using radar altimetry at a temporal resolution between 10 and 35 days, depending on the satellite, but hydrologists are typically interested in river flows rather than levels and require predictions at daily or even sub-daily temporal resolutions. One way to exploit satellite radar altimetry is therefore to combine the data with hydrological models in a data assimilation framework. In this study, radar altimetry data from 6 ENVISAT virtual stations were assimilated to a routing model of the main reach of the Brahmaputra River driven by the outputs of a calibrated rainfall runoff model. The Extended Kalman Filter was used to update the routed water volumes for the years 2008 to 2010. Model performance was improved with the Nash-Sutcliffe model efficiency for daily discharge increasing from 0.78 to 0.84. The method uses very little in situ data and is easily implemented as an add-on to hydrological models and it therefore has the potential for large scale application to improve hydrological predictions in many river basins.

Description: Management of water temperatures in the Columbia River Basin (Washington) is critical because water projects have substantially altered the habitat of Endangered Species Act (ESA) listed species, such as salmon, throughout the basin. This is most important in tributaries to the Columbia, such as the Methow River, where the spawning and rearing life stages of these cold water fishes occurs. Climate change projections generally predict increasing air temperatures across the western United States, with less confidence regarding shifts in precipitation. As air temperatures rise, we anticipate a corresponding increase in water temperatures, which may alter the timing and availability of habitat for fish reproduction and growth. To assess the impact of future climate change in the Methow River, we couple historical climate and future climate projections with a statistical modeling framework to predict daily mean stream temperatures. A K -nearest neighbor algorithm is also employed to: (i) adjust the climate projections for biases compared to the observed record and (ii) provide a reference for performing spatiotemporal disaggregation in future hydraulic modeling of stream habitat. The statistical models indicate the primary drivers of stream temperature are maximum and minimum air temperature and streamflow and show reasonable skill in predictability. When compared to the historical reference time period of 1916-2006, we conclude that increases in stream temperature are expected to occur at each subsequent time horizon representative of the year 2020, 2040, and 2080, with an increase of 0.8 ± 1.9 °C by the year 2080.

Description: Thermal remote sensing methods for mapping evapotranspiration (ET) exploit the physical interconnection that exists between land-surface temperature (LST) and evaporative cooling, employing principles of surface energy balance (SEB). Unfortunately, while many applications in water resource management require ET information at daily and field spatial scales, current satellite-based thermal sensors are characterized by either low spatial resolution and high repeatability or by moderate/high spatial resolution and low frequency. Here we introduce a novel approach to ET mapping that fuses characteristics of both classes of sensors to provide optimal spatiotemporal coverage. In this approach, coarse resolution daily ET maps generated with a SEB model using geostationary satellite data are spatially disaggregated using daily MODIS (MODerate resolution Imaging Spectroradiometer) 1-km and bi-weekly Landsat LST imagery sharpened to 30-m. These ET fields are then fused to obtain daily ET maps at 30-m spatial resolution. The accuracy of the fused Landsat-MODIS daily ET maps was evaluated over Iowa using observations collected at 8 flux towers sited in corn and soybean fields during the Soil Moisture Experiment of 2002 (SMEX02), as well as in comparison with a Landsat-only retrieval. A significant improvement in ET accuracy (reducing errors from 0.75 to 0.58 mm/d on average) was obtained by fusing MODIS and Landsat data in comparison with the Landsat-only case, with most notable improvements when a rainfall event occurred between two successive Landsat acquisitions. The improvements are further evident at the seasonal timescale, where a 3% error is obtained using Landsat-MODIS fusion vs. a 9% Landsat-only systematic underestimation.

Description: Widespread changes in gene expression underlie B cell development and activation, yet our knowledge of which chromatin-remodeling factors are essential is limited. Here, we demonstrate that the BRG1 catalytic subunit of SWI/SNF complexes was dispensable for murine B cell development but played an important, albeit selective, role during activation. Although BRG1 was dispensable for CD69 induction and differentiation into plasma cells based on the ability of mutant B cells to undergo hypertrophy and secrete IgM antibodies, it was required for robust cell proliferation in response to activation. Accordingly, BRG1 was required for only ∼100 genes to be expressed at normal levels in naïve B cells but 〉1,000 genes during their activation. BRG1 upregulated 5-fold more genes than it downregulated, and the toll-like receptor pathway and JAK/STAT cytokine-signaling pathways were particularly dependent on BRG1. The importance of BRG1 in B cell activation was underscored by the occurrence of opportunistic Pasteurella infections in conditionally mutant mice. B cell activation has long served as a model of inducible gene expression, and the results presented here identify BRG1 as a chromatin-remodeling factor that upregulates the transcriptome of B cells during their activation to promote rapid cell proliferation and to mount an effective immune response. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: Optical tweezers were used to scan individual Chronic Myelogenous Leukemia cells to determine if the cell death depends on the scanning conditions. Although increasing the scanning frequency or amplitude means greater force applied to the cells, their effects on cell death are not a simple increasing trend, as observed in the optical microscopy. Indeed, cell death sharply increased at particular screening frequencies and amplitudes, whereas other frequencies or amplitudes were less detrimental. These results suggest that cell damage was more sensitive to certain scanning conditions, rather than simply high applied forces. J. Cell. Physiol. © 2013 Wiley Periodicals, Inc.

Description: This study reports on two strategies for accelerating posterior inference of a highly parameterized and CPU-demanding groundwater flow model. Our method builds on previous stochastic collocation approaches [e.g., Marzouk and Xiu , 2009; Marzouk and Najm , 2009] and uses generalized polynomial chaos (gPC) theory to emulate the output of a large-scale groundwater flow model. The resulting surrogate model is CPU-efficient and serves to explore the posterior distribution at a much lower computational cost using two-stage MCMC simulation. The case study reported in this paper demonstrates a 2-5 times speed up in sampling efficiency.

Description: An earlier infiltration equation relied on curve fitting of infiltration data for the determination of one of the parameters, which limits its usefulness in practice. This handicap is removed here and the parameter is now evaluated by linking it directly to soil-water properties. The new predictions of infiltration using this evaluation are quite accurate. Positions and shapes of soil-water profiles are also examined in detail and found to be predicted analytically with great precision.

Description: Odontoblasts, which derive from dental papilla, are a type of terminally differentiated matrix-secreting cells. Previous studies have identified various transcription factors involved in the differentiation process of odontoblasts. We have recently found that Krüppel-like factor 4 ( Klf4 ) was expressed in the polarizing and elongating odontoblasts, but the function of Klf4 in the differentiation of odontoblasts is still unclear. We hypothesized Klf4 promoted the differentiation of odontoblasts by up-regulating some odontoblast-related genes. In this study, we found that the expression of Klf4 increased significantly during the odontoblastic differentiation of primary mouse dental papilla cells and the mouse dental papilla cell line-mDPC6T. Overexpression of Klf4 significantly up-regulated odontoblast-related genes, such as Dmp1 , Dspp , and Alp , and promoted the accumulation of mineral nodules. Knock-down of Klf4 down-regulated expression of Dmp1 , Dspp , and Alp , and inhibited mineral deposition. We applied in silico analysis and identified one target gene of Klf4 — Dmp1 . Based on further analysis of ChIP data, EMSA and dual luciferase activity assays, we confirmed that Klf4 was able to specifically bind to the Dmp1 promoter and transactivate its expression. Furthermore, forced expression of Dmp1 in the Klf4 knock-down mDPC6T cell line significantly recovered its odontoblastic differentiation ability. Our data confirmed our hypothesis that Klf4 promotes the differentiation of odontoblasts via the up-regulation of Dmp1 . © 2013 Wiley Periodicals, Inc.

Description: Nociception is the sensory mechanism used to detect cues that can harm an organism. The understanding of the neural networks and molecular controls of the reception of pain remains an ongoing challenge for biologists. While we have made significant progress in identifying a number of molecules and pathways that are involved in transduction of noxious stimuli, from the skin through the sensory receptor cell and from this to the spinal cord on into the central nervous system, we still lack a clear understanding of the perceptual processes, the responses to pain and the regulation of pain perception. Mice and rat animal models have been extensively used for nociception studies. However, the study of pain and noiception in these organisms can be rather laborious, costly and time consuming. Conversely the use of Drosophila and C. elegans may be affected by the large evolutionary distance between these animals and humans. We outline here the reasons why zebrafish presents a new and attractive model for studying pain reception and responses and the most interesting findings in the study of nociception that have been obtained using the zebrafish model. © 2013 Wiley Periodicals, Inc.

Description: Transforming growth factor (TGF)-β is a multifunctional cytokine acting during development, tissue homeostasis, regeneration processes and disease progression. Due to its pleiotropic effects, tight regulation of the induced signaling cascades is mandatory. Caveolin proteins regulate a specific endocytic pathway and modulate diverse signaling pathways and thus have been related to severe disorders, e.g. cancer and fibrosis. Caveolin affects TGF-β/-Smad and non-Smad signaling in many ways and thus can determine the cellular outcome upon TGF-β challenge. Reciprocal regulation of caveolin and TGF-β is also evident, ranging from gene expression to miRNA regulation. Finally, there is in vivo evidence that this crosstalk influences disease development and progression. This review gives an overview about the multifaceted relations of caveolin and TGF-β. © 2013 Wiley Periodicals, Inc.

Description: Fibre-optic Distributed Temperature Sensing (FO-DTS) has been frequently applied for analysing thermal patterns, including the identification of groundwater-surface water exchange fluxes across aquifer-river interfaces. However, the impacts of a) seasonal variability in signal strength (given by the difference between groundwater and surface water temperatures) and b) monitoring modes on the accuracy of FO-DTS surveys has not yet been determined. This study uses a well investigated field site as model system for quantifying the accuracy and uncertainty of FO-DTS surveys in dependency of seasonal signal variation and monitoring mode. The analysis of the relationship between seasonal variability in signal strength and diurnal oscillations in end-member temperatures at the study site revealed that winter conditions, with substantially lower diurnal temperature oscillations provide the highest temporal stability in signal strength. The choice of monitoring mode proved to have significant impact on the accuracy of FO-DTS surveys. The proposed two-way single-ended averaging of FO-DTS surveys had significant advantages compared to single-ended or double-ended surveys, with a higher accuracy in signal detection in particular for small-scale temperature variations. Since FO-DTS surveys in two-way single-ended averaging mode were better suited for detecting the full complexity of spatial temperature patterns for the investigated aquifer-river interface, we recommend its wider application in similarly complex systems with small-scale thermal patterns.

Description: The paper presents a semianalytical method to solve the multispecies reactive solute-transport equation coupled with a sequential first-order reaction network under spatially or temporally varying flow velocities and dispersion coefficients. This method employs the generalized integral transform technique (GITT) and general linear transformation method by Clement [2001] to transform the set of coupled multispecies reactive transport equations into a set of independent uncoupled equations and to solve these independent equations for spatially or temporally varying flow velocities and dispersion coefficients, as well for temporally varying inlet concentration. The proposed semianalytical solution is compared against previously published analytical solutions of Srinivasan and Clement [2008b] and van Genuchten [1985]. An example is used to show application of the solution to a hypothetical multilayered medium. The solution of proposed approach is compared also with a numerical solution using the 2DFATMIC. Three scenarios are illustrated to show the capabilities of the proposed semianalytical method to deal with aquifer heterogeneity and transient situations. We also show a practical implementation of the solution to an actual field, single-well push-pull test (PPT) example designed to obtain the concentration distribution of reactants consumed and products formed at the end of the injection phase.

Description: Transforming growth factor (TGF)-β1 regulates diverse cellular functions. Particularly, TGF-β1 induces monocyte migration to sites of injury or inflammation in early period, whereas TGF-β1 inhibits cell migration in late phase. In this study, we attempted to understand how TGF-β1 suppresses cell migration in late phase. We found that TGF-β1 of short exposure induces the production of chemokines, such as macrophage inflammatory protein (MIP)-1α, by Raw 264.7 cells. However, knock-down of small GTPase RhoA by sh-RhoA inhibited the production of MIP-1α and macrophage migration, suggesting that RhoA is essential for expression of this chemokine. An activator of Epac ( e xchange p roteins directly a ctivated by c AMP; a guanine nucleotide exchange factor of Rap1), 8CPT-2Me-cAMP which leads to Rap1 activation abrogated MIP-1α expression and macrophage migration. Indeed, GTP-RhoA and GTP-Rap1 levels were reciprocally regulated in a time-dependent manner following TGF-β1 stimulation. 8CPT-2Me-cAMP suppressed GTP-RhoA levels, whereas si-Rap1 augmented GTP-RhoA levels and cell migration. TGF-β1 produced cAMP in late period and si-RNAs of Epac1 (exchange protein directly activated by cAMP 1) and Epac2 reduced GTP-Rap1 levels leading to promotion of GTP-RhoA levels. Furthermore, si-RNA of ARAP3 (Rap-dependent RhoGAP) increased GTP-RhoA level and cell migration. Therefore, we propose the mechanism that prolonged TGF-β1 treatment produce cAMP, which activates sequentially Epac, Rap1 and ARAP3, resulting in suppression of RhoA, chemokine expression, and macrophage migration. Contrary to the general concept that Rap1 stimulates cell migration, we demonstrated in this study that Rap1 inhibits cell migration by suppression of RhoA activity in response to TGF-β1. © 2013 Wiley Periodicals, Inc.

Description: Polycyclic Aromatic Hydrocarbons (PAHs) are the products of incomplete combustion of organic materials, which are present in cigarette smoke, deep-fried food, and in natural crude oil. Since PAH-metabolites form DNA adducts and cause oxidative DNA damage, we asked if these environmental carcinogens could affect transforming potential of the human Polyomavirus JC oncoprotein, T-antigen (JCV T-antigen). We extracted DMSO soluble PAHs from Deepwater Horizon oil spill in the Gulf of Mexico (oil-PAHs), and detected several carcinogenic PAHs. The oil-PAHs were tested in exponentially growing cultures on normal mouse fibroblasts (R508), and in R508 stably expressing JCV T-antigen (R508/T). The oil-PAHs were cytotoxic only at relatively high doses (1:50–1:100 dilution), and at 1:500 dilution the growth and cell survival rates were practically unaffected. This non-toxic dose triggered however, a significant accumulation of reactive oxygen species (ROS), caused oxidative DNA damage and the formation of DNA double strand breaks (DSBs). Although oil-PAHs induced similar levels of DNA damage in R508 and R508/T cells, only T-antigen expressing cells demonstrated inhibition of high fidelity DNA repair by homologous recombination (HRR). In contrast, low-fidelity repair by non-homologous end joining (NHEJ) was unaffected. This potential mutagenic shift between DNA repair mechanisms was accompanied by a significant increase in clonal growth of R508/T cells chronically exposed to low doses of the oil-PAHs. Our results indicate for the first time carcinogenic synergy in which oil-PAHs trigger oxidative DNA damage and JCV T-antigen compromises DNA repair fidelity. © 2013 Wiley Periodicals, Inc.

Description: The intracellular pH is regulated by a delicate balance of ion distribution across the plasma membrane and the physico-chemical properties of intra- and extracellular components. We analysed the effects of glycosaminoglycans on the intracellular pH of fibroblasts by using the fluorescent pH indicator BCECF-AM. Addition of hyaluronan, hyaluronan oligosaccharides, chondroitin sulfate or heparin to the culture medium of fibroblasts caused intracellular acidification from pH 7.2 to pH 6.7 in a concentration dependent manner. High molecular weight hyaluronan acidified more than hyaluronan oligosaccharides at the same concentrations. Hyaluronidase treatment or inhibition of hyaluronan export with xanthohumol led to intracellular alkalization. These observations indicated that extracellular glycosaminoglycans participate in intracellular pH regulation. The mechanism was explained by Donnan effects and molecular crowding. © 2013 Wiley Periodicals, Inc.

Description: Purpose To test whether the use of a striatum weighted image may improve registration accuracy and diagnostic outcome in patients with parkinsonian syndromes (PS). Methods Weighted images were generated by increasing signal intensity of striatal voxels and used as intermediate dataset for co-registering the brain image onto template. Experimental validation was performed using an anthropomorphic striatal phantom. 123 I-FP-CIT SPECT binding ratios were manually determined in 67 PS subjects an and compared to those obtained using unsupervised standard (UWR) and weighted registered (WR) approach. Normalized cost function was used to evaluate the accuracy of phantom and subjects registered images to the template. Reproducibility between unsupervised and manual ratios was assessed by using intra-class correlation coefficient (ICC) and Bland and Altman analysis. Correlation coefficient was used to assess the dependence of semi-quantitative ratios on clinical findings. Results Weighted method improves accuracy of brain registration onto template as determined by cost function in phantom (0.86 ± 0.06vs.0.98 ± 0.02; Student's t test, P = 0.04) and in subject scans (0.69 ± 0.06vs.0.53 ± 0.06; Student's t test, P 〈 0.0001). Agreement between manual and unsupervised derived binding ratios as measured by ICC was significantly higher on WR as compared to UWR images (0.91vs.0.76). Motor UPDRS score was significantly correlated with manual and unsupervised derived binding potential. In phantom as well as in subjects studies, correlations were more significant using the WR method (BPm: R 2  = 0.36,p = 0.0001; BPwr: R 2  = 0.368, P  = 0.0001; BPuwr: R 2  = 0.300, P  = 0.0008). Conclusion Weighted registration improves accuracy of binding potential estimates and may be a promising approach to enhance the diagnostic outcome of SPECT imaging, correlation with disease severity, and for monitoring disease progression in parkinsonian syndromes. © 2013 Wiley Periodicals, Inc.

Description: The acquisition of reliable datasets representative of hydrological regimes and their variations is a critical concern for water resource assessment. For the subsurface, traditional approaches based on probe measurements, core analysis and well data can be laborious, expensive, and highly intrusive, while only yielding sparse data sets. For this study, an innovative field survey, merging relative microgravimetry, magnetic resonance soundings and hydrological measurements, was conducted to evaluate both surface and subsurface water storage variations in a semi-arid Sahelian area. The instrumental setup was implemented in the lower part of a typical hillslope feeding to a temporary pond. Weekly measurements were carried out using relative spring gravimeters during three months of the rainy season in 2009 over a 350 × 500 m 2 network of twelve microgravity stations. Gravity variations of small to medium amplitude (≤ 220 nm s 2 ) were measured with accuracies better than 50 nm s -2 , revealing significant variations of the water storage at small time (from one week up to three months) and space (from a couple of meters up to a few hundred meters) scales. Consistent spatial organization of the water storage variations were detected, suggesting high infiltration at the outlet of a small gully. The comparison with hydrological measurements and magnetic resonance soundings involved that most of the microgravity variations came from the heterogeneity in the vadose zone. The results highlights the potential of time lapse microgravity surveys for detecting intraseasonal water storage variations and providing rich space-time datasets for process investigation or hydrological model calibration/evaluation.

Description: The instantaneous turbulent flow fields over a smooth bed and a bed containing large-scale roughness elements are characterized by the presence of elongated low and high streamwise momentum regions, or streaks. If the bed contains large-scale roughness elements (e.g., dunes), the size of the streaks increases and is of the order of the size of these elements and the flow depth. The present large eddy simulation (LES) study focuses on the case of developing flow within wide channels containing at the bottom a long array of spanwise-oriented sinusoidal 2D dunes (2a/h=0.1, λ/h=1, λ is the wavelength, 2a is the dune height, h is the mean flow depth) and, respectively, an array of 2D asymmetric dunes (2a/h=0.25, λ/h=3.75) of closer shape to the ones observed in natural streams. For the case of an incoming steady flow, the instantaneous flow fields, in the region where the flow transitions toward a fully-developed turbulent flow regime, contain arrays of highly-organized hairpin vortices whose dimensions are larger than the dune height. LES shows that for relatively shallow channels (e.g., channels with 2a/h=0.25), the large-scale hairpins and the streaks penetrate regularly up to the free surface, thus affecting mass transport and mixing over the whole water column. The paper explains the mechanism for the formation of these arrays of hairpin vortices and discusses changes between a case with asymmetric dunes that are characterized by a large value of λ/2a (=15) and a long upslope face, and a case with symmetric dunes for which λ/2a=10, the upslope face is relatively short and the rate of change of the bed curvature around the dune's crest is relatively small. The study discusses the main mechanisms through which large-scale hairpin form and how these mechanisms change between two dune geometries (sinusoidal vs. asymmetric dunes). We also show that hairpin eddies play the primary role in the formation of the streaks over the region containing dunes and we characterize the average dimensions of these streaks. The presence of resolved turbulence in the incoming flow reduces the streamwise distance needed for the streaks to develop over region containing dunes, but does not affect qualitatively the transition process toward the fully-developed flow regime, nor the spacing of the streaks in the fully-developed flow region.

Description: Parlange and Brutsaert [1987] derived a modified Boussinesq equation to account for the capillary effect on watertable dynamics in unconfined aquifers. Barry et al . [1996] solved this equation subject to a periodic boundary condition. Their solution shows significant influence of capillarity on watertable fluctuations, which evolve to finite-amplitude standing waves at the high frequency limit. Here, we propose a new governing equation for the watertable, which considers both horizontal and vertical flows in an unsaturated zone of finite thickness. An approximate analytical solution for periodic watertable fluctuations based on the new equation was derived. In agreement with previous results, the analytical solution shows that the unsaturated zone's storage capacity permits watertable fluctuations to propagate more readily than predicted by the Boussinesq equation. Furthermore, the new solution reveals a capping effect of the unsaturated zone on both the amplitude and phase of the watertable fluctuations as well as the watertable overheight. Due to the finite thickness of the unsaturated zone, the capillary effect on watertable fluctuations is modified mainly with reduced amplitude damping and phase shift.

Description: Impacts of rising sea level on the hydraulic balance between aquifers and the ocean threaten fresh water resources and aquatic ecosystems along many world coastlines. Understanding the vulnerability of groundwater systems to these changes and the primary factors that determine the magnitude of system response is critical to developing effective management and adaptation plans in coastal zones. We assessed the vulnerability of two types of groundwater systems, recharge-limited and topography-limited, to changes caused by sea-level rise over a range of hydrogeologic settings. Vulnerability in this context is defined by the rate and magnitude of salinization of coastal aquifers and changes in groundwater flow to the sea. Two-dimensional variable-density groundwater flow and salt transport simulations indicate that the response of recharge-limited systems is largely minimal, whereas topography-limited systems are vulnerable for various combinations of permeability, vertical anisotropy in permeability, and recharge. World coastlines were classified according to system type as a vulnerability indicator. Results indicate that ~70% of world coastlines may be topography-limited, though variability in hydrogeologic conditions strongly affects classification. Future recharge and sea-level rise scenarios have much less influence on the proportion of vulnerable coastlines than differences in permeability, distance to a hydraulic divide, and recharge, indicating that hydrogeologic properties and setting are more important factors to consider in determining vulnerability than uncertainties in the magnitude of sea-level rise and hydrologic shifts associated with future climate change.

Description: ABSTRACT Given the range of future uncertainty, there is increasing interest in developing and evaluating water management strategies that are robust to an uncertain future. As part of a process termed “decision scaling”, a climate response function was developed to isolate the impact of climate change on a water system in terms of hazards identified by stakeholders. The climate response function was then used to evaluate system performance over a wide range of climate conditions and to define robustness indicators. The robustness indicators, which measure system performance as a function of climate state, are conditioned on explicit assumptions about climate variable probability distributions. To illustrate this process, it is applied to the Upper Great Lakes to evaluate system robustness related to water management decisions and assess the impact of climate probability assumptions. The robustness indicators were used to identify decisions that outperformed other courses of action regardless of assumptions of future climate probabilities.