349 research outputs found
Wavelet transform-based de-noising for two-photon imaging of synaptic Ca2+ transients.
PublishedJournal ArticleResearch Support, Non-U.S. Gov'tThis is an open access article.Postsynaptic Ca(2+) transients triggered by neurotransmission at excitatory synapses are a key signaling step for the induction of synaptic plasticity and are typically recorded in tissue slices using two-photon fluorescence imaging with Ca(2+)-sensitive dyes. The signals generated are small with very low peak signal/noise ratios (pSNRs) that make detailed analysis problematic. Here, we implement a wavelet-based de-noising algorithm (PURE-LET) to enhance signal/noise ratio for Ca(2+) fluorescence transients evoked by single synaptic events under physiological conditions. Using simulated Ca(2+) transients with defined noise levels, we analyzed the ability of the PURE-LET algorithm to retrieve the underlying signal. Fitting single Ca(2+) transients with an exponential rise and decay model revealed a distortion of τ(rise) but improved accuracy and reliability of τ(decay) and peak amplitude after PURE-LET de-noising compared to raw signals. The PURE-LET de-noising algorithm also provided a ∼30-dB gain in pSNR compared to ∼16-dB pSNR gain after an optimized binomial filter. The higher pSNR provided by PURE-LET de-noising increased discrimination accuracy between successes and failures of synaptic transmission as measured by the occurrence of synaptic Ca(2+) transients by ∼20% relative to an optimized binomial filter. Furthermore, in comparison to binomial filter, no optimization of PURE-LET de-noising was required for reducing arbitrary bias. In conclusion, the de-noising of fluorescent Ca(2+) transients using PURE-LET enhances detection and characterization of Ca(2+) responses at central excitatory synapses.C.M.T. and J.R.M. were supported by the Wellcome Trust, and K.T.-A. was supported by grant No. EP/I018638/1 from the Engineering and Physical Sciences Research Council
Numerical study of circulation on the inner Amazon Shelf
Author Posting. © Springer, 2008. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Ocean Dynamics 58 (2008): 187-198, doi:10.1007/s10236-008-0139-4.We studied the circulation on the coastal
domain of the Amazon Shelf by applying the hydrodynamic
module of the Estuarine and Coastal Ocean
Model and Sediment Transport - ECOMSED. The first
barotropic experiment aimed to explain the major bathymetric
effects on tides and those generated by anisotropy
in sediment distribution. We analyzed the continental
shelf response of barotropic tides under realistic bottom
stress parametrization (Cd), considering sediment granulometry
obtained from a faciologic map, where river
mud deposits and reworked sediments areas are well distinguished,
among others classes of sediments. Very low
Cd values were set in the fluid mud regions off the Amapa
coast (1.0 10-4 ), in contrast to values around 3:5 10-3
for coarser sediment regions off the Para coast. Three-dimensional
experiments represented the Amazon River
discharge and trade winds, combined to barotropic tide
influences and induced vertical mixing. The quasi-resonant
response of the Amazon Shelf to the M2 tide act on
the local hydrodynamics by increasing tidal admittance,
along with tidal forcing at the shelf break and extensive
fluid mud regions. Harmonic analysis of modeled
currents agreed well with analysis of the AMASSEDS
observational data set. Tidal-induced vertical shear provided
strong homogenization of threshold waters, which
are subject to a kind of hydraulic control due to the topographic
steepness. Ahead of the hydraulic jump, the
low-salinity plume is disconnected from the bottom and
acquires negative vorticity, turning southeastward. Tides
act as a generator mechanism and topography, via hydraulic
control, as a maintainer mechanism for the low-salinity
frontal zone positioning. Tidally induced southeastward
plume fate is overwhelmed by northwestward
trade winds so that, along with background circulation,
probably play the most important role on the plume fate
and variability over the Amazon Shelf
Increased insolation threshold for runaway greenhouse processes on Earth like planets
Because the solar luminosity increases over geological timescales, Earth
climate is expected to warm, increasing water evaporation which, in turn,
enhances the atmospheric greenhouse effect. Above a certain critical
insolation, this destabilizing greenhouse feedback can "runaway" until all the
oceans are evaporated. Through increases in stratospheric humidity, warming may
also cause oceans to escape to space before the runaway greenhouse occurs. The
critical insolation thresholds for these processes, however, remain uncertain
because they have so far been evaluated with unidimensional models that cannot
account for the dynamical and cloud feedback effects that are key stabilizing
features of Earth's climate. Here we use a 3D global climate model to show that
the threshold for the runaway greenhouse is about 375 W/m, significantly
higher than previously thought. Our model is specifically developed to quantify
the climate response of Earth-like planets to increased insolation in hot and
extremely moist atmospheres. In contrast with previous studies, we find that
clouds have a destabilizing feedback on the long term warming. However,
subsident, unsaturated regions created by the Hadley circulation have a
stabilizing effect that is strong enough to defer the runaway greenhouse limit
to higher insolation than inferred from 1D models. Furthermore, because of
wavelength-dependent radiative effects, the stratosphere remains cold and dry
enough to hamper atmospheric water escape, even at large fluxes. This has
strong implications for Venus early water history and extends the size of the
habitable zone around other stars.Comment: Published in Nature. Online publication date: December 12, 2013.
Accepted version before journal editing and with Supplementary Informatio
Energy- and flux-budget (EFB) turbulence closure model for the stably stratified flows. Part I: Steady-state, homogeneous regimes
We propose a new turbulence closure model based on the budget equations for
the key second moments: turbulent kinetic and potential energies: TKE and TPE
(comprising the turbulent total energy: TTE = TKE + TPE) and vertical turbulent
fluxes of momentum and buoyancy (proportional to potential temperature).
Besides the concept of TTE, we take into account the non-gradient correction to
the traditional buoyancy flux formulation. The proposed model grants the
existence of turbulence at any gradient Richardson number, Ri. Instead of its
critical value separating - as usually assumed - the turbulent and the laminar
regimes, it reveals a transition interval, 0.1< Ri <1, which separates two
regimes of essentially different nature but both turbulent: strong turbulence
at Ri<<1; and weak turbulence, capable of transporting momentum but much less
efficient in transporting heat, at Ri>1. Predictions from this model are
consistent with available data from atmospheric and lab experiments, direct
numerical simulation (DNS) and large-eddy simulation (LES).Comment: 40 pages, 6 figures, Boundary-layer Meteorology, resubmitted, revised
versio
Validating the turbulence parameterization schemes of a numerical model using eddy dissipation rate and turbulent kinetic energy measurements in terrain-disrupted airflow
Analysis of Vertical Turbulent Heat Flux Limit in Stable Conditions with a Local Equilibrium, Turbulence Closure Model
Metabolic alterations during the growth of tumour spheroids
Solid tumours undergo considerable alterations in their metabolism of nutrients in order to generate sufficient energy and biomass for sustained growth and proliferation. During growth, the tumour microenvironment exerts a number of influences (e.g. hypoxia and acidity) that affect cellular biology and the flux or utilisation of fuels including glucose. The tumour spheroid model was used to characterise the utilisation of glucose and describe alterations to the activity and expression of key glycolytic enzymes during the tissue growth curve. Glucose was avidly consumed and associated with the production of lactate and an acidified medium, confirming the reliance on glycolytic pathways and a diminution of oxidative phosphorylation. The expression levels and activities of hexokinase, phosphofructokinase-1, pyruvate kinase and lactate dehydrogenase in the glycolytic pathway were measured to assess glycolytic capacity. Similar measurements were made for glucose-6-phosphate dehydrogenase, the entry point and regulatory step of the pentose-phosphate pathway (PPP) and for cytosolic malate dehydrogenase, a key link to TCA cycle intermediates. The parameters for these key enzymes were shown to undergo considerable variation during the growth curve of tumour spheroids. In addition, they revealed that the dynamic alterations were influenced by both transcriptional and posttranslational mechanisms
Metabolic alterations during the growth of tumour spheroids
Solid tumours undergo considerable alterations in their metabolism of nutrients in order to generate sufficient energy and biomass for sustained growth and proliferation. During growth, the tumour microenvironment exerts a number of influences (e.g. hypoxia and acidity) that affect cellular biology and the flux or utilisation of fuels including glucose. The tumour spheroid model was used to characterise the utilisation of glucose and describe alterations to the activity and expression of key glycolytic enzymes during the tissue growth curve. Glucose was avidly consumed and associated with the production of lactate and an acidified medium, confirming the reliance on glycolytic pathways and a diminution of oxidative phosphorylation. The expression levels and activities of hexokinase, phosphofructokinase-1, pyruvate kinase and lactate dehydrogenase in the glycolytic pathway were measured to assess glycolytic capacity. Similar measurements were made for glucose-6-phosphate dehydrogenase, the entry point and regulatory step of the pentose-phosphate pathway (PPP) and for cytosolic malate dehydrogenase, a key link to TCA cycle intermediates. The parameters for these key enzymes were shown to undergo considerable variation during the growth curve of tumour spheroids. In addition, they revealed that the dynamic alterations were influenced by both transcriptional and posttranslational mechanisms
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