Quantitative Deconvolution Research Articles

Quantitative deconvolution of autocorrelations and cross correlations from two-dimensional lifetime decay maps in fluorescence lifetime correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a widely used method for measuring molecular diffusion and chemical kinetics. However, when a mixture of fluorescent species is taken into account, the conventional FCS method has limitations in extracting autocorrelations for different species and cross correlations between different species. Recently developed fluorescence lifetime correlation spectroscopy (FLCS) based on time-tagged time-resolved (TTTR) photon recording, which can record the global and micro arrival time for each individual photon, has been used to discriminate different species according to fluorescence lifetime. Here, based on two-dimensional lifetime decay maps constructed from TTTR photon stream, we have developed a quantitative lifetime-deconvolution FCS model (LDFCS) to extract precise chemical rates for chemical conversions in multi-species systems. The key point of LDFCS model is separation of different species according to the global distribution of fluorescence lifetime and then deconvolution of autocorrelations and cross-correlations from the two-dimensional lifetime decay maps constructed by the micro arrival times of photon pairs at each delay time.

Neodymium in the oceans: a global database, a regional comparison and implications for palaeoceanographic research.

The neodymium (Nd) isotopic composition of seawater has been used extensively to reconstruct ocean circulation on a variety of time scales. However, dissolved neodymium concentrations and isotopes do not always behave conservatively, and quantitative deconvolution of this non-conservative component can be used to detect trace metal inputs and isotopic exchange at ocean–sediment interfaces. In order to facilitate such comparisons for historical datasets, we here provide an extended global database for Nd isotopes and concentrations in the context of hydrography and nutrients. Since 2010, combined datasets for a large range of trace elements and isotopes are collected on international GEOTRACES section cruises, alongside classical nutrient and hydrography measurements. Here, we take a first step towards exploiting these datasets by comparing high-resolution Nd sections for the western and eastern North Atlantic in the context of hydrography, nutrients and aluminium (Al) concentrations. Evaluating those data in tracer–tracer space reveals that North Atlantic seawater Nd isotopes and concentrations generally follow the patterns of advection, as do Al concentrations. Deviations from water mass mixing are observed locally, associated with the addition or removal of trace metals in benthic nepheloid layers, exchange with ocean margins (i.e. boundary exchange) and/or exchange with particulate phases (i.e. reversible scavenging). We emphasize that the complexity of some of the new datasets cautions against a quantitative interpretation of individual palaeo Nd isotope records, and indicates the importance of spatial reconstructions for a more balanced approach to deciphering past ocean changes.This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’.

Oxygen Evolution Reaction Dynamics, Faradaic Charge Efficiency, and the Active Metal Redox States of Ni-Fe Oxide Water Splitting Electrocatalysts.

Mixed Ni-Fe oxides are attractive anode catalysts for efficient water splitting in solar fuels reactors. Because of conflicting past reports, the catalytically active metal redox state of the catalyst has remained under debate. Here, we report an in operando quantitative deconvolution of the charge injected into the nanostructured Ni-Fe oxyhydroxide OER catalysts or into reaction product molecules. To achieve this, we explore the oxygen evolution reaction dynamics and the individual faradaic charge efficiencies using operando differential electrochemical mass spectrometry (DEMS). We further use X-ray absorption spectroscopy (XAS) under OER conditions at the Ni and Fe K-edges of the electrocatalysts to evaluate oxidation states and local atomic structure motifs. DEMS and XAS data consistently reveal that up to 75% of the Ni centers increase their oxidation state from +2 to +3, while up to 25% arrive in the +4 state for the NiOOH catalyst under OER catalysis. The Fe centers consistently remain in the +3 state, regardless of potential and composition. For mixed Ni100-xFex catalysts, where x exceeds 9 atomic %, the faradaic efficiency of O2 sharply increases from ∼30% to 90%, suggesting that Ni atoms largely remain in the oxidation state +2 under catalytic conditions. To reconcile the apparent low level of oxidized Ni in mixed Ni-Fe catalysts, we hypothesize that a kinetic competition between the (i) metal oxidation process and the (ii) metal reduction step during O2 release may account for an insignificant accumulation of detectable high-valent metal states if the reaction rate of process (ii) outweighs that of (i). We conclude that a discussion of the superior catalytic OER activity of Ni-FeOOH electrocatalysts in terms of surface catalysis and redox-inactive metal sites likely represents an oversimplification that fails to capture essential aspects of the synergisms at highly active Ni-Fe sites.

Rare earth elements (REEs) in the tropical South Atlantic and quantitative deconvolution of their non-conservative behavior

This study presents new concentration measurements of dissolved rare earth elements (dREEs) along a full-depth east–west section across the tropical South Atlantic (∼12°S), and uses these data to investigate the oceanic cycling of the REEs. Enrichment of dREEs, associated with the redox cycling of Fe–Mn oxides, is observed in the oxygen minimum zone (OMZ) off the African shelf. For deeper-waters, a multi-parameter mixing model was developed to deconvolve the relative importance of physical transport (i.e., water mass mixing) from biogeochemical controls on the dREE distribution in the deep Atlantic. This approach enables chemical processes involved in REE cycling, not apparent from the measurements alone, to be distinguished and quantified. Results show that the measured dREE concentrations below ∼1000m are dominantly controlled (>75%) by preformed REE concentrations resulting from water mass mixing. This result indicates that the linear correlation between dREEs and dissolved Si observed in Atlantic deep waters results from the dominantly conservative behavior of these tracers, rather than from similar chemical processes influencing both dREEs and Si. Minor addition of dREEs (∼10% of dNd and ∼5% of dYb) is observed in the deep (>∼4000m) Brazil Basin, resulting from either remineralization of particles in-situ or along the flow path. Greater addition of dREEs (up to 25% for dNd and 20% for dYb) is found at ∼1500m and below ∼4000m in the Angola Basin near the African continental margin. Cerium anomalies suggest that different sources are responsible for these dREE addition plumes. The 1500m excess is most likely attributed to dREE release from Fe oxides, whereas the 4000m excess may be due to remineralization of calcite. Higher particulate fluxes and a more sluggish ocean circulation in the Angola Basin may explain why the dREE excesses in this basin are significantly higher than that observed in the Brazil Basin. Hydrothermal venting over the mid-Atlantic ridge acts as a regional net sink for light REEs, but has little influence on the net budget of heavy REEs. The combination of dense REE measurements with water mass deconvolution is shown to provide quantitative assessment of the relative roles of physical and biogeochemical processes in the oceanic cycling of REEs.

Catalytic Kinetics of Different Types of Surface Atoms on Shaped Pd Nanocrystals.

To understand the catalytic properties or roles of different types of surface atoms on metal nanocatalysts, the catalytic kinetics and dynamics of the different types of surface atoms (plane and edge) were revealed for the first time by a statistical quantitative deconvolution of observables obtained from traditional single-molecule nanocatalysis of Pd nanocrystals.It was found that the edge and plane of Pd nanocubes show similar size-dependent product formation processes, but inverse product dissociation processes. This work helps push the traditional single-molecule nanocatalysis method towards the sub-particle level.

Catalytic Kinetics of Different Types of Surface Atoms on Shaped Pd Nanocrystals

AbstractTo understand the catalytic properties or roles of different types of surface atoms on metal nanocatalysts, the catalytic kinetics and dynamics of the different types of surface atoms (plane and edge) were revealed for the first time by a statistical quantitative deconvolution of observables obtained from traditional single‐molecule nanocatalysis of Pd nanocrystals.It was found that the edge and plane of Pd nanocubes show similar size‐dependent product formation processes, but inverse product dissociation processes. This work helps push the traditional single‐molecule nanocatalysis method towards the sub‐particle level.

Local Linear Convergence of the ADMM/Douglas--Rachford Algorithms without Strong Convexity and Application to Statistical Imaging

We consider the problem of minimizing the sum of a convex function and a convex function composed with an injective linear mapping. For such problems, subject to a coercivity condition at fixed points of the corresponding Picard iteration, iterates of the alternating directions method of multipliers converge locally linearly to points from which the solution to the original problem can be computed. Our proof strategy uses duality and strong metric subregularity of the Douglas--Rachford fixed point mapping. Our analysis does not require strong convexity and yields error bounds to the set of model solutions. We show in particular that convex piecewise linear-quadratic functions naturally satisfy the requirements of the theory, guaranteeing eventual linear convergence of both the Douglas--Rachford algorithm and the alternating directions method of multipliers for this class of objectives under mild assumptions on the set of fixed points. We demonstrate this result on quantitative image deconvolution and deno...

Pooled Nucleic Acid Testing to Detect Antiretroviral Treatment Failure in HIV-Infected Patients in Mozambique.

In resource-limited settings, viral load monitoring of HIV-infected patients receiving antiretroviral therapy (ART) is not readily available because of high costs. Here, we compared the accuracy and costs of quantitative and qualitative pooled methods with standard viral load testing. Blood was collected prospectively from 461 patients receiving first-line ART in Mozambique who had not been evaluated previously with viral load testing. Screening for virologic failure of ART was performed quantitatively (ie, standard viral loads) and qualitatively [one and 2 rounds of polymerase chain reaction (PCR)]. Individual samples and minipools of 5 samples were then analyzed using both methods. The relative efficiency, accuracy, and costs of each method were calculated based on viral load thresholds for ART failure. Standard viral load testing of individual samples revealed a high rate of ART failure (19%-23%) across all virologic failure thresholds, and the majority of the patients (93%) with viral loads >1500 copies per milliliter had genotypic resistance to drugs in their ART regimen. Pooled quantitative screening and deconvolution testing had positive and negative predictive values exceeding 95% with cost savings of $11,250 compared with quantitative testing of each sample individually. Pooled qualitative screening and deconvolution testing had a higher cost savings of $30,147 for 1 PCR round and $25,535 for 2 PCR rounds compared with quantitative testing each sample individually. Both pooled qualitative PCR methods had positive and negative predictive values ≥90%, but the pooled 1-round PCR method had a sensitivity of 64%. Given the high rate of undiagnosed ART failure and drug resistance in this cohort, it is clear that virologic monitoring is urgently needed in this population. Here, we compared alternative methods of virologic monitoring with standard viral load testing of individual samples and found these methods to be cost saving and accurate. The test characteristics of each method will likely need to be considered for each local population before it is adopted.

Hydrolysis contributions in U(VI) spectroscopic speciation in acetate media

An analysis of 17 UV–Vis absorption spectra is presented, collected in a region of the pH/lg(acetate) diagram where the UO2CH3COO+ species prevails. The study was conducted (a) to test a previously determined single component of the UO2CH3COO+ species, (b) to assess the impact of (UO2)2(OH)22+ hydrolysis species into numerical peak deconvolution and (c) to study statistical properties of peak deconvolution procedures as a basis for measurement uncertainty assessment. Comparative speciation was performed for a two-species and three-species model, which resulted in different values of U(VI)-acetato formation quotients. The numerical analysis corroborated a detectability of (UO2)2(OH)22+ at relative amounts >1%. Lower relative contributions remain ambiguous due to the large Pearson correlation of U(VI) UV–Vis single component spectra. The results of the study show the quantitative deconvolution of U(VI) spectra into single components of UO22+, UO2(CH3COO)+ and (UO2)2(OH)22+ species. Theoretical U(VI) concentrations are reproduced within a few percent.

Direct spectroscopic speciation of the complexation of U(VI) in acetate solution.

As a result of systematic UV–Vis absorption spectroscopy studies in the U(VI) acetate system, the single component spectrum of [UO2CH3COO]+ with characteristic parameters was evaluated and applied in quantitative deconvolution of multicomponent spectra. Free acetate concentrations were obtained by the use of geochemical and probabilistic modelling codes. A total of 51 UV–Vis spectra were collected in a wide range of experimental conditions where coordination of U(VI) by acetate ion was indicated by characteristic variations in the spectra structure as compared to UO2 2+. Using chemometric data analysis, the resulting factor structure was evaluated to obtain a subset of 14 spectra holding only one coordinated species next to UO2 2+ (aq). The molar absorption coefficient for the U(VI) monoaceto species was estimated as ε 418 = 17.8 ± 1 dm3 mol−1 cm−1. Spectral deconvolution was used to obtain an estimate of the species concentrations which allowed to calculate for each sample the free acetate concentration, the total U(VI) amount and, eventually, to estimate the formation quotient lg β 11 = 2.8 ± 0.3 of UO2(CH3COO)+.Graphical

FlowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies

Herein we introduce flowFit, a Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The software, distributed as an R Bioconductor library, is based on a mathematical model that takes into account the height of each peak, the size and position of the parental population (labeled but not proliferating) and the estimated distance between the brightness of a cell and the brightness of its daughter (in which the dye is assumed to undergo a 2-fold dilution). Although the algorithm does not make any inference on cell types, rates of cell divisions or rates of cell death, it deconvolutes the actual collected data into a set of peaks, whereby each peak corresponds to a subpopulation of cells that have divided N times. We validated flowFit by retrospective analysis of published proliferation-tracking experiments and demonstrated that the algorithm predicts the same percentage of cells/generation either in samples with discernible peaks (in which the peaks are visible in the collected raw data) or in samples with non-discernible peaks (in which the peaks are fused together). To the best of our knowledge, flowFit represents the first open-source algorithm in its category and might be applied to numerous areas of cell biology in which quantitative deconvolution of tracking dye-based experiments is desired, including stem cell research. http://www.bioconductor.org/packages/devel/bioc/html/flowFit.html (Bioconductor software page). http://www.bioconductor.org/packages/2.13/bioc/vignettes/flowFit/inst/doc/HowTo-flowFit.pdf (package vignette). http://rpubs.com/tucano/flowFit (online tutorial).

Feasibility of quantitative perfusion CMR in patients with poor left ventricular function

Background First pass perfusion CMR is a well-validated technique for the detection of inducible myocardial ischaemia. However, limited data are available on the feasibility of first pass perfusion CMR and quantitative deconvolution analysis in the context of reduced LV function. The aim of this study was to assess effects of reduced LV function and LV dilatation on the characteristics of signal in the left ventricle (arterial input function, AIF) and in the myocardium (MSI), and to test the feasibility of quantitative perfusion analysis with Fermi deconvolution in this cohort of patients.

Quantitative Deconvolution of Human Thermal Infrared Emittance

The bioheat transfer models conventionally employed in etiology of human thermal infrared (TIR) emittance rely upon two assumptions; universal graybody emissivity and significant transmission of heat from subsurface tissue layers. In this work, a series of clinical and laboratory experiments were designed and carried out to conclusively evaluate the validity of the two assumptions. Results obtained from the objective analyses of TIR images of human facial and tibial regions demonstrated significant variations in spectral thermophysical properties at different anatomic locations on human body. The limited validity of the two assumptions signifies need for quantitative deconvolution of human TIR emittance in clinical, psychophysiological and critical applications. A novel approach to joint inversion of the bioheat transfer model is also introduced, levering the deterministic temperature-dependency of proton resonance frequency in low-lipid human soft tissue for characterizing the relationship between subsurface 3D tissue temperature profiles and corresponding TIR emittance.

Desulfurization of phosphorothioate oligonucleotides via the sulfur‐by‐oxygen replacement induced by the hydroxyl radical during negative electrospray ionization mass spectrometry

While the occurrence of desulfurization of phosphorothioate oligonucleotides in solution is well established, this study represents the first attempt to investigate the basis of the unexpected desulfurization via the net sulfur-by-oxygen (S-O) replacement during negative electrospray ionization (ESI). The current work, facilitated by quantitative mass deconvolution, demonstrates that considerable desulfurization can take place even under common negative ESI operating conditions. The extent of desulfurization is dependent on the molar phosphorothioate oligonucleotide-to-hydroxyl radical ratio, which is consistent with the corona discharge-induced origin of the hydroxyl radical leading to the S-O replacement. This hypothesis is supported by the fact that an increase of the high-performance liquid chromatography (HPLC) flow rate and the on-column concentration of a phosphorothioate oligonucleotide, as well as a decrease of the electrospray voltage reduce the degree of desulfurization. Comparative LC-tandem mass spectrometry (MS/MS) sequencing of a phosphorothioate oligonucleotide and its corresponding desulfurization product revealed evidence that the S-O replacement occurs at multiple phosphorothioate internucleotide linkage sites. In practice, the most convenient and effective strategy for minimizing this P = O artifact is to increase the LC flow rate and the on-column concentration of phosphorothioate oligonucleotides. Another approach to mitigate possible detrimental effects of the undesired desulfurization is to operate the ESI source at a very low electrospray voltage to diminish the corona discharge; however this will significantly compromise sensitivity when analyzing the low-level P = O impurities in phosphorothioate oligonucleotides.

Characterization of lithium borophosphate glass thin film electrolytes deposited by RF-magnetron sputtering for micro-batteries

Lithium ion conducting thin film electrolytes, Li2O-B2O3-P2O5 glass systems, were prepared with a wide range of chemical composition by co-sputtering method with multi-targets. The maximum ionic conductivity at room temperature was 1.22×10−6S/cm and the activation energy of this specimen was 0.54eV when enhanced by the mixed former effect and the high network modifier content. The increased ion conductivity of the films appeared to be associated with the formation of stable tetrahedral borate at high lithium concentration and this structural change facilitated faster ion migrations. The relationship between the glass structure and electrical performance of the mixed former glasses was investigated by the infrared spectra analysis of borate networks. The conductivity of the mixed former electrolytes increased gradually with increasing the RF power on Li2O target, and the maximum conductivity was obtained at 100W. The structural role of the network modifier in xLi2O-(1-x)(B2O3-P2O5) glasses was analyzed by the O1s spectra of X-ray Photoelectron Spectroscopy. A quantitative deconvolution of O1s spectra suggests that the increased conductivity with increasing lithium content is due to the formation of non-bridging oxygen.

CCR5-deficiency abrogates microglial activation and neuronal injury in HIV gp120-transgenic mice. (108.5)

Abstract AIDS patients and mice expressing the envelope glycoprotein gp120 of human immunodeficiency virus-1 (HIV-1) as transgene in the brain (gp120tg) share key features of viral neuropathology, such as a decrease of neurites and synapses, pronounced astrocytosis, and activated microglia and macrophages. Virus-associated or soluble HIV-1 gp120 interacts with CD4 and co-receptors CCR5 and CXCR4 leading to infection and/or cellular signaling. In the present study we crossed HIVgp120tg with CCR5KO mice. Microarray analysis of brain tissue from 6 month-old mice showed that HIV-1 gp120 affected the expression of about 800 genes in the presence of CCR5 but of only 51 genes in the absence of the co-receptor. Differentially expressed genes in CCR5 wild type (wt)/gp120tg mice compared to non-transgenic controls primarily belong in the nervous and immune systems. CCR5KO/gp120tg mice and non-transgenic CCR5KO controls differed mostly in expression of an astrocytic protein and factors of the innate immune system. Using quantitative fluorescence and deconvolution microscopy, we assessed neuronal injury and glial cell activation in brain sections. CCR5wt/gp120tg mice displayed a significant reduction in neuronal dendrites and pre-synaptic terminals besides microglial activation (increased Iba1 immuno-reactivity) in comparison to all of the three other genotypes. Thus, in our model CCR5 is required for HIV-1 gp120 to activate microglia and to cause damage to neuronal processes and synapses.

Biophotonic techniques for the study of malaria-infected red blood cells

Investigation of the homeostasis of red blood cells upon infection by Plasmodium falciparum poses complex experimental challenges. Changes in red cell shape, volume, protein, and ion balance are difficult to quantify. In this article, we review a wide range of optical techniques for quantitative measurements of critical homeostatic parameters in malaria-infected red blood cells. Fluorescence lifetime imaging and tomographic phase microscopy, quantitative deconvolution microscopy, and X-ray microanalysis, are used to measure haemoglobin concentration, cell volume, and ion contents. Atomic force microscopy is briefly reviewed in the context of these optical methodologies. We also describe how optical tweezers and optical stretchers can be usefully applied to empower basic malaria research to yield diagnostic information on cell compliance changes upon malaria infection. The combined application of these techniques sheds new light on the detailed mechanisms of malaria infection providing potential for new diagnostic or therapeutic approaches.

Depth-dependent local structures in thin films unraveled by grazing-incidence X-ray absorption spectroscopy

A method of using X-ray absorption spectroscopy together with resolved grazing-incidence geometry for depth profiling of atomic, electronic or chemical local structures in thin films is presented. The quantitative deconvolution of thickness-dependent spectral features is performed by fully considering both scattering and absorption formalisms. Surface oxidation and local structural depth profiles in nanometric FePt films are determined, exemplifying the application of the method.

Glomerular Protein Levels of Matrix Metalloproteinase-1 and Tissue Inhibitor of Metalloproteinase-1 Are Lower in Diabetic Subjects

Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) regulate extracellular matrix turnover throughout the body, including in renal glomeruli. We investigated protein levels of multiple MMPs (MMP-1, MMP-2, MMP-3, and MMP-9) and TIMP-1 in glomeruli and investigated whether disease phenotypes were associated with levels of these proteins. Renal cortex was collected from 100 adult autopsy subjects arrayed across 17 tissue microarrays. Immunohistochemical staining intensity for each MMP and TIMP-1 was determined using quantitative color deconvolution techniques. We observed significantly decreased glomerular MMP-1 and TIMP-1 staining in subjects with diabetes, hypertension, and an estimated glomerular filtration rate <30 ml/min/1.73 m(2) in univariate analyses. MMP-1 staining, but not TIMP-1 staining, was inversely correlated with increased glomerular fibrosis (r = -0.40). In multivariable analysis, diabetes was robustly associated with decreased staining intensity. This study indicates that in human subjects, the long-term sequelae of diseases such as diabetes that cause chronic renal failure result in decreased TIMP-1 and MMP-1 proteins in renal glomeruli. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

Water‐Dragging Ability of Aromatic Compounds in Octanol‐Water Systems: A Quantitative Approach by Spectra Deconvolution

AbstractThis is the first time that the water‐dragging ability of aromatic compounds partitioning in octanolwater biphasic systems is experimentally estimated by a quantitative spectral deconvolution model. The water‐dragging amount, Δ f value, measured by the quantitative model is based on the integrations of peak area increments of component peaks deconvoluted from O‐H modes of water and octanol molecule, recorded by a Fourier‐transformed infrared spectrophotometer. The stoichiometry hydration capacity, Δ fw, is derived from the corresponding Δ f values. Without any tedious experimental procedure or complicated modeling calculation, the Δ fw value is able to give the required solute‐water hydration information. Such an advantage can't be provided by other techniques applied in the field of water‐dragging ability investigation. Six aromatic compounds were used for the method validation. The Δ fw data obtained by this model are generally consistent with literature‐known values. The efficiency of this quantitative spectral deconvolution model can solve the state of aggregations and the structure of hydrates existing in the organic phase. Moreover, this deconvolution model also has the ability to be extended further to investigate the environmental and biological problems related to the organic chemical portioning in the aqueous and non‐aqueous phases.