Nonlinear speech analysis algorithms mapped to a standard metric achieve clinically useful quantification of average Parkinson's disease symptom severity

The standard reference clinical score quantifying average Parkinson's disease (PD) symptom severity is the Unified Parkinson's Disease Rating Scale (UPDRS). At present, UPDRS is determined by the subjective clinical evaluation of the patient's ability to adequately cope with a range of tasks. In this study, we extend recent findings that UPDRS can be objectively assessed to clinically useful accuracy using simple, self-administered speech tests, without requiring the patient's physical presence in the clinic. We apply a wide range of known speech signal processing algorithms to a large database (approx. 6000 recordings from 42 PD patients, recruited to a six-month, multi-centre trial) and propose a number of novel, nonlinear signal processing algorithms which reveal pathological characteristics in PD more accurately than existing approaches. Robust feature selection algorithms select the optimal subset of these algorithms, which is fed into non-parametric regression and classification algorithms, mapping the signal processing algorithm outputs to UPDRS. We demonstrate rapid, accurate replication of the UPDRS assessment with clinically useful accuracy (about 2 UPDRS points difference from the clinicians' estimates, p < 0.001). This study supports the viability of frequent, remote, cost-effective, objective, accurate UPDRS telemonitoring based on self-administered speech tests. This technology could facilitate large-scale clinical trials into novel PD treatments.

The quantification of hazards at LPG installations

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A novel dried blood spot-LCMS method for the quantification of methotrexate polyglutamates as a potential marker for methotrexate use in children

Objective: Development and validation of a selective and sensitive LCMS method for the determination of methotrexate polyglutamates in dried blood spots (DBS). Methods: DBS samples [spiked or patient samples] were prepared by applying blood to Guthrie cards which was then dried at room temperature. The method utilised 6-mm disks punched from the DBS samples (equivalent to approximately 12 μl of whole blood). The simple treatment procedure was based on protein precipitation using perchloric acid followed by solid phase extraction using MAX cartridges. The extracted sample was chromatographed using a reversed phase system involving an Atlantis T3-C18 column (3 μm, 2.1x150 mm) preceded by Atlantis guard column of matching chemistry. Analytes were subjected to LCMS analysis using positive electrospray ionization. Key Results: The method was linear over the range 5-400 nmol/L. The limits of detection and quantification were 1.6 and 5 nmol/L for individual polyglutamates and 1.5 and 4.5 nmol/L for total polyglutamates, respectively. The method has been applied successfully to the determination of DBS finger-prick samples from 47 paediatric patients and results confirmed with concentrations measured in matched RBC samples using conventional HPLC-UV technique. Conclusions and Clinical Relevance: The methodology has a potential for application in a range of clinical studies (e.g. pharmacokinetic evaluations or medication adherence assessment) since it is minimally invasive and easy to perform, potentially allowing parents to take blood samples at home. The feasibility of using DBS sampling can be of major value for future clinical trials or clinical care in paediatric rheumatology. © 2014 Hawwa et al.

Development of an enantiomer selective microsampling assay for the quantification of ketorolac suitable for paediatric pharmacokinetic studies

Background: Ketorolac, a potent nonsteroidal anti-inflammatory drug used for pain control in children, exists as a racemate of inactive R (+) and active S (-) enantiomers. Aim: To develop a microsampling assay for the enantioselective analysis of ketorolac in children. Methods: Ketorolac enantiomers were extracted from 50 µl of plasma by liquid–liquid extraction and separated on a ChiralPak AD-RH. Detection was by a TSQ quantum triple quadrupole mass spectrometer with an electrospray ionisation source operating in a positive ion mode. Five children (age 13.8 (1.6) years, weight 52.7 (7.2) kg), were administered intravenous ketorolac 0.5 mg/kg (maximum 10 mg) and blood samples were taken at 0, 0.25, 0.5, 1, 2, 4, 6, 8 and 12 h post administration. CL, VD and t1/2 were calculated based on non-compartmental methods. Results: The standard curves for R (+) and S (-) ketorolac were linear in the range 0–2000 ng/ml. The LLOQs of the method were 0.15 ng on column and 0.31 ng on column for R (+) and S (-) ketorolac, respectively. The median (range) VD and CL of R (+) and S (-) ketorolac were 0.12 l/kg (0.07–0.17), 0.017 l/h/kg (0.12–0.29) and 0.17 (0.09–0.31) l/kg, 0.049 (0.02–0.1) l/h/kg, p = 0.043), respectively. The median (range) elimination half-life (t1/2) of the R (+) and S (-) ketorolac was 5.0 h (2.5–5.8) and 3.1 h (1.8–4.4), p = 0.043), respectively. Conclusion: The development of a simple, rapid and reliable ketorolac assay suitable for paediatric PK studies is reported. Copyright © 2013 John Wiley & Sons, Ltd.

A simple bioanalytical method for the quantification of antiepileptic drugs in dried blood spots

An increasing number of publications on the dried blood spot (DBS) sampling approach for the quantification of drugs and metabolites have been spurred on by the inherent advantages of this sampling technique. In the present research, a selective and sensitive high-performance liquid chromatography method for the concurrent determination of multiple antiepileptic drugs (AEDs) [levetiracetam (LVT), lamotrigine (LTG), phenobarbital (PHB)], carbamazepine (CBZ) and its active metabolite carbamazepine-10,11 epoxide (CBZE)] in a single DBS has been developed and validated. Whole blood was spotted onto Guthrie cards and dried. Using a standard punch (6 mm diameter), a circular disc was punched from the card and extracted with methanol: acetonitrile (3:1, v/v) containing hexobarbital (Internal Standard) and sonicated prior to evaporation. The extract was then dissolved in water and vortex mixed before undergoing solid phase extraction using HLB cartridges. Chromatographic separation of the AEDs was achieved using Waters XBridge™ C18 column with a gradient system. The developed method was linear over the concentration ranges studied with r ≥ 0.995 for all compounds. The lower limits of quantification (LLOQs) were 2, 1, 2, 0.5 and 1 μg/mL for LVT, LTG, PHB, CBZE and CBZ, respectively. Accuracy (%RE) and precision (%CV) values for within and between day were <20% at the LLOQs and <15% at all other concentrations tested. This method was successfully applied to the analysis of the AEDs in DBS samples taken from children with epilepsy for the assessment of their adherence to prescribed treatments.

Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells

Introduction: Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell. Methods: In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis. Findings: We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles. Conclusions: The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein. © 2014 Jiwaji et al.

Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy

Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy. (Graph Presented).

Detection and quantification of protein oxidation in sarcopenic models:a mass spectrometry study

Oxidised biomolecules in aged tissue could potentially be used as biomarkers for age-related diseases; however, it is still unclear whether they causatively contribute to ageing or are consequences of the ageing process. To assess the potential of using protein oxidation as markers of ageing, mass spectrometry (MS) was employed for the identification and quantification of oxidative modifications in obese (ob/ob) mice. Lean muscle mass and strength is reduced in obesity, representing a sarcopenic model in which the levels of oxidation can be evaluated for different muscular systems including calcium homeostasis, metabolism and contractility. Several oxidised residues were identified by tandem MS (MS/MS) in both muscle homogenate and isolated sarcoplasmic reticulum (SR), an organelle that regulates intracellular calcium levels in muscle. These modifications include oxidation of methionine, cysteine, tyrosine, and tryptophan in several proteins such as sarcoplasmic reticulum calcium ATPase (SERCA), glycogen phosphorylase, and myosin. Once modifications had been identified, multiple reaction monitoring MS (MRM) was used to quantify the percentage modification of oxidised residues within the samples. Preliminary data suggests proteins in ob/ob mice are more oxidised than the controls. For example SERCA, which constitutes 60-70% of the SR, had approximately a 2-fold increase in cysteine trioxidation of Cys561 in the obese model when compared to the control. Other obese muscle proteins have also shown a similar increase in oxidation for various residues. Further analysis with complex protein mixtures will determine the potential diagnostic use of MRM experiments for analysing protein oxidation in small biological samples such as muscle needle biopsies.

QuantUn:quantification of uncertainty for the reassessment of requirements

Self-adaptive systems (SASs) should be able to adapt to new environmental contexts dynamically. The uncertainty that demands this runtime self-adaptive capability makes it hard to formulate, validate and manage their requirements. QuantUn is part of our longer-term vision of requirements reflection, that is, the ability of a system to dynamically observe and reason about its own requirements. QuantUn's contribution to the achievement of this vision is the development of novel techniques to explicitly quantify uncertainty to support dynamic re-assessment of requirements and therefore improve decision-making for self-adaption. This short paper discusses the research gap we want to fill, present partial results and also the plan we propose to fill the gap.

Quantification of white matter abnormalities in neurodegenerative disease

Degeneration of white matter fibre tracts occurs in several neurodegenerative disorders and results in various histological abnormalities including loss of axons, vacuolation, gliosis, axonal varicosities and spheroids, corpora amylacea, extracellular protein deposits, and glial inclusions (GI). This chapter describes quantitative studies that have been carried out on white matter pathology in a variety of neurodegenerative disease. First, in Alzheimer’s disease (AD), axonal loss quantified in histological sections stained with toluidine blue, occurs in several white matter fibre tracts including the optic nerve, olfactory tract, and corpus callosum. Second, in Creutzfeldt-Jakob disease (CJD), sections of cerebral cortex stained with haematoxylin and eosin (H/E) or immunolabelled with antibodies against the disease form of prion protein (PrPsc), reveal extensive vacuolation, gliosis of white matter, and deposition of PrPsc deposits. Third, GI immunolabelled with antibodies against various pathological proteins including tau, -synuclein, TDP-43, and FUS, have been recorded in white matter of a number of disorders including frontotemporal lobar degeneration (FTLD), progressive supranuclear palsy (PSP), multiple system atrophy (MSA), and neuronal intermediate filament inclusion disease (NIFID). Axonal varicosities have also been observed in NIFID. There are two important questions regarding white matter pathology that need further investigation: (1) what is the relative importance of white and gray matter pathologies in different disorders and (2) do white matter abnormalities precede or are they the consequence of gray matter pathology?

Airborne laser quantification of Florida shoreline and beach volume change caused by hurricanes

This dissertation combines three separate studies that measure coastal change using airborne laser data. The initial study develops a method for measuring subaerial and subaqueous volume change incrementally alongshore, and compares those measurements to shoreline change in order to quantify their relationship in Palm Beach County, Florida. A poor correlation (R2 = 0.39) was found between shoreline and volume change before the hurricane season in the northern section of Palm Beach County because of beach nourishment and inlet dynamics. However, a relatively high R2 value of 0.78 in the southern section of Palm Beach County was found due to little disturbance from tidal inlets and coastal engineering projects. The shoreline and volume change caused by the 2004 hurricane season was poorly correlated with R 2 values of 0.02 and 0.42 for the north and south sections, respectively. The second study uses airborne laser data to investigate if there is a significant relationship between shoreline migration before and after Hurricane Ivan near Panama City, Florida. In addition, the relationship between shoreline change and subaerial volume was quantified and a new method for quantifying subaqueous sediment change was developed. No significant spatial relationship was found between shoreline migration before and after the hurricane. Utilization of a single coefficient to represent all relationships between shoreline and subaerial volume change was found to be problematic due to the spatial variability in the linear relationship. Differences in bathymetric data show only a small portion of sediment was transported beyond the active zone and most sediment remained within the active zone despite the occurrence of a hurricane. The third study uses airborne laser bathymetry to measure the offshore limit of change, and compares that location with calculated depth of closures and subaqueous geomorphology. There appears to be strong geologic control of the depth of closure in Broward and Miami-Dade Counties. North of Hillsboro Inlet, hydrodynamics control the geomorphology which in turn indicates the location of the depth of closure.

Plasma and cold sprayed aluminum carbon nanotube composites: Quantification of nanotube distribution and multi-scale mechanical properties

Carbon nanotubes (CNT) could serve as potential reinforcement for metal matrix composites for improved mechanical properties. However dispersion of carbon nanotubes (CNT) in the matrix has been a longstanding problem, since they tend to form clusters to minimize their surface area. The aim of this study was to use plasma and cold spraying techniques to synthesize CNT reinforced aluminum composite with improved dispersion and to quantify the degree of CNT dispersion as it influences the mechanical properties. Novel method of spray drying was used to disperse CNTs in Al-12 wt.% Si prealloyed powder, which was used as feedstock for plasma and cold spraying. A new method for quantification of CNT distribution was developed. Two parameters for CNT dispersion quantification, namely Dispersion parameter (DP) and Clustering Parameter (CP) have been proposed based on the image analysis and distance between the centers of CNTs. Nanomechanical properties were correlated with the dispersion of CNTs in the microstructure. Coating microstructure evolution has been discussed in terms of splat formation, deformation and damage of CNTs and CNT/matrix interface. Effect of Si and CNT content on the reaction at CNT/matrix interface was thermodynamically and kinetically studied. A pseudo phase diagram was computed which predicts the interfacial carbide for reaction between CNT and Al-Si alloy at processing temperature. Kinetic aspects showed that Al4C3 forms with Al-12 wt.% Si alloy while SiC forms with Al-23wt.% Si alloy. Mechanical properties at nano, micro and macro-scale were evaluated using nanoindentation and nanoscratch, microindentation and bulk tensile testing respectively. Nano and micro-scale mechanical properties (elastic modulus, hardness and yield strength) displayed improvement whereas macro-scale mechanical properties were poor. The inversion of the mechanical properties at different scale length was attributed to the porosity, CNT clustering, CNT-splat adhesion and Al 4C3 formation at the CNT/matrix interface. The Dispersion parameter (DP) was more sensitive than Clustering parameter (CP) in measuring degree of CNT distribution in the matrix.

Positron emission tomography (PET) tumor segmentation and quantification: Development of new algorithms

Tumor functional volume (FV) and its mean activity concentration (mAC) are the quantities derived from positron emission tomography (PET). These quantities are used for estimating radiation dose for a therapy, evaluating the progression of a disease and also use it as a prognostic indicator for predicting outcome. PET images have low resolution, high noise and affected by partial volume effect (PVE). Manually segmenting each tumor is very cumbersome and very hard to reproduce. To solve the above problem I developed an algorithm, called iterative deconvolution thresholding segmentation (IDTS) algorithm; the algorithm segment the tumor, measures the FV, correct for the PVE and calculates mAC. The algorithm corrects for the PVE without the need to estimate camera's point spread function (PSF); also does not require optimizing for a specific camera. My algorithm was tested in physical phantom studies, where hollow spheres (0.5-16 ml) were used to represent tumors with a homogeneous activity distribution. It was also tested on irregular shaped tumors with a heterogeneous activity profile which were acquired using physical and simulated phantom. The physical phantom studies were performed with different signal to background ratios (SBR) and with different acquisition times (1-5 min). The algorithm was applied on ten clinical data where the results were compared with manual segmentation and fixed percentage thresholding method called T50 and T60 in which 50% and 60% of the maximum intensity respectively is used as threshold. The average error in FV and mAC calculation was 30% and -35% for 0.5 ml tumor. The average error FV and mAC calculation were ~5% for 16 ml tumor. The overall FV error was ∼10% for heterogeneous tumors in physical and simulated phantom data. The FV and mAC error for clinical image compared to manual segmentation was around -17% and 15% respectively. In summary my algorithm has potential to be applied on data acquired from different cameras as its not dependent on knowing the camera's PSF. The algorithm can also improve dose estimation and treatment planning.^

Putting the Green in Bureaucracy: Practices of Quantification and Valuation in Environmental Regulation

While researchers have devoted considerable attention to exploring the ways that intentional environmental reregulation creates new avenues for capital accumulation (e.g. Smith, 2007; Castree, 2008), it remains somewhat unclear how the less grandiose day-to-day work of environmental regulators may also help create new sources of ecological value. Through an ethnographic study of environmental regulators tasked with enforcing key environmental laws, I shed light on the subtle ways that rule interpretation and scientific practice structure the frames, models, and methodologies regulators use to enact “best professional judgments” about ecological systems, and ultimately to assign particular values to nature. I also show the ways that non-human nature pushes back against such assessments, which in combination with the interpretive work of environmental regulation, opens spaces of conflict in at least two arenas: one focused on modes of quantification, where actors contend between economistic, ecological, statutory, and moral frames for making value assessments; and one focused on presentations of value, where actors contend between value assessments that best represent their self-defined interests. The ‘value settlements’ environmental regulators reach in these contested spaces allow processes of commensuration to proceed, and ultimately make nature legible for capitalization and exchange. Accounting for the ways that these basic regulatory practice help create ecological value is essential for creating a fuller picture of the ways capital and natural capital relate.

Airborne Laser Quantification of Florida Shoreline and Beach Volume Change Caused by Hurricanes

This dissertation combines three separate studies that measure coastal change using airborne laser data. The initial study develops a method for measuring subaerial and subaqueous volume change incrementally alongshore, and compares those measurements to shoreline change in order to quantify their relationship in Palm Beach County, Florida. A poor correlation (R2 = 0.39) was found between shoreline and volume change before the hurricane season in the northern section of Palm Beach County because of beach nourishment and inlet dynamics. However, a relatively high R2 value of 0.78 in the southern section of Palm Beach County was found due to little disturbance from tidal inlets and coastal engineering projects. The shoreline and volume change caused by the 2004 hurricane season was poorly correlated with R2 values of 0.02 and 0.42 for the north and south sections, respectively. The second study uses airborne laser data to investigate if there is a significant relationship between shoreline migration before and after Hurricane Ivan near Panama City, Florida. In addition, the relationship between shoreline change and subaerial volume was quantified and a new method for quantifying subaqueous sediment change was developed. No significant spatial relationship was found between shoreline migration before and after the hurricane. Utilization of a single coefficient to represent all relationships between shoreline and subaerial volume change was found to be problematic due to the spatial variability in the linear relationship. Differences in bathymetric data show only a small portion of sediment was transported beyond the active zone and most sediment remained within the active zone despite the occurrence of a hurricane. The third study uses airborne laser bathymetry to measure the offshore limit of change, and compares that location with calculated depth of closures and subaqueous geomorphology. There appears to be strong geologic control of the depth of closure in Broward and Miami-Dade Counties. North of Hillsboro Inlet, hydrodynamics control the geomorphology which in turn indicates the location of the depth of closure.