A comparison of variational and Markov chain Monte Carlo methods for inference in partially observed stochastic dynamic systems

In recent work we have developed a novel variational inference method for partially observed systems governed by stochastic differential equations. In this paper we provide a comparison of the Variational Gaussian Process Smoother with an exact solution computed using a Hybrid Monte Carlo approach to path sampling, applied to a stochastic double well potential model. It is demonstrated that the variational smoother provides us a very accurate estimate of mean path while conditional variance is slightly underestimated. We conclude with some remarks as to the advantages and disadvantages of the variational smoother. © 2008 Springer Science + Business Media LLC.

Complementary methods to investigate the development of clogging within a horizontal sub-surface flow tertiary treatment wetland

A combination of experimental methods was applied at a clogged, horizontal subsurface flow (HSSF) municipal wastewater tertiary treatment wetland (TW) in the UK, to quantify the extent of surface and subsurface clogging which had resulted in undesirable surface flow. The three dimensional hydraulic conductivity profile was determined, using a purpose made device which recreates the constant head permeameter test in-situ. The hydrodynamic pathways were investigated by performing dye tracing tests with Rhodamine WT and a novel multi-channel, data-logging, flow through Fluorimeter which allows synchronous measurements to be taken from a matrix of sampling points. Hydraulic conductivity varied in all planes, with the lowest measurement of 0.1 md1 corresponding to the surface layer at the inlet, and the maximum measurement of 1550 md1 located at a 0.4m depth at the outlet. According to dye tracing results, the region where the overland flow ceased received five times the average flow, which then vertically short-circuited below the rhizosphere. The tracer break-through curve obtained from the outlet showed that this preferential flow-path accounted for approximately 80% of the flow overall and arrived 8 h before a distinctly separate secondary flow-path. The overall volumetric efficiencyof the clogged system was 71% and the hydrology was simulated using a dual-path, dead-zone storage model. It is concluded that uneven inlet distribution, continuous surface loading and high rhizosphere resistance is responsible for the clog formation observed in this system. The average inlet hydraulic conductivity was 2 md1, suggesting that current European design guidelines, which predict that the system will reach an equilibrium hydraulic conductivity of 86 md1, do not adequately describe the hydrology of mature systems.

Potassium canrenoate treatment in paediatric patients:a population pharmacokinetic study using novel dried blood spot sampling

Objective: To characterize the population pharmacokinetics of canrenone following administration of potassium canrenoate (K-canrenoate) in paediatric patients. Methods: Data were collected prospectively from 37 paediatric patients (median weight 2.9 kg, age range 2 days–0.85 years) who received intravenous K-canrenoate for management of retained fluids, for example in heart failure and chronic lung disease. Dried blood spot (DBS) samples (n = 213) from these were analysed for canrenone content and the data subjected to pharmacokinetic analysis using nonlinear mixed-effects modelling. Another group of patients (n = 16) who had 71 matching plasma and DBS samples was analysed separately to compare canrenone pharmacokinetic parameters obtained using the two different matrices. Results: A one-compartment model best described the DBS data. Significant covariates were weight, postmenstrual age (PMA) and gestational age. The final population models for canrenone clearance (CL/F) and volume of distribution (V/F) in DBS were CL/F (l/h) = 12.86 ×  (WT/70.0)0.75 × e [0.066 ×  (PMA - 40]) and V/F (l) = 603.30 ×  (WT/70) × (GA/40)1.89 where weight is in kilograms. The corresponding values of CL/F and V/F in a patient with a median weight of 2.9 kg are 1.11 l/h and 20.48 l, respectively. Estimated half-life of canrenone based on DBS concentrations was similar to that based on matched plasma concentrations (19.99 and 19.37 h, respectively, in 70 kg patient). Conclusion: The range of estimated CL/F in DBS for the study population was 0.12–9.62 l/h; hence, bodyweight-based dosage adjustment of K-canrenoate appears necessary. However, a dosing scheme that takes into consideration both weight and age (PMA/gestational age) of paediatric patients seems more appropriate.

Source localization methods

One of the most pressing demands on electrophysiology applied to the diagnosis of epilepsy is the non-invasive localization of the neuronal generators responsible for brain electrical and magnetic fields (the so-called inverse problem). These neuronal generators produce primary currents in the brain, which together with passive currents give rise to the EEG signal. Unfortunately, the signal we measure on the scalp surface doesn't directly indicate the location of the active neuronal assemblies. This is the expression of the ambiguity of the underlying static electromagnetic inverse problem, partly due to the relatively limited number of independent measures available. A given electric potential distribution recorded at the scalp can be explained by the activity of infinite different configurations of intracranial sources. In contrast, the forward problem, which consists of computing the potential field at the scalp from known source locations and strengths with known geometry and conductivity properties of the brain and its layers (CSF/meninges, skin and skull), i.e. the head model, has a unique solution. The head models vary from the computationally simpler spherical models (three or four concentric spheres) to the realistic models based on the segmentation of anatomical images obtained using magnetic resonance imaging (MRI). Realistic models – computationally intensive and difficult to implement – can separate different tissues of the head and account for the convoluted geometry of the brain and the significant inter-individual variability. In real-life applications, if the assumptions of the statistical, anatomical or functional properties of the signal and the volume in which it is generated are meaningful, a true three-dimensional tomographic representation of sources of brain electrical activity is possible in spite of the ‘ill-posed’ nature of the inverse problem (Michel et al., 2004). The techniques used to achieve this are now referred to as electrical source imaging (ESI) or magnetic source imaging (MSI). The first issue to influence reconstruction accuracy is spatial sampling, i.e. the number of EEG electrodes. It has been shown that this relationship is not linear, reaching a plateau at about 128 electrodes, provided spatial distribution is uniform. The second factor is related to the different properties of the source localization strategies used with respect to the hypothesized source configuration.

Effect of sampling effort and sampling frequency on the composition of the planktonic crustacean assemblage: a case study of the river Danube

Although numerous studies have focused on the seasonal dynamics of riverine zooplankton, little is known about its short-term variation. In order to examine the effects of sampling frequency and sampling effort, microcrustacean samples were collected at daily intervals between 13 June and 21 July of 2007 in a parapotamal side arm of the river Danube, Hungary. Samples were also taken at biweekly intervals from November 2006 to May 2008. After presenting the community dynamics, the effect of sampling effort was evaluated with two different methods; the minimal sample size was also estimated. We introduced a single index (potential dynamic information loss; to determine the potential loss of information when sampling frequency is reduced. The formula was calculated for the total abundance, densities of the dominant taxa, adult/larva ratios of copepods and for two different diversity measures. Results suggest that abundances may experience notable fluctuations even within 1 week, as do diversities and adult/larva ratios.

A distance education case study: A comparison of instructional delivery methods practiced by higher education faculty and emerging standards

The purpose of this research was to compare the delivery methods as practiced by higher education faculty teaching distance courses with recommended or emerging standard instructional delivery methods for distance education. Previous research shows that traditional-type instructional strategies have been used in distance education and that there has been no training to distance teach. Secondary data, however, appear to suggest emerging practices which could be pooled toward the development of standards. This is a qualitative study based on the constant comparative analysis approach of grounded theory.^ Participants (N = 5) of this study were full-time faculty teaching distance education courses. The observation method used was unobtrusive content analysis of videotaped instruction. Triangulation of data was accomplished through one-on-one in-depth interviews and from literature review. Due to the addition of non-media content being analyzed, a special time-sampling technique was designed by the researcher--influenced by content analyst theories of media-related data--to sample portions of the videotape instruction that were observed and counted. A standardized interview guide was used to collect data from in-depth interviews. Coding was done based on categories drawn from review of literature, and from Cranton and Weston's (1989) typology of instructional strategies. The data were observed, counted, tabulated, analyzed, and interpreted solely by the researcher. It should be noted however, that systematic and rigorous data collection and analysis led to credible data.^ The findings of this study supported the proposition that there are no standard instructional practices for distance teaching. Further, the findings revealed that of the emerging practices suggested by proponents and by faculty who teach distance education courses, few were practiced even minimally. A noted example was the use of lecture and questioning. Questioning, as a teaching tool was used a great deal, with students at the originating site but not with distance students. Lectures were given, but were mostly conducted in traditional fashion--long in duration and with no interactive component.^ It can be concluded from the findings that while there are no standard practices for instructional delivery for distance education, there appears to be sufficient information from secondary and empirical data to initiate some standard instructional practices. Therefore, grounded in this research data is the theory that the way to arrive at some instructional delivery standards for televised distance education is a pooling of the tacitly agreed-upon emerging practices by proponents and practicing instructors. Implicit in this theory is a need for experimental research so that these emerging practices can be tested, tried, and proven, ultimately resulting in formal standards for instructional delivery in television education. ^

Headspace analysis of smokeless powders: Development of mass calibration methods using microdrop printing for chromatographic and ion mobility spectrometric detection

Smokeless powder additives are usually detected by their extraction from post-blast residues or unburned powder particles followed by analysis using chromatographic techniques. This work presents the first comprehensive study of the detection of the volatile and semi-volatile additives of smokeless powders using solid phase microextraction (SPME) as a sampling and pre-concentration technique. Seventy smokeless powders were studied using laboratory based chromatography techniques and a field deployable ion mobility spectrometer (IMS). The detection of diphenylamine, ethyl and methyl centralite, 2,4-dinitrotoluene, diethyl and dibutyl phthalate by IMS to associate the presence of these compounds to smokeless powders is also reported for the first time. A previously reported SPME-IMS analytical approach facilitates rapid sub-nanogram detection of the vapor phase components of smokeless powders. A mass calibration procedure for the analytical techniques used in this study was developed. Precise and accurate mass delivery of analytes in picoliter volumes was achieved using a drop-on-demand inkjet printing method. Absolute mass detection limits determined using this method for the various analytes of interest ranged between 0.03–0.8 ng for the GC-MS and between 0.03–2 ng for the IMS. Mass response graphs generated for different detection techniques help in the determination of mass extracted from the headspace of each smokeless powder. The analyte mass present in the vapor phase was sufficient for a SPME fiber to extract most analytes at amounts above the detection limits of both chromatographic techniques and the ion mobility spectrometer. Analysis of the large number of smokeless powders revealed that diphenylamine was present in the headspace of 96% of the powders. Ethyl centralite was detected in 47% of the powders and 8% of the powders had methyl centralite available for detection from the headspace sampling of the powders by SPME. Nitroglycerin was the dominant peak present in the headspace of the double-based powders. 2,4-dinitrotoluene which is another important headspace component was detected in 44% of the powders. The powders therefore have more than one headspace component and the detection of a combination of these compounds is achievable by SPME-IMS leading to an association to the presence of smokeless powders.

Headspace Analysis of Smokeless Powders: Development of Mass Calibration Methods using Microdrop Printing for Chromatographic and Ion Mobility Spectrometric Detection

Smokeless powder additives are usually detected by their extraction from post-blast residues or unburned powder particles followed by analysis using chromatographic techniques. This work presents the first comprehensive study of the detection of the volatile and semi-volatile additives of smokeless powders using solid phase microextraction (SPME) as a sampling and pre-concentration technique. Seventy smokeless powders were studied using laboratory based chromatography techniques and a field deployable ion mobility spectrometer (IMS). The detection of diphenylamine, ethyl and methyl centralite, 2,4-dinitrotoluene, diethyl and dibutyl phthalate by IMS to associate the presence of these compounds to smokeless powders is also reported for the first time. A previously reported SPME-IMS analytical approach facilitates rapid sub-nanogram detection of the vapor phase components of smokeless powders. A mass calibration procedure for the analytical techniques used in this study was developed. Precise and accurate mass delivery of analytes in picoliter volumes was achieved using a drop-on-demand inkjet printing method. Absolute mass detection limits determined using this method for the various analytes of interest ranged between 0.03 - 0.8 ng for the GC-MS and between 0.03 - 2 ng for the IMS. Mass response graphs generated for different detection techniques help in the determination of mass extracted from the headspace of each smokeless powder. The analyte mass present in the vapor phase was sufficient for a SPME fiber to extract most analytes at amounts above the detection limits of both chromatographic techniques and the ion mobility spectrometer. Analysis of the large number of smokeless powders revealed that diphenylamine was present in the headspace of 96% of the powders. Ethyl centralite was detected in 47% of the powders and 8% of the powders had methyl centralite available for detection from the headspace sampling of the powders by SPME. Nitroglycerin was the dominant peak present in the headspace of the double-based powders. 2,4-dinitrotoluene which is another important headspace component was detected in 44% of the powders. The powders therefore have more than one headspace component and the detection of a combination of these compounds is achievable by SPME-IMS leading to an association to the presence of smokeless powders.

Properties of seawater and particulate matter from a WETLabs AC-S spectrophotometer and a WETLabs chlorophyll fluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of evironmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication provides permanent links to original and updated versions of validated data files containing measurements from the Continuous Surface Sampling System [CSSS]. Water was pumped at the front of the vessel from ~2m depth, then de-bubbled and circulated to a WETLabs AC-S spectrophotometer and a WETLabs chlorophyll fluorometer. Systems maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive legs. All data were stamped with a GPS.

Integrated geoarchaeological methods for the determination of site activity areas : A study of a Viking Age house in Reykjavik, Iceland

Acknowledgements The excavation was funded by the City of Reykjavík, and the geoarchaeological research was funded by a SSHRCC Doctoral Fellowship from the government of Canada, an Overseas Research Studentship, the Cambridge Commonwealth Trust, Pelham Roberts and Muriel Onslow Research Studentships from Newnham College, Cambridge, and Canadian Centennial Scholarships from the Canadian High Commission in London. Garðar Guðmundsson took the micromorphology samples, and supervised sampling on site. The bones were counted by Clayton Tinsley, the thin sections were made by Julie Boreham, and Steve Boreham and his team in the Department of Geography, University of Cambridge, provided technical support for all of the bulk geochemical analyses that were conducted by K. Milek, except for ICP–AES, which was conducted by ALS Chemex. Our gratitude is extended to Charles French, Catherine Hills, Peter Jordan and two anonymous reviewers for their support and helpful comments on earlier drafts of this paper, and to Óskar Gísli Sveinbjarnarson for his assistance with the figures.

Integrated geoarchaeological methods for the determination of site activity areas : A study of a Viking Age house in Reykjavik, Iceland

Acknowledgements The excavation was funded by the City of Reykjavík, and the geoarchaeological research was funded by a SSHRCC Doctoral Fellowship from the government of Canada, an Overseas Research Studentship, the Cambridge Commonwealth Trust, Pelham Roberts and Muriel Onslow Research Studentships from Newnham College, Cambridge, and Canadian Centennial Scholarships from the Canadian High Commission in London. Garðar Guðmundsson took the micromorphology samples, and supervised sampling on site. The bones were counted by Clayton Tinsley, the thin sections were made by Julie Boreham, and Steve Boreham and his team in the Department of Geography, University of Cambridge, provided technical support for all of the bulk geochemical analyses that were conducted by K. Milek, except for ICP–AES, which was conducted by ALS Chemex. Our gratitude is extended to Charles French, Catherine Hills, Peter Jordan and two anonymous reviewers for their support and helpful comments on earlier drafts of this paper, and to Óskar Gísli Sveinbjarnarson for his assistance with the figures.

Assessment of exposure to the Penicillium glabrum complex in cork industry using complementing methods

Cork oak is the second most dominant forest species in Portugal and makes this country the world leader in cork export. Occupational exposure to Chrysonilia sitophila and the Penicillium glabrum complex in cork industry is common, and the latter fungus is associated with suberosis. However, as conventional methods seem to underestimate its presence in occupational environments, the aim of our study was to see whether information obtained by polymerase chain reaction (PCR), a molecular-based method, can complement conventional findings and give a better insight into occupational exposure of cork industry workers. We assessed fungal contamination with the P. glabrum complex in three cork manufacturing plants in the outskirts of Lisbon using both conventional and molecular methods. Conventional culturing failed to detect the fungus at six sampling sites in which PCR did detect it. This confirms our assumption that the use of complementing methods can provide information for a more accurate assessment of occupational exposure to the P. glabrum complex in cork industry.

Sampling strategies for characterization of neuropeptides using mass spectrometry and functional implications into cell-cell signaling

In this dissertation, there are developed different analytical strategies to discover and characterize mammalian brain peptides using small amount of tissues. The magnocellular neurons of rat supraoptic nucleus in tissue and cell culture served as the main model to study neuropeptides, in addition to hippocampal neurons and mouse embryonic pituitaries. The neuropeptidomcis studies described here use different extraction methods on tissue or cell culture combined with mass spectrometry (MS) techniques, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). These strategies lead to the identification of multiple peptides from the rat/mouse brain in tissue and cell cultures, including novel compounds One of the goals in this dissertation was to optimize sample preparations on samples isolated from well-defined brain regions for mass spectrometric analysis. Here, the neuropeptidomics study of the SON resulted in the identification of 85 peptides, including 20 unique peptides from known prohormones. This study includes mass spectrometric analysis even from individually isolated magnocellular neuroendocrine cells, where vasopressin and several other peptides are detected. At the same time, it was shown that the same approach could be applied to analyze peptides isolated from a similar hypothalamic region, the suprachiasmatic nucleus (SCN). Although there were some overlaps regarding the detection of the peptides in the two brain nuclei, different peptides were detected specific to each nucleus. Among other peptides, provasopressin fragments were specifically detected in the SON while angiotensin I, somatostatin-14, neurokinin B, galanin, and vasoactive-intestinal peptide (VIP) were detected in the SCN only. Lists of peptides were generated from both brain regions for comparison of the peptidome of SON and SCN nuclei. Moving from analysis of magnocellular neurons in tissue to cell culture, the direct peptidomics of the magnocellular and hippocampal neurons led to the detection of 10 peaks that were assigned to previously characterized peptides and 17 peaks that remain unassigned. Peptides from the vasopressin prohormone and secretogranin-2 are attributed to magnocellular neurons, whereas neurokinin A, peptide J, and neurokinin B are attributed to cultured hippocampal neurons. This approach enabled the elucidation of cell-specific prohormone processing and the discovery of cell-cell signaling peptides. The peptides with roles in the development of the pituitary were analyzed using transgenic mice. Hes1 KO is a genetically modified mouse that lives only e18.5 (embryonic days). Anterior pituitaries of Hes1 null mice exhibit hypoplasia due to increased cell death and reduced proliferation and in the intermediate lobe, the cells differentiate abnormally into somatotropes instead of melanotropes. These previous findings demonstrate that Hes1 has multiple roles in pituitary development, cell differentiation, and cell fate. AVP was detected in all samples. Interestingly, somatostatin [92-100] and provasopressin [151-168] were detected in the mutant but not in the wild type or heterozygous pituitaries while somatostatin-14 was detected only in the heterozygous pituitary. In addition, the putative peptide corresponding to m/z 1330.2 and POMC [205-222] are detected in the mutant and heterozygous pituitaries, but not in the wild type. These results indicate that Hes1 influences the processing of different prohormones having possible roles during development and opens new directions for further developmental studies. This research demonstrates the robust capabilities of MS, which ensures the unbiased direct analysis of peptides extracted from complex biological systems and allows addressing important questions to understand cell-cell signaling in the brain.

Analysis of Sampling Data

A Similar Exposure Group (SEG) can be created through the evaluation of workers performing the same or similar task, hazards they are exposed to, frequency and duration of their exposures, engineering controls available during their operations, personal protective equipment used, and exposure data. For this report, the samples of one facility that has collected nearly 40,000 various types of samples will be evaluated to determine if the creation of a SEG can be supported. The data will be reviewed for consistency with collection methods and laboratory detection limits. A subset of the samples may be selected based on the review. Data will also be statistically evaluated in order to determine whether the data is sufficient to terminate the sampling. IHDataAnalyst V1.27 will be used to assess the data. This program uses Bayesian Analysis to assist in making determinations. The 95 percent confidence interval will be calculated and evaluated in making decisions. This evaluation will be used to determine if a SEG can be created for any of the workers and determine the need for future sample collection. The data and evaluation presented in this report have been selected and evaluated specifically for the purposes of this project.

Exploration of Ground Penetrating Radar and Time Domain Reflectometry Methods for the Determination of Pavement Dielectric Constant

Traditionally, densities of newly built roadways are checked by direct sampling (cores) or by nuclear density gauge measurements. For roadway engineers, density of asphalt pavement surfaces is essential to determine pavement quality. Unfortunately, field measurements of density by direct sampling or by nuclear measurement are slow processes. Therefore, I have explored the use of rapidly-deployed ground penetrating radar (GPR) as an alternative means of determining pavement quality. The dielectric constant of pavement surface may be a substructure parameter that correlates with pavement density, and can be used as a proxy when density of asphalt is not known from nuclear or destructive methods. The dielectric constant of the asphalt can be determined using ground penetrating radar (GPR). In order to use GPR for evaluation of road surface quality, the relationship between dielectric constants of asphalt and their densities must be established. Field measurements of GPR were taken at four highway sites in Houghton and Keweenaw Counties, Michigan, where density values were also obtained using nuclear methods in the field. Laboratory studies involved asphalt samples taken from the field sites and samples created in the laboratory. These were tested in various ways, including, density, thickness, and time domain reflectometry (TDR). In the field, GPR data was acquired using a 1000 MHz air-launched unit and a ground-coupled unit at 200 and 500 MHz. The equipment used was owned and operated by the Michigan Department of Transportation (MDOT) and available for this study for a total of four days during summer 2005 and spring 2006. The analysis of the reflected waveforms included “routine” processing for velocity using commercial software and direct evaluation of reflection coefficients to determine a dielectric constant. The dielectric constants computed from velocities do not agree well with those obtained from reflection coefficients. Perhaps due to the limited range of asphalt types studied, no correlation between density and dielectric constant was evident. Laboratory measurements were taken with samples removed from the field and samples created for this study. Samples from the field were studied using TDR, in order to obtain dielectric constant directly, and these correlated well with the estimates made from reflection coefficients. Samples created in the laboratory were measured using 1000 MHz air-launched GPR, and 400 MHz ground-coupled GPR, each under both wet and dry conditions. On the basis of these observations, I conclude that dielectric constant of asphalt can be reliably measured from waveform amplitude analysis of GJPR data, based on the consistent agreement with that obtained in the laboratory using TDR. Because of the uniformity of asphalts studied here, any correlation between dielectric constant and density is not yet apparent.