Advances in methods for determining fecundity: application of the new methods to some marine fishes

Estimation of individual egg production (realized fecundity) is a key step either to understand the stock and recruit relationship or to carry out fisheries-independent assessment of spawning stock biomass using egg production methods. Many fish are highly fecund and their ovaries may weigh over a kilogram; therefore the work time can be consuming and require large quantities of toxic fixative. Recently it has been shown for Atlantic cod (Gadus morhua) that image analysis can automate fecundity determination using a power equation that links follicles per gram ovary to the mean vitellogenic follicular diameter (the autodiametric method). In this article we demonstrate the precision of the autodiametric method applied to a range of species with different spawning strategies during maturation and spawning. A new method using a solid displacement pipette to remove quantitative fecundity samples (25, 50, 100, and 200 milligram [mg]) is evaluated, as are the underlying assumptions to effectively fix and subsample the ovary. Finally, we demonstrate the interpretation of dispersed formaldehyde-fixed ovarian samples (whole mounts) to assess the presence of atretic and postovulatory follicles to replace labor intensive histology. These results can be used to estimate down regulation (production of atretic follicles) of fecundity during maturation.

Decision analysis applied to the fishery of the sea snail Concholepas concholepas from central northern coast of Chile

Formal decision analysis was applied to the management of loco (Concholepas concholepas, Fam. Muricidae) in Chile, 29-35 degrees S. Four interested groups were considered "Fishers", "Scientists", "Buyers" and the "State", along with three fishing effort levels and four subobjectives. The method was found to encourage the emergence of a consensus (here: halving of effort), and is recommended for use in other fisheries.

TIME RESOLVED REFLECTIVITY MEASUREMENTS APPLIED TO RAPID ISOTHERMAL ANNEALING OF ION IMPLANTED SILICON.

The annealing of ion implantation damage in silicon by rapid isothermal heating has been monitored by the time resolved reflectivity (TRR) method. This technique was applied simultaneously at a wavelength of 632. 8nm and also at 1152nm, where the optical absorption coefficient of silicon is less. The two wavelength method simplifies the interpretation of TRR results, extends the measurement depth and allows good resolution of the position of the interface between amorphous and crystalline silicon. The regrowth of amorphous layers in silicon, created by self implantation and implanted with electrically active impurities, was observed. Regrowth in rapid isothermal annealing occurs during the heating up stage of typical thermal cycles. Impurities such as B, P, and As increase the regrowth rate in a manner consistent with a vacancy model for regrowth. The maximum regrowth rate in boron implanted silicon is limited by the solid solubility.

A probabilistic energy model for non-domestic building sectors applied to analysis of school buildings in greater London

The diversity of non-domestic buildings at urban scale poses a number of difficulties to develop models for large scale analysis of the stock. This research proposes a probabilistic, engineering-based, bottom-up model to address these issues. In a recent study we classified London's non-domestic buildings based on the service they provide, such as offices, retail premise, and schools, and proposed the creation of one probabilistic representational model per building type. This paper investigates techniques for the development of such models. The representational model is a statistical surrogate of a dynamic energy simulation (ES) model. We first identify the main parameters affecting energy consumption in a particular building sector/type by using sampling-based global sensitivity analysis methods, and then generate statistical surrogate models of the dynamic ES model within the dominant model parameters. Given a sample of actual energy consumption for that sector, we use the surrogate model to infer the distribution of model parameters by inverse analysis. The inferred distributions of input parameters are able to quantify the relative benefits of alternative energy saving measures on an entire building sector with requisite quantification of uncertainties. Secondary school buildings are used for illustrating the application of this probabilistic method. © 2012 Elsevier B.V. All rights reserved.

Threshold reduction in strained-layer InGaAs/GaAs quantum well lasers by liquid phase epitaxy regrowth

When liquid phase epitaxy regrowth at 780 degrees C for 2 h is applied to the samples after molecular beam epitaxy, a decrease of the threshold current density in strained InGaAs/GaAs quantum well lasers by a factor of 3 to 4 is obtained. We suggest that this improvement is attributed to the reduction of nonradiative centers associated with deep levels at the three regions of the active region, the graded layer and the cladding layer. Indeed, a significant reduction of deep center densities has been observed by using minority and majority carrier injection deep level transient spectroscopy measurements. (C) 1998 Elsevier Science B.V. All rights reserved.

Field-amplified sample stacking capillary electrophoresis with electrochemiluminescence applied to the determination of illicit drugs on banknotes

Capillary electrophoresis (CE) with Ru(bpy)(3)(2+) electrochemiluminescence. (ECL) detection system was established to the determination of contamination of banknotes with controlled drugs and a high efficiency on-column field-amplified sample stacking (FASS) technique was also optimized to increase the ECL intensity. The method was illustrated using heroin and cocaine, which are two typical and popular illicit drugs. Highest sample stacking was obtained when 0.01 mM acetic acid was chosen for sample dissolution with electrokinetical injection for 6 s at 17 kV. Under the optimized conditions: ECL detection at 1.2 V, separation voltage 10.0 kV, 20 mM phosphate-acetate (pH 7.2) as running buffer, 5 mM Ru(bpy)(3)(2+) with 50 mM phosphate-acetate (pH 7.2) in the detection cell, the standard curves were linear in the range of 7.50 x 10(-8) to 1.00 x 10(-5) M for heroin and 2.50 x 10(-7) to 1.00 x 10(-4) M for cocaine and detection limits of 50 nM for heroin and 60 nM for cocaine were achieved (S/N = 3), respectively. Relative standard derivations of the ECL intensity and the migration time were 3.50 and 0.51% for heroin and 4.44 and 0.12% for cocaine, respectively.The developed method was successfully applied to the determination of heroin and cocaine on illicit drug contaminated banknotes without any damage of the paper currency.

FACTOR-ANALYSIS APPLIED TO X-RAY-DIFFRACTION DIAGRAMS OF POLYMER BLENDS

The feasibility of applying the method of factor analysis to X-ray diffraction diagrams of binary blends of polypropylene and ethylene-propylene-diene terpolymer (PP/EPDM) was examined. The result of mathematical treatment was satisfactory. The number of scattering species and their concentrations in six kinds of PP/EPDM blends were determined. The separation of the spectral peaks of each species in the blends, contributing spectral intensities, was carried out.

Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes.

The quantification of protein-ligand interactions is essential for systems biology, drug discovery, and bioengineering. Ligand-induced changes in protein thermal stability provide a general, quantifiable signature of binding and may be monitored with dyes such as Sypro Orange (SO), which increase their fluorescence emission intensities upon interaction with the unfolded protein. This method is an experimentally straightforward, economical, and high-throughput approach for observing thermal melts using commonly available real-time polymerase chain reaction instrumentation. However, quantitative analysis requires careful consideration of the dye-mediated reporting mechanism and the underlying thermodynamic model. We determine affinity constants by analysis of ligand-mediated shifts in melting-temperature midpoint values. Ligand affinity is determined in a ligand titration series from shifts in free energies of stability at a common reference temperature. Thermodynamic parameters are obtained by fitting the inverse first derivative of the experimental signal reporting on thermal denaturation with equations that incorporate linear or nonlinear baseline models. We apply these methods to fit protein melts monitored with SO that exhibit prominent nonlinear post-transition baselines. SO can perturb the equilibria on which it is reporting. We analyze cases in which the ligand binds to both the native and denatured state or to the native state only and cases in which protein:ligand stoichiometry needs to treated explicitly.

2D-drop model applied to the calculation of step formation energies on a (111) substrate

A model is presented for obtaining the step formation energy for metallic islands on (1 1 1) surfaces from Monte Carlo simulations. This model is applied to homo (Cu/Cu(1 1 1), Ag/Ag(1 1 1)) and heteroepitaxy (Ag/Pt(1 1 1)) systems. The embedded atom method is used to represent the interaction between the particles of the system, but any other type of potential could be used as well. The formulation can also be employed to consider the case of other single crystal surfaces, since the higher barriers for atom motion on other surfaces are not a hindrance for the simulation scheme proposed.

Molecular diagnosis for heterogeneous genetic diseases with high-throughput DNA sequencing applied to retinitis pigmentosa

BACKGROUND:
The genetic heterogeneity of many Mendelian disorders, such as retinitis pigmentosa which results from mutations in over 40 genes, is a major obstacle to obtaining a molecular diagnosis in clinical practice. Targeted high-throughput DNA sequencing offers a potential solution and was used to develop a molecular diagnostic screen for patients with retinitis pigmentosa.
METHODS:
A custom sequence capture array was designed to target the coding regions of all known retinitis pigmentosa genes and used to enrich these sequences from DNA samples of five patients. Enriched DNA was subjected to high-throughput sequencing singly or in pools, and sequence variants were identified by alignment of up to 10 million reads per sample to the normal reference sequence. Potential pathogenicity was assessed by functional predictions and frequency in controls.
RESULTS AND CONCLUSIONS:
Known homozygous PDE6B and compound heterozygous CRB1 mutations were detected in two patients. A novel homozygous missense mutation (c.2957A?T; p.N986I) in the cyclic nucleotide gated channel ß1 (CNGB1) gene predicted to have a deleterious effect and absent in 720 control chromosomes was detected in one case in which conventional genetic screening had failed to detect mutations. The detection of known and novel retinitis pigmentosa mutations in this study establishes high-throughput DNA sequencing with DNA pooling as an effective diagnostic tool for heterogeneous genetic diseases.

Association between tortilla consumption and human urinary fumonisin B1 levels in a Mexican population

Fumonisins are mycotoxins produced by Fusarium spp. and commonly contaminate maize and maize products worldwide. Fumonisins are rodent carcinogens and have been associated with human esophageal cancer. However, the lack of a valid exposure biomarker has hindered both the assessment of human exposure and the evaluation of disease risk. A sensitive liquid chromatography-mass spectrometry method to measure urinary fumonisin B1 (FB1) following extraction on Oasis MAX cartridges was established and applied to urine samples from women in a cohort recruited in Morelos County, Mexico. Urinary FB1 was compared with dietary information on tortilla consumption. FB1 recovery in spiked samples averaged 94% as judged by deuterium-labeled FB1 internal standard. Urinary FB1 was determined in 75 samples from women selected based on low, medium, or high consumption of maize-based tortillas. The geometric mean (95% confidence interval) of urinary FB1 was 35.0 (18.8-65.2), 63.1 (36.8-108.2), and 147.4 (87.6-248.0) pg/mL and the frequency of samples above the detection limit (set at 20 pg FB1/mL urine) was 45%, 80%, and 96% for the low, medium, and high groups, respectively. Women with high intake had a 3-fold higher average FB1 levels compared with the "low intake" group (F = 7.3; P = 0.0015). Urinary FB1 was correlated with maize intake (P-trend = 0.001); the correlation remained significant after adjusting for age, education, and place of residence. This study suggests that measurement of urinary FB1 is sufficiently sensitive for fumonisin exposure assessment in human populations and could be a valuable tool in investigating the associated health effects of exposure.

Time-dependent R-matrix theory applied to two-photon double ionization of He

We introduce a time-dependent R-matrix theory generalized to describe double-ionization processes. The method is used to investigate two-photon double ionization of He by intense XUV laser radiation. We combine a detailed B-spline-based wave-function description in an extended inner region with a single-electron outer region containing channels representing both single ionization and double ionization. A comparison of wave-function densities for different box sizes demonstrates that the flow between the two regions is described with excellent accuracy. The obtained two-photon double-ionization cross sections are in excellent agreement with other cross sections available. Compared to calculations fully contained within a finite inner region, the present calculations can be propagated over the time it takes the slowest electron to reach the boundary.

On the Assumption of Bivariate Normality in Selection Models: A Copula Approach Applied to Estimating HIV Prevalence

Background: Heckman-type selection models have been used to control HIV prevalence estimates for selection bias when participation in HIV testing and HIV status are associated after controlling for observed variables. These models typically rely on the strong assumption that the error terms in the participation and the outcome equations that comprise the model are distributed as bivariate normal.
Methods: We introduce a novel approach for relaxing the bivariate normality assumption in selection models using copula functions. We apply this method to estimating HIV prevalence and new confidence intervals (CI) in the 2007 Zambia Demographic and Health Survey (DHS) by using interviewer identity as the selection variable that predicts participation (consent to test) but not the outcome (HIV status).
Results: We show in a simulation study that selection models can generate biased results when the bivariate normality assumption is violated. In the 2007 Zambia DHS, HIV prevalence estimates are similar irrespective of the structure of the association assumed between participation and outcome. For men, we estimate a population HIV prevalence of 21% (95% CI = 16%–25%) compared with 12% (11%–13%) among those who consented to be tested; for women, the corresponding figures are 19% (13%–24%) and 16% (15%–17%).
Conclusions: Copula approaches to Heckman-type selection models are a useful addition to the methodological toolkit of HIV epidemiology and of epidemiology in general. We develop the use of this approach to systematically evaluate the robustness of HIV prevalence estimates based on selection models, both empirically and in a simulation study.

A comprehensive strategy to detect the fraudulent adulteration of herbs: The oregano approach

Fraud in the global food supply chain is becoming increasingly common due to the huge profits associated with this type of criminal activity. Food commodities and ingredients that are expensive and are part of complex supply chains are particularly vulnerable. Both herbs and spices fit these criteria perfectly and yet strategies to detect fraudulent adulteration are still far from robust. An FT-IR screening method coupled to data analysis using chemometrics and a second method using LC-HRMS were developed, with the latter detecting commonly used adulterants by biomarker identification. The two tier testing strategy was applied to 78 samples obtained from a variety of retail and on-line sources. There was 100% agreement between the two tests that over 24% of all samples tested had some form of adulterants present. The innovative strategy devised could potentially be used for testing the global supply chains for fraud in many different forms of herbs.

New methodologies for directed functional connectivity applied to brain neuroimaging research

Tese de doutoramento, Engenharia Biomédica e Biofísica, Universidade de Lisboa, Faculdade de Ciências, 2015