Molecular docking and geographical information systems as tools to assess the potential impact of veterinary medicines on non-target organisms and the environment

Veterinary medicines (VMs) from agricultural industry can enter the environment in a number of ways. This includes direct exposure through aquaculture, accidental spillage and disposal, and indirect entry by leaching from manure or runoff after treatment. Many compounds used in animal treatments have ecotoxic properties that may have chronic or sometimes lethal effects when they come into contact with non-target organisms. VMs enter the environment in mixtures, potentially having additive effects. Traditional ecotoxicology tests are used to determine the lethal and sometimes reproductive effects on freshwater and terrestrial organisms. However, organisms used in ecotoxicology tests can be unrepresentative of the populations that are likely to be exposed to the compound in the environment. Most often the tests are on single compound toxicity but mixture effects may be significant and should be included in ecotoxicology testing. This work investigates the use, measured environmental concentrations (MECs) and potential impact of sea lice treatments on salmon farms in Scotland. Alternative methods for ecotoxicology testing including mixture toxicity, and the use of in silico techniques to predict the chronic impact of VMs on different species of aquatic organisms were also investigated. The Scottish Environmental Protection Agency (SEPA) provided information on the use of five sea lice treatments from 2008-2011 on Scottish salmon farms. This information was combined with the recently available data on sediment MECs for the years 2009-2012 provided by SEPA using ArcGIS 10.1. In depth analysis of this data showed that from a total of 55 sites, 30 sites had a MEC higher than the maximum allowable concentration (MAC) as set out by SEPA for emamectin benzoate and 7 sites had a higher MEC than MAC for teflubenzuron. A number of sites that were up to 16 km away from the nearest salmon farm reported as using either emamectin benzoate or teflubenzuron measured positive for the two treatments. There was no relationship between current direction and the distribution of the sea lice treatments, nor was there any evidence for alternative sources of the compounds e.g. land treatments. The sites that had MECs higher than the MAC could pose a risk to non-target organisms and disrupt the species dynamics of the area. There was evidence that some marine protected sites might be at risk of exposure to these compounds. To complement this work, effects on acute mixture toxicity of the 5 sea lice treatments, plus one major metabolite 3-phenoxybenzoic acid (3PBA), were measured using an assay using the bioluminescent bacteria Aliivibrio fischeri. When exposed to the 5 sea lice treatments and 3PBA A. fischeri showed a response to 3PBA, emamectin benzoate and azamethiphos as well as combinations of the three. In order to establish any additive effect of the sea lice treatments, the efficacy of two mixture prediction equations, concentration addition (CA) and independent action ii(IA) were tested using the results from single compound dose response curves. In this instance IA was the more effective prediction method with a linear regression confidence interval of 82.6% compared with 22.6% of CA. In silico molecular docking was carried out to predict the chronic effects of 15 VMs (including the five used as sea lice control). Molecular docking has been proposed as an alternative screening method for the chronic effects of large animal treatments on non-target organisms. Oestrogen receptor alpha (ERα) of 7 non-target bony fish and the African clawed frog Xenopus laevis were modelled using SwissModel. These models were then ‘docked’ to oestradiol, the synthetic oestrogen ethinylestradiol, two known xenoestrogens dichlorodiphenyltrichloroethane (DDT) and bisphenol A (BPA), the antioestrogen breast cancer treatment tamoxifen and 15 VMs using Auto Dock 4. Based on the results of this work, four VMs were identified as being possible xenoestrogens or anti-oestrogens; these were cypermethrin, deltamethrin, fenbendazole and teflubenzuron. Further investigation, using in vitro assays, into these four VMs has been suggested as future work. A modified recombinant yeast oestrogen screen (YES) was attempted using the cDNA of the ERα of the zebrafish Danio rerio and the rainbow trout Oncorhynchus mykiss. Due to time and difficulties in cloning protocols this work was unable to be completed. Use of such in vitro assays would allow for further investigation of the highlighted VMs into their oestrogenic potential. In conclusion, VMs used as sea lice treatments, such as teflubenzuron and emamectin benzoate may be more persistent and have a wider range in the environment than previously thought. Mixtures of sea lice treatments have been found to persist together in the environment, and effects of these mixtures on the bacteria A. fischeri can be predicted using the IA equation. Finally, molecular docking may be a suitable tool to predict chronic endocrine disrupting effects and identify varying degrees of impact on the ERα of nine species of aquatic organisms.

Time of Flight Measurements for Neutrons Produced in Reactions Driven by Laser-Target Interactions at Petawatt level

Abstract Short intense pulses of fast neutrons were produced in a two stage laser-driven experiment. Protons were accelerated by means of the Target Normal Sheath Acceleration (TNSA) method using the TITAN facility at the Lawrence Livermore National Laboratory. Neutrons were obtained following interactions of the protons with a secondary lithium fluoride (LiF) target. The properties of the neutron flux were studied using BC-400 plastic scintillation detectors and the neutron time of flight (nTOF) technique. The detector setup and the experimental conditions were simulated with the Geant4 toolkit. The effects of different components of the experimental setup on the nTOF were studied. Preliminary results from a comparison between experimental and simulated nTOF distributions are presented.

Streptolysin-O reversible permeabilisation is an effective method to transfect siRNAs into myeloma cells

RNA interference (RNAi) has been shown to be a valuable tool to specifically target gene expression in a number of organisms becoming an indispensable weapon in the arsenal in functional genomics. In this study, we demonstrate that streptolysin-O (SLO) reversible permeabilisation is an efficient method to deliver small interfering RNAs (siRNAs) to hard-to-transfect human myeloma cell lines. We used published, pre-validated siRNAs for ERK2 and non-silencing siRNA control. We transfected siRNAs into human myeloma cell lines using SLO reversible permeabilisation method. Flow cytometry and western blot analysis were performed to assess the effect of SLO on transfection efficiency and ERK2 knockdown. These experiments demonstrate that SLO reversible permeabilisation method is an efficient and easy-to-use method to deliver siRNAs into human myeloma cell lines. Optimised SLO permeabilisation method showed to transfect >80% of JIM-3, H929, RPM18226 and U266 cells, with minimal effect on cell viability (<10%) and cell cycle. Equally important, SLO permeabilisation induced a substantial knockdown of ERK2 at the protein level. These studies demonstrate that reversible SLO permeabilisation can successfully be applied to hard-to-transfect human myeloma cell lines to effectively silence genes. (C) 2008 Published by Elsevier B.V.

A low overhead error confinement method based on application statistical characteristics

Reliability has emerged as a critical design constraint especially in memories. Designers are going to great lengths to guarantee fault free operation of the underlying silicon by adopting redundancy-based techniques, which essentially try to detect and correct every single error. However, such techniques come at a cost of large area, power and performance overheads which making many researchers to doubt their efficiency especially for error resilient systems where 100% accuracy is not always required. In this paper, we present an alternative method focusing on the confinement of the resulting output error induced by any reliability issues. By focusing on memory faults, rather than correcting every single error the proposed method exploits the statistical characteristics of any target application and replaces any erroneous data with the best available estimate of that data. To realize the proposed method a RISC processor is augmented with custom instructions and special-purpose functional units. We apply the method on the proposed enhanced processor by studying the statistical characteristics of the various algorithms involved in a popular multimedia application. Our experimental results show that in contrast to state-of-the-art fault tolerance approaches, we are able to reduce runtime and area overhead by 71.3% and 83.3% respectively.

Oncology research and clinical decisions based on immunohistochemistry: the importance of the technical aspects that support a complex method

Immunohistochemistry (IHC) is the group of techniques that use antibodies as specific reagents to identify and demonstrate several cell and tissue components that are antigens. This linking allows locating and identifying the in situ presence of various substances by means of color that is associated with the formed antigen-antibody complexes. The practical value of this biotechnology area, widely used in Pathology and Oncology, in diagnostic, prognostic, theranostic and research context, results from the possibility of combining a colour marker with an antibody without causing any damage to specific binding established between antibody and antigen. This provides the microscopic observation of the target locations where the antibody and hence the antigen are present. IHC is presented as a powerful means for identification of several cellular and tissue structures that can be associated with pathologies, and of the consequences, at functional and morphological level, of these same elements action.

Time Reversed Electromagnetic Wave Propagation as a Novel Method of Wireless Power Transfer

We investigate the application of time-reversed electromagnetic wave propagation to transmit energy in a wireless power transmission system. “Time reversal” is a signal focusing method that exploits the time reversal invariance of the lossless wave equation to direct signals onto a single point inside a complex scattering environment. In this work, we explore the properties of time reversed microwave pulses in a low-loss ray-chaotic chamber. We measure the spatial profile of the collapsing wavefront around the target antenna, and demonstrate that time reversal can be used to transfer energy to a receiver in motion. We demonstrate how nonlinear elements can be controlled to selectively focus on one target out of a group. Finally, we discuss the design of a rectenna for use in a time reversal system. We explore the implication of these results, and how they may be applied in future technologies.

Adoption of catamaran fishing method for mukene (Rastrineobola argentea) in off shore waters of Lake Victoria

This report presents information on the development of a system for commercial harvesting of Rastrineobola argentea (Mukene) in Lake Victoria. The objective of this work is to develop a system for commercial Harvesting of Mukene with: •Targeted output above 1,000 kg per working night per boat. •Target area to be off shore waters of Lake Victoria. •Drying under hygienic conditions for production of high quality poultry and animal feeds. •Supply to be continuous with predicable prices

Measurement of target single-spin asymmetry in charged kaon electroproduction on a transversely polarized 3He target

The subject of quark transverse spin and transverse momentum distribution are two current research frontier in understanding the spin structure of the nucleons. The goal of the research reported in this dissertation is to extract new information on the quark transversity distribution and the novel transverse-momentum-dependent Sivers function in the neutron. A semi-inclusive deep inelastic scattering experiment was performed at the Hall A of the Jefferson laboratory using 5.9 GeV electron beam and a transversely polarized ^{3}He target. The scattered electrons and the produced hadrons (pions, kaons, and protons) were detected in coincidence with two large magnetic spectrometers. By regularly flipping the spin direction of the transversely polarized target, the single-spin-asymmetry (SSA) of the semi-inclusive deep inelastic reaction ^{3}He^{uparrow}(e,e'h^{\pm})X was measured over the kinematic range 0.13 < x < 0.41 and 1.3 < Q^{2} < 3.1 (GeV)^{2}. The SSA contains several different azimuthal angular modulations which are convolutions of quarks distribution functions in the nucleons and the quark fragmentation functions into hadrons. It is from the extraction of the various ``moments'' of these azimuthal angular distributions (Collins moment and Sivers moment) that we obtain information on the quark transversity distribution and the novel T-odd Sivers function. In this dissertation, I first introduced the theoretical background and experimental status of nucleon spins and the physics of SSA. I will then present the experimental setup and data collection of the JLab E06-010 experiment. Details of data analysis will be discussed next with emphasis on the kaon particle identification and the Ring-Imaging Cherenkov detector which are my major responsibilities in this experiment. Finally, results on the kaon Collins and Sivers moments extracted from the Maximum Likelihood method will be presented and interpreted. I will conclude with a discussion on the future prospects for this research.

Inertial dissipation method applied to derive turbulent fluxed over the ocean during the Surface of the Ocean, Fluxes and Interactions with the Atmosphere Atlantic Stratocumulus Transition Experiment (SOFIA/ASTEX) and Structure des Echanges Mer-Atmosphere, Proprietes des Heterogeneites Oceaniques: Recherche Experimentale (SEMAPHORE) experiments with low to moderate wind speed

The transfer coefficients for momentum and heat have been determined for 10 m neutral wind speeds (U-10n) between 0 and 12 m/s using data from the Surface of the Ocean, Fluxes and Interactions with the Atmosphere (SOFIA) and Structure des Echanges Mer-Atmosphere, Proprietes des Heterogeneites Oceaniques: Recherche Experimentale (SEMAPHORE) experiments. The inertial dissipation method was applied to wind and pseudo virtual temperature spectra from a sonic anemometer, mounted on a platform (ship) which was moving through the turbulence held. Under unstable conditions the assumptions concerning the turbulent kinetic energy (TKE) budget appeared incorrect. Using a bulk estimate for the stability parameter, Z/L (where Z is the height and L is the Obukhov length), this resulted in anomalously low drag coefficients compared to neutral conditions. Determining Z/L iteratively, a low rate of convergence was achieved. It was concluded that the divergence of the turbulent transport of TKE was not negligible under unstable conditions. By minimizing the dependence of the calculated neutral drag coefficient on stability, this term was estimated at about -0.65Z/L. The resulting turbulent fluxes were then in close agreement with other studies at moderate wind speed. The drag and exchange coefficients for low wind speeds were found to be C-en x 10(3) = 2.79U(10n)(-1) + 0.66 (U-10n < 5.2 m/s), C-en x 10(3) = C-hn x 10(3) = 1.2 (U-10n greater than or equal to 5.2 m/s), and C-dn x 10(3) = 11.7U(10n)(-2) + 0.668 (U-10n < 5.5 m/s), which imply a rapid increase of the coefficient values as the wind decreased within the smooth flow regime. The frozen turbulence hypothesis and the assumptions of isotropy and an inertial subrange were found to remain valid at these low wind speeds for these shipboard measurements. Incorporation of a free convection parameterization had little effect.

Biomarkers of Nitrosative Stress: Development and validation of a new analytical method for 3-Nitrotyrosine quantification

Background: The nitration of tyrosine residues in proteins is associated with nitrosative stress, resulting in the formation of 3-nitrotyrosine (3-NT). 3-NT levels in biological samples have been associated with numerous physiological and pathological conditions. For this reason, several attempts have been made in order to develop methods that accurately quantify 3-NT in biological samples. Regarding chromatographic methods, they seem to be very accurate, showing very good sensibility and specificity. However, accurate quantification of this molecule, which is present at very low concentrations both at physiological and pathological states, is always a complex task and a target of intense research. Objectives: We aimed to develop a simple, rapid, low-cost and sensitive 3-NT quantification method for use in medical laboratories as an additional tool for diagnosis and/or treatment monitoring of a wide range of pathologies. We also aimed to evaluate the performance of the HPLC-based method developed here in a wide range of biological matrices. Material and methods: All experiments were performed on a Hitachi LaChrom Elite® HPLC system and separation was carried out using a Lichrocart® 250-4 Lichrospher 100 RP-18 (5μm) column. The method was further validated according to ICH guidelines. The biological matrices tested were serum, whole blood, urine, B16 F-10 melanoma cell line, growth medium conditioned with the same cell line, bacterial and yeast suspensions. Results: From all the protocols tested, the best results were obtained using 0.5% CH3COOH:MeOH:H2O (15:15:70) as the mobile phase, with detection at wavelengths 215, 276 and 356 nm, at 25ºC, and using a flow rate of 1 mL/min. By using this protocol, it was possible to obtain a linear calibration curve (correlation coefficient = 1), limits of detection and quantification in the order of ng/mL, and a short analysis time (<15 minutes per sample). Additionally, the developed protocol allowed the successful detection and quantification of 3-NT in all biological matrices tested, with detection at 356 nm. Conclusion: The method described in this study, which was successfully developed and validated for 3-NT quantification, is simple, cheap and fast, rendering it suitable for analysis in a wide range of biological matrices.

Texture-Detail Preservation Measurement in Camera Phones: An Updated Approach

Recent advances in mobile phone cameras have poised them to take over compact hand-held cameras as the consumer’s preferred camera option. Along with advances in the number of pixels, motion blur removal, face-tracking, and noise reduction algorithms have significant roles in the internal processing of the devices. An undesired effect of severe noise reduction is the loss of texture (i.e. low-contrast fine details) of the original scene. Current established methods for resolution measurement fail to accurately portray the texture loss incurred in a camera system. The development of an accurate objective method to identify the texture preservation or texture reproduction capability of a camera device is important in this regard. The ‘Dead Leaves’ target has been used extensively as a method to measure the modulation transfer function (MTF) of cameras that employ highly non-linear noise-reduction methods. This stochastic model consists of a series of overlapping circles with radii r distributed as r−3, and having uniformly distributed gray level, which gives an accurate model of occlusion in a natural setting and hence mimics a natural scene. This target can be used to model the texture transfer through a camera system when a natural scene is captured. In the first part of our study we identify various factors that affect the MTF measured using the ‘Dead Leaves’ chart. These include variations in illumination, distance, exposure time and ISO sensitivity among others. We discuss the main differences of this method with the existing resolution measurement techniques and identify the advantages. In the second part of this study, we propose an improvement to the current texture MTF measurement algorithm. High frequency residual noise in the processed image contains the same frequency content as fine texture detail, and is sometimes reported as such, thereby leading to inaccurate results. A wavelet thresholding based denoising technique is utilized for modeling the noise present in the final captured image. This updated noise model is then used for calculating an accurate texture MTF. We present comparative results for both algorithms under various image capture conditions.

Equity research – CTT Correios de Portugal, S.A.

Dissertação de Mestrado, Gestão Empresarial, Faculdade de Economia, Universidade do Algarve, 2016

Influência da gestão do habitat na distribuição e abundância do coelho-bravo no Sítio Natura 2000 Monchique

O coelho-bravo, devido à sua importância ecológica e económica, tem sido alvo de diversos planos de gestão e vários esforços têm sido empreendidos no sentido de contrariar o decréscimo das suas populações. Este estudo foi realizado em três zonas de caça do Sítio Monchique e o principal objectivo é determinar se as medidas de gestão implementadas influenciam a distribuição e abundância da espécie na área de estudo. A abundância relativa foi interpolada com o método "Inverso do Peso da Distância" {IDW), e as relações entre presença de coelho e os descritores ambientais foram analisadas através de Modelos Lineares Generalizados (GLM). Os resultados da modelação estatística mostraram que as medidas de melhoria de habitat parecem ter sido determinantes para um aumento da área de distribuição do coelho-bravo nos locais intervencionados. São propostas novas medidas de gestão, cujo objectivo será promover a continuação do aumento da ocorrência e abundância da espécie neste local. /ABSTRACT: The wild rabbit, due to its ecological and economical role, has been the target of several management plans and considerable efforts have been made to enhance its populations. This study was held in three game estates located inside Monchique Natura 2000. Site and aims to determine if the habitat management actions implemented in the study area influence rabbit distribution and abundance. The relative abundance was interpolated to all study area with lnverse Distance Weight method {IDW} and the relationships between rabbit presence and the environmental descriptors were evaluated with Generalized Linear Models (GLM). The results of the statistical modelling showed that the management actions seem to have contributed significantly to an enhancement on the rabbit occurrence in the studied game estates. Several new management actions are proposed with the aim to continue to increase rabbit occurrence and abundance in this site.

“Albedo dome”: a method for measuring spectral flux-reflectance in a laboratory for media with long optical paths

A method is presented for accurate measurement of spectral flux-reflectance (albedo) in a laboratory, for media with long optical path lengths, such as snow and ice. The approach uses an acrylic hemispheric dome, which, when placed over the surface being studied, serves two functions: (i) it creates an overcast “sky” to illuminate the target surface from all directions within a hemisphere, and (ii) serves as a platform for measuring incident and backscattered spectral radiances, which can be integrated to obtain fluxes. The fluxes are relative measurements and because their ratio is used to determine flux-reflectance, no absolute radiometric calibrations are required. The dome and surface must meet minimum size requirements based on the scattering properties of the surface. This technique is suited for media with long photon path lengths since the backscattered illumination is collected over a large enough area to include photons that reemerge from the domain far from their point of entry because of multiple scattering and small absorption. Comparison between field and laboratory albedo of a portable test surface demonstrates the viability of this method.

Congenital thoracic vertebral malformations in brachycephalic “screw-tailed” dog breeds: Validation of a human classification scheme and a method of Cobb angle measurement in the assessment of vertebral column deformity

Congenital vertebral malformations are common in brachycephalic “screw-tailed” dog breeds such as French bulldogs, English bulldogs, Boston terriers, and Pugs. Those vertebral malformations disrupt the normal vertebral column anatomy and biomechanics, potentially leading to deformity of the vertebral column and subsequent neurological dysfunction. The initial aim of this work was to study and determine whether the congenital vertebral malformations identified in those breeds could be translated in a radiographic classification scheme used in humans to give an improved classification, with clear and well-defined terminology, with the expectation that this would facilitate future study and clinical management in the veterinary field. Therefore, two observers who were blinded to the neurologic status of the dogs classified each vertebral malformation based on the human classification scheme of McMaster and were able to translate them successfully into a new classification scheme for veterinary use. The following aim was to assess the nature and the impact of vertebral column deformity engendered by those congenital vertebral malformations in the target breeds. As no gold standard exists in veterinary medicine for the calculation of the degree of deformity, it was elected to adapt the human equivalent, termed the Cobb angle, as a potential standard reference tool for use in veterinary practice. For the validation of the Cobb angle measurement method, a computerised semi-automatic technique was used and assessed by multiple independent observers. They observed not only that Kyphosis was the most common vertebral column deformity but also that patients with such deformity were found to be more likely to suffer from neurological deficits, more especially if their Cobb angle was above 35 degrees.