Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

This project was carried out during CD’s BBSRC Eastbio PIPS placement at Marine Scotland. The authors are grateful to Dr Milena Monte (University of Aberdeen) for help with the FACS analysis. The authors wish to thank Dr Filippo Del Bene (Neuronal Circuit Development, Institut Curie) and Dr Wenbiao Chen (School of Medicine, Vanderbilt University) for the Addgene plasmids, #61051 and #47929, respectively, and Prof. Nancy C. Reich Marshall (Department of Molecular Genetics and Microbiology, Stony Brooks University) for the plasmid pmEGFP-N1.

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

This project was carried out during CD’s BBSRC Eastbio PIPS placement at Marine Scotland. The authors are grateful to Dr Milena Monte (University of Aberdeen) for help with the FACS analysis. The authors wish to thank Dr Filippo Del Bene (Neuronal Circuit Development, Institut Curie) and Dr Wenbiao Chen (School of Medicine, Vanderbilt University) for the Addgene plasmids, #61051 and #47929, respectively, and Prof. Nancy C. Reich Marshall (Department of Molecular Genetics and Microbiology, Stony Brooks University) for the plasmid pmEGFP-N1.

Organometallic derivatives of cyclotriphosphazene as precursors of nanostructured metallic materials: a new solid state method

The cyclic phosphazene trimers [N3P3(OC6H5)5OC5H4N·Ti(Cp)2Cl][PF6] (3), [N3P3(OC6H4CH2CN·Ti(Cp)2Cl)6][PF6]6 (4), [N3P3(OC6H4-But)5(OC6H4CH2CN·Ti(Cp)2Cl)][PF6] (5), [N3P3(OC6H5)5C6H4CH2CN·Ru(Cp)(PPh3)2][PF6] (6), [N3P3(OC6H5)5C6H4CH2CN·Fe(Cp)(dppe)][PF6] (7) and N3P3(OC6H5)5OC5H4N·W(CO)5 (8) were prepared and characterized. As a model, the simple compounds [HOC5H5N·Ti(Cp)2Cl]PF6 (1) and [HOC6H4CH2CN·Ti(Cp)2Cl]PF6 (2) were also prepared and characterized. Pyrolysis of the organometallic cyclic trimers in air yields metallic nanostructured materials, which according to transmission and scanning electron microscopy (TEM/SEM), energy-dispersive X-ray microanalysis (EDX), and IR data, can be formulated as either a metal oxide, metal pyrophosphate or a mixture in some cases, depending on the nature and quantity of the metal, characteristics of the organic spacer and the auxiliary substituent attached to the phosphorus cycle. Atomic force microscopy (AFM) data indicate the formation of small island and striate nanostructures. A plausible formation mechanism which involves the formation of a cyclomatrix is proposed, and the pyrolysis of the organometallic cyclic phosphazene polymer as a new and general method for obtaining metallic nanostructured materials is discussed.

Collimation of a D-D Neutron Generator for Clinical Implementation of Neutron Stimulated Emission Computed Tomography: a Monte Carlo Study

This work is an investigation into collimator designs for a deuterium-deuterium (DD) neutron generator for an inexpensive and compact neutron imaging system that can be implemented in a hospital. The envisioned application is for a spectroscopic imaging technique called neutron stimulated emission computed tomography (NSECT).

Previous NSECT studies have been performed using a Van-de-Graaff accelerator at the Triangle Universities Nuclear Laboratory (TUNL) in Duke University. This facility has provided invaluable research into the development of NSECT. To transition the current imaging method into a clinically feasible system, there is a need for a high-intensity fast neutron source that can produce collimated beams. The DD neutron generator from Adelphi Technologies Inc. is being explored as a possible candidate to provide the uncollimated neutrons. This DD generator is a compact source that produces 2.5 MeV fast neutrons with intensities of 1012 n/s (4π). The neutron energy is sufficient to excite most isotopes of interest in the body with the exception of carbon and oxygen. However, a special collimator is needed to collimate the 4π neutron emission into a narrow beam. This work describes the development and evaluation of a series of collimator designs to collimate the DD generator for narrow beams suitable for NSECT imaging.

A neutron collimator made of high-density polyethylene (HDPE) and lead was modeled and simulated using the GEANT4 toolkit. The collimator was designed as a 52 x 52 x 52 cm3 HDPE block coupled with 1 cm lead shielding. Non-tapering (cylindrical) and tapering (conical) opening designs were modeled into the collimator to permit passage of neutrons. The shape, size, and geometry of the aperture were varied to assess the effects on the collimated neutron beam. Parameters varied were: inlet diameter (1-5 cm), outlet diameter (1-5 cm), aperture diameter (0.5-1.5 cm), and aperture placement (13-39 cm). For each combination of collimator parameters, the spatial and energy distributions of neutrons and gammas were tracked and analyzed to determine three performance parameters: neutron beam-width, primary neutron flux, and the output quality. To evaluate these parameters, the simulated neutron beams are then regenerated for a NSECT breast scan. Scan involved a realistic breast lesion implanted into an anthropomorphic female phantom.

This work indicates potential for collimating and shielding a DD neutron generator for use in a clinical NSECT system. The proposed collimator designs produced a well-collimated neutron beam that can be used for NSECT breast imaging. The aperture diameter showed a strong correlation to the beam-width, where the collimated neutron beam-width was about 10% larger than the physical aperture diameter. In addition, a collimator opening consisting of a tapering inlet and cylindrical outlet allowed greater neutron throughput when compared to a simple cylindrical opening. The tapering inlet design can allow additional neutron throughput when the neck is placed farther from the source. On the other hand, the tapering designs also decrease output quality (i.e. increase in stray neutrons outside the primary collimated beam). All collimators are cataloged in measures of beam-width, neutron flux, and output quality. For a particular NSECT application, an optimal choice should be based on the collimator specifications listed in this work.

Method to Improve the Linearity of Active Commutating Mixers Using Dynamic Current Injection

A double balanced (DBM) CMOS mixer providing high linearity is presented in this paper. A cross-coupled pair used in the IF stage of the mixer to dynamically inject current into the to mixer provide a high linearity. The proposed DBM was fabricated using a standard 130-nm CMOS process and was tested on-wafer. The double balanced mixer delivers 10 dB conversion gain, 9.5 dBm IIP3, and input P1dB of -2.4 dBm. RF bandwidth of the proposed mixer is 6 GHz, covering 0.5 GHz to 6.5 GHz with IF bandwidth of 300 MHz. RF to IF and LO to IF isolation are also better than 59 dB in the whole frequency band. The circuit uses an area of 0.015 mm2 excluding bonding pads and draw 4.5mW from a 1.2V supply.

Attack simulation based software protection assessment method

Software protection is an essential aspect of information security to withstand malicious activities on software, and preserving software assets. However, software developers still lacks a methodology for the assessment of the deployed protections. To solve these issues, we present a novel attack simulation based software protection assessment method to assess and compare various protection solutions. Our solution relies on Petri Nets to specify and visualize attack models, and we developed a Monte Carlo based approach to simulate attacking processes and to deal with uncertainty. Then, based on this simulation and estimation, a novel protection comparison model is proposed to compare different protection solutions. Lastly, our attack simulation based software protection assessment method is presented. We illustrate our method by means of a software protection assessment process to demonstrate that our approach can provide a suitable software protection assessment for developers and software companies.

A deformation model of flexible, high area-to-mass ratio debris under perturbations and validation method

A new type of space debris was recently discovered by Schildknecht in near -geosynchronous orbit (GEO). These objects were later identified as exhibiting properties associated with High Area-to-Mass ratio (HAMR) objects. According to their brightness magnitudes (light curve), high rotation rates and composition properties (albedo, amount of specular and diffuse reflection, colour, etc), it is thought that these objects are multilayer insulation (MLI). Observations have shown that this debris type is very sensitive to environmental disturbances, particularly solar radiation pressure, due to the fact that their shapes are easily deformed leading to changes in the Area-to-Mass ratio (AMR) over time. This thesis proposes a simple effective flexible model of the thin, deformable membrane with two different methods. Firstly, this debris is modelled with Finite Element Analysis (FEA) by using Bernoulli-Euler theory called “Bernoulli model”. The Bernoulli model is constructed with beam elements consisting 2 nodes and each node has six degrees of freedom (DoF). The mass of membrane is distributed in beam elements. Secondly, the debris based on multibody dynamics theory call “Multibody model” is modelled as a series of lump masses, connected through flexible joints, representing the flexibility of the membrane itself. The mass of the membrane, albeit low, is taken into account with lump masses in the joints. The dynamic equations for the masses, including the constraints defined by the connecting rigid rod, are derived using fundamental Newtonian mechanics. The physical properties of both flexible models required by the models (membrane density, reflectivity, composition, etc.), are assumed to be those of multilayer insulation. Both flexible membrane models are then propagated together with classical orbital and attitude equations of motion near GEO region to predict the orbital evolution under the perturbations of solar radiation pressure, Earth’s gravity field, luni-solar gravitational fields and self-shadowing effect. These results are then compared to two rigid body models (cannonball and flat rigid plate). In this investigation, when comparing with a rigid model, the evolutions of orbital elements of the flexible models indicate the difference of inclination and secular eccentricity evolutions, rapid irregular attitude motion and unstable cross-section area due to a deformation over time. Then, the Monte Carlo simulations by varying initial attitude dynamics and deformed angle are investigated and compared with rigid models over 100 days. As the results of the simulations, the different initial conditions provide unique orbital motions, which is significantly different in term of orbital motions of both rigid models. Furthermore, this thesis presents a methodology to determine the material dynamic properties of thin membranes and validates the deformation of the multibody model with real MLI materials. Experiments are performed in a high vacuum chamber (10-4 mbar) replicating space environment. A thin membrane is hinged at one end but free at the other. The free motion experiment, the first experiment, is a free vibration test to determine the damping coefficient and natural frequency of the thin membrane. In this test, the membrane is allowed to fall freely in the chamber with the motion tracked and captured through high velocity video frames. A Kalman filter technique is implemented in the tracking algorithm to reduce noise and increase the tracking accuracy of the oscillating motion. The forced motion experiment, the last test, is performed to determine the deformation characteristics of the object. A high power spotlight (500-2000W) is used to illuminate the MLI and the displacements are measured by means of a high resolution laser sensor. Finite Element Analysis (FEA) and multibody dynamics of the experimental setups are used for the validation of the flexible model by comparing with the experimental results of displacements and natural frequencies.

Aplicación de la medicina ancestral en los usuarios del Centro de Salud Carlos Elizalde. Cuenca 2015

ANTECEDENTES: En gran parte del mundo la medicina tradicional es el pilar principal de la prestación de servicios de salud, por ello en algunos países suele denominarse medicina complementaria. La medicina tradicional ha sufrido transformaciones, y los valores de este tipo de medicina están desapareciendo con rapidez a pesar que la OMS dicta estrategias para su implementación y el MSP del Ecuador reconoce su valor. OBJETIVO GENERAL: Caracterización de la aplicación de la medicina ancestral en los usuarios y usuarias del Centro de Salud “Carlos Elizalde”. METODOLOGIA: Es un estudio cuantitativo descriptivo en el que caracteriza la aplicación de la medicina ancestral en los usuarios del Centro de Salud “Carlos Elizalde”. El método utilizado fue la entrevista previo consentimiento informado realizada, según criterios de inclusión y exclusión a un universo de 110 usuarios, en la tabulación de datos se utilizó el programa SPSS Windows y Excel, y estos fueron analizados en tablas simples y gráficos. RESULTADOS: Los resultados obtenidos han servido para identificar la aplicación la Medicina Ancestral en los usuarios que acuden al Centro de Salud “Carlos Elizalde” de la Parroquia Yanuncay, identificando a las personas que más acuden al tratamiento son adultos con 71% y adultos mayores con un 16%, la mayoría son amas de casa en un 38%, con instrucción de primaria incompleta, es las enfermedades más frecuentes son espanto con un 36%, mal aire 18% y 10% caída de zhungo; para el tratamiento utilizan plantas o hiervas en un 54%

Evaluating tests for convergence of economic series using Monte Carlo methods with an application to real GDP's per head.

Doutoramento em Economia.

Análise de DFA e de agrupamento do perfil de densidade de poços de petróleo

In recent years, the DFA introduced by Peng, was established as an important tool capable of detecting long-range autocorrelation in time series with non-stationary. This technique has been successfully applied to various areas such as: Econophysics, Biophysics, Medicine, Physics and Climatology. In this study, we used the DFA technique to obtain the Hurst exponent (H) of the profile of electric density profile (RHOB) of 53 wells resulting from the Field School of Namorados. In this work we want to know if we can or not use H to spatially characterize the spatial data field. Two cases arise: In the first a set of H reflects the local geology, with wells that are geographically closer showing similar H, and then one can use H in geostatistical procedures. In the second case each well has its proper H and the information of the well are uncorrelated, the profiles show only random fluctuations in H that do not show any spatial structure. Cluster analysis is a method widely used in carrying out statistical analysis. In this work we use the non-hierarchy method of k-means. In order to verify whether a set of data generated by the k-means method shows spatial patterns, we create the parameter Ω (index of neighborhood). High Ω shows more aggregated data, low Ω indicates dispersed or data without spatial correlation. With help of this index and the method of Monte Carlo. Using Ω index we verify that random cluster data shows a distribution of Ω that is lower than actual cluster Ω. Thus we conclude that the data of H obtained in 53 wells are grouped and can be used to characterize space patterns. The analysis of curves level confirmed the results of the k-means

Propuesta de una metodología de entrenamiento funcional para el personal docente de la Unidad Educativa Técnico Salesiano campus Carlos Crespi de la ciudad de Cuenca 2015

El presente trabajo de titulación comprende la elaboración de una propuesta metodológica, a través del Entrenamiento Funcional en Docentes, como un método de Recreación, siendo estas actividades una manera diferente de ejercitarse y teniendo como carga el propio peso corporal, haciendo que el trabajo físico sea más fácil de ejecutar. A su vez este programa se aplica a un universo de 20 personas pertenecientes a la Unidad Educativa Técnico Salesiano Campus Carlos Crespi de la ciudad de Cuenca La realización de este trabajo de graduación consta de 4 capítulos donde se detallará en cada uno de ellos: el Entrenamiento Funcional y la Cultura Física, Particularidades del Docente y del Entrenamiento Funcional, Planificación del Macrociclo de Entrenamiento Funcional para el docente escolar, y la Aplicación de la Propuesta. Al realizar esta propuesta considero que es de gran utilidad, ya que en la actualidad este es un novedoso método de ejercitación en la Ciudad de Cuenca y en el país. Por lo tanto el Entrenamiento Funcional se está convirtiendo en una nueva forma de hacer ejercitarse, el cual se puede ejecutar con personas de diferentes edad, capacidad y condición física.

Evocation to the Dr. Carlos J. Finlay Barres on the centennial of his death

About the editorial of the Professor Guillermo Llanos: "Carlos J. Finlay: the forgotten Pasteur of America", a hundred years after his death and through a documental review, a summary of the life and work of this great man of science was conducted. Finlay was a notable figure of the American medicine, he conceived a new infection way able to explain the propagation of the yellow fever, and added the possibility of their scientific confirmation by an experimental method. For all the above-mentioned Finlay was recognized as the humanity's benefactor.

VALIDATION OF A 'DISPLACEMENT TOMOGRAPHY' INVERSION METHOD FOR MODELING SHEET INTRUSIONS

The study of volcano deformation data can provide information on magma processes and help assess the potential for future eruptions. In employing inverse deformation modeling on these data, we attempt to characterize the geometry, location and volume/pressure change of a deformation source. Techniques currently used to model sheet intrusions (e.g., dikes and sills) often require significant a priori assumptions about source geometry and can require testing a large number of parameters. Moreover, surface deformations are a non-linear function of the source geometry and location. This requires the use of Monte Carlo inversion techniques which leads to long computation times. Recently, ‘displacement tomography’ models have been used to characterize magma reservoirs by inverting source deformation data for volume changes using a grid of point sources in the subsurface. The computations involved in these models are less intensive as no assumptions are made on the source geometry and location, and the relationship between the point sources and the surface deformation is linear. In this project, seeking a less computationally intensive technique for fracture sources, we tested if this displacement tomography method for reservoirs could be used for sheet intrusions. We began by simulating the opening of three synthetic dikes of known geometry and location using an established deformation model for fracture sources. We then sought to reproduce the displacements and volume changes undergone by the fractures using the sources employed in the tomography methodology. Results of this validation indicate the volumetric point sources are not appropriate for locating fracture sources, however they may provide useful qualitative information on volume changes occurring in the surrounding rock, and therefore indirectly indicate the source location.

Hybrid Monte Carlo algorithm for the double exchange model

The Hybrid Monte Carlo algorithm is adapted to the simulation of a system of classical degrees of freedom coupled to non self-interacting lattices fermions. The diagonalization of the Hamiltonian matrix is avoided by introducing a path-integral formulation of the problem, in d + 1 Euclidean space–time. A perfect action formulation allows to work on the continuum Euclidean time, without need for a Trotter–Suzuki extrapolation. To demonstrate the feasibility of the method we study the Double Exchange Model in three dimensions. The complexity of the algorithm grows only as the system volume, allowing to simulate in lattices as large as 163 on a personal computer. We conclude that the second order paramagnetic–ferromagnetic phase transition of Double Exchange Materials close to half-filling belongs to the Universality Class of the three-dimensional classical Heisenberg model.

The Power of the Synthetic Control Method

The synthetic control method (SCM) is a new, popular method developed for the purpose of estimating the effect of an intervention when only one single unit has been exposed. Other similar, unexposed units are combined into a synthetic control unit intended to mimic the evolution in the exposed unit, had it not been subject to exposure. As the inference relies on only a single observational unit, the statistical inferential issue is a challenge. In this paper, we examine the statistical properties of the estimator, study a number of features potentially yielding uncertainty in the estimator, discuss the rationale for statistical inference in relation to SCM, and provide a Web-app for researchers to aid in their decision of whether SCM is powerful for a specific case study. We conclude that SCM is powerful with a limited number of controls in the donor pool and a fairly short pre-intervention time period. This holds as long as the parameter of interest is a parametric specification of the intervention effect, and the duration of post-intervention period is reasonably long, and the fit of the synthetic control unit to the exposed unit in the pre-intervention period is good.