Disposable polyester-toner electrophoresis microchips for DNA analysis

Microchip electrophoresis has become a powerful tool for DNA separation, offering all of the advantages typically associated with miniaturized techniques: high speed, high resolution, ease of automation, and great versatility for both routine and research applications. Various substrate materials have been used to produce microchips for DNA separations, including conventional (glass, silicon, and quartz) and alternative (polymers) platforms. In this study, we perform DNA separation in a simple and low-cost polyester-toner (PeT)-based electrophoresis microchip. PeT devices were fabricated by a direct-printing process using a 600 dpi-resolution laser printer. DNA separations were performed on PeT chip with channels filled with polymer solutions (0.5% m/v hydroxyethylcellulose or hydroxypropylcellulose) at electric fields ranging from 100 to 300Vcm(-1). Separation of DNA fragments between 100 and 1000 bp, with good correlation of the size of DNA fragments and mobility, was achieved in this system. Although the mobility increased with increasing electric field, separations showed the same profile regardless of the electric field. The system provided good separation efficiency (215 000 plates per m for the 500 bp fragment) and the separation was completed in 4 min for 1000 bp fragment ladder. The cost of a given chip is approximately $0.15 and it takes less than 10 minutes to prepare a single device.

Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus)

Abstract Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.

A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks

The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical behavior displaying the degree of robustness typical of the biological cell cycle. The structure of our PGN model was inspired in well-established biological facts such as the existence of integrator subsystems, negative and positive feedback loops, and redundant signaling pathways. Our model represents genes interactions as stochastic processes and presents strong robustness in the presence of moderate noise and parameters fluctuations. A recently published deterministic yeast cell-cycle model does not perform as well as our PGN model, even upon moderate noise conditions. In addition, self stimulatory mechanisms can give our PGN model the possibility of having a pacemaker activity similar to the observed in the oscillatory embryonic cell cycle.

Six-month evaluation of a resin/dentin interface created by methacrylate and silorane-based materials

Objectives: This study aimed to compare the micro-tensile bond strength of methacrylate resin systems to a silorane-based restorative system on dentin after 24 hours and six months water storage. Material and Methods: The restorative systems Adper Single Bond 2/Filtek Z350 (ASB), Clearfil SE Bond/Z350 (CF), Adper SE Plus/Z350 (ASEP) and P90 Adhesive System/Filtek P90 (P90) were applied on flat dentin surfaces of 20 third molars (n=5). The restored teeth were sectioned perpendicularly to the bonding interface to obtain sticks (0.8 mm2) to be tested after 24 hours (24 h) and 6 months (6 m) of water storage, in a universal testing machine at 0.5 mm/min. The data was analyzed via two-way Analysis of Variance/Bonferroni post hoc tests at 5% global significance. Results: Overall outcomes did not indicate a statistical difference for the resin systems (p=0.26) nor time (p=0.62). No interaction between material × time was detected (p=0.28). Mean standard-deviation in MPa at 24 h and 6 m were: ASB 31.38 (4.53) and 30.06 (1.95), CF 34.26 (3.47) and 32.75 (4.18), ASEP 29.54 (4.14) and 33.47 (2.47), P90 30.27 (2.03) and 31.34 (2.19). Conclusions: The silorane-based system showed a similar performance to methacrylate-based materials on dentin. All systems were stable in terms of bond strength up to 6 month of water storage.

Recent advances in the development of magnetically recoverable metal nanoparticle catalysts

The aim of this Account is to provide an overview of our current research activities on the design and modification of superparamagnetic nanomaterials for application in the field of magnetic separation and catalysis. First, an introduction of magnetism and magnetic separation is done. Then, the synthetic strategies that have been developed for generating superparamagnetic nanoparticles spherically coated by silica and other oxides, with a focus on well characterized systems prepared by methods that generate samples of high quality and easy to scale-up, are discussed. A set of magnetically recoverable catalysts prepared in our research group by the unique combination of superparamagnetic supports and metal nanoparticles is highlighted. This Account is concluded with personal remarks and perspectives on this research field.

Matrix-vector multiplication and triangular linear solver using GPGPU for symmetric positive definite matrices derived from elliptic equations

The modern GPUs are well suited for intensive computational tasks and massive parallel computation. Sparse matrix multiplication and linear triangular solver are the most important and heavily used kernels in scientific computation, and several challenges in developing a high performance kernel with the two modules is investigated. The main interest it to solve linear systems derived from the elliptic equations with triangular elements. The resulting linear system has a symmetric positive definite matrix. The sparse matrix is stored in the compressed sparse row (CSR) format. It is proposed a CUDA algorithm to execute the matrix vector multiplication using directly the CSR format. A dependence tree algorithm is used to determine which variables the linear triangular solver can determine in parallel. To increase the number of the parallel threads, a coloring graph algorithm is implemented to reorder the mesh numbering in a pre-processing phase. The proposed method is compared with parallel and serial available libraries. The results show that the proposed method improves the computation cost of the matrix vector multiplication. The pre-processing associated with the triangular solver needs to be executed just once in the proposed method. The conjugate gradient method was implemented and showed similar convergence rate for all the compared methods. The proposed method showed significant smaller execution time.

Resonant States in Negative Ions

Resonant states are multiply excited states in atoms and ions that have enough energy to decay by emitting an electron. The ability to emit an electron and the strong electron correlation (which is extra strong in negative ions) makes these states both interesting and challenging from a theoretical point of view. The main contribution in this thesis is a method, which combines the use of B splines and complex rotation, to solve the three-electron Schrödinger equation treating all three electrons equally. It is used to calculate doubly excited and triply excited states of 4S symmetry with even parity in He-. For the doubly excited states there are experimental and theoretical data to compare with. For the triply excited states there is only theoretical data available and only for one of the resonances. The agreement is in general good. For the triply excited state there is a significant and interesting difference in the width between our calculation and another method. A cause for this deviation is suggested. The method is also used to find a resonant state of 4S symmetry with odd parity in H2-. This state, in this extremely negative system, has been predicted by two earlier calculations but is highly controversial. Several other studies presented here focus on two-electron systems. In one, the effect of the splitting of the degenerate H(n=2) thresholds in H-, on the resonant states converging to this threshold, is studied. If a completely degenerate threshold is assumed an infinite series of states is expected to converge to the threshold. Here states of 1P symmetry and odd parity are examined, and it is found that the relativistic and radiative splitting of the threshold causes the series to end after only three resonant states. Since the independent particle model completely fails for doubly excited states, several schemes of alternative quantum numbers have been suggested. We investigate the so called DESB (Doubly Excited Symmetry Basis) quantum numbers in several calculations. For the doubly excited states of He- mentioned above we investigate one resonance and find that it cannot be assigned DESB quantum numbers unambiguously. We also investigate these quantum numbers for states of 1S even parity in He. We find two types of mixing of DESB states in the doubly excited states calculated. We also show that the amount of mixing of DESB quantum numbers can be inferred from the value of the cosine of the inter-electronic angle. In a study on Li- the calculated cosine values are used to identify doubly excited states measured in a photodetachment experiment. In particular a resonant state that violates a propensity rule is found.

Microalgae production improvement for the ICCM´s Marine Fish Hatchery

Máster Oficial en Cultivos Marinos. VI Máster Internacional en Acuicultura. Trabajo presentado como requisito parcial para la obtención del Título de Máster Oficial en Cultivos Marinos, otorgado por la Universidad de Las Palmas de Gran Canaria (ULPGC), el Instituto Canario de Ciencias Marinas (ICCM), y el Centro Internacional de Altos Estudios Agronómicos Mediterráneos de Zaragoza (CIHEAM)

Detección, seguimiento y análisis de personas en streams de vídeo

[ES] El presente TFG consiste en una aplicación para la detección de personas de cuerpo entero. La idea es aplicar este detector a las continuas imágenes recogidas en tiempo real a través de una web-cam, o de un archivo con formato de vídeo que se encuentre ubicado en el propio sistema. El código está escrito en C++. Para conseguir este objetivo nos basamos en el uso conjunto de dos sistemas de detección ya existentes: primero, OpenCV, mediante un método de histograma de gradientes orientados, el cual ya proporciona propiamente un detector de personas que será aplicado a cada una de las imágenes del stream de vídeo; por otro lado, el detector facial de la librería Encara que se aplica a cada una de las detecciones de supuestas personas obtenidas en el método de OpenCV, para comprobar si hay una cara en la supuesta persona detectada. En caso de ser así, y de haber una cara más o menos correctamente situada, determinamos que es realmente una persona. Para cada persona detectada se guardan sus datos de situación en la imagen, en una lista, para posteriormente compararlos con los datos obtenidos en frames anteriores, e intentar hacer un  seguimiento de todas las personas. Visualmente se observaría como se va recuadrando cada persona con un color determinado aleatorio asignado a cada una, mientras se visualiza el vídeo. También se registra la hora y frame de aparición, y la hora y frame de salida, de cada persona detectada, quedando estos datos guardados tanto en un fichero de log, como en una base de datos. Los resultados son, bastante satisfactorios, aunque con posibilidades de mejora, ya que es un trabajo que permite combinar otras técnicas diferentes a las descritas. Debido a la complejidad de los métodos empleados se destaca la necesidad de alta capacidad de computación para poder ejecutar la aplicación en tiempo real sin ralentizaciones. 

Temporal constraints in large optical flow estimation

[EN] The aim of this work is to propose a model for computing the optical flow in a sequence of images. We introduce a new temporal regularizer that is suitable for large displacements. We propose to decouple the spatial and temporal regularizations to avoid an incongruous formulation. For the spatial regularization we use the Nagel-Enkelmann operator and a newly designed temporal regularization. Our model is based on an energy functional that yields a partial differential equation (PDE). This PDE is embedded into a multipyramidal strategy to recover large displacements. A gradient descent technique is applied at each scale to reach the minimum.

Diseño, implementación y verificación de un controlador para robots educativos

[EN] This project briefly analyzes the scope and applications of Industrial Robotics, as well as the importance that this technical discipline has gained in the past decades. In addition, it proposes a modern platform to assist in teaching this discipline in colleges and universities. This new educational platform for the teaching of Industrial Robotics is based on the robotic systems from Rhino Robotics Ltd., using the existing robotic arms and replacing the control electronics by a newer, modern and yet backwards-compatible controller. In addition to the controller, this platform also provides new, up-to-date software utilities that are more intuitive than those provided with the old system. The work to be done consists essentially in receiving commands from a personal computer which the controller must interpret in order to control the motors of the robotic arm. The controller itself will be implemented as an embedded system based on microcontrollers. This requires the implementation of a communication protocol between the personal computer and the microcontroller, the design of a command interpreter, the design of the electronics for motor control using PWM and H-bridges, and the implementation of control techniques (more precisely, PID control). Hence, this project combines software and hardware design and integration techniques with motor control techniques and feedback control methods from Control Engineering, along with the kinematic analysis of the Rhino XR-4 robotic arm. 

3D reconstruction from a vascular tree model

[EN] In this paper, we present a vascular tree model made with synthetic materials and which allows us to obtain images to make a 3D reconstruction.We have used PVC tubes of several diameters and lengths that will let us evaluate the accuracy of our 3D reconstruction. In order to calibrate the camera we have used a corner detector. Also we have used Optical Flow techniques to follow the points through the images going and going back. We describe two general techniques to extract a sequence of corresponding points from multiple views of an object. The resulting sequence of points will be used later to reconstruct a set of 3D points representing the object surfaces on the scene. We have made the 3D reconstruction choosing by chance a couple of images and we have calculated the projection error. After several repetitions, we have found the best 3D location for the point.

Studio di biomateriali usati come scaffold per Tissue Engineering e loro caratterizzazione con tecniche spettroscopiche vibrazionali e di analisi termica

This research investigated someone of the main problems connected to the application of Tissue Engineering in the prosthetic field, in particular about the characterization of the scaffolding materials and biomimetic strategies adopted in order to promote the implant integration. The spectroscopic and thermal analysis techniques were usefully applied to characterize the chemico-physical properties of the materials such as – crystallinity; – relative composition in case of composite materials; – Structure and conformation of polymeric and peptidic chains; – mechanism and degradation rate; – Intramolecular and intermolecular interactions (hydrogen bonds, aliphatic interactions). This kind of information are of great importance in the comprehension of the interactions that scaffold undergoes when it is in contact with biological tissues; this information are fundamental to predict biodegradation mechanisms and to understand how chemico-physical properties change during the degradation process. In order to fully characterize biomaterials, this findings must be integrated by information relative to mechanical aspects and in vitro and in vivo behavior thanks to collaborations with biomedical engineers and biologists. This study was focussed on three different systems that correspond to three different strategies adopted in Tissue Engineering: biomimetic replica of fibrous 3-D structure of extracellular matrix (PCL-PLLA), incorporation of an apatitic phase similar to bone inorganic phase to promote biomineralization (PCL-HA), surface modification with synthetic oligopeptides that elicit the interaction with osteoblasts. The characterization of the PCL-PLLA composite underlined that the degradation started along PLLA fibres, which are more hydrophylic, and they serve as a guide for tissue regeneration. Moreover it was found that some cellular lines are more active in the colonization of the scaffold. In the PCL-HA composite, the weight ratio between the polymeric and the inorganic phase plays an essential role both in the degradation process and in the biomineralization of the material. The study of self-assembling peptides allowed to clarify the influence of primary structure on intermolecular and intermolecular interactions, that lead to the formation of the secondary structure and it was possible to find a new class of oligopeptides useful to functionalize materials surface. Among the analytical techniques used in this study, Raman vibrational spectroscopy played a major role, being non-destructive and non-invasive, two properties that make it suitable to degradation studies and to morphological characterization. Also micro-IR spectroscopy was useful in the comprehension of peptide structure on oxidized titanium: up to date this study was one of the first to employ this relatively new technique in the biomedical field.

Adattamento e acclimatazione a diverse temperature di lieviti psicrofili obbligati e facoltativi e di lieviti mesofili. Studio della produzione di acidi grassi polinsaturi omega-3 e omega-6 per via fermentativa.

Adaptation and acclimation to different temperatures of obligate psychrophilic, facultative psychrophilic and mesophilic yeasts. Production of ω-3 and ω-6 polyunsaturated fatty acids by fermentative way. Obligate psychrophilic, facultative psychrophilic and mesophilic yeasts were cultured in a carbon rich medium at different temperatures to investigate if growth parameters, lipid accumulation and fatty acid composition were adaptive and/or acclimatory responses. Acclimation of facultative psychrophiles and mesophiles to lower temperature negatively affected their specific growth rate. Obligate psychrophiles exhibited the highest biomass yield (YX/S), followed by facultative psychrophiles, then by mesophiles. The growth temperature did not influence the YX/S of facultative psychrophiles and mesophiles. Acclimation to lower temperature caused the increase in lipid yield (YL/X) in mesophilic yeasts, but did not affect YL/X in facultative psychrophiles. Similar YL/X were found in both facultative and obligated psychrophiles, suggesting that lipid accumulation is not a distinctive character of adaptation to permanently cold environments. The extent of unsaturation of fatty acids was one major adaptive feature of the yeasts which colonize permanently cold ecosystems. Remarkable amounts of α-linolenic acid were found in obligate psychrophiles at the expenses of linoleic acid, whereas it was generally scarce or absent in all the others strains. Increased unsaturation of fatty acids was also an acclimatory response of mesophiles and facultative psychrophiles to lower temperature. It’s well known that omega-3 polyunsaturated fatty acids (PUFAs) display a variety of beneficial effects on various organ systems and diseases, therefore a process for the microbial production of omega-3 PUFAs would be of great interest. This work sought also to investigate if one of the better psychrophilic yeast, Rhodotorula glacialis DBVPG 4785, stimulated by acclamatory responses, produced omega-3 PUFAs. In fact, the adaptation of psychrophilic yeasts to cold niches is related to the production of higher amounts of lipids and to increased unsaturation degree of fatty acids, presumably to maintain membrane fluidity and functionality at low temperatures. Bioreactor fermentations of Rhodotorula glacialis DBVPG 4785 were carried out at 25, 20, 15, 10, 5, 0, and -3°C in a complex medium with high C:N ratio for 15 days. High biomass production was attained at all the temperatures with a similar biomass/glucose yield (YXS), between 0.40 and 0.45, but the specific growth rate of the strain decreased as the temperature diminished. The coefficients YL/X have been measured between a minimum of 0.50 to a maximum of 0.67, but it was not possible to show a clear effect of temperature. Similarly, the coefficient YL/S ranges from a minimum of 0.22 to a maximum of 0.28: again, it does not appear to be any significant changes due to temperature. Among omega-3 PUFAs, only α-linolenic acid (ALA, 18:3n-3) was found at temperatures below to 0°C, while, it’s remarkable, that the worthy arachidonic acid (C20:4,n-6), stearidonic acid (C20:4,n-3) C22:0 and docosahexaenoic acid (C22:6n-3) were produced only at the late exponential phase and the stationary phase of batch fermentations at 0 and -3°C. The docosahexaenoic acid (DHA) is a beneficial omega-3 PUFA that is usually found in fatty fish and fish oils. The results herein reported improve the knowledge about the responses which enable psychrophilic yeasts to cope with cold and may support exploitation of these strains as a new resource for biotechnological applications.