Establishment of a fully automatized microfluidic platform for the screening and characterization of novel Hepatitis B virus capsid assembly modulators

El procés de descobriment de fàrmacs s'enfronta a importants desafiaments a causa de la constant disminució dels guanys per medicament atesa la disminució en les noves aprovacions de la FDA combinada amb el constant augment dels costos i el temps de desenvolupament. Les plataformes integrades de detecció usant microfluídica van sorgir com a possibles solucions per accelerar el desenvolupament de molècules actives i reduir els requisits de temps i costos. El projecte VIRO-FLOW té com a objectiu identificar nous agents curatius per al virus de l'hepatitis B (VHB), integrant els avantatges de la química de flux continu amb tecnologies de bioassaigs in vitro en microfluídica. Durant aquesta tesi es va construir un sistema microfluídic aplicant dispositius modulars automatitzats. Es van redactar protocols d'avaluació per a les dades de fluorescència i reflexió, permetent el càlcul del factor Z, les desviacions estàndard, les corbes de dilució i els valors de concentracions efectives mitjanes màximes (EC50). La proteïna central del VHB (HBc) es va seleccionar com a objectiu principalEl proceso de descubrimiento de fármacos se enfrenta a importantes desafíos debido a la constante disminución de las ganancias por medicamento dada la disminución en las nuevas aprobaciones de la FDA combinada con el constante aumento de los costes y el tiempo de desarrollo. Las plataformas integradas de detección usando microfluídica surgieron como posibles soluciones para acelerar el desarrollo de moléculas activas y reducir los requisitos de tiempo y costes. El proyecto VIRO-FLOW tiene como objetivo la identificación de nuevos agentes curativos para el virus de la hepatitis B (VHB), integrando las ventajas de la química de flujo continuo con tecnologías de bioensayos in vitro en microfluídica. Durante la presente tesis se construyó un sistema microfluídico aplicando dispositivos modulares automatizados. Se redactaron protocolos de evaluación para los datos de fluorescencia y reflexión, permitiendo el cálculo del factor Z, desviaciones estándar, curvas de dilución y valores de concentraciones efectivas medias máximas (EC50). La proteína central del VHB (HBc) se seleccionó como objetivo principal.Drug Discovery as known today faces major challenges due to the constant decrease of earnings per drug given the decrease in new FDA approvements combined with the steadily rising development costs and time. Integrated microfluidic screening platforms emerged as possible solutions by accelerating the hit-to-lead development cycle and reducing time and cost requirements. The VIRO-FLOW project aims at the fast and efficient identification of novel curative agents for the Hepatitis B Virus (HBV), integrating the advantages of continuous flow chemistry with in vitro microfluidic bioassay technologies. During the present thesis a microfluidic system was built, applying automatized modular devices. Evaluation protocols were written for the fluorescence and reflection data, allowing the Z´-factor calculation, standard deviations, dilution curves, and half‐maximal effective concentrations (EC50) values. HBV core protein (HBc) was selected as primary target due to the ongoing demand for a functional cure to reduce the economic and social challenges imposed by the chronic diseas

Master slave en-face OCT/SLO

Master Slave optical coherence tomography (MS-OCT) is an OCT method that does not require resampling of data and can be used to deliver en-face images from several depths simultaneously. As the MS-OCT method requires important computational resources, the number of multiple depth en-face images that can be produced in real-time is limited. Here, we demonstrate progress in taking advantage of the parallel processing feature of the MS-OCT technology. Harnessing the capabilities of graphics processing units (GPU)s, information from 384 depth positions is acquired in one raster with real time display of up to 40 en-face OCT images. These exhibit comparable resolution and sensitivity to the images produced using the conventional Fourier domain based method. The GPU facilitates versatile real time selection of parameters, such as the depth positions of the 40 images out of the set of 384 depth locations, as well as their axial resolution. In each updated displayed frame, in parallel with the 40 en-face OCT images, a scanning laser ophthalmoscopy (SLO) lookalike image is presented together with two B-scan OCT images oriented along rectangular directions. The thickness of the SLO lookalike image is dynamically determined by the choice of number of en-face OCT images displayed in the frame and the choice of differential axial distance between them

Optical Indoor Positioning System Based on TFT Technology

A novel indoor positioning system is presented in the paper. Similarly to the camera-based solutions, it is based on visual detection, but it conceptually differs from the classical approaches. First, the objects are marked by LEDs, and second, a special sensing unit is applied, instead of a camera, to track the motion of the markers. This sensing unit realizes a modified pinhole camera model, where the light-sensing area is fixed and consists of a small number of sensing elements (photodiodes), and it is the hole that can be moved. The markers are tracked by controlling the motion of the hole, such that the light of the LEDs always hits the photodiodes. The proposed concept has several advantages: Apart from its low computational demands, it is insensitive to the disturbing ambient light. Moreover, as every component of the system can be realized by simple and inexpensive elements, the overall cost of the system can be kept low

ENER-BI: Integrating Energy and Spatial Data for Cities’ Decarbonisation Planning

Given the current climate emergency, our planet is suffering. Mitigation measures must be urgently deployed in urban environments, which are responsible for more than 70% of global CO2 emissions. In this sense, a deeper integration between energy and urban planning disciplines is a key factor for effective decarbonisation in urban environments. This is addressed in the Cities4ZERO decarbonisation methodology. This method specifically points out the need for technology-based solutions able to support that integration among both disciplines at a local level, enriching decision-making in urban decarbonisation policy-making, diagnosis, planning, and follow-up tasks, incorporating the spatial dimension to the whole process (GIS-based), as well as the possibilities of the digital era. Accordingly, this paper explores the demands of both integrated urban energy planning and European/Basque energy directives, to set the main requisites and functionalities that Decision Support Systems (DSSs) must fulfil to effectively support city managers and the urban decarbonisation process.This research was funded by European Commission, grant number 691883

ENER-BI: Integrating Energy and Spatial Data for Cities’ Decarbonisation Planning

Given the current climate emergency, our planet is suffering. Mitigation measures must be urgently deployed in urban environments, which are responsible for more than 70% of global CO2 emissions. In this sense, a deeper integration between energy and urban planning disciplines is a key factor for effective decarbonisation in urban environments. This is addressed in the Cities4ZERO decarbonisation methodology. This method specifically points out the need for technology-based solutions able to support that integration among both disciplines at a local level, enriching decision-making in urban decarbonisation policy-making, diagnosis, planning, and follow-up tasks, incorporating the spatial dimension to the whole process (GIS-based), as well as the possibilities of the digital era. Accordingly, this paper explores the demands of both integrated urban energy planning and European/Basque energy directives, to set the main requisites and functionalities that Decision Support Systems (DSSs) must fulfil to effectively support city managers and the urban decarbonisation process.This research was funded by European Commission, grant number 691883

Neural correlates of the processing of co-speech gestures

In communicative situations, speech is often accompanied by gestures. For example, speakers tend to illustrate certain contents of speech by means of iconic gestures which are hand movements that bear a formal relationship to the contents of speech. The meaning of an iconic gesture is determined both by its form as well as the speech context in which it is performed. Thus, gesture and speech interact in comprehension. Using fMRI, the present study investigated what brain areas are involved in this interaction process. Participants watched videos in which sentences containing an ambiguous word (e.g. She touched the mouse) were accompanied by either a meaningless grooming movement, a gesture supporting the more frequent dominant meaning (e.g. animal) or a gesture supporting the less frequent subordinate meaning (e.g. computer device). We hypothesized that brain areas involved in the interaction of gesture and speech would show greater activation to gesture-supported sentences as compared to sentences accompanied by a meaningless grooming movement. The main results are that when contrasted with grooming, both types of gestures (dominant and subordinate) activated an array of brain regions consisting of the left posterior superior temporal sulcus (STS), the inferior parietal lobule bilaterally and the ventral precentral sulcus bilaterally. Given the crucial role of the STS in audiovisual integration processes, this activation might reflect the interaction between the meaning of gesture and the ambiguous sentence. The activations in inferior frontal and inferior parietal regions may reflect a mechanism of determining the goal of co-speech hand movements through an observation-execution matching process

Automatic image analysis of C-arm Computed Tomography images for ankle joint surgeries

Open reduction and internal fixation is a standard procedure in ankle surgery for treating a fractured fibula. Since fibula fractures are often accompanied by an injury of the syndesmosis complex, it is essential to restore the correct relative pose of the fibula relative to the adjoining tibia for the ligaments to heal. Otherwise, the patient might experience instability of the ankle leading to arthritis and ankle pain and ultimately revision surgery. Incorrect positioning referred to as malreduction of the fibula is assumed to be one of the major causes of unsuccessful ankle surgery. 3D C-arm imaging is the current standard procedure for revealing malreduction of fractures in the operating room. However, intra-operative visual inspection of the reduction result is complicated due to high inter-individual variation of the ankle anatomy and rather based on the subjective experience of the surgeon. A contralateral side comparison with the patient’s uninjured ankle is recommended but has not been integrated into clinical routine due to the high level of radiation exposure it incurs. This thesis presents the first approach towards a computer-assisted intra-operative contralateral side comparison of the ankle joint. The focus of this thesis was the design, development and validation of a software-based prototype for a fully automatic intra-operative assistance system for orthopedic surgeons. The implementation does not require an additional 3D C-arm scan of the uninjured ankle, thus reducing time consumption and cumulative radiation dose. A 3D statistical shape model (SSM) is used to reconstruct a 3D surface model from three 2D fluoroscopic projections representing the uninjured ankle. To this end, a 3D SSM segmentation is performed on the 3D image of the injured ankle to gain prior knowledge of the ankle. A 3D convolutional neural network (CNN) based initialization method was developed and its outcome was incorporated into the SSM adaption step. Segmentation quality was shown to be improved in terms of accuracy and robustness compared to the pure intensity-based SSM. This allows us to overcome the limitations of the previously proposed methods, namely inaccuracy due to metal artifacts and the lack of device-to-patient orientation of the C-arm. A 2D-CNN is employed to extract semantic knowledge from all fluoroscopic projection images. This step of the pipeline both creates features for the subsequent reconstruction and also helps to pre-initialize the 3D-SSM without user interaction. A 2D-3D multi-bone reconstruction method has been developed which uses distance maps of the 2D features for fast and accurate correspondence optimization and SSM adaption. This is the central and most crucial component of the workflow. This is the first time that a bone reconstruction method has been applied to the complex ankle joint and the first reconstruction method using CNN based segmentations as features. The reconstructed 3D-SSM of the uninjured ankle can be back-projected and visualized in a workflow-oriented manner to procure clear visualization of the region of interest, which is essential for the evaluation of the reduction result. The surgeon can thus directly compare an overlay of the contralateral ankle with the injured ankle. The developed methods were evaluated individually using data sets acquired during a cadaver study and representative clinical data acquired during fibular reduction. A hierarchical evaluation was designed to assess the inaccuracies of the system on different levels and to identify major sources of error. The overall evaluation performed on eleven challenging clinical datasets acquired for manual contralateral side comparison showed that the system is capable of accurately reconstructing 3D surface models of the uninjured ankle solely using three projection images. A mean Hausdorff distance of 1.72 mm was measured when comparing the reconstruction result to the ground truth segmentation and almost achieved the high required clinical accuracy of 1-2 mm. The overall error of the pipeline was mainly attributed to inaccuracies in the 2D-CNN segmentation. The consistency of these results requires further validation on a larger dataset. The workflow proposed in this thesis establishes the first approach to enable automatic computer-assisted contralateral side comparison in ankle surgery. The feasibility of the proposed approach was proven on a limited amount of clinical cases and has already yielded good results. The next important step is to alleviate the identified bottlenecks in the approach by providing more training data in order to further improve the accuracy. In conclusion, the new approach presented gives the chance to guide the surgeon during the reduction process, improve the surgical outcome while avoiding additional radiation exposure and reduce the number of revision surgeries in the long term

Theoretical and experimental evidence of level repulsion states and evanescent modes in sonic crystal stubbed waveguides

The complex band structures calculated using the Extended Plane Wave Expansion (EPWE) reveal the presence of evanescent modes in periodic systems, never predicted by the classical \omega(\vec{k}) methods, providing novel interpretations of several phenomena as well as a complete picture of the system. In this work we theoretically and experimentally observe that in the ranges of frequencies where a deaf band is traditionally predicted, an evanescent mode with the excitable symmetry appears changing drastically the interpretation of the transmission properties. On the other hand, the simplicity of the sonic crystals in which only the longitudinal polarization can be excited, is used to interpret, without loss of generality, the level repulsion between symmetric and antisymmetric bands in sonic crystals as the presence of an evanescent mode connecting both repelled bands. These evanescent modes, obtained using EPWE, explain both the attenuation produced in this range of frequencies and the transfer of symmetry from one band to the other in good agreement with both experimental results and multiple scattering predictions. Thus, the evanescent properties of the periodic system have been revealed necessary for the design of new acoustic and electromagnetic applications based on periodicity

Optical Feedback Loop in Paraxial Fluids of Light: A Gate to new phenomena in analogue physical simulations

Easily accessible through tabletop experiments based on laser propagation inside nonlinear optical media, Paraxial Fluids of Light are emerging as promising platforms for the simulation and exploration of quantum-like phenomena. In particular, the analogy builds on a formal equivalence between the governing model for a Bose-Einstein Condensate under the mean-field approximation and the model of laser propagation under the paraxial approximation. Yet, the fact that the role of time is played by the propagation distance in the optical analogue system may impose strong bounds on the range of accessible phenomena due to the limited length of the nonlinear medium. In this manuscript, we present a novel experimental approach to solve this limitation in the form of an optical feedback loop, which consists of the reconstruction of the optical states at the end of the system followed by their subsequent re-injection exploiting wavefront shaping techniques. The results enclosed demonstrate the potential of this approach to access unprecedented dynamics, paving for the observation of novel phenomena in these systems