Modelling and segmentation of the vocal track during speech production by using deformable models in magnetic resonance images

The first and second authors would like to thank the support of the PhD grants with references SFRH/BD/28817/2006 and SFRH/PROTEC/49517/2009, respectively, from Fundação para a Ciência e Tecnol ogia (FCT). This work was partially done in the scope of the project “Methodologies to Analyze Organs from Complex Medical Images – Applications to Fema le Pelvic Cavity”, wi th reference PTDC/EEA- CRO/103320/2008, financially supported by FCT.Since ancient times, speech production has attracted particularly interest aiming at reaching a deeper understanding of the mechanisms involved by considering both morphological and speech acoustic aspects. The central anatomical aspects and the physiology of the human vocal tract are common to all individuals. However, speech production is an exceptionally complex and individualistic process. Therefore, the modelling of the mechanisms involved in speech production implies the enclosing of adequate flexibility in order to consider individual variations accurately. In this work, the shape of vocal tract in the articulation of some European Portuguese (EP) sounds is evaluated by using deformable models applied in Magnetic Resonance (MR) images. Additionally, the deformable models built are afterwards used to automatically segment the modelled vocal tract in MR images. From the imaging modalities that have been take n into consideration in order to study the vocal tract shape and articulators, Magnetic Resonance Imaging (MRI) has been the most commonly accepted. Actually, the use of MRI allows the study of the entire human vocal tract and, in addition, the quality and resolution of soft-tissues and the use of non-ionizing radiation are key advantages presented by MRI. The deformable model used, commonly known as Point Distribution Model (PDM), was built from a set of training images acquired du ring artificially sustained articulations of 21 EP sounds. In a brief review, one can assert that PDM’s are obtained by a statistical analysis done on the co-ordinates of landmark points that represent the shape to be modelled: after aligning the training shapes, a Principal Component Analysis is performed in order to obtain the model mean shape and the modes of variation relatively to this mean shap e. Combining the geometrical information of the PDM with the grey levels of the landmark points us ed in its building one can build the Active Shape Models (ASM) and the Active Appearance Models (AAM). With these enhanced models is possible to segment the modelled shape in new images in a fully automated way. From the experimental results obtained in this work, one may conclude that the PDM built could efficiently characterize the behaviour of the voca l tract shape during the production of the EP sounds studied with MRI. Furthermore, one can ve rify that the ASM and the AAM built could be used to segment the modelled vocal tract in MR images in a successful manner. Therefore, the deformable models built should be considered towards the efficient and automatic study of the vocal tract during speech production with MRI, in particular for enhanced speech production simulation and speech rehabilitation therapies.Fundação para a Ciência e Tecnologia (FCT

Comando de um Servomecanismo usando Visão Computacional

Neste artigo é apresentada uma metodologia para controlar um servomecanismo usando visão computacional. As imagens de controlo,baseadas na linguagem gestual, são obtidas por intermédio de uma webcam genérica e processadas praticamente em tempo real. Aordem de comando em causa é reconhecida por diferença dos histogramas de orientação da imagem associada e das imagens deordens preestabelecidas. Estas imagens de ordens são guardadas durante o processo de aprendizagem do sistema de controlo.In this paper a methodology to control a servomechanism using computational vision is presented. The control images, based in hand language, are acquired by a generic webcam and processed in quasi real time. The command order in cause is recognized by the difference of the orientation histograms for the associated and preset orders images. These preset orders images are acquired in the learning process of the control system

Magnetic resonance imaging of the vocal tract: techniques and applications

Magnetic resonance (MR) imaging has been used to analyse and evaluate the vocal tract shape through different techniques and with promising results in several fields. Our purpose is to demonstrate the relevance of MR and image processing for the vocal tract study. The extraction of contours of the air cavities allowed the set-up of a number of 3D reconstruction image stacks by means of the combination of orthogonally oriented sets of slices for each articulatory gesture, as a new approach to solve the expected spatial under sampling of the imaging process. In result these models give improved information for the visualization of morphologic and anatomical aspects and are useful for partial measurements of the vocal tract shape in different situations. Potential use can be found in Medical and therapeutic applications as well as in acoustic articulatory speech modelling

Segmentation and 3D reconstruction of the vocal tract from MR images - a comparative study

Speech production is an important human function involving a set of organs with specific morphological and dynamic aspects. The inter-speaker variability, the coarticulation or the nasality are some interesting aspects to improve a realistic 3D modeling of the vocal tract. For this, the understanding of the mechanism of speech production is crucial, as the current image data is not sufficient to reproduce truthfully the speakers anatomy and articulation. Hence, the goal of 3D modeling is to generate the complete geometrical and dynamical information concerning the vocal tract from medical images, such as from magnetic reso-nance imaging (MRI). This work aims to describe and compare two different segmentation techniques to at-tain the 3D shape of the vocal tract during speech production from MR images: the former based on manual tracing of the vocal tract contours and the latter based on image thresholding. Thus, the segmented cross-sectional areas were measured, and 3D models were built from the sagittal data by blending the contours ob-tained from the two segmentation techniques. The mean error of the measures computed were low for both segmentation techniques, which let us conclude that the techniques are useful to evaluate the vocal tract ge-ometry accurately. Additionally, the 3D models built using both segmentation techniques were also very similar and truthful. However, when the coronal data was used, various difficulties occurred

A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard

This work was supported by the Associate Laboratory for Green Chemistry—LAQV which is financed by national funds from FCT/MCTES (UIDB/50006/2020 and UIDP/50006/2020). This work has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 870292 (BioICEP project). J.P. acknowledges a PhD grant (SFRD/BD14610472019), Fundação para a Ciência e Tecnologia (FCT) and R.S.C. the contract CEECIND/01399/2017In this paper, a computational framework is proposed that merges mechanistic modeling with deep neural networks obeying the Systems Biology Markup Language (SBML) standard. Over the last 20 years, the systems biology community has developed a large number of mechanistic models that are currently stored in public databases in SBML. With the proposed framework, existing SBML models may be redesigned into hybrid systems through the incorporation of deep neural networks into the model core, using a freely available python tool. The so-formed hybrid mechanistic/neural network models are trained with a deep learning algorithm based on the adaptive moment estimation method (ADAM), stochastic regularization and semidirect sensitivity equations. The trained hybrid models are encoded in SBML and uploaded in model databases, where they may be further analyzed as regular SBML models. This approach is illustrated with three well-known case studies: the Escherichia coli threonine synthesis model, the P58IPK signal transduction model, and the Yeast glycolytic oscillations model. The proposed framework is expected to greatly facilitate the widespread use of hybrid modeling techniques for systems biology applications.publishersversionpublishe

Stereoselective synthesis of 2,3-unsaturated-O-Glycosides promoted by TeBr4

The use of a catalytic amount of tellurium(IV) tetrabromide to promote the O-glycosylation of glycals to yield 2,3-unsaturated-O-glycosides is described. The desired compounds were obtained in good yields and high α-selectivity

Climate- and fire-smart landscape scenarios call for redesigning protection regimes to achieve multiple management goals

Integrated management of biodiversity and ecosystem services (ES) in heterogeneous landscapes requires considering the potential trade-offs between conflicting objectives. The UNESCO's Biosphere Reserve zoning scheme is a suitable context to address these trade-offs by considering multiple management zones that aim to minimise conflicts between management objectives. Moreover, in Mediterranean ecosystems, management and planning also needs to consider drivers of landscape dynamics such as wildfires and traditional farming and forestry practices that have historically shaped landscapes and the biodiversity they host. In this study, we applied a conservation planning approach to prioritise the allocation of management zones under future landscape and climate scenarios. We tested different landscape management scenarios reflecting the outcomes of climate-smart and fire-smart policies. We projected the expected landscape dynamics and associated changes on the distribution of 207 vertebrate species, 4 ES and fire hazard under each scenario. We used Marxan with Zones to allocate three management zones, replicating the Biosphere Reserves zoning scheme (“Core area”, “Buffer zone” and “Transition area”) to address the various management objectives within the Biosphere Reserve. Our results show that to promote ES supply and biodiversity conservation, while also minimising fire hazard, the reserve will need to: i) Redefine its zoning, especially regarding Core Areas, which need a considerable expansion to help mitigate changes in biodiversity and accommodate ES supply under expected changes in climate and species distribution. ii) Revisit current management policies that will result in encroached landscapes prone to high intensity, uncontrollable wildfires with the potential to heavily damage ecosystems and compromise the supply of ES. Our results support that both climate- and fire-smart policies in the Meseta Ibérica can help develop multifunctional landscapes that help mitigate and adapt to climate change and ensure the best possible maintenance of biodiversity and ES supply under uncertain future climate conditions.This study was supported by national funds - Portuguese Foundation for Science and Technology, under the “FirESmart” project (PCIF/MOG/0083/2017), and the project UIDB/04033/2020. CCS is supported by the “Financiamento Programático” UIDP/04050/2020 funded by national funds through the FCT I.P. VH was funded by the Junta de Andalucía through an Emergia contract (EMERGIA20_00135). AR is supported by ‘Juan de la Cierva’ fellowship program funded by the Spanish Ministry of Science and Innovation (IJC2019-041033-I). ÂS received support from the Portuguese Foundation for Science and Technology (FCT) through Ph.D. Grant SFRH/BD/132838/2017, funded by the Ministry of Science, Technology and Higher Education, and by the European Social Fund - Operational Program Human Capital within the 2014–2020 EU Strategic Framework.info:eu-repo/semantics/publishedVersio

Long-term sustainability of cork oak agro-forests in the Iberian Peninsula: A model-based approach aimed at supporting the best management options for the montado conservation

The future of the montado, a human shaped agro-forestry ecosystem of South Western Europe, is questioned due to the observed lack of cork oak health and low natural regeneration. We developed a System Dynamics Modelling approach to predict the long-term sustainability of this agro-forest, by recreating cork-oak population dynamics, management practices and the main environmental and biological constrains associated with this ecosystem. Our results indicate that the leading limitations to cork oak regeneration in montado ecosystems result from the intensity and interaction of land management practices, namely livestock and the use of heavy machinery. The main conclusions indicate that limiting the quantity of livestock up to 0.40 LU.ha -1 , and considering soil ploughing with a minimum periodicity of 5 years, are crucial to maintaining sustainable cork oak populations. This study represents a first step to support strategic options for cork oak montado management by providing projections of long-term population trends under realistic social-ecological change scenarios.This work was supported by the FCT (Portuguese Foun-dation for Science and Technology) under a Ph.D. grant[SFRH/BD/70708/2010]. R. Bastos is funded by FCT through the doc-toral grant SFRH/BD/102428/2014. S. Costa is funded by the FCTthrough the post-doctoral grant SFRH/BPD/102438/2014. We aregrateful to Alfredo Sendim from Herdade do Freixo do Meio whokindly allowed us to develop this work at his property.info:eu-repo/semantics/publishedVersio