Branching Boogaloo: Botanical Adventures in Multi-Mediated Morphologies

FormaLeaf is a software interface for exploring leaf morphology using parallel string rewriting grammars called L-systems. Scanned images of dicotyledonous angiosperm leaves removed from plants around Bard’s campus are displayed on the left and analyzed using the computer vision library OpenCV. Morphometrical information and terminological labels are reported in a side-panel. “Slider mode” allows the user to control the structural template and growth parameters of the generated L-system leaf displayed on the right. “Vision mode” shows the input and generated leaves as the computer ‘sees’ them. “Search mode” attempts to automatically produce a formally defined graphical representation of the input by evaluating the visual similarity of a generated pool of candidate leaves. The system seeks to derive a possible internal structural configuration for venation based purely off a visual analysis of external shape. The iterations of the generated L-system leaves when viewed in succession appear as a hypothetical development sequence. FormaLeaf was written in Processing

A Topology-Based Approach for Nonlinear Time Series with Applications in Computer Performance Analysis

We present a topology-based methodology for the analysis of experimental data generated by a discrete-time, nonlinear dynamical system. This methodology has significant applications in the field of computer performance analysis. Our approach consists of two parts. In the first part, we propose a novel signal separation algorithm that exploits the continuity of the dynamical system being studied. We use established tools from computational topology to test the connectedness of various regions of state space. In particular, a connected region of space that has a disconnected image under the experimental dynamics suggests the presence of multiple signals in the data. Using this as a guideline, we are able to model experimental data as an Iterated Function System (IFS). We demonstrate the success of our algorithm on several synthetic examples--including a Henon-like IFS. Additionally, we successfully model experimental computer performance data as an IFS. In the second part of the analysis, we represent an experimental dynamical system with an algebraic structure that allows for the computation of algebraic topological invariants. Previous work has shown that a cubical grid and the associated cubical complex are effective tools that can be used to identify isolating neighborhoods and compute the corresponding Conley Index--thereby rigorously verifying the existence of periodic orbits and/or chaotic dynamics. Our contribution is to adapt this technique by altering the underlying data structure--improving flexibility and efficiency. We represent the state space of the dynamical system with a simplicial complex and its induced simplicial multivalued map. This contains information about both geometry and dynamics, whereas the cubical complex is restricted by the geometry of the experimental data. This representation has several advantages; most notably, the complexity of the algorithm that generates the associated simplicial multivalued map is linear in the number of data points--as opposed to exponential in dimension for the cubical multivalued map. The synthesis of the two parts of our methodology results in a nonlinear time-series analysis framework that is particularly well suited for computer performance analysis. Complex computer programs naturally switch between `regimes\u27 and are appropriately modeled as IFSs by part one of our program. Part two of our methodology provides the correct tools for analyzing each regime independently

Differentiating population spatial behaviour using a standard feature set

Moving through space, consuming services at locations, transitioning and dwelling are all aspects of spatial behavior that can be recorded with unprecedented ease and accuracy using the GPS and other sensor systems on commodity smartphones. Collection of GPS data is becoming a standard experimental method for studies ranging from public health interventions to studying the browsing behavior of large non-human mammals. However, the millions of records collected in these studies do not lend themselves to traditional geographic analysis. GPS records need to be reduced to a single feature or combination of features, which express the characteristic of interest. While features for spatial behavior characterization have been proposed in different disciplines, it is not always clear which feature should be appropriate for a specific dataset. The substantial effort on subjective selection or design of feature may or may not lead to an insight into GPS datasets. In this thesis we describe a feature set drawn from three different mathematical heritages: buffer area, convex hull and its variations from activity space, fractal dimension of the recorded GPS traces, and entropy rate of individual paths. We analyze these features against six human mobility datasets. We show that the standard feature set could be used to distinguish disparate human mobility patterns while single feature could not distinguish them alone. The feature set can be efficiently applied to most datasets, subject to the assumptions about data quality inherent in the features

3D Composer: A Software for Micro-composition

The aim of this compositional research project is to find new paradigms of expression and representation of musical information, supported by technology. This may further our understanding of how artistic intention materialises during the production of a musical work. A further aim is to create a software device, which will allow the user to generate, analyse and manipulate abstract musical information within a multi-dimensional environment. The main intent of this software and composition portfolio is to examine the process involved during the development of a compositional tool to verify how transformations applied to the conceptualisation of musical abstraction will affect musical outcome, and demonstrate how this transformational process would be useful in a creative context. This thesis suggests a reflection upon various technological and conceptual aspects within a dynamic multimedia framework. The discussion situates the artistic work of a composer within the technological sphere, and investigates the role of technology and its influences during the creative process. Notions of space are relocated in the scope of a personal compositional direction in order to develop a new framework for musical creation. The author establishes theoretical ramifications and suggests a definition for micro-composition. The main aspect focuses on the ability to establish a direct conceptual link between visual elements and their correlated musical output, ultimately leading to the design of a software called 3D-Composer, a tool for the visualisation of musical information as a means to assist composers to create works within a new methodological and conceptual realm. Of particular importance is the ability to transform musical structures in three-dimensional space, based on the geometric properties of micro-composition. The compositions Six Electroacoustic Studies and Dada 2009 display the use of the software. The formalisation process was derived from a transposition of influences of the early twentieth century avant-garde period, to a contemporary digital studio environment utilising new media and computer technologies for musical expression

Propriétés invariantes d'échelle et anisotropes de morphologies d'érosion fluviatile

Les propriétés statistiques invariantes d'échelle isotropes et anisotropes de morphologies terrestres d'érosion fluviatile ont été caractérisées dans cette étude à l'aide d'images satellitaires. En premier lieu, les propriétés invariantes d'échelle isotrope de différentes sections du réseau de drainage du Plateau éthiopien ont été déterminées à partir d'images de régions spectrales variées des satellites Landsat TM 5 et ERS-1. Ensuite, une méthode a été développée pour évaluer les propriétés anisotropes invariantes d'échelle de surfaces d'érosion fluvio-tectonique. Deux types de réseau de drainage ont alors été choisis: le réseau de la Rivière Jaune sur le Plateau de L?ss en Chine et celui de la Green River dans le Utah aux États-Unis. Dans cette deuxième partie, des images du visible du satellite TERRA ASTER ont été analysées. Enfin, la méthode de caractérisation de l'anisotropie indépendante de l'échelle a été appliquée sur les données du Plateau éthiopien afin de mieux y cerner les processus impliqués; les données satellitaires Landsat TM 5 et TERRA ASTER ont été utilisées pour cette partie de la recherche. Les deux régions sélectionnées sur le Plateau éthiopien, "plateau" et "canyon", possèdent des degrés d'érosion très différents. Une première distinction des propriétés invariantes d'échelle isotropes a été trouvée à l'aide d'images Landsat TM 5 dans le visible et d'images ERS-1 dans les micro-ondes. Cette différence a été liée au degré d'érosion mécanique entre ces deux régions, "plateau" (peu érodé) et "canyon" (très érodé). Une deuxième différence statistique a été révélée par les analyses d'invariance d'échelle isotrope des images Landsat TM 5 dans l'infrarouge moyen, qui sont plus sensibles aux argiles. Cette distinction est associée à la présence d'une couche d'altération des minéraux sur le "plateau", couche qui n'est pas retrouvée dans la région "canyon" à cause de l'érosion mécanique plus importante. Ainsi, ces analyses statistiques révèlent la présence active de deux processus distincts agissant sur le Plateau éthiopien, soit l'érosion mécanique et l'érosion chimique. L'étude de l'anisotropie sur des images de réseaux fluviaux a permis de trouver des différences statistiques significatives entre les différents réseaux de drainage. Les analyses de l'anisotropie montrent aussi que celle-ci doit être caractérisée dans un cadre d'invariance d'échelle. Les analyses d'invariance d'échelle isotrope (paramètre fi) permettent de différencier les images très dendritiques (densité de drainage très élevée) du réseau de drainage du Plateau de Loess chinois des autres images moins densément dendritiques. Cependant, elles ne donnent pas la possibilité de distinguer les images du Utah de celles de la Chine où l'érosion est plus poussée et les réseaux plus développés. Dans ce cas, les propriétés anisotropes distinctes reliées aux différentes lithologies des régions permettent de les différencier. De plus, l'anisotropie invariante d'échelle permet de distinguer les images de différentes parties d'un même réseau, par exemple le Plateau de Loess chinois, qui présente des contrastes associés au degré de maturité (ou au développement) du réseau et aux différences lithologiques et structurales régionales. Les analyses effectuées sur l'anisotropie du réseau de drainage du Plateau éthiopien ont confirmé les différences associées aux processus d'érosion et d'altération chimique des sols. Dans l'ensemble, cette étude montre la portée de l'utilisation des images satellitaires en relation avec les analyses d'invariance d'échelle sur les champs de données. Les analyses statistiques anisotropes des structures sur une grande gamme d'échelles complémentent de façon adéquate les analyses isotropes. La méthode développée dans cette étude est d'utilisation relativement simple et pourrait fournir une caractérisation quantitative plus systématique échelle par échelle des surfaces terrestres et des processus dynamiques sous-jacents

Biophysical Sources of 1/f Noises in Neurological Tissue

High levels of random noise are a defining characteristic of neurological signals at all levels, from individual neurons up to electroencephalograms (EEG). These random signals degrade the performance of many methods of neuroengineering and medical neuroscience. Understanding this noise also is essential for applications such as real-time brain-computer interfaces (BCIs), which must make accurate control decisions from very short data epochs. The major type of neurological noise is of the so-called 1/f-type, whose origins and statistical nature has remained unexplained for decades. This research provides the first simple explanation of 1/f-type neurological noise based on biophysical fundamentals. In addition, noise models derived from this theory provide validated algorithm performance improvements over alternatives. Specifically, this research defines a new class of formal latent-variable stochastic processes called hidden quantum models (HQMs) which clarify the theoretical foundations of ion channel signal processing. HQMs are based on quantum state processes which formalize time-dependent observation. They allow the quantum-based calculation of channel conductance autocovariance functions, essential for frequency-domain signal processing. HQMs based on a particular type of observation protocol called independent activated measurements are shown to be distributionally equivalent to hidden Markov models yet without an underlying physical Markov process. Since the formal Markov processes are non-physical, the theory of activated measurement allows merging energy-based Eyring rate theories of ion channel behavior with the more common phenomenological Markov kinetic schemes to form energy-modulated quantum channels. These unique biophysical concepts developed to understand the mechanisms of ion channel kinetics have the potential of revolutionizing our understanding of neurological computation. To apply this theory, the simplest quantum channel model consistent with neuronal membrane voltage-clamp experiments is used to derive the activation eigenenergies for the Hodgkin-Huxley K+ and Na+ ion channels. It is shown that maximizing entropy under constrained activation energy yields noise spectral densities approximating S(f) = 1/f, thus offering a biophysical explanation for this ubiquitous noise component. These new channel-based noise processes are called generalized van der Ziel-McWhorter (GVZM) power spectral densities (PSDs). This is the only known EEG noise model that has a small, fixed number of parameters, matches recorded EEG PSD\u27s with high accuracy from 0 Hz to over 30 Hz without infinities, and has approximately 1/f behavior in the mid-frequencies. In addition to the theoretical derivation of the noise statistics from ion channel stochastic processes, the GVZM model is validated in two ways. First, a class of mixed autoregressive models is presented which simulate brain background noise and whose periodograms are proven to be asymptotic to the GVZM PSD. Second, it is shown that pairwise comparisons of GVZM-based algorithms, using real EEG data from a publicly-available data set, exhibit statistically significant accuracy improvement over two well-known and widely-used steady-state visual evoked potential (SSVEP) estimators

Characterisation of disuse-related osteoporosis in an animal model of spinal cord injury

Injury to the spinal cord can result in paralysis below the level of injury. A secondary complication of the removal of muscle-driven bone stimulation is the development of rapid osteoporosis in the bones of the paralysed limbs. The severe deterioration of both bone quantity and quality means that spinal cord injury (SCI) patients are at a significantly higher risk of fragility fractures in the lower extremities than the able-bodied population.;These fractures occur most commonly around the knee (distal femur and proximal tibia). This thesis presents a characterisation of the time-course effects a complete SCI has on the fracture-prone distal femur in a rat model. The aims are to characterise the quality and distribution of bone and to provide a uniquely detailed description of its response to SCI at various time points post-injury.;Bone quality is assessed using i) ex vivo micro-Computed Tomography (μCT) for global and site-specific analysis of both trabecular and cortical bone morphometry and densitometry, and ii) three-point bending and torsional mechanical testing to provide whole-bone structural and material level properties.;Evidence is presented that SCI-induced osteoporosis is site-specific within the same appendicular bone. A rapid and severe deterioration of metaphyseal trabecular bone was observed, after just 2 weeks trabecular volume fraction (BV/TV) had decreased by 59% compared to age-matched sham-operated controls. This resulted in a compromised structure composed of on average 53% fewer and 15% thinner trabeculae compared to control.;At later time points post-SCI there were no further significant reductions in metaphyseal BV/TV, although significant microstructural changes did occur. On the other hand, the more distally located epiphyseal trabecular bone was structurally more resistant to SCI-induced osteoporosis. There was a 23% decrease in BV/TV at 2 weeks post-SCI compared to control, characterised by a 15% decrease in trabecular thickness, thus unlike metaphyseal trabecular structures, the epiphyseal structure's connectivity was maintained. At later time points post-SCI there was a growth-related increase in epiphyseal BV/TV.;Rapid changes to cortical bone were also seen, with distal-metaphyseal regions experiencing the most severe decrease in cortical area at 2 weeks post-SCI compared to control. The varying degrees of change in the amount of both trabecular and cortical bone appears concomitant with each region's bone surface to volume ratio. Analysis of more chronic time points post-SCI (6, 10 and 16 weeks) highlights that caution must be exercised when interpreting results from rodent studies.;The analysis performed here indicates that SCI-induced bone changes are a combination of bone loss and suppressed bone growth. No difference in cortical tissue mineral density was observed between SCI and control groups at any time-points assessed, indicating that the decreases in whole-bone mechanical properties observed due to SCI were primarily a result of changes to the spatial distribution of bone.;Cumulatively, this thesis illustrates that SCI-induced osteoporosis has detrimentally affected the spatial distribution of both trabecular and cortical bone in site-specific ways, but the bone material itself does not appear affected.Injury to the spinal cord can result in paralysis below the level of injury. A secondary complication of the removal of muscle-driven bone stimulation is the development of rapid osteoporosis in the bones of the paralysed limbs. The severe deterioration of both bone quantity and quality means that spinal cord injury (SCI) patients are at a significantly higher risk of fragility fractures in the lower extremities than the able-bodied population.;These fractures occur most commonly around the knee (distal femur and proximal tibia). This thesis presents a characterisation of the time-course effects a complete SCI has on the fracture-prone distal femur in a rat model. The aims are to characterise the quality and distribution of bone and to provide a uniquely detailed description of its response to SCI at various time points post-injury.;Bone quality is assessed using i) ex vivo micro-Computed Tomography (μCT) for global and site-specific analysis of both trabecular and cortical bone morphometry and densitometry, and ii) three-point bending and torsional mechanical testing to provide whole-bone structural and material level properties.;Evidence is presented that SCI-induced osteoporosis is site-specific within the same appendicular bone. A rapid and severe deterioration of metaphyseal trabecular bone was observed, after just 2 weeks trabecular volume fraction (BV/TV) had decreased by 59% compared to age-matched sham-operated controls. This resulted in a compromised structure composed of on average 53% fewer and 15% thinner trabeculae compared to control.;At later time points post-SCI there were no further significant reductions in metaphyseal BV/TV, although significant microstructural changes did occur. On the other hand, the more distally located epiphyseal trabecular bone was structurally more resistant to SCI-induced osteoporosis. There was a 23% decrease in BV/TV at 2 weeks post-SCI compared to control, characterised by a 15% decrease in trabecular thickness, thus unlike metaphyseal trabecular structures, the epiphyseal structure's connectivity was maintained. At later time points post-SCI there was a growth-related increase in epiphyseal BV/TV.;Rapid changes to cortical bone were also seen, with distal-metaphyseal regions experiencing the most severe decrease in cortical area at 2 weeks post-SCI compared to control. The varying degrees of change in the amount of both trabecular and cortical bone appears concomitant with each region's bone surface to volume ratio. Analysis of more chronic time points post-SCI (6, 10 and 16 weeks) highlights that caution must be exercised when interpreting results from rodent studies.;The analysis performed here indicates that SCI-induced bone changes are a combination of bone loss and suppressed bone growth. No difference in cortical tissue mineral density was observed between SCI and control groups at any time-points assessed, indicating that the decreases in whole-bone mechanical properties observed due to SCI were primarily a result of changes to the spatial distribution of bone.;Cumulatively, this thesis illustrates that SCI-induced osteoporosis has detrimentally affected the spatial distribution of both trabecular and cortical bone in site-specific ways, but the bone material itself does not appear affected

Changes in surface electromyography characteristics and foot-tapping rate of force development as measures of spasticity in patients with multiple sclerosis

Spasticity is a common symptom experienced by individuals with upper motor neuron lesions such as those with stroke, spinal cord injury, traumatic brain injury, cerebral palsy, amyotrophic lateral sclerosis, and multiple sclerosis. Although the etiology and progression of spasticity differs between these clinical populations, it shares many of the same consequences: muscle pain, weakness, fatigue, increased disability, depression, medication side effects, and a reduced quality of life. For this reason, there has been increased interest in the measurement and treatment of spasticity symptoms. Subjective measures of spasticity like the Modified Ashworth Scale (MAS) and Tardieu Scale have shown questionable validity/reliability and poorly correlate to functional outcome measures but continue to be used in clinical and research settings. Objective measures like myotonometry, electrogoniometry, and inertial sensors on the other hand provide much more reliable measures but at the expense of increased costs, time, and equipment. Therefore, to properly assess and treat spasticity symptoms, a timelier and cost-effective objective measure of spasticity is needed. PURPOSE: To reexamine a previously collected dataset from a sample of patients with multiple sclerosis before and after dry-needling and functional electrically stimulated walking spasticity treatments. Specifically, we wished to know whether there were: 1.) Acute (within visit) and chronic (between visit) changes in sEMG and Foot-tapping rate of force development measures after treatment, 2.) Between leg differences before and after treatments, 3.) significant correlations between EMG, foot-tapping, and functional outcome measures. METHODS: 16 MS patients (10 relapsing-remitting and 6 progressive MS) participated in the original study. The study consisted of 14 visits: 2 pre/post visits, 4 visits of dry-needling + functional electrically stimulated walking (FESW), and 8 visits with FESW only. The more spastic leg (involved leg) was given the treatment, making the other the control. Dry-needling was performed on the involved leg’s gastrocnemius medial and lateral heads by inserting monofilament needles and electrically stimming the muscles until visible twitches occurred. Dry-needling was done 30 seconds on and 30 seconds off for a total of 90 seconds of treatment. FESW was performed on the involved leg by attaching electrodes to the tibialis anterior and gastrocnemius muscles. Patients walked 20-minutes at a self-selected pace while the involved leg was stimmed. sEMG was collected before and after each treatment by having the patient perform a single maximal heel raise. Foot-tapping ability was assessed using the 10-second foot-tapping test (FTT) and a small force plate. Functional measures also included the 25-foot walk test (25FWT) 6-minute walk test (6MWT), modified fatigue impact score (MFIS), and number of heel raises performed. RESULTS: No significant between leg differences were noted for any of the sEMG measures (p>0.05). No significant chronic changes occurred in any of the sEMG measures. For the Dry-needling + FESW visits, sEMG sample entropy was significantly increased in the involved leg at post-needling (p = 0.035) and post-FESW (p = 0.027). The non-involved leg’s sample entropy was significantly higher at post-FESW only (p = 0.017). The non-involved leg’s, mean frequency was significantly higher at post-FESW compared pre-needling (p = 0.033) and post-needling (p = 0.032). For the FESW only visits, there were no significant changes in the involved leg. The Non-involved leg’s mean frequency was significantly higher at Post-FESW (p = 0.006). Median frequency was significantly higher at Post-FESW (p = 0.009). The number of foot-taps was significantly increased from Pre to Post-intervention in both the Involved (p = 0.006) and Non-involved legs (p 0.002). There was a significantly higher number of foot-taps in the Non-involved leg compared to the Involved leg at both Pre (p =0.008) and Post (p = 0.015) timepoints. AUC was significantly higher in the Involved leg at Post-treatment (p = 0.030). Time to peak was found to be higher in the Involved leg compared to the Non-involved leg at both Pre (p = 0.037) and Post-intervention (p = 0.019). Time to base was higher in the Involved leg compared to the Non-involved leg at both Pre (p = 0.031) and Post-intervention (p = 0.004). Total tap time was higher in the Involved leg at both Pre (p = 0.010) and Post-intervention (p = 0.007). Percent time to peak was significantly lower in the involved limb at Pre-intervention (p = 0.026) and Post intervention (p = 0.037). Percent time to base was significantly higher in the Involved leg at Pre-intervention (p = 0.026) and Post intervention (p = 0.037). The sEMG measures tended to poorly or non-significantly correlate with the functional outcome measures. The foot-tapping measures, especially the involved leg, tended to exhibit stronger correlations with the functional outcome measures. CONCLUSION: sEMG Sample entropy and foot-tapping ability are significantly improved by dry-needling treatments and walking. sEMG measures did not tend to correlate well with functional outcome measures but the foot-tapping measures did. This suggests that foot-tapping rate and related measures may be a useful measure of spasticity and treatment effects

Etude expérimentale des dynamiques temporelles du comportement normal et pathologique chez le rat et la souris

155 p.Modern neuroscience highlights the need for designing sophisticated behavioral readout of internal cognitive states. From a thorough analysis of classical behavioral test, my results supports the hypothesis that sensory ypersensitivity might be the cause of other behavioural deficits, and confirm the potassium channel BKCa as a potentially relevant molecular target for the development of drug medication against Fragile X Syndrome/Autism Spectrum Disorders. I have also used an innovative device, based on pressure sensors that can non-invasively detect the slightest animal movement with unprecedented sensitivity and time resolution, during spontaneous behaviour. Analysing this signal with sophisticated computational tools, I could demonstrate the outstanding potential of this methodology for behavioural phenotyping in general, and more specifically for the investigation of pain, fear or locomotion in normal mice and models of neurodevelopmental and neurodegenerative disorders

Articles publicats per investigadors de l'ETSEIB. Producció científica a Futur 2015

Postprint (author's final draft