Unsupervised classification to improve the quality of a bird song recording dataset

Open audio databases such as Xeno-Canto are widely used to build datasets to explore bird song repertoire or to train models for automatic bird sound classification by deep learning algorithms. However, such databases suffer from the fact that bird sounds are weakly labelled: a species name is attributed to each audio recording without timestamps that provide the temporal localization of the bird song of interest. Manual annotations can solve this issue, but they are time consuming, expert-dependent, and cannot run on large datasets. Another solution consists in using a labelling function that automatically segments audio recordings before assigning a label to each segmented audio sample. Although labelling functions were introduced to expedite strong label assignment, their classification performance remains mostly unknown. To address this issue and reduce label noise (wrong label assignment) in large bird song datasets, we introduce a data-centric novel labelling function composed of three successive steps: 1) time-frequency sound unit segmentation, 2) feature computation for each sound unit, and 3) classification of each sound unit as bird song or noise with either an unsupervised DBSCAN algorithm or the supervised BirdNET neural network. The labelling function was optimized, validated, and tested on the songs of 44 West-Palearctic common bird species. We first showed that the segmentation of bird songs alone aggregated from 10% to 83% of label noise depending on the species. We also demonstrated that our labelling function was able to significantly reduce the initial label noise present in the dataset by up to a factor of three. Finally, we discuss different opportunities to design suitable labelling functions to build high-quality animal vocalizations with minimum expert annotation effort

Nonlinear ultrasound monitoring of fatigue microdamage accumulation in cortical bone

Accumulation of bone micro-damage is suspected to lead to severe impairment of mechanical properties with an increase in skeletal fragility and fracture risk. The objective of the study was to evaluate the potential of Nonlinear Resonant Ultrasound Spectroscopy (NRUS) for measuring micro-damage accumulation in cortical bone using four-point bending cycling fatigue. Sixteen human cortical bone specimens were machined as parallelepiped beams. Damage progression was controlled by measuring the linear elastic beam theory modulus (E LEBT ), known to reflect microdamage accumulation. Before and between each damage step, the nonlinear ultrasonic elastic coefficient was measured by NRUS. At the end of each cycling fatigue, a subset of bone samples was measured by μCT at the European Synchrotron Radiation Facility. Results showing a progressive increase of nonlinear ultrasonic elastic coefficient along fatigue cycling suggest that NRUS measurements are sensitive to micro-damage accumulation. The results mentioned above were validated using synchrotron radiation μCT. The variation of elastic nonlinearity was found to be significantly correlated to the variation of number density of small microcracks which almost doubled in damaged regionsThis research was supported by the Agence Nationale pour la Recherche (ANR), France (Grant BONUS_07BLAN0197

Lentiviral gene transfer of RPE65 rescues survival and function of cones in a mouse model of Leber congenital amaurosis.

BACKGROUND: RPE65 is specifically expressed in the retinal pigment epithelium and is essential for the recycling of 11-cis-retinal, the chromophore of rod and cone opsins. In humans, mutations in RPE65 lead to Leber congenital amaurosis or early-onset retinal dystrophy, a severe form of retinitis pigmentosa. The proof of feasibility of gene therapy for RPE65 deficiency has already been established in a dog model of Leber congenital amaurosis, but rescue of the cone function, although crucial for human high-acuity vision, has never been strictly proven. In Rpe65 knockout mice, photoreceptors show a drastically reduced light sensitivity and are subject to degeneration, the cone photoreceptors being lost at early stages of the disease. In the present study, we address the question of whether application of a lentiviral vector expressing the Rpe65 mouse cDNA prevents cone degeneration and restores cone function in Rpe65 knockout mice. METHODS AND FINDINGS: Subretinal injection of the vector in Rpe65-deficient mice led to sustained expression of Rpe65 in the retinal pigment epithelium. Electroretinogram recordings showed that Rpe65 gene transfer restored retinal function to a near-normal pattern. We performed histological analyses using cone-specific markers and demonstrated that Rpe65 gene transfer completely prevented cone degeneration until at least four months, an age at which almost all cones have degenerated in the untreated Rpe65-deficient mouse. We established an algorithm that allows prediction of the cone-rescue area as a function of transgene expression, which should be a useful tool for future clinical trials. Finally, in mice deficient for both RPE65 and rod transducin, Rpe65 gene transfer restored cone function when applied at an early stage of the disease. CONCLUSIONS: By demonstrating that lentivirus-mediated Rpe65 gene transfer protects and restores the function of cones in the Rpe65(-/-) mouse, this study reinforces the therapeutic value of gene therapy for RPE65 deficiencies, suggests a cone-preserving treatment for the retina, and evaluates a potentially effective viral vector for this purpose

Evaluation du micro-endommagement osseux par spectroscopie ultrasonore non-linéaire : vers une mesure quantitative

Bone microdamage characterization as well as its involvement in bone metabolism or bone fragility remains a challenge, especially because no existing techniques are well suited to its measurement. Non invasive techniques for detecting and monitoring bone microcracks accumulation and propagation are thus highly desirable. The objective of this thesis was to evaluate the sensitivity of nonlinear resonant ultrasound spectroscopy (NRUS) measurements to the accumulation of damage in cortical bone by fatigue or by controlled crack propagation. First, NRUS method was optimized to achieve highly sensitive and reproducible bone nonlinearity measurements. Then, two groups of human cortical bone specimens were machined from the femoral mid-diaphysis. The first group was taken through a progressive fatigue protocol consisting of four steps of cyclic four-point bending. The second group was taken through a toughness protocol consisting of initiation and controlled propagation of a stable crack induced by 4-point bending mechanical loading. Our results evidenced a progressive increase of the nonlinear elastic parameter during fatigue testing or during toughness experiments. Moreover, the relative variation of nonlinear elasticity of the fatigued specimens was significantly related to the relative variation of the number density of small cracks assessed with micro-computed tomography, whereas in crack propagation experiments a significant relationship was found between the level of nonlinearity and total crack length. These results strongly suggest that NRUS measurements are sensitive to damage accumulation and bone non-linearity can be used as a marker of bone damage.La caractérisation du micro-endommagement et la compréhension de son rôle dans le métabolisme ou dans la fragilisation osseuse restent des challenges, tout particulièrement en raison de l'absence de techniques de mesures bien adaptées à son étude. Il apparaît donc nécessaire de développer de nouvelles techniques non-invasives pour détecter et suivre l'accumulation de micro-endommagement osseux, en particulier celui qui se manifeste par la présence de microfissures. L'objectif de la thèse est d'évaluer la sensibilité de la spectroscopie ultrasonore non-linéaire (NRUS) à l'accumulation du micro-endommagement osseux. La sensibilité et la reproductibilité de la technique NRUS ont tout d'abord été optimisées. Puis, deux groupes d'échantillons d'os cortical ont été prélevés sur des diaphyses fémorales humaines. Les spécimens du premier groupe ont été endommagés progressivement par fatigue en flexion 4-points. Le second groupe a subi un test de ténacité pour initier et propager de manière contrôlée une fissure unique. Nos résultats montrent que la non-linéarité mesurée des échantillons fatigués et fissurés augmente de manière significative après les étapes de fatigue ou le test de ténacité. De plus, nous observons une corrélation significative entre la variation relative du paramètre non-linéaire et l'augmentation de la densité de petites fissures (évaluée par microtomographie par rayonnement synchrotron). Enfin, le niveau de non-linéarité des spécimens fissurés est significativement corrélé à la longueur totale de la fissure. Ces résultats suggèrent que la technique NRUS optimisée est sensible à l'accumulation du micro-endommagement osseux

Evaluation du micro-endommagement osseux par spectroscopie ultrasonore non-linéaire (vers une mesure quantitative)

La caractérisation du micro-endommagement et la compréhension de son rôle dans le métabolisme ou dans la fragilisation osseuse restent des challenges, tout particulièrement en raison de l absence de techniques de mesures bien adaptées à son étude. Il apparaît donc nécessaire de développer de nouvelles techniques non-invasives pour détecter et suivre l accumulation de micro-endommagement osseux, en particulier celui qui se manifeste par la présence de microfissures. L objectif de la thèse est d évaluer la sensibilité de la spectroscopie ultrasonore non-linéaire (NRUS) à l accumulation du micro-endommagement osseux. La sensibilité et la reproductibilité de la technique NRUS ont tout d abord été optimisées. Puis, deux groupes d échantillons d os cortical ont été prélevés sur des diaphyses fémorales humaines. Les spécimens du premier groupe ont été endommagés progressivement par fatigue en flexion 4-points. Le second groupe a subi un test de ténacité pour initier et propager de manière contrôlée une fissure unique. Nos résultats montrent que la non-linéarité mesurée des échantillons fatigués et fissurés augmente de manière significative après les étapes de fatigue ou le test de ténacité. De plus, nous observons une corrélation significative entre la variation relative du paramètre non-linéaire et l augmentation de la densité de petites fissures (évaluée par microtomographie par rayonnement synchrotron). Enfin, le niveau de non-linéarité des spécimens fissurés est significativement corrélé à la longueur totale de la fissure. Ces résultats suggèrent que la technique NRUS optimisée est sensible à l accumulation du micro-endommagement osseux.Bone microdamage characterization as well as its involvement in bone metabolism or bone fragility remains a challenge, especially because no existing techniques are well suited to its measurement. Non invasive techniques for detecting and monitoring bone microcracks accumulation and propagation are thus highly desirable. The objective of this thesis was to evaluate the sensitivity of nonlinear resonant ultrasound spectroscopy (NRUS) measurements to the accumulation of damage in cortical bone by fatigue or by controlled crack propagation. First, NRUS method was optimized to achieve highly sensitive and reproducible bone nonlinearity measurements. Then, two groups of human cortical bone specimens were machined from the femoral mid-diaphysis. The first group was taken through a progressive fatigue protocol consisting of four steps of cyclic four-point bending. The second group was taken through a toughness protocol consisting of initiation and controlled propagation of a stable crack induced by 4-point bending mechanical loading. Our results evidenced a progressive increase of the nonlinear elastic parameter during fatigue testing or during toughness experiments. Moreover, the relative variation of nonlinear elasticity of the fatigued specimens was significantly related to the relative variation of the number density of small cracks assessed with micro-computed tomography, whereas in crack propagation experiments a significant relationship was found between the level of nonlinearity and total crack length. These results strongly suggest that NRUS measurements are sensitive to damage accumulation and bone non-linearity can be used as a marker of bone damage.PARIS-BIUSJ-Biologie recherche (751052107) / SudocSudocFranceF

Physics-based model to predict the acoustic detection distance of terrestrial autonomous recording units over the diel cycle and across seasons: insights from an Alpine and a Neotropical forest

International audience1. Passive acoustic monitoring of biodiversity is growing fast, as it offers an alternative to traditional aural point count surveys, with the possibility to deploy long-term acoustic surveys in large and complex natural environments. However, there is still a clear need to evaluate how the frequency-and distancedependent attenuation of sound as well as the ambient sound level impact the acoustic detection distance of the soniferous species in natural environments over the diel cycles and across seasons. This is of great importance to avoid pseudoreplication and to provide relevant biodiversity indicators, including species richness, species abundance and species density. 2. To address the issue of detection distance, we tested a field-based protocol in a Neotropical rainforest (French Guiana, France) and in an Alpine coniferous forest (Jura, France). This standardized and repeatable method consists in a recording session of the ambient sound directly followed by an experiment using a calibrated white noise sound broadcast at different positions along a 100 m linear transect. We then used acoustic laws to reveal the basic physics behind sound propagation attenuation. 3. We demonstrate that habitat attenuation in two different kinds of forests can be modelled by an exponential decay law with a linear dependence on frequency and distance. We also report that habitat attenuation, as first approximation, can be summarized by a single value, the coefficient of attenuation of the habitat. 4. Finally, we show that the detection distance can be predicted knowing the contribution of each attenuation factor, the coefficient of attenuation of the habitat, the ambient sound pressure level and the amplitude and frequency bandwidth characteristics of the transmitted sound. We show that the detection 1 distance mostly depends on the ambient sound and may vary by a factor of up to 5 over the diel cycle and across seasons. These results reinforce the need to take into account the variation of the detection distance when performing passive acoustic surveys and producing reliable biodiversity indicators

Ultrasonic imaging of nonlinear scatterers buried in a medium

International audienceIn this paper, an ultrasonic technique for imaging nonlinear scatterers, such as cracks, buried in a medium is proposed. The method called amplitude modulation consists of a sequence of three acquisitions for each line of the image. The first acquisition is obtained by transmitting with all elements of the phased array. Next the second and third acquisitions are obtained by transmitting with odd elements only and even elements only, respectively. An image revealing nonlinear scattering from the medium is reconstructed line by line by subtracting the responses measured with second and third acquisitions (odd elements and even elements) from the response obtained with all elements transmitting. The method was implemented on three different conventional multi-channel electronic platforms equipped with different ultrasonic probes (center frequency 3MHz to 5MHz, 64 or 128 elements). A crack (6mm-deep x 24mm-long) in a stainless steel block was investigated. With all probes and multi-channel electronic platforms, higher detection specificity of the crack was obtained with amplitude modulation compared with conventional ultrasound imaging. Image contrast (ratio between crack response amplitude over background amplitude) was increased by 5dB with amplitude modulation compared with conventional ultrasound imaging

Fundamental wave amplitude difference imaging for detection and characterization of embedded cracks

International audienceAn ultrasonic technique for imaging nonlinear scatterers, such as partially-closed cracks, buried in a medium has been recently proposed. The method called fundamental wave amplitude difference (FAD) consists of a sequence of acquisitions with different subsets of elements for each line of the image. An image revealing nonlinear scatterers in the medium is reconstructed line by line by subtracting the responses measured with the subsets of elements from the response obtained with all elements transmitting. In order to get a better insight of the capabilities of FAD, two metallic samples having a fatigue or thermal crack are inspected by translating the probe with ultrasonic beam perpendicular (i.e. parallel) to the crack direction which is the most (i.e. less) favorable case. Each time, the responses of the linear scatterers (i.e. conventional image) and nonlinear scat-terers (i.e. FAD image) are compared in term of intensity and spatial repartition. FAD exhibits higher detection specificity of the crack with a better contrast than conventional ultrasound imaging. Moreover, we observe that both methods give complementary results as nonlinear and linear scatterers are mostly not co-localized. In addition, we show experimentally that FAD resolution in elevation and lateral follows the same rule as the theoretical resolution of conventional ultrasonic technique. Finally, we report that FAD gives the possibility to perform parametric studies which let the opportunity to address the physical mechanisms causing the distortion of the signal. FAD is a promising and reliable tool which can be directly implemented on a conventional open scanner ultrasound device for real-time imaging. This might contribute to its fast and wide spread in the industry

Comparative study of nonlinear ultrasonic methods applied to experimental models of prostheses osseointegration

International audienceThis study is part of the long-term perspective to implement in vivo some new noninvasive methods to monitor the bone prostheses sealing or osseointegration (dental implants, hip prostheses). Although the most widely used clinically, X-ray radiography suffers from low sensitivity, limiting for instance its ability to detect early loosening of a prosthesis. The potential of methods developed over the past twenty years and based on elasticity measurements has been shown in vitro, but their in vivo effectiveness is still questionable. Our objective was to evaluate the potential of new methods based on nonlinear elasticity measurements that have emerged in the fields of geophysics and nondestructive testing, and which showed greater sensitivity than the linear elastic response to the presence of weak contacts within a rigid structure, such as cracks. For this, several osseointegration and sealing models (with manifold damping and boundary conditions) have been studied experimentally using different nonlinear elasticity techniques. Finally, this experimental study allowed the extraction of the most promising nonlinear parameters and the evaluation of their respective advantages and limitations for an in vivo application

Nonlinear ultrasound monitoring of single crack propagation in cortical bone

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