Learning midlevel image features for natural scene and texture classification

This paper deals with coding of natural scenes in order to extract semantic information. We present a new scheme to project natural scenes onto a basis in which each dimension encodes statistically independent information. Basis extraction is performed by independent component analysis (ICA) applied to image patches culled from natural scenes. The study of the resulting coding units (coding filters) extracted from well-chosen categories of images shows that they adapt and respond selectively to discriminant features in natural scenes. Given this basis, we define global and local image signatures relying on the maximal activity of filters on the input image. Locally, the construction of the signature takes into account the spatial distribution of the maximal responses within the image. We propose a criterion to reduce the size of the space of representation for faster computation. The proposed approach is tested in the context of texture classification (111 classes), as well as natural scenes classification (11 categories, 2037 images). Using a common protocol, the other commonly used descriptors have at most 47.7% accuracy on average while our method obtains performances of up to 63.8%. We show that this advantage does not depend on the size of the signature and demonstrate the efficiency of the proposed criterion to select ICA filters and reduce the dimensio

Drug-induced toxicity on mitochondria and lipid metabolism: mechanistic diversity and deleterious consequences for the liver.

International audienceNumerous investigations have shown that mitochondrial dysfunction is a major mechanism of drug-induced liver injury, which involves the parent drug or a reactive metabolite generated through cytochromes P450. Depending of their nature and their severity, the mitochondrial alterations are able to induce mild to fulminant hepatic cytolysis and steatosis (lipid accumulation), which can have different clinical and pathological features. Microvesicular steatosis, a potentially severe liver lesion usually associated with liver failure and profound hypoglycemia, is due to a major inhibition of mitochondrial fatty acid oxidation (FAO). Macrovacuolar steatosis, a relatively benign liver lesion in the short term, can be induced not only by a moderate reduction of mitochondrial FAO but also by an increased hepatic de novo lipid synthesis and a decreased secretion of VLDL-associated triglycerides. Moreover, recent investigations suggest that some drugs could favor lipid deposition in the liver through primary alterations of white adipose tissue (WAT) homeostasis. If the treatment is not interrupted, steatosis can evolve toward steatohepatitis, which is characterized not only by lipid accumulation but also by necroinflammation and fibrosis. Although the mechanisms involved in this aggravation are not fully characterized, it appears that overproduction of reactive oxygen species by the damaged mitochondria could play a salient role. Numerous factors could favor drug-induced mitochondrial and metabolic toxicity, such as the structure of the parent molecule, genetic predispositions (in particular those involving mitochondrial enzymes), alcohol intoxication, hepatitis virus C infection, and obesity. In obese and diabetic patients, some drugs may induce acute liver injury more frequently while others may worsen the pre-existent steatosis (or steatohepatitis)

Limiting shapes for deterministic centrally seeded growth models

We study the rotor router model and two deterministic sandpile models. For the rotor router model in $\mathbb{Z}^d$, Levine and Peres proved that the limiting shape of the growth cluster is a sphere. For the other two models, only bounds in dimension 2 are known. A unified approach for these models with a new parameter $h$ (the initial number of particles at each site), allows to prove a number of new limiting shape results in any dimension $d \geq 1$. For the rotor router model, the limiting shape is a sphere for all values of $h$. For one of the sandpile models, and $h=2d-2$ (the maximal value), the limiting shape is a cube. For both sandpile models, the limiting shape is a sphere in the limit $h \to -\infty$. Finally, we prove that the rotor router shape contains a diamond.Comment: 18 pages, 3 figures, some errors corrected and more explanation added, to appear in Journal of Statistical Physic

Qualitative response of interaction networks: application to the validation of biological models

International audienceWe advocate the use of qualitative models for the analysis of shift equilibria in large biological systems. We present a mathematical method, allowing qualitative predictions to be made of the behaviour of a biological system. These predictions are not dependent on specific values of the kinetic constants. We show how these methods can be used to improve understanding of a complex regulatory system

Use Scenarios & Practical Examples of AI Use in Education

This report presents a set of use scenarios based on existing resources that teachers can use as inspiration to create their own, with the aim of introducing artificial intelligence (AI) at different pre-university levels, and with different goals. The Artificial Intelligence Education field (AIEd) is very active, with new resources and tools arising continuously. Those included in this document have already been tested with students and selected by experts in the field, but they must be taken just as practical examples to guide and inspire teachers creativity.Comment: Developed within the AI in Education working group of the European Digital Education Hu

Advancing measurements and representations of subsurface heterogeneity and dynamic processes: towards 4D hydrogeology

Essentially all hydrogeological processes are strongly influenced by the subsurface spatial heterogeneity and the temporal variation of environmental conditions, hydraulic properties, and solute concentrations. This spatial and temporal variability generally leads to effective behaviors and emerging phenomena that cannot be predicted from conventional approaches based on homogeneous assumptions and models. However, it is not always clear when, why, how, and at what scale the 4D (3D + time) nature of the subsurface needs to be considered in hydrogeological monitoring, modeling, and applications. In this paper, we discuss the interest and potential for the monitoring and characterization of spatial and temporal variability, including 4D imaging, in a series of hydrogeological processes: (1) groundwater fluxes, (2) solute transport and reaction, (3) vadose zone dynamics, and (4) surface–subsurface water interactions. We first identify the main challenges related to the coupling of spatial and temporal fluctuations for these processes. We then highlight recent innovations that have led to significant breakthroughs in high-resolution space–time imaging and modeling the characterization, monitoring, and modeling of these spatial and temporal fluctuations. We finally propose a classification of processes and applications at different scales according to their need and potential for high-resolution space–time imaging. We thus advocate a more systematic characterization of the dynamic and 3D nature of the subsurface for a series of critical processes and emerging applications. This calls for the validation of 4D imaging techniques at highly instrumented observatories and the harmonization of open databases to share hydrogeological data sets in their 4D components

C11orf70 Mutations Disrupting the Intraflagellar Transport-Dependent Assembly of Multiple Axonemal Dyneins Cause Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a genetically and phenotypically heterogeneous disorder characterized by destructive respiratory disease and laterality abnormalities due to randomized left-right body asymmetry. PCD is mostly caused by mutations affecting the core axoneme structure of motile cilia that is essential for movement. Genes that cause PCD when mutated include a group that encode proteins essential for the assembly of the ciliary dynein motors and the active transport process that delivers them from their cytoplasmic assembly site into the axoneme. We screened a cohort of affected individuals for disease-causing mutations using a targeted next generation sequencing panel and identified two unrelated families (three affected children) with mutations in the uncharacterized C11orf70 gene (official gene name CFAP300). The affected children share a consistent PCD phenotype from early life with laterality defects and immotile respiratory cilia displaying combined loss of inner and outer dynein arms (IDA+ODA). Phylogenetic analysis shows C11orf70 is highly conserved, distributed across species similarly to proteins involved in the intraflagellar transport (IFT)-dependant assembly of axonemal dyneins. Paramecium C11orf70 RNAi knockdown led to combined loss of ciliary IDA+ODA with reduced cilia beating and swim velocity. Tagged C11orf70 in Paramecium and Chlamydomonas localizes mainly in the cytoplasm with a small amount in the ciliary component. IFT139/TTC21B (IFT-A protein) and FLA10 (IFT kinesin) depletion experiments show that its transport within cilia is IFT dependent. During ciliogenesis, C11orf70 accumulates at the ciliary tips in a similar distribution to the IFT-B protein IFT46. In summary, C11orf70 is essential for assembly of dynein arms and C11orf70 mutations cause defective cilia motility and PCD

Inferring the role of transcription factors in regulatory networks

<p>Abstract</p> <p>Background</p> <p>Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneous sources of information, as well as to comply with practical observability issues: measurements can be scarce or noisy. In this work, we show how to combine a network of genetic regulations with a set of expression profiles, in order to infer the functional effect of the regulations, as inducer or repressor. Our approach is based on a consistency rule between a network and the signs of variation given by expression arrays.</p> <p>Results</p> <p>We evaluate our approach in several settings of increasing complexity. First, we generate artificial expression data on a transcriptional network of <it>E. coli </it>extracted from the literature (1529 nodes and 3802 edges), and we estimate that 30% of the regulations can be annotated with about 30 profiles. We additionally prove that at most 40.8% of the network can be inferred using our approach. Second, we use this network in order to validate the predictions obtained with a compendium of real expression profiles. We describe a filtering algorithm that generates particularly reliable predictions. Finally, we apply our inference approach to <it>S. cerevisiae </it>transcriptional network (2419 nodes and 4344 interactions), by combining ChIP-chip data and 15 expression profiles. We are able to detect and isolate inconsistencies between the expression profiles and a significant portion of the model (15% of all the interactions). In addition, we report predictions for 14.5% of all interactions.</p> <p>Conclusion</p> <p>Our approach does not require accurate expression levels nor times series. Nevertheless, we show on both data, real and artificial, that a relatively small number of perturbation experiments are enough to determine a significant portion of regulatory effects. This is a key practical asset compared to statistical methods for network reconstruction. We demonstrate that our approach is able to provide accurate predictions, even when the network is incomplete and the data is noisy.</p

Mutations in Outer Dynein Arm Heavy Chain DNAH9 Cause Motile Cilia Defects and Situs Inversus

International audienceMotile cilia move body fluids and gametes and the beating of cilia lining the airway epithelial surfaces ensures that they are kept clear and protected from inhaled pathogens and consequent respiratory infections. Dynein motor proteins provide mechanical force for cilia beating. Dynein mutations are a common cause of primary ciliary dyskinesia (PCD), an inherited condition characterized by deficient mucociliary clearance and chronic respiratory disease coupled with laterality disturbances and subfertility. Using next-generation sequencing, we detected mutations in the ciliary outer dynein arm (ODA) heavy chain gene DNAH9 in individuals from PCD clinics with situs inversus and in one case male infertility. DNAH9 and its partner heavy chain DNAH5 localize to type 2 ODAs of the distal cilium and in DNAH9-mutated nasal respiratory epithelial cilia we found a loss of DNAH9/DNAH5-containing type 2 ODAs that was restricted to the distal cilia region. This confers a reduced beating frequency with a subtle beating pattern defect affecting the motility of the distal cilia portion. 3D electron tomography ultrastructural studies confirmed regional loss of ODAs from the distal cilium, manifesting as either loss of whole ODA or partial loss of ODA volume. Paramecium DNAH9 knockdown confirms an evolutionarily conserved function for DNAH9 in cilia motility and ODA stability. We find that DNAH9 is widely expressed in the airways, despite DNAH9 mutations appearing to confer symptoms restricted to the upper respiratory tract. In summary, DNAH9 mutations reduce cilia function but some respiratory mucociliary clearance potential may be retained, widening the PCD disease spectrum