71,482 research outputs found
A bio-inspired image coder with temporal scalability
We present a novel bio-inspired and dynamic coding scheme for static images.
Our coder aims at reproducing the main steps of the visual stimulus processing
in the mammalian retina taking into account its time behavior. The main novelty
of this work is to show how to exploit the time behavior of the retina cells to
ensure, in a simple way, scalability and bit allocation. To do so, our main
source of inspiration will be the biologically plausible retina model called
Virtual Retina. Following a similar structure, our model has two stages. The
first stage is an image transform which is performed by the outer layers in the
retina. Here it is modelled by filtering the image with a bank of difference of
Gaussians with time-delays. The second stage is a time-dependent
analog-to-digital conversion which is performed by the inner layers in the
retina. Thanks to its conception, our coder enables scalability and bit
allocation across time. Also, our decoded images do not show annoying artefacts
such as ringing and block effects. As a whole, this article shows how to
capture the main properties of a biological system, here the retina, in order
to design a new efficient coder.Comment: 12 pages; Advanced Concepts for Intelligent Vision Systems (ACIVS
2011
MOPED: Model Organism Protein Expression Database
Large numbers of mass spectrometry proteomics studies are being conducted to understand all types of biological processes. The size and complexity of proteomics data hinders efforts to easily share, integrate, query and compare the studies. The Model Organism Protein Expression Database (MOPED, htttp://moped.proteinspire.org) is a new and expanding proteomics resource that enables rapid browsing of protein expression information from publicly available studies on humans and model organisms. MOPED is designed to simplify the comparison and sharing of proteomics data for the greater research community. MOPED uniquely provides protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis. Data can be queried for specific proteins, browsed based on organism, tissue, localization and condition and sorted by false discovery rate and expression. MOPED empowers users to visualize their own expression data and compare it with existing studies. Further, MOPED links to various protein and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED contains over 43 000 proteins with at least one spectral match and more than 11 million high certainty spectra
Streaming an image through the eye: The retina seen as a dithered scalable image coder
We propose the design of an original scalable image coder/decoder that is
inspired from the mammalians retina. Our coder accounts for the time-dependent
and also nondeterministic behavior of the actual retina. The present work
brings two main contributions: As a first step, (i) we design a deterministic
image coder mimicking most of the retinal processing stages and then (ii) we
introduce a retinal noise in the coding process, that we model here as a dither
signal, to gain interesting perceptual features. Regarding our first
contribution, our main source of inspiration will be the biologically plausible
model of the retina called Virtual Retina. The main novelty of this coder is to
show that the time-dependent behavior of the retina cells could ensure, in an
implicit way, scalability and bit allocation. Regarding our second
contribution, we reconsider the inner layers of the retina. We emit a possible
interpretation for the non-determinism observed by neurophysiologists in their
output. For this sake, we model the retinal noise that occurs in these layers
by a dither signal. The dithering process that we propose adds several
interesting features to our image coder. The dither noise whitens the
reconstruction error and decorrelates it from the input stimuli. Furthermore,
integrating the dither noise in our coder allows a faster recognition of the
fine details of the image during the decoding process. Our present paper goal
is twofold. First, we aim at mimicking as closely as possible the retina for
the design of a novel image coder while keeping encouraging performances.
Second, we bring a new insight concerning the non-deterministic behavior of the
retina.Comment: arXiv admin note: substantial text overlap with arXiv:1104.155
A Path to Implement Precision Child Health Cardiovascular Medicine.
Congenital heart defects (CHDs) affect approximately 1% of live births and are a major source of childhood morbidity and mortality even in countries with advanced healthcare systems. Along with phenotypic heterogeneity, the underlying etiology of CHDs is multifactorial, involving genetic, epigenetic, and/or environmental contributors. Clear dissection of the underlying mechanism is a powerful step to establish individualized therapies. However, the majority of CHDs are yet to be clearly diagnosed for the underlying genetic and environmental factors, and even less with effective therapies. Although the survival rate for CHDs is steadily improving, there is still a significant unmet need for refining diagnostic precision and establishing targeted therapies to optimize life quality and to minimize future complications. In particular, proper identification of disease associated genetic variants in humans has been challenging, and this greatly impedes our ability to delineate gene-environment interactions that contribute to the pathogenesis of CHDs. Implementing a systematic multileveled approach can establish a continuum from phenotypic characterization in the clinic to molecular dissection using combined next-generation sequencing platforms and validation studies in suitable models at the bench. Key elements necessary to advance the field are: first, proper delineation of the phenotypic spectrum of CHDs; second, defining the molecular genotype/phenotype by combining whole-exome sequencing and transcriptome analysis; third, integration of phenotypic, genotypic, and molecular datasets to identify molecular network contributing to CHDs; fourth, generation of relevant disease models and multileveled experimental investigations. In order to achieve all these goals, access to high-quality biological specimens from well-defined patient cohorts is a crucial step. Therefore, establishing a CHD BioCore is an essential infrastructure and a critical step on the path toward precision child health cardiovascular medicine
Typing tumors using pathways selected by somatic evolution.
Many recent efforts to analyze cancer genomes involve aggregation of mutations within reference maps of molecular pathways and protein networks. Here, we find these pathway studies are impeded by molecular interactions that are functionally irrelevant to cancer or the patient's tumor type, as these interactions diminish the contrast of driver pathways relative to individual frequently mutated genes. This problem can be addressed by creating stringent tumor-specific networks of biophysical protein interactions, identified by signatures of epistatic selection during tumor evolution. Using such an evolutionarily selected pathway (ESP) map, we analyze the major cancer genome atlases to derive a hierarchical classification of tumor subtypes linked to characteristic mutated pathways. These pathways are clinically prognostic and predictive, including the TP53-AXIN-ARHGEF17 combination in liver and CYLC2-STK11-STK11IP in lung cancer, which we validate in independent cohorts. This ESP framework substantially improves the definition of cancer pathways and subtypes from tumor genome data
- …