Search results for "SYSTEMS"
showing 10 items of 11952 documents
Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
2018
AbstractAptamers have in recent years emerged as a viable alternative to antibodies. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Despite the availability and advantages of HTS compared to Sanger sequencing, there are only 50 aptamer HTS sequencing samples available on public databases. HTS data in aptamer research are primarily used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because the enrichment of sequences during selection can be due to inefficient negative selection when using live…
Motor-skill learning in an insect inspired neuro-computational control system
2017
In nature, insects show impressive adaptation and learning capabilities. The proposed computational model takes inspiration from specific structures of the insect brain: after proposing key hypotheses on the direct involvement of the mushroom bodies (MBs) and on their neural organization, we developed a new architecture for motor learning to be applied in insect-like walking robots. The proposed model is a nonlinear control system based on spiking neurons. MBs are modeled as a nonlinear recurrent spiking neural network (SNN) with novel characteristics, able to memorize time evolutions of key parameters of the neural motor controller, so that existing motor primitives can be improved. The ad…
The Drosophila Larval Locomotor Circuit Provides a Model to Understand Neural Circuit Development and Function
2021
It is difficult to answer important questions in neuroscience, such as: “how do neural circuits generate behaviour?,” because research is limited by the complexity and inaccessibility of the mammalian nervous system. Invertebrate model organisms offer simpler networks that are easier to manipulate. As a result, much of what we know about the development of neural circuits is derived from work in crustaceans, nematode worms and arguably most of all, the fruit fly, Drosophila melanogaster. This review aims to demonstrate the utility of the Drosophila larval locomotor network as a model circuit, to those who do not usually use the fly in their work. This utility is explored first by discussion…
Network Analysis: Ten Years Shining Light on Host–Parasite Interactions
2020
Biological interactions are key drivers of ecological and evolutionary processes. The complexity of such interactions hinders our understanding of ecological systems and our ability to make effective predictions in changing environments. However, network analysis allows us to better tackle the complexity of ecosystems because it extracts the properties of an ecological system according to the number and distribution of links among interacting entities. The number of studies using network analysis to solve ecological and evolutionary questions in parasitology has increased over the past decade. Here, we synthesise the contribution of network analysis toward disentangling host-parasite proces…
Low-energy Tests of Fundamental Physics
2018
This article presents a personal perspective on why it is interesting and important to test all kinds of fundamental laws and search for as-yet-undiscovered particles and interactions using laboratory-based non-accelerator techniques. Such room-scale experiments are already spearheading discovery, and can be expected to become even more important as accelerators reach seemingly inevitable limits.
miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal
2017
Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and …
Revealing community structures by ensemble clustering using group diffusion
2018
We propose an ensemble clustering approach using group diffusion to reveal community structures in data. We represent data points as a directed graph and assume each data point belong to single cluster membership instead of multiple memberships. The method is based on the concept of ensemble group diffusion with a parameter to represent diffusion depth in clustering. The ability to modulate the diffusion-depth parameter by varying it within a certain interval allows for more accurate construction of clusters. Depending on the value of the diffusion-depth parameter, the presented approach can determine very well both local clusters and global structure of data. At the same time, the ability …
SpCLUST: Towards a fast and reliable clustering for potentially divergent biological sequences
2019
International audience; This paper presents SpCLUST, a new C++ package that takes a list of sequences as input, aligns them with MUSCLE, computes their similarity matrix in parallel and then performs the clustering. SpCLUST extends a previously released software by integrating additional scoring matrices which enables it to cover the clustering of amino-acid sequences. The similarity matrix is now computed in parallel according to the master/slave distributed architecture, using MPI. Performance analysis, realized on two real datasets of 100 nucleotide sequences and 1049 amino-acids ones, show that the resulting library substantially outperforms the original Python package. The proposed pac…
Hyperosmolarity and Benzalkonium Chloride Differently Stimulate Inflammatory Markers in Conjunctiva-Derived Epithelial Cells in vitro
2017
Tear hyperosmolarity is known to cause ocular surface inflammation in dry eye syndrome. Benzalkonium chloride (BAK), an eyedrop preservative, is known to induce dry eye in long-term-treated patients. Analyzing the modulation of the proinflammatory potential of hyperosmolarity in the presence of BAK on the conjunctiva could give new insights into the effect of this preservative on the disease. In a hyperosmolar model on a conjunctiva-derived cell line, and in the presence of BAK, we evaluated key inflammatory markers [CCL2, IL-8, IL-6, macrophage migration inhibitory factor (MIF) and intercellular adhesion molecule (ICAM)-1] as well as the osmoprotectant element nuclear factor of activated T…
Non-cognate bystander cytolysis by clonal epitope-specific CTL lines through CD28-CD80 interaction inhibits antibody production: A potential caveat t…
2015
Abstract Adoptive transfer of virus epitope-specific CD8 T cells is an immunotherapy option to control cytomegalovirus (CMV) infection and prevent CMV organ disease in immunocompromised solid organ transplantation (SOT) and hematopoietic cell transplantation (HCT) recipients. The therapy aims at an early, selective recognition and cytolysis of infected cells for preventing viral spread in tissues with no adverse immunopathogenic side-effects by attack of uninfected bystander cells. Here we describe that virus epitope-specific, cloned T-cell lines lyse target cells that present the cognate antigenic peptide to the TCR, but simultaneously have the potential to lyse uninfected cells expressing…