Biomedical subjects

Netta Cohen

Publications and source records attributed to Netta Cohen.

5 recordsLinked to original sources

PubMed2006

Real time computation: zooming in on population codes.

Information processing in nervous systems intricately combines computation at the neuronal and network levels. Many computations may be envisioned as sequences of signal processing steps along some pathway. How can information encoded by single cells be mapped onto network population codes, and how do different modules or layers in the computation synchronize their communication and computation? These fundamental questions are particularly severe when dealing with real time streams of inputs. Here we study this problem within the context of a minimal signal perception task. In particular, we encode neuronal information by externally applying a space- and time-localized stimulus to individual neurons within a network. We show that a pulse-coupled recurrent neural network can successfully handle this task in real time, and obeys three key requirements: (i) stimulus dependence, (ii) initial-conditions independence, and (iii) accessibility by a readout mechanism. In particular, we suggest that the network's overall level of activity can be used as a temporal cue for a robust readout mechanism. Within this framework, the network can rapidly map a local stimulus onto a population code that can then be reliably read out during some narrow but well defined window of time.

Computer Simulation↗

PubMed2005

GC composition of the human genome: in search of isochores.

The isochore theory, proposed nearly three decades ago, depicts the mammalian genome as a mosaic of long, fairly homogeneous genomic regions that are characterized by their guanine and cytosine (GC) content. The human genome, for instance, was claimed to consist of five distinct isochore families: L1, L2, H1, H2, and H3, with GC contents of <37%, 37%-42%, 42%-47%, 47%-52%, and >52%, respectively. In this paper, we address the question of the validity of the isochore theory through a rigorous sequence-based analysis of the human genome. Toward this end, we adopt a set of six attributes that are generally claimed to characterize isochores and statistically test their veracity against the available draft sequence of the complete human genome. By the selection criteria used in this study: distinctiveness, homogeneity, and minimal length of 300 kb, we identify 1,857 genomic segments that warrant the label "isochore." These putative isochores are nonuniformly scattered throughout the genome and cover about 41% of the human genome. We found that a four-family model of putative isochores is the most parsimonious multi-Gaussian model that can be fitted to the empirical data. These families, however, are GC poor, with mean GC contents of 35%, 38%, 41%, and 48% and do not resemble the five isochore families in the literature. Moreover, due to large overlaps among the families, it is impossible to classify genomic segments into isochore families reliably, according to compositional properties alone. These findings undermine the utility of the isochore theory and seem to indicate that the theory may have reached the limits of its usefulness as a description of genomic compositional structures.

Base Composition↗

PubMed2002

Immune response and virus population composition: HIV as a case study.

Based on the current understanding of the immune response, we present what we believe to be a new model of intrahost virus dynamics. The model takes into account the relationship between virus replication rate and the level of antigen displayed by infected cells, and shows how the cell-directed immune response controls both virus load and virus replication rate. In contrast to conventional wisdom, it shows that the predominant virus variant does not necessarily have the highest replication rate. A strong immune response produces a selective advantage for latent viruses, whereas a deteriorating immune response invites in viruses of higher replication rates. The model is analysed in light of the well-studied HIV/AIDS disease progression, and shows how a wide range of major, seemingly unrelated issues in the study of HIV may be accounted for in a simple and unified manner.

Antiretroviral Therapy, Highly Active↗

PubMed2002

Long term behavior of lithographically prepared in vitro neuronal networks.

We measured the long term spontaneous electrical activity of neuronal networks with different sizes, grown on lithographically prepared substrates and recorded with multi-electrode-array technology. The time sequences of synchronized bursting events were used to characterize network dynamics. All networks exhibit scale-invariant Lévy distributions and long-range correlations. These observations suggest that different-size networks self-organize to adjust their activities over many time scales. As predictions of current models differ from our observations, this calls for revised models.

Electrodes↗

PubMed2002

The locust frontal ganglion: a central pattern generator network controlling foregut rhythmic motor patterns.

The frontal ganglion (FG) is part of the insect stomatogastric nervous system and is found in most insect orders. Previous work has shown that in the desert locust, Schistocerca gregaria, the FG constitutes a major source of innervation to the foregut. In an in vitro preparation, isolated from all descending and sensory inputs, the FG spontaneously generated rhythmic multi-unit bursts of action potentials that could be recorded from all its efferent nerves. The consistent endogenous FG rhythmic pattern indicates the presence of a central pattern generator network. We found the appearance of in vitro rhythmic activity to be strongly correlated with the physiological state of the donor locust. A robust pattern emerged only after a period of saline superfusion, if the locust had a very full foregut and crop, or if the animal was close to ecdysis. Accordingly, haemolymph collected at these stages inhibited an ongoing rhythmic pattern when applied onto the ganglion. We present this novel central pattern generating system as a basis for future work on the neural network characterisation and its role in generating and controlling behaviour.

Animals↗