Search results for "Modeling"

The Sea Urchin sns5 Insulator Protects Retroviral Vectors From Chromosomal Position Effects by Maintaining Active Chromatin Structure

2009

Silencing and position-effect (PE) variegation (PEV), which is due to integration of viral vectors in heterochromatin regions, are considered significant obstacles to obtaining a consistent level of transgene expression in gene therapy. The inclusion of chromatin insulators into vectors has been proposed to counteract this position-dependent variegation of transgene expression. Here, we show that the sea urchin chromatin insulator, sns5, protects a recombinant gamma-retroviral vector from the negative influence of chromatin in erythroid milieu. This element increases the probability of vector expression at different chromosomal integration sites, which reduces both silencing and PEV. By chr…

Epigenetic Transcriptional Regulation of the Growth Arrest-Specific gene 1 (Gas1) in Hepatic Cell Proliferation at Mononucleosomal Resolution

2011

Background Gas1 (growth arrest-specific 1) gene is known to inhibit cell proliferation in a variety of models, but its possible implication in regulating quiescence in adult tissues has not been examined to date. The knowledge of how Gas1 is regulated in quiescence may contribute to understand the deregulation occurring in neoplastic diseases. Methodology/Principal Findings Gas1 expression has been studied in quiescent murine liver and during the naturally synchronized cell proliferation after partial hepatectomy. Chromatin immunoprecipitation at nucleosomal resolution (Nuc-ChIP) has been used to carry out the study preserving the in vivo conditions. Transcription has been assessed at real …

The nucleosome remodeling factor ISWI functionally interacts with an evolutionarily conserved network of cellular factors

2010

Abstract ISWI is an evolutionarily conserved ATP-dependent chromatin remodeling factor playing central roles in DNA replication, RNA transcription, and chromosome organization. The variety of biological functions dependent on ISWI suggests that its activity could be highly regulated. Our group has previously isolated and characterized new cellular activities that positively regulate ISWI in Drosophila melanogaster. To identify factors that antagonize ISWI activity we developed a novel in vivo eye-based assay to screen for genetic suppressors of ISWI. Our screen revealed that ISWI interacts with an evolutionarily conserved network of cellular and nuclear factors that escaped previous genetic…

Chromatin remodeling redulation by small molecules and metabolites

2010

ORGANIZATION OF HIGHER-LEVEL CHROMATIN STRUCTURES (CHROMOMERE, CHROMONEMA AND CHROMATIN BLOCK) EXAMINED USING VISIBLE LIGHT-INDUCED CHROMATIN PHOTO-S…

2002

The method of chromatin photo-stabilization by the action of visible light in the presence of ethidium bromide was used for investigation of higher-level chromatin structures in isolated nuclei. As a model we used rat hepatocyte nuclei isolated in buffers which stabilized or destabilized nuclear matrix. Several higher-level chromatin structures were visualized: 100 nm globules—chromomeres, chains of chromomeres—chromonemata, aggregates of chromomeres—blocks of condensed chromatin. All these structures were completely destroyed by 2 M NaCl extraction independent of the matrix state, and DNA was extruded from the residual nuclei (nuclear matrices) into a halo. These results show that nuclear …

Musical pitch quantization as an eigenvalue problem

2020

How can discrete pitches and chords emerge from the continuum of sound? Using a quantum cognition model of tonal music, we prove that the associated Schrödinger equation in Fourier space is invariant under continuous pitch transpositions. However, this symmetry is broken in the case of transpositions of chords, entailing a discrete cyclic group as transposition symmetry. Our research relates quantum mechanics with music and is consistent with music theory and seminal insights by Hermann von Helmholtz.

Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit

2013

In the olfactory bulb, lateral inhibition mediated by granule cells has been suggested to modulate the timing of mitral cell firing, thereby shaping the representation of input odorants. Current experimental techniques, however, do not enable a clear study of how the mitral-granule cell network sculpts odor inputs to represent odor information spatially and temporally. To address this critical step in the neural basis of odor recognition, we built a biophysical network model of mitral and granule cells, corresponding to 1/100th of the real system in the rat, and used direct experimental imaging data of glomeruli activated by various odors. The model allows the systematic investigation and g…

Combining workload balance and patient priority maximisation in operating room planning through hierarchical multi-objective optimisation

2022

Abstract Previous analysis suggested the opportunity to consider the preferences of different stakeholders (hospital, patients, doctors and nurses) through the adoption of both patient priority maximisation and workload balance as performance criteria. The aim of this paper is to develop an effective and efficient solution approach for the operating room planning and scheduling capable to take into account the patient priority maximisation and workload balance criteria at the same time. This work is inspired by the need of a deeper understanding of the quality of the solutions obtained when a combination of the two criteria leads the OR planning decisions. Starting from a hierarchical multi…

The development of school well-being in secondary school: High academic buoyancy and supportive class- and school climate as buffers

2021

Abstract Students experience increasing pressure to perform well and worry about their academic performance before critical school transitions. These challenges may compromise students' school well-being. Drawing on the Model of Personality and Affect for Education (Matthews et al., 2005) as well as on the Conservation of Resources Theory (Hobfoll, 1989), we investigated the buffering role of high academic buoyancy and supportive class- and school climate against decreases in school well-being (i.e., school-related stress, anti-school attitude, and satisfaction with school) among Finnish lower secondary school students (N = 1024) from grades seven to nine. Controlling for gender, fluid inte…

The PASSI and Agile PASSI MAS Meta-models Compared with a Unifying Proposal

2005

A great number of processes for multi-agent systems design have been presented in last years to support the different approaches to agent-oriented design; each process is specific for a particular class of problems and it instantiates a specific MAS meta-model. These differences produce inconsistences and overlaps: a MAS meta-model may define a term not referred by another, or the same term can be used with a different meaning. We think that the lack of a standardization may cause a significant delay to the diffusion of the agent paradigm outside research context. Working for this unification goal, it is also necessary to define in unambiguous way the terms of the agent model and their rela…