Aspects of integrability in a classical model for non-interacting fermionic fields

In this work we investigate the issue of integrability in a classical model for noninteracting fermionic fields. This model is constructed via classical-quantum correspondence obtained from the semiclassical treatment of the quantum system. Our main finding is that the classical system, contrary to the quantum system, is not integrablein general. Regarding this contrast it is clear that in general classical models for fermionic quantum systems have to be handled with care. Further numerical investigation of the system showed that there may be islands of stability in the phase space. We also investigated a similar model that is used in theoretical chemistry and found this one to be most probably integrable, although also here the integrability is not assured by the quantum-classical correspondence principle

Signatures of irreversibility in microscopic models of flocking

Flocking in $d=2$ is a genuine non-equilibrium phenomenon for which irreversibility is an essential ingredient. We study a class of minimal flocking models whose only source of irreversibility is self-propulsion and use the entropy production rate (EPR) to quantify the departure from equilibrium across their phase diagrams. The EPR is maximal in the vicinity of the order-disorder transition, where reshuffling of the interaction network is fast. We show that signatures of irreversibility come in the form of asymmetries in the steady state distribution of the flock's microstates. They occur as consequences of the time reversal symmetry breaking in the considered self-propelled systems, independently of the interaction details. In the case of metric pairwise forces, they reduce to local asymmetries in the distribution of pairs of particles. This study suggests a possible use of pair asymmetries both to quantify the departure from equilibrium and to learn relevant information about aligning interaction potentials from data.Comment: 8 pages + Appendix; 6 figure

Dynamics of Genome Organization

A human cell contains about 2m of DNA, packed into a nucleus with diameter ~10μm. The three-dimensional structure of this packing has been the subject of intense investigation essentially since the discovery of DNA itself, with an explosion of the field over the past 15 years, following the advent of chromosome conformation capture techniques. The fourth dimension---time---however, has remained elusive and the dynamics underlying the organization of the genome are much less known. In this thesis I present my contributions to our understanding of these dynamics, working towards a full four-dimensional characterization of genome organization. First, by pulling on a genomic locus in live cells, we revealed the rather liquid-like material properties of chromatin and dispelled the idea that chromatin in interphase forms a gel. Second, by tracking genomic elements known to act as boundary elements for loop formation, we quantified the dynamics of chromatin loops in live cells. My contribution to both projects lay in the development and application of novel data analysis, modeling, and inference methods, implementations of which have been made available to the community for future use. Finally, we devised a simple scaling argument to reconcile the orthogonal observations of chromosome structure, dynamics, and mechanics. In sum, these contributions further our understanding of the dynamical behavior of chromatin in living cells and provide valuable tools and directions for future research.Ph.D

Electroconvulsive therapy hasn’t negative effects on short-term memory function, as assessed using a bedside hand-held device

Electroconvulsive therapy (ECT) is effective in the treatment of treatment-resistant major depression. The fear of cognitive impairment after ECT often deters patients from choosing this treatment option. There is little reliable information regarding the effects of ECT on overall cognitive performance, while short-term memory deficits are well known but not easy to measure within clinical routines. In this pilot study, we examined ECT recipients’ pre- and posttreatment performances on a digital ascending number tapping test. We found that cognitive performance measures exhibited good reproducibility in individual patients and that ECT did not significantly alter cognitive performance up to 2 hours after this therapy was applied. Our results can help patients and physicians make decisions regarding the administration of ECT. Digital measurements are recommended, especially when screening for the most common side effects on cognitive performance and short-term memory

Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm

Background Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is used a measure for spot signal. Other methods use the optical density, i.e. the intensity of the most intense pixel of a spot, or calculate the volume from the parameters of a fitted function. Results In this study we compare the performance of different spot quantification methods using synthetic and real data. We propose a ready-to-use algorithm for spot detection and quantification that uses fitting of two dimensional Gaussian function curves for the extraction of data from two dimensional gel electrophoresis (2-DE) images. The algorithm implements fitting using logical compounds and is computationally efficient. The applicability of the compound fitting algorithm was evaluated for various simulated data and compared with other quantification approaches. We provide evidence that even if an incorrect bell-shaped function is used, the fitting method is superior to other approaches, especially when spots overlap. Finally, we validated the method with experimental data of urea-based 2-DE of Aβ peptides andre-analyzed published data sets. Our methods showed higher precision and accuracy than other approaches when applied to exposure time series and standard gels. Conclusion Compound fitting as a quantification method for 2-DE spots shows several advantages over other approaches and could be combined with various spot detection methods. The algorithm was scripted in MATLAB (Mathworks) and is available as a supplemental file

Bone marrow edema in traumatic vertebral compression fractures: Diagnostic accuracy of dual-layer detector CT using calcium suppressed images

Purpose: To evaluate calcium suppressed images (CaSupp) in dual-layer detector computed tomography (DLCT) for the detection of bone marrow edema (BME) in vertebral fractures. Materials and methods: The retrospective study was approved by the institutional review board. 34 patients with synchronous DLCT and MRI, who were diagnosed with one or more acute vertebral fractures, were included. MRI were systematically analyzed as reference standard. Two blinded and independent readers evaluated CaSupp for vertebral BME. Additionally, both readers determined the optimal calcium suppression indices (CaSupp-I) for visualization of BME in consensus and correlated the CaSupp-I with parallel measurement of trabecular density as surrogate parameter for bone mineral density. ROI-based measurements of the contrast-to-noise ratios (CNR) were also conducted. Interrater agreement was determined by kappa-statistics. CNR were analyzed using Wilcoxon signed rank test. Results: Fifty-seven acute fractured vertebrae out of 383 vertebrae (14.9%) were found. CaSupp yielded an average sensitivity of 87% and specificity of 99%, a positive predictive value of 95%, a negative predictive value of 98% and an accuracy of 97% for the detection of fracture-associated edema. Interrater agreement was excellent (kappa 0.91). Increase in CNR of BME correlated with increasing CaSupp-I. Edema adjacent to the cortical endplates was better visualized using CaSupp-I of 70 and 80, while extensive edema was better visualized using a CaSupp-I of 90 and 100 (chi2 0.2). Conclusion: CaSupp reconstructed from DLCT enable visualization and detection of BME in traumatic fractured vertebrae with high diagnostic accuracy using CaSupp-I of 70-100

Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

Our understanding of the physical principles organizing the genome in the nucleus is limited by the lack of tools to directly exert and measure forces on interphase chromosomes in vivo and probe their material nature. Here, we present a novel approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. We observe viscoelastic displacements over microns within minutes in response to near-picoNewton forces, which are well captured by a Rouse polymer model. Our results highlight the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing the minor role of crosslinks and topological effects and challenging the view that interphase chromatin is a gel-like material. Our new technology opens avenues for future research, from chromosome mechanics to genome functions

Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

International audienceOur understanding of the physical principles organizing the genome in the nucleus is limited by the lack of tools to directly exert and measure forces on interphase chromosomes in vivo and probe their material nature. Here, we introduce an approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. We observed viscoelastic displacements over micrometers within minutes in response to near-piconewton forces, which are consistent with a Rouse polymer model. Our results highlight the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing minor roles for cross-links and topological effects and challenging the view that interphase chromatin is a gel-like material. Our technology opens avenues for future research in areas from chromosome mechanics to genome functions