3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

Global Topological Order Emerges through Local Mechanical Control of Cell Divisions in the Arabidopsis Shoot Apical Meristem

The control of cell position and division act in concert to dictate multicellular organization in tissues and organs. How these processes shape global order and molecular movement across organs is an outstanding problem in biology. Using live 3D imaging and computational analyses, we extracted networks capturing cellular connectivity dynamics across the Arabidopsis shoot apical meristem (SAM) and topologically analyzed the local and global properties of cellular architecture. Locally generated cell division rules lead to the emergence of global tissue-scale organization of the SAM, facilitating robust global communication. Cells that lie upon more shorter paths have an increased propensity to divide, with division plane placement acting to limit the number of shortest paths their daughter cells lie upon. Cell shape heterogeneity and global cellular organization requires KATANIN, providing a multiscale link between cell geometry, mechanical cell-cell interactions, and global tissue order

"Pi of the Sky" - all-sky, real-time search for fast optical transients

An apparatus to search for optical flashes in the sky is described. It has been optimized for gamma ray bursts (GRB) optical counterparts. It consists of 2x16 cameras covering all the sky. The sky is monitored continuously and the data are analysed on-line. It has self-triggering capability and can react to external triggers with negative delay. The prototype with two cameras has been installed at Las Campanas (Chile) and is operational from July 2004. The paper presents general idea and describes the apparatus in detail. Performance of the prototype is briefly reviewed and perspectives for the future are outlined

The SERRATE protein is involved in alternative splicing in <em>Arabidopsis thaliana</em>

Howalternative splicing (AS) is regulated in plants has not yet been elucidated. Previously, we have shown that the nuclear cap-binding protein complex (AtCBC) is involved in AS in Arabidopsis thaliana. Here we show that both subunits of AtCBC (AtCBP20 and AtCBP80) interact with SERRATE (AtSE), a protein involved in the microRNA biogenesis pathway. Moreover, using a high-resolution reverse transcript-ase-polymerase chain reaction AS system we have found that AtSE influences AS in a similar way to the cap-binding complex (CBC), preferentially affecting selection of 50 splice site of first introns. The AtSE protein acts in cooperation with AtCBC: many changes observed in the mutant lacking the correct SERRATE activity were common to those observed in the cbp mutants. Interestingly, significant changes in AS of some genes were also observed in other mutants of plant microRNA biogenesis pathway, hyl1-2 and dcl1-7, but a majority of them did not cor-respond to the changes observed in the se-1mutant. Thus, the role of SERRATE in AS regulation is distinct from that of HYL1andDCL1, and is similar to the regu-lation of AS in which CBC is involved

Active target TPC for study of photonuclear reactions at astrophysical energies

A setup designed to study photonuclear reactions at astrophysical energies - an active target Time Projection Chamber was developed and constructed at the Faculty of Physics, University of Warsaw. The device was successfully employed in two experiments at the Institute of Nuclear Physics Polish Academy of Sciences in Cracow, in which {\gamma}- and neutron-induced reactions with CO2 gas target were measured. The reaction products were detected and their momenta reconstructed. Preliminary results are shown.Comment: Presented at Zakopane Conference on Nuclear Physics 202

An RPC-based Technical Trigger for the CMS Experiment

In the CMS experiment, sub-detectors may send special trigger signals, called "Technical Triggers", for special purposes like test and calibration. The Resistive Plate Chambers are part of the Muon Trigger System of the experiment, but might also produce a cosmic muon trigger as Technical Trigger to be used during the commissioning to the detectors, the CMS magnet Test Cosmic Challenge and the later running of CMS. The proposed implementation is based on the development of a new board, the RBC Balcony Collector (RBC); the test results on prototypes and their performance during the recent CMS Cosmic Challenge are presented

First measurements of the performance of the Barrel RPC system in CMS

During the summer 2006, a first integrated test of a part of the CMS experiment was performed at CERN collecting a data sample of several millions of cosmic rays events. A fraction of the Resistive Plate Chambers system was successfully operated. Results on the RPC performance are reported

Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set

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A finite strain fibre-reinforced viscoelasto-viscoplastic model of plant cell wall growth

A finite strain fibre-reinforced viscoelasto-viscoplastic model implemented in a finite element (FE) analysis is presented to study the expansive growth of plant cell walls. Three components of the deformation of growing cell wall, i.e. elasticity, viscoelasticity and viscoplasticity-like growth, are modelled within a consistent framework aiming to present an integrative growth model. The two aspects of growth—turgor-driven creep and new material deposition—and the interplay between them are considered by presenting a yield function, flow rule and hardening law. A fibre-reinforcement formulation is used to account for the role of cellulose microfibrils in the anisotropic growth. Mechanisms in in vivo growth are taken into account to represent the corresponding biologycontrolled behaviour of a cell wall. A viscoelastic formulation is proposed to capture the viscoelastic response in the cell wall. The proposed constitutive model provides a unique framework for modelling both the in vivo growth of cell wall dominated by viscoplasticity-like behaviour and in vitro deformation dominated by elastic or viscoelastic responses. A numerical scheme is devised, and FE case studies are reported and compared with experimental data