339 research outputs found
Effect of an electric field on a floating lipid bilayer: a neutron reflectivity study
We present here a neutron reflectivity study of the influence of an
alternative electric field on a supported phospholipid double bilayer. We
report for the first time a reproducible increase of the fluctuation amplitude
leading to the complete unbinding of the floating bilayer. Results are in good
agreement with a semi-quantitative interpretation in terms of negative
electrostatic surface tension.Comment: 12 pages, 7 figures, 1 table accepted for publication in European
Physical Journal E Replaced with with correct bibliograph
From supported membranes to tethered vesicles: lipid bilayers destabilisation at the main transition
We report results concerning the destabilisation of supported phospholipid
bilayers in a well-defined geometry. When heating up supported phospholipid
membranes deposited on highly hydrophilic glass slides from room temperature
(i.e. with lipids in the gel phase), unbinding was observed around the main gel
to fluid transition temperature of the lipids. It lead to the formation of
relatively monodisperse vesicles, of which most remained tethered to the
supported bilayer. We interpret these observations in terms of a sharp decrease
of the bending rigidity modulus in the transition region, combined
with a weak initial adhesion energy. On the basis of scaling arguments, we show
that our experimental findings are consistent with this hypothesis.Comment: 11 pages, 3 figure
Electrostatic and electrokinetic contributions to the elastic moduli of a driven membrane
We discuss the electrostatic contribution to the elastic moduli of a cell or
artificial membrane placed in an electrolyte and driven by a DC electric field.
The field drives ion currents across the membrane, through specific channels,
pumps or natural pores. In steady state, charges accumulate in the Debye layers
close to the membrane, modifying the membrane elastic moduli. We first study a
model of a membrane of zero thickness, later generalizing this treatment to
allow for a finite thickness and finite dielectric constant. Our results
clarify and extend the results presented in [D. Lacoste, M. Cosentino
Lagomarsino, and J. F. Joanny, Europhys. Lett., {\bf 77}, 18006 (2007)], by
providing a physical explanation for a destabilizing term proportional to
\kps^3 in the fluctuation spectrum, which we relate to a nonlinear ()
electro-kinetic effect called induced-charge electro-osmosis (ICEO). Recent
studies of ICEO have focused on electrodes and polarizable particles, where an
applied bulk field is perturbed by capacitive charging of the double layer and
drives flow along the field axis toward surface protrusions; in contrast, we
predict "reverse" ICEO flows around driven membranes, due to curvature-induced
tangential fields within a non-equilibrium double layer, which hydrodynamically
enhance protrusions. We also consider the effect of incorporating the dynamics
of a spatially dependent concentration field for the ion channels.Comment: 22 pages, 10 figures. Under review for EPJ
TeCNO: Surgical Phase Recognition with Multi-Stage Temporal Convolutional Networks
Automatic surgical phase recognition is a challenging and crucial task with
the potential to improve patient safety and become an integral part of
intra-operative decision-support systems. In this paper, we propose, for the
first time in workflow analysis, a Multi-Stage Temporal Convolutional Network
(MS-TCN) that performs hierarchical prediction refinement for surgical phase
recognition. Causal, dilated convolutions allow for a large receptive field and
online inference with smooth predictions even during ambiguous transitions. Our
method is thoroughly evaluated on two datasets of laparoscopic cholecystectomy
videos with and without the use of additional surgical tool information.
Outperforming various state-of-the-art LSTM approaches, we verify the
suitability of the proposed causal MS-TCN for surgical phase recognition.Comment: 10 pages, 2 figure
Examining the Connections within the Startup Ecosystem: A Case Study of St. Louis
This paper documents the resurgence of entrepreneurial activity in St. Louis by reporting on the collaboration and local learning within the startup community. This activity is happening both between entrepreneurs and between organizations that provide support, such as mentoring and funding, to entrepreneurs. As these connections deepen, the strength of the entrepreneurial ecosystem grows. Another finding from the research is that activity-based events, where entrepreneurs have the chance to use and practice the skills needed to grow their businesses, are most useful. St. Louis provides a multitude of these activities, such as Startup Weekend, 1 Million Cups, Code Until Dawn, StartLouis, and GlobalHack. Some of these are St. Louis specific, but others have nationwide or global operations, providing important implications for other cities
Repression of RNA Polymerase II Transcription by a Drosophila Oligopeptide
Background: Germline progenitors resist signals that promote differentiation into somatic cells. This occurs through the transient repression in primordial germ cells of RNA polymerase II, specifically by disrupting Ser2 phosphorylation on its C-terminal domain. Methodology/Principal Findings: Here we show that contrary to expectation the Drosophila polar granule component (pgc) gene functions as a protein rather than a non-coding RNA. Surprisingly, pgc encodes a 71-residue, dimeric, alphahelical oligopeptide repressor. In vivo data show that Pgc ablates Ser2 phosphorylation of the RNA polymerase II C-terminal domain and completely suppresses early zygotic transcription in the soma. Conclusions/Significance: We thus identify pgc as a novel oligopeptide that readily inhibits gene expression. Germ cell repression of transcription in Drosophila is thus catalyzed by a small inhibitor protein
RNAmute: RNA secondary structure mutation analysis tool
BACKGROUND: RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation. RESULTS: Selecting a category in each one of the processed tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical drawing of the single point mutation and the wild type, and includes basic information such as associated energies, representations and distances. RNAMute can be used successfully with very little previous experience and without choosing any parameter value alongside the initial RNA sequence. The package runs under LINUX operating system. CONCLUSION: RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs. In several cases of substantial interest, notably in virology, a point mutation may lead to a loss of important functionality such as the RNA virus replication and translation initiation because of a conformational rearrangement in the secondary structure
Global parameter estimation methods for stochastic biochemical systems
<p>Abstract</p> <p>Background</p> <p>The importance of stochasticity in cellular processes having low number of molecules has resulted in the development of stochastic models such as chemical master equation. As in other modelling frameworks, the accompanying rate constants are important for the end-applications like analyzing system properties (e.g. robustness) or predicting the effects of genetic perturbations. Prior knowledge of kinetic constants is usually limited and the model identification routine typically includes parameter estimation from experimental data. Although the subject of parameter estimation is well-established for deterministic models, it is not yet routine for the chemical master equation. In addition, recent advances in measurement technology have made the quantification of genetic substrates possible to single molecular levels. Thus, the purpose of this work is to develop practical and effective methods for estimating kinetic model parameters in the chemical master equation and other stochastic models from single cell and cell population experimental data.</p> <p>Results</p> <p>Three parameter estimation methods are proposed based on the maximum likelihood and density function distance, including probability and cumulative density functions. Since stochastic models such as chemical master equations are typically solved using a Monte Carlo approach in which only a finite number of Monte Carlo realizations are computationally practical, specific considerations are given to account for the effect of finite sampling in the histogram binning of the state density functions. Applications to three practical case studies showed that while maximum likelihood method can effectively handle low replicate measurements, the density function distance methods, particularly the cumulative density function distance estimation, are more robust in estimating the parameters with consistently higher accuracy, even for systems showing multimodality.</p> <p>Conclusions</p> <p>The parameter estimation methodologies described in this work have provided an effective and practical approach in the estimation of kinetic parameters of stochastic systems from either sparse or dense cell population data. Nevertheless, similar to kinetic parameter estimation in other modelling frameworks, not all parameters can be estimated accurately, which is a common problem arising from the lack of complete parameter identifiability from the available data.</p
Using Visual Cues to Enhance Haptic Feedback for Palpation on Virtual Model of Soft Tissue
This paper explores methods that make use of visual cues aimed at generating actual haptic sensation to the user, namely pseudo-haptics. We propose a new pseudo-haptic feedback based method capable of conveying 3D haptic information and combining visual haptics with force feedback to enhance the user’s haptic experience. We focused on an application related to tumor identification during palpation and evaluated the proposed method in an experimental study where users interacted with a haptic device and graphical interface while exploring a virtual model of soft tissue, which represented stiffness distribution of a silicone phantom tissue with embedded hard inclusions. The performance of hard inclusion detection using force feedback only, pseudo-haptic feedback only, and the combination of the two feedbacks were compared with the direct hand touch. The combination method and direct hand touch had no significant difference in the detection results. Compared with the force feedback alone, our method increased the sensitivity by 5%, the positive predictive value by 4%, and decreased detection time by 48.7%. The proposed methodology has great potential for robot-assisted minimally invasive surgery and in all applications where remote haptic feedback is needed
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