An executable subset of VDM-SL in an SA/RT framework

In this article we present the executable specification language IPTES Meta-IV based on the formal specification language VDM-SL. The language has been fitted to work in an SA/RT framework and the article presents how it supports the specification of the data transformation part of SA/RT. Furthermore we present some of the advanced constructs of the language seen as an executable specification language in its own right. Finally we present how an IPTES Meta-IV interpreter is used in combination with a high-level timed Petri net executor to execute SA/RT models.     

Musculoskeletal complaints among nurses related to patient handling tasks and psychosocial factors--based on logbook registrations

The aims were to evaluate the inter-method reliability of a registration sheet for patient handling tasks, to study the day-to-day variation of musculoskeletal complaints (MSC) and to examine whether patient handling tasks and psychosocial factors were associated with MSC.Nurses (n = 148) fulfilled logbooks for three consecutive working days followed by a day off. Low back pain (LBP), neck/shoulder pain (NSP), knee pain (KP), psychosocial factors (time pressure, stress, conscience of the quality of work) and patient transfers and care tasks were reported.The logbook was reliable for both transfer and care tasks. The numbers of nurses reporting MSC and the level of pain increased significantly during the three working days (15%-30% and 17%-37%, respectively) and decreased on the day off. Stress and transfer task were associated with LPB and transfer tasks were associated with KP.Our results confirm a relationship between work factors and MSC and indicate that logs could be one way to obtain a better understanding of the complex interaction of various nursing working conditions in relation to MSC.     

tweezercalib 2.0: Faster version of MatLab package for precise calibration of optical tweezers

We present a vectorized version of the MatLab (MathWorks Inc.) package tweezercalib for calibration of optical tweezers with precision. The calibration is based on the power spectrum of the Brownian motion of a dielectric bead trapped in the tweezers. Precision is achieved by accounting for a number of factors that affect this power spectrum, as described in vs. 1 of the package [I.M. Toli?-Nørrelykke, K. Berg-Sørensen, H. Flyvbjerg, Matlab program for precision calibration of optical tweezers, Comput. Phys. Comm. 159 (2004) 225-240]. The graphical user interface allows the user to include or leave out each of these factors. Several “health tests” are applied to the experimental data during calibration, and test results are displayed graphically. Thus, the user can easily see whether the data comply with the theory used for their interpretation. Final calibration results are given with statistical errors and covariance matrix.

New version program summary

Title of program: tweezercalibCatalogue identifier: ADTV_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTV_v2_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: I.M. Toli?-Nørrelykke, K. Berg-Sørensen, H. Flyvbjerg, Comput. Phys. Comm. 159 (2004) 225Catalogue identifier of previous version: ADTVDoes the new version supersede the original program: YesComputer for which the program is designed and others on which it has been tested: General computer running MatLab (Mathworks Inc.)Operating systems under with the program has been tested: Windows2000, Windows-XP, LinuxProgramming language used: MatLab (Mathworks Inc.), standard licenseMemory required to execute with typical data: Of order four times the size of the data fileHigh speed storage required: noneNo. of lines in distributed program, including test data, etc.: 135 989No. of bytes in distributed program, including test data, etc.: 1 527 611Distribution format: tar. gzNature of physical problem: Calibrate optical tweezers with precision by fitting theory to experimental power spectrum of position of bead doing Brownian motion in incompressible fluid, possibly near microscope cover slip, while trapped in optical tweezers. Thereby determine spring constant of optical trap and conversion factor for arbitrary-units-to-nanometers for detection system.Method of solution: Elimination of cross-talk between quadrant photo-diode's output channels for positions (optional). Check that distribution of recorded positions agrees with Boltzmann distribution of bead in harmonic trap. Data compression and noise reduction by blocking method applied to power spectrum. Full accounting for hydrodynamic effects: Frequency-dependent drag force and interaction with nearby cover slip (optional). Full accounting for electronic filters (optional), for “virtual filtering” caused by detection system (optional). Full accounting for aliasing caused by finite sampling rate (optional). Standard non-linear least-squares fitting. Statistical support for fit is given, with several plots facilitating inspection of consistency and quality of data and fit.Summary of revisions: A faster fitting routine, adapted from [J. Nocedal, Y.x. Yuan, Combining trust region and line search techniques, Technical Report OTC 98/04, Optimization Technology Center, 1998; W.H. Press, B.P. Flannery, S.A. Teukolsky, W.T. Vetterling, Numerical Recipes. The Art of Scientific Computing, Cambridge University Press, Cambridge, 1986], is applied. It uses fewer function evaluations, and the remaining function evaluations have been vectorized. Calls to routines in Toolboxes not included with a standard MatLab license have been replaced by calls to routines that are included in the present package. Fitting parameters are rescaled to ensure that they are all of roughly the same size (of order 1) while being fitted. Generally, the program package has been updated to comply with MatLab, vs. 7.0, and optimized for speed.Restrictions on the complexity of the problem: Data should be positions of bead doing Brownian motion while held by optical tweezers. For high precision in final results, data should be time series measured over a long time, with sufficiently high experimental sampling rate: The sampling rate should be well above the characteristic frequency of the trap, the so-called corner frequency. Thus, the sampling frequency should typically be larger than 10 kHz. The Fast Fourier Transform used works optimally when the time series contain n² data points, and long measurement time is obtained with n>12-15. Finally, the optics should be set to ensure a harmonic trapping potential in the range of positions visited by the bead. The fitting procedure checks for harmonic potential.Typical running time: SecondsUnusual features of the program: NoneReferences: The theoretical underpinnings for the procedure are found in [K. Berg-Sørensen, H. Flyvbjerg, Power spectrum analysis for optical tweezers, Rev. Sci. Ins. 75 (2004) 594-612].     

Hot-nanoparticle-mediated fusion of selected cells

Complete fusion of two selected cells allows for the creation of novel hybrid cells with inherited genetic properties from both original cells.Alternatively,via fusion of a selected cell with a selected vesicle,chemicals or genes can be directly delivered into the cell of interest,to control cellular reactions or gene expression.Here,we demonstrate how to perform an optically controlled fusion of two selected cells or of one cell and one vesicle.Fusion is mediated by laser irradiating plasmonic gold nanoparticles optically trapped between two cells (or a vesicle and a cell) of interest.This hot-particle-mediated fusion causes total mixing of the two cytoplasms and the two cell membranes resulting in formation of a new hybrid cell with an intact cell membrane and enzymatic activity following fusion.Similarly,fusion between a vesicle and a cell results in delivery of the vesicle cargo to the cytoplasm,and after fusion,the cell shows signs of viability.The method is an implementation of targeted drug delivery at the single-cell level and has a great potential for cellular control and design.     

Effects of Particle Crushing in Stress Drop-Relaxation Experiments on Crushed Coral Sand

Stress relaxation and stress drop-relaxation tests have been performed to complement a test series performed to study strain rate, creep, and stress drop-creep effects on crushed coral sand. Drained experiments with constant effective confining pressure of 200 kPa were performed in which triaxial specimens of crushed coral sand were loaded to initial stress differences of 500, 700, and 900 kPa, followed by stress drops of 0, 100, 200, 300, and 400 kPa at which points the axial strains were kept constant while the axial stress relaxation and the volumetric strains were observed. The stress drops produced delays in initiation of stress relaxation that were proportional with the magnitudes of the stress drops. The experiments show that sands do not exhibit classic viscous effects, and their behavior is indicated as “nonisotach,” while the typical viscous behavior of clay is termed “isotach.” Thus, there are significant differences in the time-dependent behavior patterns of sands and clay. A mechanistic picture of time effects in sands is proposed.     

Aequorin-based functional assays for G-protein-coupled receptors,ion channels,and tyrosine kinase receptors

Aequorin is a photoprotein originating from jellyfish, whose luminescent activity is dependent on the concentration of calcium ions. Due to the high sensitivity and low background linked to luminescent assays, as well as to its absence of toxicity and its large linear dynamic range, aequorin has been used as an intracellular calcium indicator since its discovery in the early 1960s. The first applications of aequorin involved its microinjection in cells. The cloning of its gene in 1985 opened the way to the stable expression of aequorin in cell lines or even entire organisms. Here we present the validation of aequorin as a functional assay for the screening of G-protein-coupled receptors, ion channels, and tyrosine kinase receptors, as well as for their pharmacological characterization in agonist and antagonist detection assays. We optimized our cell suspension-based assay and determined that the most sensitive assay was performed at room temperature, with mitochondrially expressed aequorin and using coelenterazine derivative h for reconstitution of aequorin. The robustness of the assay and the current availability of luminometers with integrated injectors allow aequorin to fit perfectly with high throughput functional assays requirements.