The application of interactive graphics to large time-dependent hydrodynamics problems

A written companion of a movie entitled "Interactive Graphics at Los Alamos Scientific Laboratory" was presented. While the movie presents the actual graphics terminal and the functions performed on it, the paper attempts to put in perspective the complexity of the application code and the complexity of the interaction that is possible

A luminosity monitor for the A4 parity violation experiment at MAMI

A water Cherenkov luminosity monitor system with associated electronics has been developed for the A4 parity violation experiment at MAMI. The detector system measures the luminosity of the hydrogen target hit by the MAMI electron beam and monitors the stability of the liquid hydrogen target. Both is required for the precise study of the count rate asymmetries in the scattering of longitudinally polarized electrons on unpolarized protons. Any helicity correlated fluctuation of the target density leads to false asymmetries. The performance of the luminosity monitor, investigated in about 2000 hours with electron beam, and the results of its application in the A4 experiment are presented.Comment: 22 pages, 12 figures, submitted to NIM

Damping of quasi-2D internal wave attractors by rigid-wall friction

The reflection of internal gravity waves at sloping boundaries leads to focusing or defocusing. In closed domains, focusing typically dominates and projects the wave energy onto 'wave attractors'. For small-amplitude internal waves, the projection of energy onto higher wave numbers by geometric focusing can be balanced by viscous dissipation at high wave numbers. Contrary to what was previously suggested, viscous dissipation in interior shear layers may not be sufficient to explain the experiments on wave attractors in the classical quasi-2D trapezoidal laboratory set-ups. Applying standard boundary layer theory, we provide an elaborate description of the viscous dissipation in the interior shear layer, as well as at the rigid boundaries. Our analysis shows that even if the thin lateral Stokes boundary layers consist of no more than 1% of the wall-to-wall distance, dissipation by lateral walls dominates at intermediate wave numbers. Our extended model for the spectrum of 3D wave attractors in equilibrium closes the gap between observations and theory by Hazewinkel et al. (2008)

A Chemical-Genetic Screen for Identifying Substrates of the Er Kinase Perk

Cells constantly encounter changing environments that challenge the ability to adapt and survive. Signal transduction networks enable cells to appropriately sense and respond to these changes, and are often mediated through the activity of protein kinases. Protein kinases are a class of enzyme responsible for regulating a broad spectrum of cellular functions by transferring phosphate groups from ATP to substrate proteins, thereby altering substrate activity and function. PERK is a resident kinase of the endoplasmic reticulum, and is responsible for sensing perturbations in the protein folding capacity of the ER. When the influx of unfolded, nascent proteins exceeds the folding capacity of the ER, PERK initiates a cascade of signaling events that enable cell adaptation and ER stress resolution. These signaling pathways are not only essential for the survival of normal cells undergoing ER stress, but are also co-opted by tumor cells in order to survive the oxygen and nutrient-restricted conditions of the tumor microenvironment. Not surprisingly, PERK signaling is known to influence a variety of pro-tumorigenic processes. Therefore, from a purely biological standpoint as well as from a clinical perspective, it is important to understand this critical cell adaptive pathway in greater detail through identifying its interacting partners and thereby elucidating additional downstream signaling branches. Prior to the work described herein, only three direct PERK substrates had been identified. Using chemical-genetic screening techniques, we have generated a significant list of putative PERK substrates, several of which have been confirmed as PERK substrates in vitro. These preliminary results suggest new connections between known UPR pathways, as well as entirely novel signaling branches downstream of PERK. This work will provide a solid foundation for launching future PERK-related discovery studies

Inertial waves and modes excited by the libration of a rotating cube

We report experimental measurements of the flow in a cubic container submitted to a longitudinal libration, i.e. a rotation modulated in time. Velocity fields in a vertical and a horizontal plane are measured in the librating frame using a corotating particle image velocimetry system. When the libration frequency $\sigma_0$ is smaller than twice the mean rotation rate $\Omega_0$, inertial waves can propagate in the interior of the fluid. At arbitrary excitation frequencies $\sigma_0<2\Omega_0$, the oscillating flow shows two contributions: (i) a basic flow induced by the libration motion, and (ii) inertial wave beams propagating obliquely upward and downward from the horizontal edges of the cube. In addition to these two contributions, inertial modes may also be excited at some specific resonant frequencies. We characterize in particular the resonance of the mode of lowest order compatible with the symmetries of the forcing, noted [2,1,+]. By comparing the measured flow fields to the expected inviscid inertial modes computed numerically [L.R.M. Maas, Fluid Dyn. Res. \textbf{33}, 373 (2003)], we show that only a subset of inertial modes, matching the symmetries of the forcing, can be excited by the libration.Comment: Phys. Fluids (in press

A tale of reviews in two history of science journals

This paper examines the role of book reviews in the discipline of the history of science by comparing their appearance in two periodicals, Isis, the flagship journal of the discipline that was founded in 1913, and the Journal for the History of Astronomy, founded in 1970 to serve a newly emerging, specialized subfield within the broader discipline. Our analysis of the reviews published in selected slices of time finds differing norms and reviewing practices within the two journals. Despite important changes during the past century in the conceptualization of the history of science and its research methods, reviewing practices in Isis remained remarkably consistent over time, with reviewers generally defending a fixed set of norms for “good” scholarship. More change appears in reviews of the Journal for the History of Astronomy, as its audience shifted from a mix of the laity, working astronomers, and historians to a specialized group of professional historians of astronomy. Scholarly norms, reflected in the reviews, shifted with these changes in readership. We conclude that book reviews offer rich sources for analyzing the evolution of scholarly disciplines and norms.Analiza recenzji w dwóch czasopismach z historii nauki W artykule przeanalizowano rolę recenzji książek w dyscyplinie historia nauki, porównując ich występowanie w dwóch czasopismach, Isis, flagowym czasopiśmie dyscypliny założonej w 1913 r., oraz Journal for the History of Astronomy, założonym w 1970 r. służącego nowo powstającej, wyspecjalizowanej poddziedzinie w ramach szerszej dyscypliny. Nasza analiza recenzji opublikowanych w wybranych wycinkach czasu wskazuje na różne normy i praktyki recenzowania w obu czasopismach. Pomimo ważnych zmian, jakie dokonały się w ciągu ostatniego stulecia w konceptualizacji historii nauki i jej metodach badawczych, praktyki recenzowania w Isis pozostawały z biegiem czasu niezwykle spójne, a recenzenci generalnie bronili ustalonego zestawu norm dotyczących „dobrej” nauki. Więcej zmian pojawia się w recenzjach czasopisma Journal for the History of Astronomy, gdy uległa zmianie jego publiczność od mieszanki laików: pracujących astronomów i historyków do wyspecjalizowanej grupy zawodowych historyków astronomii. Wraz z tymi zmianami czytelnictwa zmieniały się normy naukowe, odzwierciedlone w recenzjach. Dochodzimy do wniosku, że recenzje książek stanowią bogate źródła do analizy ewolucji dyscyplin i norm naukowych

Accuracy and feasibility of dual fluoroscopy and model-based tracking to quantify in vivo hip kinematics during clinical exams

pre-printAccurate measurements of in-vivo hip kinematics may elucidate the mechanisms responsible for impaired function and chondrolabral damage in hips with femoroacetabular impingement (FAI). The objectives of this study were to quantify the accuracy and demonstrate the feasibility of using dual fluoroscopy to measure in-vivo hip kinematics during clinical exams used in the assessment of FAI. Steel beads were implanted into the pelvis and femur of two cadavers. Specimens were imaged under dual fluoroscopy during the impingement exam, FABER test, and rotational profile. Bead locations measured with model-based tracking were compared to those measured using dynamic radiostereometric analysis. Error was quantified by bias and precision, defined as the average and standard deviation of the differences between tracking methods, respectively. A normal male volunteer was also imaged during clinical exams. Bias and precision along a single axis did not exceed 0.17 and 0.21 mm, respectively. Comparing kinematics, positional error was less than 0.48 mm and rotational error was less than 0.58°. For the volunteer, kinematics were reported as joint angles and bone-bone distance. These results demonstrate that dual fluoroscopy and model-based tracking can accurately measure hip kinematics in living subjects during clinical exams of the hip