A Minimal Model of Metabolism Based Chemotaxis

Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption. Recent studies have shown, however, that many metabolism-dependent chemotactic patterns occur in bacteria. We hereby present the simplest artificial protocell model capable of performing metabolism-based chemotaxis. The model serves as a proof of concept to show how even the simplest metabolism can sustain chemotactic patterns of varying sophistication. It also reproduces a set of phenomena that have recently attracted attention on bacterial chemotaxis and provides insights about alternative mechanisms that could instantiate them. We conclude that relaxing the metabolism-independent assumption provides important theoretical advances, forces us to rethink some established pre-conceptions and may help us better understand unexplored and poorly understood aspects of bacterial chemotaxis

Significance Tests for Periodogram Peaks

We discuss methods currently in use for determining the significance of peaks in the periodograms of time series. We discuss some general methods for constructing significance tests, false alarm probability functions, and the role played in these by independent random variables and by empirical and theoretical cumulative distribution functions. We also discuss the concept of "independent frequencies" in periodogram analysis. We propose a practical method for estimating the significance of periodogram peaks, applicable to all time series irrespective of the spacing of the data. This method, based on Monte Carlo simulations, produces significance tests that are tailor-made for any given astronomical time series.Comment: 22 pages, 11 Encapsulated Postscript figures, AAS LaTeX v5.2 Submitted to Ap

Habitable Zones in the Universe

Habitability varies dramatically with location and time in the universe. This was recognized centuries ago, but it was only in the last few decades that astronomers began to systematize the study of habitability. The introduction of the concept of the habitable zone was key to progress in this area. The habitable zone concept was first applied to the space around a star, now called the Circumstellar Habitable Zone. Recently, other, vastly broader, habitable zones have been proposed. We review the historical development of the concept of habitable zones and the present state of the research. We also suggest ways to make progress on each of the habitable zones and to unify them into a single concept encompassing the entire universe.Comment: 71 pages, 3 figures, 1 table; to be published in Origins of Life and Evolution of Biospheres; table slightly revise

Status Of The FAIR Synchrotron Projects SIS18 And SIS100

A large fraction of the program to upgrade the existingheavy ion synchrotron SIS18 as injector for the FAIR synchrotron SIS100 has been successfully completed. With the achieved technical status, a major increase of theaccelerated number of heavy ions could be reached. Thenow available performance especially demonstrates thefeasibility of high intensity beams of medium charge stateheavy ions with a sufficient control of the dynamicvacuum and connected charge exchange loss. Two furtherupgrade measures, the installation of additional magneticalloy (MA) acceleration cavities and the exchange of themain dipole power converter, are presently beingimplemented. For the FAIR synchrotron SIS100, theprocurement of all major components with longproduction times has been started. With the delivery andtesting of several pre-series components, the phase ofoutstanding technical reserach and developments could becompleted and the readiness for series productionachieved

An improved parameterization of tidal mixing for ocean models

Two modifications to an existing scheme of tidal mixing are implemented in the coarse resolution ocean component of a global climate model. First, the vertical distribution of energy flux out of the barotropic tide is determined using high resolution bathymetry. This shifts the levels of mixing higher up in the water column and leads to a stronger mid-depth meridional overturning circulation in the model. Second, the local dissipation efficiency for diurnal tides is assumed to be larger than that for the semi-diurnal tides poleward of 30°. Both modifications are shown to improve agreement with observational estimates of diapycnal diffusivities based on microstructure measurements and circulation indices. We also assess impacts of different spatial distributions of the barotropic energy loss. Estimates based on satellite altimetry lead to larger diffusivities in the deep ocean and hence a stronger deep overturning circulation in our climate model that is in better agreement with observation based estimates compared to those based on a tidal model.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Copernicus Publications on behalf of the European Geosciences Union. The published article can be found at: http://www.geoscientific-model-development.net/home.html

Robust principal component analysis of electromagnetic arrays with missing data

We describe a new algorithm for robust principal component analysis (PCA) of electromagnetic (EM) array data, extending previously developed multivariate methods to include arrays with large data gaps, and only partial overlap between site occupations. Our approach is based on a criss-cross regression scheme in which polarization parameters and spatial modes are alternately estimated with robust regression procedures. The basic scheme can be viewed as an expectation robust (ER) algorithm, of the sort that has been widely discussed in the statistical literature in the context of robust PCA, but with details of the scheme tailored to the physical specifics of EM array observations. We have tested our algorithm with synthetic and real data, including data denial experiments where we have created artificial gaps, and compared results obtained with full and incomplete data arrays. These tests reveal that for modest amounts of missing data (up to 20 per cent or so) the algorithm performs well, reproducing essentially the same dominant spatial modes that would be obtained from analysis of the complete array. The algorithm thus makes multivariate analysis practical for the first time for large heterogeneous arrays, as we illustrate by application to two different EM arrays.Keywords: Time series analysis, Geomagnetic induction, Magnetotelluri

Reproducibility of quantitative F-18-3'-deoxy-3'-fluorothymidine measurements using positron emission tomography

Positron emission tomography (PET) using F-18-3'-deoxy-3'-fluorothymidine ([F-18]FLT) allows noninvasive monitoring of tumour proliferation. For serial imaging in individual patients, good reproducibility is essential. The purpose of the present study was to evaluate the reproducibility of quantitative [F-18]FLT measurements. Nine patients with non-small-cell lung cancer (NSCLC) and six with head-and-neck cancer (HNC) underwent [F-18]FLT PET twice within 7 days prior to therapy. The maximum pixel value (SUVmax) and a threshold defined volume (SUV41%) were defined for all delineated lesions. The plasma to tumour transfer constant (K-i) was estimated using both Patlak graphical analysis and nonlinear regression (NLR). NLR was also used to estimate k(3), which, at least in theory, selectively reflects thymidine kinase 1 activity. The level of agreement between test and retest values was assessed using the intraclass correlation coefficient (ICC) and Bland-Altman analysis. All primary tumours and > 90% of clinically suspected locoregional metastases could be delineated. In total, 24 lesions were defined. NLR-derived K-i, Patlak-derived K-i, SUV41% and SUVmax showed excellent reproducibility with ICCs of 0.92, 0.95, 0.98 and 0.93, and SDs of 16%, 12%, 7% and 11%, respectively. Reproducibility was poor for k(3) with an ICC of 0.43 and SD of 38%. Quantitative [F-18]FLT measurements are reproducible in both NSCLC and HNC patients. When monitoring response in individual patients, changes of more than 15% in SUV41%, 20-25% in SUVmax and Patlak-derived K-i, and 32% in NLR3k-derived K-i are likely to represent treatment effect

Ionospheric current source modeling and global geomagnetic induction using ground geomagnetic observatory data

Long-period global-scale electromagnetic induction studies of deep Earth conductivity are based almost exclusively on magnetovariational methods and require accurate models of external source spatial structure. We describe approaches to inverting for both the external sources and three-dimensional (3-D) conductivity variations and apply these methods to long-period (T≥1.2 days) geomagnetic observatory data. Our scheme involves three steps: (1) Observatory data from 60 years (only partly overlapping and with many large gaps) are reduced and merged into dominant spatial modes using a scheme based on frequency domain principal components. (2) Resulting modes are inverted for corresponding external source spatial structure, using a simplified conductivity model with radial variations overlain by a two-dimensional thin sheet. The source inversion is regularized using a physically based source covariance, generated through superposition of correlated tilted zonal (quasi-dipole) current loops, representing ionospheric source complexity smoothed by Earth rotation. Free parameters in the source covariance model are tuned by a leave-one-out cross-validation scheme. (3) The estimated data modes are inverted for 3-D Earth conductivity, assuming the source excitation estimated in step 2. Together, these developments constitute key components in a practical scheme for simultaneous inversion of the catalogue of historical and modern observatory data for external source spatial structure and 3-D Earth conductivity.This is the publisher’s final pdf. The article is copyrighted by the American Geophysical Union and published by John Wiley & Sons, Inc. It can be found at: http://agupubs.onlinelibrary.wiley.com/agu/jgr/journal/10.1002/%28ISSN%292169-9356/Keywords: simultaneous inversion, external source fields, mantle conductivity, global inductio

Long-term monitoring of ULF electromagnetic fields at Parkfield, CA

Electric and magnetic fields in the (10{sup -4}-1.0) Hz band were monitored at two sites adjacent to the San Andreas Fault near Parkfield and Hollister, California from 1995 to present. A data window [2002-2005], enclosing the September 28, 2004 M6 Parkfield earthquake, was analyzed to determine if anomalous electric or magnetic fields, or changes in ground conductivity, occurred before the earthquake. The data were edited, removing intervals of instrument malfunction leaving 875 days in the four-year period. Frequent, spike-like disturbances were common, but were not more frequent around the time of the earthquake; these were removed before subsequent processing. Signal to noise amplitude spectra, estimated via magnetotelluric processing showed the behavior of the ULF fields to be remarkably constant over the period of analysis. These first-order plots make clear that most of the recorded energy is coherent over the spatial extent of the array. Three main statistical techniques were employed to separate local anomalous electrical or magnetic fields from the dominant coherent natural fields: transfer function estimates between components at each site were employed to subtract the dominant field, and look deeper at the 'residual' fields; the data were decomposed into principal components to identify the dominant coherent array modes; and the technique of canonical coherences was employed to distinguish anomalous fields which are spatially broad from anomalies which occur at a single site only, and furthermore to distinguish anomalies which are present in both the electric and magnetic fields from those which are present in only one field type. Standard remote reference apparent resistivity estimates were generated daily at Parkfield. A significant seasonal component of variability was observed suggesting local distortion due to variations in near surface resistance. In all cases, high levels of sensitivity to subtle electromagnetic effects were demonstrated, but no effects which can be reasonably characterized as precursors to the Parkfield earthquake were found