Ouabain-induced cytoplasmic vesicles and their role in cell volume maintenance

Cellular swelling is controlled by an active mechanism of cell volume regulation driven by a Na+/K+-dependent ATPase and by aquaporins which translocate water along the osmotic gradient. Na+/K+-pump may be blocked by ouabain, a digitalic derivative, by inhibition of ATP, or by drastic ion alterations of extracellular fluid. However, it has been observed that some tissues are still able to control their volume despite the presence of ouabain, suggesting the existence of other mechanisms of cell volume control. In 1977, by correlating electron microscopy observation with ion and water composition of liver slices incubated in differentmetabolic conditions in the presence or absence of ouabain, we observed that hepatocytes were able to control their volume extruding water and recovering ion composition in the presence of ouabain. In particular, hepatocytes were able to sequester ions and water in intracellular vesicles and then secrete themat the bile canaliculus pole.We named this “vesicularmechanismof cell volume control.” Afterward, thismechanism has been confirmed by us and other laboratories in several mammalian tissues.This review summarizes evidences regarding this mechanism, problems that are still pending, and questions that need to be answered. Finally, we shortly review the importance of cell volume control in some human pathological conditions

rPICARD: A CASA-based Calibration Pipeline for VLBI Data

Currently, HOPS and AIPS are the primary choices for the time-consuming process of (millimeter) Very Long Baseline Interferometry (VLBI) data calibration. However, for a full end-to-end pipeline, they either lack the ability to perform easily scriptable incremental calibration or do not provide full control over the workflow with the ability to manipulate and edit calibration solutions directly. The Common Astronomy Software Application (CASA) offers all these abilities, together with a secure development future and an intuitive Python interface, which is very attractive for young radio astronomers. Inspired by the recent addition of a global fringe-fitter, the capability to convert FITS-IDI files to measurement sets, and amplitude calibration routines based on ANTAB metadata, we have developed the the CASA-based Radboud PIpeline for the Calibration of high Angular Resolution Data (rPICARD). The pipeline will be able to handle data from multiple arrays: EHT, GMVA, VLBA and the EVN in the first release. Polarization and phase-referencing calibration are supported and a spectral line mode will be added in the future. The large bandwidths of future radio observatories ask for a scalable reduction software. Within CASA, a message passing interface (MPI) implementation is used for parallelization, reducing the total time needed for processing. The most significant gain is obtained for the time-consuming fringe-fitting task where each scan be processed in parallel.Comment: 6 pages, 1 figure, EVN 2018 symposium proceeding

Ions and energy metabolism in duck salt‐gland: possible role of furosemide‐sensitive co‐transport of sodium and chloride

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110010/1/tjp19823251333.pd

A New Type of Intensity Correlation in Random Media

A monochromatic point source, embedded in a three-dimensional disordered medium, is considered. The resulting intensity pattern exhibits a new type of long-range correlations. The range of these correlations is infinite and their magnitude, normalized to the average intensity, is of order $1/k_0 \ell$, where $k_0$ and $\ell$ are the wave number and the mean free path respectively.Comment: RevTeX, 8 pages, 3 figures, Accepted to Phys. Rev. Let

The effect of neural adaptation of population coding accuracy

Most neurons in the primary visual cortex initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. The functional consequences of adaptation are unclear. Typically a reduction of firing rate would reduce single neuron accuracy as less spikes are available for decoding, but it has been suggested that on the population level, adaptation increases coding accuracy. This question requires careful analysis as adaptation not only changes the firing rates of neurons, but also the neural variability and correlations between neurons, which affect coding accuracy as well. We calculate the coding accuracy using a computational model that implements two forms of adaptation: spike frequency adaptation and synaptic adaptation in the form of short-term synaptic plasticity. We find that the net effect of adaptation is subtle and heterogeneous. Depending on adaptation mechanism and test stimulus, adaptation can either increase or decrease coding accuracy. We discuss the neurophysiological and psychophysical implications of the findings and relate it to published experimental data.Comment: 35 pages, 8 figure

User interfaces for computational science: a domain specific language for OOMMF embedded in Python

Computer simulations are used widely across the engineering and science disciplines, including in the research and development of magnetic devices using computational micromagnetics. In this work, we identify and review different approaches to configuring simulation runs: (i) the re-compilation of source code, (ii) the use of configuration files, (iii) the graphical user interface, and (iv) embedding the simulation specification in an existing programming language to express the computational problem. We identify the advantages and disadvantages of different approaches and discuss their implications on effectiveness and reproducibility of computational studies and results. Following on from this, we design and describe a domain specific language for micromagnetics that is embedded in the Python language, and allows users to define the micromagnetic simulations they want to carry out in a flexible way. We have implemented this micromagnetic simulation description language together with a computational backend that executes the simulation task using the Object Oriented MicroMagnetic Framework (OOMMF). We illustrate the use of this Python interface for OOMMF by solving the micromagnetic standard problem 4. All the code is publicly available and is open source

Universal conductance fluctuations in non-integer dimensions

We propose an Ansatz for Universal conductance fluctuations in continuous dimensions from 0 up to 4. The Ansatz agrees with known formulas for integer dimensions 1, 2 and 3, both for hard wall and periodic boundary conditions. The method is based solely on the knowledge of energy spectrum and standard assumptions. We also study numerically the conductance fluctuations in 4D Anderson model, depending on system size L and disorder W. We find a small plateau with a value diverging logarithmically with increasing L. Universality gets lost just in 4D.Comment: 4 pages, 4 figures submitted to Phys. Rev.

SLIMS—a user-friendly sample operations and inventory management system for genotyping labs

Summary: We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers