TurbuStat: Turbulence Statistics in Python

We present TurbuStat (v1.0): a Python package for computing turbulence statistics in spectral-line data cubes. TurbuStat includes implementations of fourteen methods for recovering turbulent properties from observational data. Additional features of the software include: distance metrics for comparing two data sets; a segmented linear model for fitting lines with a break-point; a two-dimensional elliptical power-law model; multi-core fast-fourier-transform support; a suite for producing simulated observations of fractional Brownian Motion fields, including two-dimensional images and optically-thin HI data cubes; and functions for creating realistic world coordinate system information for synthetic observations. This paper summarizes the TurbuStat package and provides representative examples using several different methods. TurbuStat is an open-source package and we welcome community feedback and contributions.Comment: Accepted in AJ. 21 pages, 8 figure

In vivo robotics: the automation of neuroscience and other intact-system biological fields

Robotic and automation technologies have played a huge role in in vitro biological science, having proved critical for scientific endeavors such as genome sequencing and high-throughput screening. Robotic and automation strategies are beginning to play a greater role in in vivo and in situ sciences, especially when it comes to the difficult in vivo experiments required for understanding the neural mechanisms of behavior and disease. In this perspective, we discuss the prospects for robotics and automation to influence neuroscientific and intact-system biology fields. We discuss how robotic innovations might be created to open up new frontiers in basic and applied neuroscience and present a concrete example with our recent automation of in vivo whole-cell patch clamp electrophysiology of neurons in the living mouse brain.National Institutes of Health (U.S.) (Single Cell Grant 1 R01 EY023173)Human Frontier Science Program (Strasbourg, France)McGovern Institute for Brain Research at MIT. Neurotechnology (MINT) ProgramMIT Media Lab ConsortiumNew York Stem Cell Foundation (Robertson Investigator Award)National Institutes of Health (U.S.) (Director's New Innovator Award 1DP2OD002002)National Institutes of Health (U.S.) (EUREKA Award 1R01GM104948)National Institutes of Health (U.S.) (Grant 1R01DA029639)National Institutes of Health (U.S.) (Grant 1R01NS067199)National Science Foundation (U.S.) (CAREER Award CBET 1053233)National Science Foundation (U.S.) (DMS1042134)Paul G. Allen Family Foundation (Distinguished Investigator in Neuroscience Award)Skolkovo Institute of Science and Technolog

Automated whole-cell patch-clamp electrophysiology of neurons in vivo

Whole-cell patch-clamp electrophysiology of neurons is a gold-standard technique for high-fidelity analysis of the biophysical mechanisms of neural computation and pathology, but it requires great skill to perform. We have developed a robot that automatically performs patch clamping in vivo, algorithmically detecting cells by analyzing the temporal sequence of electrode impedance changes. We demonstrate good yield, throughput and quality of automated intracellular recording in mouse cortex and hippocampus.National Institutes of Health (U.S.) (NIH EUREKA Award program (1R01NS075421))National Institutes of Health (U.S.) ((NIH) Director′s New Innovator Award (DP2OD002002)National Science Foundation (U.S.) ((NSF) CAREER award (CBET 1053233))New York Stem Cell Foundation (Robertson Neuroscience Award)Dr. Gerald Burnett and Marjorie BurnettNational Science Foundation (U.S.) (grant CISE 1110947)National Science Foundation (U.S.) (grant EHR 0965945)American Heart Association (10GRNT4430029

Acute optogenetic silencing of orexin/hypocretin neurons induces slow wave sleep in mice

Orexin/hypocretin neurons have a crucial role in the regulation of sleep and wakefulness. To help determine how these neurons promote wakefulness, we generated transgenic mice in which orexin neurons expressed halorhodopsin (orexin/Halo mice), an orange light-activated neuronal silencer. Slice patch-clamp recordings of orexin neurons that expressed halorhodopsin demonstrated that orange light photic illumination immediately hyperpolarized membrane potential and inhibited orexin neuron discharge in proportion to illumination intensity. Acute silencing of orexin neurons in vivo during the day (the inactive period) induced synchronization of the electroencephalogram and a reduction in amplitude of the electromyogram that is characteristic of slow-wave sleep (SWS). In contrast, orexin neuron photoinhibition was ineffective during the night (active period). Acute photoinhibition of orexin neurons during the day in orexin/Halo mice also reduced discharge of neurons in an orexin terminal field, the dorsal raphe (DR) nucleus. However, serotonergic DR neurons exhibited normal discharge rates in mice lacking orexin neurons. Thus, although usually highly dependent on orexin neuronal activity, serotonergic DR neuronal activity can be regulated appropriately in the chronic absence of orexin input. Together, these results demonstrate that acute inhibition of orexin neurons results in time-of-day-dependent induction of SWS and in reduced firing rate of neurons in an efferent projection site thought to be involved in arousal state regulation. The results presented here advance our understanding of the role of orexin neurons in the regulation of sleep/wakefulness and may be relevant to the mechanisms that underlie symptom progression in narcolepsy.National Institutes of Health (U.S.) (Grant R01NS057464

Assessing the Impact of Astrochemistry on Molecular Cloud Turbulence Statistics

We analyze hydrodynamic simulations of turbulent, star-forming molecular clouds that are post-processed with the photo-dissociation region astrochemistry code 3D-PDR. We investigate the sensitivity of 15 commonly applied turbulence statistics to post-processing assumptions, namely variations in gas temperature, abundance and external radiation field. We produce synthetic $^{12}$CO(1-0) and CI($^{3}$P$_{1}$-$^{3}$P$_{0}$) observations and examine how the variations influence the resulting emission distributions. To characterize differences between the datasets, we perform statistical measurements, identify diagnostics sensitive to our chemistry parameters, and quantify the statistic responses by using a variety of distance metrics. We find that multiple turbulent statistics are sensitive not only to the chemical complexity but also to the strength of the background radiation field. The statistics with meaningful responses include principal component analysis, spatial power spectrum and bicoherence. A few of the statistics, such as the velocity coordinate spectrum, are primarily sensitive to the type of tracer being utilized, while others, like the delta-variance, strongly respond to the background radiation field. Collectively, these findings indicate that more realistic chemistry impacts the responses of turbulent statistics and is necessary for accurate statistical comparisons between models and observed molecular clouds.Comment: 27 pages, 21 figures, accepted to Ap

Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics

We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing in fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach for mapping whole-mammalian-brain connectomes with rich molecular annotations

Dynamic Stability Instrumentation System (DSIS)

The paper is an operating manual for the Dynamic Stability Instrumentation System in specific NASA Langley wind tunnels. The instrumentation system performs either a synchronous demodulation or a Fast Fourier Transform on dynamic balance strain gage signals, and ultimately computes aerodynamic coefficients. The dynamic balance converts sting motor rotation into pitch or yaw plane or roll axis oscillation, with timing information provided by a shaft encoder. Additional instruments control model attitude and balance temperature and monitor sting vibrations. Other instruments perform self-calibration and diagnostics. Procedures for conducting calibrations and wind-off and wind-on tests are listed

Synthetic Physiology

Optogenetic tools are DNA-encoded molecules that, when genetically targeted to cells, enable the control of specific physiological processes within those cells through exposure to light. These tools can pinpoint how these specific processes affect the emergent properties of a complex biological system, such as a mammalian organ or even an entire animal. They can also allow control of a biological system for therapeutic or bioengineering purposes. Many of the optical control tools explored to date are single-component reagents containing a photoactive signaling domain. An interesting question is raised by comparing optogenetics to synthetic biology. In the latter, interchangeable and modular DNA-encoded parts are assembled into complex biological circuits, thus enabling sophisticated logic and computation as well as the production of biologics and reagents (1, 2). Is it possible to devise strategies for the temporally precise cell-targeted optical control of complex engineered biological computational or chemical-synthetic pathways? Such a marriage of optogenetics and synthetic biology—which one might call synthetic physiology—would open up the ability to use optogenetics to trigger and regulate engineered synthetic biology systems, which in turn could execute computational and biological programs of great complexity (3). On page 1565 of this issue, Ye et al. (4) explore such a hybrid approach to controlling a biological system, as well as the bioengineering and preclinical capabilities opened up by such an approach