Mechanisms associated with activation of intracellular metabotropic glutamate receptor, mGluR5

The group 1 metabotropic glutamate receptor, mGluR5, is found on the cell surface as well as on intracellular membranes where it can mediate both overlapping and unique signaling effects. Previously we have shown that glutamate activates intracellular mGluR5 by entry through sodium-dependent transporters and/or cystine glutamate exchangers. Calibrated antibody labelling suggests that the glutamate concentration within neurons is quite high (~10 mM) raising the question as to whether intracellular mGluR5 is maximally activated at all times or whether a different ligand might be responsible for receptor activation. To address this issue, we used cellular, optical and molecular techniques to show that intracellular glutamate is largely sequestered in mitochondria; that the glutamate concentration necessary to activate intracellular mGluR5 is about ten-fold higher than what is necessary to activate cell surface mGluR5; and uncaging caged glutamate within neurons can directly activate the receptor. Thus these studies further the concept that glutamate itself serves as the ligand for intracellular mGluR5

ChimpCheck: Property-Based Randomized Test Generation for Interactive Apps

We consider the problem of generating relevant execution traces to test rich interactive applications. Rich interactive applications, such as apps on mobile platforms, are complex stateful and often distributed systems where sufficiently exercising the app with user-interaction (UI) event sequences to expose defects is both hard and time-consuming. In particular, there is a fundamental tension between brute-force random UI exercising tools, which are fully-automated but offer low relevance, and UI test scripts, which are manual but offer high relevance. In this paper, we consider a middle way---enabling a seamless fusion of scripted and randomized UI testing. This fusion is prototyped in a testing tool called ChimpCheck for programming, generating, and executing property-based randomized test cases for Android apps. Our approach realizes this fusion by offering a high-level, embedded domain-specific language for defining custom generators of simulated user-interaction event sequences. What follows is a combinator library built on industrial strength frameworks for property-based testing (ScalaCheck) and Android testing (Android JUnit and Espresso) to implement property-based randomized testing for Android development. Driven by real, reported issues in open source Android apps, we show, through case studies, how ChimpCheck enables expressing effective testing patterns in a compact manner.Comment: 20 pages, 21 figures, Symposium on New ideas, New Paradigms, and Reflections on Programming and Software (Onward!2017

Expert-level detection of acute intracranial hemorrhage on head computed tomography using deep learning.

Computed tomography (CT) of the head is used worldwide to diagnose neurologic emergencies. However, expertise is required to interpret these scans, and even highly trained experts may miss subtle life-threatening findings. For head CT, a unique challenge is to identify, with perfect or near-perfect sensitivity and very high specificity, often small subtle abnormalities on a multislice cross-sectional (three-dimensional [3D]) imaging modality that is characterized by poor soft tissue contrast, low signal-to-noise using current low radiation-dose protocols, and a high incidence of artifacts. We trained a fully convolutional neural network with 4,396 head CT scans performed at the University of California at San Francisco and affiliated hospitals and compared the algorithm's performance to that of 4 American Board of Radiology (ABR) certified radiologists on an independent test set of 200 randomly selected head CT scans. Our algorithm demonstrated the highest accuracy to date for this clinical application, with a receiver operating characteristic (ROC) area under the curve (AUC) of 0.991 ± 0.006 for identification of examinations positive for acute intracranial hemorrhage, and also exceeded the performance of 2 of 4 radiologists. We demonstrate an end-to-end network that performs joint classification and segmentation with examination-level classification comparable to experts, in addition to robust localization of abnormalities, including some that are missed by radiologists, both of which are critically important elements for this application

Bio-logic: gene expression and the laws of combinatorial logic

Original article can be found at: http://www.mitpressjournals.org/ Copyright MIT Press DOI: 10.1162/artl.2008.14.1.121At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection and multiplexing is performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This paper presents a systematic investigation into the effect of TF binding dependencies on the predicted regulatory function of this “bio-logic”. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each other’s affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: 1) the laws of combinatorial logic hold only for systems with independently binding TFs; 2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and 3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be more robustly controlled than that of single TF or (quasi-) logical multi-TF systems. Keywords: Transcription regulation, Genetic regulatory networks, Enzyme kinetics, Combinatorial logic, Non-Boolean continuous logic, Modelling.Peer reviewe

Sequences within the C terminus of the metabotropic glutamate receptor 5 (mGluR5) are responsible for inner nuclear membrane localization

Traditionally, G-protein-coupled receptors (GPCR) are thought to be located on the cell surface where they transmit extracellular signals to the cytoplasm. However, recent studies indicate that some GPCRs are also localized to various subcellular compartments such as the nucleus where they appear required for various biological functions. For example, the metabotropic glutamate receptor 5 (mGluR5) is concentrated at the inner nuclear membrane (INM) where it mediates Ca(2+) changes in the nucleoplasm by coupling with G(q/11). Here, we identified a region within the C-terminal domain (amino acids 852–876) that is necessary and sufficient for INM localization of the receptor. Because these sequences do not correspond to known nuclear localization signal motifs, they represent a new motif for INM trafficking. mGluR5 is also trafficked to the plasma membrane where it undergoes re-cycling/degradation in a separate receptor pool, one that does not interact with the nuclear mGluR5 pool. Finally, our data suggest that once at the INM, mGluR5 is stably retained via interactions with chromatin. Thus, mGluR5 is perfectly positioned to regulate nucleoplasmic Ca(2+) in situ

Meso-beta scale numerical simulation studies of terrain-induced jet streak mass/momentum perturbations

An in-depth analysis of observed gravity waves and their relationship to precipitation bands over the Montana mesonetwork during the 1981 CCOPE case study indicates that there were two episodes of coherent internal gravity waves. One of the fundamental unanswered questions from this research, however, concerns the dynamical processes which generated the observed waves, all of which originated from the region encompassing the borders of Montana, Idaho, and Wyoming. While geostrophic adjustment, shearing instability, and terrain where all implicated separately or in concert as possible wave generation mechanisms, the lack of upper-air data within the wave genesis region made it difficult to rigorously define the genesis processes from observations alone. In this report we employ a mesoscale numerical model to help diagnose the intricate early wave generation mechanisms during the first observed wave episode

An Operational Computational Terminal Area PBL Prediction System

There are two fundamental goals of this research project which are listed here in terms of priority, i.e., a primary and secondary goal. The first and primary goal is to develop a prognostic system which could satisfy the operational weather prediction requirements of the meteorological subsystem within the Aircraft Vortex Spacing System (AVOSS), i.e., an operational computational Terminal Area PBL Prediction System (TAPPS). The second goal is to perform indepth diagnostic analyses of the meteorological conditions during the special wake vortex deployments at Memphis and Dallas during August 95 and September 97, respectively. These two goals are interdependent because a thorough understanding of the atmospheric dynamical processes which produced the unique meteorology during the Memphis and Dallas deployments will help us design a prognostic system for the planetary boundary layer (PBL) which could be utilized to support the meteorological subsystem within AVOSS. Concerning the primary goal, TAPPS Stage 2 was tested on the Memphis data and is about to be tested on the Dallas case studies. Furthermore benchmark tests have been undertaken to select the appropriate platform to run TAPPS in real time in support of the DFW AVOSS system. In addition, a technique to improve the initial data over the region surrounding Dallas was also tested and modified for potential operational use in TAPPS. The secondary goal involved several sensitivity simulations and comparisons to Memphis observational data sets in an effort to diagnose what specific atmospheric phenomena where occurring which may have impacted the dynamics of atmospheric wake vortices

Meso-beta scale numerical simulation studies of terrain-induced jet streak mass and momentum perturbations

An in-depth analysis of observed gravity waves and their relationship to precipitation bands over the Montana mesonetwork during the 11-12 July 1981 CCOPE case study indicated two episodes of coherent waves. While geostrophic adjustment, shearing instability, and terrain were all implicated separately or in combination as possible wave generation mechanisms, the lack of upper-air data within the wave genesis region made it difficult to define the genesis processes from observations alone. The first part of this paper, 3D Numerical Modeling Studies of Terrain-Induced Mass/Momentum Perturbations, employs a mesoscale numerical model to help diagnose the intricate early wave generation mechanisms during the first observed gravity wave episode. The meso-beta scale numerical model is used to study various simulations of the role of multiple geostrophic adjustment processes in focusing a region for gravity wave genesis. The second part of this paper, Linear Theory and Theoretical Modeling, investigates the response of non-resting rotating homogeneous and continuously stratified Boussinesq models of the terrestrial atmosphere to temporally impulsive and uniformly propagating three-dimensional localized zonal momentum sources representative of midlatitude jet streaks. The methods of linear perturbation theory applied to the potential vorticity (PV) and wave field equations are used to study the geostrophic adjustment dynamics. The total zonal and meridional wind perturbations are separated into geostrophic and ageostrophic components in order to define and follow the evolution of both the primary and secondary mesocirculations accompanying midlatitude jetogenesis forced by geostrophic adjustment processes. This problem is addressed to help fill the gap in understanding the dynamics and structure of mesoscale inertia-gravity waves forced by geostrophic adjustment processes in simple two-dimensional quiescent current systems and those produced by mesoscale numerical models simulating the orographic and diabatic perturbation of three-dimensional quasi-geostrophically balanced synoptic scale jet streaks associated with complex baroclinic severe storm producing environments

Meso-beta scale numerical simulation studies of terrain-induced jet streak mass/momentum perturbations

Work performed during the report period is summarized. The first numerical experiment which was performed on the North Carolina Supercomputer Center's CRAY-YMP machine during the second half of FY92 involved a 36 hour simulation of the CCOPE case study. This first coarse-mesh simulation employed the GMASS model with a 178 x 108 x 32 matrix of grid points spaced approximately 24 km apart. The initial data was comprised of the global 2.5 x 2.5 degree analyses as well as all available North American rawinsonde data valid at 0000 UTC 11 July 1981. Highly-smoothed LFM-derived terrain data were utilized so as to determine the mesoscale response of the three-dimensional atmosphere to weak terrain forcing prior to including the observed highly complex terrain of the northern Rocky Mountain region. It was felt that the model should be run with a spectrum of terrain geometries, ranging from observed complex terrain to no terrain at all, to determine how crucial the terrain was in forcing the mesoscale phenomena. Both convection and stratiform (stable) precipitation were not allowed in this simulation so that their relative importance could be determined by inclusion in forth-coming simulations. A full suite of planetary boundary layer forcing was allowed in the simulation, including surface sensible and latent heat fluxes employing the Blakadar PBL formulation. The details of this simulation, which in many ways could be considered the control simulation, including the important synoptic-scale, meso-alpha scale, and meso-beta scale circulations is described. These results are compared to the observations diagnosed by Koch and his colleagues as well as hypotheses set forth in the project proposal for terrain-influences upon the jet stream and their role in the generation of mesoscale wave phenomenon. The fundamental goal of the analyses being the discrimination among background geostrophic adjustment, terrain influences, and shearing instability in the initiation and maintainance of mesoscale internal wave phenomena. Based upon these findings, FY93 plans are discussed. A review of linear theory and theoretical modeling of a geostrophic zonal wind anomaly is included

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure