Network mechanisms of grid cells

One of the major breakthroughs in neuroscience is the emerging understanding of how signals from the external environment are extracted and represented in the primary sensory cortices of the mammalian brain. The operational principles of the rest of the cortex, however, have essentially remained in the dark. The discovery of grid cells, and their functional organization, opens the door to some of the first insights into the workings of the association cortices, at a stage of neural processing where firing properties are shaped not primarily by the nature of incoming sensory signals but rather by internal self-organizing principles. Grid cells are place-modulated neurons whose firing locations define a periodic triangular array overlaid on the entire space available to a moving animal. The unclouded firing pattern of these cells is rare within the association cortices. In this paper, we shall review recent advances in our understanding of the mechanisms of grid-cell formation which suggest that the pattern originates by competitive network interactions, and we shall relate these ideas to new insights regarding the organization of grid cells into functionally segregated modules.     

Computational models of grid cells

Grid cells are space-modulated neurons with periodic firing fields. In moving animals, the multiple firing fields of an individual grid cell form a triangular pattern tiling the entire space available to the animal. Collectively, grid cells are thought to provide a context-independent metric representation of the local environment. Since the discovery of grid cells in 2005, a number of models have been proposed to explain the formation of spatially repetitive firing patterns as well as the conversion of these signals to place signals one synapse downstream in the hippocampus. The present article reviews the most recent developments in our understanding of how grid patterns are generated, maintained, and transformed, with particular emphasis on second-generation computational models that have emerged during the past 2-3 years in response to criticism and new data.     

How to build a grid cell

Neurons in the medial entorhinal cortex fire action potentials at regular spatial intervals, creating a striking grid-like pattern of spike rates spanning the whole environment of a navigating animal. This remarkable spatial code may represent a neural map for path integration. Recent advances using patch-clamp recordings from entorhinal cortex neurons in vitro and in vivo have revealed how the microcircuitry in the medial entorhinal cortex may contribute to grid cell firing patterns, and how grid cells may transform synaptic inputs into spike output during firing field crossings. These new findings provide key insights into the ingredients necessary to build a grid cell.     

Collagen deposition on a preformed grid

Appearance of collagen fibrils in the cuticle was seen by electron microscopy to be preceded by fonnation of a finely filamentous matrix material. At first, the fine filaments of the matrix are unorganized. However, signs of orthogonal ordering soon appear in the most superficial portion of the cuticle, and subsequently appear more basally and closer to the underlying epidermis. Meanwhile, fibrils of different staining properties and identifiable as collagen begin to be deposited in the superficial portion of the cuticle, the same region which first showed organized fine filaments. Then, like the fine filaments before them, the collagen fibrils polymerize more basally. Collagen appears to polymerize on the preformed skeleton of fine filaments as though the fine filaments caused the collagen to assemble. Neither the polymerization nor ordering of collagen fibrils seems to require direct cellular intervention but occur first in that portion of the cuticle which is furthest away from the underlying epidermis. The fine filaments may be self ordering, extracellular macromolecules which in turn determine the polymerization of collagen fibrils.     

Talisman--rapid application development for the grid

In order to make use of the emerging grid and network services offered by various institutes and mandated by many current research projects, some kind of user accessible client is required. In contrast with attempts to build generic workbenches, Talisman is designed to allow a bioinformatics expert to rapidly build custom applications, immediately visible using standard web technology, for users who wish to concentrate on the biology of their problem rather than the informatics aspects. As a component of the MyGrid project, it is intended to allow access to arbitrary resources, including but not limited to relational, object and flat file data sources, analysis programs and grid based storage, tracking and distributed annotation systems.     

Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid

This paper describes a prototype grid infrastructure, called the “eMinerals minigrid”, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.     

Scalable and effective peer-to-peer desktop grid system

We have designed a set of protocols that use peer-to-peer techniques to efficiently implement a distributed and decentralized desktop grid. Incoming jobs with different resource requirements are matched with system nodes through proximity in an N-dimensional Content-Addressable Network, where each resource type is represented as a distinct dimension. In this paper, we describe a comprehensive suite of techniques that cooperate to maximize throughput, and to ensure that load is balanced across all peers. We balance load induced by job executions through randomly generated virtual dimension values, which act to disaggregate clusters of nodes/jobs, and also by a job pushing mechanism based on an approximate global view of the system. We improve upon initial job assignments by using a job-stealing mechanism to overcome load imbalance caused by heterogeneity of nodes/jobs and stale load information. We also describe a set of optimizations that combine to reduce the system load created by the management of the underlying peer-to-peer system and the job-monitoring infrastructure. Unlike other systems, we can effectively support resource constraints of jobs during the course of load balancing since we simplify the problem of matchmaking through building a multi-dimensional resource space and mapping jobs and nodes to this space. We use extensive simulation results to show that the new techniques improve scalability, system throughput, and average response time.     

A relatively cheap photographic film eye-piece grid

A ‘signaller’ (for example, a prey) can avoid detection by a ‘receiver’ (for example, a predator) if its visual signals are difficult to separate from the background. There are two ways by which signallers match the coloration of their background— ‘crypsis’ and ‘masquerade’. We draw attention to the relationships between these two phenomena and how they differ from Batesian mimicry, another adaptation against detection.     

A taxonomy of peer-to-peer desktop grid paradigms

Desktop grid systems and applications have generated significant impacts on science and engineering. The emerging convergence of grid and peer-to-peer (P2P) computing technologies further opens new opportunities for enabling P2P Desktop Grid systems. This paper presents a taxonomy for classifying P2P desktop grid implementation paradigms, aiming to summarize the state-of-the-art technologies and explore the current and potential solution space. To have a comprehensive taxonomy for P2P desktop grid paradigms, we investigate both computational and data grid systems. Moreover, to ease the understanding, the taxonomy is applied to selected case studies of P2P desktop grid systems. The taxonomy is expected to be used as a survey of the state-of-the-art, a design map, a guideline for novice researchers, a common vocabulary, or a design space for simulation and benchmark, and to be extended as the technologies rapidly evolve.     

Hierarchical genetic-based grid scheduling with energy optimization

An optimization of power and energy consumptions is the important concern for a design of modern-day and future computing and communication systems. Various techniques and high performance technologies have been investigated and developed for an efficient management of such systems. All these technologies should be able to provide good performance and to cope under an increased workload demand in the dynamic environments such as Computational Grids (CGs), clusters and clouds. In this paper we approach the independent batch scheduling in CG as a bi-objective minimization problem with makespan and energy consumption as the scheduling criteria. We use the Dynamic Voltage Scaling (DVS) methodology for scaling and possible reduction of cumulative power energy utilized by the system resources. We develop two implementations of Hierarchical Genetic Strategy-based grid scheduler (Green-HGS-Sched) with elitist and struggle replacement mechanisms. The proposed algorithms were empirically evaluated versus single-population Genetic Algorithms (GAs) and Island GA models for four CG size scenarios in static and dynamic modes. The simulation results show that proposed scheduling methodologies fairly reduce the energy usage and can be easily adapted to the dynamically changing grid states and various scheduling scenarios.     

Integrating ARC grid middleware with Taverna workflows

Summary: This work presents two independent approaches for aseamless integration of computational grids with the bioinformaticsworkflow suite Taverna. These are supported by a unique relationaldatabase to link applications with grid resources and presentsthose as workflow elements. A web portal facilitates its collaborativemaintenance. The first approach implements a gateway serviceto handle authentication certificates and all communicationwith the grid. It reads the database to spawn web services forworkflow elements which are in turn used by Taverna. The secondapproach lets Taverna communicate with the grid on its own,by means of a newly developed plug-in. It reads the databaseand executes the needed tasks directly on the grid. While thegateway service is non-intrusive, the plug-in has technicaladvantages, e.g. by allowing data to remain on the grid whilebeing passed between workflow elements. Availability: http://grid.inb.uni-luebeck.de/ Contact: bayer{at}inb.uni-luebeck.de Associate Editor: Alfonso Valencia     

An isomorphic mapping hypothesis of the grid representation

We introduce a grid cell microcircuit hypothesis. We propose the ‘grid in the world’ (evident in grid cell discharges) is generated by a ‘grid in the cortex’. This cortical grid is formed by patches of calbindin-positive pyramidal neurons in layer 2 of medial entorhinal cortex (MEC). Our isomorphic mapping hypothesis assumes three types of isomorphism: (i) metric correspondence of neural space (the two-dimensional cortical sheet) and the external two-dimensional space within patches; (ii) isomorphism between cellular connectivity matrix and firing field; (iii) isomorphism between single cell and population activity. Each patch is a grid cell lattice arranged in a two-dimensional map of space with a neural : external scale of approximately 1 : 2000 in the dorsal part of rat MEC. The lattice behaves like an excitable medium with neighbouring grid cells exciting each other. Spatial scale is implemented as an intrinsic scaling factor for neural propagation speed. This factor varies along the dorsoventral cortical axis. A connectivity scheme of the grid system is described. Head direction input specifies the direction of activity propagation. We extend the theory to neurons between grid patches and predict a rare discharge pattern (inverted grid cells) and the relative location and proportion of grid cells and spatial band cells.     

Ocular stereometric grid for research on the liver

A new ocular network of the light microscope and the method of its application for histometric investigation of hepatocytes, and microcirculatory bed of the liver lobe based on the morphofunctional peculiarities of peripheral and central lobular zones are described. Histometry of biopsy material from the dog liver has demonstrated that with a smaller volume of sinusoids in normal animals, the nuclear-cytoplasmic hepatocyte ratio was greater in the peripheral than in the central lobular zones.     

Temporal summation and reaction time for grid detection

We studied the stimulus-duration effect on the reaction time (RT) to gratings with different spatial frequencies. At each duration value, the product of the contrast and the duration, i.e. the contrast "energy" was kept constant. We found that at near-threshold "energy" levels the RT was constant for up to 15 ms at lower spatial frequencies and up to 30 ms at higher spatial frequencies. At higher "energy" levels, this critical interval was the same (up to 15 ms) for both lower and higher spatial frequencies. The effect of the duration of gradual onset of the stimulus on RT was also studied. An increase of onset duration (up to 60 ms) at low spatial frequencies substantially delayed reaction time for the contrasts under study. Conversely, at high spatial frequencies, this effect was present only for gratings with a high contrast. These results suggest that reaction time is determined by two types of mechanisms (transient and sustained) at a near threshold contrast, and by one type (transient) mechanism at higher contrasts.     

Solving navigational uncertainty using grid cells on robots

To successfully navigate their habitats, many mammals use a combination of two mechanisms, path integration and calibration using landmarks, which together enable them to estimate their location and orientation, or pose. In large natural environments, both these mechanisms are characterized by uncertainty: the path integration process is subject to the accumulation of error, while landmark calibration is limited by perceptual ambiguity. It remains unclear how animals form coherent spatial representations in the presence of such uncertainty. Navigation research using robots has determined that uncertainty can be effectively addressed by maintaining multiple probabilistic estimates of a robot's pose. Here we show how conjunctive grid cells in dorsocaudal medial entorhinal cortex (dMEC) may maintain multiple estimates of pose using a brain-based robot navigation system known as RatSLAM. Based both on rodent spatially-responsive cells and functional engineering principles, the cells at the core of the RatSLAM computational model have similar characteristics to rodent grid cells, which we demonstrate by replicating the seminal Moser experiments. We apply the RatSLAM model to a new experimental paradigm designed to examine the responses of a robot or animal in the presence of perceptual ambiguity. Our computational approach enables us to observe short-term population coding of multiple location hypotheses, a phenomenon which would not be easily observable in rodent recordings. We present behavioral and neural evidence demonstrating that the conjunctive grid cells maintain and propagate multiple estimates of pose, enabling the correct pose estimate to be resolved over time even without uniquely identifying cues. While recent research has focused on the grid-like firing characteristics, accuracy and representational capacity of grid cells, our results identify a possible critical and unique role for conjunctive grid cells in filtering sensory uncertainty. We anticipate our study to be a starting point for animal experiments that test navigation in perceptually ambiguous environments.     

myGrid: personalised bioinformatics on the information grid

MOTIVATION: The (my)Grid project aims to exploit Grid technology, with an emphasis on the Information Grid, and provide middleware layers that make it appropriate for the needs of bioinformatics. (my)Grid is building high level services for data and application integration such as resource discovery, workflow enactment and distributed query processing. Additional services are provided to support the scientific method and best practice found at the bench but often neglected at the workstation, notably provenance management, change notification and personalisation. RESULTS: We give an overview of these services and their metadata. In particular, semantically rich metadata expressed using ontologies necessary to discover, select and compose services into dynamic workflows.