Visual cortex: Looking into a Klein bottle

AbstractArguments based on mathematical topology may help in understanding the organization of topographic maps in the cerebral cortex

Productivity of Florida Springs: final report to Biology Branch, Office of Naval Research progress from December 31, 1955 to May 31, 1956

CONTENTS: Factors that control species numbers in Silver Springs, by James L. Yount. Study of the biomass of parasites in the stumpknockers, by Wanda Hunter. Macrophytic communities in Florida inland waters, by Delle N. Swindale. Comment in retrospect, by Howard T. Odum. (15pp.

Symmetry considerations and development of pinwheels in visual maps

Neurons in the visual cortex respond best to rod-like stimuli of given orientation. While the preferred orientation varies continuously across most of the cortex, there are prominent pinwheel centers around which all orientations a re present. Oriented segments abound in natural images, and tend to be collinear}; neurons are also more likely to be connected if their preferred orientations are aligned to their topographic separation. These are indications of a reduced symmetry requiring joint rotations of both orientation preference and the underl ying topography. We verify that this requirement extends to cortical maps of mo nkey and cat by direct statistical analysis. Furthermore, analytical arguments and numerical studies indicate that pinwheels are generically stable in evolving field models which couple orientation and topography

Python for Large-Scale Electrophysiology

Electrophysiology is increasingly moving towards highly parallel recording techniques which generate large data sets. We record extracellularly in vivo in cat and rat visual cortex with 54-channel silicon polytrodes, under time-locked visual stimulation, from localized neuronal populations within a cortical column. To help deal with the complexity of generating and analysing these data, we used the Python programming language to develop three software projects: one for temporally precise visual stimulus generation (“dimstim”); one for electrophysiological waveform visualization and spike sorting (“spyke”); and one for spike train and stimulus analysis (“neuropy”). All three are open source and available for download (http://swindale.ecc.ubc.ca/code). The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three. Here we present our software as a showcase of the extensive capabilities of Python in neuroscience

Reorganization of columnar architecture in the growing visual cortex

Many cortical areas increase in size considerably during postnatal development, progressively displacing neuronal cell bodies from each other. At present, little is known about how cortical growth affects the development of neuronal circuits. Here, in acute and chronic experiments, we study the layout of ocular dominance (OD) columns in cat primary visual cortex (V1) during a period of substantial postnatal growth. We find that despite a considerable size increase of V1, the spacing between columns is largely preserved. In contrast, their spatial arrangement changes systematically over this period. While in young animals columns are more band-like, layouts become more isotropic in mature animals. We propose a novel mechanism of growth-induced reorganization that is based on the `zigzag instability', a dynamical instability observed in several inanimate pattern forming systems. We argue that this mechanism is inherent to a wide class of models for the activity-dependent formation of OD columns. Analyzing one member of this class, the Elastic Network model, we show that this mechanism can account for the preservation of column spacing and the specific mode of reorganization of OD columns that we observe. We conclude that neurons systematically shift their selectivities during normal development and that this reorganization is induced by the cortical expansion during growth. Our work suggests that cortical circuits remain plastic for an extended period in development in order to facilitate the modification of neuronal circuits to adjust for cortical growth.Comment: 8+13 pages, 4+8 figures, paper + supplementary materia

Coordinated optimization of visual cortical maps (I) Symmetry-based analysis

In the primary visual cortex of primates and carnivores, functional architecture can be characterized by maps of various stimulus features such as orientation preference (OP), ocular dominance (OD), and spatial frequency. It is a long-standing question in theoretical neuroscience whether the observed maps should be interpreted as optima of a specific energy functional that summarizes the design principles of cortical functional architecture. A rigorous evaluation of this optimization hypothesis is particularly demanded by recent evidence that the functional architecture of OP columns precisely follows species invariant quantitative laws. Because it would be desirable to infer the form of such an optimization principle from the biological data, the optimization approach to explain cortical functional architecture raises the following questions: i) What are the genuine ground states of candidate energy functionals and how can they be calculated with precision and rigor? ii) How do differences in candidate optimization principles impact on the predicted map structure and conversely what can be learned about an hypothetical underlying optimization principle from observations on map structure? iii) Is there a way to analyze the coordinated organization of cortical maps predicted by optimization principles in general? To answer these questions we developed a general dynamical systems approach to the combined optimization of visual cortical maps of OP and another scalar feature such as OD or spatial frequency preference.Comment: 90 pages, 16 figure

Numerical modelling of river rehabilitation schemes

This thesis is based on the application of hydraulic modelling techniques to the study of river rehabilitation schemes. River channelization and rehabilitation techniques are reviewed and the restoration of the River Idle is detailed. The rehabilitation of the Idle, consisting principally of the installation of a number of flow deflectors, forms the basis of the modelling work carried out. Open channel modelling techniques are reviewed and the packages ISIS, HEC-RAS, SSIIM and CFX are applied to the River Idle. Results from SSIIM (two dimensional) and CFX (three dimensional) are validated against site measured velocities. SSIIM predicted velocities calibrate poorly against site data whilst CFX results are considerably more encouraging. Reasons for the increased accuracy of the three dimensional results are discussed. The effect of the installation of the flow deflectors on aquatic habitat is simulated using the techniques underlying the Instream Flow Incremental Methodology (IFIM). The results from the one dimensional model ISIS and the three dimensional package CFX are used to make available habitat predictions. Results indicate an improvement in habitat for adult and spawning chub but a worsening of habitat for roach fry. However, habitat for roach fry can be expected to improve with time as the geomorphology of the river responds to the installation of the deflectors. The results from the habitat modelling exercise also indicate significant discrepancies between the results obtained by applying the one and three dimensional models. Greater improvements in habitat are indicated in the results from the three dimensional modelling approach. This can be attributed to a number of factors but most significantly the fact that the three dimensional model, in solving two further momentum balance equations, accurately simulates a plume of higher velocity which is produced by the narrowing of the channel width at the deflector. This plume of higher velocity is propagated downstream for some distance beyond the deflector and is associated with improved habitat suitability in the case of adult and spawning chub. The effect of the deflectors on the movement of sediments in the Idle is simulated using ISIS Sediment, a module of the ISIS package, and SHEAR. SHEAR is a FORTRAN program, written for this thesis, which calculates bed shear stresses from the vertical velocity distribution predicted by CFX. The predicted bed shear stresses are compared with a critical shear stress for erosion which is calculated from the Shields criteria. Deposition areas can be implied from zones of reduced bed shear stress. Thus, SHEAR is able to describe the spatial detail of erosion and deposition, for any given sediment particle size, at a specific discharge. Results from ISIS Sediment and SHEAR are compared qualitatively with site measurements of bed erosion that has taken place at a single deflector site. Results indicate that the programs have successfully reproduced the major features of the movement of sediments observed on site. These consist of the erosion of a scour pool adjacent to the deflector tip and deposition in the lee of the deflector leading to the development of a bank of sediment. Overall, significant benefits are indicated in a three dimensional approach over the more traditional one dimensional models. These are evident in both improved calibration with site measured velocities, better available habitat prediction and the ability to describe the spatial detail of erosion and deposition

Retinal Wave Behavior through Activity- Dependent Refractory Periods

In the developing mammalian visual system, spontaneous retinal ganglion cell (RGC) activity contributes to and drives several aspects of visual system organization. This spontaneous activity takes the form of spreading patches of synchronized bursting that slowly advance across portions of the retina. These patches are non-repeating and tile the retina in minutes. Several transmitter systems are known to be involved, but the basic mechanism underlying wave production is still not well-understood. We present a model for retinal waves that focuses on acetylcholine mediated waves but whose principles are adaptable to other developmental stages. Its assumptions are that a) spontaneous depolarizations of amacrine cells drive wave activity; b) amacrine cells are locally connected, and c) cells receiving more input during their depolarization are subsequently less responsive and have longer periods between spontaneous depolarizations. The resulting model produces waves with non-repeating borders and randomly distributed initiation points. The wave generation mechanism appears to be chaotic and does not require neural noise to produce this wave behavior. Variations in parameter settings allow the model to produce waves that are similar in size, frequency, and velocity to those observed in several species. Our results suggest that retinal wave behavior results from activity-dependent refractory periods and that the average velocity of retinal waves depends on the duration a cell is excitatory: longer periods of excitation result in slower waves. In contrast to previous studies, we find that a single layer of cells is sufficient for wave generation. The principles described here are very general and may be adaptable to the description of spontaneous wave activity in other areas of the nervous system

A time for rainfed agriculture: Eleventh Coromandel Lecture

In this lecture a plea is made for the study and promotion of increased agricultural production and stabilization of crop yields in rainfed areas of India, based on experience gained by the author in different parts of the world and particularly at ICRISAT. The increasing pressure of population on land resources in India, and particularly the weather, makes it essential to get the maximum food production both from irrigated and rainfed areas. Out of 142 ha of cultivated land in India, about 108 mill ha depend on rainfed agriculture, accounting for 42% of foodgrains production. Average yields are low, generally below 800 kg/ha. It is possible to increase the yields by 50 to 100% with the existing technologies. The contribution of improved, input-responsive seeds and fertilizers, improved management of soil and rainfall, proper choice of cropping systems, supplementary irrigation and water harvesting in rainfed areas, and adoption of full packages of practices will enable modern agriculture and higher production and farm incomes to spread throughout the rainfed area