a code generation approach to neural simulations on parallel hardware

Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions

Equivariant Ricci-Flow with Surgery

In dieser Arbeit untersuchen wir Perelmans Ricci-Fluss mit Chirurgie auf geschlossenen 3–Mannigfaltigkeiten, deren Ausgangsmetrik invariant unter einer vorgegebenen glatten Wirkung einer endlichen Gruppe ist. Eine solche Metrik kann stets durch Mittelung einer beliebigen Riemannschen Metrik erzeugt werden, und wegen der Eindeutigkeit des Ricci-Flusses bleibt dieser bis zum Auftreten von Singularitäten invariant unter der Gruppenwirkung. Die technische Schwierigkeit besteht nun darin, Symmetrien der evolvierenden Metrik zu kontrollieren, wenn sich der Fluss einer Singularität nähert. Zu diesem Zweck konstruieren wir eine invariante singuläre S²–Blätterung auf dem Bereich der Mannigfaltigkeit, der von der Chirurgie betroffen ist. Insbesondere ermöglicht es diese, den Chirurgieprozess äquivariant durchzuführen und die Gruppenwirkung auf solchen Komponenten zu analysieren, die bei der Chirurgie komplett entfernt werden. Darüber hinaus lässt sich mit Hilfe der Blätterung beschreiben, wie die Gruppenwirkungen vor und nach der Chirurgie zusammenhängen. Dadurch lassen sich aus dem Langzeitverhalten des Ricci-Flusses und der Gruppenwirkung Rückschlüsse auf die ursprüngliche Wirkung ziehen. Als Anwendung zeigen wir, dass jede glatte endliche Gruppenwirkung auf einer geschlossenen geometrischen 3–dimensionalen Mannigfaltigkeit mit sphärischer, hyperbolischer oder (S²×R)–Geometrie verträglich mit der geometrischen Struktur ist, dass also eine invariante vollständige lokalhomogene Riemannsche Metrik existiert. Dies löst eine von William Thurston aufgestellte Frage zu Gruppenwirkungen auf geometrischen 3–Mannigfaltigkeiten, die für die übrigen fünf Geometrien bereits von Meeks und Scott gelöst wurde.In this thesis we study Perelman’s Ricci-flow with surgery on closed 3–manifolds on which the initial metric is invariant under a given smooth finite group action. Such a metric can always be obtained by averaging an arbitrary metric, and due to its uniqueness the Ricci-flow stays invariant until the first singular time. The main technical difficulty is to control the symmetries of the evolving metric when the flow approaches a singular time. In order to get such a control, we construct an invariant singular S²–foliation on the part of the manifold which is affected by the surgery. In particular this foliation enables us to perform the surgery process in an equivariant way and to analyze the action on those components which get extinct at the surgery time, since they are completely covered by the foliation. Moreover, it relates the group actions before and after a surgery. Thus, we can conclude properties of the initial group action from the long time behavior of the equivariant flow. As an application we show that any smooth finite group action on a closed geometric 3-manifold with spherical, hyperbolic or (S²×R)–geometry is compatible with the geometric structure, i. e. there exists an invariant complete locally homogeneous Riemannian metric. This solves a question of William Thurston for smooth group actions on geometric 3–manifolds, which was proved for the other five geometries by Meeks and Scott

GeNN: a code generation framework for accelerated brain simulations

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/

Case report: Life threatening hyponatremia in infants with urinary tract infections: two cases of type III pseudohypoaldosteronism and review of the literature

We describe two female infants at the age of five and six months with urinary tract infections presenting with vomiting and reduced drinking behavior. On laboratory analysis, severe hyponatremia (106 mmol/L and 109 mmol/L) was seen with hyperkalemia and compensated metabolic acidosis. Endocrinological analyses revealed massively increased levels of aldosterone and renin, leading to the diagnosis of type III pseudohypoaldosteronism (PHA). A review of the current literature 2013–2023 revealed 26 type III PHA cases aged up to ten months with reduced drinking behavior, weight loss and/or failure to thrive being the most common clinical presentations. Given the severe presentation of PHA electrolyte measurements in infants with urinary tract infections and/or in infants with congenital anomalies of the kidney and urinary tract (CAKUT) are strongly recommended

Virtual deep brain stimulation: Multiscale co-simulation of a spiking basal ganglia model and a whole-brain mean-field model with The Virtual Brain

Deep brain stimulation (DBS) has been successfully applied in various neurodegenerative diseases as an effective symptomatic treatment. However, its mechanisms of action within the brain network are still poorly understood. Many virtual DBS models analyze a subnetwork around the basal ganglia and its dynamics as a spiking network with their details validated by experimental data. However, connectomic evidence shows widespread effects of DBS affecting many different cortical and subcortical areas. From a clinical perspective, various effects of DBS besides the motoric impact have been demonstrated. The neuroinformatics platform The Virtual Brain (TVB) offers a modeling framework allowing us to virtually perform stimulation, including DBS, and forecast the outcome from a dynamic systems perspective prior to invasive surgery with DBS lead placement. For an accurate prediction of the effects of DBS, we implement a detailed spiking model of the basal ganglia, which we combine with TVB via our previously developed co-simulation environment. This multiscale co-simulation approach builds on the extensive previous literature of spiking models of the basal ganglia while simultaneously offering a whole-brain perspective on widespread effects of the stimulation going beyond the motor circuit. In the first demonstration of our model, we show that virtual DBS can move the firing rates of a Parkinson's disease patient's thalamus - basal ganglia network towards the healthy regime while, at the same time, altering the activity in distributed cortical regions with a pronounced effect in frontal regions. Thus, we provide proof of concept for virtual DBS in a co-simulation environment with TVB. The developed modeling approach has the potential to optimize DBS lead placement and configuration and forecast the success of DBS treatment for individual patients

Pathogen burden, inflammation, proliferation and apoptosis in human in-stent restenosis - Tissue characteristics compared to primary atherosclerosis

Pathogenic events leading to in-stent restenosis (ISR) are still incompletely understood. Among others, inflammation, immune reactions, deregulated cell death and growth have been suggested. Therefore, atherectomy probes from 21 patients with symptomatic ISR were analyzed by immunohistochemistry for pathogen burden and compared to primary target lesions from 20 stable angina patients. While cytomegalovirus, herpes simplex virus, Epstein-Barr virus and Helicobacter pylori were not found in ISR, acute and/or persistent chlamydial infection were present in 6/21 of these lesions (29%). Expression of human heat shock protein 60 was found in 8/21 of probes (38%). Indicated by distinct signals of CD68, CD40 and CRP, inflammation was present in 5/21 (24%), 3/21 (14%) and 2/21 (10%) of ISR cases. Cell density of ISR was significantly higher than that of primary lesions ( 977 +/- 315 vs. 431 +/- 148 cells/mm(2); p < 0.001). There was no replicating cell as shown by Ki67 or PCNA. TUNEL+ cells indicating apoptosis were seen in 6/21 of ISR specimens (29%). Quantitative analysis revealed lower expression levels for each intimal determinant in ISR compared to primary atheroma (all p < 0.05). In summary, human ISR at the time of clinical presentation is characterized by low frequency of pathogen burden and inflammation, but pronounced hypercellularity, low apoptosis and absence of proliferation. Copyright (C) 2004 S. Karger AG, Basel