State-Dependent Computation Using Coupled Recurrent Networks

Although conditional branching between possible behavioral states is a hallmark of intelligent behavior, very little is known about the neuronal mechanisms that support this processing. In a step toward solving this problem, we demonstrate by theoretical analysis and simulation how networks of richly interconnected neurons, such as those observed in the superficial layers of the neocortex, can embed reliable, robust finite state machines. We show how a multistable neuronal network containing a number of states can be created very simply by coupling two recurrent networks whose synaptic weights have been configured for soft winner-take-all (sWTA) performance. These two sWTAs have simple, homogeneous, locally recurrent connectivity except for a small fraction of recurrent cross-connections between them, which are used to embed the required states. This coupling between the maps allows the network to continue to express the current state even after the input that elicited that state iswithdrawn. In addition, a small number of transition neurons implement the necessary input-driven transitions between the embedded states. We provide simple rules to systematically design and construct neuronal state machines of this kind. The significance of our finding is that it offers a method whereby the cortex could construct networks supporting a broad range of sophisticated processing by applying only small specializations to the same generic neuronal circuit

Simulation of Laser Propagation in a Plasma with a Frequency Wave Equation

The aim of this work is to perform numerical simulations of the propagation of a laser in a plasma. At each time step, one has to solve a Helmholtz equation in a domain which consists in some hundreds of millions of cells. To solve this huge linear system, one uses a iterative Krylov method with a preconditioning by a separable matrix. The corresponding linear system is solved with a block cyclic reduction method. Some enlightments on the parallel implementation are also given. Lastly, numerical results are presented including some features concerning the scalability of the numerical method on a parallel architecture

A tilted grating interferometer for full vector field differential x-ray phase contrast tomography

We report on a setup for differential x-ray phase-contrast imaging and tomography, that measures the full 2D phase-gradient information. The setup uses a simple one-dimensional x-ray grating interferometer, in which the grating structures of the interferometer are oriented at a tilt angle with respect to the sample rotation axis. In such a configuration, the differential phase images from opposing tomography projections can be combined to yield both components of the gradient vector. We show how the refractive index distribution as well as its x, y, and z gradient components can be reconstructed directly from the recorded projection data. The method can equally well be applied at conventional x-ray tube sources, to analyzer based x-ray imaging or neutron imaging. It is demonstrated with measurements of an x-ray phantom and a rat brain using synchrotron radiation

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task

A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory

A Historical Perspective of Bladderworts (Utricularia): Traps, Carnivory and Body Architecture

The genus Utricularia includes around 250 species of carnivorous plants, commonly known as bladderworts. The generic name Utricularia was coined by Carolus Linnaeus in reference to the carnivorous organs (Utriculus in Latin) present in all species of the genus. Since the formal proposition by Linnaeus, many species of Utricularia were described, but only scarce information about the biology for most species is known. All Utricularia species are herbs with vegetative organs that do not follow traditional models of morphological classification. Since the formal description of Utricularia in the 18th century, the trap function has intrigued naturalists. Historically, the traps were regarded as floating organs, a common hypothesis that was maintained by different botanists. However, Charles Darwin was most likely the first naturalist to refute this idea, since even with the removal of all traps, the plants continued to float. More recently, due mainly to methodological advances, detailed studies on the trap function and mechanisms could be investigated. This review shows a historical perspective on Utricularia studies which focuses on the traps and body organization

A Collaboratory, Multi-Disciplinary Approach to Risk Mitigation during HIV Analytical Treatment Interruption

Analytic treatment interruptions (ATIs) are currently the standard for assessing the impact of experimental interventions aimed at inducing sustained antiretroviral therapy (ART)-free remission in trials related to HIV cure. ATIs are associated with substantial risk to both study participants and their sexual partner(s). Two documented HIV transmissions occurring in the context of ATIs have been recently reported, but recommendations for mitigating the risk of such events during ATIs are limited. We outline a practical approach to risk mitigation during ATI studies and describe strategies we are utilising in an upcoming clinical trial that may be applicable to other centres

Risk assessment of released cellulose nanocrystals – mimicking inhalatory exposure

Cellulose nanocrystals (CNCs) exhibit advantageous chemical and mechanical properties that render them attractive for a wide range of applications. During the life-cycle of CNC containing materials the nanocrystals could be released and become airborne, posing a potential inhalatory exposure risk towards humans. Absent reliable and dose-controlled models that mimic this exposure in situ is a central issue in gaining an insight into the CNC-lung interaction. Here, an Air Liquid Interface Cell Exposure system (ALICE), previously designed for studies of spherical nanoparticles, was used for the first time to establish a realistic physiological exposure test method for inhaled fiber shaped nano-objects; in this case, CNCs isolated from cotton. Applying a microscopy based approach the spatially homogenous deposition of CNCs was demonstrated as a prerequisite of the functioning of the ALICE. Furthermore, reliability and controllability of the system to nebulise high aspect ratio nanomaterials (HARN, e.g. CNCs) was shown. This opens the potential to thoroughly investigate the inhalatory risk of CNCs in vitro using a realistic exposure system

Collective and single cell behavior in epithelial contact inhibition

Control of cell proliferation is a fundamental aspect of tissue physiology central to morphogenesis, wound healing and cancer. Although many of the molecular genetic factors are now known, the system level regulation of growth is still poorly understood. A simple form of inhibition of cell proliferation is encountered in vitro in normally differentiating epithelial cell cultures and is known as "contact inhibition". The study presented here provides a quantitative characterization of contact inhibition dynamics on tissue-wide and single cell levels. Using long-term tracking of cultured MDCK cells we demonstrate that inhibition of cell division in a confluent monolayer follows inhibition of cell motility and sets in when mechanical constraint on local expansion causes divisions to reduce cell area. We quantify cell motility and cell cycle statistics in the low density confluent regime and their change across the transition to epithelial morphology which occurs with increasing cell density. We then study the dynamics of cell area distribution arising through reductive division, determine the average mitotic rate as a function of cell size and demonstrate that complete arrest of mitosis occurs when cell area falls below a critical value. We also present a simple computational model of growth mechanics which captures all aspects of the observed behavior. Our measurements and analysis show that contact inhibition is a consequence of mechanical interaction and constraint rather than interfacial contact alone, and define quantitative phenotypes that can guide future studies of molecular mechanisms underlying contact inhibition