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The Four-Plate Test in Mice

The four-plate test (FPT) is an animal model of anxiety based on spontaneous response. Animals are exposed to a novel environment. The exploration of this novel surrounding is suppressed by the delivery of mild electric foot shock contingent to quadrant crossing. Animal can only escape from th ...

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Novelty-Suppressed Feeding in the Mouse

The use of hyponeophagia, in which exposure to a novel environment suppresses feeding behavior, has been used to assess anxiety-related behavior in animals for over seven decades. More recent work has shown that variations of hyponeophagia, such as the novelty-suppressed feeding test, h ...

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Managing Knowledge in Neuroscience

Processing text from scientific literature has become a necessity due to the burgeoning amounts of information that are fast becoming available, stemming from advances in electronic information technology. We created a program, NeuroText (http://senselab.med.yale.edu/tex ...

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Interoperability Across Neuroscience Databases

Data interoperability between well-defined domains is currently performed by leveraging Web services. In the biosciences, more specifically in neuroscience, robust data interoperability is more difficult to achieve due to data heterogeneity, continuous domain changes, and ...

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Database Architectures for Neuroscience Applications

To determine effective database architecture for a specific neuroscience application, one must consider the distinguishing features of research databases and the requirements that the particular application must meet. Research databases manage diverse types of data, and th ...

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XML for Data Representation and Model Specification in Neuroscience

EXtensible Markup Language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed ...

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Creating Neuroscience Ontologies

The insufficiency of terminological standards in neuroscience is increasingly recognized as a serious obstacle to interoperability. Adoption of a controlled vocabulary is a successful solution for small numbers of groups that work closely together but is impractical for large n ...

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Computational Exploration of Neuron and Neural Network Models in Neurobiology

The electrical activity of individual neurons and neuronal networks is shaped by the complex interplay of a large number of non-linear processes, including the voltage-dependent gating of ion channels and the activation of synaptic receptors. These complex dynamics make it difficult ...

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Constructing Realistic Neural Simulations with GENESIS

The GEneral NEural SImulation System (GENESIS) is an open source simulation platform for realistic modeling of systems ranging from subcellular components and biochemical reactions to detailed models of single neurons, simulations of large networks of realistic neurons, and sy ...

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Brain Atlases and Neuroanatomic Imaging

Quantifying the effect of a genetic manipulation or disease is a complicated process in a population of animals. Probabilistic brain atlases can capture population variability and be used to quantify those variations in anatomy as measured by structural imaging. Minimum deformation ...

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Brain Mapping with High-Resolution fMRI Technology

This chapter describes the use of high-resolution functional magnetic resonance imaging (fMRI) technology in brain odor mapping and a suite of informatics tools for building, databasing, and analyzing fMRI odor maps. OdorMapBuilder is a software program that extracts the olfactory ...

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Workflow-Based Approaches to Neuroimaging Analysis

Analysis of functional and structural magnetic resonance imaging (MRI) brain images requires a complex sequence of data processing steps to proceed from raw image data to the final statistical tests. Neuroimaging researchers have begun to apply workflow-based computing techniq ...

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An Informatics Approach to Systems Neurogenetics

We outline the theory behind complex trait analysis and systems genetics and describe web-accessible resources including GeneNetwork (GN) that can be used for rapid exploratory analysis and hypothesis testing. GN, in particular, is a tightly integrated suite of bioinformatics too ...

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Databasing Receptor Distributions in the Brain

Receptor distributions in the brain are studied by autoradiographic mapping in brain slices, which is a labor-intensive and expensive procedure. To keep track of the results of such studies, we have designed CoReDat, a multi-user relational database system that is available for download f ...

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Computational Models of Dementia and Neurological Problems

A critical goal of neuroscience is to fully understand neural processes and their relations to mental processes, and cognitive, affective, and behavioral disorders. Computational modeling, although still in its infancy, continues to play a central role in this endeavor. Presented he ...

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Integrating Genetic, Functional Genomic, and Bioinformatics Data in a Systems Biology Approach to Complex Diseases: Application to Schizophrenia

The search for DNA alterations that cause human disease has been an area of active research for more than 50 years, since the time that the genetic code was first solved. In the absence of data implicating chromosomal aberrations, researchers historically have performed whole genome linkage a ...

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Real-Time Imaging of Tumors Using Replication-Competent Light-Emitting Microorganisms

Early detection of cancer and metastases is pivotal to the success of subsequent treatment intervention. In recent years, the use of live microorganisms, such as viruses and bacteria, has gained substantial research and clinical interest in both detection and therapy of cancer. Many of the ...

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Real-Time Fluorescence Imaging of Abdominal, Pleural, and Lymphatic Metastases

Virally-directed fluorescence imaging has the potential to revolutionize intra-operative oncologic staging and tumor resection. Many viruses genetically engineered to specifically infect tumor cells as cancer therapy can be further modified to have a visible marker gene for ...

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In Vivo Imaging of Pancreatic Cancer with Fluorescent Proteins in Mouse Models

In this chapter, we describe protocols for clinically-relevant, metastatic orthotopic mouse models of pancreatic cancer, made imageable with genetic reporters. These models utilize human pancreatic-cancer cell lines which have been genetically engineered to selectively e ...

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Three-Dimensional In Vivo Imaging of Tumors Expressing Red Fluorescent Proteins

3D imaging of genetically-engineered fluorescent tumors enables quantitative monitoring of tumor growth/regression, metastatic processes, including during anticancer therapy in real-time. Fluorescent tumor models for 3D imaging require stable expression of geneti ...

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