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 JoVE Biology

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

1Department of Chemical and Biological Engineering, Princeton University


JoVE 50476

We developed computational de novo protein design methods capable of tackling several important areas of protein design. To disseminate these methods we present Protein WISDOM, an online tool for protein design (http://www.proteinwisdom.org). Starting from a structural template, design of monomeric proteins for increased stability and complexes for increased binding affinity can be performed.

 JoVE Behavior

Cortical Source Analysis of High-Density EEG Recordings in Children

1Cognitive Neuroscience & Neuropsychiatry Section, UCL Institute of Child Health, 2Academic Division of Neonatology, Institute for Women's Health, University College London


JoVE 51705

In recent years, there has been increasing interest in estimating the cortical sources of scalp measured electrical activity for cognitive neuroscience experiments. This article describes how high density EEG is acquired and how recordings are processed for cortical source estimation in children from the age of 2 years at the London Baby Lab.

 JoVE Clinical and Translational Medicine

Detection of Architectural Distortion in Prior Mammograms via Analysis of Oriented Patterns

1Department of Electrical and Computer Engineering, Schulich School of Engineering, University of Calgary, 2Department of Radiology, University of Calgary


JoVE 50341

We demonstrate methods for the detection of architectural distortion in prior mammograms. Oriented structures are analyzed using Gabor filters and phase portraits to detect sites of radiating tissue patterns. Each site is characterized and classified using measures to represent spiculating patterns. The methods should assist in the detection of breast cancer.

 JoVE Bioengineering

Patient-specific Modeling of the Heart: Estimation of Ventricular Fiber Orientations

1Institute for Computational Medicine and the Department of Biomedical Engineering, Johns Hopkins University


JoVE 50125

A methodology to estimate ventricular fiber orientations from in vivo images of patient heart geometries for personalized modeling is described. Validation of the methodology performed using normal and failing canine hearts demonstrate that that there are no significant differences between estimated and acquired fiber orientations at a clinically observable level.

 JoVE Neuroscience

Simultaneous Long-term Recordings at Two Neuronal Processing Stages in Behaving Honeybees

1Department of Behavioral Physiology and Sociobiology (Zoology II) Biozentrum, University of Würzburg


JoVE 51750

Simultaneous extracellular long term recordings from two different brain neuropiles or two different anatomical tracts were established in honeybees. These recordings allow the investigation of temporal aspects of neuronal processing across different brain areas at the single neuron as well as at the ensemble level in a behaving animal.

 JoVE Clinical and Translational Medicine

Near Infrared Optical Projection Tomography for Assessments of β-cell Mass Distribution in Diabetes Research

1Umeå Centre for Molecular Medicine, Umeå University, 2Cell Transplant Center, Diabetes Research Institute, University of Miami,, 3EMBL-CRG Systems Biology Program, Centre for Genomic Regulation, Catalan Institute of Research and Advanced Studies, 4Dept. of Computing Science, Umeå University


JoVE 50238

We describe the adaptation of optical projection tomography (OPT)1 to imaging in the near infrared spectrum, and the implementation of a number of computational tools. These protocols enable assessments of pancreatic β-cell mass (BCM) in larger specimens, increase the multichannel capacity of the technique and increase the quality of OPT data.

 JoVE Bioengineering

Designing Silk-silk Protein Alloy Materials for Biomedical Applications

1Department of Physics and Astronomy, Rowan University, 2Department of Biomedical and Translational Sciences, Rowan University, 3Department of Biomedical Sciences, Cooper Medical School of Rowan University, 4Department of Chemistry and Biochemistry, Rowan University


JoVE 50891

Blending is an efficient approach to generate biomaterials with a broad range of properties and combined features. By predicting the molecular interactions between different natural silk proteins, new silk-silk protein alloy platforms with tunable mechanical resiliency, electrical response, optical transparency, chemical processability, biodegradability, or thermal stability can be designed.

 JoVE Clinical and Translational Medicine

Lesion Explorer: A Video-guided, Standardized Protocol for Accurate and Reliable MRI-derived Volumetrics in Alzheimer's Disease and Normal Elderly

1LC Campbell Cognitive Neurology Research Unit, Heart & Stroke Foundation Canadian Partnership for Stroke Recovery, Brain Sciences Research Program, Sunnybrook Health Sciences Centre, 2Department of Medicine (Neurology), Institute of Medical Science, University of Toronto


JoVE 50887

Lesion Explorer (LE) is a semi-automatic, image-processing pipeline developed to obtain regional brain tissue and subcortical hyperintensity lesion volumetrics from structural MRI of Alzheimer's disease and normal elderly. To ensure a high level of accuracy and reliability, the following is a video-guided, standardized protocol for LE's manual procedures.

 JoVE Biology

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

1Max von Pettenkofer Institute, 2Department of Medicine, University of Cambridge, 3Institute for Informatics, Ludwig-Maximilians-University Munich


JoVE 50195

Total cellular RNA provides a poor template for studying short-term changes in RNA synthesis and decay as well as the kinetics of RNA processing. Here, we describe metabolic labeling of newly transcribed RNA with 4-thiouridine followed by thiol-specific biotinylation and purification of newly transcribed RNA allowing to overcome these limitations.

 JoVE Neuroscience

Creating Objects and Object Categories for Studying Perception and Perceptual Learning

1Brain and Behavior Discovery Institute, Georgia Health Sciences University, 2Vision Discovery Institute, Georgia Health Sciences University, 3Department of Opthalmology, Georgia Health Sciences University, 4Intelligent Systems Laboratory, Palo Alto Research Center, 5Pattern Recognition Systems, Palo Alto Research Center, 6Department of Psychology, University of Minnesota


JoVE 3358

We describe a novel methodology for creating naturalistic 3-D objects and object categories with precisely defined feature variations. We use simulations of the biological processes of morphogenesis and phylogenesis to create novel, naturalistic virtual 3-D objects and object categories that can then be rendered as visual images or haptic objects.

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