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Valentine Svensson, Sarah A Teichmann, Oliver Stegle
Technological advances have made it possible to measure spatially resolved gene expression at high throughput. However, methods to analyze these data are not established. Here we describe SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed imaging or spatial RNA-sequencing data. SpatialDE also implements 'automatic expression histology', a spatial gene-clustering approach that enables expression-based tissue histology.
March 19, 2018: Nature Methods
Daniel Edsgärd, Per Johnsson, Rickard Sandberg
As methods for measuring spatial gene expression at single-cell resolution become available, there is a need for computational analysis strategies. We present trendsceek, a method based on marked point processes that identifies genes with statistically significant spatial expression trends. trendsceek finds these genes in spatial transcriptomic and sequential fluorescence in situ hybridization data, and also reveals significant gene expression gradients and hot spots in low-dimensional projections of dissociated single-cell RNA-seq data...
March 19, 2018: Nature Methods
Tara Nietzold, Bradley M West, Michael Stuckelberger, Barry Lai, Stefan Vogt, Mariana I Bertoni
The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical composition and elemental distribution within a material. Synchrotron-based XRF has become an integral characterization technique for a variety of research topics, particularly due to its non-destructive nature and its high sensitivity. Today, synchrotrons can acquire fluorescence data at spatial resolutions well below a micron, allowing for the evaluation of compositional variations at the nanoscale...
February 17, 2018: Journal of Visualized Experiments: JoVE
Madeleine S Durkee, Landon D Nash, Fatemeh Nooshabadi, Jeffrey D Cirillo, Duncan J Maitland, Kristen C Maitland
The rapid development of new optical imaging techniques is dependent on the availability of low-cost, customizable, and easily reproducible standards. By replicating the imaging environment, costly animal experiments to validate a technique may be circumvented. Predicting and optimizing the performance of in vivo and ex vivo imaging techniques requires testing on samples that are optically similar to tissues of interest. Tissue-mimicking optical phantoms provide a standard for evaluation, characterization, or calibration of an optical system...
February 12, 2018: Journal of Visualized Experiments: JoVE
Harmen B Gudde, Debra Griffiths, Kenny R Coventry
The memory game paradigm is a behavioral procedure to explore the relationship between language, spatial memory, and object knowledge. Using two different versions of the paradigm, spatial language use and memory for object location are tested under different, experimentally manipulated conditions. This allows us to tease apart proposed models explaining the influence of object knowledge on spatial language (e.g., spatial demonstratives), and spatial memory, as well as understanding the parameters that affect demonstrative choice and spatial memory more broadly...
February 19, 2018: Journal of Visualized Experiments: JoVE
Kensuke Ihara, Koji Sugiyama, Kentaro Takahashi, Masahiro Yamazoe, Tetsuo Sasano, Tetsushi Furukawa
Recent genome-wide association studies targeting atrial fibrillation (AF) have indicated a strong association between the genotype and electrophysiological phenotype in the atria. That encourages us to utilize a genetically-engineered mouse model to elucidate the mechanism of AF. However, it is difficult to evaluate the electrophysiological properties in murine atria due to their small size. This protocol describes the electrophysiological evaluation of atria using an optical mapping system with a high temporal and spatial resolution in Langendorff perfused murine hearts...
February 22, 2018: Journal of Visualized Experiments: JoVE
Andrey Zavadsky, Lev Shemer
This manuscript describes an experimental procedure that allows obtaining diverse quantitative information on temporal and spatial evolution of water waves excited by time-dependent and steady wind forcing. Capacitance-type wave gauge and Laser Slope Gauge (LSG) are used to measure instantaneous water surface elevation and two components of the instantaneous surface slope at a number of locations along the test section of a wind-wave facility. The computer-controlled blower provides airflow over the water in the tank whose rate can vary in time...
February 13, 2018: Journal of Visualized Experiments: JoVE
Waldemar Kaiser, Tim Albes, Alessio Gagliardi
Low charge carrier mobility is one key factor limiting the performance and applicability of devices based on organic semiconductors. Theoretical studies on mobility using the kinetic Monte Carlo or master equation are mainly based on a Gaussian energetic disorder and regular cubic lattices. The dependence of mobility on the electric field, temperature and charge carrier density is well studied for the Gaussian disorder model. In this work, we investigate the influence of spatially correlated site energies and spatial disorder in the lattice sites on the mobility using kinetic Monte Carlo simulations...
March 19, 2018: Physical Chemistry Chemical Physics: PCCP
Gembu Maryu, Haruko Miura, Yoichi Uda, Akira T Komatsubara, Michiyuki Matsuda, Kazuhiro Aoki
Protein kinases play pivotal roles in intracellular signal transduction, and dysregulation of kinases leads to pathological results such as malignant tumors. Kinase activity has hitherto been measured by biochemical methods such as in vitro phosphorylation assay and western blotting. However, these methods are less useful to explore spatial and temporal changes in kinase activity and its cell-to-cell variation. Recent advances in fluorescent proteins and live-cell imaging techniques enable us to visualize kinase activity in living cells with high spatial and temporal resolutions...
March 17, 2018: Cell Structure and Function
Joan M King, Chetan Tiwari, Armin R Mikler, Martin O'Neill
Ebola is a high consequence infectious disease-a disease with the potential to cause outbreaks, epidemics, or pandemics with deadly possibilities, highly infectious, pathogenic, and virulent. Ebola's first reported cases in the United States in September 2014 led to the development of preparedness capabilities for the mitigation of possible rapid outbreaks, with the Centers for Disease Control and Prevention (CDC) providing guidelines to assist public health officials in infectious disease response planning...
March 19, 2018: Disaster Medicine and Public Health Preparedness
Yu-Ru Guo, Hsiu-Chuan Lee, Yun-Chun Lo, Shao-Chuan Yu, Shih-Yi Huang
Nutritional deficit of n-3 polyunsaturated fatty acids (PUFAs) is closely related to cognitive impairment and depression in later life. Cognitive impairment and depression lead to comorbidities, such as metabolic syndrome, in elderly people. The aim of this study is to evaluate the effects of dietary n-3 PUFAs on cognition and depressive-like behavior in an accelerated senescence rat model with prediabetic status. Rats were cotreated with d-gal and sucrose solution for 7 months and then fed fish-oil- or flaxseed-oil-rich diets for 3 months...
March 19, 2018: Food & Function
Alexandra K Eicher, H Matthew Berns, James M Wells
Gastric diseases, including peptic ulcer disease and gastric cancer, are highly prevalent in human beings. Despite this, the cellular biology of the stomach remains poorly understood relative to other gastrointestinal organs such as the liver, intestine, and colon. In particular, little is known about the molecular basis of stomach development and the differentiation of gastric lineages. Although animal models are useful for studying gastric development, function, and disease, there are major structural and physiological differences in human stomachs that render these models insufficient...
March 2018: Cellular and Molecular Gastroenterology and Hepatology
Timm Oberwahrenbrock, Ghislaine L Traber, Sebastian Lukas, Iñigo Gabilondo, Rachel Nolan, Christopher Songster, Lisanne Balk, Axel Petzold, Friedemann Paul, Pablo Villoslada, Alexander U Brandt, Ari J Green, Sven Schippling
Objective: To evaluate the inter-rater reliability of semiautomated segmentation of spectral domain optical coherence tomography (OCT) macular volume scans. Methods: Macular OCT volume scans of left eyes from 17 subjects (8 patients with MS and 9 healthy controls) were automatically segmented by Heidelberg Eye Explorer (v1.9.3.0) beta-software (Spectralis Viewing Module v6.0.0.7), followed by manual correction by 5 experienced operators from 5 different academic centers...
May 2018: Neurology® Neuroimmunology & Neuroinflammation
Amandine Bastide, Jonathan W Yewdell, Alexandre David
While isotopic labeling of amino acids remains the reference method in the field for quantifying translation rate, it does not provide any information on spatial localization of translation sites. The rationale behind developing the ribopuromycylation method (RPM) was primarily to map translation sites at the sub-cellular level while avoiding detection of newly synthesized proteins released from ribosomes. RPM visualizes actively translating ribosomes in cells via standard immunofluorescence microscopy in fixed and permeabilized cells using a puromycin-specific monoclonal antibody to detect puromycylated nascent chains trapped on ribosomes treated with a chain elongation inhibitor...
January 5, 2018: Bio-protocol
Etienne Cavaignac, Gregoire Laumond, Nicolas Reina, Karine Wytrykowski, Jérôme Murgier, Marie Faruch, Philippe Chiron
Ultrasonography (US) is a nonirradiating, low-cost, real-time imaging modality that has very good spatial resolution. US can be used to view the anterolateral ligament (ALL) and injuries to the ALL. Several authors have sought to analyze the anterolateral aspect of the knee using US with varying luck. All of them analyzed the ALL statically only. The goal of this Technical Note is to describe in detail the technique that we use to analyze the anterolateral aspect of the knee in patients with an anterior cruciate ligament tear...
January 2018: Arthroscopy Techniques
Nancy L Chabot, Evangela E Shread, John K Harmon
There is strong evidence that Mercury's polar deposits are water ice hosted in permanently shadowed regions. In this study, we present new Arecibo radar observations of Mercury's south pole, which reveal numerous radar-bright deposits and substantially increase the radar imaging coverage. We also use images from MESSENGER's full mission to determine the illumination conditions of Mercury's south polar region at the same spatial resolution as the north polar region, enabling comparisons between the two poles...
February 2018: Journal of Geophysical Research. Planets
Pu Wang, Gianluca Turcatel, Cosimo Arnesano, David Warburton, Scott E Fraser, Francesco Cutrale
Hyperspectral endoscopic imaging has the potential to enhance clinical diagnostics and outcome. Most commercial endoscopes utilize imaging fiber bundles to transmit the collected signal from the patient to the medical operator. These bundles consist of several fiber cores surrounded by a cladding layer creating comb structure-like artifacts, which complicate further analysis, both spatially and spectrally. Here we present an optical fiber pattern removal algorithm which we applied to hyperspectral bronchoscopic images robustly and quantitatively without the need for specific optical or electrical hardware...
February 1, 2018: Biomedical Optics Express
Shang Wang, Manmohan Singh, Thuy Tien Tran, John Leach, Salavat R Aglyamov, Irina V Larina, James F Martin, Kirill V Larin
Myocardial infarction (MI) leads to cardiomyocyte loss, impaired cardiac function, and heart failure. Molecular genetic analyses of myocardium in mouse models of ischemic heart disease have provided great insight into the mechanisms of heart regeneration, which is promising for novel therapies after MI. Although biomechanical factors are considered an important aspect in cardiomyocyte proliferation, there are limited methods for mechanical assessment of the heart in the mouse MI model. This prevents further understanding the role of tissue biomechanics in cardiac regeneration...
February 1, 2018: Biomedical Optics Express
Vivian Pera, Kavon Karrobi, Syeda Tabassum, Fei Teng, Darren Roblyer
Spatial frequency domain imaging (SFDI) is a wide-field diffuse optical imaging modality that has attracted considerable interest in recent years. Typically, diffuse reflectance measurements of spatially modulated light are used to quantify the optical absorption and reduced scattering coefficients of tissue, and with these, chromophore concentrations are extracted. However, uncertainties in estimated absorption and reduced scattering coefficients are rarely reported, and we know of no method capable of providing these when look-up table (LUT) algorithms are used to recover the optical properties...
February 1, 2018: Biomedical Optics Express
Mikhail E Kandel, Michael Fanous, Catherine Best-Popescu, Gabriel Popescu
As a label-free, nondestructive method, phase contrast is by far the most popular microscopy technique for routine inspection of cell cultures. However, features of interest such as extensions near cell bodies are often obscured by a glow, which came to be known as the halo . Advances in modeling image formation have shown that this artifact is due to the limited spatial coherence of the illumination. Nevertheless, the same incoherent illumination is responsible for superior sensitivity to fine details in the phase contrast geometry...
February 1, 2018: Biomedical Optics Express
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