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Madison, WI, United States

Ajeti V.,University of Wisconsin - Madison | Ajeti V.,Laboratory for Optical and Computational Instrumentation | Lien C.-H.,University of Wisconsin - Madison | Chen S.-J.,National Cheng Kung University | And 12 more authors.
Optics Express | Year: 2013

Multiphoton excited photochemistry is a powerful 3D fabrication tool that produces sub-micron feature sizes. Here we exploit the freeform nature of the process to create models of the extracellular matrix (ECM) of several tissues, where the design blueprint is derived directly from high resolution optical microscopy images (e.g. fluorescence and Second Harmonic Generation). To achieve this goal, we implemented a new form of instrument control, termed modulated raster scanning, where rapid laser shuttering (10 MHz) is used to directly map the greyscale image data to the resulting protein concentration in the fabricated scaffold. Fidelity in terms of area coverage and relative concentration relative to the image data is 95%. We compare the results to an STL approach, and find the new scheme provides significantly improved performance. We suggest the method will enable a variety of cell-matrix studies in cancer biology and also provide insight into generating scaffolds for tissue engineering. ©2013 Optical Society of America. Source


Keles S.,1300 University Avenue
Bioinformatics | Year: 2014

Motivation: ChIP-seq technology enables investigators to study genome-wide binding of transcription factors and mapping of epigenomic marks. Although the availability of basic analysis tools for ChIP-seq data is rapidly increasing, there has not been much progress on the related design issues. A challenging question for designing a ChIP-seq experiment is how deeply should the ChIP and the control samples be sequenced? The answer depends on multiple factors some of which can be set by the experimenter based on pilot/preliminary data. The sequencing depth of a ChIP-seq experiment is one of the key factors that determine whether all the underlying targets (e.g. binding locations or epigenomic profiles) can be identified with a targeted power.Results: We developed a statistical framework named CSSP (ChIP-seq Statistical Power) for power calculations in ChIP-seq experiments by considering a local Poisson model, which is commonly adopted by many peak callers. Evaluations with simulations and data-driven computational experiments demonstrate that this framework can reliably estimate the power of a ChIP-seq experiment at different sequencing depths based on pilot data. Furthermore, it provides an analytical approach for calculating the required depth for a targeted power while controlling the false discovery rate at a user-specified level. Hence, our results enable researchers to use their own or publicly available data for determining required sequencing depths of their ChIP-seq experiments and potentially make better use of the multiplexing functionality of the sequencers. Evaluation of power for multiple public ChIP-seq datasets indicate that, currently, typical ChIP-seq studies are powered well for detecting large fold changes of ChIP enrichment over the control sample, but they have considerably less power for detecting smaller fold changes. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved. Source


Toops K.A.,University of Wisconsin - Madison | Hagemann T.L.,University of Wisconsin - Madison | Messing A.,University of Wisconsin - Madison | Nickells R.W.,University of Wisconsin - Madison | Nickells R.W.,1300 University Avenue
BMC Research Notes | Year: 2012

Background: Increased expression of glial fibrillary acidic protein (GFAP) within macroglia is commonly seen as a hallmark of glial activation after damage within the central nervous system, including the retina. The increased expression of GFAP in glia is also considered part of the pathologically inhibitory environment for regeneration of axons from damaged neurons. Recent studies have raised the possibility that reactive gliosis and increased GFAP cannot automatically be assumed to be negative events for the surrounding neurons and that the context of the reactive gliosis is critical to whether neurons benefit or suffer. We utilized transgenic mice expressing a range of Gfap to titrate the amount of GFAP in retinal explants to investigate the relationship between GFAP concentration and the regenerative potential of retinal ganglion cells. Findings. Explants from Gfap -/- and Gfap +/- mice did not have increased neurite outgrowth compared with Gfap +/+ or Gfap over-expressing mice as would be expected if GFAP was detrimental to axon regeneration. In fact, Gfap over-expressing explants had the most neurite outgrowth when treated with a neurite stimulatory media. Transmission electron microscopy revealed that neurites formed bundles, which were surrounded by larger cellular processes that were GFAP positive indicating a close association between growing axons and glial cells in this regeneration paradigm. Conclusions: We postulate that glial cells with increased Gfap expression support the elongation of new neurites from retinal ganglion cells possibly by providing a scaffold for outgrowth. © 2012 Toops et al.; licensee BioMed Central Ltd. Source


Zuo C.,1300 University Avenue
Bioinformatics (Oxford, England) | Year: 2014

ChIP-seq technology enables investigators to study genome-wide binding of transcription factors and mapping of epigenomic marks. Although the availability of basic analysis tools for ChIP-seq data is rapidly increasing, there has not been much progress on the related design issues. A challenging question for designing a ChIP-seq experiment is how deeply should the ChIP and the control samples be sequenced? The answer depends on multiple factors some of which can be set by the experimenter based on pilot/preliminary data. The sequencing depth of a ChIP-seq experiment is one of the key factors that determine whether all the underlying targets (e.g. binding locations or epigenomic profiles) can be identified with a targeted power. We developed a statistical framework named CSSP (ChIP-seq Statistical Power) for power calculations in ChIP-seq experiments by considering a local Poisson model, which is commonly adopted by many peak callers. Evaluations with simulations and data-driven computational experiments demonstrate that this framework can reliably estimate the power of a ChIP-seq experiment at different sequencing depths based on pilot data. Furthermore, it provides an analytical approach for calculating the required depth for a targeted power while controlling the false discovery rate at a user-specified level. Hence, our results enable researchers to use their own or publicly available data for determining required sequencing depths of their ChIP-seq experiments and potentially make better use of the multiplexing functionality of the sequencers. Evaluation of power for multiple public ChIP-seq datasets indicate that, currently, typical ChIP-seq studies are powered well for detecting large fold changes of ChIP enrichment over the control sample, but they have considerably less power for detecting smaller fold changes. Available at www.stat.wisc.edu/~zuo/CSSP. keles@stat.wisc.edu Supplementary data are available at Bioinformatics online. Source


Thein-Nissenbaum J.M.,University of Wisconsin - Madison | Thein-Nissenbaum J.M.,1300 University Avenue | Carr K.E.,University of Wisconsin - Madison
Physical Therapy in Sport | Year: 2011

Female sports participation at the high school level has significantly increased since the 1970s. Physical activity in females has numerous positive benefits, including improved body image and overall health. Unfortunately, a select population of exercising females may experience symptoms related to the " female athlete triad," which refers to the interrelationships among energy availability, menstrual function, and bone mineral density. Clinically, these conditions can manifest as disordered eating behaviors, menstrual irregularity, and stress fractures. Athletes with conditions related to the triad are distributed along a spectrum between optimal health and disease and may not experience all conditions simultaneously.Previous research related to the triad has primarily focused on collegiate and elite athletes. However, mounting evidence demonstrates that the triad is present in the high school population. High school athletes should be assessed for triad components at preparticipation physicals. In addition, parents, coaches, and health care professionals should be educated and informed about the female athlete triad syndrome. In the presence of triad symptoms, further evaluation and treatment by a multidisciplinary team is strongly recommended for the athlete. © 2011. Source

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