51,092 research outputs found
Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs
Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments
Convolutional Deblurring for Natural Imaging
In this paper, we propose a novel design of image deblurring in the form of
one-shot convolution filtering that can directly convolve with naturally
blurred images for restoration. The problem of optical blurring is a common
disadvantage to many imaging applications that suffer from optical
imperfections. Despite numerous deconvolution methods that blindly estimate
blurring in either inclusive or exclusive forms, they are practically
challenging due to high computational cost and low image reconstruction
quality. Both conditions of high accuracy and high speed are prerequisites for
high-throughput imaging platforms in digital archiving. In such platforms,
deblurring is required after image acquisition before being stored, previewed,
or processed for high-level interpretation. Therefore, on-the-fly correction of
such images is important to avoid possible time delays, mitigate computational
expenses, and increase image perception quality. We bridge this gap by
synthesizing a deconvolution kernel as a linear combination of Finite Impulse
Response (FIR) even-derivative filters that can be directly convolved with
blurry input images to boost the frequency fall-off of the Point Spread
Function (PSF) associated with the optical blur. We employ a Gaussian low-pass
filter to decouple the image denoising problem for image edge deblurring.
Furthermore, we propose a blind approach to estimate the PSF statistics for two
Gaussian and Laplacian models that are common in many imaging pipelines.
Thorough experiments are designed to test and validate the efficiency of the
proposed method using 2054 naturally blurred images across six imaging
applications and seven state-of-the-art deconvolution methods.Comment: 15 pages, for publication in IEEE Transaction Image Processin
How to Ask for a Favor: A Case Study on the Success of Altruistic Requests
Requests are at the core of many social media systems such as question &
answer sites and online philanthropy communities. While the success of such
requests is critical to the success of the community, the factors that lead
community members to satisfy a request are largely unknown. Success of a
request depends on factors like who is asking, how they are asking, when are
they asking, and most critically what is being requested, ranging from small
favors to substantial monetary donations. We present a case study of altruistic
requests in an online community where all requests ask for the very same
contribution and do not offer anything tangible in return, allowing us to
disentangle what is requested from textual and social factors. Drawing from
social psychology literature, we extract high-level social features from text
that operationalize social relations between recipient and donor and
demonstrate that these extracted relations are predictive of success. More
specifically, we find that clearly communicating need through the narrative is
essential and that that linguistic indications of gratitude, evidentiality, and
generalized reciprocity, as well as high status of the asker further increase
the likelihood of success. Building on this understanding, we develop a model
that can predict the success of unseen requests, significantly improving over
several baselines. We link these findings to research in psychology on helping
behavior, providing a basis for further analysis of success in social media
systems.Comment: To appear at ICWSM 2014. 10pp, 3 fig. Data and other info available
at http://www.mpi-sws.org/~cristian/How_to_Ask_for_a_Favor.htm
LEGaTO: first steps towards energy-efficient toolset for heterogeneous computing
LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft
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