scholarly journals Evaluation of ChIC-based data requires normalization that properly retains signal-to-noise ratios

2021 ◽  
Author(s):  
Bofeng Liu ◽  
Fengling Chen ◽  
Wei Xie
Keyword(s):  
Transcription Factors ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Signal To Noise Ratio ◽  
Complete Loss ◽  
Open Chromatin ◽  
Dramatic Reduction ◽  
Signal To Noise ◽  
Noise Ratio ◽  
Tn5 Transposase

Several chromatin immunocleavage-based (ChIC) methods using Tn5 transposase have been developed to profile histone modifications and transcription factors bindings. A recent preprint by Wang et al. raised potential concerns that these methods are prone to open chromatin bias. While the authors are appreciated for alerting the community for this issue, it has been previously described and discussed by Henikoff and colleagues in the original CUT&Tag paper. However, as described for CUT&Tag, the signal-to-noise ratio is essential for Tn5-based profiling methods and all antibody-based enrichment assays. Based on this notion, we would like to point out a major analysis issue in Wang et al. that caused a complete loss or dramatic reduction of enrichment at true targets for datasets generated by Tn5-based methods, which in turn artificially enhanced the relative enrichment of potential open chromatin bias. Such analysis issue is caused by distinct background normalizations used towards ChIP-based (chromatin immunoprecipitation) data and Tn5-based data in Wang et al. Only the normalization for Tn5-based data, but not ChIP-seq based data, yielded such effects. Distortion of such signal-to-noise ratio would consequently lead to misleading results.

scholarly journals TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay

2019 ◽  
Vol 2 (4) ◽  
pp. e201900318 ◽  
Author(s):  
Junaid Akhtar ◽  
Piyush More ◽  
Steffen Albrecht ◽  
Federico Marini ◽  
Waldemar Kaiser ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Signal To Noise Ratio ◽  
High Signal ◽  
Signal To Noise ◽  
Chromatin Immunoprecipitation Assay ◽  
High Agreement ◽  
Genome Wide ◽  
Sequencing Method ◽  
Noise Ratio ◽  
Generation Sequencing

Chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) is a powerful technique to study transcriptional regulation. However, the requirement of millions of cells to generate results with high signal-to-noise ratio precludes it in the study of small cell populations. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high-quality histone profiles from low cell numbers. The data obtained from the TAF-ChIP approach are amenable to standard tools for ChIP-Seq analysis, owing to its high signal-to-noise ratio. The epigenetic profiles from TAF-ChIP approach showed high agreement with conventional ChIP-Seq datasets, thereby underlining the utility of this approach.

scholarly journals TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay

2018 ◽  
Author(s):  
Junaid Akhtar ◽  
Piyush More ◽  
Steffen Albrecht ◽  
Federico Marini ◽  
Waldemar Kaiser ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Signal To Noise Ratio ◽  
High Signal ◽  
Signal To Noise ◽  
Chromatin Immunoprecipitation Assay ◽  
High Agreement ◽  
Genome Wide ◽  
Sequencing Method ◽  
Noise Ratio ◽  
Generation Sequencing

AbstractChromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) is powerful technique to study transcriptional regulation. However, the requirement of millions of cells to generate results with high signal-to-noise ratio precludes it in the study of small cell populations. Here, we present a Tagmentation-Assisted Fragmentation ChIP (TAF-ChIP) and sequencing method to generate high-quality results from low cell numbers. The data obtained from the TAF-ChIP approach is amenable to standard tools for ChIP-Seq analysis, owing to its high signal-to-noise ratio. The epigenetic profiles from TAF-ChIP approach showed high agreement with conventional ChIP-Seq datasets, thereby underlining the utility of this approach.

Determination of the Best Emulsion for the Microscopy of Crystals

1981 ◽  
Vol 39 ◽  
pp. 32-33
Author(s):  
David A. Grano ◽  
Kenneth H. Downing
Keyword(s):  
Spatial Frequency ◽  
Information Transfer ◽  
Signal To Noise Ratio ◽  
Experimental Situation ◽  
Photographic Emulsion ◽  
Modulation Transfer ◽  
Signal To Noise ◽  
Frequency Space ◽  
Noise Ratio

The retrieval of high-resolution information from images of biological crystals depends, in part, on the use of the correct photographic emulsion. We have been investigating the information transfer properties of twelve emulsions with a view toward 1) characterizing the emulsions by a few, measurable quantities, and 2) identifying the “best” emulsion of those we have studied for use in any given experimental situation. Because our interests lie in the examination of crystalline specimens, we've chosen to evaluate an emulsion's signal-to-noise ratio (SNR) as a function of spatial frequency and use this as our critereon for determining the best emulsion.The signal-to-noise ratio in frequency space depends on several factors. First, the signal depends on the speed of the emulsion and its modulation transfer function (MTF). By procedures outlined in, MTF's have been found for all the emulsions tested and can be fit by an analytic expression 1/(1+(S/S0)2). Figure 1 shows the experimental data and fitted curve for an emulsion with a better than average MTF. A single parameter, the spatial frequency at which the transfer falls to 50% (S0), characterizes this curve.

Experiments in Bright-Field Imaging with Hollow-Cone Illumination

1981 ◽  
Vol 39 ◽  
pp. 226-227
Author(s):  
W. Kunath ◽  
K. Weiss ◽  
E. Zeitler
Keyword(s):  
Signal To Noise Ratio ◽  
Carbon Support ◽  
Electronic System ◽  
Optic Axis ◽  
Hollow Cone ◽  
Signal To Noise ◽  
Bright Field ◽  
Noise Ratio ◽  
Single Field ◽  
Field Imaging

Bright-field images taken with axial illumination show spurious high contrast patterns which obscure details smaller than 15 ° Hollow-cone illumination (HCI), however, reduces this disturbing granulation by statistical superposition and thus improves the signal-to-noise ratio. In this presentation we report on experiments aimed at selecting the proper amount of tilt and defocus for improvement of the signal-to-noise ratio by means of direct observation of the electron images on a TV monitor.Hollow-cone illumination is implemented in our microscope (single field condenser objective, Cs = .5 mm) by an electronic system which rotates the tilted beam about the optic axis. At low rates of revolution (one turn per second or so) a circular motion of the usual granulation in the image of a carbon support film can be observed on the TV monitor. The size of the granular structures and the radius of their orbits depend on both the conical tilt and defocus.

Information capacity and bandwidth limitations in the SEM

1989 ◽  
Vol 47 ◽  
pp. 84-85
Author(s):  
D. C. Joy ◽  
R. D. Bunn
Keyword(s):  
Signal To Noise Ratio ◽  
Critical Dimension ◽  
Information Capacity ◽  
Acquisition Time ◽  
Signal To Noise ◽  
Sem Image ◽  
Probe Size ◽  
Minimum Number ◽  
Noise Ratio ◽  
Signal Channel

The information available from an SEM image is limited both by the inherent signal to noise ratio that characterizes the image and as a result of the transformations that it may undergo as it is passed through the amplifying circuits of the instrument. In applications such as Critical Dimension Metrology it is necessary to be able to quantify these limitations in order to be able to assess the likely precision of any measurement made with the microscope.The information capacity of an SEM signal, defined as the minimum number of bits needed to encode the output signal, depends on the signal to noise ratio of the image - which in turn depends on the probe size and source brightness and acquisition time per pixel - and on the efficiency of the specimen in producing the signal that is being observed. A detailed analysis of the secondary electron case shows that the information capacity C (bits/pixel) of the SEM signal channel could be written as :

Speech Reception in the Presence of Classroom Noise

1979 ◽  
Vol 10 (4) ◽  
pp. 221-230 ◽  
Author(s):  
Veronica Smyth
Keyword(s):  
Signal To Noise Ratio ◽  
Learning Processes ◽  
Speech Discrimination ◽  
Signal To Noise ◽  
Speech Reception ◽  
Monosyllabic Words ◽  
Noise Ratio

Three hundred children from five to 12 years of age were required to discriminate simple, familiar, monosyllabic words under two conditions: 1) quiet, and 2) in the presence of background classroom noise. Of the sample, 45.3% made errors in speech discrimination in the presence of background classroom noise. The effect was most marked in children younger than seven years six months. The results are discussed considering the signal-to-noise ratio and the possible effects of unwanted classroom noise on learning processes.

Quantifying the Effects of Background Speech Babble on Preschool Children's Novel Word Learning in a Multisession Paradigm: A Preliminary Study

2020 ◽  
Vol 63 (1) ◽  
pp. 345-356
Author(s):  
Meital Avivi-Reich ◽  
Megan Y. Roberts ◽  
Tina M. Grieco-Calub
Keyword(s):  
Word Learning ◽  
Signal To Noise Ratio ◽  
Preschool Age ◽  
Exposure Condition ◽  
Signal To Noise ◽  
Verbal Recall ◽  
Referent Selection ◽  
Main Effect ◽  
Noise Ratio ◽  
Novel Word Learning

Purpose This study tested the effects of background speech babble on novel word learning in preschool children with a multisession paradigm. Method Eight 3-year-old children were exposed to a total of 8 novel word–object pairs across 2 story books presented digitally. Each story contained 4 novel consonant–vowel–consonant nonwords. Children were exposed to both stories, one in quiet and one in the presence of 4-talker babble presented at 0-dB signal-to-noise ratio. After each story, children's learning was tested with a referent selection task and a verbal recall (naming) task. Children were exposed to and tested on the novel word–object pairs on 5 separate days within a 2-week span. Results A significant main effect of session was found for both referent selection and verbal recall. There was also a significant main effect of exposure condition on referent selection performance, with more referents correctly selected for word–object pairs that were presented in quiet compared to pairs presented in speech babble. Finally, children's verbal recall of novel words was statistically better than baseline performance (i.e., 0%) on Sessions 3–5 for words exposed in quiet, but only on Session 5 for words exposed in speech babble. Conclusions These findings suggest that background speech babble at 0-dB signal-to-noise ratio disrupts novel word learning in preschool-age children. As a result, children may need more time and more exposures of a novel word before they can recognize or verbally recall it.

On the Signal-to-Noise Ratio for Boolean Functions

2020 ◽  
Vol E103.A (12) ◽  
pp. 1659-1665
Author(s):  
Yu ZHOU ◽  
Wei ZHAO ◽  
Zhixiong CHEN ◽  
Weiqiong WANG ◽  
Xiaoni DU
Keyword(s):  
Boolean Functions ◽  
Signal To Noise Ratio ◽  
Signal To Noise ◽  
Noise Ratio

An Over 120dB Dynamic Range Linear Response Single Exposure CMOS Image Sensor with Two-stage Lateral Overflow Integration Trench Capacitors

2020 ◽  
Vol 2020 (7) ◽  
pp. 143-1-143-6 ◽  
Author(s):  
Yasuyuki Fujihara ◽  
Maasa Murata ◽  
Shota Nakayama ◽  
Rihito Kuroda ◽  
Shigetoshi Sugawa
Keyword(s):  
Linear Response ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Cmos Image Sensor ◽  
Image Sensor ◽  
Signal To Noise ◽  
Single Exposure ◽  
Two Stage ◽  
Noise Ratio ◽  
Maximum Signal

This paper presents a prototype linear response single exposure CMOS image sensor with two-stage lateral overflow integration trench capacitors (LOFITreCs) exhibiting over 120dB dynamic range with 11.4Me- full well capacity (FWC) and maximum signal-to-noise ratio (SNR) of 70dB. The measured SNR at all switching points were over 35dB thanks to the proposed two-stage LOFITreCs.

Image Quality Enhancing by Efficient Histogram Equalization

2014 ◽  
Vol 2 (2) ◽  
pp. 47-58
Author(s):  
Ismail Sh. Baqer
Keyword(s):  
Image Quality ◽  
Contrast Enhancement ◽  
Mean Squared Error ◽  
Signal To Noise Ratio ◽  
Histogram Equalization ◽  
Gray Level ◽  
Signal To Noise ◽  
Squared Error ◽  
Noise Ratio

A two Level Image Quality enhancement is proposed in this paper. In the first level, Dualistic Sub-Image Histogram Equalization DSIHE method decomposes the original image into two sub-images based on median of original images. The second level deals with spikes shaped noise that may appear in the image after processing. We presents three methods of image enhancement GHE, LHE and proposed DSIHE that improve the visual quality of images. A comparative calculations is being carried out on above mentioned techniques to examine objective and subjective image quality parameters e.g. Peak Signal-to-Noise Ratio PSNR values, entropy H and mean squared error MSE to measure the quality of gray scale enhanced images. For handling gray-level images, convenient Histogram Equalization methods e.g. GHE and LHE tend to change the mean brightness of an image to middle level of the gray-level range limiting their appropriateness for contrast enhancement in consumer electronics such as TV monitors. The DSIHE methods seem to overcome this disadvantage as they tend to preserve both, the brightness and contrast enhancement. Experimental results show that the proposed technique gives better results in terms of Discrete Entropy, Signal to Noise ratio and Mean Squared Error values than the Global and Local histogram-based equalization methods

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