MicroRNA annotation in plants: current status and challenges

2021 ◽  
Author(s):  
Yongxin Zhao ◽  
Zheng Kuang ◽  
Ying Wang ◽  
Lei Li ◽  
Xiaozeng Yang
Keyword(s):  
Small Rna ◽  
Signal To Noise Ratio ◽  
Current Status ◽  
Mirna Biogenesis ◽  
Plant Mirnas ◽  
Signal To Noise ◽  
Advantages And Disadvantages ◽  
Plant Mirna ◽  
History Of ◽  
Mirna Biogenesis Pathway

Abstract Last two decades, the studies on microRNAs (miRNAs) and the numbers of annotated miRNAs in plants and animals have surged. Herein, we reviewed the current progress and challenges of miRNA annotation in plants. Via the comparison of plant and animal miRNAs, we pinpointed out the difficulties on plant miRNA annotation and proposed potential solutions. In terms of recalling the history of methods and criteria in plant miRNA annotation, we detailed how the major progresses made and evolved. By collecting and categorizing bioinformatics tools for plant miRNA annotation, we surveyed their advantages and disadvantages, especially for ones with the principle of mimicking the miRNA biogenesis pathway by parsing deeply sequenced small RNA (sRNA) libraries. In addition, we summarized all available databases hosting plant miRNAs, and posted the potential optimization solutions such as how to increase the signal-to-noise ratio (SNR) in these databases. Finally, we discussed the challenges and perspectives of plant miRNA annotations, and indicated the possibilities offered by an all-in-one tool and platform according to the integration of artificial intelligence.

Current Status of Immunofluorescent Methodology for Salmonellae1

1981 ◽  
Vol 44 (5) ◽  
pp. 381-384 ◽  
Author(s):  
BERENICE M. THOMASON
Keyword(s):  
Fluorescent Antibody ◽  
Screening Method ◽  
Rapid Screening ◽  
Current Status ◽  
Official Method ◽  
Pathogenic Microorganisms ◽  
Advantages And Disadvantages ◽  
Food And Feed ◽  
History Of ◽  
Feed Samples

The fluorescent antibody (FA) method for detecting salmonellae in food and feed samples is now an official method of the Association of Official Analytical Chemists. The need for a rapid screening method for detecting these pathogenic microorganisms in suspect products led to development of the FA method. A brief history of the development of the FA test, its evaluation by various investigators and its use by food laboratories are described in this report. Advantages and disadvantages of the method are discussed with suggestions for improvement of the technique.

scholarly journals Enrichment of the gynecologic cytologic specimen.

1977 ◽  
Vol 25 (7) ◽  
pp. 504-507 ◽  
Author(s):  
W E Tolles ◽  
G L Garcia
Keyword(s):  
Signal To Noise Ratio ◽  
Enrichment Factors ◽  
Spatial Spectrum ◽  
Current Status ◽  
Differential Analysis ◽  
Signal To Noise ◽  
Principal Objective ◽  
Enrichment Techniques ◽  
Non Destructive ◽  
Destructive Methods

The principal objective of our group has been and continues to be the improvement of the biologic signal-to-noise ratio of the gynecologic cytologic specimen through: the dispersal of clusters and clumps, enrichment of the abnormal component of the dispersed specimen by the method of rate-zonal sedimentation under unit gravity, and monitoring the effects of these manipulations with biophysical non-destructive methods. This report is concerned only with presenting the current status of the effectiveness of our enrichment techniques both qualitatively and quantitatively. Zonal sedimentation creates a broad spatial spectrum of cells by virtue of their different velocities which are directly related to their areas. Certain fractions of this spectrum are extracted, concentrated and deposited on slides for subsequent manual differential analysis, evaluation and documentation. Qualitatively, fractions M1 and M2 show impressive removal of erythrocytes, leukocytes and debris. Quantitatively, enrichment factors vary from 0.1 (depletion) to as high as 26 yielding an average enrichment of about 6, a most rewarding improvement.

Retrieval of chlorine dioxide columns from Sentinel-5p observations

2020 ◽  
Author(s):  
Andreas Carlos Meier ◽  
Andreas Richter ◽  
Gaia Pinardi ◽  
Michel Van Roozendael ◽  
John Philip Burrows
Keyword(s):  
Chlorine Dioxide ◽  
Signal To Noise Ratio ◽  
Stratospheric Ozone ◽  
Polar Vortex ◽  
Current Status ◽  
Innovation Activity ◽  
Signal To Noise ◽  
Fine Spatial Resolution ◽  
Global Coverage ◽  
Good Signal

<p>The Sentinel-5-precursor (S5p) satellite with the TROPOMI payload was launched on 13 October 2017. It is part of the European Copernicus program and provides a set of operational products of atmospheric constituents related to air quality and climate change with almost daily global coverage. The good signal to noise ratio of the instrument enables precise measurements despite the fine spatial resolution of 3.5 x 5.5 km2. </p><p><br>The ESA S5p+ Innovation activity aims at extending the list of S5p products with scientific products, which are not yet part of the operational processor, to exploit the potential of the Sentinel-5p mission’s capabilities beyond its primary objectives. The retrieval of chlorine dioxide (OClO) from S5p is among the seven funded sub projects. Chlorine dioxide is an indicator for chlorine activation in the stratosphere and thus of importance for the understanding of stratospheric ozone chemistry, in particular in the polar vortex. Chlorine dioxide was retrieved from heritage instruments (GOME, SCIAMACHY, GOME2, OMI) and the S5p OClO product will act as a continuation of these time-series.</p><p><br>Here we present the current status of the IUP-Bremen S5p OClO product developed within the ESA S5p+ Innovation framework. The new S5p product will be put into context with products from previous and current (e.g. GOME-2c) satellite missions as well as ground-based measurements used for validation.</p>

scholarly journals ANALYSIS OF INSTALLATIONS TO CONTROL THE OF RATION SIGNAL-TO-NOISE OF VACUUM UNIT ELECTRO-OPTICAL CONVERTER

2020 ◽  
Vol 6 (1) ◽  
pp. 167-172
Author(s):  
Oleg A. Kvitovskiy ◽  
Dmitry M. Nikulin
Keyword(s):  
State Standard ◽  
Signal To Noise Ratio ◽  
Signal To Noise ◽  
Vacuum Unit ◽  
Advantages And Disadvantages ◽  
Noise Ratio

The article considers and compares different installations to measure the signal-to-noise ratio of the electron-optical converter. Advantages and disadvantages described in State Standard 21815.19-90 of the installations design for signal-to-noise ratio control are analysed. Prospects for improving the method of measuring the signal-to-noise ratio of the electron-optical converter are outlined.

scholarly journals The Pristine survey – VI. The first three years of medium-resolution follow-up spectroscopy of Pristine EMP star candidates

2019 ◽  
Vol 490 (2) ◽  
pp. 2241-2253 ◽  
Author(s):  
David S Aguado ◽  
Kris Youakim ◽  
Jonay I González Hernández ◽  
Carlos Allende Prieto ◽  
Else Starkenburg ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Current Status ◽  
Success Rates ◽  
Signal To Noise ◽  
Stellar Spectra ◽  
Carbon Abundance ◽  
Medium Resolution ◽  
Carbon Determination ◽  
William Herschel

ABSTRACT We present the results of a 3-yr long, medium-resolution spectroscopic campaign aimed at identifying very metal-poor stars from candidates selected with the CaHK, metallicity-sensitive Pristine survey. The catalogue consists of a total of 1007 stars, and includes 146 rediscoveries of metal-poor stars already presented in previous surveys, 707 new very metal-poor stars with $\rm [Fe/H] \lt -2.0$, and 95 new extremely metal-poor stars with $\rm [Fe/H] \lt -3.0$. We provide a spectroscopic [Fe/H] for every star in the catalogue, and [C/Fe] measurements for a subset of the stars (10 per cent with $\rm [Fe/H] \lt -3$ and 24 per cent with $-3 \lt \rm [Fe/H] \lt -2$) for which a carbon determination is possible, contingent mainly on the carbon abundance, effective temperature and signal-to-noise ratio of the stellar spectra. We find an average carbon enhancement fraction ([C/Fe] ≥ +0.7) of 41 ± 4 per cent for stars with $-3 \lt \rm [Fe/H] \lt -2$ and 58 ± 14 per cent for stars with $\rm [Fe/H] \lt -3$, and report updated success rates for the Pristine survey of 56 per cent and 23 per cent to recover stars with $\rm [Fe/H] \lt -2.5$ and $\lt -3$, respectively. Finally, we discuss the current status of the survey and its preparation for providing targets to upcoming multi-object spectroscopic surveys such as William Herschel Telescope Enhanced Area Velocity Explorer.

scholarly journals Evolutionary footprints reveal insights into plant microRNA biogenesis

2017 ◽  
Author(s):  
Uciel Chorostecki ◽  
Belen Moro ◽  
Arantxa M.L. Rojas ◽  
Juan M. Debernardi ◽  
Arnaldo L. Schapire ◽  
...  
Keyword(s):  
Binding Sites ◽  
Small Rnas ◽  
Target Genes ◽  
Graphical Representation ◽  
Mirna Biogenesis ◽  
Plant Mirnas ◽  
Structural Determinants ◽  
Plant Mirna ◽  
Conservation Patterns

AbstractMicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity. They are processed from longer precursors that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing machinery in different ways. However, ancient miRNAs and their binding sites in target genes are conserved during evolution. Here, we designed a strategy to systematically analyze MIRNAs from different species generating a graphical representation of the conservation of the primary sequence and secondary structure. We found that plant MIRNAs have evolutionary footprints that go beyond the small RNA sequence itself, yet, their location along the precursor depends on the specific MIRNA. We show that these conserved regions correspond to structural determinants recognized during the biogenesis of plant miRNAs. Furthermore, we found that the members of the miR166 family have unusual conservation patterns and demonstrated that the recognition of these precursors in vivo differs from other known miRNAs. Our results describe a link between the evolutionary conservation of plant MIRNAs and the mechanisms underlying the biogenesis of these small RNAs, and show that the MIRNA pattern of conservation can be used to infer the mode of miRNA biogenesis.

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.

Correlation averaging of two-dimensional crystals: basic strategy and refinements

1986 ◽  
Vol 44 ◽  
pp. 136-139
Author(s):  
W. Baumeister ◽  
R. Rachel ◽  
R. Guckenberger ◽  
R. Hegerl
Keyword(s):  
Low Dose ◽  
Signal To Noise Ratio ◽  
Real Space ◽  
Fourier Domain ◽  
Two Dimensional ◽  
Signal To Noise ◽  
Unit Cells ◽  
Lateral Displacements ◽  
Established Technique ◽  
Crystalline Array

IntroductionCorrelation averaging (CAV) is meanwhile an established technique in image processing of two-dimensional crystals /1,2/. The basic idea is to detect the real positions of unit cells in a crystalline array by means of correlation functions and to average them by real space superposition of the aligned motifs. The signal-to-noise ratio improves in proportion to the number of motifs included in the average. Unlike filtering in the Fourier domain, CAV corrects for lateral displacements of the unit cells; thus it avoids the loss of resolution entailed by these distortions in the conventional approach. Here we report on some variants of the method, aimed at retrieving a maximum of information from images with very low signal-to-noise ratios (low dose microscopy of unstained or lightly stained specimens) while keeping the procedure economical.

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 :

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