scholarly journals Quantitative modeling of the function of kinetically driven transcriptional riboswitches

2019 ◽  
Author(s):  
César Parra-Rojas ◽  
Boris Fürtig ◽  
Harald Schwalbe ◽  
Esteban A. Hernandez-Vargas
Keyword(s):  
Dynamic Range ◽  
Metabolite Concentration ◽  
Time Dependent ◽  
Current View ◽  
Transcription Rate ◽  
Site Location ◽  
Modeling Framework ◽  
Wide Range ◽  
Kinetic Mechanisms ◽  
Concentration Result

AbstractWe propose a generalized modeling framework for the kinetic mechanisms of transcriptional riboswitches. The formalism accommodates time-dependent transcription rates and changes of metabolite concentration and permits incorporation of variations in transcription rate depending on transcript length. We derive explicit analytical expressions for the fraction of transcripts that determine repression or activation of gene expression, pause site location and its slowing down of transcription for the case of the (2’dG)-sensing riboswitch from Mesoplasma florum. Our modeling challenges the current view on the exclusive importance of metabolite binding to transcripts containing only the aptamer domain. Numerical simulations of transcription proceeding in a continuous manner under time-dependent changes of metabolite concentration further suggest that rapid modulations in concentration result in a reduced dynamic range for riboswitch function regardless of transcription rate, while a combination of slow modulations and small transcription rates ensures a wide range of finely tuneable regulatory outcomes.

scholarly journals Detectivity optimization to detect of ultraweak light fluxes with an EM-CCD as binary photon counter array

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ibtissame Khaoua ◽  
Guillaume Graciani ◽  
Andrey Kim ◽  
François Amblard
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Photon Counting ◽  
Detection Methods ◽  
Strong Nonlinearity ◽  
Wide Range ◽  
Depth Analysis ◽  
Spatially Extended ◽  
Extended Sources ◽  
Photon Counting Mode

AbstractFor a wide range of purposes, one faces the challenge to detect light from extremely faint and spatially extended sources. In such cases, detector noises dominate over the photon noise of the source, and quantum detectors in photon counting mode are generally the best option. Here, we combine a statistical model with an in-depth analysis of detector noises and calibration experiments, and we show that visible light can be detected with an electron-multiplying charge-coupled devices (EM-CCD) with a signal-to-noise ratio (SNR) of 3 for fluxes less than $$30\,{\text{photon}}\,{\text{s}}^{ - 1} \,{\text{cm}}^{ - 2}$$ 30 photon s - 1 cm - 2 . For green photons, this corresponds to 12 aW $${\text{cm}}^{ - 2}$$ cm - 2 ≈ $$9{ } \times 10^{ - 11}$$ 9 × 10 - 11 lux, i.e. 15 orders of magnitude less than typical daylight. The strong nonlinearity of the SNR with the sampling time leads to a dynamic range of detection of 4 orders of magnitude. To detect possibly varying light fluxes, we operate in conditions of maximal detectivity $${\mathcal{D}}$$ D rather than maximal SNR. Given the quantum efficiency $$QE\left( \lambda \right)$$ Q E λ of the detector, we find $${ \mathcal{D}} = 0.015\,{\text{photon}}^{ - 1} \,{\text{s}}^{1/2} \,{\text{cm}}$$ D = 0.015 photon - 1 s 1 / 2 cm , and a non-negligible sensitivity to blackbody radiation for T > 50 °C. This work should help design highly sensitive luminescence detection methods and develop experiments to explore dynamic phenomena involving ultra-weak luminescence in biology, chemistry, and material sciences.

scholarly journals Bulk Relativistic Motion in a Complete Sample of Radio Selected AGN

1987 ◽  
Vol 121 ◽  
pp. 287-293
Author(s):  
C.J. Schalinski ◽  
P. Biermann ◽  
A. Eckart ◽  
K.J. Johnston ◽  
T.Ph. Krichbaum ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Radio Sources ◽  
Relativistic Motion ◽  
Complete Sample ◽  
Superluminal Motion ◽  
Spectrum Radio ◽  
Wide Range ◽  
Show Evidence

A complete sample of 13 flat spectrum radio sources is investigated over a wide range of frequencies and spatial resolutions. SSC-calculations lead to the prediction of bulk relativistic motion in all sources. So far 6 out of 7 sources observed with sufficient dynamic range by means of VLBI show evidence for apparent superluminal motion.

scholarly journals EXPRESS: Overcoming the Cold Start Problem of CRM using a Probabilistic Machine Learning Approach

2021 ◽  
pp. 002224372110329
Author(s):  
Nicolas Padilla ◽  
Eva Ascarza
Keyword(s):  
Machine Learning ◽  
Cold Start ◽  
Customer Relationship ◽  
Exponential Families ◽  
Modeling Framework ◽  
Wide Range ◽  
The Moment ◽  
Probabilistic Machine Learning ◽  
Marketing Actions ◽  
Cold Start Problem

The success of Customer Relationship Management (CRM) programs ultimately depends on the firm's ability to identify and leverage differences across customers — a very diffcult task when firms attempt to manage new customers, for whom only the first purchase has been observed. For those customers, the lack of repeated observations poses a structural challenge to inferring unobserved differences across them. This is what we call the “cold start” problem of CRM, whereby companies have difficulties leveraging existing data when they attempt to make inferences about customers at the beginning of their relationship. We propose a solution to the cold start problem by developing a probabilistic machine learning modeling framework that leverages the information collected at the moment of acquisition. The main aspect of the model is that it exibly captures latent dimensions that govern the behaviors observed at acquisition as well as future propensities to buy and to respond to marketing actions using deep exponential families. The model can be integrated with a variety of demand specifications and is exible enough to capture a wide range of heterogeneity structures. We validate our approach in a retail context and empirically demonstrate the model's ability at identifying high-value customers as well as those most sensitive to marketing actions, right after their first purchase.

scholarly journals Optical whispering-gallery mode barcodes for high-precision and wide-range temperature measurements

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Jie Liao ◽  
Lan Yang
Keyword(s):  
High Precision ◽  
Dynamic Range ◽  
Single Mode ◽  
Whispering Gallery Mode ◽  
Temperature Measurements ◽  
Laser Source ◽  
Multiple Modes ◽  
Whispering Gallery ◽  
Wide Range ◽  
Thermal Sensing

AbstractTemperature is one of the most fundamental physical properties to characterize various physical, chemical, and biological processes. Even a slight change in temperature could have an impact on the status or dynamics of a system. Thus, there is a great need for high-precision and large-dynamic-range temperature measurements. Conventional temperature sensors encounter difficulties in high-precision thermal sensing on the submicron scale. Recently, optical whispering-gallery mode (WGM) sensors have shown promise for many sensing applications, such as thermal sensing, magnetic detection, and biosensing. However, despite their superior sensitivity, the conventional sensing method for WGM resonators relies on tracking the changes in a single mode, which limits the dynamic range constrained by the laser source that has to be fine-tuned in a timely manner to follow the selected mode during the measurement. Moreover, we cannot derive the actual temperature from the spectrum directly but rather derive a relative temperature change. Here, we demonstrate an optical WGM barcode technique involving simultaneous monitoring of the patterns of multiple modes that can provide a direct temperature readout from the spectrum. The measurement relies on the patterns of multiple modes in the WGM spectrum instead of the changes of a particular mode. It can provide us with more information than the single-mode spectrum, such as the precise measurement of actual temperatures. Leveraging the high sensitivity of WGMs and eliminating the need to monitor particular modes, this work lays the foundation for developing a high-performance temperature sensor with not only superior sensitivity but also a broad dynamic range.

Contributions of Time Dependent and Cyclic Crack Growth to the Crack Growth Behavior of Non Strain-Crystallizing Elastomers

2002 ◽  
Vol 75 (4) ◽  
pp. 643-656 ◽  
Author(s):  
J. J. C. Busfield ◽  
K. Tsunoda ◽  
C. K. L. Davies ◽  
A. G. Thomas
Keyword(s):  
Crack Growth ◽  
Growth Behavior ◽  
Time Dependent ◽  
Crack Growth Behavior ◽  
Wide Range ◽  
Dependent Component ◽  
Tearing Energy ◽  
Quasi Crystals ◽  
Crack Growth Rates ◽  
Time Dependent Crack Growth

Abstract Engineering components are observed to fail more rapidly under cyclic loading than under static loading. This reflects features of the underlying crack growth behavior. This behavior is characterized by the relation between the tearing energy, T, and the crack growth per cycle, dc/dn. The increment of crack growth during each cycle is shown here to result from the sum of time dependent and cyclic crack growth components. The time dependent component represents the crack growth behavior that would be present in a conventional constant T crack growth test. Under repeated stressing additional crack growth, termed the cyclic crack growth component, occurs. For a non-crystallizing elastomer, significant effects of frequency have been found on the cyclic crack growth behavior, reflecting the presence of this cyclic element of crack growth. The cyclic crack growth behavior over a wide range of frequencies was investigated for unfilled and swollen SBR materials. The time dependent crack growth component was calculated from constant T crack growth tests and the cyclic contribution derived from comparison with the observed cyclic growth. It is shown that decreasing the frequency or increasing the maximum tearing energy during a cycle results in the cyclic crack growth behavior being dominated by time dependent crack growth. Conversely at high frequency and at low tearing energy, cyclic crack growth is dominated by the cyclic crack growth component. A large effect of frequency on cyclic crack growth behavior was observed for highly swollen SBR. The cyclic crack growth behavior was dominated by the time dependent crack growth component over the entire range of tearing energy and/or crack growth rate. The origin of the cyclic component may be the formation/melting of quasi crystals at the crack tip, which is absent at fast crack growth rates in the unswollen SBR and is absent at all rates in the swollen SBR.

Detector commissioning and development for PETRA-III

2010 ◽  
Vol 1 (SRMS-7) ◽  
Author(s):  
David Pennicard ◽  
Heinz Graafsma ◽  
Michael Lohmann
Keyword(s):  
High Speed ◽  
Materials Science ◽  
Dynamic Range ◽  
Photon Counting ◽  
High Energy ◽  
X Rays ◽  
Silicon Detectors ◽  
Time Resolved ◽  
Wide Range ◽  
Synchrotron Light

The new synchrotron light source PETRA-III produced its first beam last year. The extremely high brilliance of PETRA-III and the large energy range of many of its beamlines make it useful for a wide range of experiments, particularly in materials science. The detectors at PETRA-III will need to meet several requirements, such as operation across a wide dynamic range, high-speed readout and good quantum efficiency even at high photon energies. PETRA-III beamlines with lower photon energies will typically be equipped with photon-counting silicon detectors for two-dimensional detection and silicon drift detectors for spectroscopy and higher-energy beamlines will use scintillators coupled to cameras or photomultiplier tubes. Longer-term developments include ‘high-Z’ semiconductors for detecting high-energy X-rays, photon-counting readout chips with smaller pixels and higher frame rates and pixellated avalanche photodiodes for time-resolved experiments.

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

Product Review: High Dynamic Range Displays

2007 ◽  
Vol 16 (1) ◽  
pp. 119-122 ◽  
Author(s):  
Patrick Ledda
Keyword(s):  
Dynamic Range ◽  
Liquid Crystal Display ◽  
Contrast Ratio ◽  
Luminance Level ◽  
High Dynamic Range ◽  
Natural World ◽  
Adaptation Level ◽  
Wide Range ◽  
High Dynamic ◽  
3D Software

In the natural world, the human eye is confronted with a wide range of colors and luminances. A surface lit by moonlight might have a luminance level of around 10−3 cd/m2, while surfaces lit during a sunny day could reach values larger than 105 cd/m2. A good quality CRT (cathode ray tube) or LCD (liquid crystal display) monitor is only able to achieve a maximum luminance of around 200 to 300 cd/m2 and a contrast ratio of not more than two orders of magnitude. In this context the contrast ratio or dynamic range is defined as the ratio of the highest to the lowest luminance. We call high dynamic range (HDR) images, those images (or scenes) in which the contrast ratio is larger than what a display can reproduce. In practice, any scene that contains some sort of light source and shadows is HDR. The main problem with HDR images is that they cannot be displayed, therefore although methods to create them do exist (by taking multiple photographs at different exposure times or using computer graphics 3D software for example) it is not possible to see both bright and dark areas simultaneously. (See Figure 1.) There is data that suggests that our eyes can see detail at any given adaptation level within a contrast of 10,000:1 between the brightest and darkest regions of a scene. Therefore an ideal display should be able to reproduce this range. In this review, we present two high dynamic range displays developed by Brightside Technologies (formerly Sunnybrook Technologies) which are capable, for the first time, of linearly displaying high contrast images. These displays are of great use for both researchers in the vision/graphics/VR/medical fields as well as professionals in the VFX/gaming/architectural industry.

Modeling framework for IoT integration of building automation systems

2017 ◽  
Vol 65 (9) ◽  
Author(s):  
Daniel Schachinger ◽  
Andreas Fernbach ◽  
Wolfgang Kastner
Keyword(s):  
Web Services ◽  
Web Service ◽  
Building Automation ◽  
Modeling Framework ◽  
Seamless Integration ◽  
Automation Systems ◽  
Wide Range ◽  
Machine To Machine Communication ◽  
Machine Communication ◽  
The Internet Of Things

AbstractAdvancements within the Internet of Things are leading to a pervasive integration of different domains including also building automation systems. As a result, device functionality becomes available to a wide range of applications and users outside of the building automation domain. In this context, Web services are identified as suitable solution for machine-to-machine communication. However, a major requirement to provide necessary interoperability is the consideration of underlying semantics. Thus, this work presents a universal framework for tag-based semantic modeling and seamless integration of building automation systems via Web service-based technologies. Using the example of the KNX Web services specification, the applicability of this approach is pointed out.

scholarly journals Airborne fine-resolution UHF radar: an approach to the study of englacial reflections, firn compaction and ice attenuation rates

2015 ◽  
Vol 61 (225) ◽  
pp. 89-100 ◽  
Author(s):  
Cameron Lewis ◽  
Sivaprasad Gogineni ◽  
Fernando Rodriguez-Morales ◽  
Ben Panzer ◽  
Theresa Stumpf ◽  
...  
Keyword(s):  
Dynamic Range ◽  
High Sensitivity ◽  
Ultra Wideband ◽  
West Antarctica ◽  
Ice Shelves ◽  
Ross Ice Shelf ◽  
Transmission Coefficients ◽  
Ice Surface ◽  
Wide Range ◽  
Fine Resolution

AbstractWe have built and operated an ultra-wideband UHF pulsed-chirp radar for measuring firn stratigraphy from airborne platforms over the ice sheets of Greenland and West Antarctica. Our analysis found a wide range of capabilities, including imaging of post firn–ice transition horizons and sounding of shallow glaciers and ice shelves. Imaging of horizons to depths exceeding 600 m was possible in the colder interior regions of the ice sheet, where scattering from the ice surface and inclusions was minimal. The radar’s high sensitivity and large dynamic range point to loss tangent variations as the dominant mechanism for these englacial reflective horizons. The radar is capable of mapping interfaces with reflection coefficients as low as −80 dB near the firn–ice transition and as low as −64 dB at depths of 600 m. We found that firn horizon reflectivity strongly mirrored density variance, a result of the near-unity interfacial transmission coefficients. Zones with differing compaction mechanisms were also apparent in the data. We were able to sound many ice shelves and areas of shallow ice. We estimated ice attenuation rates for a few locations, and our attenuation estimates for the Ross Ice Shelf, West Antarctica, appear to agree well with earlier reported results.

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