scholarly journals AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Asa Thibodeau ◽  
Alper Eroglu ◽  
Christopher S. McGinnis ◽  
Nathan Lawlor ◽  
Djamel Nehar-Belaid ◽  
...  
Keyword(s):  
High Precision ◽  
Pancreatic Islet ◽  
Human Blood ◽  
Dynamic Range ◽  
Read Depth ◽  
Read Count ◽  
Data Sparsity ◽  
High Recall ◽  
Single Nucleus

AbstractDetecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved.

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.

scholarly journals Novel Electrochemiluminescent Assays for Drug Discovery

2000 ◽  
Vol 5 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Maura C. Kibbey ◽  
David MacAllan ◽  
James W. Karaszkiewicz
Keyword(s):  
Drug Discovery ◽  
High Precision ◽  
High Throughput ◽  
High Performance ◽  
Dynamic Range ◽  
Wide Dynamic Range ◽  
Receptor Ligand ◽  
Enzymatic Assays ◽  
Detection Systems ◽  
Protein Assays

IGEN's ORIGEN® technology, which is based on electrochemiluminescence, has been adopted by a number of research and bioanalytical laboratories who have recognized its exquisite sensitivity, high precision, wide dynamic range, and flexibility in formatting a wide variety of applications. IGEN's M-SERIES™ marks the introduction of the second generation of detection systems employing the ORIGEN technology specifically repackaged to address the needs of the high throughput laboratories involved in drug discovery. Assays are formatted without wash steps. Users realize the high performance of a heterogeneous technology with the convenience of a homogeneous format. The M-SERIES platform can address enzymatic assays (kinases, proteases, helicases, etc.), receptor-ligand or protein-protein assays, immunoassays, quantitation of nucleic acids, as well as other applications. Recent assay formats will be explored in detail.

scholarly journals NULL Convention Floating Point Multiplier

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Anitha Juliette Albert ◽  
Seshasayanan Ramachandran
Keyword(s):  
High Precision ◽  
Dynamic Range ◽  
Digital Signal ◽  
High Dynamic Range ◽  
Floating Point ◽  
Single Precision ◽  
Critical Part ◽  
Point Multiplication ◽  
Null Convention Logic ◽  
High Dynamic

Floating point multiplication is a critical part in high dynamic range and computational intensive digital signal processing applications which require high precision and low power. This paper presents the design of an IEEE 754 single precision floating point multiplier using asynchronous NULL convention logic paradigm. Rounding has not been implemented to suit high precision applications. The novelty of the research is that it is the first ever NULL convention logic multiplier, designed to perform floating point multiplication. The proposed multiplier offers substantial decrease in power consumption when compared with its synchronous version. Performance attributes of the NULL convention logic floating point multiplier, obtained from Xilinx simulation and Cadence, are compared with its equivalent synchronous implementation.

scholarly journals Curating GitHub for engineered software projects

2016 ◽  
Author(s):  
Nuthan Munaiah ◽  
Steven Kroh ◽  
Craig Cabrey ◽  
Meiyappan Nagappan
Keyword(s):  
Software Engineering ◽  
High Precision ◽  
Ground Truth ◽  
Software Project ◽  
Software Projects ◽  
Data Set ◽  
High Recall ◽  
Home Work ◽  
Reference Implementation ◽  
Engineering Practices

Software forges like GitHub host millions of repositories. Software engineering researchers have been able to take advantage of such a large corpora of potential study subjects with the help of tools like GHTorrent and Boa. However, the simplicity in querying comes with a caveat: there are limited means of separating the signal (e.g. repositories containing engineered software projects) from the noise (e.g. repositories containing home work assignments). The proportion of noise in a random sample of repositories could skew the study and may lead to researchers reaching unrealistic, potentially inaccurate, conclusions. We argue that it is imperative to have the ability to sieve out the noise in such large repository forges. We propose a framework, and present a reference implementation of the framework as a tool called reaper, to enable researchers to select GitHub repositories that contain evidence of an engineered software project. We identify software engineering practices (called dimensions) and propose means for validating their existence in a GitHub repository. We used reaper to measure the dimensions of 1,994,977 GitHub repositories. We then used the data set train classifiers capable of predicting if a given GitHub repository contains an engineered software project. The performance of the classifiers was evaluated using a set of 200 repositories with known ground truth classification. We also compared the performance of the classifiers to other approaches to classification (e.g. number of GitHub Stargazers) and found our classifiers to outperform existing approaches. We found stargazers-based classifier to exhibit high precision (96%) but an inversely proportional recall (27%). On the other hand, our best classifier exhibited a high precision (82%) and a high recall (83%). The stargazer-based criteria offers precision but fails to recall a significant potion of the population.

scholarly journals Single-Element Dual-Interferometer for Precision Inertial Sensing

Sensors ◽  
2020 ◽  
Vol 20 (17) ◽  
pp. 4986
Author(s):  
Yichao Yang ◽  
Kohei Yamamoto ◽  
Victor Huarcaya ◽  
Christoph Vorndamme ◽  
Daniel Penkert ◽  
...  
Keyword(s):  
High Precision ◽  
Degrees Of Freedom ◽  
Dynamic Range ◽  
Inertial Sensor ◽  
Single Element ◽  
Inertial Sensing ◽  
Optical Readout ◽  
One Step ◽  
Isolation Systems ◽  
Laser Interferometers

Tracking moving masses in several degrees of freedom with high precision and large dynamic range is a central aspect in many current and future gravitational physics experiments. Laser interferometers have been established as one of the tools of choice for such measurement schemes. Using sinusoidal phase modulation homodyne interferometry allows a drastic reduction of the complexity of the optical setup, a key limitation of multi-channel interferometry. By shifting the complexity of the setup to the signal processing stage, these methods enable devices with a size and weight not feasible using conventional techniques. In this paper we present the design of a novel sensor topology based on deep frequency modulation interferometry: the self-referenced single-element dual-interferometer (SEDI) inertial sensor, which takes simplification one step further by accommodating two interferometers in one optic. Using a combination of computer models and analytical methods we show that an inertial sensor with sub-picometer precision for frequencies above 10 mHz, in a package of a few cubic inches, seems feasible with our approach. Moreover we show that by combining two of these devices it is possible to reach sub-picometer precision down to 2 mHz. In combination with the given compactness, this makes the SEDI sensor a promising approach for applications in high precision inertial sensing for both next-generation space-based gravity missions employing drag-free control, and ground-based experiments employing inertial isolation systems with optical readout.

A CMOS Image Sensor with a Novel Passive Pixel Array and High Precision Current Amplifier for a Compact Digital X-ray Detector

2020 ◽  
Vol 10 (11) ◽  
pp. 2745-2753
Author(s):  
Jimin Cheon ◽  
Dongmyung Lee ◽  
Hojong Choi
Keyword(s):  
High Precision ◽  
Dynamic Range ◽  
Cmos Image Sensor ◽  
Image Sensor ◽  
Total Power ◽  
Cmos Process ◽  
Current Amplifier ◽  
X Ray ◽  
Total Power Consumption ◽  
Pixel Array

An active pixel sensor (APS) in a digital X-ray detector is the dominant circuitry for a CMOS image sensor (CIS) despite its lower fill factor (FF) compared to that of a passive pixel sensor (PPS). Although the PPS provides higher FF, its overall signal-to-noise ratio (SNR) is lower than that of the APS. The required high resolution and small focal plane can be achieved by reducing the number of transistors and contacts per pixel. We proposed a novel passive pixel array and a high precision current amplifier to improve the dynamic range (DR) without minimizing the sensitivity for diagnostic compact digital X-ray detector applications. The PPS can be an alternative to improve the FF. However, size reduction of the feedback capacitor causes degradation of SNR performance. This paper proposes a novel PPS based on readout and amplification circuits with a high precision current amplifier to minimize performance degradation. The expected result was attained with a 0.35-μm CMOS process parameter with power supply voltage of 3.3 V. The proposed PPS has a saturation signal of 1.5 V, dynamic range of 63.5 dB, and total power consumption of 13.47 mW. Therefore, the proposed PPS readout circuit improves the dynamic range without sacrificing the sensitivity.

Quantitative Imaging of FRET-Based Biosensors for Cell- and Organelle-Specific Analyses in Plants

2016 ◽  
Vol 22 (2) ◽  
pp. 300-310 ◽  
Author(s):  
Swayoma Banerjee ◽  
Luis Rene Garcia ◽  
Wayne K. Versaw
Keyword(s):  
High Precision ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Dynamic Range ◽  
Quantitative Imaging ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
High Dynamic Range ◽  
Imaging Data ◽  
Protein Protein Interactions

AbstractGenetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein–protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.

Sign in / Sign up

Export Citation Format

Share Document