Accurate determination of DNA in agarose gels using the novel algorithm GelScann(1.0)

1995 ◽  
Vol 11 (2) ◽  
pp. 187-194
Author(s):  
Michael L. Metzker ◽  
Kyle M. Allain ◽  
Richard A. Gibbs
Keyword(s):  
Accurate Determination ◽  
The Novel ◽  
Agarose Gels ◽  
Novel Algorithm

scholarly journals Computer programs for accurate determination of size of DNA fragments in agarose gels.

1987 ◽  
Vol 40 (6) ◽  
pp. 692-695 ◽  
Author(s):  
J Ling ◽  
K L Ling ◽  
K W Chan ◽  
G L French
Keyword(s):  
Accurate Determination ◽  
Computer Programs ◽  
Dna Fragments ◽  
Agarose Gels

scholarly journals RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Leanne S. Whitmore ◽  
Bernard Nguyen ◽  
Ali Pinar ◽  
Anthe George ◽  
Corey M. Hudson
Keyword(s):  
Efficient Production ◽  
The Novel ◽  
Ranking Criteria ◽  
Complex Process ◽  
Target Yield ◽  
Balance Analysis ◽  
Target Production ◽  
Biological Solutions ◽  
Novel Algorithm

Abstract Background The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical in a chassis organism is computationally intractable. Many current methods provide a single solution to this problem, but fail to provide all optimal pathways, optional sub-optimal solutions or hybrid biological/non-biological solutions. Results Here we present RetSynth, software with a novel algorithm for determining all optimal biological pathways given a starting biological chassis and target chemical. By dynamically selecting constraints, the number of potential pathways scales by the number of fully independent pathways and not by the number of overall reactions or size of the metabolic network. This feature allows all optimal pathways to be determined for a large number of chemicals and for a large corpus of potential chassis organisms. Additionally, this software contains other features including the ability to collect data from metabolic repositories, perform flux balance analysis, and to view optimal pathways identified by our algorithm using a built-in visualization module. This software also identifies sub-optimal pathways and allows incorporation of non-biological chemical reactions, which may be performed after metabolic production of precursor molecules. Conclusions The novel algorithm designed for RetSynth streamlines an arduous and complex process in metabolic engineering. Our stand-alone software allows the identification of candidate optimal and additional sub-optimal pathways, and provides the user with necessary ranking criteria such as target yield to decide which route to select for target production. Furthermore, the ability to incorporate non-biological reactions into the final steps allows determination of pathways to production for targets that cannot be solely produced biologically. With this comprehensive suite of features RetSynth exceeds any open-source software or webservice currently available for identifying optimal pathways for target production.

scholarly journals Analysis of Inactivation of SARS-CoV-2 by Specimen Transport Media, Nucleic Acid Extraction Reagents, Detergents, and Fixatives

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Stephen R. Welch ◽  
Katherine A. Davies ◽  
Hubert Buczkowski ◽  
Nipunadi Hettiarachchi ◽  
Nicole Green ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Infectious Virus ◽  
Clinical Sample ◽  
Accurate Determination ◽  
Acid Extraction ◽  
The Novel ◽  
Nucleic Acid Extraction ◽  
Human Coronavirus ◽  
Critical Data

ABSTRACT The COVID-19 pandemic has necessitated a multifaceted rapid response by the scientific community, bringing researchers, health officials, and industry together to address the ongoing public health emergency. To meet this challenge, participants need an informed approach for working safely with the etiological agent, the novel human coronavirus SARS-CoV-2. Work with infectious SARS-CoV-2 is currently restricted to high-containment laboratories, but material can be handled at a lower containment level after inactivation. Given the wide array of inactivation reagents that are being used in laboratories during this pandemic, it is vital that their effectiveness is thoroughly investigated. Here, we evaluated a total of 23 commercial reagents designed for clinical sample transportation, nucleic acid extraction, and virus inactivation for their ability to inactivate SARS-CoV-2, as well as seven other common chemicals, including detergents and fixatives. As part of this study, we have also tested five filtration matrices for their effectiveness at removing the cytotoxic elements of each reagent, permitting accurate determination of levels of infectious virus remaining following treatment. In addition to providing critical data informing inactivation methods and risk assessments for diagnostic and research laboratories working with SARS-CoV-2, these data provide a framework for other laboratories to validate their inactivation processes and to guide similar studies for other pathogens.

scholarly journals Inactivation analysis of SARS-CoV-2 by specimen transport media, nucleic acid extraction reagents, detergents and fixatives

2020 ◽  
Author(s):  
Stephen R. Welch ◽  
Katherine A. Davies ◽  
Hubert Buczkowski ◽  
Nipunadi Hettiarachchi ◽  
Nicole Green ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Infectious Virus ◽  
Clinical Sample ◽  
Accurate Determination ◽  
Acid Extraction ◽  
The Novel ◽  
Nucleic Acid Extraction ◽  
Human Coronavirus ◽  
Critical Data

AbstractThe COVID-19 pandemic has necessitated a rapid multi-faceted response by the scientific community, bringing researchers, health officials and industry together to address the ongoing public health emergency. To meet this challenge, participants need an informed approach for working safely with the etiological agent, the novel human coronavirus SARS-CoV-2. Work with infectious SARS-CoV-2 is currently restricted to high-containment laboratories, but material can be handled at a lower containment level after inactivation. Given the wide array of inactivation reagents that are being used in laboratories during this pandemic, it is vital that their effectiveness is thoroughly investigated. Here, we evaluated a total of 23 commercial reagents designed for clinical sample transportation, nucleic acid extraction and virus inactivation for their ability to inactivate SARS-CoV-2, as well as seven other common chemicals including detergents and fixatives. As part of this study, we have also tested five filtration matrices for their effectiveness at removing the cytotoxic elements of each reagent, permitting accurate determination of levels of infectious virus remaining following treatment. In addition to providing critical data informing inactivation methods and risk assessments for diagnostic and research laboratories working with SARS-CoV-2, these data provide a framework for other laboratories to validate their inactivation processes and to guide similar studies for other pathogens.

A quantitative approach to inner shell losses

1978 ◽  
Vol 36 (1) ◽  
pp. 526-527 ◽  
Author(s):  
R.D. Leapman ◽  
P. Rez ◽  
D.F. Mayers
Keyword(s):  
Energy Transfer ◽  
Cross Section ◽  
Cross Sections ◽  
Accurate Determination ◽  
Background Intensity ◽  
Core Excitation ◽  
Quantitative Basis ◽  
Cross Section Differential ◽  
Bound Electrons

Microanalysis by EELS has been developing rapidly and though the general form of the spectrum is now understood there is a need to put the technique on a more quantitative basis (1,2). Certain aspects important for microanalysis include: (i) accurate determination of the partial cross sections, σx(α,ΔE) for core excitation when scattering lies inside collection angle a and energy range ΔE above the edge, (ii) behavior of the background intensity due to excitation of less strongly bound electrons, necessary for extrapolation beneath the signal of interest, (iii) departures from the simple hydrogenic K-edge seen in L and M losses, effecting σx and complicating microanalysis. Such problems might be approached empirically but here we describe how computation can elucidate the spectrum shape.The inelastic cross section differential with respect to energy transfer E and momentum transfer q for electrons of energy E0 and velocity v can be written as

Fast calibration of CBED patterns for quantitative analysis

1993 ◽  
Vol 51 ◽  
pp. 674-675
Author(s):  
M.A. Gribelyuk ◽  
M. Rühle
Keyword(s):  
Reciprocal Lattice ◽  
Accurate Determination ◽  
Incident Beam ◽  
Crystal Thickness ◽  
Structure Model ◽  
Beam Direction ◽  
Transmitted Beam ◽  
Reciprocal Vector ◽  
On Line

A new method is suggested for the accurate determination of the incident beam direction K, crystal thickness t and the coordinates of the basic reciprocal lattice vectors V1 and V2 (Fig. 1) of the ZOLZ plans in pixels of the digitized 2-D CBED pattern. For a given structure model and some estimated values Vest and Kest of some point O in the CBED pattern a set of line scans AkBk is chosen so that all the scans are located within CBED disks.The points on line scans AkBk are conjugate to those on A0B0 since they are shifted by the reciprocal vector gk with respect to each other. As many conjugate scans are considered as CBED disks fall into the energy filtered region of the experimental pattern. Electron intensities of the transmitted beam I0 and diffracted beams Igk for all points on conjugate scans are found as a function of crystal thickness t on the basis of the full dynamical calculation.

Computer-Assisted High-Re Solution TEM

1990 ◽  
Vol 48 (1) ◽  
pp. 162-163
Author(s):  
F.A. Ponce ◽  
H. Hikashi
Keyword(s):  
Signal To Noise Ratio ◽  
Accurate Determination ◽  
Computer Software ◽  
Video Camera ◽  
Image Contrast ◽  
Objective Lens ◽  
Computer Assisted ◽  
Optical Parameters ◽  
Astigmatism Correction

The determination of the atomic positions from HRTEM micrographs is only possible if the optical parameters are known to a certain accuracy, and reliable through-focus series are available to match the experimental images with calculated images of possible atomic models. The main limitation in interpreting images at the atomic level is the knowledge of the optical parameters such as beam alignment, astigmatism correction and defocus value. Under ordinary conditions, the uncertainty in these values is sufficiently large to prevent the accurate determination of the atomic positions. Therefore, in order to achieve the resolution power of the microscope (under 0.2nm) it is necessary to take extraordinary measures. The use of on line computers has been proposed [e.g.: 2-5] and used with certain amount of success.We have built a system that can perform operations in the range of one frame stored and analyzed per second. A schematic diagram of the system is shown in figure 1. A JEOL 4000EX microscope equipped with an external computer interface is directly linked to a SUN-3 computer. All electrical parameters in the microscope can be changed via this interface by the use of a set of commands. The image is received from a video camera. A commercial image processor improves the signal-to-noise ratio by recursively averaging with a time constant, usually set at 0.25 sec. The computer software is based on a multi-window system and is entirely mouse-driven. All operations can be performed by clicking the mouse on the appropiate windows and buttons. This capability leads to extreme friendliness, ease of operation, and high operator speeds. Image analysis can be done in various ways. Here, we have measured the image contrast and used it to optimize certain parameters. The system is designed to have instant access to: (a) x- and y- alignment coils, (b) x- and y- astigmatism correction coils, and (c) objective lens current. The algorithm is shown in figure 2. Figure 3 shows an example taken from a thin CdTe crystal. The image contrast is displayed for changing objective lens current (defocus value). The display is calibrated in angstroms. Images are stored on the disk and are accessible by clicking the data points in the graph. Some of the frame-store images are displayed in Fig. 4.

A novel method for the determination of linting propensity of paper

TAPPI Journal ◽  
2012 ◽  
Vol 11 (10) ◽  
pp. 9-17
Author(s):  
ALESSANDRA GERLI ◽  
LEENDERT C. EIGENBROOD
Keyword(s):  
Ash Content ◽  
The Novel ◽  
Offset Printing ◽  
Excellent Correlation ◽  
End Conditions ◽  
Bottom Side ◽  
Novel Method ◽  
Total Fraction

A novel method was developed for the determination of linting propensity of paper based on printing with an IGT printability tester and image analysis of the printed strips. On average, the total fraction of the surface removed as lint during printing is 0.01%-0.1%. This value is lower than those reported in most laboratory printing tests, and more representative of commercial offset printing applications. Newsprint paper produced on a roll/blade former machine was evaluated for linting propensity using the novel method and also printed on a commercial coldset offset press. Laboratory and commercial printing results matched well, showing that linting was higher for the bottom side of paper than for the top side, and that linting could be reduced on both sides by application of a dry-strength additive. In a second case study, varying wet-end conditions were used on a hybrid former machine to produce four paper reels, with the goal of matching the low linting propensity of the paper produced on a machine with gap former configuration. We found that the retention program, by improving fiber fines retention, substantially reduced the linting propensity of the paper produced on the hybrid former machine. The papers were also printed on a commercial coldset offset press. An excellent correlation was found between the total lint area removed from the bottom side of the paper samples during laboratory printing and lint collected on halftone areas of the first upper printing unit after 45000 copies. Finally, the method was applied to determine the linting propensity of highly filled supercalendered paper produced on a hybrid former machine. In this case, the linting propensity of the bottom side of paper correlated with its ash content.

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