scholarly journals ORF Capture-Seq: a versatile method for targeted identification of full-length isoforms

2019 ◽  
Author(s):  
Gloria M. Sheynkman ◽  
Katharine S. Tuttle ◽  
Elizabeth Tseng ◽  
Jason G. Underwood ◽  
Liang Yu ◽  
...  
Keyword(s):  
Cost Effective ◽  
Full Length ◽  
Proof Of Concept ◽  
Protein Coding ◽  
Reading Frame ◽  
Cost Effective Method ◽  
Reasonable Cost ◽  
Order Of Magnitude ◽  
Human Isoforms ◽  
Alternative Isoforms

AbstractMost human protein-coding genes are expressed as multiple isoforms. This in turn greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every gene, the majority of alternative isoforms remains uncharacterized experimentally. This is primarily due to: i) vast differences of overall levels between different isoforms expressed from common genes, and ii) the difficulty of obtaining contiguous full-length ORF sequences. Here, we present ORF Capture-Seq (OCS), a flexible and cost-effective method that addresses both challenges for targeted full-length isoform sequencing applications using collections of cloned ORFs as probes. As proof-of-concept, we show that an OCS pipeline focused on genes coding for transcription factors increases isoform detection by an order of magnitude, compared to unenriched sample. In short, OCS enables rapid discovery of isoforms from custom-selected genes and will allow mapping of the full set of human isoforms at reasonable cost.

Enzyme entrapment in polyaniline films observed via fluorescence anisotropy and antiquenching

2014 ◽  
Vol 28 (11) ◽  
pp. 1430004
Author(s):  
Louis R. Nemzer ◽  
Marisa McCaffrey ◽  
Arthur J. Epstein
Keyword(s):  
Fluorescence Anisotropy ◽  
Cost Effective ◽  
Hydrophobic Collapse ◽  
Cost Effective Method ◽  
Proposed Model ◽  
Order Of Magnitude ◽  
Polyaniline Films ◽  
Oxidoreductase Enzymes ◽  
Electron Donation ◽  
Phosphate Buffered Saline

The facile entrapment of oxidoreductase enzymes within polyaniline polymer films by inducing hydrophobic collapse using phosphate buffered saline (PBS) has been shown to be a cost-effective method for fabricating organic biosensors. Here, we use fluorescence anisotropy measurements to verify enzyme immobilization and subsequent electron donation to the polymer matrix, both prerequisites for an effective biosensor. Specifically, we measure a three order of magnitude decrease in the ratio of the fluorescence to rotational lifetimes. In addition, the observed fluorescence antiquenching supports the previously proposed model that the polymer chain assumes a severely coiled conformation when exposed to PBS. These results help to empirically reinforce the theoretical basis previously laid out for this biosensing platform.

scholarly journals An Overview of the Photocatalytic Water Splitting over Suspended Particles

Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 60
Author(s):  
Muhammad Amtiaz Nadeem ◽  
Mohd Adnan Khan ◽  
Ahmed Abdeslam Ziani ◽  
Hicham Idriss
Keyword(s):  
Water Splitting ◽  
Large Scale ◽  
Cost Effective ◽  
Synthetic Methods ◽  
Scale Production ◽  
Practical Applications ◽  
Co Catalysts ◽  
Large Scale Production ◽  
Cost Effective Method ◽  
Order Of Magnitude

The conversion of solar to chemical energy is one of the central processes considered in the emerging renewable energy economy. Hydrogen production from water splitting over particulate semiconductor catalysts has often been proposed as a simple and a cost-effective method for large-scale production. In this review, we summarize the basic concepts of the overall water splitting (in the absence of sacrificial agents) using particulate photocatalysts, with a focus on their synthetic methods and the role of the so-called “co-catalysts”. Then, a focus is then given on improving light absorption in which the Z-scheme concept and the overall system efficiency are discussed. A section on reactor design and cost of the overall technology is given, where the possibility of the different technologies to be deployed at a commercial scale and the considerable challenges ahead are discussed. To date, the highest reported efficiency of any of these systems is at least one order of magnitude lower than that deserving consideration for practical applications.

Gene Set to Diseases (GS2D): disease enrichment analysis on human gene sets with literature data

2016 ◽  
Vol 2 (1) ◽  
pp. 33 ◽  
Author(s):  
Jean Fred Fontaine ◽  
Miguel A Andrade-Navarro
Keyword(s):  
Experimental Data ◽  
Enrichment Analysis ◽  
Cost Effective ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Protein Coding ◽  
Gene Set ◽  
Gene Sets ◽  
Cost Effective Method ◽  
Disease Associations

Large sets of candidate genes derived from high-throughput biological experiments can be characterized by functional enrichment analysis. The analysis consists of comparing the functions of one gene set against that of a background gene set. Then, functions related to a significant number of genes in the gene set are expected to be relevant. Web tools offering disease enrichment analysis on gene sets are often based on gene-disease associations from manually curated or experimental data that is accurate but does not cover all diseases discussed in the literature. Using associations automatically derived from literature data could be a cost effective method to improve the coverage of diseases for enrichment analysis at comparable levels of accuracy. We have implemented a method named Gene set to Diseases, GS2D, as a web tool performing disease enrichment analysis on human protein coding gene sets. It uses an automatically built dataset of more than 63 thousand gene-disease associations defined as statistically significant co-occurrences of genes and diseases in annotations of biomedical citations from PubMed. The dataset covers more diseases for enrichment analysis than the largest comparable curated database, Comparative Toxicogenomics Database, and its performance compared favourably to similar approaches based on manually curated or experimental data. Graphical and programmatic interfaces are available at http://cbdm.uni-mainz.de/geneset2diseases.

scholarly journals Modeling the effectiveness of olfactory testing to limit SARS-2-CoV transmission

2020 ◽  
Author(s):  
Daniel B. Larremore ◽  
Derek Toomre ◽  
Roy Parker
Keyword(s):  
Low Cost ◽  
Onset Time ◽  
Cost Effective ◽  
Olfactory Dysfunction ◽  
Molecular Tests ◽  
Point Of Entry ◽  
Screening And Surveillance ◽  
Cost Effective Method ◽  
Olfactory Testing ◽  
Order Of Magnitude

AbstractA central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Molecular tests that detect viral RNAs or antigens will be unable to rise to this challenge unless testing capacity increases by at least an order of magnitude while decreasing turnaround times. Here, we evaluate an alternative strategy based on the monitoring of olfactory dysfunction, a symptom identified in 76-83% of SARS-CoV-2 infections—including those that are otherwise asymptomatic—when a standardized olfaction test is used. We model how screening for olfactory dysfunction, with reflexive molecular tests, could be beneficial in reducing community spread of SARS-CoV-2 by varying testing frequency and the prevalence, duration, and onset time of olfactory dysfunction. We find that monitoring olfactory dysfunction could reduce spread via regular screening, and could reduce risk when used at point-of-entry for single-day events. In light of these estimated impacts, and because olfactory tests can be mass produced at low cost and self-administered, we suggest that screening for olfactory dysfunction could be a high impact and cost effective method for broad COVID-19 screening and surveillance.

scholarly journals Modeling the effectiveness of olfactory testing to limit SARS-CoV-2 transmission

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Daniel B. Larremore ◽  
Derek Toomre ◽  
Roy Parker
Keyword(s):  
Low Cost ◽  
Onset Time ◽  
Cost Effective ◽  
Olfactory Dysfunction ◽  
Molecular Tests ◽  
Point Of Entry ◽  
Screening And Surveillance ◽  
Cost Effective Method ◽  
Olfactory Testing ◽  
Order Of Magnitude

AbstractA central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Molecular tests that detect viral RNAs or antigens will be unable to rise to this challenge unless testing capacity increases by at least an order of magnitude while decreasing turnaround times. Here, we evaluate an alternative strategy based on the monitoring of olfactory dysfunction, a symptom identified in 76–83% of SARS-CoV-2 infections—including those with no other symptoms—when a standardized olfaction test is used. We model how screening for olfactory dysfunction, with reflexive molecular tests, could be beneficial in reducing community spread of SARS-CoV-2 by varying testing frequency and the prevalence, duration, and onset time of olfactory dysfunction. We find that monitoring olfactory dysfunction could reduce spread via regular screening, and could reduce risk when used at point-of-entry for single-day events. In light of these estimated impacts, and because olfactory tests can be mass produced at low cost and self-administered, we suggest that screening for olfactory dysfunction could be a high impact and cost-effective method for broad COVID-19 screening and surveillance.

scholarly journals Badges to Acknowledge Open Practices: A Simple, Low-Cost, Effective Method for Increasing Transparency

2016 ◽  
Author(s):  
Mallory Kidwell ◽  
Ljiljana B. Lazarevic ◽  
Erica Baranski ◽  
Tom Elis Hardwicke ◽  
Sarah Piechowski ◽  
...  
Keyword(s):  
Data Sharing ◽  
Low Cost ◽  
Open Data ◽  
Cost Effective ◽  
Change Over Time ◽  
Psychological Science ◽  
Cost Effective Method ◽  
Order Of Magnitude ◽  
Open Materials ◽  
Over Time

Beginning January 2014, Psychological Science gave authors the opportunity to signal open data and materials if they qualified for badges that accompanied published articles. Before badges, less than 3% of Psychological Science articles reported open data. After badges, 23% reported open data, with an accelerating trend; 39% reported open data in the first half of 2015, an increase of more than an order of magnitude from baseline. There was no change over time in the low rates of data sharing among comparison journals. Moreover, reporting openness does not guarantee openness. When badges were earned, reportedly available data were more likely to be actually available, correct, usable, and complete than when badges were not earned. Open materials also increased to a weaker degree, and there was more variability among comparison journals. Badges are simple, effective signals to promote open practices and improve preservation of data and materials by using independent repositories.

CAD Of Anticorrosive Protection Of Steel Structures

2019 ◽  
pp. 18-23
Keyword(s):  
Protective Coating ◽  
Computer Aided Design ◽  
Steel Structures ◽  
Cost Effective ◽  
Operating Conditions ◽  
Computational Tool ◽  
Protection Method ◽  
Cost Effective Method ◽  
The Cost ◽  
Aided Design

The choice of cost-effective method of anticorrosive protection of steel structures is an urgent and time consuming task, considering the significant number of protection ways, differing from each other in the complex of technological, physical, chemical and economic characteristics. To reduce the complexity of solving this problem, the author proposes a computational tool that can be considered as a subsystem of computer-aided design and used at the stage of variant and detailed design of steel structures. As a criterion of the effectiveness of the anti-corrosion protection method, the cost of the protective coating during the service life is accepted. The analysis of existing methods of steel protection against corrosion is performed, the possibility of their use for the protection of the most common steel structures is established, as well as the estimated period of effective operation of the coating. The developed computational tool makes it possible to choose the best method of protection of steel structures against corrosion, taking into account the operating conditions of the protected structure and the possibility of using a protective coating.

Monitoring effluent quality in hypertrophic wastewater reservoirs using remote sensing

1996 ◽  
Vol 33 (8) ◽  
pp. 23-29 ◽  
Author(s):  
I. Dor ◽  
N. Ben-Yosef
Keyword(s):  
Water Quality ◽  
Theoretical Model ◽  
Principal Component ◽  
Cost Effective ◽  
Operational Parameters ◽  
Effluent Quality ◽  
Optical Images ◽  
Routine Monitoring ◽  
Cost Effective Method ◽  
Wastewater Quality

About one hundred and fifty wastewater reservoirs store effluents for irrigation in Israel. Effluent qualities differ according to the inflowing wastewater quality, the degree of pretreatment and the operational parameters. Certain aspects of water quality like concentration of organic matter, suspended solids and chlorophyll are significantly correlated with the water column transparency and colour. Accordingly optical images of the reservoirs obtained from the SPOT satellite demonstrate pronounced differences correlated with the water quality. The analysis of satellite multispectral images is based on a theoretical model. The model calculates, using the radiation transfer equation, the volume reflectance of the water body. Satellite images of 99 reservoirs were analyzed in the chromacity space in order to classify them according to water quality. Principal Component Analysis backed by the theoretical model increases the method sensitivity. Further elaboration of this approach will lead to the establishment of a time and cost effective method for the routine monitoring of these hypertrophic wastewater reservoirs.

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