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This single primer design is cost-effective and it reduces the risk of sequence errors during synthesis of long oligos.
Sequencing was performed on approximately 20 40 clones derived from each tissue by ELIM Biopharmaceuticals, Hayward, CA. Because of the large amount of sequence data produced for the study and the risk of sequence contamination or PCR over-representation at the many levels of experimentation, a computational pipeline for screening the entire data base of sequences was developed.
Background: European studies suggest that living near high-density livestock production increases the risk of sequence type (ST) 398 methicillin-resistant Staphylococcus aureus (MRSA) colonization.
The risk of sequence artifacts due to interfering variants at primer binding sites is reduced through amplicon tiling in all but the terminal primers of gene regions.
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The VISA approach sequences PCR products directly, without subcloning, which reduces the risk of sequencing contaminating products [201].
Using smaller fractions of the genome reduces the risk of sequencing template derived from both orthologous chromosomes but increases the number of libraries required.
Note that our exclusion of all singletons due to risk of sequencing errors may have caused us to also discard many true positives, especially in phylogenetically isolated strains.
We will evaluate the following domains for risk of bias: sequence generation, allocation sequence concealment, blinding of participants and personnel and outcome assessors, incomplete outcome data, selective outcome reporting and other sources of bias.
The assessment of the risk of bias (sequence generation, allocation concealment, blinding outcome assessor, incomplete outcome data, selective outcome reporting, other sources of bias) was based on the Cochrane Risk of Bias tool [46].
We evaluated the following fields as at low, high or unclear risk of bias: sequence generation (selection bias), allocation concealment (selection bias), blinding of participants and personnel (performance bias), blinding of outcome assessors (detection bias), incomplete outcome data addressed (attrition bias), selective outcome reporting (reporting bias) and other bias.
The two before-after studies were judged to be at high risk of selection, sequence concealment and performance bias.
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