Characterization of Readback Signal, Distortion, and Noise and Estimation of Error Rates Based on Spectral Measurements Only

2012 ◽  
Vol 48 (6) ◽  
pp. 2073-2079 ◽  
Author(s):  
Roger Wood ◽  
Michael Salo ◽  
Helen Dang
Keyword(s):  
Error Rates ◽  
Signal Distortion ◽  
Spectral Measurements ◽  
Estimation Of Error

scholarly journals Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1338
Author(s):  
Morgan E. Meissner ◽  
Emily J. Julik ◽  
Jonathan P. Badalamenti ◽  
William G. Arndt ◽  
Lauren J. Mills ◽  
...  
Keyword(s):  
Error Rates ◽  
Maximum Depth ◽  
Sequencing Data ◽  
Background Error ◽  
High Background ◽  
Immunodeficiency Virus ◽  
User Friendly ◽  
Viral Mutagenesis ◽  
Hiv 1

Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

scholarly journals The synthesis and characterization of some new diazoamino derivatives

2010 ◽  
Vol 16 (1) ◽  
pp. 89-95
Author(s):  
Mihaela Mocanu
Keyword(s):  
1H Nmr ◽  
Bioactive Compounds ◽  
Elemental Analysis ◽  
Analysis Data ◽  
Biological Properties ◽  
Synthesis And Characterization ◽  
Elemental Analysis Data ◽  
Spectral Measurements ◽  
Inflammatory Processes

The sulfonamidic moiety is much encountered in structures of bioactive compounds. In the present paper the studies on the sulfonamidated aryloxyalkylcarboxylic acids are extended by their attaching on certain substrata able to confer some special biological properties to the final products, such as anti-tumor and antioxidant actions useful in treating inflammatory processes, ulcer, convulsions and diabetes, as well as a herbicidal action. The stepwise syntheses of the sulfonamidated aryloxyalkylcarboxylic acid derivatives and their characterization by elemental analysis data and IR, 1H-NMR and UV-Vis spectral measurements are described. The newly obtained compounds could show potential pharmaceutical and herbicide properties.

scholarly journals debar, a sequence-by-sequence denoiser for COI-5P DNA barcode data

2021 ◽  
Author(s):  
Cameron M. Nugent ◽  
Tyler A. Elliott ◽  
Sujeevan Ratnasingham ◽  
Paul D. N. Hebert ◽  
Sarah J. Adamowicz
Keyword(s):  
High Throughput Sequencing ◽  
Dna Barcode ◽  
R Package ◽  
Error Rates ◽  
Real World Data ◽  
Species Discovery ◽  
Consensus Sequences ◽  
In Silico Studies ◽  
Coi Sequences

AbstractDNA barcoding and metabarcoding are now widely used to advance species discovery and biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume and scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates of biodiversity. Denoising —the separation of biological signal from instrument (technical) noise—of barcode and metabarcode data currently employs abundance-based methods which do not capitalize on the highly conserved structure of the cytochrome c oxidase subunit I (COI) region employed as the animal barcode. This manuscript introduces debar, an R package that utilizes a profile hidden Markov model to denoise indel errors in COI sequences introduced by instrument error. In silico studies demonstrated that debar recognized 95% of artificially introduced indels in COI sequences. When applied to real-world data, debar reduced indel errors in circular consensus sequences obtained with the Sequel platform by 75%, and those generated on the Ion Torrent S5 by 94%. The false correction rate was less than 0.1%, indicating that debar is receptive to the majority of true COI variation in the animal kingdom. In conclusion, the debar package improves DNA barcode and metabarcode workflows by aiding the generation of more accurate sequences aiding the characterization of species diversity.

Monothiocarbamate complexes of divalent nickel, palladium, and platinum

1973 ◽  
Vol 26 (8) ◽  
pp. 1645 ◽  
Author(s):  
EM Krankovits ◽  
RJ Magee ◽  
MJ O'Conner
Keyword(s):  
Proton Magnetic Resonance ◽  
Resonance Spectrum ◽  
Proton Magnetic Resonance Spectrum ◽  
Spectral Measurements ◽  
Infrared Measurements ◽  
Divalent Nickel ◽  
Infrared Spectral ◽  
Definite Structure ◽  
First Time

The preparation of a number of polymeric, octahedral bis(N- alkylmonothiocarbamato)nickel(II) complexes and some of their base adducts is described. ��� The preparation and characterization of some bis(phosphine)bis(N- alkylmono-thiocarbamato)palladium(II) compounds are also described for the first time. The butyl compound is monomeric in chloroform and infrared spectral measurements of all compounds indicate that the monothiocarbamate ligands are bonded to palladium through the sulphur atoms only. The proton magnetic resonance spectrum of the dimethylphenylphosphine complex shows clearly that the phosphine groups are trans in the complexes. ��� Simple bis(monothiocarbamato)-palladium(II) or -platinum(II) have not been isolated but pyrrolidinium tetra(N- pyrrolidylmonothiocarbamato)-palladium(II) or -platinum(II) compounds are formed. Infrared measurements indicate that the mono-thiocarbamate ligands are bonded to the metal through both oxygen and sulphur atoms but no definite structure can be proposed for these compounds at present.

scholarly journals Multifaceted aspects of chunking enable robust algorithms

2014 ◽  
Vol 112 (8) ◽  
pp. 1849-1856 ◽  
Author(s):  
Daniel E. Acuna ◽  
Nicholas F. Wymbs ◽  
Chelsea A. Reynolds ◽  
Nathalie Picard ◽  
Robert S. Turner ◽  
...  
Keyword(s):  
Motor Behavior ◽  
Response Times ◽  
Reaction Times ◽  
Error Rates ◽  
Physiological Data ◽  
Bayesian Algorithm ◽  
Robust Algorithms ◽  
Sequence Production ◽  
Standard Tool

Sequence production tasks are a standard tool to analyze motor learning, consolidation, and habituation. As sequences are learned, movements are typically grouped into subsets or chunks. For example, most Americans memorize telephone numbers in two chunks of three digits, and one chunk of four. Studies generally use response times or error rates to estimate how subjects chunk, and these estimates are often related to physiological data. Here we show that chunking is simultaneously reflected in reaction times, errors, and their correlations. This multimodal structure enables us to propose a Bayesian algorithm that better estimates chunks while avoiding overfitting. Our algorithm reveals previously unknown behavioral structure, such as an increased error correlations with training, and promises a useful tool for the characterization of many forms of sequential motor behavior.

Characterization of semiconductor laser frequency chirp based on signal distortion in dispersive optical fiber

2006 ◽  
Vol 14 (2) ◽  
Author(s):  
P. Krehlik
Keyword(s):  
Single Mode ◽  
Laser Frequency ◽  
Single Mode Fiber ◽  
Distributed Feedback ◽  
Parameters Estimation ◽  
Signal Distortion ◽  
Measuring Time ◽  
Simple Method ◽  
Laser Chirp

AbstractIn the paper, the simple method of laser chirp parameters estimation is presented. It is based on measuring time-domain distortions of chirped signal transmitted through dispersive fiber and finding laser chirp parameters by matching measured distortions to calculated ones. Experiments undertaken with 1.55 μm telecommunication grade distributed feedback (DFB) lasers and standard single-mode fiber are described, together with some practical remarks on measurement setup and main conclusions.

scholarly journals Spectral Characterization of Fungal Metabolites in Aqueous Medium with Humus Substances

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
D. A. Khundzhua ◽  
S. V. Patsaeva ◽  
V. A. Terekhova ◽  
V. I. Yuzhakov
Keyword(s):  
Organic Matter ◽  
Natural Waters ◽  
Culture Medium ◽  
Molecular Size ◽  
Aquatic Environments ◽  
Fungal Metabolites ◽  
Microscopic Fungi ◽  
Spectral Measurements ◽  
Humus Substances

The work is targeted to confirm participation of microscopic fungi in transformation of humus substances in aquatic environments. The research is focused on the spectroscopic study of the collection of fungal strains with different pigmentation of mycelium. Spectral properties of fungal metabolites were measured and compared to that of natural aquatic nonliving organic matter and commercial humus substances in aqueous solutions. The experiments revealed that the effect of microscopic fungi growing in the culture medium with added humate appeared as changes in the humic-type fluorescence: its characteristics became more similar to that of nonliving organic matter in natural waters than to original humate preparation. The experiments demonstrated degradation of coal-originated humate due to microbial activity into compounds of smaller molecular size and increased heterogeneity. We resume that transformation of humus substances by fungal cultures can be monitored and characterized using spectral measurements.

Characterization of published errors in high-impact oncology journals

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 6627-6627
Author(s):  
A. Molckovsky ◽  
M. M. Vickers ◽  
P. A. Tang
Keyword(s):  
Error Rate ◽  
Error Propagation ◽  
Web Of Science ◽  
Citation Index ◽  
Error Rates ◽  
High Impact ◽  
Typographical Error ◽  
Survey Results ◽  
Erroneous Data

6627 Background: Knowledge within oncology is disseminated primarily via peer-reviewed journals. The potential for dissemination of erroneous data exists, an issue that has not been explored in oncology. We evaluated errata from the Journal of Clinical Oncology and the Journal of the National Cancer Institute published between 2004–2007. Methods: Two authors independently abstracted data regarding errata and classified them as trivial (eg typographical error) or serious (eg change in outcome). For serious errors, the frequency of citation and error propagation was determined using the Science Citation Index in Web of Science. For publications cited > 150 times, a random sample of 10% were evaluated for error propagation. Canadian oncologists were surveyed regarding attitudes towards published errata. Results: There were 190 published errors, out of a total of 5118 papers, for an error rate of 4 ± 1% (SD) per year. 26/190 errors were identified as serious (14%). The median time from publication of the original article to publication of the erratum was 3.5 mo for trivial errors compared to 8.3 mo for serious errors (p = 0.03). A median of 1 error per article was reported for papers with trivial errors compared to a median of 2 errors per article with serious errors (p < 0.01). The 26 articles with serious errors were cited 256 times before publication of the error and 1056 times afterwards; of these, 96 and 527, respectively, were evaluated for propagation. Error propagation occurred in 14.6% of the citations published before error publication, and in 3.4% of citations published afterwards (p < 0.001). Survey results indicate that 30% of oncologists do not read the erratum section of journals, and that 45% of oncologists have only read the abstract of an article before citing it in a publication. Although 58% of oncologists have noticed errors in cancer publications, only 15% of these errors were reported. Conclusions: Error rates in high impact oncology journals average 4% per year, but this is likely an underestimate since errors noticed by readers are not consistently reported to the journal. The accuracy of articles submitted for publication is of utmost importance; while error propagation decreases after erratum publication, serious errors continue to be propagated in the literature. No significant financial relationships to disclose.

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