Double Indexing Synchronizer - To Amplify the Synchronizer Capacity

2012 ◽  
Author(s):  
Amit Sandooja
Keyword(s):  
Double Indexing

Clonal Diversity Analysis Of Integrating Vector Transduced Hematopoietic Cells Using LAM-PCR Followed By Illumina-Based Next-Generation Sequencing Is Affected By False Positivity That Arises From Both Reaction Biochemistry and Bioinformatic Analysis

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1662-1662
Author(s):  
Michael R. Greene ◽  
Michael Rusch ◽  
Chunlao Tang ◽  
Jinghui Zhang ◽  
Brian P. Sorrentino
Keyword(s):  
Human Genome ◽  
Sensitivity And Specificity ◽  
False Positive ◽  
Conflicts Of Interest ◽  
Fragment Size ◽  
Bioinformatic Analysis ◽  
Read Length ◽  
False Positivity ◽  
Insertion Sites ◽  
Double Indexing

Abstract We have previously reported that LAM-PCR libraries derived from non-vector transduced NSG repopulating cells, even those proven negative by high-resolution gel analysis, subsequently prepared following standard Illumina library preparation and sequencing protocol, yielded thousands of reads that contained full length LTR (30nt) fragments, met all quality control filters, were mappable to loci within the human genome, and were thus indistinguishable from true reads. We observed 430,385 of these reads in two mocks, with one having 106 identified vector insertion sites (VIS) and the other 27. To determine the source of this mock positivity, we modified our LAM biochemistry to include a 6nt barcode sequence in the linker fragment that could provide a second identity verification in addition to the Illumina adaptor index (double-indexing). Now when we performed LAM-NGS we were able to filter out any read where the linker barcode did not match with the identified Illumina index, which resulted in the elimination of all but 2 reads, neither of which could be mapped. As the sequencing libraries generated from the vector treated NSG repopulating cell LAM-PCR products were also double-indexed, we could identify any read that had been assigned to the incorrect source (mis-indexing). This occurred at a rate of approximately 0.1-1% in polyclonally reconstituted animals, but could be as high as 100% in mice with one or two identified VIS. This risk of mis-indexing appears constant, such that reads derived from vector insertion sites with the highest read counts are most likely to result in mock positivity, therefore the simple subtraction of the VIS found in mock will result in the loss of true signal and cannot be recommended. For any assay to be successfully translated to the clinic, one must have an understanding of its performance characteristics, so we sought to determine the sensitivity and specificity of the LAM-NGS assay. To this end, we developed a set of controls consisting of genomic DNA purified from mixtures of Jurkat cell clones that contained known VIS to derive LAM-NGS libraries of predictable complexity (a 15 VIS and a 32 VIS library). Using these controls with standard LAM-PCR/ Illumina biochemistry followed by standard bioinformatic analysis, even with the incorporation of the double indexing strategy to remove all mis-indexed reads, numerous predicted VIS still remain as false positive calls. Our 15 VIS control had a sensitivity of 100% but a specificity 21% (55 false positive of 70 total VIS identified), and our 32 VIS control performed even worse with a sensitivity/specificity of 53%/13% (119 false positive of 136 total VIS identified). Several factors were common to the non mis-indexed false positive reads: 1. False positive VIS usually arise from shorter reads (<90nt) which, due to the highly repetitive nature of the human genome, can be mapped to multiple locations or map better to different locations depending on how long the read is and 2. False positive VIS are more prevalent in reads with lower read counts (<100, with many of them =1) where a read is likely a synthesis artifact where regions of low complexity such as a run of poly-T will result in indels or other PCR induced artifacts such as chimera formation that alter the best mapping location. Neither of these criteria was sufficient as filters and many true VIS became undetectable when arbitrary limits were placed on read length or total read count. Using different mapping algorithms (we tested BLAT, BWA, BFast, and GSNAP), while altering the absolute number and where many of these false positive reads mapped, none could eliminate this problem and all showed some degree of both success and failure. By using a set of defined controls and double indexing biochemistry, we have been able to assess the sensitivity and specificity of the LAM-NGS assay and to elucidate the mechanism underlying much of the assay’s false positivity. By using this double indexing strategy, we have eliminated mis-indexed reads, but false positivity from real reads mapped to incorrect locations as well as low numbers of reads arising from still unclear sources are present in the LAM-NGS assay. As much of these false positive reads are due to PCR artifact we are currently testing low PCR cycle approaches and as read length is also an issue, controlling LAM fragment size using sonication instead of restriction endonucleases is also being evaluated. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

2011 ◽  
Vol 40 (1) ◽  
pp. e3-e3 ◽  
Author(s):  
Martin Kircher ◽  
Susanna Sawyer ◽  
Matthias Meyer
Keyword(s):  
Illumina Platform ◽  
Multiplex Sequencing ◽  
Double Indexing

scholarly journals The equative sentence in Finnish Sign Language

2007 ◽  
Vol 10 (2) ◽  
pp. 113-143 ◽  
Author(s):  
Tommi Jantunen
Keyword(s):  
Sign Language ◽  
The Other ◽  
External Position ◽  
General Schema ◽  
Textual Cohesion ◽  
Double Indexing

It is argued in this paper that equative sentences in Finnish Sign Language (FinSL) conform to the general schema of (NP) NP+(PI+)NP, parenthesis marking optionality of elements. With respect to this schema, it is further argued, (a) that the function of the first NP in equative sentences is always topic; (b) that topics are marked syntactically, prosodically, and morphologically in FinSL; (c) that the preferred organisation of equative sentences in general is topic-comment; (d) that there are two structurally distinct topic-comment structures in FinSL, one having the topic at the beginning of the clause and the other having the topic in the left-detached clause-external position; (e) that the double-indexing phenomenon (cf. pronoun copy) is functionally a means to increase textual cohesion; and (f) that the sign PI in equative sentences is a certainty expressing modal device, although it may be in the process of grammaticalising into a copula.

John Buridan’s Theory of Truth and the Paradox of the Liar

Vivarium ◽  
2011 ◽  
Vol 49 (1-3) ◽  
pp. 184-213
Author(s):  
Ernesto Perini-Santos
Keyword(s):  
Philosophy Of Language ◽  
Liar Paradox ◽  
Truth Conditions ◽  
Truth Values ◽  
Truth Value ◽  
Correct Understanding ◽  
The Liar ◽  
The Liar Paradox ◽  
Double Indexing

AbstractThe solution John Buridan offers for the Paradox of the Liar has not been correctly placed within the framework of his philosophy of language. More precisely, there are two important points of the Buridanian philosophy of language that are crucial to the correct understanding of his solution to the Liar paradox that are either misrepresented or ignored in some important accounts of his theory. The first point is that the Aristotelian formula, ‘propositio est vera quia qualitercumque significat in rebus significatis ita est’, once amended, is a correct way to talk about the truth of a sentence. The second one is that he has a double indexing theory of truth: a sentence is true in a time about a time, and such times should be distinguished in the account of the truth-conditions of sentences. These two claims are connected in an important way: the Aristotelian formula indicates the time about which a sentence is true. Some interpreters of the Buridanian solution to the paradox, following the lead of Herzberger, have missed these points and have been led to postulate truth-values gaps, or surrogates of truth-value gaps, when there is nothing of this sort in his theory. I argue against this tradition of interpretation of Buridan and propose an interpretation of his solution to the Liar.

scholarly journals Optimization of Microblog Representation Using Deep Learning Approach

2018 ◽  
Vol 7 (2) ◽  
pp. 133-138
Author(s):  
K. H. Walse
Keyword(s):  
Real Time ◽  
Online Communication ◽  
Daily Lives ◽  
Time News ◽  
Indexing Method ◽  
Similarity Algorithm ◽  
Indexing Technique ◽  
Share Information ◽  
Extract Information ◽  
Double Indexing

Microblogging, as a new form of online communication in which users talk about their daily lives, to gather real-time news, opinion about people or share information by short posts, has become one of the most popular social networking services today, e.g. to stay in touch with friends . Finding proper representations of microblog texts is a challenging issue. The overview of microblog included how to extract information from microblog, also discuss about Microblogging and Twitter. This paper included existing research on Optimization of Microblog Representation by using existing techniques and methods as well as microblogging services.Current approaches, for microblog reduction are single indexing. In this work, we have proposed double indexing method for microblog reduction. We have used our own generated dataset for microblog reduction. We have collected tweets from real time twitter for both single and double indexing technique. Also, we have use LDA with Semantic Similarity algorithm. We compared our results with single indexing. Experimental results shows that double indexing gives better performance than single indexing. This may happen because we will show both original and reduced tweets, so it will be known to user which tweet are removed and relevant part shows as output. We have also compared our results with the state-of-art. The proposed double indexing gives better performance than existing 1-ROCA of improved online SVM technique.

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