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Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter

Mohamed Hashim EK, Abdullah R

J Theor Biol, 2015 Dec 21;387:88-100.
PMID: 26427337 DOI: 10.1016/j.jtbi.2015.09.014

Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets.

Matched MeSH terms: Dinucleoside Phosphates
Fulltext Polymer-free sirolimus-eluting stents in a large-scale all-comers population

Krackhardt F, Kočka V, Waliszewski MW, Utech A, Lustermann M, Hudec M, et al.

Open Heart, 2017 06 06;4(2):e000592.
PMID: 28761678 DOI: 10.1136/openhrt-2017-000592

OBJECTIVE: The objective of this study was to assess the safety and efficacy of a polymer-free sirolimus coated, ultrathin strut drug-eluting stent (PF-SES) in an unselected patient population with a focus on acute coronary syndrome (ACS). Furthermore, stable coronary artery disease (CAD) with short (≤6 months) versus long (>6 months) dual antiplatelet therapy (DAPT) were also studied.
METHODS: Patients who received PF-SES were investigated in an unselected large-scale international, single-armed, multicenter, 'all comers' observational study. The primary endpoint was the 9-month target lesion revascularisation (TLR) rate, whereas secondary endpoints included the 9-month major adverse cardiac events (MACE) and procedural success rates. A priori defined subgroups such as patients with ACS, diabetes, lesion subsets and procedural characteristics relative to DAPT were investigated.
RESULTS: A total of 2877 patients of whom 1084 had ACS were treated with PF-SES (1.31±0.75 stents per patient). At 9 months, the accumulated overall TLR rate was 2.3% (58/2513). There was no significant difference between ACS and stable CAD (2.6% vs 2.1%, p=0.389). However, the overall MACE rate was 4.3% (108/2513) with a higher rate in patients with ACS when compared with the stable CAD subgroup (6.1%, 58/947 vs 3.2%, 50/1566, p<0.001).
CONCLUSIONS: PF-SES angioplasty is safe and effective in the daily clinical routine with low rates of TLR and MACE in an unselected patient population. Our data are in agreement with prior clinical findings that extended DAPT duration beyond 6 months do not improve clinical outcomes in patients with stable CAD (ClinicalTrials.gov Identifier NCT02629575).
TRIAL REGISTRATION NUMBER: NCT02629575.

Matched MeSH terms: Dinucleoside Phosphates
Fulltext Polymer-free sirolimus-eluting stent use in Europe and Asia: Ethnic differences in demographics and clinical outcomes

Krackhardt F, Waliszewski M, Wan Ahmad WA, Kočka V, Toušek P, Janek B, et al.

PLoS One, 2020;15(1):e0226606.
PMID: 31929543 DOI: 10.1371/journal.pone.0226606

BACKGROUND: The objective of this study was to assess regional and ethnic differences in an unselected patient population treated with polymer-free sirolimus-eluting stents (PF-SES) in Asia and Europe.
METHODS: Two all-comers observational studies based on the same protocol (ClinicalTrials.gov Identifiers: NCT02629575 and NCT02905214) were combined for data analysis to assure sufficient statistical power. The primary endpoint was the accumulated target lesion revascularization (TLR) rate at 9-12 months.
RESULTS: Of the total population of 7243 patients, 44.0% (3186) were recruited in the Mediterranean region and 32.0% (2317) in central Europe. The most prominent Asian region was South Korea (17.6%, 1274) followed by Malaysia (5.7%, 413). Major cardiovascular risk factors varied significantly across regions. The overall rates for accumulated TLR and MACE were low with 2.2% (140/6374) and 4.4% (279/6374), respectively. In ACS patients, there were no differences in terms of MACE, TLR, MI and accumulated mortality between the investigated regions. Moreover, dual antiplatelet therapy (DAPT) regimens were substantially longer in Asian countries even in patients with stable coronary artery disease as compared to those in Europe.
CONCLUSIONS: PF-SES angioplasty is associated with low clinical event rates in all regions. Further reductions in clinical event rates seem to be associated with longer DAPT regimens.

Matched MeSH terms: Dinucleoside Phosphates

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