Browsing large scale cheminformatics data with dimension reduction

Visualization of large-scale high dimensional data tool is highly valuable for scientific discovery in many fields. We present PubChemBrowse, a customized visualization tool for cheminformatics research. It provides a novel 3D data point browser that displays complex properties of massive data on commodity clients. As in GIS browsers for Earth and Environment data, chemical compounds with similar properties are nearby in the browser. PubChemBrowse is built around in-house high performance parallel MDS (Multi-Dimensional Scaling) and GTM (Generative Topographic Mapping) services and supports fast interaction with an external property database. These properties can be overlaid on 3D mapped compound space or queried for individual points. We prototype the use with Chem2Bio2RDF system using SPARQL query language to access over 20 publicly accessible bioinformatics databases. We describe our design and implementation of the integrated PubChemBrowse application and outline its use in drug discovery. The same core technologies can be used to develop similar high dimensional browsers in other scientific areas. 1

Clonazepam-induced lichenoid drug eruption: a case report

Background Lichenoid drug eruption is rare and can mimic idiopathic lichen planus and other dermatoses. Clonazepam, a commonly used drug for the treatment of anxiety-related disorders and seizures, is known to be an unlikely cause of cutaneous adverse effects. Only one case report of LDE due to clonazepam has been reported. Case presentation A 81-year-old male patient with Alzheimers disease developed a lichenoid eruption after taking clonazepam. He developed a violaceous scaly patch on his lower extremities, from both buttocks to the feet. The cutaneous eruption resolved 2 months after cessation of clonazepam and with initiation of corticosteroid therapy. Conclusion A skin eruption that develops after clonazepam administration can be a lichenoid drug eruption, which is less likely to resolve spontaneously and requires discontinuation of clonazepam administration

Sirolimus-eluting stent is superior to paclitaxel-eluting stent for coronary intervention in patients with renal insufficiency: Long-term clinical outcomes

Background: Renal insufficiency (RI) is an independent risk factor for the adverse cardiovascular events. Long-term clinical outcome of percutaneous coronary intervention (PCI) in patients with RI is unknown especially in the era of first generation drug-eluting stents (DES). This study aims at comparing clinical outcomes between sirolimus-eluting stents (SES) and paclitaxel-eluting stents (PES) based on large scaled registry.Methods: Patients who underwent PCI with DES from January 2004 to December 2009 in the Catholic University of Korea-PCI (COACT) registry were prospectively enrolled. A group of 1,033 patients with RI, defined as estimated glomerular filtration rate under 60 mL/min, were analyzed. Major adverse cardiac events (MACE), including all-cause death, non-fatal myocardial infarction (MI), target lesion revascularization (TLR), and target vessel revascularization (TVR) according to the type of stents were compared.Results: Median follow-up period was 810 days (interquartile range: from 361 to 1,354 days). A group of 612 (59.2%) patients were treated with SES and 421 (40.8%) patients were treated with PES. The PES vs. SES group had significantly higher rate of MACE (35.9% vs. 28.3%, p = 0.01). In multivariate Cox hazard regression analysis, PES vs. SES group had significantly higher rate of MACE (adjusted hazard ratio [AHR] 1.29, 95% confidence interval [CI] 1.02–1.64, p = 0.033), particularly pronounced by all-cause death (AHR 1.34, 95% CI 1.008–1.770; p = 0.044). In further analysis with propensity score matching, overall findings were consistent.Conclusions: In patients with RI, PCI using PES provides poorer clinical outcomes than SES in terms of MACE and all-cause death

Smaller pineal gland is associated with rapid eye movement sleep behavior disorder in Alzheimers disease

Background To investigate the association between pineal gland volume and symptoms of rapid eye movement (REM) sleep behavior disorder (RBD) in Alzheimers disease (AD) patients without any feature of dementia with Lewy bodies. Methods We enrolled 296 community-dwelling probable AD patients who did not meet the diagnostic criteria for possible or probable dementia with Lewy bodies. Among them, 93 were amyloid beta (Aβ) positive on 18F-florbetaben amyloid brain positron emission tomography. We measured RBD symptoms using the REM Sleep Behavior Disorder Screening Questionnaire (RBDSQ) and defined probable RBD (pRBD) as the RBDSQ of 5 or higher. We manually segmented pineal gland on 3T structural T1-weighted brain magnetic resonance imaging. Results The participants with pRBD had smaller pineal parenchyma volume (VPP) than those without pRBD (p <  0.001). The smaller the VPP, the more severe the RBD symptoms (p <  0.001). VPP was inversely associated with risk of prevalent pRBD (odds ratio = 0.909, 95% confidence interval [CI] = 0.878–0.942, p <  0.001). Area under the receiver operator characteristic curve for pRBD of VPP was 0.80 (95% CI = 0.750–0.844, p <  0.0001). These results were not changed when we analyzed the 93 participants with Aβ-positive AD separately. Conclusions In AD patients, reduced pineal gland volume may be associated with RBD.This study was supported by the grants from the Korean Health Technology R&D Project, Ministry of Health and Welfare, Republic of Korea (grant no.HI09C1379 [A092077]) and the Institute for Information & Communications Technology Promotion (IITP) grant funded by the Korea government (MSIT) (2018-2-00861, Intelligent SW Technology Development for Medical Data Analysis)

Genetic Predisposition of Donors Affects the Allograft Outcome in Kidney Transplantation; Polymorphisms of Stromal-Derived Factor-1 and CXC Receptor 4

Genetic interaction between donor and recipient may dictate the impending responses after transplantation. In this study, we evaluated the role of the genetic predispositions of stromal-derived factor-1 (SDF1) [rs1801157 (G>A)] and CXC receptor 4 (CXCR4) [rs2228014 (C>T)] on renal allograft outcomes. A total of 335 pairs of recipients and donors were enrolled. Biopsy-proven acute rejection (BPAR) and long-term graft survival were traced. Despite similar allele frequencies between donors and recipients, minor allele of SDF1 rs1801157 (GA+AA) from donor, not from recipients, has a protective effect on the development of BPAR compared to wild type donor (GG) (P = 0.005). Adjustment for multiple covariates did not affect this result (odds ratio 0.39, 95% C.I 0.20–0.76, P = 0.006). CXCR4 rs2228014 polymorphisms from donor or recipient did not affect the incidence of acute rejection. SDF1 was differentially expressed in renal tubular epithelium with acute rejection according to genetic variations of donor rs1801157 showing higher expressions in the grafts from GG donors. Contrary to the development of BPAR, the presence of minor allele rs1801157 A, especially homozygocity, predisposed poor graft survival (P = 0.001). This association was significant after adjusting for several risk factors (hazard ratio 3.01; 95% C.I = 1.19–7.60; P = 0.020). The allelic variation of recipients, however, was not associated with graft loss. A donor-derived genetic polymorphism of SDF1 has influenced the graft outcome. Thus, the genetic predisposition of donor should be carefully considered in transplantation

Efficacies of the new Paclitaxel-eluting Coroflex Please™ Stent in percutaneous coronary intervention; comparison of efficacy between Coroflex Please™ and Taxus™ (ECO-PLEASANT) trial: study rationale and design

<p>Abstract</p> <p>Background</p> <p>Previous randomized trials have showed the superiority of Paclitaxel-eluting stent over bare metal stent in angiographic and clinical outcomes. Coroflex Please™ stent is a newly developed drug eluting stent using the Coroflex™ stent platform combined with the drug paclitaxel contained in a polymer coating. PECOPS I trial, one-arm observational study, showed that the clinical and angiographic outcomes of Coroflex Please™ stent were within the range of those of Taxus, the 1^stgeneration paclitaxel-eluting stent (PES). However, there have been no studies directly comparing the Coroflex Please™ stent with the Taxus Liberte™ stent that is the newest version of Taxus. Therefore, prospective, randomized trial is required to demonstrate the non-inferiority of Coroflex Please™ stent compared with Taxus Liberte™ stent in a head-to-head manner.</p> <p>Methods</p> <p>In the comparison of Efficacy between COroflex PLEASe™ ANd Taxus™ stent(ECO-PLEASANT) trial, approximately 900 patients are being prospectively and randomly assigned to the either type of Coroflex Please™ stent and Taxus Liberte™ stent via web-based randomization. The primary endpoint is clinically driven target vessel revascularization at 9 months. The secondary endpoints include major cardiac adverse events, target vessel failure, stent thrombosis and angiographic efficacy endpoints.</p> <p>Discussion</p> <p>The ECO-PLEASANT trial is the study not yet performed to directly compare the efficacy and safety of the Coroflex Please™ versus Taxus Liberte™ stent. On the basis of this trial, we will be able to find out whether the Coroflex Please™ stent is non-inferior to Taxus Liberte™ stent or not.</p> <p>Trial registration</p> <p>ClinicalTrials.gov number, NCT00699543.</p

Fabrication of Trapezoidal Re-entrant Structure with UV and X-ray Lithography

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