SOLiDzipper: A High Speed Encoding Method for the Next-Generation Sequencing Data

Background Next-generation sequencing (NGS) methods pose computational challenges of handling large volumes of data. Although cloud computing offers a potential solution to these challenges, transferring a large data set across the internet is the biggest obstacle, which may be overcome by efficient encoding methods. When encoding is used to facilitate data transfer to the cloud, the time factor is equally as important as the encoding efficiency. Moreover, to take advantage of parallel processing in cloud computing, a parallel technique to decode and split compressed data in the cloud is essential. Hence in this review, we present SOLiDzipper, a new encoding method for NGS data. Methods The basic strategy of SOLiDzipper is to divide and encode. NGS data files contain both the sequence and non-sequence information whose encoding efficiencies are different. In SOLiDzipper, encoded data are stored in binary data block that does not contain the characteristic information of a specific sequence platform, which means that data can be decoded according to a desired platform even in cases of Illumina, Solexa or Roche 454 data. Results The main calculation time using Crossbow was 173 minutes when 40 EC2 nodes were involved. In that case, an analysis preparation time of 464 minutes is required to encode data in the latest DNA compression method like G-SQZ and transmit it on a 183 Mbit/s bandwidth. However, it takes 194 minutes to encode and transmit data with SOLiDzipper under the same bandwidth conditions. These results indicate that the entire processing time can be reduced according to the encoding methods used, under the same network bandwidth conditions. Considering the limited network bandwidth, high-speed, high-efficiency encoding methods such as SOLiDzipper can make a significant contribution to higher productivity in labs seeking to take advantage of the cloud as an alternative to local computing. Availability http://szipper.dinfree.com . Academic/non-profit: Binary available for direct download at no cost. For-profit: Submit request for for-profit license from the web-site

Solitary Cutaneous Myofibroma on the Sole: An Unusual Localization

Solitary cutaneous myofibroma is a circumscribed benign neoplasm of superficial soft tissue in adolescents and adults; it represents the adult counterpart of infantile myofibromatosis1. Clinically, it typically presents as a painless, slow-growing, firm cutaneous or subcutaneous nodule with an occasional bluish hue. There is a predilection for it to occur on the head and neck, shoulder girdle, lower extremity and hand2, 3. Oral and genital solitary cutaneous myofibromas have also been identified. Plantar involvement is exceptionally rare, and there has been only one case of solitary cutaneous myofibroma affecting the sole in the literature3. Histological findings reveal a distinctive appearance, well recognized in children but much less so in adults. It manifests as a biphasic pattern or a zoning arrangement of two cell types4. Among them, the hemangiopericytomatous components, which are typical of infantile myofibromatosis, may sometimes be inconspicuous or even absent in adult lesions, as in our case3. Spindle cells have eosinophilic cytoplasm arranged in short bundles and fascicles resembling leiomyoma. These cells demonstrate features of both myofibroblasts and fibroblasts. Myofibroblastic differentiation of the tumor cells is supported by their immunophenotype. The spindle cells are desmin negative, but smooth muscle actin positive. The Masson trichrome stain, in which thick fibrous bundles with random, irregularly intersecting angles are prominent, can be used to assist in differentiating myofibromas from smooth muscle lesions5. In contrast, smooth muscle lesions show delicate fibrous tissues surrounding the smooth muscle cells and in the septa between the smooth muscle masses. The limited follow-up of solitary cutaneous myofibromas suggests that they tend to follow a benign clinical course with no evidence of recurrence or metastasi

Electrical Characterization of Proposed Transpositional Acupoints on the Urinary Bladder Meridian in a Rat Model

Specific electrical characteristicsof acupointswere investigated on the urinary bladder (BL) meridian in 14 rats. BL acupointsand non-acupoints on the back were selected and their electrical voltages were measured by using aSPACsystem.The mean voltages of each point or each line were statistically analyzed by using the ANOVA test.The BL meridian showed voltages higher than those of the reference line (P < .05). Bilateral 1st BL lines presented higher voltages than bilateral 2nd BL lines (P < .05). Most BL acupoints had voltageshigher than those for the corresponding reference points (P < .05). In particular, theright BL16 exhibited the biggest difference from the reference point, followed by the left extra BL point-2, the right BL27, the left BL17, and theleft BL45. Additionally, the distributions of neurofilamentsfor several points were investigated by using immunohistochemistry. There was a trend for the BL acupoints to have larger numbers of neurofilaments than the reference points, and that trend seemed to be directly proportional to the difference in voltage between the points.In conclusion, BL acupoints on the back in ratsexhibited specific electric and histologic characteristics. Therefore, those acupointsmay be utilized to investigate the efficacy of acupuncturewith laboratory animals

Predicting factors of present hepatitis C virus infection among patients positive for the hepatitis C virus antibody

Background/AimsTo identify the predicting factors of present hepatitis C virus (HCV) infection among patients with positivity for antibodies to HCV (anti-HCV).MethodsWe analyzed patients who showed positive enzyme immunoassay (EIA) results and performed an HCV RNA test as a confirmatory test at Kyung Hee University Hospital at Gangdong from June 2006 to July 2012. The features distinguishing the groups with positive and negative HCV RNA results were reviewed.ResultsIn total, 490 patients were included. The results of the HCV RNA test were positive and negative in 228 and 262 patients, respectively. The index value of anti-HCV, mean age, platelet counts, total bilirubin, prothrombin time international normalized ratio, albumin and alanine transaminase (ALT) levels differed significantly between the two groups. On multivariable analysis, an index value of anti-HCV >10 [odds ratio (OR)=397.27, P40 IU/L (OR=3.64, P=0.001), and albumin <3.8 g/dL (OR=2.66, P=0.014) were related to present HCV infection.ConclusionsAlthough EIA is not a quantitative test, considering the anti-HCV titer with ALT and albumin levels may be helpful in predicting present of HCV infection

The impact of transferring patients with ST-segment elevation myocardial infarction to percutaneous coronary intervention-capable hospitals on clinical outcomes

Background: Primary percutaneous coronary intervention (PCI) is recommended for ST-segment elevation myocardial infarction (STEMI) patients even when the patient must be transported to a PCI-capable hospital. This study aimed to evaluate the long-term clinical outcomes of STEMI patients who were transferred for primary PCI compared to patients who arrived directly to PCI-capable hospitals. Methods: A total of 3,576 STEMI patients with less than 12 h of symptom onset-to-door time from the Korea Acute Myocardial Infarction Registry were divided into transfer (n = 2,176) and direct-arrival (n = 1,400) groups according to their status. The primary outcome was the composite of major adverse cardiac event (MACE), defined as death, non-fatal myocardial infarction, and revascularization at 1 year. Results: In the transfer vs. the direct-arrival group, the median symptom onset-to-firstmedical contact time was significantly shorter (60 vs. 80 min, p &lt; 0.001), but the median symptom onset-to-door time was significantly longer (194 vs. 90 min, p &lt; 0.001). The median door-to-balloon time was significantly shorter in the transfer group vs. the direct-arrival group (75 vs. 91 min, p &lt; 0.001). Total death and the composite of MACE were not significantly different during hospitalization (5.1 vs. 3.9%, p = 0.980; 5.4 vs. 4.8%, p = 0.435, respectively) and at 1-year (8.2 vs. 6.6%, p = 0.075; 13.7 vs. 13.9%, p = 0.922, respectively). Conclusions: Transferring STEMI patients to PCI-capable hospitals with a time delay did not affect clinical outcomes after 1 year. This study suggests that inter-hospital transfer should be encouraged even with delay for STEMI patients who require primary PCI in areas with a similar geographic accessibility

Epitaxial Growth of a Single-Crystal Hybridized Boron Nitride and Graphene layer on a Wide-Band Gap Semiconductor

Vertical and lateral heterogeneous structures of two-dimensional (2D) materials have paved the way for pioneering studies on the physics and applications of 2D materials. A hybridized hexagonal boron nitride (h-BN) and graphene lateral structure, a heterogeneous 2D structure, has been fabricated on single-crystal metals or metal foils by chemical vapor deposition (CVD). However, once fabricated on metals, the h-BN/graphene lateral structures require an additional transfer process for device applications, as reported for CVD graphene grown on metal foils. Here, we demonstrate that a single-crystal h-BN/graphene lateral structure can be epitaxially grown on a wide-gap semiconductor, SiC(0001). First, a single-crystal h-BN layer with the same orientation as bulk SiC was grown on a Si-terminated SiC substrate at 850 oC using borazine molecules. Second, when heated above 1150 oC in vacuum, the h-BN layer was partially removed and, subsequently, replaced with graphene domains. Interestingly, these graphene domains possess the same orientation as the h-BN layer, resulting in a single-crystal h-BN/graphene lateral structure on a whole sample area. For temperatures above 1600 oC, the single-crystal h-BN layer was completely replaced by the single-crystal graphene layer. The crystalline structure, electronic band structure, and atomic structure of the h-BN/graphene lateral structure were studied by using low energy electron diffraction, angle-resolved photoemission spectroscopy, and scanning tunneling microscopy, respectively. The h-BN/graphene lateral structure fabricated on a wide-gap semiconductor substrate can be directly applied to devices without a further transfer process, as reported for epitaxial graphene on a SiC substrate.Comment: 23 pages, 7 figure

Anaphylactic Shock Caused by Ingestion of Polyethylene Glycol

Colonoscopy is the current standard method for evaluation of the colon. The diagnostic accuracy and therapeutic safety of colonoscopy depend on the quality of colonic cleansing and preparation. Generally, all these preparations have been demonstrated to be safe for use in healthy individuals without significant comorbid conditions. Based on safety and efficacy concerns, polyethylene glycol (PEG) is most commonly utilized as a bowel preparation solution for colonoscopy. Adverse events in patients receiving PEG are mostly clinically non-significant. However, fatal adverse events rarely have been shown to occur in the few individuals who experience vomiting or aspiration. Anaphylactic shock associated with ingestion of PEG electrolyte solution is an extremely rare fatal complication, and reported mainly in Western countries. Here, we report the first case of anaphylactic shock following the ingestion of PEG solution in Korea