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

Anxiety Control and Periodontal Practice

Chronic periodontitis is one of the most common diseases in clinical dentistry, which requires various surgical interventions to treat the moderately to severely destructed supporting periodontium. Most patients have anxiety and fear to those surgical procedures and dentists often have problems dealing with those patients. By applying the conscious sedation technique in outpatient units, periodontists have become able to manage their patients successfully with less anxiety or fear. Also, we have experienced the increased level of patients\u27 satisfaction. Generally, periodontal treatments are time consuming procedures and patients are usually reluctant to the periodontal instruments. This study is focused on the sedation procedure with intravenous midazolam infusion performed in Department of Periodontology of Ewha Womans University Hospital. Using questionnaires, we evaluated 80 randomly selected patients for the anxiolytic effect of intravenous midazolam. Anxiety control using IV sedation was very helpful in performing various periodontal reconstructive and advanced surgical procedures in implant dentistry

Highly p-doped graphene obtained by fluorine intercalation

We present a method for decoupling epitaxial graphene grown on SiC(0001) by intercalation of a layer of fluorine at the interface. The fluorine atoms do not enter into a covalent bond with graphene, but rather saturate the substrate Si bonds. This configuration of the fluorine atoms induces a remarkably large hole density of p \approx 4.5 \times 1013 cm-2, equivalent to the location of the Fermi level at 0.79 eV above the Dirac point ED .Comment: 4 pages, 2 figures, in print AP

Genotypic Characterization of Vibrio vulnificus Clinical Isolates in Korea

AbstractObjectivesVibrio vunificus is known to cause septicemia and severe wound infections in patients with chronic liver diseases or an immuno-compromised condition. We carried out the molecular characterization of V. vulnificus isolates from human Vibrio septicemia cases based on pulsed-field gel electrophoresis (PFGE) using NotI and SfiI.Methods and ResultsPFGE was used to characterize a total of 78 strains from clinical cases after NotI or SfiI digestion. The geographical distribution of PFGE patterns for the strains from the southern part of Korea, a high-risk region for Vibrio septicemia, indicated that the isolates from southeastern Korea showed a comparatively higher degree of homology than those from southwestern Korea.ConclusionsWe report the genetic distribution of V. vulnficus isolated from Vibrio septicemia cases during 2000–2004 in Korea. This method has potential use as a subspecies-typing tool for V. vulnificus strains isolated from distant geographic regions

Handheld photoacoustic tomography probe built using optical-fiber parallel acoustic delay lines

The development of the first miniaturized parallel acoustic delay line (PADL) probe for handheld photoacoustic tomography (PAT) is reported. Using fused-silica optical fibers with low acoustic attenuation, we constructed two arrays of eight PADLs. Precision laser micromachining was conducted to produce robust and accurate mechanical support and alignment structures for the PADLs, with minimal acoustic distortion and interchannel coupling. The 16 optical-fiber PADLs, each with a different time delay, were arranged to form one input port and two output ports. A handheld PADL probe was constructed using two single-element transducers and two data acquisition channels (equal to a channel reduction ratio of 8:1). Photoacoustic (PA) images of a black-ink target embedded in an optically scattering phantom were successfully acquired. After traveling through the PADLs, the eight channels of differently time-delayed PA signals reached each single-element ultrasonic transducer in a designated nonoverlapping time series, allowing clear signal separation for PA image reconstruction. Our results show that the PADL technique and the handheld probe can potentially enable real-time PAT, while significantly reducing the complexity and cost of the ultrasound receiver system

Experimental Study on the Acellular Demal Matrix Graft for the Root Coverage in Dog

Mucogingival surgery is a plastic surgical procedure designed to correct defects in the morphology, position, and dimensions of the gingiva surrounding the teeth. Many surgical techniques have been reported in mucogingival surgery. Since these procedures also include the soft tissue esthetic approach, the term periodontal plastic surgery has been proposed to be more appropriate.1 Root coverage is a procedure that falls with this definition, and it has attracted more interest than others

Anti-Inflammatory Effects of Inonotus obliquus in Colitis Induced by Dextran Sodium Sulfate

A total of 28 male BALB/c mice (average weight 20.7 ± 1.6 g) were divided into 4 treatment groups and fed a commercial diet (A), a commercial diet + induced colitis by dextran sodium sulfate (DSS) (B), Inonotus obliquus (IO) administration (C), and IO administration + induced colitis by DSS (D). IO treatment (C, D) decreased the expression of tumor necrosis factor (TNF)-α and signal transducers and activators of transcription (STAT)1 compared to those of the colitis induced group (B). The expressions of IL-4 and STAT6 were decreased in group D compared to the colitis induced group (B). The serum immunoglobulin (Ig)E level decreased in IO treatment groups (C, D) compared to no IO treatment groups (A and B) although there was no significant difference between the IO treatment groups. Extract from IO itself had a weak cytotoxic effect on murine macrophage cell line (RAW264.7 cells). Extract from IO inhibited lipopolysaccharide- (LPS-) induced, TNF-α, STAT1, pSTAT1, STAT6, and pSTAT6 production in RAW264.7 cells