GBParsy: A GenBank flatfile parser library with high speed

<p>Abstract</p> <p>Background</p> <p>GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory.</p> <p>Results</p> <p>We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5 - 100× faster than current parsers in benchmark tests.</p> <p>Conclusion</p> <p>GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.</p

Single-stage C6-7 ACDF with T1-2 Oblique Keyhole Transcorporeal Disectomy to Treat Cervico-thoracic Tandem Disc Herniation: A Case Report

Symptomatic cervico-thoracic tandem disc herniation occurs very rarely. On the other hand, cervical disc herniations are common and may be treated via a variety of surgical procedures. Symptomatic upper thoracic disc herniations are extremely rare, and use of a surgical approach in their treatment is controversial due to the narrow operative space within which surgical procedures must be performed. We report an extremely rare case of symptomatic tandem C6-7 and T1-2 disc herniation successfully treated via single-stage, single-incision, C6-7 anterior cervical decompression and fusion, and T1-2 oblique keyhole transcorporeal discectomy. This is the first symptomatic cervico-thoracic tandem disc herniation with its treatment

The Effects of Aerobic Exercise Training on Blood Lipid Profiles, Fibrinolytic Activities, and Nitric Oxide Levels in High-fat-diet induced Rats

Although exercise training has been utilized to improve vascular function in animals and humans, the impact of moderate intensity exercise training on fibrinolytic activities and nitric oxide (NO) bioavailability has not been well documented. Therefore, the purpose of the current study was to examine the impact of moderate intensity aerobic exercise training on fat mass, blood lipid profiles, fibrinolytic activity, and NO levels in high-fat-diet induced rats. The body weight, fat mass, blood lipid profiles, fibrinolytic activity, and nitrite/nitrate were measured pre- and postexercise (10 weeks) training. The body weight and fat mass reduced significantly in the exercise (EX) group compared to the control (CON) group. Blood lipid profiles and low-density lipoprotein were unchanged in the EX group compared to the CON group. However, triglyceride and free fatty acid were significantly lower in the EX group compared to the CON group, and high-density lipoprotein was significantly greater in the EX group compared to the CON group. In addition, fibrinolytic activity and nitrite/nitrate were significantly greater in the EX compared to the CON group. These results suggest that 10 weeks of the moderated intensity aerobic exercise training improves blood lipid profiles, fibrinolytic activity, and the nitrite/nitrate ratio, which may improve vascular health and reduce obesity-related cardiovascular disease risks in high-fat- diet induced rats

Large Cell Neuroendocrine Carcinoma of the Thymus: A Two-Case Report

A large cell neuroendocrine carcinoma (LCNEC) of the thymus is a very rare malignant tumor that has a very poor prognosis. The detailed clinical features of LCNEC are still unknown, including the long term prognoses and the definitive modalities of the treatment for LCNEC of the thymus. We are reporting 2 cases of an enlarged LCNEC of the thymus, both of which were diagnosed and treated by surgical resection followed by postoperative adjuvant chemoradiation therapy. Although recurrences and metastases of the LCNEC were noticed 1 and 4 years postoperatively for each case, aggressive surgical resection and adjuvant chemoradiation therapy may be helpful for a patient's long term survival

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

<p>Abstract</p> <p>Background</p> <p>The interaction between a transcription factor and DNA motif (<it>cis</it>-acting element) is an important regulatory step in gene regulation. Comprehensive genome-wide methods have been developed to characterize protein-DNA interactions. Recently, the universal protein binding microarray (PBM) was introduced to determine if a DNA motif interacts with proteins in a genome-wide manner.</p> <p>Results</p> <p>We facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the <it>cis</it>-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified <it>cis</it>-acting element of the OsNAC6 rice transcription factor.</p> <p>Conclusion</p> <p>Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.</p

Unilateral Biportal Endoscopic Translaminar Keyhole Approach to Treat High-grade Up-migrated Lumbar Disc Herniation: Technical Note

The incidence of lumbar disc fragment migration is approximately 35%–72% of which 34% are high-grade up-migrated discs. Translaminar keyhole approach is a minimally invasive and true tissue sparing technique which has been applied to approach migrated disc herniation. The unilateral biportal endoscopic approach is an emerging technique among endoscopic spine surgery that combines the advantages of microscopic surgery with endoscopic surgery. In this technical report we demonstrate the surgical technique of performing the translaminar keyhole approach with unilateral biportal endoscopic spine surgery to treat high-grade up-migrated discs. As far as we know, this is the first technical report of unilateral biportal endoscopy with translaminar keyhole approach to treat high-grade up migrated lumbar disc herniation