Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on k-mers from short reads and detects polymorphic edges with k-mers for which there is no match between target and control, making it possible to detect SNPs by direct comparison of short-reads in two datasets (target and control) without a reference genome sequence. The second method is based on bidirectional alignment to detect polymorphic edges, not only SNPs but also insertions, deletions, inversions and translocations. Using these two methods, we succeed in making a high-quality comparison map between rice cultivars showing good match to the theoretical value of introgression, and in detecting specific large deletions across cultivars.Using Polymorphic Edge Detection (PED), the k-mer method is able to detect SNPs by direct comparison of short-reads in two datasets without genomic alignment step, and the bidirectional alignment method is able to detect SNPs and structural variations from even single-end short-reads. The PED is an efficient tool to obtain accurate data for both SNPs and structural variations.The PED software is available at: https://github.com/akiomiyao/ped .
We report a case of pseudomigraine with pleocytosis (PMP) characterized by temporary neurological deficits and elevated cell counts in cerebrospinal fluid (CSF). A 28-year-old woman was admitted to our hospital with a second episode of right side throbbing headache accompanied by hemianopsia without scintillating scotoma of left side, hand numbness and weakness of left hand. Two months before the admission, she experienced a first identical episode, which lasted several hours. On admission to our hospital, neurological examination showed left hemianopsia, mild left hemiparesis, dysesthesia of left hand, exceeded tendon reflex of left upper limb, stiff-neck and positive Kerning's sign. CSF examination showed mild elevation of mononuclear cell counts. No abnormal findings on brain CT and MRI (including diffusion weighted image) were observed. 99mTc-HMPAO single photon emission computed tomography (SPECT) demonstrated extensive hypoperfusion at right cerebral hemisphere, corresponding to her neurological deficits. Her electroencephalography (EEG) showed reduced amplitude on the right occipital area. The reduced amplitude of cortical component of somatosensory evoked potential (SEP) by left median nerve stimulation were observed. On the third day after the admission, her symptoms improved and cell count of CSF was normalized. One week after the onset her SEP, EEG and SPECT were normalized on their retrials. She has never recurred these symptoms. We established a diagnosed of psedomigraine with pleocytosis as the first Japanese case.
Positional MEDLINE (PosMed; http://biolod.org/PosMed) is a powerful Semantic Web Association Study engine that ranks biomedical resources such as genes, metabolites, diseases and drugs, based on the statistical significance of associations between user-specified phenotypic keywords and resources connected directly or inferentially through a Semantic Web of biological databases such as MEDLINE, OMIM, pathways, co-expressions, molecular interactions and ontology terms. Since 2005, PosMed has long been used for in silico positional cloning studies to infer candidate disease-responsible genes existing within chromosomal intervals. PosMed is redesigned as a workbench to discover possible functional interpretations for numerous genetic variants found from exome sequencing of human disease samples. We also show that the association search engine enhances the value of mouse bioresources because most knockout mouse resources have no phenotypic annotation, but can be associated inferentially to phenotypes via genes and biomedical documents. For this purpose, we established text-mining rules to the biomedical documents by careful human curation work, and created a huge amount of correct linking between genes and documents. PosMed associates any phenotypic keyword to mouse resources with 20 public databases and four original data sets as of May 2013.
Background: Gastric cancer requiring lymph node dissection is not often approached laparoscopically because of the surgical difficulty. However, in cases of gastric submucosal tumor, such as gastroin-testinal stromal tumor (GIST), lymph node dissection is not usually necessary. Local resection is generally sufficient, and GIST, then, is a good indication for reduced-port surgery (RPS). We describe RPS performed through two ports—one in the umbilicus and one in the left epigastric region. Two devices have been developed for this procedure: the free jaw (FJ) clip, which is used to grasp organs in the abdominal cavity, and the free loop plus, which is used pull suture threads from inside the abdominal cavity to outside the body. We have used the new devices with good outcomes in 11 patients undergoing resection of GIST. We describe the new devices, their use in RPS for GIST, and the case outcomes.
Methods: The FJ clip is a short clip designed to assist with organ elevation. The clip comes in two sizes, one for use in a 5-mm port and the other for use in a 12-mm port, and in two lengths, 29.4 and 35.6 mm, respectively. Both clips are made of stainless steel, and they can be easily maneuvered with commonly-used laparoscopy forceps. The clips have a powerful grasping force (200±20 and 300±30 gf, respectively) but cause no or only negligible organ damage. The jaw surface is textured in a lattice-like relief to resist slippage. The free loop plus is used to puncture the abdominal wall and pull suture threads from inside the abdominal cavity to outside the body. It is fitted with a φ 0.1-mm NiTi alloy suture thread that passes through a 90-mm 21 G stainless steel needle. Generally, the device is attached to the FJ clip and used to guide the traction suture to outside the body.
Results: In the 11 cases noted above, mean operation time was 156 minutes (78–287 minutes). The blood loss volume was ≤30 g per patient and so low in 8 patients that it could not be measured. In all 11 patients, the surgery was performed via two ports, one in the umbilicus and the other in the left epigastric region. Laparoscopic endoscopic cooperative surgery was performed in 4 of the 11 patients. There were no intraoperative or postoperative complications, and the mean postoperative hospital stay was 9.9 days (range, 8–11 days).
Conclusions: Our success with the devices leads us to believe that the FJ clip will assume the role of forceps in many laparoscopic surgery settings in fields such as obstetrics and gynecology and urology. We are also led to believe that the FJ clip will pave the way for new developments in RPS.
The periodic maintenance method is well known as one of the best methods in the preventive maintenance. Its properties in the strictly periodic maintenance have been studied theoretically, but the case where there is randomness in the periodic maintenance interval has never been investigated so far. On the other hand, the field maintenance data have suggested us difficulties of keeping the interval of periodic maintenance strictly.Therefore, this paper deals with the characteristics of the MTBF (Mean Time Between Failures) under the periodic maintenance with random interval. First we choose a Weibull distribution as the reliability function of the items and next set up the maintenance model which exists the random interval in the periodic maintenance. Under these conditions, we investigate how the randomness of the maintenance interval effects on the MTBF of the items from the theoretical viewpoints. Finally, we show the usefulness on the basis of results obtained here.
