ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

<p>Abstract</p> <p>Background</p> <p>Structural variations (SVs) change the structure of the genome and are therefore the causes of various diseases. Next-generation sequencing allows us to obtain a multitude of sequence data, some of which can be used to infer the position of SVs.</p> <p>Methods</p> <p>We developed a new method and implementation named ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome. For comparison, we selected BreakDancer, CNVnator and Pindel, each of which adopts a different approach to detect SVs, e.g. discordant pair approach, depth of coverage approach and split read approach, respectively.</p> <p>Results</p> <p>Our method outperformed BreakDancer and CNVnator in both discovering rate and call accuracy in any type of SV. Pindel offered a similar performance as our method, but our method crucially outperformed for detecting small duplications. From our experiments, ClipCrop infer reliable SVs for the data set with more than 50 bases read lengths and 20x depth of coverage, both of which are reasonable values in current NGS data set.</p> <p>Conclusions</p> <p>ClipCrop can detect SVs with higher discovering rate and call accuracy than any other tool in our simulation data set.</p

Patterns of Consensus Building in Research Meetings for Elementary-School Physical Education Teachers: Focusing on Problem Solving Situations

本研究の目的は，小学校の体育研究主任研究会において課題分析をする際に，教師がどのような合意形成パターンを取りながらコミュニケーションしていくのかを明らかにすることである．「コンセンサス」と「アコモデーション」という2つの「合意形成」概念を視点に会話分析した結果，6個の合意形成パターンを抽出することができた．「コンセンサス」をめぐる合意形成では，「単語の共有」，「言い換えによる納得」が抽出され，「アコモデーション」をめぐる合意形成では，「実体験への共感」，「概念をめぐる差異の許容」，「つぶやきの強化」，「視点の転換」が抽出された．これらの概念を合意される内容（「コンセンサス」，「アコモデーション」）を縦軸，話題への参加構造（「単線的」，「複線的」）を横軸にとる合意形成パターン構造に整理した．このことにより，教員研修内の発話がどのようになされているのかを認識する枠組みを提示することができた．The purpose of this study is to elucidate the kinds of patterns of consensus building employed by teachers in communication during analysis of issues in physical education classes conducted in research meetings for elementary-school physical education teachers. Grounded in the perspective of social constructivism, which holds that people’ s understandings are determined by consensus achieved through dialogue, conversational analysis was conducted regarding group discussions conducted during research meetings for elementary-school physical education teachers, employing as analytical perspectives the two consensusbuilding concepts of consensus and accommodation. From the results of analysis, six concepts could be identified from teachers’ patterns of consensus building. Patterns of communication identified with regard to consensus were sharing of terminology and assent through rephrasing, while patterns of communication identified with regard to accommodation were sharing of real-world experiences with humor, tolerance of differences regarding abstract concepts, emphasis by grumbling, and diversion of perspectives through rephrasing questions. Furthermore, these concepts were plotted in four quadrants along two axes, with the results of agreement (consensus, accommodation) on the vertical axis and the structures of participation in dialogue (unilinear, multilinear) on the horizontal axis. This suggested possibilities for use in facilitation of groupwork in teacher training

Assessment of Neutrophil Functional Activity following Prolonged Endurance Exercise

ntroduction: Neutrophils not only play an important role in host defense by migrating to the site of infection and producing reactive oxygen species (RO S), but also mediate pathological process in inflammatory tissue damage. Therefore, it is import ant not only to assess but also modulate neutrophil activities for disease prevention. We hav e reported that exhaustive exercise causes neutrophil priming (Suzuki et al. J. Appl. Physiol. , 81, 1213-1222, 1996) which might be associated wi th muscle damage (Suzuki et al. J. Appl. Physiol. , 87, 1360-1367, 1999), but antioxidant capacity is also activated following exercise (Suzuki et al. Med. Sci. Sports Exerc. , 35, 348-355, 2003). In the present study, we examined the effects of endurance exercis e on neutrophil activation in relation with muscle damage (Sugama et al. EIR , 18, 115-126, 2012) and report the ex vivo findings based on a newly- developed neutrophil activity measurement system (S uzuki et al. Anticancer Res, 32, 2369-2376, 2012). Methods: Fourteen male triathletes participated in a duathlo n race consisted of 5 km of running, 40 km of cycling and 5 km of running. Venous blood sam ples were collected before, immediately after, 1.5 h and 3 h after the race. A mixture of blood an d luminol was layered on hydrogel (Mebiol Co., Kanagawa, Japan) in each tube and incubated for 60 min. The cell counts in the hydrogel were quantified as the migratory activity of neutrophils , whereas the ROS production was measured by luminol-dependent chemiluminescence. Serum concentr ation of myoglobin (Mb) as a marker of muscle damage and plasma reactive oxygen metabolite s (d-ROMs) as a marker of oxidative stress were also measured. Results: The migratory activity of neutrophils was significa ntly elevated immediately after exercise, further increased 1.5 h, and slightly decreased but remained significantly elevated 3 h after the race . ROS production of neutrophils was significantly ele vated 3 h after the race. Serum Mb concentration increased significantly after exercise and correlat ed positively with the migratory activity of neutrophils, suggesting that neutrophils could infi ltrate into the injured muscle. On the other hand, plasma d-ROMs tended to correlate with ROS producti on, indicating that exercise-induced oxidative stress can be explained at least in part by the ROS production from neutrophils. Conclusions: This new method for measuring neutrophil activitie s can be applied not only for assessing the status of inflammation and oxidative stress in exhaustive exercise, but also as a method for evaluating the efficacy of antioxidant and anti -inflammatory substances for reducing muscle damage

Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome.

Somatic mutations in the spliceosome gene ZRSR2-located on the X chromosome-are associated with myelodysplastic syndrome (MDS). ZRSR2 is involved in the recognition of 3'-splice site during the early stages of spliceosome assembly; however, its precise role in RNA splicing has remained unclear. Here we characterize ZRSR2 as an essential component of the minor spliceosome (U12 dependent) assembly. shRNA-mediated knockdown of ZRSR2 leads to impaired splicing of the U12-type introns and RNA-sequencing of MDS bone marrow reveals that loss of ZRSR2 activity causes increased mis-splicing. These splicing defects involve retention of the U12-type introns, while splicing of the U2-type introns remain mostly unaffected. ZRSR2-deficient cells also exhibit reduced proliferation potential and distinct alterations in myeloid and erythroid differentiation in vitro. These data identify a specific role for ZRSR2 in RNA splicing and highlight dysregulated splicing of U12-type introns as a characteristic feature of ZRSR2 mutations in MDS

Changes in Anterior Segment Morphology of Iris Bombe before and after Laser Peripheral Iridotomy in Patients with Uveitic Secondary Glaucoma

Purpose. To quantify changes in anterior segment (AS) parameters after laser peripheral iridotomy (LPI) using AS-optical coherence tomography (OCT) of iris bombe. Method. AS images of eight eyes were captured before and after iris bombe and more than 2 weeks after LPI (post-LPI) using AS-OCT. We compared the following AS parameters: anterior chamber depth (ACD), anterior chamber volume (ACV), iris curvature (IC), iris thickness at 500 μm from the scleral spur (IT-1) in the middle between the iris root and pupillary margin (IT-2) and 500 μm from the pupillary margin (IT-3) to the anterior chamber angle (ACA) (angle opening distance [AOD750]), and trabecular iris space area. Results. Mean IT-1 and IT-3, but not IT-2, were lower after iris bombe (IT-1, P=0.001; IT-2, P=0.081; and IT-3, P=0.001). There were no significant differences between ACD at pre-LPI and before iris bombe (P=0.096). The mean ACV and AOD750 of iris bombe increased at post-LPI (ACV, P<0.01, and AOD750, P<0.05). The mean IT-1, IT-2, and IT-3 increased at post-LPI (all, P≤0.01). IC decreased at post-LPI (P<0.001), and ACD at post-LPI did not change. Conclusions. The iris extends and becomes thinner during iris bombe. LPI during bombe decreases the IC and increases the ACV and ACA