The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

<p>Abstract</p> <p>Background</p> <p>The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009.</p> <p>Results</p> <p>Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs.</p> <p>Conclusions</p> <p>Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.</p

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

切迫性ならびに腹圧性尿失禁に対するプロビベリンの臨床効果に関する検討

プロピベリン(20mg/日, 28日間)の臨床効果を49名の患者を対象に多施設協同研究で調査した.排尿回数の中等度以上の改善を切迫性及び腹圧性尿失禁で52%及び54%の患者で達成出来た.尿意切迫感はそれぞれ91%及び58%の症例で改善した.尿失禁はそれぞれ97%及び71%の症例で改善した.日常生活の制限はそれぞれ94%及び64%の症例で改善が見られた.軽度の副作用を5名に, 臨床検査値の変動を2名に認めたThe efficacy and tolerability of propiverine hydrochloride (20 mg/day) were evaluated in the treatment of a total of 49 Japanese patients (35 with urge incontinence and 14 with stress incontinence) in an open multicenter trial lasting 28 days. The effects on the frequency of urination, urinary incontinence, urinary urgency, and daily living activities were evaluated through the voiding diaries filled out by the patients. Moderate or greater degree of improvement was attained in micturition frequency by 52 and 54% of the patients with urge incontinence and with stress incontinence, respectively, in urinary urgency by 91 and 58%, in urinary incontinence by 97 and 71%, and in daily living activities by 94 and 64%. Although minor adverse reactions (5 patients) and abnormal values in blood chemistry (2 patients) were recorded in 7 patients, all of these patients completed the trial. These results suggest that propiverine hydrochloride is a safe and effective drug of choice for the treatment of not only urge incontinence but also stress incontinence in patients diagnosed in a clinical setting

Efficacy of Combining Flexible and Rigid Ureteroscopy for Transurethral Lithotripsy

Transurethral lithotripsy (TUL) is a common procedure in urology. However, controversy persists about how to deal with stones pushed up into kidney from the ureter during the procedure of TUL. This study investigated the efficacy of combining flexible ureteroscopy and rigid ureteroscopy for pushed-up stones into kidney during TUL. Fotry-one patients underwent TUL by a single surgeon from July 2007 to May 2009. Eight cases resulted in pushed-up stones during operation or involved existing kidney stones. We used a Zero-tipR or Litho Catch BasketR catheter and a flexible ureteroscope to carry these stones in kidney down into the ureter where the rigid ureteroscope could then reach and handle the stone for lithotripsy or being taken away. A LithoclastR system was used for lithotripsy. Five cases involved stones pushed up during surgery and 3 cases involved stones already in the kidney in detail. We pulled the stones down into the ureter in all cases and successfully completed lithotripsy or removed the stone, thus avoiding the performance of additional extracorporeal shock wave lithotripsy (ESWL). In conclusions, combined use of flexible ureteroscopy and rigid ureteroscopy for upper urinary tract stones pushed up into the kidney during TUL or renal stones could be useful for avoiding additional ESWL

遊離回腸を利用した膀胱拡張術後に発生した膀胱腺癌の1例

47歳男子にみられた, 結核性萎縮膀胱に対するU字型遊離回腸移植膀胱拡張術後20年目に同移植回腸上皮より発生したと考えられる膀胱低分化腺癌の1例を報告し, 若干の文献的考察を加えた.This is a report of a case of poorly differentiated adenocarcinoma found 20 years after bladder augmentation ileoplasty. The origin of this tumor was proved to be the ileal part of bladder augmentation. Autopsy revealed metastatic lesions in the stoma (sigmoid conduit), lungs, liver, left femur, adrenal glands and lymph nodes. A review of the literature revealed only one other such case. This is a rare case of adenocarcinoma in the ileal part of bladder augmentation

難治性精巣腫瘍に対する末梢血幹細胞移植併用大量抗癌化学療法時の感染予防に関する検討

The side effects of high-dose anti-cancer drug chemotherapy with peripheral blood stem cell transplantation (PBCST) for the treatment of intractable testicular tumor are very serious. In particular, agranulocytosis in bone marrow suppression may be life threatening. In this study, we examined opportunistic infectious diseases and preventive counter measures in the compromised conditions of anti-cancer drug chemotherapy. The patients underwent anti-cancer drug chemotherapy with PBCST for the treatment of intractable testicular tumors at Kobe University Hospital from September 1996 to September 2002. The high-dose chemotherapy regimen consisted of total doses per course of 1, 250 mg/m2 carboplatin, 1, 500 mg/m2 etoposide, and 7, 500 mg/m2 ifosfamide. Twenty-four men (median age, 30 years; range, 18-70 years) received 50 courses of chemotherapy in total. The nadir of peripheral leukocyte counts was less than 1, 000/mm3 in all courses, and the mean period was for 7.1 days. None of these patients developed critical sepsis leading to disseminated intravascular coagulation or treatment-related death. Our detailed data show that we can perform high-dose anti-cancer drug chemotherapy with PBSCT for intractable testicular tumors without serious infectious complications if we take sufficient preventive countermeasures for infectious diseases.難治性精巣腫瘍に対する末梢血幹細胞移植併用大量抗癌化学療法の副作用はとても重篤である.とくに骨髄抑制における無顆粒球症は時に患者を死に至らしめることもある.今回われわれは抗癌剤投与による免疫力低下状態における日和見感染症とその予防策について検討した.対象は1996年9月から2002年9月までの期間に神戸大学医学部付属病院において難治性精巣腫瘍にて末梢血幹細胞移植併用大量抗癌化学療法を施行した患者である.大量抗癌化学療法のregimenはtotal doseで1コースあたり1, 250mg/m2 carboplatin, 1, 500mg/m2 etoposide, 7, 500mg/m2 ifosfamideを用いた.計24人, のべ50コースの当療法が行われ, 患者の年齢は中間値30歳, 範囲は18歳から70歳であった.全50コースにおいて, 末梢白血球数のnadirは1, 000/mm3以下となり, その平均期間は7.1日間であった.播種性血管内凝固を起こした重篤敗血症症例や治療関連死は認めなかった.当データにより難治性精巣腫瘍に対する末梢血幹細胞移植併用大量抗癌化学療法は十分な感染症に対する予防策がとられれば, 重篤な感染性合併症なく施行しうることが示された(著者抄録