Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/

自閉症スペクトラム障害児の症状特性と日中活動，及び夜間睡眠の関係

研究報告Original Articles　［目的］自閉症スペクトラム障害（Autism Spectrum Disorders：ASD）は，社会参加に関する発達障害であるコミュニケーションの障害，パターン化した興味や活動，感覚の偏りという特徴を持っている．本研究の目的は学童期におけるASD 児の症状特性と日中活動，夜間睡眠の関係性を分析し，生活指導時の考慮すべき要因を検討することとした．［方法］ASD と診断された通院中の学童期男児14 例を対象とし，広汎性発達障害の重症度の評価として広汎性発達障害日本自閉症協会評定尺度，感覚過敏性の評価として日本感覚インベントリー，日中活動量，夜間睡眠の評価として3 軸加速度計を用いた身体活動量計測を行った．［結果］対象児に夜間睡眠の質低下が認められ，感覚過敏性と夜間睡眠時の中途覚醒の間に正の相関関係が認められた．また，夜間覚醒時間と日中活動時間の間に負の相関関係が認められた．［結論］ASD 児における感覚過敏性の特性や日中活動時間の短縮が，睡眠の質の低下に影響していることが示唆された．そのため，ASD 児の睡眠の質向上に向けた生活指導時には，各個人の感覚刺激の特性を考慮する必要性が示唆された．　［Background］Autism spectrum disorders (ASD) is characterized by failure of communication is a developmental disorder related to social participation, interests and activities patterned, bias of the senses.　［Purpose］The purpose of this study during the day and symptoms characteristic, the night sleep to analyze the relationship of ASD children in school age activities, it was decided to examine the factors to be taken into account at the time of lifestyle guidance.　［Method］ School-age boys 14 cases (The average 9 year-old and 9 months, IQ 90.3 ± 10.9 points) participated in this study. Intended for school-age boys 14 cases in the diagnosis have been visits to the ASD assessment of pervasive developmental disorder Autism Society Japan rating scale (PARS), Japan sensation inventory (JSI-R), Actigraph.　［Result］The result is a decrease in the quality of sleep, it was recognized positive correlation to feeling irritable and nighttime of wake after sleep onset, negative correlation at night waking time and daytime activity time.　［Conclusion］In other words, the approach according to each individualʼs characteristics due to sensory evaluation of ASD children were contribute to the improvement of nighttime sleep. Therefore, as a factor to be considered at the time of lifestyle guidance, given the approach of the extension and the sensory stimulation of daytime activity time, as they improve the quality of sleep of ASD children become a cranial nerve development

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

ジョウ チョウキュウ ニホンゴ ガクシュウシャ ニオケル ハツワブンセキ ハツワ ナイヨウ リョウイキ トノ カカワリ カラ

本研究は、上・超級日本語学習者の発話の特徴を明らかにすることを目指し、ACTFL (全米外国語教育協会)から日本語の OPI テスト(口頭面接テスト)のテスター認定を受けた試験官が行なったものである。OPI テストの録音テープから、超級、上級の上・中・下の各々の典型的なものを選んで分析対象とし、母語話者とも比較した。まず、話題の種類と述べ方から発話内容領域という概念を設け、それを3つの領域---I.身近な具体的事実を直接的に言う、II.個人的一般的関心事の具体的事実を詳述する、III.抽象的内容を論じる--- に分けた。各被験者の発話について、この発話内容領域を軸として、試験官の要求への対応・発話の構成・談話の形・文法能力(語彙の広がり、誤用、言い直し、接続表現)を分析した結果、上・超級話者の各レベルの発話の特徴を具体的に示した。また、上級から超級への移行の過程が明らかになった。全分析項目において、なだらかな発達がみられるわけではなく、発話の構成・抽象的表現の使用・言い直し・接続表現・誤用などの項目では、上級と超級で大きい違いがみられた。また、発話内容領域によっても、レベル差が大きく現れる項目が異なっていた。これらの結果から、いくつかの分析項目では、ACTFL-OPI の基準で示されているレベル変化とは異なる、大きく変化する段階があることも分かった。さらに今回行なった母語話者との比較から、超級話者のほうが母語話者より論理的に話したり、和語を多く使用することが認められた。This research was conducted by a group of Japanese-language Oral Proficiency Interview (OPI) testers certified by the American Council on the Teaching of Foreign Languages (ACTFL). The purpose of the research is to clarify major characteristics of advanced- and superior-level non-native speakers. This research began by selecting tapes that represent typical lower advanced, middle advanced, upper advanced, and superior speech for detailed analysis. Tapes of Japanese native speakers were also selected and included for comparison. This article first categorizes the topics or themes of conversation into three fields: (1) predictable, familiar topics; (2) topics of personal general interest; and (3) wide range of general-interest topics. Second, in relation to these categorized content fields, this research explains the discourse structure, the rate of success in structuring an extended discourse and a paragraph, the variety of conjunctions, kango, and wago used,idiomatic expressions and onomatopoeic words used, and the number and the types of self-corrections. The result of this research shows a clear picture of major characteristics of advanced and superior-level speakers. It also suggests the feature of the progress from advanced to superior levels. Distinct difference was observed between advanced and superior level speakers in discourse structure, usage of abstract expressions, self-corrections, usage of conjunctions, and grammatical mistakes. In case of accomplishments of the tasks and the text types in treating the second field theme, clear difference was observed between advanced-low and advanced-mid speakers. Whereas in case of the text types in treating the third field theme, there was a clear distinction between advanced-mid and advanced-high speakers. The above results suggest the existence of some other levels than the one described in OPI criteria

Treatment strategy changes for inflammatory bowel diseases in biologic era: results from a multicenter cohort in Japan, Far East 1000

Abstract Many molecular targeted agents, including biologics, have emerged for inflammatory bowel diseases (IBD), but their high prices have prevented their widespread use. This study aimed to reveal the changes in patient characteristics and the therapeutic strategies of IBD before and after the implementation of biologics in Japan, where the unique health insurance system allows patients with IBD and physicians to select drugs with minimum patient expenses. The analysis was performed using a prospective cohort, including IBD expert and nonexpert hospitals in Japan. In this study, patients were classified into two groups according to the year of diagnosis based on infliximab implementation as the prebiologic and biologic era groups. The characteristics of therapeutic strategies in both groups were evaluated using association analysis. This study analyzed 542 ulcerative colitis (UC) and 186 Crohn’s disease (CD). The biologic era included 53.3% of patients with UC and 76.2% with CD, respectively. The age of UC (33.9 years vs. 38.8 years, P < 0.001) or CD diagnosis (24.3 years vs. 31.9 years, P < 0.001) was significantly higher in the biologic era group. The association analysis of patients with multiple drug usage histories revealed that patients in the prebiologic era group selected anti-tumor necrosis factor (TNF)-α agents, whereas those in the biologic era group preferred biologic agents with different mechanisms other than anti-TNF-α. In conclusion, this study demonstrated that both patient characteristics and treatment preferences in IBD have changed before and after biologic implementation