Multi-quark baryons and color screening at finite temperature

We study baryons in SU(N) gauge theories at finite temperature according to the gauge/string correspondence based on IIB string theory. The baryon is constructed out of D5 brane and $N$ fundamental strings to form a color singlet $N$-quark bound state. At finite temperature and in the deconfining phase, we could find $k(<N)$-quark ``baryons''. Thermal properties of such $k$-quark baryons and also of the $N$-quark baryon are examined. We study the temperature dependence of color screening distance and Debye length of the baryon of $k$-quark and $N$-quark. We also estimate the melting temperature, where the baryons decay into quarks and gluons completely.Comment: 16 pages, 12 figure

Whole-exome sequencing of fibroblast and its iPS cell lines derived from a patient diagnosed with xeroderma pigmentosum

AbstractCells from a patient with a DNA repair-deficiency disorder are anticipated to bear a large number of somatic mutations. Because such mutations occur independently in each cell, there is a high degree of mosaicism in patients' tissues. While major mutations that have been expanded in many cognate cells are readily detected by sequencing, minor ones are overlaid with a large depth of non-mutated alleles and are not detected. However, cell cloning enables us to observe such cryptic mutations as well as major mutations. In the present study, we focused on a fibroblastic cell line that is derived from a patient diagnosed with xeroderma pigmentosum (XP), which is an autosomal recessive disorder caused by a deficiency in nucleotide excision repair. By making a list of somatic mutations, we can expect to see a characteristic pattern of mutations caused by the hereditary disorder. We cloned a cell by generating an iPS cell line and performed a whole-exome sequencing analysis of the progenitor and its iPS cell lines. Unexpectedly, we failed to find causal mutations in the XP-related genes, but we identified many other mutations including homozygous deletion of GSTM1 and GSTT1. In addition, we found that the long arm of chromosome 9 formed uniparental disomy in the iPS cell line, which was also confirmed by a structural mutation analysis using a SNP array. Type and number of somatic mutations were different from those observed in XP patients. Taken together, we conclude that the patient might be affected by a different type of the disorder and that some of the mutations that we identified here may be responsible for exhibiting the phenotype. Sequencing and SNP-array data have been submitted to SRA and GEO under accession numbers SRP059858 and GSE55520, respectively

Logical Operation Based Literature Association with Genes and its application, PosMed.

PosMed prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses an inferential process similar to an artificial neural network comprising documental neurons (or &#x27;documentrons&#x27;) that represent each document contained in databases such as MEDLINE and OMIM (Yoshida, _et al_. 2009, Makita, _et al_. 2009). PosMed immediately ranks the candidate genes by connecting phenotypic keywords to the genes through connections representing gene&#x2013;gene interactions other biological relationships, such as metabolite&#x2013;gene, mutant mouse&#x2013;gene, drug&#x2013;gene, disease&#x2013;gene, and protein&#x2013;protein interactions, ortholog data, and gene&#x2013;literature connections.&#xd;&#xa;&#xd;&#xa;To make proper relationships between genes and literature, we manually curate queries, which are defined by logical operation rules, against MEDLINE. For example, to detect a set of MEDLINE documents for the AT1G03880 gene in _A. thaliana_, we applied the following logical query: (&#x2018;AT1G03880&#x2019; OR &#x2018;CRU2&#x2019; OR &#x2018;CRB&#x2019; OR &#x2018;CRUCIFERIN 2&#x27; OR &#x2018;CRUCIFERIN B&#x2019;) AND (&#x2018;Arabidopsis&#x2019;) NOT (&#x2018;chloroplast RNA binding&#x2019;). Curators refined these queries in mouse, rice and _A. thaliana_. For human and rat genes, we use mouse curation results via ortholog genes in PosMed.&#xd;&#xa;&#xd;&#xa;PosMed is available at &#x22;http://omicspace.riken.jp/PosMed&#x22;:http://omicspace.riken.jp/PosMed&#xd;&#xa;&#xd;&#xa;References:&#xd;&#xa;Yoshida Y, et al. _Nucleic Acids Res_. 37(Web Server issue):W147-52. 2009. &#xd;&#xa;Makita Y, et al. _Plant Cell Physiol_. 2009 Jul;50(7):1249-59.&#xd;&#xa

Providing Advanced Explanation Capability in ITS for Object Understanding Support: Explanation Structure Model: EXSEL

本論文では，人間によって設計された電気回路などの対象の理解支援を取り上げ，ITSにおける説明による教育的支援の高度化について検討する．一般に，一つの対象はさまざまに説明することができる．その対象の理解を説明によって教育的に支援する場合，対象領域内で設定されるいくつかの支援目的に応じてさまざまな説明を使い分ける機能が，支援の高度化に重要である．このような機能を有するITSを設計・開発するためには，（1）支援目的に基づく説明の整理，（2）整理した説明を可能とする説明機能の開発，を行うことが必要である．本論文では，電気回路のように構造，振舞い，機能（目的）の三つのレベルでとらえることができる対象を題材として，対象モデルおよび視点の概念を導入し，支援目的である対象理解を定式化することによって対象に関する説明を整理する．また，整理した説明を可能とする説明機能のためのモデル，EXSEL（EXplanation Structure modEL）を提案する．EXSELは，説明の資源となる説明構造を生成するモデルであり，ITSに用いることを前提として設計されている．EXSELに対して学生の理解状態などを考慮した運用機構を付与することによって，説明による高度な教育的支援を可能とするITSを構築することができる

Load-Oriented Tutoring to Enhance Student's Explanation Understanding: An Explanation Planner and a Self-explanation Envitonment

This paper discusses the design of an ITS to realize a load-oriented tutoring to enhance the student's explanation understanding. In the explanation understanding, it is to be hoped that a student not only memorizes the new information from an explanation, but also relates the acquired information with his/her own knowledge to recognize what it means. This relating process can be viewed as the one in which the student structures his/her knowledge with the explanation. In our ITS, we regard the knowledge-structuring activities as the explanation understanding. In this paper, we propose an explanation, called a load-oriented explanation, with the intention of applying a load to the student's knowledge-structuring activities purposefully. If the proper load is applied, the explanation can induce the student to think by himself/herself. Therefore he/she will have a chance of gaining the deeper understanding. The important point toward the load-oriented explanation generation is to control the load heaviness appropriately, which a student will bear in understanding the explanation. This requires to estimate how an explanation promotes the understanding activities and how much the load is applied to the activities. In order to provide ITS with the estimation, we have built an Explanation Effect Model, EEM for short. Our ITS consists of an explanation planner and a self-explanation environment. The planner generates the load-oriented explanation based on EEM. The system also makes a student explain the explanation understanding process to himself/herself. Such self-explanation is useful to let the student be conscious of the necessity of structuring his/her knowledge with the explanation. The self-explanation environment supports the student's self-explanation. Furthermore, if the student reaches an impasse in self-explaining, the planner can generate the supporting explanation for the impasse.This research is supported in part by Grant-in-Aid for Scientific Research No. 05780163 from the Ministry of Education, Science and Culture of Japan

A Tutoring for Behavior-Based Recursive Programming

プログラミングを行うためには,プログラムは少なくとも,プログラムの動作について明確に理解しておく必要がある.しかしながら初心者の場合プログラムの個々の命令の振舞いを理解できても,プログラム全体の動作を正しく理解できなかったり,プログラム仕様から動作を想定できない場合がよく見られる.このような初心者を対象とする場合,動作とプログラムコード,動作とプログラム仕様の対応関係について説明することが重要となる.本論文では動作の理解が特に難しい再帰プログラムを対象に,プログラムの動作を介したプログラミングを支援する知的教育システムについて述べる.筆者らは再帰プログラミングのモデルを想定した上で,学習者にとって理解が容易となるようにプログラムの動作を表現し,これをプログラムの振舞いと呼んでいる.本論文ではこの振舞い表現を用いて,再帰プログラムの設計過程および理解過程を支援する方法について論じる.特に,雛形を用いた解法による設計過程の支援ならびに,振舞い表現の可視化による理解過程の支援について述べる.更に振舞い表現の評価実験についても述べる

Development of Support Facilities for Exercising Arithmetical Word Problems in ITS

算数の文章題の問題解決においては，解法を同定するまでの過程が最も重要となる．従って，問題解決，問題生成，問題解説といったITSにおける問題演習支援のための基本機能を，解法の同定に関する支援を指向して設計・開発する必要がある．本論文では，問題解決モデルMIPSに基づいてこれら三つの基本機能をそれぞれ実現した．問題解決モジュール，問題生成モジュール，問題解説モジュール，について述べた．問題解決モジュールは，算数の文章題を解けるだけでなく，解法の同定過程に関する記述を生成することができる．また，問題生成モジュールは，解法の同定過程に関する指定に応じた問題を生成することができる．更に，問題解説モジュールは，解法の同定の支援を目的として，基本的な問題と応用問題の解法の同定に関する等価性を指摘する問題解説を生成することができる