CMap 1.01: a comparative mapping application for the Internet

Summary:CMap is a web-based tool for displaying and comparing maps of any type and from any species. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components

Case Report: Generalized Mutual Information (GMI) Analysis of Sensory Motor Rhythm in a Subject Affected by Facioscapulohumeral Muscular Dystrophy after Ken Ware Treatment

In this case report we study the dynamics of the SMR band in a subject affected from Facioscapulohumeral Muscular Dystrophy and subjected to Ken Ware Neuro Physics treatment. We use the Generalized Mutual Information (GMI) to analyze in detail the SMR band at rest during the treatment. Brain dynamics responds to a chaotic-deterministic regime with a complex behaviour that constantly self-rearranges and self-organizes such dynamics in function of the outside requirements. We demonstrate that the SMR chaotic dynamics responds directly to such regime and that also decreasing in EEG during muscular activity really increases its ability of self-arrangement and self-organization in brain. The proposed novel method of the GMI is arranged by us so that it may be used in several cases of clinical interest. In the case of muscular dystrophy here examined, GMI enables us to quantify with accuracy the improvement that the subject realizes during such treatment

Text-organizing metadiscourse: Tracking changes in rhetorical persuasion

Published academic writing often seems to be an unchanging form of discourse with its frozen informality remaining stable over time. Recent work has shown, however, that these texts are highly interactive and dialogic as writers anticipate and take into account readers' likely objections, background knowledge, rhetorical expectations and processing needs. In this paper, we explore one aspect of these interactions and how it has changed over the past fifty years. Focusing on what has been called interactive metadiscourse (Hyland 2005; Hyland and Tse 2004), or the ways authors organise their material for particular readers, we analyze a corpus of 2.2 million words compiled from articles in the top journals in four disciplines to discover whether, and to what extent, interactive metadiscourse has changed in different disciplines since 1965. The results show a considerable increase in an orientation to the reader over this period, reflecting changes in both research and publication practices

Survivorship and Growth in Staghorn Coral (Acropora cervicornis) Outplanting Projects in the Florida Keys National Marine Sanctuary

Significant population declines in Acropora cervicornis and A. palmata began in the 1970s and now exceed over 90%. The losses were caused by a combination of coral disease and bleaching, with possible contributions from other stressors, including pollution and predation. Reproduction in the wild by fragment regeneration and sexual recruitment is inadequate to offset population declines. Starting in 2007, the Coral Restoration Foundation™ evaluated the feasibility of outplanting A. cervicornis colonies to reefs in the Florida Keys to restore populations at sites where the species was previously abundant. Reported here are the results of 20 coral outplanting projects with each project defined as a cohort of colonies outplanted at the same time and location. Photogrammetric analysis and in situ monitoring (2007 to 2015) measured survivorship, growth, and condition of 2419 colonies. Survivorship was initially high but generally decreased after two years. Survivorship among projects based on colony counts ranged from 4% to 89% for seven cohorts monitored at least five years. Weibull survival models were used to estimate survivorship beyond the duration of the projects and ranged from approximately 0% to over 35% after five years and 0% to 10% after seven years. Growth rate averaged 10 cm/year during the first two years then plateaued in subsequent years. After four years, approximately one-third of surviving colonies were ≥ 50 cm in maximum diameter. Projects used three to sixteen different genotypes and significant differences did not occur in survivorship, condition, or growth. Restoration times for three reefs were calculated based on NOAA Recovery Plan (NRP) metrics (colony abundance and size) and the findings from projects reported here. Results support NRP conclusions that reducing stressors is required before significant population growth and recovery will occur. Until then, outplanting protects against local extinction and helps to maintain genetic diversity in the wild

The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species

The Genetic Diversity module of the Gramene database ("http://www.gramene.org/diversity":http://www.gramene.org/diversity) is specifically designed to handle data from high-throughput sequencing and array-based genotyping plateforms. Empowered by the Genomic Diversity and Phenotype Data Model, Gramene Genetic Diversity module provides live database connectivities of RFLP, SSR and SNP allele data, information about QTL, passport data for wild and cultivated germplasm from rice, maize, wheat, and _Arabidopsis_, and quantitative phenotypic data for some of these accessions. Large datasets of SNP variation are searchable via genomic positions of interest by SNP Query tool on a sequenced genome; and, trait associations, patterns of linkage disequilibrium and diversity can be evaluated using TASSEL. The Gramene database is updated twice a year, with the most recent release (Build #31) completed in May 2010

Classroom Use of Critical Thinking Skills : Student and Teacher Surveys

本稿は,亜細亜大学のフレッシュマン・イングリッシュを受講している1年生351名を対象に,バードと松田によって実施された英語と日本語による授業でのクリティカル・シンキング(CT)の使用に関する調査結果について検討している,アンケートの結果から,学生は日本語の授業よりも英語の授業においてより積極的にCTを使用していることがわかった.ブルームの分類のより高度なレベルのCT活動を行うことについては,学生の反応は消極的になっている.また,単に知識を問う活動よりも内容の理解を問う活動により高い満足度を示している.留学生は,日本人学生よりも頻繁に意見,気持ち,考えを授業で率先して述べたり,教師の期待よりも高いレベルのCT活動に対して積極的な姿勢を示している.これに関しては,留学生の動機付けや本国での教育環境などさまざまな要因が考えられるが,留学生と一緒の授業が,日本人学生にとって異なる文化的価値感や意見を考える機会を与えており,CTを促進する学習環境を提供しているようである

Gramene database in 2010: updates and extensions

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data

Gramene: a bird's eye view of cereal genomes

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, ; USDA 1997, ). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of ∼400 Mbp, has been sequenced and annotated. The Gramene database () takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606–1613], the database has undergone extensive changes that are described in this publication

Gramene: a bird's eye view of cereal genomes

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, ; USDA 1997, ). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of ∼400 Mbp, has been sequenced and annotated. The Gramene database () takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606–1613], the database has undergone extensive changes that are described in this publication

Gramene: a bird's eye view of cereal genomes

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, ; USDA 1997, ). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of ∼400 Mbp, has been sequenced and annotated. The Gramene database () takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606–1613], the database has undergone extensive changes that are described in this publication