487 research outputs found
John Jenkins and \u3ci\u3eThe Art of Writing\u3c/i\u3e: Handwriting and Identity in the Early American Republic
A literary critique of the 1791 and 1813 editions of the American penmanship and handwriting text The Art of Writing, Reduced to a Plain and Easy System, by John Jenkins is presented. It considers aspects of national identity and individual identity, noting Jenkins\u27 concern for national unity in the first edition. The author explores social and economic facets of handwriting, reflecting on gentility, opportunity, and aesthetics
Querying the public databases for sequences using complex keywords contained in the feature lines
BACKGROUND: High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords. RESULTS: We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing of large data files, and we embedded these scripts in a user friendly interface (OS independent) for easy use. CONCLUSION: Although not as fast as the public tools that use prebuilt indexes, parsing the complete entries using a script is often necessary in order to retrieve the exact data searched for. Embedding in a user friendly interface allows biologists to use the scripts, which can easily be modified, if necessary, by bioinformaticians for unforeseen needs
Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci
Background: Cryptosporidium is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, C. parvum and C. hominis are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of Cryptosporidium clinical isolates and reference strains. Results: The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes. Conclusions: Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia
Vigabatrin-Induced Peripheral Visual Field Defects in Patients With Refractory Partial Epilepsy
Purpose:
Vigabatrin can cause retinopathy, resulting in bilateral visual field constriction. Previous analyses of results from a prospective, observational study assessing vigabatrin-induced visual field constriction (described below) employed a partially subjective interpretation of static perimetery. In an effort to affirm these previous findings through more objective, quantitative methodology, we now report data from a subset analysis of refractory partial epilepsy patients in the study who underwent Goldmann kinetic perimetry.
Methods:
Patients aged â„8 years with refractory partial seizures were enrolled and grouped: those receiving vigabatrin for â„6 months (Group I); those who had received vigabatrin for â„6 months and then had discontinued for â„6 months (Group II); and those naĂŻve to vigabatrin (Group III). Patients underwent static or kinetic perimetry or both every 4â6 months for â€3 years. For kinetic perimetry, the temporal and nasal visual fields were measured along the horizontal meridian with the largest (V4e, IV4e) and smallest (I2e, I1e) isopters, respectively.
Results:
Of 735 patients enrolled, 341 had Goldmann perimetry data. Of these, 258 received vigabatrin. Sixteen percent of vigabatrin-exposed patients had moderate visual field defects (30°â60° retained temporal vision), and 3% had severe defects (\u3c30° retained temporal vision). Visual function questionnaire results indicated a weak correlation between visual field constriction severity and visual symptoms.
Conclusions:
These results affirm both an analysis of the same study based primarily on static perimetry and findings from cross-sectional studies. The present analysis verifies that visual field constriction, when it occurs, is most often mild or moderate and is not associated with symptoms of abnormal visual function. The clinical decision to prescribe vigabatrin should be based on a benefit-risk analysis for each individual patient
A catalog of Nearby Poor Clusters of Galaxies
A catalog of 732 optically selected, nearby poor clusters of galaxies
covering the entire sky north of declination is presented. The
poor clusters, called WBL clusters, were identified as concentrations of 3 or
more galaxies with photographic magnitudes brighter than 15.7, possessing a
galaxy surface overdensity of . These criteria are consistent with
those used in the identification of the original Yerkes poor clusters, and this
new catalog substantially increases the sample size of such objects. These poor
clusters cover the entire range of galaxy associations up to and including
Abell clusters, systematically including poor and rich galaxy systems spanning
over three orders of magnitude in the cluster mass function. As a result, this
new catalog contains a greater diversity of richness and structures than other
group catalogs, such as the Hickson or Yerkes catalogs. The information on
individual galaxies includes redshifts and cross-references to other galaxy
catalogs. The entries for the clusters include redshift (where available) and
cross-references to other group and cluster catalogs.Comment: 27 pages, 7 figures, + one 20-page landscape table, accepted for
publication in A
Defining Reference Sequences for Nocardia Species by Similarity and Clustering Analyses of 16S rRNA Gene Sequence Data
The intra- and inter-species genetic diversity of bacteria and the absence of
'reference', or the most representative, sequences of individual species
present a significant challenge for sequence-based identification. The aims of
this study were to determine the utility, and compare the performance of
several clustering and classification algorithms to identify the species of 364
sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences
of 16S rRNA gene with no defined species, all within the genus Nocardia. A
total of 364 16S rRNA gene sequences of Nocardia species were studied. In
addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level
at the time of submission to GenBank were used for machine learning
classification experiments. Different clustering algorithms were compared with
a novel algorithm or the linear mapping (LM) of the distance matrix. Principal
Components Analysis was used for the dimensionality reduction and
visualization. Results: The LM algorithm achieved the highest performance and
classified the set of 364 16S rRNA sequences into 80 clusters, the majority of
which (83.52%) corresponded with the original species. The most representative
16S rRNA sequences for individual Nocardia species have been identified as
'centroids' in respective clusters from which the distances to all other
sequences were minimized; 110 16S rRNA gene sequences with identifications
recorded only at the genus level were classified using machine learning
methods. Simple kNN machine learning demonstrated the highest performance and
classified Nocardia species sequences with an accuracy of 92.7% and a mean
frequency of 0.578
Apport des nouvelles gĂ©nĂ©rations de sĂ©quençage pour accĂ©der Ă la diversitĂ© des communautĂ©s microbiennes du sol : nĂ©cessitĂ© dâun âpipelineâ bio-informatique pour les biologistes
Communication orale, rĂ©sumĂ©La diversitĂ© microbienne dâun sol est difficile Ă caractĂ©riser. Ceci sâexplique par une accessibilitĂ© plus ou moins importante des populations au sein dâune matrice hĂ©tĂ©rogĂšne et structurĂ©e, mais aussi par lâincapacitĂ© Ă rĂ©soudre une information constituĂ©e de 100 000 Ă 1 000 000 dâespĂšces diffĂ©rentes par gramme de sol. Toutefois, rĂ©cemment, dâimportantes avancĂ©es en biologie molĂ©culaire ont permis de mieux caractĂ©riser la diversitĂ© des communautĂ©s microbiennes du sol in situ et ce sans a priori. Ainsi, la puissance des nouvelles gĂ©nĂ©rations de sĂ©quençage comme le pyrosĂ©quençage permettent de travailler en haut-dĂ©bit afin dâobtenir plusieurs dizaines, voire plusieurs centaines de milliers de sĂ©quences Ă partir dâun ADN mĂ©ta-gĂ©nomique. De premiĂšres Ă©tudes ont dĂ©jĂ Ă©tĂ© rĂ©alisĂ©es avec cette technique afin dâaborder la diversitĂ© bactĂ©rienne des sols. Ces Ă©tudes ont, pour la premiĂšre fois, permis de quantifier de façon exhaustive la diversitĂ© microbienne de sols en termes de richesse spĂ©cifique et de dĂ©montrer la pertinence, la faisabilitĂ© et la robustesse de cette approche. Cette approche est maintenant unanimement reconnue pour sa pertinence et ses potentialitĂ©s trĂšs importantes, et ce afin de dĂ©terminer la diversitĂ© des microorganismes telluriques. Notre approche consiste en la caractĂ©risation de la diversitĂ© taxonomique (bactĂ©rienne et fongique) de sols sur des Ă©chantillonnages de grande ampleur dans le temps et dans lâespace, avec comme objectifs : (i) de faire un inventaire exhaustif de la diversitĂ© microbienne tellurique, (ii) dâĂ©valuer sa distribution spatiale, (iii) de mieux comprendre sa rĂ©gulation et, (iv) in fine, de pouvoir relier cette diversitĂ© en fonctionnement biologique du sol et en services Ă©cosystĂ©miques [1-3]. Cependant, lâĂ©tude dâun aussi grand nombre dâĂ©chantillons va entraĂźner la production massive de sĂ©quences. Ce caractĂšre massif, ainsi que les caractĂ©ristiques inhĂ©rentes aux sĂ©quences obtenues par cette technique requiĂšrent le dĂ©veloppement dâoutils bioinformatiques adaptĂ©s, optimisĂ©s et Ă©valuĂ©s, afin dâanalyser rapidement et efficacement ce type de donnĂ©es. Ce nouveau pipeline dâanalyse doit tout dâabord ĂȘtre facile dâutilisation et rĂ©pondre aux attentes des diffĂ©rents utilisateurs, quâils soient compĂ©tents en bio-informatique, ou novices dans lâanalyse de tels jeux de donnĂ©es. Il doit Ă©galement permettre de gĂ©rer un grand nombre de sĂ©quences et dâautomatiser les grandes Ă©tapes dâanalyse (prĂ©traitement, filtration, clustĂ©risation, assignation taxonomique, calculs dâindices dâabondance et de diversitĂ©, taux de couverture,âŠ). Lâensemble du systĂšme devra enfin ĂȘtre transfĂ©rĂ© sur un serveur de calcul et accessible au travers dâun serveur Web pour ĂȘtre accessible Ă la collectivitĂ© des Ă©cologistes microbiens. Lâobjectif Ă©tant de coupler, sur un grand nombre dâĂ©chantillons, cette approche avec des mesures dâactivitĂ©s et de faire le lien entre la diversitĂ© microbienne et lâaptitude des sols Ă rendre des services
Measuring Cross-Linguistic Influence in First- and Second-Generation Bilinguals: ERP vs. Acceptability Judgments
Two types of Spanish-English bilinguals were tested in an event-related potential (ERP) experiment on a contrast in the two languages exemplified in (1) and (2) in order to investigate linguistic permeability during processing of Spanish (1a and 2a). In Spanish, but not English, absence of the complementizer que is ungrammatical.
(1) a. QuĂ© hermana confesĂł InĂ©s que habĂa comido la tarta?
b. *What sister did Inés confess that had eaten the cake?
(2) a. *QuĂ© hermana confesĂł InĂ©s Ă habĂa comido la tarta?
b. What sister did Inés confess à had eaten the cake?
In a first analysis, we grouped subjects by generation and compared ERP responses to que-less vs. que-full sentences. A significant N400 effect was found for first-, but not second-generation, suggesting reduced sensitivity to missing que for the latter. However, a second analysis, using linear mixed modeling to test predictiveness of individual speaker variables revealed generation to be non-predictive of N400 amplitude. Instead, current language use, cumulative exposure to English, and socioeconomic status (SES) were significant predictors for all subjects: increased English use, exposure, and SES resulted in smaller N400 amplitude to the anomaly in Spanish shown in (2a). Our results show that a priori classification of bilinguals masks gradient cross-linguistic effects, and processing is permeable in all bilinguals depending on amount of language use. Results from an acceptability judgment task administered to the same subjects using a subset of the same stimuli show that both subject groups judge que-less and que-full to be equally natural. These results suggest that behavioral measures that rely on metalinguistic judgments may not be good indicators of processing, and that having to appeal to metalinguistic knowledge may mask intrinsic knowledge
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