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 ≥8 years with refractory partial seizures were enrolled and grouped: those receiving vigabatrin for ≥6 months (Group I); those who had received vigabatrin for ≥6 months and then had discontinued for ≥6 months (Group II); and those naïve to vigabatrin (Group III). Patients underwent static or kinetic perimetry or both every 4–6 months for ≤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°–60° 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 $\rm -3^{\circ}$ 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 $10^{4/3}$. 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

Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Communication orale, résuméLa diversité microbienne d’un sol est difficile à caractériser. Ceci s’explique par une accessibilité plus ou moins importante des populations au sein d’une matrice hétérogène et structurée, mais aussi par l’incapacité à résoudre une information constituée de 100 000 à 1 000 000 d’espèces différentes par gramme de sol. Toutefois, récemment, d’importantes avancées en biologie moléculaire ont permis de mieux caractériser la diversité des communautés microbiennes du sol in situ et ce sans a priori. Ainsi, la puissance des nouvelles générations de séquençage comme le pyroséquençage permettent de travailler en haut-débit afin d’obtenir plusieurs dizaines, voire plusieurs centaines de milliers de séquences à partir d’un ADN méta-génomique. De premières études ont déjà été réalisées avec cette technique afin d’aborder la diversité bactérienne des sols. Ces études ont, pour la première fois, permis de quantifier de façon exhaustive la diversité microbienne de sols en termes de richesse spécifique et de démontrer la pertinence, la faisabilité et la robustesse de cette approche. Cette approche est maintenant unanimement reconnue pour sa pertinence et ses potentialités très importantes, et ce afin de déterminer la diversité des microorganismes telluriques. Notre approche consiste en la caractérisation de la diversité taxonomique (bactérienne et fongique) de sols sur des échantillonnages de grande ampleur dans le temps et dans l’espace, avec comme objectifs : (i) de faire un inventaire exhaustif de la diversité microbienne tellurique, (ii) d’évaluer sa distribution spatiale, (iii) de mieux comprendre sa régulation et, (iv) in fine, de pouvoir relier cette diversité en fonctionnement biologique du sol et en services écosystémiques [1-3]. Cependant, l’étude d’un aussi grand nombre d’échantillons va entraîner la production massive de séquences. Ce caractère massif, ainsi que les caractéristiques inhérentes aux séquences obtenues par cette technique requièrent le développement d’outils bioinformatiques adaptés, optimisés et évalués, afin d’analyser rapidement et efficacement ce type de données. Ce nouveau pipeline d’analyse doit tout d’abord être facile d’utilisation et répondre aux attentes des différents utilisateurs, qu’ils soient compétents en bio-informatique, ou novices dans l’analyse de tels jeux de données. Il doit également permettre de gérer un grand nombre de séquences et d’automatiser les grandes étapes d’analyse (prétraitement, filtration, clustérisation, assignation taxonomique, calculs d’indices d’abondance et de diversité, taux de couverture,…). L’ensemble du système devra enfin être transféré sur un serveur de calcul et accessible au travers d’un serveur Web pour être accessible à la collectivité des écologistes microbiens. L’objectif étant de coupler, sur un grand nombre d’échantillons, cette approche avec des mesures d’activités et de faire le lien entre la diversité microbienne et l’aptitude des sols à rendre des services

Hydrogen production by the hyperthermophilic bacterium Thermotoga maritima part I: effects of sulfured nutriments, with thiosulfate as model, on hydrogen production and growth

International audienceBackground: Thermotoga maritima and T. neapolitana are hyperthermophile bacteria chosen by many research teams to produce bio-hydrogen because of their potential to ferment a wide variety of sugars with the highest theoretical H-2/glucose yields. However, to develop economically sustainable bio-processes, the culture medium formulation remained to be optimized. The main aim of this study was to quantify accurately and specifically the effect of thiosulfate, used as sulfured nutriment model, on T. maritima growth, yields and productivities of hydrogen. The results were obtained from batch cultures, performed into a bioreactor, carefully controlled, and specifically designed to prevent the back-inhibition by hydrogen. Results: Among sulfured nutriments tested, thiosulfate, cysteine, and sulfide were found to be the most efficient to stimulate T. maritima growth and hydrogen production. In particular, under our experimental conditions (glucose 60 mmol L-1 and yeast extract 1 g L-1), the cellular growth was limited by thiosulfate concentrations lower than 0.06 mmol L-1. Under these conditions, the cellular yield on thiosulfate (Y X/Thio) could be determined at 3617 mg mmol(-1). In addition, it has been shown that the limitations of T. maritima growth by thiosulfate lead to metabolic stress marked by a significant metabolic shift of glucose towards the production of extracellular polysaccharides (EPS). Finally, it has been estimated that the presence of thiosulfate in the T. maritima culture medium significantly increased the cellular and hydrogen productivities by a factor 6 without detectable sulfide production. Conclusions: The stimulant effects of thiosulfate at very low concentrations on T. maritima growth have forced us to reconsider its role in this species and more probably also in all thiosulfato-reducer hyperthermophiles. Henceforth, thiosulfate should be considered in T. maritima as (1) an essential sulfur source for cellular materials when it is present at low concentrations (about 0.3 mmol g(-1) of cells), and (2) as both sulfur source and detoxifying agent for H-2 when thiosulfate is present at higher concentrations and, when, simultaneously, the pH(2) is high. Finally, to improve the hydrogen production in bio-processes using Thermotoga species, it should be recommended to incorporate thiosulfate in the culture medium

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. Qué hermana confesó Inés que había comido la tarta? b. *What sister did Inés confess that had eaten the cake? (2) a. *Qué hermana confesó Inés Ø había comido la tarta? b. What sister did Inés confess Ø 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