The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Surface modification of biomaterials for conjugation with human fetal osteoblasts.

Surface functionalization of hydroxyapatite (HA) and beta-tricalcium phosphate (TCP) bioceramics with chemical ligands containing a pyrrogallol moiety was developed to improve the adhesion of bone cell precursors to the biomaterials. Fast and biocompatible copper-free click reaction with azido-modified human fetal osteoblasts resulted in improved cell binding to both HA and TCP bioceramics, opening the way for using this methodology in the preparation of cell-engineered bone implants.

What impact do systemically administrated bisphosphonates have on oral implant therapy? A systematic review.

OBJECTIVES: The aim of this systematic review is to evaluate, analysing the dental literature, whether: * Patients on intravenous (IV) or oral bisphosphonates (BPs) can receive oral implant therapy and what could be the risk of developing bisphosphonate-related osteonecrosis of the jaw (BRONJ)? * Osseointegrated implants could be affected by BP therapy. MATERIAL AND METHODS: A Medline search was conducted and all publications fulfilling the inclusion and exclusion criteria from 1966 until December 2008 were included in the review. Moreover, the Cochrane Data Base of Systematic Reviews, and the Cochrane Central Register of Controlled Trials and EMBASE (from 1980 to December 2008) were searched for English-language articles published between 1966 and 2008. Literature search was completed by a hand research accessing the references cited in all identified publications. RESULTS: The literature search rendered only one prospective and three retrospective studies. The prospective controlled non-randomized clinical study followed patients with and without BP medication up to 36 months after implant therapy. The patients in the experimental group had been on oral BPs before implant therapy for periods ranging between 1 and 4 years. None of the patients developed BRONJ and implant outcome was not affected by the BP medication. The three selected retrospective studies (two case-controls and one case series) yielded very similar results. All have followed patients on oral BPs after implant therapy, with follow-up ranging between 2 and 4 years. BRONJ was never reported and implant survival rates ranged between 95% and 100%. The literature search on BRONJ including guidelines and recommendations found 59 papers, from which six were retrieved. Among the guidelines, there is a consensus on contraindicating implants in cancer patients under IV-BPs and not contraindicating dental implants in patients under oral-BPs for osteoporosis. CONCLUSIONS: From the analysis of the one prospective and the three retrospective series (217 patients), the placement of an implant may be considered a safe procedure in patients taking oral BPs for <5 years with regard to the occurrence of BRONJ since in these studies no BRONJ has been reported. Moreover, the intake of oral-BPs did not influence short-term (1-4 years) implant survival rates.

Fonder un nouveau mode de redistribution des aides sociales sur une philosophie de la personne?

Cet article présente un nouveau modèle de redistribution des aides sociales en France, le mécanisme de "l'allocation personnelle", fondé sur une nouvelle conception des mutuelles auxquelles est assigné un rôle de redistribution. L'enjeu de ce papier est de mettre en avant les fondements philosophiques qui sous-tendent cette nouvelle conception de la redistribution, en particulier la philosophie personnaliste.

Introducció als Estudis Fichteans

En la línia iniciada per la Introducció als estudis cartesians (Anuari de la Socierat Catalana de Filosofia, IV, 1990-91, pp. 125-176; reeditada a Societat Catalana de Filosofia, Estudis Cartesians, Barcelona, 1996, pp. 131 -217) i seguida per la lntroducció als estudis hobbeians (Anuari de la Socierar Catalana de Filosofia, VII, 1995, pp. 73-152), presentem aquesta Introduaió als estudis fichteanS com a crítica bibliogràfica amb una doble funció: per a l'orientació de l'esrudiant de filosofia en l'evolució de la literatura fichteana, i coma drecera pera apropar-se a l'estat de la qüestió en la recerca historiogràfica especialitzada. Aquesta publicació és resultat de la tasca dura a terme en dos seminaris consagrats a la filosofia transcendental de Kant a Fichte, dins del pro­grama de doctorar Idealisme i modernitat de la Universitat de Barcelona (1996-98), i s'inscriu en el projecre de recerca El model transcedental en la filosofía moderna i contemporania reconegut i finançat at pel Ministeri d'Educació i Cultura (PB 97-0884). Esperem que sigui una comtribució útil per a la incorporació de la recerca universitària al nostre país -més enlla dels capricis de les modes i de les actualitats efímeres- a les línies de treball rigoroses i internacionalment reconegudes sobre l'idealisme alemany i sobre Fichte en concret.

Subduction of continental crust in the Western Alps

As a result of recent deep reflection and refraction seismology the crustal structure of the Western Alps is now quite well-defined. However, this raises the question of what is present below the Moho, such as a crustal eclogitic root. This study attempts to estimate the volume of this eclogitic root on the basis of palinspastic reconstructions. Even with a minimum estimate of the crustal material involved in the subduction processes which took place during the Alpine orogeny, a significant eclogitized crustal root must be present down to depths of around 100 km below the Po plain. A maximum estimate suggests that a large part of this root could now be recycled in the asthenosphere.

Cancer chronotherapeutics: experimental, theoretical, and clinical aspects.

The circadian timing system controls cell cycle, apoptosis, drug bioactivation, and transport and detoxification mechanisms in healthy tissues. As a consequence, the tolerability of cancer chemotherapy varies up to several folds as a function of circadian timing of drug administration in experimental models. Best antitumor efficacy of single-agent or combination chemotherapy usually corresponds to the delivery of anticancer drugs near their respective times of best tolerability. Mathematical models reveal that such coincidence between chronotolerance and chronoefficacy is best explained by differences in the circadian and cell cycle dynamics of host and cancer cells, especially with regard circadian entrainment and cell cycle variability. In the clinic, a large improvement in tolerability was shown in international randomized trials where cancer patients received the same sinusoidal chronotherapy schedule over 24h as compared to constant-rate infusion or wrongly timed chronotherapy. However, sex, genetic background, and lifestyle were found to influence optimal chronotherapy scheduling. These findings support systems biology approaches to cancer chronotherapeutics. They involve the systematic experimental mapping and modeling of chronopharmacology pathways in synchronized cell cultures and their adjustment to mouse models of both sexes and distinct genetic background, as recently shown for irinotecan. Model-based personalized circadian drug delivery aims at jointly improving tolerability and efficacy of anticancer drugs based on the circadian timing system of individual patients, using dedicated circadian biomarker and drug delivery technologies.

Seismic Wave Velocity as a Means of In-Place Density Measurement, Part 1, HR-114

Velocity-density tests conducted in the laboratory involved small 4-inch diameter by 4.58-inch-long compacted soil cylinders made up of 3 differing soil types and for varying degrees of density and moisture content, the latter being varied well beyond optimum moisture values. Seventeen specimens were tested, 9 with velocity determinations made along two elements of the cylinder, 180 degrees apart, and 8 along three elements, 120 degrees apart. Seismic energy was developed by blows of a small tack hammer on a 5/8-inch diameter steel ball placed at the center of the top of the cylinder, with the detector placed successively at four points spaced 1/2-inch apart on the side of the specimen involving wave travel paths varying from 3.36 inches to 4.66 inches in length. Time intervals were measured using a model 217 micro-seismic timer in both laboratory and field measurements. Forty blows of the hammer were required for each velocity determination, which amounted to 80 blows on 9 laboratory specimens and 120 blows on the remaining 8 cylinders. Thirty-five field tests were made over the three selected soil types, all fine-grained, using a 2-foot seismic line with hammer-impact points at 6-inch intervals. The small tack hammer and 5/8-inch steel ball was, again, used to develop seismic wave energy. Generally, the densities obtained from the velocity measurements were lower than those measured in the conventional field testing. Conclusions were reached that: (1) the method does not appear to be usable for measurement of density of essentially fine-grained soils when the moisture content greatly exceeds the optimum for compaction, and (2) due to a gradual reduction in velocity upon aging, apparently because of gradual absorption of pore water into the expandable interlayer region of the clay, the seismic test should be conducted immediately after soil compaction to obtain a meaningful velocity value.

Spontaneous viral clearance, viral load, and genotype distribution of hepatitis C virus (HCV) in HIV-infected patients with anti-HCV antibodies in Europe.

BACKGROUND: Variables influencing serum hepatitis C virus (HCV) RNA levels and genotype distribution in individuals with human immunodeficiency virus (HIV) infection are not well known, nor are factors determining spontaneous clearance after exposure to HCV in this population. METHODS: All HCV antibody (Ab)-positive patients with HIV infection in the EuroSIDA cohort who had stored samples were tested for serum HCV RNA, and HCV genotyping was done for subjects with viremia. Logistic regression was used to identify variables associated with spontaneous HCV clearance and HCV genotype 1. RESULTS: Of 1940 HCV Ab-positive patients, 1496 (77%) were serum HCV RNA positive. Injection drug users (IDUs) were less likely to have spontaneously cleared HCV than were homosexual men (20% vs. 39%; adjusted odds ratio [aOR], 0.36 [95% confidence interval {CI}, 0.24-0.53]), whereas patients positive for hepatitis B surface antigen (HBsAg) were more likely to have spontaneously cleared HCV than were those negative for HBsAg (43% vs. 21%; aOR, 2.91 [95% CI, 1.94-4.38]). Of patients with HCV viremia, 786 (53%) carried HCV genotype 1, and 53 (4%), 440 (29%), and 217 (15%) carried HCV genotype 2, 3, and 4, respectively. A greater HCV RNA level was associated with a greater chance of being infected with HCV genotype 1 (aOR, 1.60 per 1 log higher [95% CI, 1.36-1.88]). CONCLUSIONS: More than three-quarters of the HIV- and HCV Ab-positive patients in EuroSIDA showed active HCV replication. Viremia was more frequent in IDUs and, conversely, was less common in HBsAg-positive patients. Of the patients with HCV viremia analyzed, 53% were found to carry HCV genotype 1, and this genotype was associated with greater serum HCV RNA levels.

Espectro de gotas de pulverização e controle da ferrugem-asiática-da-soja em cultivares com diferentes arquiteturas de planta

O objetivo deste trabalho foi determinar o espectro de gotas de pulverização ideal para o controle da ferrugem-asiática-da-soja (Phakopsora pachyrhizi), em cultivares com diferentes arquiteturas de planta. O experimento foi conduzido na safra de 2009/2010. A aplicação de fungicida (piraclostrobina + epoxiconazol, com óleo mineral) foi avaliada com quatro espectros de gotas de pulverização - muito fino, <119 μm; fino, 119 a 216 μm; médio, 217 a 352 μm; e grosso, 353 a 464 μm -, em quatro cultivares de soja (BMX Apollo RR, NA 7636 RR, Fcep 53 RR e TMG 4001 RR) contrastantes quanto a índice de área foliar, estatura de plantas e número de ramos por planta. Foram quantificadas as variáveis: número de gotas por cm², diâmetro mediano volumétrico das gotas, área abaixo da curva de progresso da ferrugem-asiática e produtividade da soja. A definição do espectro de gotas a ser utilizado deve considerar a cultivar e as condições ambientais em que a pulverização será realizada. A magnitude da proteção exercida pelo fungicida varia de acordo com a cobertura de plantas e a penetração de gotas no dossel, proporcionada pelos diferentes espectros de gota. O espectro de gotas fino proporciona boa deposição de gotas, controle da doença e produtividade, independentemente da cultivar avaliada.

The fixation of metacentric chromosomes during the chromosomal evolution in the common shrew (Sorex araneus, Insectivora)

Rb fusions between acrocentric chromosomes leading to metacentrics tend to become fixed during the chromosomal evolution in the common shrew. Using microsatellite markers preliminary results show that populations are only slightly subdivided and genetic drift seems not to play an important role for the fixation of metacentrics. A significant segregation distortion in favour of metacentric chromosomes was found during male meiosis. This suggests that cytological factors such as facilitated fusion between acrocentric chromosomes or choice-effects at the level of gametes are more likely to play a role for the chromosomal evolution in the common shrew.

[1 lettre autographe signée de Jules Barbier et Ambroise Thomas à Vaucorbeil, 18 juin 1880]

Au sujet de "Françoise de Rimini" et de Madame Adler-Devriès

Enjeux d'une didactique plurilingue : entre représentations et pratiques courantes

Résumé:S'inscrivant dans le projet Construction intégrée des savoirs linguistiques et disciplinaires dans l'enseignement bilingue au secondaire et au tertiaire, dirigé par L. Gajo, notre étude met en relation des données concernant les représentations des acteurs de l'enseignement bilingue avec des exemples d'interactions effectives. Plusieurs décalages sont ainsi mis à jour, les pratiques s'avérant souvent largement plus complexes que les représentations qui leur sont sous-jacentes. Dans ce cadre, nous accordons une attention particulière aux spécificités disciplinaires, et interrogeons la traditionnelle représentation associant les mathématiques à une "langue en soi". Enfin, l'examen de séquences-types illustrera la richesse du travail effectivement réalisé en classe bilingue - tant dans les sciences humaines que dans les sciences exactes - et nous conclurons sur quelques propositions didactiques découlant directement de nos observations.Abstract:In der vorliegenden Studie (durchgeführt im Rahmen des von L. Gajo geleiteten Projekts Construction intégrée des savoirs linguistiques et disciplinaires dans l'enseignement bilingue au secondaire et au tertiaire) werden Vorstellungen der betroffenen Akteure über bilingualen Sachfachunterricht in Bezug zu Beispielen von real beobachteten Interaktionen gesetzt. Dabei können eine Reihe von Diskrepanzen aufgedeckt werden, da sich die Praxis häufig als wesentlich komplexer als die ihr zugrunde liegenden Vorstellungen erweist. Des Weiteren wird den fachspezifischen Eigenheiten besondere Aufmerksamkeit geschenkt und die Vorstellung hinterfragt, die die Mathematik als eine "Sprache an sich" ansieht. Die Analyse einiger Mustersequenzen veranschaulicht die vielseitige Realität der Arbeit in bilingualen Klassen - sowohl in den Geistes- und Sozialwissenschaften als auch in den Naturwissenschaften. Letztlich werden einige fachdidaktischen Empfehlungen abgegeben, die sich aus unseren Beobachtungen ableiten lassen.