Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

The geographical concentration of industry across Spanish Regions, 1856-1995

New economic geography models show that there may be a strong relationship between economic integration and the geographical concentration of industries. Nevertheless, this relationship is neither unique nor stable, and may follow a ?-shaped pattern in the long term. The aim of the present paper is to analyze the evolution of the geographical concentration of manufacturing across Spanish regions during the period 1856-1995. We construct several geographical concentration indices for different points in time over these 140 years. The analysis is carried out at two levels of aggregation, in regions corresponding to the NUTS-II and NUTS-III classifications. We confirm that the process of economic integration stimulated the geographical concentration of industrial activity. Nevertheless, the localization coefficients only started to fall after the beginning of the integration of the Spanish Economy into the international markets in the mid-70s, and this new path was not interrupted by Spain¿s entry in the European Union some years later

Design and Performance Verifcation of Ultra-High Performance Concrete Piles for Deep Foundations Final Report, November 2008

The strategic plan for bridge engineering issued by AASHTO in 2005 identified extending the service life and optimizing structural systems of bridges in the United States as two grand challenges in bridge engineering, with the objective of producing safer bridges that have a minimum service life of 75 years and reduced maintenance cost. Material deterioration was identified as one of the primary challenges to achieving the objective of extended life. In substructural applications (e.g., deep foundations), construction materials such as timber, steel, and concrete are subjected to deterioration due to environmental impacts. Using innovative and new materials for foundation applications makes the AASHTO objective of 75 years service life achievable. Ultra High Performance Concrete (UHPC) with compressive strength of 180 MPa (26,000 psi) and excellent durability has been used in superstructure applications but not in geotechnical and foundation applications. This study explores the use of precast, prestressed UHPC piles in future foundations of bridges and other structures. An H-shaped UHPC section, which is 10-in. (250-mm) deep with weight similar to that of an HP10×57 steel pile, was designed to improve constructability and reduce cost. In this project, instrumented UHPC piles were cast and laboratory and field tests were conducted. Laboratory tests were used to verify the moment-curvature response of UHPC pile section. In the field, two UHPC piles have been successfully driven in glacial till clay soil and load tested under vertical and lateral loads. This report provides a complete set of results for the field investigation conducted on UHPC H-shaped piles. Test results, durability, drivability, and other material advantages over normal concrete and steel indicate that UHPC piles are a viable alternative to achieve the goals of AASHTO strategic plan.

Development of LRFD Procedures for Bridge Pile Foundations in Iowa Final Report, June 2010

For well over 100 years, the Working Stress Design (WSD) approach has been the traditional basis for geotechnical design with regard to settlements or failure conditions. However, considerable effort has been put forth over the past couple of decades in relation to the adoption of the Load and Resistance Factor Design (LRFD) approach into geotechnical design. With the goal of producing engineered designs with consistent levels of reliability, the Federal Highway Administration (FHWA) issued a policy memorandum on June 28, 2000, requiring all new bridges initiated after October 1, 2007, to be designed according to the LRFD approach. Likewise, regionally calibrated LRFD resistance factors were permitted by the American Association of State Highway and Transportation Officials (AASHTO) to improve the economy of bridge foundation elements. Thus, projects TR-573, TR-583 and TR-584 were undertaken by a research team at Iowa State University’s Bridge Engineering Center with the goal of developing resistance factors for pile design using available pile static load test data. To accomplish this goal, the available data were first analyzed for reliability and then placed in a newly designed relational database management system termed PIle LOad Tests (PILOT), to which this first volume of the final report for project TR-573 is dedicated. PILOT is an amalgamated, electronic source of information consisting of both static and dynamic data for pile load tests conducted in the State of Iowa. The database, which includes historical data on pile load tests dating back to 1966, is intended for use in the establishment of LRFD resistance factors for design and construction control of driven pile foundations in Iowa. Although a considerable amount of geotechnical and pile load test data is available in literature as well as in various State Department of Transportation files, PILOT is one of the first regional databases to be exclusively used in the development of LRFD resistance factors for the design and construction control of driven pile foundations. Currently providing an electronically organized assimilation of geotechnical and pile load test data for 274 piles of various types (e.g., steel H-shaped, timber, pipe, Monotube, and concrete), PILOT (http://srg.cce.iastate.edu/lrfd/) is on par with such familiar national databases used in the calibration of LRFD resistance factors for pile foundations as the FHWA’s Deep Foundation Load Test Database. By narrowing geographical boundaries while maintaining a high number of pile load tests, PILOT exemplifies a model for effective regional LRFD calibration procedures.

Stable alpha-synuclein oligomers strongly inhibit chaperone activity of the Hsp70 system by weak interactions with J-domain co-chaperones.

α-Synuclein aggregation and accumulation in Lewy bodies are implicated in progressive loss of dopaminergic neurons in Parkinson disease and related disorders. In neurons, the Hsp70s and their Hsp40-like J-domain co-chaperones are the only known components of chaperone network that can use ATP to convert cytotoxic protein aggregates into harmless natively refolded polypeptides. Here we developed a protocol for preparing a homogeneous population of highly stable β-sheet enriched toroid-shaped α-Syn oligomers with a diameter typical of toxic pore-forming oligomers. These oligomers were partially resistant to in vitro unfolding by the bacterial Hsp70 chaperone system (DnaK, DnaJ, GrpE). Moreover, both bacterial and human Hsp70/Hsp40 unfolding/refolding activities of model chaperone substrates were strongly inhibited by the oligomers but, remarkably, not by unstructured α-Syn monomers even in large excess. The oligomers acted as a specific competitive inhibitor of the J-domain co-chaperones, indicating that J-domain co-chaperones may preferably bind to exposed bulky misfolded structures in misfolded proteins and, thus, complement Hsp70s that bind to extended segments. Together, our findings suggest that inhibition of the Hsp70/Hsp40 chaperone system by α-Syn oligomers may contribute to the disruption of protein homeostasis in dopaminergic neurons, leading to apoptosis and tissue loss in Parkinson disease and related neurodegenerative diseases.

Pouchography, CT, and MRI features of ileal J pouch-anal anastomosis

OBJECTIVE: Our objective is to describe pouchography, CT, and MRI features of the J-shaped pouch, both normal and with pouch-related complications. CONCLUSION: Pouchography is performed before closure of the loop ileostomy to assess the integrity of the ileal pouch and anastomosis. CT and MRI can be performed when postoperative complications, such as small-bowel obstruction, pouchitis, leakage, abscess, intramural hematoma, desmoid tumor, or recurrent Crohn's disease, are suspected.

Analysis of gene expression patterns in animals

During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals. Gene expression patterns (when and where a gene is expressed) are a key feature in understanding gene function, notably in development. It appears clear now that the evolution of developmental processes and of phenotypes is shaped both by evolution at the coding sequence level, and at the gene expression level.Studying gene expression evolution in animals, with complex expression patterns over tissues and developmental time, is still challenging. No tools are available to routinely compare expression patterns between different species, with precision, and on a large-scale basis. Studies on gene expression evolution are therefore performed only on small genes datasets, or using imprecise descriptions of expression patterns.The aim of my PhD was thus to develop and use novel bioinformatics resources, to study the evolution of gene expression. To this end, I developed the database Bgee (Base for Gene Expression Evolution). The approach of Bgee is to transform heterogeneous expression data (ESTs, microarrays, and in-situ hybridizations) into present/absent calls, and to annotate them to standard representations of anatomy and development of different species (anatomical ontologies). An extensive mapping between anatomies of species is then developed based on hypothesis of homology. These precise annotations to anatomies, and this extensive mapping between species, are the major assets of Bgee, and have required the involvement of many co-workers over the years. My main personal contribution is the development and the management of both the Bgee database and the web-application.Bgee is now on its ninth release, and includes an important gene expression dataset for 5 species (human, mouse, drosophila, zebrafish, Xenopus), with the most data from mouse, human and zebrafish. Using these three species, I have conducted an analysis of gene expression evolution after duplication in vertebrates.Gene duplication is thought to be a major source of novelty in evolution, and to participate to speciation. It has been suggested that the evolution of gene expression patterns might participate in the retention of duplicate genes. I performed a large-scale comparison of expression patterns of hundreds of duplicated genes to their singleton ortholog in an outgroup, including both small and large-scale duplicates, in three vertebrate species (human, mouse and zebrafish), and using highly accurate descriptions of expression patterns. My results showed unexpectedly high rates of de novo acquisition of expression domains after duplication (neofunctionalization), at least as high or higher than rates of partitioning of expression domains (subfunctionalization). I found differences in the evolution of expression of small- and large-scale duplicates, with small-scale duplicates more prone to neofunctionalization. Duplicates with neofunctionalization seemed to evolve under more relaxed selective pressure on the coding sequence. Finally, even with abundant and precise expression data, the majority fate I recovered was neither neo- nor subfunctionalization of expression domains, suggesting a major role for other mechanisms in duplicate gene retention.

Nonequilibrium patterns and shape fluctuations in reactive membranes

A simple kinetic model of a two-component deformable and reactive bilayer is presented. The two differently shaped components are interconverted by a nonequilibrium reaction, and a phenomenological coupling between local composition and curvature is proposed. When the two components are not miscible, linear stability analysis predicts, and numerical simulations show, the formation of stationary nonequilibrium composition/curvature patterns whose typical size is determined by the reactive process. For miscible components, a linearization of the dynamic equations is performed in order to evaluate the correlation function for shape fluctuations from which the behavior of these systems in micropipet aspiration experiments can be predicted.

The geographical concentration of industry across Spanish Regions, 1856-1995

New economic geography models show that there may be a strong relationship between economic integration and the geographical concentration of industries. Nevertheless, this relationship is neither unique nor stable, and may follow a ?-shaped pattern in the long term. The aim of the present paper is to analyze the evolution of the geographical concentration of manufacturing across Spanish regions during the period 1856-1995. We construct several geographical concentration indices for different points in time over these 140 years. The analysis is carried out at two levels of aggregation, in regions corresponding to the NUTS-II and NUTS-III classifications. We confirm that the process of economic integration stimulated the geographical concentration of industrial activity. Nevertheless, the localization coefficients only started to fall after the beginning of the integration of the Spanish Economy into the international markets in the mid-70s, and this new path was not interrupted by Spain¿s entry in the European Union some years later

Alcohol drinking, the metabolic syndrome and diabetes in a population with high mean alcohol consumption.

AIMS: To investigate the relationship of alcohol consumption with the metabolic syndrome and diabetes in a population-based study with high mean alcohol consumption. Few data exist on these conditions in high-risk drinkers. METHODS: In 6172 adults aged 35-75 years, alcohol consumption was categorized as 0, 1-6, 7-13, 14-20, 21-27, 28-34 and ≥ 35 drinks/week or as non-drinkers (0), low-risk (1-13), medium-to-high-risk (14-34) and very-high-risk (≥ 35) drinkers. Alcohol consumption was objectively confirmed by biochemical tests. In multivariate analysis, we assessed the relationship of alcohol consumption with adjusted prevalence of the metabolic syndrome, diabetes and insulin resistance, determined with the homeostasis model assessment of insulin resistance (HOMA-IR). RESULTS: Seventy-three per cent of participants consumed alcohol, 16% were medium-to-high-risk drinkers and 2% very-high-risk drinkers. In multivariate analysis, the prevalence of the metabolic syndrome, diabetes and mean HOMA-IR decreased with low-risk drinking and increased with high-risk drinking. Adjusted prevalence of the metabolic syndrome was 24% in non-drinkers, 19% in low-risk (P<0.001 vs. non-drinkers), 20% in medium-to-high-risk and 29% in very-high-risk drinkers (P=0.005 vs. low-risk). Adjusted prevalence of diabetes was 6.0% in non-drinkers, 3.6% in low-risk (P<0.001 vs. non-drinkers), 3.8% in medium-to-high-risk and 6.7% in very-high-risk drinkers (P=0.046 vs. low-risk). Adjusted HOMA-IR was 2.47 in non-drinkers, 2.14 in low-risk (P<0.001 vs. non-drinkers), 2.27 in medium-to-high-risk and 2.53 in very-high-risk drinkers (P=0.04 vs. low-risk). These relationships did not differ according to beverage types. CONCLUSIONS: Alcohol has a U-shaped relationship with the metabolic syndrome, diabetes and HOMA-IR, without differences between beverage types.

Horae secundum usum romanum.

F. A-B. Bifolium contenant la fin de l’office du Saint Esprit ; cf. le même texte aux ff. 156-156v. XVe siècle. Copie inachevée dont les initialesont été laissées en blanc. Le f. B réglé est blanc. La justification est la même que celle du corps du manuscrit.F. 1-12v. Calendrier écrit à l’encre rouge et bleue et à l’or: nombreux saints méridionaux, en particulier de la vallée du Rhône et du Languedoc : « Fulcrani ep. [Lodevensis] » (13 févr.) ; « translatio s. Pauli » (20 février) ; « translatio s.Augustini » (28 février) ; « Pauli archi. Narbo[nensis] » (22 mars) ; « translatio b. Ferreoli [ ?] (1er avril) ; « Baudilii mart. [Nemausiensis] (20 mai) ; « Quiterie (21 mai) ; « Eutropii [ep. Arausicani] (27 mai) ; « translatio s. Saturnini » (22 juin) ; « Petri de Lucemburgo » (5 juillet) ; « Roqui mart. [Montispessulani] » (16 août) ; « Ludovici regis fratris [ep. Toletani]» (19 août) ; « Privati conf. [ep. Gabalitanus (Gévaudan)] » (21 août) ; « Fereoli mart. [Viennae] (18 sept.) ; « Apolinaris ep. [Valentinensis] » (10 oct.) ; « Firmini ep. [Ucetensis] » (11 oct.] ; « Florencii ep. [Arausicani] » (17 oct.] ; « Amancii ep. [Ruthenensis] » (5 nov.) ; « Restituti ep. [Tricastini] » (8 nov.) ; « Rufi ep. [Avenionensis] » (14 nov.) ; « Pauli ep. [Narbonensis] » (11 déc.) ; « Dominici conf. [de Silos] » (20 déc.). Mentions zodiacales et de comput, parmi lesquelles on note une « renovatio indicionum », le 24 septembre. F. 13-17. Extraits des quatre Evangiles : Io (13-14) ; Lc (14-15) ; Mt (15-16v) ; Mc (16v-17).F. 17v-71. [Horae beatae Mariae virginis secundum usum romanum]. [Ad matutinas], psaumes répartis selon les jours de la semaine (18-32v) ; — « In laudibus » (32v-42v) ; — « Ad primam » (43-46v) ; — « Ad tertiam » (46v-49) ; — « Ad sextam » (49v-52) ; « Ad IXa » (52-55) ; — « Ad vesperas » (55-60) ; — « Ad comple[c]torium » (60-64) ; — Antiennes, psaumes, leçons et répons pour les différents temps de l’année (64v-71) .F. 71-77v. Messe votive. « Missa beate Marie virginis ». « Salve sancta parens... » F. 78-85. Prières et hymnes. [Septem gaudia spiritualia b. Mariae virginis], incomplet des quatre premiers vers par lacune matérielle. « [Gaude flore virginali...] et sanctorum decoratum//...-... per eterna secula » (AH, XXXI, n° 198) ; « O sponsa Dei electa// Esto nobis via recta... » ; « ...Oratio. Domine Jhesu Christe qui beatissimam gloriosam virginem...-... pervenire mereamur » ; « Gaudia. Gaude virgo mater Christi// Que per aurem concepisti// ...-... perhemni gaudio. » (AH, XXIV, n° 57) ; cf. Leroquais, Livres d’heures, I, XXVI-XXVII ; « ... Oratio. Deus qui beatissimam virginem Mariam in consceptu... pervenire. Per... » ; « Gaudia beate Marie spiritualia. Gaude stirpe regis nata// Ab angelo saluta[ta]...-... et celorum mansio » (AH, XXXI, n° 182) ; « Oratio. Consolator mitissime Deus... sempiternis perfrui. Per... » ; « Alia oratio. Deus qui Gabrielem archangelum... mereamur habere. Qui... » ; « Devota oratio ad beatam virginem Mariam. Obsecro te domina... et michi famulo tuo pauperrimo N. ... » (Leroquais, Livres d’heures, II, 346-347).F. 85v blanc.F.86-91v. [Horae Trinitatis].F.91v-93v. Messe votive. « Missa de Trinitate ».F. 93v-97. « Devota oratio. Deus omnipotens propicius esto michi peccatori, custos mei omnibus diebus et horis vite mee, Deus Abraham... Omnes sancti angeli et archangeli Dei succurrite et subvenite michi peccatori... horis vite mee » ; cf. Leroquais, Livres d’heures, II, 396 ; — « O bone Jhesu illumina oculos meos ne unquam obdormiam... impietatem peccati mei » ; cf. Leroquais, Livres d’heures, I, XXX-XXXI ; — « Omnipotens, sempiterne et clementissime Deus qui Ezechie regi ... merear et optinere. Per... », à la forme masculine ; cf. Leroquais, Livres d’heures, II, 438 ; — « Oratio. Omnipotens sempiterne Deus te supplices exoramus ut celesti... consequantur. Per... » (Corpus orationum, VI, n° 4076).F. 97v blanc.F. 98-108. [Psaumes de la pénitence]. F. 108-117v. « Letania ». A noter parmi les confesseurs, la séquence inattendue de trois évêques de Toul honorés en Lorraine : « ... s. Mansuete, s. Gerarde, s. Aper ». Parmi les saintes : « ... s. Martha, s. Eulalia... s. Radegundis... ». — Oraisons diverses : « Propicius esto, parce nobis Domine... ut michi indigno famulo tuo N... exaudire digneris » ; — ... « Omnipotens sempiterne Deus miserere michi indigno famulo tuo N.... perficiat. Per... » ; — « Pie et exaudibilis domine Jhesu Christe Deus noster clementiam tuam... digneris eternam » ; cf. Leroquais, Psautiers, I, 25 ; — « Pietate tua quesumus Domine nostrorum solve vincula delictorum et intercedente pro nobis... virgine Dei genitrice Maria cum beatis apostolis tuis Petro et Paulo atque Andrea... eternam concede. Per... » (Corpus orationum, VI, n° 4227)...F. 118-145. [Officium mortuorum secundum usum romanum]F. 145-147v. Messe votive. « Missa pro omnibus fidelibus defunctis ». F. 148-151. [Horae sancti Spiritus].F. 151-153v. Messe votive. « Missa de sancto Spiritu », incomplet de la fin par lacune matérielle.F. 154-156v. [Horae omnium sanctorum], incomplet du premier feuillet.F. 156v-159v. Messe votive. « Missa de omnibus sanctis. F. 160-162v. [Horae sancti Sacramentis], incomplet du début par lacune matérielle. F. 162v-164v. Messe votive. « Missa de corpore Christi ».F. 164v-169v. Prières et hymnes. « ... salutatio sacratissimi corporis domini nostri Jhesu Christi. Ave Jhesu Christe verbum Patris filius [Virginis] agnus Dei...-... requies nostra vita perhemnis » ; cf. ms NAL 3211, 342 ; — « Alia oratio. Salve sancta caro Dei per quam salvi...-... da michi sedem justorum. Qui... » (ed. Leroquais, Livres d’heures, II, 348) ; — In elevatione corporis Christi. Anima Christi sanctifica me // Corpus Christi salva me... secula seculorum. Amen » ; (ed. Leroquais, Livres d’heures, II, 340 variantes) ; — « Alia. Ave verum corpus natum... o pia... ora pro nobis » (AH, LIV, n° 257) ; — « Alia devota oratio. Domine Jhesu Christe qui hanc sacratissimam carnem tuam... et periculis et in eternum » ; cf.ms NAL 3203, 26v ; — « Dum volueris communicare dic orationem. Omnipotens et misericors Deus ecce accedo ad sacratissimum accedo inquam infirmus ad medicum...-... tutela finalis in morte. Qui... » ; — « Alia oratio ante communionem. Domine sancte Pater, omnipotens eterne Deus, da mihi corpus et sanguinem... in infinita secula... » ; cf. Leroquais, Livres d’heures, II, 108 ; — « Post communionem. Gratias tibi ago Domine sancte pater omnipotens eterne Deus qui me peccatorem indignum famulum tuum saciare... et gaudium sempiternum... » ; cf. Leroquais, Livres d’heures, I, 51 ; — « Post communionem ad beatam Virginem. Serenissima Virgo et inclita mater nostri Jhesu Christi, sancta Maria regina celi et terre que eundem creatorem... hodie veracis [incomplet de la fin par lacune matérielle] ; cf. Leroquais, Livres d’heures, I, 156, 299.F. 170-173. [Horae sanctae Crucis], incomplet du début.F. 173-178. Messe votive. « Missa in honore sancte Crucis ». « Crucem tuam adoramus et veneramur domine Jhesu Christe, et per ipsam tuam sanctissimam recolimus passionem...-...defunctis vitam et gloriam sempiternam... » ; — « Alia oratio. Domine Jhesu Christe plasmator tocius creature, rex glorie obsecro miserere mei quia locutus sum... semper benedictus... » ; — « Alia oratio. Domine Jhesu Christe qui voluisti pro redemptione mundi nasci et circumcidi... ego miserrimus, vilissimus, nequissimus atque indignissimus peccator...-... latronem crucifixum. Qui... » ; — « Alia oratio. Precor te, piissime domine Jhesu Christe, per illam eximiam caritatem qua tu rex celestis... mihi tribuere digneris. Qui... » ; — « Alia oratio. Deus propicius esto michi peccatori. Quid est Jhesus nisi salvator ergo Jhesus per te ipsum redemptus sum... miserere michi Deus » ; — « Dic totum deinde dic oracionem. Tribulacionem nobis [sic], quesumus, Domine propicius respice... clementer averte. Per... ». F. 178-200. « ... suffragia sanctorum ». « ... de Trinitate » ; — « De sancto Michaele archangelo » ; — « De sancto Johanne Baptista » ; — « De sancto Petro et Paulo » ; — « De sancto Andrea apostolo » ; — « De sancto Johanne evangelista » ; — « De sancto Jacobo minori » ; — « Sanctorum Philippi et Jacobi » ; — « De innocentibus » ; — « De apostolis et evvangelistis » ; — « De sancto Stephano » ; — « De sancto Laurencio » ; — « De sancto Eutropio... Eutropium martyrem tuum (f. 183v)... » ; — « De sancto Georgio » ; — « De sancto Blasio » ; — « De sancto Dyonisio » ; — « De sancto Yppolito » ; — « De sancto Christophoro » ; — « De sancto Sebastiano. Omnipotens sempiterne Deus qui meritis beati Sebastiani martyris gloriosissimi quemdam pestem epydimie generalem hominibus mortiferam revocasti, presta supplicibus tuis ut qui hanc orationem super se portavit aut in domibus vel mansionibus scriptam aut alias de ea in tuo nomine memoriam habuerint sive in die aut in nocte legerint a simili a peste et morbo epydimie sub ejus confidencia ad te confugerint ipsius meritis et precibus ab ipsis peste et morbo epydimie et ab omnibus nocumentis venenosis necnon ab omnibus periculis corporis et anime atque a subitanea et improvisa morte et ab omnibus inimicis visibilibus et invisibilibus singulis diebus et noctibus horis atque momentis liberemur. Per Dominum. Pater noster. Ave Maria. Credo. Salva regina. Ave stella matutina, rosa sine spinis, cum reliquis ». — « Unius martyris communis » ; — « De martyribus communis » ; — « De sancto Martino » ; — « De sancto Nicholao » ; — « De sancto Anthonio » ; — « De sancto Lazaro » ; — « De sancto Restituto... Deus qui per merita beati Restituti confessoris atque pontificis a multorum oculis dolorem sanas, labem removes et visum clarificas... (189v-190) » ; — « Unius confessoris » ; — « De confessoribus communis » ; — « De beata Maria Magdalena prosa. Gaude pia Magdalena // Spes salutis // Vite vena // Lapsorum fiducia // Gaude dulcis advocata // ... » ; — « De beata Catherina. Gaude virgo Catherina /// Quam refecit lux divina // Ter quaternis noctibus //... » ; — « De beata Lucia » ; — « De beata Apollonia » ; — « De beata Agatha » ; — « De virginibus » ; — « De omnibus sanctis » ; — « De pace » ; — « De sancto Petro de Lucemburgo » ; le suffrage commence par la prière attribuée à s. Pierre de Luxembourg : « Deus pater qui creasti // Mundum et illuminasti // Suscipe...-... requiescant in pace. Amen » ; cf.ms NAL 3196, 152.F. 200v-204, feuillets réglés blancs.

Statistical Modeling of the Eye for Multimodal Treatment Planning for External Beam Radiation Therapy of Intraocular Tumors.

PURPOSE: Ocular anatomy and radiation-associated toxicities provide unique challenges for external beam radiation therapy. For treatment planning, precise modeling of organs at risk and tumor volume are crucial. Development of a precise eye model and automatic adaptation of this model to patients' anatomy remain problematic because of organ shape variability. This work introduces the application of a 3-dimensional (3D) statistical shape model as a novel method for precise eye modeling for external beam radiation therapy of intraocular tumors. METHODS AND MATERIALS: Manual and automatic segmentations were compared for 17 patients, based on head computed tomography (CT) volume scans. A 3D statistical shape model of the cornea, lens, and sclera as well as of the optic disc position was developed. Furthermore, an active shape model was built to enable automatic fitting of the eye model to CT slice stacks. Cross-validation was performed based on leave-one-out tests for all training shapes by measuring dice coefficients and mean segmentation errors between automatic segmentation and manual segmentation by an expert. RESULTS: Cross-validation revealed a dice similarity of 95% ± 2% for the sclera and cornea and 91% ± 2% for the lens. Overall, mean segmentation error was found to be 0.3 ± 0.1 mm. Average segmentation time was 14 ± 2 s on a standard personal computer. CONCLUSIONS: Our results show that the solution presented outperforms state-of-the-art methods in terms of accuracy, reliability, and robustness. Moreover, the eye model shape as well as its variability is learned from a training set rather than by making shape assumptions (eg, as with the spherical or elliptical model). Therefore, the model appears to be capable of modeling nonspherically and nonelliptically shaped eyes.

Die Behandlung von Acetabulumfrakturen bei geriatrischen Patienten mittels modifizierter Kabelcerclage und primärer Hüfttotalprothese. Erste Ergebnisse [Treatment of acetabular fractures in the elderly with primary total hip arthroplasty and modified cerclage. Early results]

This prospective study addresses early results of the treatment of acute acetabular fractures in elderly patients by total hip arthroplasty and cerclage wiring.Fifteen patients with an average age of 81 years were treated at our institution between February 1998 and December 2000. There were two transverse fractures, eight T-shaped fractures, two transverse fractures with associated posterior wall fracture, two posterior column fractures with associated posterior wall fracture, and one fracture of both columns. Treatment consisted of cerclage wiring of the fracture and primary non-cemented total hip replacement.All of the patients were followed for a mean of 36 months. Although there was one patient with three hip dislocations during the first 10 months after the operation, we found an excellent or good result for the entire group. During this relatively short follow-up period, we have not found a radiological loss of fracture reduction of more than 1 mm or a cup migration of more than 3.2 mm. All of the fractures healed and no loosening of the implant was evident.Primary total hip arthroplasty combined with internal fixation is a valid treatment option for acetabular fractures in the elderly. Preliminary results are convincing, but a bigger patient population and a longer follow-up time are necessary before we are able to draw final conclusions.

Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.

The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.

Foster carers influence brood pathogen resistance in ants.

Social organisms face a high risk of epidemics, and respond to this threat by combining efficient individual and collective defences against pathogens. An intriguing and little studied feature of social animals is that individual pathogen resistance may depend not only on genetic or maternal factors, but also on the social environment during development. Here, we used a cross-fostering experiment to investigate whether the pathogen resistance of individual ant workers was shaped by their own colony of origin or by the colony of origin of their carers. The origin of care-giving workers significantly influenced the ability of newly eclosed cross-fostered Formica selysi workers to resist the fungal entomopathogen Beauveria bassiana. In particular, carers that were more resistant to the fungal entomopathogen reared more resistant workers. This effect occurred in the absence of post-infection social interactions, such as trophallaxis and allogrooming. The colony of origin of eggs significantly influenced the survival of the resulting individuals in both control and pathogen treatments. There was no significant effect of the social organization (i.e. whether colonies contain a single or multiple queens) of the colony of origin of either carers or eggs. Our experiment reveals that social interactions during development play a central role in moulding the resistance of emerging workers.