A graphical tool for parasite genome annotation

A graphical tool to facilitate rapid primary annotation of genomic sequence has been developed. Within a single interface the user can import sequences or database entries, run feature prediction programs and similarity searches, filter results, add additional manually found features and notes, and finally export annotations for database submission. Integrated rule-based feature corroboration and a novel decision support heuristic using ORF orientation, length and base-composition further enhances the efficiency of the annotation process without compromising flexibility. The program has been explicitly tailored to use in protozoan parasite genome projects, but can constitute a useful tool for prokaryote annotation as well. It is successfully being used by our lab in the Trypanosoma cruzi genome project, and can be obtained from the authors upon request.     

Measuring transport injuries in a developing country: an application of the capture-recapture method

The purposes of this study are to provide an estimation of the incidence of transport injuries in a defined local community in Nicaragua by using the capture-recapture method, and to compare results using this method when data at different levels of severity are utilized.Two sources of injury data were used to monitor injuries: hospital data (inpatient and outpatient) and traffic police records. Characteristics available for matching included name, age, sex, and date of occurrence. The methodology of capture-recapture was used to estimate the ascertainment degree of both sources of data and the estimate mortality and incidence rates. Estimates were calculated both when all hospital data were taken into account (inpatient and outpatient combined) and when only inpatient records were matched against police records.First, including police records and all hospital data, the mortality and morbidity estimates were 35.5/100000 and 43.7/1000 per year, respectively. Second, when outpatients were excluded from the analysis, the corresponding estimates were 28.6/100000 and 7.5/1000, respectively. In non-fatal cases, the ascertainment-corrected coverage through police records was 2.6% and through hospital surveillance 19.0% when both inpatients and outpatients were included. In fatal cases, the corresponding rates were 56.1 and 22.8%, respectively. The combined data set pointed out pedestrians and cyclists as the main risk groups. Most fatalities were due to head injuries.Our results show that neither police records nor hospital records nor the aggregate database provided acceptable coverage of transport-related injuries. Combining police and hospital data by means of capture-recapture analysis produces more valid estimates, but caution must be given to the issue of severity heterogeneity between the two sources.     

A critical evaluation of the strategy project

The STRATEGY project (sustainable restoration and long-term management of contaminated rural, urban and industrial ecosystems; www.strategy-ec.org.uk) addressed the need for a holistic decision framework for the selection of optimal remediation strategies for long-term sustainable management of contaminated areas in Western Europe. The project considered both technical and social aspects of implementing restoration strategies for urban and rural environments. The importance of considering socially relevant objectives in addition to the dose reduction was emphasised. A critical evaluation was carried out on 101 selected countermeasures, (including rural waste disposal options), a model was developed to aid optimising countermeasure strategies and a method of carrying out participatory decision-making suggested. The outputs of the project are described and critically evaluated.     

Surface energy measurements from Griffith cracks in boron fibres

Journal of Materials Science -     

1.4 Fast volume determination using a differential capacitance manometer

The reliable pressure readings with a capacitance manometer are the basis for a new type of instrument designed for accurate and rapid measurements of capillary volumes. The basic measuring principle is based on expansion of air atmospheric pressure enclosed in a known volume into a pre-evacuated cylinder so that the enclosed volume will cause a reduced pressure in the cyllinder. The same is done with the air in an unknown volume into another identical pre-evacuated cylinder. A differential capacitance manometer is then used to measure the difference in pressure between the two cylinders with a high degree of accuracy. This difference in pressure is shown to be ainear function of the difference in volume between the unknown and the known volume. The accuracy and repeatability of the instrument is better than 0.5%.     

Adrenergic and Cholinergic Nerves of the Human Urethra and Urinary Bladder. A histochemical study

The occurrence and distribution of adrenergic and acetylcholine esterase (AChE) positive nerves in the human urethra and urinary bladder were studied histochemically with the fluorescence method of Falck and Hillarp, and the copper thiocholine method of Koelle and Friedenwald. Both types of nerves were mainly confined to the layers of smooth muscle cells in the walls of the organs. In all parts of the urethra, there was a scanty supply of adrenergic nerves. Few adrenergic nerves were also found in the urinary bladder, except in the trigone area, where they were abundant. AChE-positive nerves were uniformly and richly distributed in the urinary bladder. Throughout the urethra the distribution of AChE-positive nerve fibres was uniform, but the number was clearly less than in the urinary bladder. No intrmurally located adrenergic or AChE-Positive ganglion cells could be demonstrated.     

Plastic deformation at a stably growing crack tip

The deformations around the tip of a straight, through-the-thickness crack in sheets of cellulose nitrate, celluloid, in tension have been studied, as well before as after the onset of stable crack growth. A tensile testing apparatus and a device for engraving a fine grid directly on the specimen sheet have been designed. The development of the plastic enclave also after the start of stable crack extension has been studied in connexion with investigations of the deformations in gross fields of size up to 30 × 40 mm² performed on a digital computer (line element length 1 or 0.5 mm, virgin crack length 80 mm). Unexpected deformations very close to the crack tip were found in the near field where line elements of length 50 µm were analyzed. A modified Dugdale model where the cohesive stresses vary linearly is examined and is applied on polyvinylehloride, PVC, specimen the thickness of which is strongly reduced near the crack tip. A method for measurement of thickness changes of the order of a few µm by tracing isohypses is described. Finally, to enable comparison with the experimental results, the elastic deformation pattern for a square mesh in the plane strain and plane stress case is obtained by a digital computer.

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Zusammenfassung Es wurden die Verformungen an der Spitze eines geraden, über die gesamte Dicke durchgehenden Risses in Spannungen unterworfenen Tafeln aus Zellulosenitrat (Zelluloïd) untersucht. Dies geschah sowohl vor als auch nach der Einstellung einer gleichmäßigen Rißfortpflanzungsgeschwindigkeit. Hierzu wurde eine Zugversuchsapparatur sowie ein Verfahren zur Gravierung eines Rasters, direkt auf die Probe, entwickelt.Die Ausbildung der plastischen Enklave, auch nach Einstellung einer gleichmäßigen Rißausweitung, wurde in Verbindung mit Studien der Verformung in Grobrastern his 30 × 40 mm mittels Digitalrechnern, untersucht (Länge einer Elementarlinie l oder 0,5 mm; Originallänge des Risses 80 mm). Direkt an der Rißspitze, wo Elementarlinien mit einer Länge von 50 µm untersucht wurden, konme man unerwartete Verformungen feststellen. Es wurde ein abgewandeltes Dugdale-Modell bei dem die Kohäsionsspannungen sich linear verändern untersucht and auf Polyvinylchlorid PVC-Proben, deren Dicke sich an der Rißspitze stark reduziert, angewandt. Es wird ein Verfahren zur Messung von Änderungen der Dicke um wenige µm beschrieben. Um einen Vergleich mit den experimentellen Ergebnissen zu ermöglichen, wird zum Schluß mit Hilfe eines Digitalrechners das elastische Verformungsmodell für Quadratraster, im Falle planer Verformung and eines planen Spannungszustandes berechnet.

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Résumé On a étudié les déformations qui se produisent au voisinage de l'extrémité d'une fissure droite et traversante dans des feuilles de nitrate de cellulose (celluloid) soumises à traction, et ce avant et après établissement d'un régime stable de propagation. A cet effet, on a mis au point un équipement d'essai de traction et une technique permettant de tracer une grille directement sur l'éprouvette. Le développement d'une enclave plastique dès que l'éxtension de la fissure devient stable a été etudie en recherchant les déformations survenant dans des réseaux grossiers, allant jusqu'à 30 × 40 mm², a l'áide d'un calculateur digital (longueur d'une ligne élémentaire: 1 ou 0,5 mm, longueur de fissure initiale: 80 mm). Dans un réseau plus fin, où les lignes élémentaires avaient une longueur de 50 microns, on a analysé, au voisinage immédiat de l'éxtrémité de la fissure, des déformations inattendues.On a examiné l'ápplication d'un modèle du Dugdale modifié, où les contraintes de cohésion varient linéairement, à des éprouvettes de PVC, dont l'épaisseur subit des réductions considérables près de l'extrémité de la fissure. On décrit une méthode de mesure des variations d'épaisseur de l'órdre de quelques microns, qui est basée sur le tracé de courbes de niveaux.Enfin, pour permettre une comparaison avec les résultats expérimentaux, on a établi par un calculateur digital l'állure de la déformation élastique dans un réseau carré pour les cas d'état plan de déformation et d'état plan de tension.

     

Accuracy in multiangle light scattering measurements for molar mass and radius estimations. Model calculations and experiments

Multiangle light scattering (MALS) is a well-established technique used to determine the size of macromolecules and particles. In this study, different extrapolation procedures used in MALS were investigated with regard to accuracy and robustness in the obtained molar mass and rms radius. Three different mathematical transformations of the light scattering function referred to as the Debye, Zimm, and Berry methods for constructing the Debye plot were investigated for two idealized polymer shapes, homogeneous spheres and random coils, with radii from 25 to 250 nm. The effect of the angular interval used for the extrapolation was investigated, as was the robustness of the different transformations toward errors in the measured light scattering intensity at low angles. For an rms radius less than 50 nm, the relative error in molar mass due to extrapolation was less than 1% independent of the method used. For larger radii, the error increased and the extrapolation procedure became more critical. For random coil polymers, the Berry method was superior in terms of accuracy and robustness. For spheres, the Debye method was superior. The Zimm method was inferior to the others. The different extrapolation methods were evaluated and compared on experimental data from a size exclusion chromatography-MALS analysis of an ultrahigh molar mass poly(ethylene oxide) (PEO). The PEO data qualitatively verified the calculations and stressed the importance of optimizing the extrapolation procedure after careful evaluation of the experimental data. A discussion of how to detect erroneous data in an experimental Debye plot is given.