Filter matrix estimation in automated DNA sequencing

In four-color fluorescence-based automated DNA sequencing, a 4×4 filter matrix parameterizes the relationship between the dye-intensity signals of interest and the data collected by an optical imaging system. The filter matrix is important because the estimated DNA sequence is based on the dye intensities that can only be recovered via inversion of the matrix. Here, the authors present a calibration method for the estimation of the columns of this matrix, using data generated through a special experiment in which DNA samples are labeled with only one fluorescent dye at a time. Simulations and applications of the method to real data are provided, with promising results     

Use of cell ELISA for the screening of neurotrophic activities on minor cell populations in retinal monolayer cultures

BACKGROUND: Whereas the secretion of the male vesicular gland in most mammals is amorphous, that of the tree shrew, Tupaia glis, was observed to be stored as globules. METHODS: Vesicular and prostate glands from Tupaia, fixed in glutaraldehyde and osmium, were studied in the light and electron microscopes. Other materials considered included the Tupaia ejaculate produced by electroejaculation and, for comparative purposes, sections of the vesicular gland from a dermopteran, the flying lemur. RESULTS: The vesicular gland epithelium in Tupaia secretes small granular aggregates and occasionally a denser aggregate that is associated with cells having obvious apical Golgi lamellae. In the alveolar lumen, these aggregates unite with others to form, respectively, granular and some dense globules of up to approximately 15 mu in diameter, which appear as such in semen produced by electroejaculation. In contrast to the prostate, however, precursor secretion vesicles were rare in the vesicular epithelium. Although poorly fixed, the vesicular gland secretion from a flying lemur also appeared to form globules. CONCLUSIONS: Although it is unlike the homogeneous secretion elaborated in most mammals, including primates and insectivores, the globular product of the Tupaia vesicular gland seems comparable to that in a variety of mega- and microbats, among representative species of which it appears to provide the bulk material for the vaginal copulation plug. Because a museum specimen examined here also indicates its occurrence in a flying lemur, the globular vesicular gland secretion common to Tupaiidae, to at least some Mega- and Microchiroptera, and apparently to Dermoptera may provide a soft tissue feature of some value in the cladistic approach to phylogenetic reconstruction within the Archonta. Anat.     

Effect of specimen size and loading conditions on spalling of concrete

Different qualities of concrete have been fire tested using different geometries of the specimens as well as different load levels and load configurations. The main objective with the study was to examine a test methodology consisting of a full‐scale test and different small scale‐tests for determining the probability of spalling and the amount of spalling of fire exposed concrete structures. A reference specimen was defined as a one‐sided fire exposed slab with the dimensions 1800 × 1200 mm² giving an exposed area of 1500 × 1200 mm². A number of concrete qualities with different probabilities for spalling, were tested using the reference specimen. These tests showed that the reference specimens worked well giving the expected test results. Small specimens were manufactured in different shapes with the same concrete as the one used in the reference tests. These small specimens were tested either at the same time as the reference specimens in the large furnace or afterwards on a small‐scale furnace where the fire exposed surface was 450 × 360 mm². The test results clearly show the increased probability and the increased amount of spalling by using external compressive loading. The results also show that by using pre‐stress through bars or wires the load can be lost due to heating of the bars/wires which results in a decreased amount of spalling. The boundary of the specimen also affects the amount of spalling. The spalling around the edges was in all tests less than the spalling on the central parts of the exposed area. It could also be noted that the spalling did not pass completely through any of the specimens. The reason for this is probably that the water/vapour could migrate out from the unexposed surface of the specimen. Copyright © 2006 John Wiley & Sons, Ltd.     

UNSTEADY-STATE SORPTION MEASUREMENTS A TEST OF DIFFERENT METHODS TO EVALUATE THE DIFFUSIVITY FROM UNSTEADY-STATE SORPTION MEASUREMENTS

Different simple methods for evaluating the diffusivity from a sorption measurement are presented and tested when there is a surface resistance (a limited mass transfer coefficient), a non-perfect step in relative humidity or non-Fickian effects. It is concluded that the different methods have different qualities and it is impossible to give a general recommendation on which method to use. The best tactic is probably to use more than one of the methods. A knowledge of the experimental conditions will help in choosing the best method.     

Crystallinity and lateral crystallite size of different UHMW PE materials

Nascent high-molecular-weight (UHMW) polyethylene (PE) samples of different origins show a rather high crystallinity of about 70–75% and contain both a major portion of orthorhombic extended chain crystallites and a minor portion of triclinic crystallites. The triclinic content is greater the higher the molecular weight of the sample and the higher the activity of the used catalyser. A melting / recooling treatment results in a reduction of crystallinity by about 15–25% and disappearance of the triclinic phase. Further, an irreversible conversion of nascent orthorhombic extended chain crystallites to orthorhombic folded chain crystallites of increased lateral dimensions and crystalline perfections takes place during the melting / recooling treatment. The results are compared to those obtained for lower-molecular-weight PE samples and for high-strength / modulus PE fibers of different origins.     

Variation in Malting Quality and Heat Resistance in the Malting Barley Variety “Alexis”

In earlier studies concerning vigour, where subsamples are heat‐treated before germination there was found heat‐sensitive as well as heat‐resistant barley samples. The vigour model developed by Ellis and Roberts and further developed at Carlsberg, could only describe the heat‐sensitive barleys. Seventeen samples of the “Alexis” variety grown widely in Europe were collected from the EBC trials in 1994 in order to see if heat resistance in barley was influenced by different growing conditions. We found both heat‐sensitive samples following the vigour model as well as pronounced heat‐resistant samples, but these were not divided according to growing conditions. The germination curves dependent on heat treatment and germination time were evaluated by Principal Component Analysis (PCA). Heat‐resistant barley samples could be differentiated from heat‐sensitive samples already after ½ h of heat treatment at 68°C (12% moisture) and after 3 days of germination. The barley samples were analysed with regard to malting quality. The PCA evaluation of the data divided the samples according to growing location, mainly due to differences in protein and β‐glucan. However, the malting analyses could not describe the differences in heat resistance and sensitivity of the barleys. The biochemical background of the heat resistance found is discussed on the basis of literature. Our findings should give an experimental basis for exploiting a biochemical principle for heat resistance, which is formed during grain filling and consumed during storage and germination.     

An efficient return algorithm for non-associated plasticity with linear yield criteria in principal stress space

An efficient return algorithm for stress update in numerical plasticity computations is presented. The yield criterion must be linear in principal stress space and can be composed of any number of yield planes. Each of these yield planes may have an associated or non-associated flow rule. The stress return and the formation of the constitutive matrix is carried out in principal stress space. Here the manipulations simplify and rely on geometrical arguments. The singularities arising at the intersection of yield planes are dealt with in a straightforward way also based on geometrical considerations. The method is exemplified on non-associated Mohr–Coulomb plasticity throughout the paper.     

An overall model for maintenance optimization

This paper presents an approach for identifying the optimal maintenance schedule for the components of a production system. Safety, health and environment objectives, maintenance costs and costs of lost production are all taken into consideration, and maintenance is thus optimized with respect to multiple objectives. Such a global approach to maintenance optimization requires expertise from various fields, e.g., decision theory, risk analysis and reliability and maintenance modelling. Further, a close co-operation between management, maintenance personnel and analysts is required to achieve a successful result. In the past this has been a major obstacle to the extensive use of proper maintenance optimization methods in practice, and techniques to promote the communication between the involved parties of the optimization process is an essential element in the suggested approach. A simple step by step presentation of the required modelling is provided. Contrary to most current methods of RCM (Reliability Centered Maintenance), the approach is based on an analytic model, and therefore gives a sound framework for carrying out a proper maintenance optimization. The approach is also flexible as it can be carried out at various levels of detail, e.g., adopted to available resources and to the managements willingness to give detailed priorities with respect to objectives on safety vs production loss.     

Design and Characterization of the CLIMPAQ,Chamber for Laboratory Investigations of Materials,Pollution and Air Quality*

A test chamber has been developed in order to provide a small and simple emission testing facility capable of testing construction products in a climate where the important climatic parameters such as temperature, ventilation rate and air velocity can be varied independently around typical indoor values. The test chamber CLIMPAQ is made of panes of window glass. Other main surface materials are stainless steel and eloxated aluminium. The chamber has a volume of 50.9 litres and is designed to meet the requirements for quantifying air pollution. In this investigation human subjects acted as air pollution judges, and chemical characterization of the air pollution was carried out. Carpet, linoleum, wall paint and seal- ant were tested simultaneously in the CLIMPAQ and in four other chambers ranging from a full-scale chamber of 28 m³ to a field and laboratory emission cell of 3.5· 10^?5m³. Product ranking is the same in all chambers for the sensory measurements. Emission rates based on sensory measurements differ for all products less than 100 % except for tests in a 3-litre chamber where emission rates were higher. Chemical measurements differ up to approximately 10 times for the same product in different chambers. Deviations appear to be the result of different environmental parameters in the various chambers. Low air concentrations or high specific ventilation rates seem to increase emissions, while differences in air velocities and sink properties may also be the cause of differences in emission rates.     

Evidence for Remote Effects of Dreissenid Mussels on the Amphipod Diporeia: Analysis of Lake Ontario Benthic Surveys, 1972–2003

The status of invasive dreissenid mussels (Dreissena polymorpha and D. bugensis) and native amphipods (Diporeia spp.) in Lake Ontario was assessed in 2003 and compared with historical data. D. polymorpha (zebra mussels) were rarely observed in 2003, having been displaced by D. bugensis (quagga mussels). D. bugensis expanded its depth range from 38 m depth in 1995 to 174 m in 2003 and this dreissenid reached densities averaging 8,000/m² at all sites < 90 m. During the same time period, Diporeia populations almost completely disappeared from 0–90 m depth, continuing a declining trend from 1994–1997 reported in previous studies. The average density of Diporeia in the 30–90 m depth interval decreased from 1,380/m² to 63/m² between 1997 and 2003. Prior to 2003, areas deeper than 90 m represented a refuge for Diporeia, but even these deep populations decreased, with densities declining from 2,181/m2 in 1999 to 545/m2 in 2003. Two common hypotheses for the decline of Diporeia in the Great Lakes are food limitation and a toxin/pathogen associated with dreissenid pseudofeces. The Diporeia decline in deep waters preceded the expansion of D. bugensis to these depths, and suggests that shallow dreissenid populations remotely influence profundal habitats. This pattern of decline is consistent with mechanisms that act from some distance including nearshore dreissenid grazing and downslope transport of pseudofeces.