Analysis of three-dimensional cell imaging obtained with optical microscopy techniques based on defocusing

The properties of an optical microscope are analyzed and analytically evaluated with a simple and effective model in order to understand the true meaning, limitations, and real capabilities of a defocusing technique. Major emphasis is given to the applications related to microscopic objects of biological interest using fluorescence and absorption light microscopy. A procedure for three-dimensional viewing is analyzed and discussed.     

A novel chromatographic method allows on-line reanalysis of the proteome

Liquid chromatography combined with electrospray ionization is widely used for direct analysis of polar and labile molecules by LCMS. The on-line coupling in LCMS is a major strength but also causes a principal limitation that each eluting analyte has to be analyzed immediately and is not available for detailed interrogation after the LCMS run. Here we developed a new chromatographic strategy, which removes this limitation. After column separation the flow is split, one portion is analyzed directly, and the other is diverted to a capture capillary. After the direct LCMS run, the flow is switched, and the portion stored in the capillary is analyzed ("replay run"). We describe a setup consisting of an analytical column, a splitting valve, and a focusing column, which performs at full sensitivity and undiminished chromatographic resolution. We demonstrate three principal advantages of this system: nearly continuous MS utilization, duplicate analysis without requirement for additional sample, and targeting of important but undersampled features in the replay run.     

A Strategic Interaction Model of Punishment Favoring Contagion of Honest Behavior

The punishment effect on social behavior is analyzed within the strategic interaction framework of Cellular Automata and computational Evolutionary Game Theory. A new game, called Social Honesty (SH), is proposed. The SH game is analyzed in spatial configurations. Probabilistic punishment is used as a dishonesty deterrence mechanism. In order to capture the intrinsic uncertainty of social environments, payoffs are described as random variables. New dynamics, with a new relation between punishment probability and punishment severity, are revealed. Punishment probability proves to be more important than punishment severity in guiding convergence towards honesty as predominant behavior. This result is confirmed by empirical evidence and reported experiments. Critical values and transition intervals for punishment probability and severity are identified and analyzed. Clusters of honest or dishonest players emerge spontaneously from the very first rounds of interaction and are determinant for the future dynamics and outcomes.     

Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra

Two procedures for analyzing overlapping optical spectra of mixtures of pyridine hemochromes are described, and extinction coefficients of pyridine hemochromes are provided for use with these methods. In the first procedure, absorbance is measured at a number of wavelengths equal to the number of components to be analyzed. This is the minimum amount of spectral data from which the concentration of each species can be calculated. In the second procedure, absorbance is measured at a number of wavelengths greater than the number of components to be analyzed. This redundancy of information makes it impossible to fit spectra which contain contributions from additional components, unless the spectra of the additional components are equal to linear combinations of the spectra of the species being analyzed. These two procedures are generally applicable to analyses of absolute or difference spectra of mixtures of components obeying Beer's law. The sensitivity to error in the absorbance measurements is only slightly greater than that for measuring a pure component at a single wavelength.     

Chromosome mosaicism in a population sample.

An analysis has been made of mosaicism found in the different types of chromosome abnormalities among the 19000 persons examined at the Cytogenetic Laboratory, Risskov. The percentage with mosaicism was 36 in both triple-X and Turner's syndrome, it was 7 and 11% in XYY and Klinefelter's syndrome, respectively, and 2 in autosomal abnormalities. We found a mosaicism frequency of 11% in population studies with 5 cells analyzed primarily compared with 7% in other studies, in which 10-50 cells were analyzed primarily. (The difference is not significant.) The total frequency of mosaicism was 8%. The first cell with the chromosome aberration establishing the mosaicism was found among the first 5 cells in 40 of the 44 cases with mosaicism, and all but one of the 44 cases would have been established as mosaics, if the guidlines indicated by Bochkov et al. (1974) had been followed; that is 11 cells analyzed primarily, and if one of these cells has a chromosome aberration, the number of cells analyzed is increased to 17; if 2 cells have the same chromosome aberration, the number of cells analyzed is extended to 23, and if 3 cells with the same chromosome aberration is found among these 23 cells, the mosaicism is established. Aneuploid or structural chromosome abnormalities present in all cells may be detected by analysis of 2-3 cells of good quality. Mosaicism with 2 or more cell clones with different chromosome patterns are extremely difficult to detect, if the percentage of cell clones with chromosome aberration is low. The incidence of chromosome abnormalities found in all cells in newborn children in the different studies is very similar as shown in a recent survey of 6 different studies by Jacobs et al. (1974). The incidence of mosaicism varies according to the frequency of artefactual aneuploidy, the variety of tissue studied, number of cells analyzed from each tissue as well as the acuity of the observer and the checking procedures.     

Effect of the fluid-structure interactions on low-density lipoprotein transport within a multi-layered arterial wall

The effects of fluid-structure interactions (FSI) and pulsation on the transport of low-density lipoprotein (LDL) through an arterial wall are analyzed in this work. To this end, a comprehensive multi-layer model for both LDL transport as well as fluid-structure interaction (FSI) is introduced. The constructed model is analyzed and compared with the existing results in the limiting cases. Excellent agreement is found between the presented model and the existing results in the limiting cases. The presented model takes into account the complete multi-layered LDL transport while incorporating the FSI aspects to enable a comprehensive study of the deformation effect on the pertinent parameters of the transport processes within an artery. Since the flow inside an artery is time-dependent, the impact of pulsatile flow is also analyzed with and without FSI. A detailed analysis is presented to illustrate the consequence of different factors on the LDL transport in an artery.     

A mathematical model for weed dispersal and control

Mathematical models for weed dispersal and control are developed, analyzed and numerically simulated. A model incorporating periodic control, e.g. herbicide application, is derived for a plant population in a spatially homogeneous setting. The model is extended to a spatially heterogeneous population where plant dispersal is incorporated. The dispersal and control model involves integrodifference equations, discrete in time and continuous in space. The models are analyzed to determine values of the control parameter that prevent weed spread. The effects of the control on travelling wave solutions are investigated numerically.     

Realization of couplings in a polynomial type mixed-mode cellular neural network

In this paper realization of couplings between cells in a polynomial type mixed-mode cellular neural network (CNN) is analyzed. The choice of the multiplier is discussed and two multiplier types are analyzed. Also, two circuits for generating the second and third order polynomial terms of cell output are described. The accuracy of the multipliers and polynomial circuits at the presence of device mismatch is analyzed.     

A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data

The phylogenetic utility of mitochondrial genomes (mtgenomes) is examined using the framework of a preliminary phylogeny of Orthoptera. This study presents five newly sequenced genomes from four orthopteran families. While all ensiferan and polyneopteran taxa retain the ancestral gene order, all caeliferan lineages including the newly sequenced caeliferan species contain a tRNA rearrangement from the insect ground plan tRNA(Lys)(K)-tRNA(Asp)(D) swapping to tRNA(Asp) (D)-tRNA(Lys) (K) confirming that this rearrangement is a possible molecular synapomorphy for this suborder. The phylogenetic signal in mtgenomes is rigorously examined under the analytical regimens of parsimony, maximum likelihood and Bayesian inference, along with how gene inclusion/exclusion, data recoding, gap coding, and different partitioning schemes influence the phylogenetic reconstruction. When all available data are analyzed simultaneously, the monophyly of Orthoptera and its two suborders, Caelifera and Ensifera, are consistently recovered in the context of our taxon sampling, regardless of the optimality criteria. When protein-coding genes are analyzed as a single partition, nearly identical topology to the combined analyses is recovered, suggesting that much of the signals of the mtgenome come from the protein-coding genes. Transfer and ribosomal RNAs perform poorly when analyzed individually, but contribute signal when analyzed in combination with the protein-coding genes. Inclusion of third codon position of the protein-coding genes does not negatively affect the phylogenetic reconstruction when all genes are analyzed together, whereas recoding of the protein-coding genes into amino acid sequences introduces artificial resolution. Over-partitioning in a Bayesian framework appears to have a negative effect in achieving convergence. Our findings suggest that the best phylogenetic inferences are made when all available nucleotide data from the mtgenome are analyzed simultaneously, and that the mtgenome data can resolve over a wide time scale from the Permian (approximately 260 MYA) to the Tertiary (approximately 50 MYA).     

固定化微生物处理氨氮废水的研究进展

生物方法因其高效、持久及无二次污染已经成为治理水污染的重要方法,固定化微生物不仅加强微生物治理效果,更能保证微生物生存稳定,是现阶段生物方法治理水污染的主要组分。近年来学者们也做了很多固定化微生物处理各类废水的研究,并取得了大量优异成果。文章对固定化微生物技术进行剖析,分析各类固定化载体材料及各种固定化方法优缺点;解析利用固定化微生物处理氨氮废水效果研究及固定化微生物处理效果影响因素;综述近年来固定化微生物处理氨氮废水应用情况;最后进行总结,并提出自己的展望。     

Homogenized stiffness matrices for mineralized collagen fibrils and lamellar bone using unit cell finite element models

Mineralized collagen fibrils have been usually analyzed like a two-phase composite material where crystals are considered as platelets that constitute the reinforcement phase. Different models have been used to describe the elastic behavior of the material. In this work, it is shown that when Halpin–Tsai equations are applied to estimate elastic constants from typical constituent properties, not all crystal dimensions yield a model that satisfy thermodynamic restrictions. We provide the ranges of platelet dimensions that lead to positive definite stiffness matrices. On the other hand, a finite element model of a mineralized collagen fibril unit cell under periodic boundary conditions is analyzed. By applying six canonical load cases, homogenized stiffness matrices are numerically calculated. Results show a monoclinic behavior of the mineralized collagen fibril. In addition, a 5-layer lamellar structure is also considered where crystals rotate in adjacent layers of a lamella. The stiffness matrix of each layer is calculated applying Lekhnitskii transformations, and a new finite element model under periodic boundary conditions is analyzed to calculate the homogenized 3D anisotropic stiffness matrix of a unit cell of lamellar bone. Results are compared with the rule-of-mixtures showing in general good agreement.     

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

SUMMARY: Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long list of genes, which are potentially interesting in the analyzed process. In order to gain biological understanding from this type of data, it is necessary to analyze the functional annotations of all genes in this list. The Gene-Ontology (GO) database provides a useful tool to annotate and analyze the functions of a large number of genes. Here, we introduce a tool that utilizes this information to obtain an understanding of which annotations are typical for the analyzed list of genes. This program automatically obtains the GO annotations from a database and generates statistics of which annotations are overrepresented in the analyzed list of genes. This results in a list of GO terms sorted by their specificity. AVAILABILITY: Our program GOstat is accessible via the Internet at http://gostat.wehi.edu.au     

A Standardized Procedure for Echoencephalography and for Analyzing Echoencephalograms

Although echoencephalography is a simple, convenient and atraumatic diagnostic technique, the accuracy and reliability of this test and whether it is reproducible can be greatly influenced by the way in which the examination is performed and subsequently analyzed. Echoencephalography in 850 patients has led to the development of a standardized technique which takes into account the positioning of the patient, the application of the transducer, the identification of the midline-echo-complex, and the elimination of observer bias. Once performed the test must meet rigid standards of acceptability. If acceptable the test is analyzed according to an established format.     

Special Relationships between Female Asian Elephants (Elephas maximus) in Zoological Gardens

Social relationships between female zoo elephants were analyzed on three different zoo groups. Interactions were defined as either affiliative or agonistic. The most frequent interactions were found to be touching of the partner's mouth, genital sinus, face and trunk. The calf was the individual involved in most social interactions. Placing the trunk tip into the partner's mouth is a well known behaviour, the correlation between this behaviour and aggression was analyzed and a further function is suggested. Aggressive behaviour was analyzed and the hypothesis derived that rank order has to be established and is flexible in a non-kin group. The hypothesis that Asian elephant females may form special relationships was tested and confirmed. The following behaviour patterns were determined as indicators of a special relationship: Spatial proximity, partner-specific reactions to arousal and to vocalizing, and omission of agonistic behaviour. An experiment confirmed the hypothesis that the removal of one member of a special relationship from the enclosure would elicit more arousal behaviour in the respective partner.     

Islands and ergodicity of the plasma current in toroidal magnetic confinement systems

Magnetic and current structures arising due to resonant perturbations of an equilibrium current-carrying magnetic configuration are analyzed using the Hamiltonian formalism. Special attention is paid to axisymmetric tokamak and pinch configurations. It is shown that, due to the very different dependences of the magnetic and current rotational transforms on the plasma pressure, the resonances (islands) of the magnetic field may not coincide with those of the current. The perturbed force-free equilibrium of a cylindrical pinch in which the field and current islands overlap is analyzed. The long-lived ribbon structures observed in the JET tokamak are explained as a manifestation of a force-free magneto-current island.     

Mechanisms of generation of signals in vertebrate photoreceptors.

The electrical responses of rods are analyzed in different ionic environments. It is shown that the dark level of the membrane potential is predominantly determined by a sodium current, while the peak of responses to bright light is controlled by the concentration of external potassium. The sag from the peak to the plateau of photoresponses seems to be generated by different ionic mechanism. The effects produced by substituting the external calcium with EGTA are also analyzed. It is suggested that calcium plays a role in different mechanisms of generation of electrical responses.     

A theory of photosensitivity of some lower animals

The two-factor nerve excitation theory is applied to the photoreactions of some lower animals along with the assumption that the threshold itself varies under the action of light, thus behaving formally like a third factor. The dependence of the reaction time upon the intensity of the stimulus is derived and is shown to follow the Bunsen-Roscoe law. The dependence of reaction time upon the time of exposure to light of a fixed intensity is derived and analyzed. The effect of dark adaptation upon the reaction time is analyzed quantitatively. Light adaptation and the effects of termination of exposure after light adaptation are discussed from the standpoint of this theory and the theory is found to be in agreement with observations.     

Linear Transformation of Electromagnetic Wave Beams of the Electron-Cyclotron Range in Toroidal Magnetic Configurations

The field structure of quasi-optical wave beams tunneled through the evanescence region in the vicinity of the plasma cutoff in a nonuniform magnetoactive plasma is analyzed. This problem is traditionally associated with the process of linear transformation of ordinary and extraordinary waves. An approximate analytical solution is constructed for a rather general magnetic configuration applicable to spherical tokamaks, optimized stellarators, and other magnetic confinement systems with a constant plasma density on magnetic surfaces. A general technique for calculating the transformation coefficient of a finite-aperture wave beam is proposed, and the physical conditions required for the most efficient transformation are analyzed.     

Pyrimidine auxotrophy and the complementation map of the Rudimentary locus of Drosophila melanogaster

Summary The complementation pattern of twelve rudimentary mutations has been analyzed at two different levels. When analyzed on the basis of complementation for a wing abnormality the mutations can be divided into three groups, each of which is believed to affect the activity of one of the first three enzymes of pyrimidine synthesis (Norby, 1973; Jarry and Falk, 1974; Rawls and Fristrom, 1975). However, when the mutants are analyzed for complementation on the basis of a second phenotype, pyrimidine auxotrophy, the distinction between two of these three groups is not evident. The disparity in the two patterns probably reflects a different threshold of gene activity required for the detection of an auxotrophic phenotype as compared to that at which a wing abnormality is detectable.The biochemical basis of these results is interpreted in light of recent data suggesting that at least the first two enzymes of pyrimidine synthesis are contained within a single multifunctional protein complex (Soderholm et al., 1975).