A Comparison of Scanning and Two-Wavelength Microspectrophotometry

Because of the absence of suitable standards, microspectrophotometry suffers from a lack of objective verification. An approach to this problem is suggested which is based on the comparison of results obtained when different techniques or instruments are applied to the same objects. The application of this approach to scanning versus two-wavelength photometry has been justified by the widely different bases of these two methods. A group of ascites tumor cells stained with gallocyanin-chrome alum was measured successively with both methods and a high degree of proportionality between the two sets of results was found. This suggests that the two methods measure the same quality of the cells within a standard deviation of 3.39 per cent. This degree of correlation is a verification of the accuracy of both of the methods and shows that either one is suitable for resolving differences in stain content between cell nuclei of the order of 10 per cent.     

Teaching Preschoolers Combinatory Experimentation

Many investigators stress the necessity of developing in preschoolers the activity of experimentation with new objects, since this is an important aspect in the self-reliance and active engagement of the child's thought [3,7,8]. Various authors have proposed their own methods for teaching children this activity [1,4,6], but I have been unable to find any studies on how preschoolers learn to experiment independently with complex, multirelational objects. In contrast to objects whose relations to each other are simple, multirelational objects reveal dependencies that are characterized by the interaction of several factors.     

Invariant visual object recognition: a model, with lighting invariance.

How are invariant representations of objects formed in the visual cortex? We describe a neurophysiological and computational approach which focusses on a feature hierarchy model in which invariant representations can be built by self-organizing learning based on the statistics of the visual input. The model can use temporal continuity in an associative synaptic learning rule with a short term memory trace, and/or it can use spatial continuity in Continuous Transformation learning. The model of visual processing in the ventral cortical stream can build representations of objects that are invariant with respect to translation, view, size, and in this paper we show also lighting. The model has been extended to provide an account of invariant representations in the dorsal visual system of the global motion produced by objects such as looming, rotation, and object-based movement. The model has been extended to incorporate top-down feedback connections to model the control of attention by biased competition in for example spatial and object search tasks. The model has also been extended to account for how the visual system can select single objects in complex visual scenes, and how multiple objects can be represented in a scene.     

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.     

DIODA: delineation and feature extraction of microscopical objects.

A computer program is described for delineation and measurement of microscopical objects, such as cells and chromosomes, which may have been scanned using absorbance, fluorescence or reflectance microscopy. The quality of the object delineation is optimized through the controur ratio, which is simply computed from the object contour. Geometrical features, like the perimeter and area are computed. A new definition is introduced for the background region, especially suited for the analysis of closely packed objects. This definition is based upon a comparison between total staining material content values resulting from a variety of methods and circumstances. The program is principally intended for use in the on-line real-time environment of a small laboratory computer, but may be used off-line as well. It has facilities for displaying the results and the process by which they are produced. A program module is described for displaying scan data on a bilevel display using an adaptation of the sigma-delta method.     

Hard-object feeding in sooty mangabeys (Cercocebus atys) and interpretation of early hominin feeding ecology

Morphology of the dentofacial complex of early hominins has figured prominently in the inference of their dietary adaptations. Recent theoretical analysis of craniofacial morphology of Australopithecus africanus proposes that skull form in this taxon represents adaptation to feeding on large, hard objects. A modern analog for this specific dietary specialization is provided by the West African sooty mangabey, Cercocebus atys. This species habitually feeds on the large, exceptionally hard nuts of Sacoglottis gabonensis, stereotypically crushing the seed casings using their premolars and molars. This type of behavior has been inferred for A. africanus based on mathematical stress analysis and aspects of dental wear and morphology. While postcanine megadontia, premolar enlargement and thick molar enamel characterize both A. africanus and C. atys, these features are not universally associated with durophagy among living anthropoids. Occlusal microwear analysis reveals complex microwear textures in C. atys unlike those observed in A. africanus, but more closely resembling textures observed in Paranthropus robustus. Since sooty mangabeys process hard objects in a manner similar to that proposed for A. africanus, yet do so without the craniofacial buttressing characteristic of this hominin, it follows that derived features of the australopith skull are sufficient but not necessary for the consumption of large, hard objects. The adaptive significance of australopith craniofacial morphology may instead be related to the toughness, rather than the hardness, of ingested foods.     

The Laplacian of Gaussian and arbitrary z-crossings approach applied to automated single particle reconstruction

The automation of single particle selection and tomographic segmentation of asymmetric particles and objects is facilitated by continuing improvement of methods based on the detection of pixel discontinuity. Here, we present the new arbitrary z-crossings approach which can be employed to enhance the accuracy of edge detection algorithms that are based on the second derivative. This is demonstrated using the Laplacian of Gaussian (LoG) filter. In its normal implementation the LoG filter uses a z value of zero to define edge contours. In contrast, the arbitrary z-crossings approach allows the user to adjust z, which causes the subsequently generated contours to tend towards lighter or darker image objects, depending on the sign of z. This functionality has been coupled with an additional feature: the ability to use the major and minor axes of bounding contours to hone automated object selection. In combination, these features significantly enhance the accuracy of particle selection and the speed of tomographic segmentation. Both features have been incorporated into the software package Swarm(PS) in which parameters are automatically adjusted based on user defined target selection.     

Use of the bioluminescent method for the determination of bacterial adenosinetriphosphate (ATP-metry) in microbiology

The attention of a wide circle of specialists has recently been attracted by different methods for rapid determination of pathogenic microorganisms in biological specimens, environmental objects and foodstuffs, as well as in cases of possible acts of bioterrorism. In this respect the bioluminescent method for determination of adenosine triphosphate (ATP) contained in microbial cells is of interest. The method is based on the interaction ATP, luciferase and luciferin, accompanied by giving off energy in the form of light emission. When compared with routine methods, the use of this method considerably reduces the duration of the analysis, and its high sensitivity is comparable with that of the polymerase chain reaction. In this review the data on the prospects of the practical use of the bioluminescent method of ATP-metry are presented.     

Quantitative genetics,version 3.0: where have we gone since 1987 and where are we headed?

The last 20 years since the previous World Congress have seen tremendous advancements in quantitative genetics, in large part due to the advancements in genomics, computation, and statistics. One central theme of this last 20 years has been the exploitation of the vast harvest of molecular markers—examples include QTL and association mapping, marker-assisted selection and introgression, scans for loci under selection, and methods to infer degree of coancestry, population membership, and past demographic history. One consequence of this harvest is that phenotyping, rather than genotyping, is now the bottleneck in molecular quantitative genetics studies. Equally important have been advances in statistics, many developed to effectively use this treasure trove of markers. Computational improvements in statistics, and in particular Markov Chain Monte Carlo (MCMC) methods, have facilitated many of these methods, as have significantly improved computational abilities for mixed models. Indeed, one could argue that mixed models have had at least as great an impact in quantitative genetics as have molecular markers. A final important theme over the past 20 years has been the fusion of population and quantitative genetics, in particular the importance of coalescence theory with its applications for association mapping, scans for loci under selection, and estimation of the demography history of a population. What are the future directions of the field? While obviously important surprises await us, the general trend seems to be moving into higher and higher dimensional traits and, in general, dimensional considerations. We have methods to deal with infinite-dimensional traits indexed by a single variable (such as a trait varying over time), but the future will require us to treat much more complex objects, such as infinite-dimensional traits indexed over several variables and with graphs and dynamical networks. A second important direction is the interfacing of quantitative genetics with physiological and developmental models as a step towards both the gene–phenotype map as well as predicting the effects of environmental changes. The high-dimensional objects we will need to consider almost certainly have most of their variation residing on a lower (likely much lower) dimensional subspace, and how to treat these constraints will be an important area of future research. Conversely, the univariate traits we currently deal with are themselves projections of more complex structures onto a lower dimensional space, and simply treating these as univariate traits can result in serious errors in understanding their selection and biology. As a field, our future is quite bright. We have new tools and techniques, and (most importantly) new talent with an exciting international group of vibrant young investigators who have received their degrees since the last Congress. One cloud for concern, however, has been the replacement at many universities of plant and animal breeders with plant and animal molecular biologists. Molecular tools are now an integral part of breeding, but breeding is not an integral part of molecular biology.     

A formalization of consensus index methods

A consensus in dex method comprises a consensus method and a consensus index that are defined on a common set of objects (e.g. classifications). For each profile of objects, the consensus method returns a consensus object representing information or structure shared among profile objects, while the consensus index returns a quantitative measure of agreement among profile objects. Since the relationship between consensus method and consensus index is poorly understood, we propose simple axioms prescribing it in the most general terms. Many taxonomic consensus index methods violate these axioms because their consensus indices measure consensus object invariants rather than profile agreement. We propose paradigms to obtain consensus index methods that measure agreement and satisfy the axioms. These paradigms salvage concepts underlying consensus index methods violating the axioms. This work was supported in part by the Faculty of Science at Memorial University of Newfoundland, and by the Natural Sciences and Engineering Research Council of Canada Under Grant A-4142.     

Comparison of preferences for object properties in the rat using paired- and free-choice paradigms

A common method for testing preference for objects is to determine which of a pair of objects is approached first in a paired-choice paradigm. In comparison, many studies of preference for environmental enrichment (EE) devices have used paradigms in which total time spent with each of a pair of objects is used to determine preference. While each of these paradigms gives a specific measure of the preference for one object in comparison to another, neither method allows comparisons between multiple objects simultaneously. Since it is possible that several EE objects would be placed in a cage together to improve animal welfare, it is important to determine measures for rats’ preferences in conditions that mimic this potential home cage environment. While it would be predicted that each type of measure would produce similar rankings of objects, this has never been tested empirically. In this study, we compared two paradigms: EE objects were either presented in pairs (paired-choice comparison) or four objects were presented simultaneously (simultaneous presentation comparison). We used frequency of first interaction and time spent with each object to rank the objects in the paired-choice experiment, and time spent with each object to rank the objects in the simultaneous presentation experiment. We also considered the behaviours elicited by the objects to determine if these might be contributing to object preference. We demonstrated that object ranking based on time spent with objects from the paired-choice experiment predicted object ranking in the simultaneous presentation experiment. Additionally, we confirmed that behaviours elicited were an important determinant of time spent with an object. This provides convergent evidence that both paired choice and simultaneous comparisons provide valid measures of preference for EE objects in rats.     

Patterns of sensitivity of association measures in numerical taxonomy

Numerical taxonomy and the related methods of multidimensional scaling (MDS) have been applied in a wide range of disciplines in the last twenty-five years. A common feature has been the initial derivation of a measure of association or proximity among pairs of objects from a multivariate data matrix. Although a large number of measures are in use, there has been little systematic study of the sensitivities of these measures to different aspects of character data. I report here a general model, for a class of these measures, that reveals basic patterns of sensitivity that underlie a wide variety of common measures and shows that there is a continuum of potential association measures which exhibit useful combinations of sensitivities. I distinguish between “separation” sensitive and “minimum value” sensitive measures and describe a new measure that is intermediate in exhibiting both minimum value and separation sensitivity. The utility of this new type of measure in three disciplines—ecology, psychology, and systematics—is briefly described.     

生物序列的聚类分析

通过不同的聚类方式,对公共数据库中生物序列数据进行生物信息的挖掘,以达到在更广泛和更深入的框架中了解它们之间的相互关系的目的。以帕金森病相关基因所对应的mRNA序列为例,使用双序列比对的得分值作为序列之间的距离定义。同时为解决不同聚类分析之间的差异,分别采用模糊聚类和层次聚类两种不同的方法进行聚类分析。并由不同聚类方法得到的一致分类聚类的结果为基因功能分类提供支持,为进一步揭示生物序列所蕴涵的生物学知识和生物学规律提供可参考的依据。     

Aerococcus viridans in the Hospital Environment

Aerococcus viridans has been described as an airborne organism prevalent in occupied rooms. It has also been described as an organism having many characteristics that might cause it to be confused with streptococci or staphylococci, and this may account for the fact that the presence of A. viridans has not been reported in the hospital environment or in clinical specimens. Swab specimens were taken from 47 objects in 11 different areas in a local hospital, cultured overnight in Trypticase Soy Broth, and streaked on blood-agar and on a selective serum agar containing potassium tellurite and crystal violet. Of 85 alpha-hemolytic cultures isolated, 11 proved to be typical A. viridans based on diagnostic tests that also were applied to a collection of gram-positive cocci, including authentic strains of A. viridans. These organisms are gram-positive cocci with a strong tendency toward tetrad formation in broth cultures. They are predominantly aerobic, have a very weak catalase activity, and lack porphyrin respiratory enzymes. Three similar cultures also were obtained from routine clinical specimens.     

The microbiological data base of the data bank project BD1

The aim of the project BD1 (Biotechnology Data Bank 1) is to improve the data processing for research in biotechnology. In BD1, data of several classes of objects and methods are compiled. A data file conception consisting of object data files, method data files and feature data files was created, which can be easily extended to further classes, and which allows the combination of different classes of features to the same class of objects. There are two main approaches to use BD1: 1. making available informations on certain biotechnological objects, 2. the identification of unknown objects by means of their feature pattern. The microbiological data base and the possibilities of data base search are presented by example of lactic acid bacteria.     

Instrumental methods for studies of structure and function of root systems of large trees

New methods using different physical principles have been successfully applied in studies of root systems of large trees. The ground-penetrating radar technique provides 3D images of coarse roots (starting with a diameter of about 20 mm) from the soil surface down to a depth of several metres. This can even be done under layers of undisturbed materials such as concrete, asphalt and water. Fine roots cannot be visualized by this method, but the total rooted volume of soil can be determined. The differential electric conductance method has been used for fast measurement of conducting (absorbing) root surfaces. However, more testing is needed. Both these methods are non-invasive. The results can be verified by an almost harmless excavation of whole root systems, including fine roots, using the ultrasonic air-stream (air-spade) method. This method is suitable for all studies, as well as practical operations on roots or objects in their vicinity, where a gentle approach is required. Sap flow measurements on their own or in tandem with soil moisture monitoring play a leading role in studying root function and hydraulic redistribution of flow in the soil. The water absorption function of roots can be studied by measuring sap flow on individual root branches directly (as on crown branches) and also indirectly, by measuring the radial pattern of sap flow in different sapwood depths at the base of a stem. Root zone architecture can also be estimated indirectly by studying its functionality. The heat field deformation method with multi-point sensors has been found to be very convenient for this purpose. A combination of several such methods is recommended whenever possible, in order to obtain detailed information about the root systems of trees.     

Computer modeling of spatial-time distribution of metabolite concentrations in phantoms of biological objects by example of rat brain pial

A method for quantitative assessment of the metabolite concentrations in digital phantoms of the biological objects has been proposed. The objects under consideration are expected to have a complex geometry of diffusive sources. We present an algorithm for calculation of non-steady state gradients of the diffusing compounds under their constant border concentration. The algorithm is based on the analytical solutions for a centrally symmetric spherical source. Spatial-time distribution of metabolites is considered by the example of glucose diffusion around blood vessels in the rat brain pial. It was shown that glucose level in the tissue was increased after glycine treatment and under condition of other biological system parameters to be unchanged.     

城市道路绿地对局地空气污染扩散的影响研究进展

城市道路绿地对局地污染物扩散的影响研究近年来比较活跃,获得了大量研究结果,但因缺乏总结梳理,尚难切实指导城市绿地建设实践.本文对道路及绿带类型进行归类,以实地监测和数值模拟两种常用方法为分类前提,对相关研究涉及的污染物浓度指标、植物特征因子及其他影响因子进行系统回顾,总结了道路绿地对局地污染扩散的影响规律,进而指出未来...     

Methods of histological treatment of the labyrinth]

The otic labyrinth presents one of the most difficult objects for histological investigations as it is situated in the thick layer of the temporal bone and has a very complex structure. At the same time, a method for treating this object is not given in general hand-books on pathological techniques. The methods for histological treatment of the otic labyrinth elaborated by Wittmaack and later on modified are presented in the article. Methods for fixation, vital fixation including, decalcination, dehydratation and saturation of the objects prepared for histological investigation are described in details. Methods for the temporal bone orientation in order to obtain sections of the internal otic structures in the most advantageous plane depending on the purpose and aim of the investigation are recommended.