Despiking Acoustic Doppler Velocimeter Data

A new method for detecting spikes in acoustic Doppler velocimeter data sequences is suggested. The method combines three concepts: (1) that differentiation enhances the high frequency portion of a signal, (2) that the expected maximum of a random series is given by the Universal threshold, and (3) that good data cluster in a dense cloud in phase space or Poincaré maps. These concepts are used to construct an ellipsoid in three-dimensional phase space, then points lying outside the ellipsoid are designated as spikes. The new method is shown to have superior performance to various other methods and it has the added advantage that it requires no parameters. Several methods for replacing sequences of spurious data are presented. A polynomial fitted to good data on either side of the spike event, then interpolated across the event, is preferred by the authors.     

Human neonatal ovary: proposal of a three-dimensional model

A model of human neonatal ovary is presented, derived from morphometric, evaluations carried out on left ovaries removed from five full-term neonates with a 46, XX karyotype, free from malformations of the genital apparatus. According to this model, the gonad can be represented by a triaxial ellipsoid with a central medullary core surrounded by a cortical stratum of constant thickness. The germinal population, consisting of follicles and primitive cortical tissue, occupies the cortex, intermingled with the interstitium or stroma. In the cortex it is then possible to describe an outer layer formed by primitive cortical tissue, and an inner portion occupied by follicles. The primary and secondary follicles fill the portion near the medulla and the primordial ones are contained in the middle and outer zones. Since the variability observed among ovaries is slight, we can propose a mean model of neonatal ovary in which the spatial relationships among the different components, the total number of follicles and their position in the cortex can be calculated.     

Geographic Information Systems-Based Three-Dimensional Critical Slope Stability Analysis and Landslide Hazard Assessment

In this paper, by combining the geographic information systems (GIS) spatial analysis function and a hydrologic analysis and modeling tool with a column-based three-dimensional (3D) slope stability analysis model, a new GIS grid-based 3D deterministic model has been developed for slope stability analysis. Assuming the initial slip as the lower half of an ellipsoid, the identification of the 3D critical slip surface in the 3D slope stability analysis is performed by means of a minimization of the 3D safety factor using Monte Carlo random simulation. By using this hydrologic analysis and modeling tool, dividing the whole study area into slope units, and taking each slope unit as a study object, the minimum 3D safety factor for each slope unit can be obtained, and the landslide hazard can then be mapped for the whole study area.     

Functional Equivalence of Spatial Representations Derived From Vision and Language: Evidence From Allocentric Judgments.

Past research (e.g., J. M. Loomis, Y. Lippa, R. L. Klatzky, & R. G. Golledge, 2002) has indicated that spatial representations derived from spatial language can function equivalently to those derived from perception. The authors tested functional equivalence for reporting spatial relations that were not explicitly stated during learning. Participants learned a spatial layout by visual perception or spatial language and then made allocentric direction and distance judgments. Experiments 1 and 2 indicated allocentric relations could be accurately reported in all modalities, but visually perceived layouts, tested with or without vision, produced faster and less variable directional responses than language. In Experiment 3, when participants were forced to create a spatial image during learning (by spatially updating during a backward translation), functional equivalence of spatial language and visual perception was demonstrated by patterns of latency, systematic error, and variability. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Computational analysis of the binding of P1 variants of domain 3 of turkey ovomucoid inhibitor to Streptomyces griseus protease B

Binding constants for complexes of variants of the ovomucoid inhibitor domain 3 from turkey (OMTKY3) and Streptomyces griseus protease B (SGPB) have been computed. On the basis of the crystallographically determined structures of the complexes, continuum electrostatic calculations have been carried out to evaluate the electrostatic contribution to the binding energy. The hydrophobic component was computed based on the change in the solvent accessible surface area on complex formation. These two terms were combined linearly and the parameters for the protein dielectric, atomic solvation parameter and a constant term were derived using a multivariate fit to the observed binding energies. The resulting fit shows a high correlation with a multiple coefficient of determination of 0.79. This indicates that 79% of the variation in the observed binding energies is explained by the electrostatic and hydrophobic terms. The analysis results in a protein dielectric of 8.2 and an atomic solvation parameter of 30 cal/mol A2. As a test, these parameters were used to calculate the binding energies of complexes of chymotrypsin and of leukocyte elastase OMTKY3, as well as three other variants of OMTKY3 bound to SGPB. As these structures were not used for the multivariate fit, they serve as an independent check on the derived parameters. The calculated energies for the three new variants of OMTKY3 are in good agreement with the observed values. However, the binding energies of the other complexes are poorly predicted. This implies that the parameters that were obtained are not transferable. The possible causes for this lack of transferability are discussed.     

Long-term depression at thalamocortical synapses in developing rat somatosensory cortex

PURPOSE: To develop and apply a method for the derivation of cancellous bone architectural parameters from in vivo magnetic resonance (MR) images of the distal radius and to evaluate these parameters as predictors of vertebral fracture status in osteopenia. MATERIALS AND METHODS: MR images (137 x 137 x 500-micron3 voxel size) were acquired with a three-dimensional partial flip-angle spin-echo pulse sequence in the distal radius of 36 women. Subjects were classified as healthy or with osteoporosis on the basis of vertebral deformity and bone mineral density (BMD). Images rated as of adequate quality in 20 subjects were processed with a method that is applicable in the limited spatial resolution regime. The method relies on histogram deconvolution to obviate binary segmentation. Cancellous bone structure was treated as a quasi-regular lattice and analyzed with spatial autocorrelation, yielding parameters that quantify intertrabecular spacing, contiguity, and a measure of longitudinal alignment called tubularity. RESULTS: Whereas neither BMD nor any of the structural parameters individually correlated significantly with vertebral deformity fraction, a simple function that involved tubularity and longitudinal spacing predicted deformity fraction well (r = .78, P < .005). CONCLUSION: Histomorphometric parameters characterizing cancellous bone in the distal radius can be derived from in vivo MR microimages and are predictive of vertebral deformity.     

Involvement of Neurospora mitochondrial tyrosyl-tRNA synthetase in RNA splicing. A new method for purifying the protein and characterization of physical and enzymatic properties pertinent to splicing

The Neurospora CYT-18 protein, the mitochondrial tyrosyl-tRNA synthetase, functions in the splicing of group I introns. Here, bacterially expressed CYT-18 protein, purified by a new procedure involving polyethyleneimine precipitation to remove tightly bound nucleic acids, was used to characterize properties pertinent to RNA splicing. Analytical ultracentrifugation and other methods showed that the CYT-18 protein is an asymmetric homodimer. The measured frictional ratio, f/fo = 1.55, corresponds to an axial ratio of 10 for a prolate ellipsoid or 12 for an oblate ellipsoid. Like bacterial TyrRSs, the CYT-18 protein exhibits half-sites reactivity, each homodimer having one active site for tyrosyl adenylation and RNA splicing. The splicing activity of CYT-18 was unaffected by aminoacylation substrates at concentrations used in aminoacylation reactions, whereas the TyrRS activity was inhibited by physiological concentrations of the splicing cofactor GTP, as well as CTP or UTP, or by low concentrations of a group I intron RNA. Kinetic measurements suggest that the binding of CYT-18 to a group I intron substrate is a two-step process, with an initial biomolecular step that is close to diffusion limited (3.24 +/- 0.03 x 10(7) M-1s-1) followed by a slower conformational change (0.54 +/- 0.07 s-1). After CYT-18 binding, splicing occurs at a rate of 0.0025 s-1, within 6-fold of the rate of self-splicing of the Tetrahymena large rRNA intron in vitro. The Kd for the complex between the CYT-18 protein and a group I intron substrate, calculated from koff/kon, was < 0.3 pM, substantially lower than determined by presumed equilibrium measurements [Guo, Q., & Lambowitz, A. M. (1992) Genes Dev. 6, 1357-1372]. As a result of this tight binding, the CYT-18 protein functions stoichiometrically in in vitro splicing reactions due to its extremely slow dissociation from the excised intron RNA. The very tight binding of the CYT-18 protein to the intron RNA raises the possibility that specific mechanisms exist for dissociating the protein from the excised intron in vivo.     

Multiple parameter cross-species protein identification using MultiIdent--a world-wide web accessible tool

Recent increases in the number of genome sequencing projects means that the amount of protein sequence in databases is increasing at an astonishing pace. In proteome studies, this is facilitating the identification of proteins from molecularly well-defined organisms. However, in studies of proteins from the majority of organisms, proteins must be identified by comparing analytical data to sequences in databases from other species. This process is known as cross-species protein identification. Here we present a new program, MultiIdent, which uses multiple protein parameters such as amino acid composition, peptide masses, sequence tags, estimated protein pI and mass, to achieve cross-species protein identification. The program is structured so that protein amino acid composition, which is highly conserved across species boundaries, first generates a set of candidate proteins. These proteins are then queried with other protein parameters such as sequence tags and peptide masses. A final list of database entries which considers all analytical parameters is presented, ranked by an integrated score. We illustrate the power of the approach with the identification of a set of standard proteins, and the identification of proteins from dog heart separated by two-dimensional gel electrophoresis. The MultiIdent program is available on the world-wide web at: http://www.expasy.ch/sprot/multiident.h tml.     

The fine structure of the digital corpuscle of the mouse toe pad, with special reference to nerve fibers

Digital corpuscles in the dermal papillae of the mouse toe pad have been studied using light and electron microscopy of serial thick and thin sections, and silver impregnations of frozen sections. These corpuscles are ellipsoid in shape and approximately 10-30 mum in diameter. They consist of one to three lamellar cells, nerve fibers and a capsule. These digital corpuscles are regarded as small Meissner corpuscles. The capsule is perineural epithelium. One or two myelinated nerve fibers and occasionally an unmyelinated nerve fiber enter the corpuscle. The axon terminals contain many mitochondria and a variable population of vesicular profiles. These terminals are ellipsoid or discoid in shape with the long axis parallel to the skin surface. The cytoplasmic plates (or lamellae) of the lamellar cells are arranged parallel to the skin surface, as is the cleft between the bilaterally symmetrical stacks of lamellae. Small processes extend from the expanded terminal of the neurite into the cleft between the lamellae. The relationship of the neurite terminal and associated lamellar cells resembles in some respects the organization of the inner core of Pacinian corpuscles. Intraepidermal fibers derived from myelinated neurites of the corpuscle may extend to the superficial epidermis. Intraepidermal fibers derived from unmyelinated neurites usually terminate in the basal regions of the epidermis.     

楔横轧铝合金轧件内部空洞演变

采用数值模拟的手段,研究了楔横轧轧制铝合金时轧件内部空洞演化的一般规律和工艺参数对空洞演化的影响.结果表明:轧件内部单空洞演化的一般规律是球形-椭球形-轧件内部轴向贯通的孔腔;多空洞演化时,位于轧件中心的空洞的变化规律和单空洞时相似,但其余位置的空洞发生了闭合,它们对中心空洞有正作用方面的影响;在模具的各个阶段中,楔入段的后期和展宽段的前期是内部空洞演化的关键阶段;在楔横轧加工的工艺参数方面,展宽角是影响空洞演化的最敏感因素,其次是断面收缩率,再次是成形角.研究证明了小的成形角、展宽角和断面收缩率均有利于轧件内部空腔的扩展.     

Phyletic relationships of protein structures based on spatial preference of residues

A structure-based scoring matrix MDPRE was derived from amino acid spatial preferences in protein structures. Sequence alignment and evolutionary studies by using MDPRE matrix gave similar results as those from ordinary sequence and structure alignments. It is interesting that a matrix derived from structure data solely could give comparable alignment results, strongly indicating the intimate connection between protein sequences and structures. The branch order and length from this approach were close to those obtained by a structure comparison method. Thus, by applying this structure-based matrix, the trees obtained should reflect evolutionary characteristics of protein structure. This approach takes advantage over a direct structure comparison in that (1) only a sequence and MDPRE matrix are needed, making it simple and widely applicable (especially in the absence of 3-dimensional protein structure data); (2) an established algorithm for sequence alignment and tree building could be employed, providing opportunities for direct comparison between matrices from different methodologies. One of the most striking features of this method is its capability to detect protein structure homologies when the sequence identities are low. This was well reflected in the given examples of the alignment of dinucleotide-binding domains.     

The influence of the spatial structure of focal hepatic lesions on volume measurements performed with two and three-dimensional sonography using the ellipsoid formula

A total of 63 patients with localized hepatic lesions were examined using two and three-dimensional sonography. The tumor volumes were calculated by means of the ellipsoid formula, compared with an experimentally determined reference volume and subsequently differentiated into correct and erroneous measurements according to the WHO criteria for tumor volumes. In a second test series, an analysis of the tumor shapes was carried out using parallel projections. It could be seen that 65% of the erroneous measurements resulted from the use of the ellipsoid formula, a procedure which is used to determine the volume of hepatic lesions. In the third part of this study, it was found that findings which are difficult to measure are frequently not recognized as such by the investigator making use of two-dimensional sonography. As a consequence, the volume measurements of focal hepatic lesions in oncology patients being considered for particular therapies should preferably be carried out with the aid of planimetric measurements rather than with the use of the ellipsoid formula.     

Prediction of membrane proteins based on classification of transmembrane segments

The number of transmembrane segments often corresponds to a structural or functional class of membrane proteins such as to seven-transmembrane receptors and six-transmembrane ion channels. We have developed a new prediction method to detect the membrane protein class that is defined by the number of transmembrane segments, as well as to locate the transmembrane segments in the amino acid sequence. Each membrane protein class is represented by a model of ordering different types of transmembrane segments. Specifically, we have classified the transmembrane segments in known membrane proteins into five groups (types) using the Mahalanobis distance with the average hydrophobicity and the periodicity of hydrophobicity as a measure of similarity. The discriminant functions derived for these groups were then used to detect transmembrane segments and to match with the models for one- to fourteen-spanning membrane proteins and for globular proteins. Using the test data set of 89 membrane proteins whose transmembrane positions are known by experimental evidence, 61.8% of the proteins and 85.1% of the transmembrane segments were correctly predicted. Because of the new feature to predict membrane protein classes, the method should be useful in the functional assignment of genomic sequences.     

Simultaneous Prediction of Saturated Hydraulic Conductivity and Drainable Porosity Using the Inverse Problem Technique

The saturated hydraulic conductivity K and the effective porosity f are two important input parameters needed for lateral drain spacing design, as well as some other applications. The technical and economic justification, of most drainage projects, is mainly connected to these two parameters. The current design procedure is based upon calculation of the lateral spacing, using some average values of K and f within the drainage area. The objectives of this study were to introduce a new method for simultaneous estimation of K and f parameters using the inverse problem technique, and to evaluate five different unsteady drainage analytical models of the Boussinesq equation, suggested by different researchers for simultaneous prediction of the parameters. Consequently, five different analytical models for predicting water table profiles were solved, using the inverse problem technique. Each model was then evaluated. A physical drainage model of 2.2?m length, 0.3?m width, and 0.5?m height was established in the laboratory and carefully packed with a sandy loam soil. A perforated drainage pipe of 4.5?cm in diameter was installed at the bottom end of the model. Many piezometers were inserted in the soil for spatial and temporal water table monitoring. Different data sets from the experiments and literature were used for model calibration. The newly proposed approach that is based upon measuring water table profiles, at different times, was then evaluated with both constant and variable f. The predicted values of the proposed approach indicated reasonable agreement with the measured data. With variable effective porosity, the method was even more accurate to predict the water table profiles. Using the inverse problem technique, all the analytical models provided good agreement with the measured data. Among these, however, the Topp and Moody model predicted more accurate results than other models.     

Fitting objects into holes: On the development of spatial cognition skills.

The authors examined 14- to 26-month-old infants' understanding of the spatial relationships between objects and apertures in an object manipulation task. The task was to insert objects with various cross-sections (circular, square, rectangular, ellipsoid, and triangular) into fitting apertures. A successful solution required the infant to mentally rotate the object to be fit into the aperture and use that information to plan the action. The object was presented standing up in half of the trials; in the other half, it was lying down. The results showed that infants solved the problem consistently from age 22 months and that a successful solution was associated with appropriate preadjustments before the hand arrived with the block to the aperture. No sex differences were found. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Reliability Analysis of Laterally Loaded Piles Involving Nonlinear Soil and Pile Behavior

An alternative approach of analyzing laterally loaded piles in the ubiquitous spreadsheet platform is presented. The numerical procedure couples nonlinear pile flexural rigidity (EpIp) with nonlinear p-y analysis. The deterministic study is then extended to carry out reliability analysis, which reflects the uncertainties and correlation structure of the underlying parameters. The reliability index is evaluated based on the alternative intuitive perspective of an expanding equivalent ellipsoid in the original space of the random variables. This paper investigates two modes of failure: deflection and bending moment, and considers non-normal random variables. Spatial variability of the soil medium is accounted for by incorporating an autocorrelation model. The spreadsheet-based reliability approach can also be coupled with stand-alone programs via the response surface method. The probabilities of failure inferred from reliability indices agree well with Monte Carlo simulations. Simple reliability-based design is demonstrated, in which the appropriate pile section or length that satisfies target reliability in one or more limit states is sought.     

Brain aging: changes in the nature of information coding by the hippocampus

Advanced age in rats is associated with a decline in spatial memory capacities dependent on hippocampal processing. As yet, however, little is known about the nature of age-related alterations in the information encoded by the hippocampus. Young rats and aged rats identified as intact or impaired in spatial learning capacity were trained on a radial arm maze task, and then multiple parameters of the environmental cues were manipulated to characterize the changes in firing patterns of hippocampal neurons corresponding to the presence of particular cues or the spatial relationships among them. The scope of information encoded by the hippocampus was reduced in memory-impaired aged subjects, even though the number of neurons responsive to salient environmental cues was not different from that in young rats. Furthermore, after repeated manipulations of the cues, memory-intact aged rats, like young rats, altered their spatial representations, whereas memory-impaired aged rats showed reduced plasticity of their representation throughout testing. Thus changes in hippocampal memory representation associated with aging and memory loss can be characterized as a rigid encoding of only part of the available information.     

Model of response-reinforcer contingency.

Presents a model of response-reinforcer contingency for guiding research, defining response-reinforcer contingency as the degree of association or correlation between reinforcer delivery and criterion responses that may be indexed by the correlation statistic known as the phi coefficient. Experimental manipulation of this contingency metric requires control of the probability of a criterion response. If the response property used to partition responses into criterion and noncriterion subsets permits the construction of an ordinal scale, then a percentile schedule can be used to control the probability of a criterion response. The model identifies 3 experimentally manipulable parameters that jointly determine phi and clarifies the nature of their interactions. Four experiments, using 100 male Wistar rats in a spatial differentiation paradigm, were conducted to test predictions derived from the model. In these experiments, reinforcer delivery was contingent on the location of a joystick displacement response, and a criterion response was one with a location close to a target value relative to the distribution of locations generated by recent responses. Higher degrees of location differentiation were produced by higher degrees of location-reinforcer contingency, as indexed by phi, and the results of all 4 experiments were parsimoniously accounted for by the model of contingency. (27 ref) (PsycINFO Database Record (c) 2011 APA, all rights reserved)