Mathematical models for nonparametric inferences from line transect data

A general mathematical theory of line transects is develoepd which supplies a framework for nonparametric density estimation based on either right angle or sighting distances. The probability of observing a point given its right angle distance (y) from the line is generalized to an arbitrary function g(y). Given only that g(O) = 1, it is shown there are nonparametric approaches to density estimation using the observed right angle distances. The model is then generalized to include sighting distances (r). Let f(y/r) be the conditional distribution of right angle distance given sighting distance. It is shown that nonparametric estimation based only on sighting distances requires we know the transformation of r given by f(O/r).     

Multiple human taste receptor sites: a molecular modeling approach

Numerous experimental data on the human peripheral taste system suggest the existence of multiple low-affinity and low-specificity receptor sites which are responsible for the detection and the complete discrimination of a very large number of organic molecules. According to this hypothesis, a given molecule interacts with numerous taste receptors and vice versa. Statistical analysis of taste intensities estimated by 58 human subjects for various molecules enables the calculation of taste intermolecular distances. For the present modeling study, we hypothesized that a short taste distance (i.e. taste similarity) between two distinct molecules indicates that they bind with similar distributions of affinities to the taste receptors, and hence display similar binding motifs. In order to find common molecular binding motifs among 14 selected organic tastants, hydrogen-bonding and hydrophobic interaction properties were mapped onto their molecular surfaces. The 14 surfaces were then cut in 240 fragments, most of which were made up of 2-4 potentially interacting zones. A correspondence index was defined to measure the analogy between two optimally superimposed fragments. The 75 most representative fragments were all matched pairwise. Twelve distinct clusters of fragments were isolated from the 2775 calculated comparisons. These 12 fragment types were used to calculate structural similarity distances. We then performed a combinatorial analysis to identify which fragment combination best reconciled structural and taste distances. We finally identified an optimal subset of seven fragment types out of the 12, which significantly and best accounted for the 91 pairwise taste distances between all 14 modeled tastants. These seven validated fragment types are therefore presented as good candidates to be recognized by the same number of distinct taste receptor sites. Potential applications of these identified binding motifs to tastant design are suggested.     

Application of total internal reflection fluorescence microscopy to study cell adhesion to biomaterials

Cell adhesion and function depend upon the formation of adhesive contacts between the cell and substrate. Determination of the cell substrate contact area is necessary in order to understand how biomaterial properties influence cell adhesion. In this review we describe the development and application of total internal reflection fluorescence microscopy (TIRFM) to quantify the separation distance of cells from a biomaterial surface. An approximate theory is presented for the straightforward calculation of separation distances when a fluor is placed in the cell membrane. The validity of this approach is discussed. TIRFM is compared to interference reflection microscopy and related techniques that measure cell/substrate separation distances. This approach is then applied to a number of important problems in cell substrate interactions, including changes in contact area and adhesion strength on biomaterial surfaces, analysis of bond strength, and real-time measurement of cell/substrate separation distances following exposure to flow.     

Tribological Investigation of Effect of Grain Size in 304 Austenitic Stainless Steel

Stainless steels are widely used in a variety of engineering applications such as food appliances, surgical instruments, nuclear reactors and cryogenic applications. The properties of stainless steel are greatly affected by the grain size. The present study investigates the effect of grain size on sliding wear behavior of AISI 304 stainless steel. The sliding wear properties are measured using a Pin-on-Disc machine. Annealing heat treatment process varies the grain size of steel at 1100 °C. The wear test is performed on different grain sizes of AISI 304 steel at various sliding speeds under dry condition. The wear rate of the steels at different sliding distances is plotted as a function of grain size. The maximum wear rate is obtained at an intermediate grain size. It is noted that frictional force and temperature initially increases and then reaches the saturation plateau. The results are used to establish a correlation between the grain size and sliding wear properties of stainless steel. The present study is useful in enhancing the life of various components made of the stainless steel.     

Estimation of Unsaturated Hydraulic Parameters from Infiltration and Internal Drainage Experiments

Inverse problem of determining unsaturated soil hydraulic properties from transient infiltration and internal drainage events are analyzed. Hydraulic properties are assumed to be described by van Genuchten’s relationships. The inverse problem is solved using Levenberg-Marquardt method while the forward problem is solved using a mass conservative finite difference numerical scheme. The bias induced by different objective functions on the parameter estimates with error free and noisy data are analyzed. Field experiments are conducted at two sites to compare the parameter estimates obtained from the infiltration and internal drainage tests. The results indicate that some objective functions induce undue bias in the estimated parameters in the presence of noise in the data and as such selecting a suitable objective function should be given due importance in the parameter estimation. The comparison of the parameter estimates from infiltration and internal drainage experiments at two sites indicates that the parameter estimates are close to each other. It is concluded that infiltration experiment, which is simpler and of short duration can be an alternative to internal drainage experiment for estimating the unsaturated soil parameters.     

Fluorescent labeling of NK2 receptor at specific sites in vivo and fluorescence energy transfer analysis of NK2 ligand-receptor complexes

A fluorescent unnatural amino acid was introduced biosynthetically at known sites into the G protein-coupled neurokinin (tachykinin) NK2 receptor by suppression of UAG nonsense codons with the aid of a chemically misacylated synthetic tRNA specifically designed for the incorporation of unnatural amino acids during heterologous expression in Xenopus oocytes. A systematic UAG-scanning mutagenesis in NK2 extra- or intracellular loops and proximal transmembrane domains established that readthrough at some UAG sites may represent a limitation to the range of applicability of the nonsense suppression methodology. Fluorescence-labeled NK2 mutants containing an unique fluorescent nitrobenzoxadiazoyl-diaminopropionic acid residue at known sites were shown to be functionnally active. Intermolecular distances were determined by measuring the fluorescence resonance energy transfer (FRET) between the fluorescent unnatural amino acid and a fluorescently labeled NK2 heptapeptide antagonist in a native membrane environment. These distances confirmed the seven transmembrane topology for G protein-coupled receptors and determined a structural model for NK2 ligand-receptor interactions. The peptide is inserted between the fifth and sixth transmembrane domains, thus suggesting that antagonism may be caused by preventing correct packing of the helices required for receptor function.     

Effect of surface topography of titanium on surface chemistry and cellular response

A number of aryl semicarbazones had been shown previously to possess significant anticonvulsant properties. The principal objective of the present investigation was to determine the importance of the primary amino group in this series of compounds by replacing it with other substituents. The results indicate that the amino group was not essential for anticonvulsant activity. However its replacement by an aryl ring generally abolished activity while a terminal phenylamino function was better tolerated. Thus both the size of the group and its hydrogen bonding capabilities appear to influence bioactivity. Alteration of the oxygen atom of the semicarbazones by isosteres did not enhance anticonvulsant properties.     

Subfamily of olfactory receptors characterized by unique structural features and expression patterns

The complex chemospecificity of the olfactory system is probably due to the large family of short-looped, heptahelical receptor proteins expressed in neurons widely distributed throughout one of the several zones within the nasal neuroepithelium. In this study, a subfamily of olfactory receptors has been identified that is characterized by distinct structural features as well as a unique expression pattern. Members of this receptor family are found in mammals, such as rodents and opossum, but not in lower vertebrates. All identified subtypes comprise an extended third extracellular loop that exhibits amphiphilic properties and contains numerous charged amino acids in conserved positions. Olfactory sensory neurons expressing these receptor types are segregated in small clusters on the tip of central turbinates, thus representing a novel pattern of expression for olfactory receptors. In mouse, genes encoding the new subfamily of receptors were found to be harbored within a small contiguous segment of genomic DNA. Based on species specificity as well as the unique structural properties and expression pattern, it is conceivable that the novel receptor subfamily may serve a special function in the olfactory system of mammals.     

SC1: a marker for astrocytes in the adult rodent brain is upregulated during reactive astrocytosis

An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biochemical properties of amino acids. As a follow-up to the previous study, we have increased the size of the database, which currently contains 402 published indices, and re-performed the single-linkage cluster analysis. The results basically confirmed the previous findings. Another important feature of amino acids that can be represented numerically is the similarity between them. Thus, a similarity matrix, also called a mutation matrix, is a set of 20 x 20 numerical values used for protein sequence alignments and similarity searches. We have collected 42 published matrices, performed hierarchical cluster analyses and identified several clusters corresponding to the nature of the data set and the method used for constructing the mutation matrix. Further, we have tried to reproduce each mutation matrix by the combination of amino acid indices in order to understand which properties of amino acids are reflected most. There was a relationship between the PAM units of Dayhoff's mutation matrix and the volume and hydrophobicity of amino acids. The database of 402 amino acid indices and 42 amino acid mutation matrices is made publicly available on the Internet.     

Calculation of the electrical conductivity of a cesium melt by an LMTO recursive method over a wide temperature range

The structure and properties of liquid cesium are calculated over a wide temperature range. The Shommers method, which is based on Winter’s experimental data, is used to construct structural models. A density of states is obtained by a recursive method using an LMTO Hamiltonian. Electrical conductivity is calculated by the Kubo-Greenwood formula. The degree of electron localization as a function of temperature is estimated, and the metal-nonmetal transition in cesium is shown to be related to electron localization at atomic clusters.     

Span-Dependent Distributions of the Bending Strength of Spruce Timber

Tests data of bending strengths of a large number of timber beams of different spans obtained at the Swedish Institute for Wood Technology Research reveal a statistical structure that can be represented in a simple probabilistic model of series system type. A particular feature of the data from one of the large test series is that unintentionally the data became randomly censored upwards. This censoring of the data rules out both the moment estimation method and the maximum likelihood method. Instead valid parameter estimates can be obtained by maximizing the posterior density defined as the likelihood function multiplied by a suitably chosen noninformative prior density (MP method). Subsequently using bias factors assessed by simulation ensures that the corrected MP estimates are unbiased. A closed form analytical expression for the distribution function of the bending strength of a beam with any given number of defect clusters follows from the obtained distribution model for the bending strength of the random single defect cluster. The empirical distribution function of bending test results for a sample of beams with two defect clusters is well predicted, and for long beams with several defect clusters the same is the case in the lower tail up to at least about the 50% probability level.     

Induction of resting microglia in culture medium devoid of glycine and serine

Cultured microglial cells usually exhibit ameboid morphology and peripheral macrophage-like properties, which are distinct from those observed in the normal mature brain. This might be caused by the inappropriate culture of microglial cells in high concentrations (approximately 200-400 microM) of Gly and Ser, although the concentrations of the amino acids in extracellular spaces of the brain parenchyma are quite low (approximately 5 microM). In the present study, we focused on the concentration-dependent effects of glycine (Gly) and serine (Ser) on microglial morphology and function. Under Gly/Ser-free and serum-free condition, the majority of rat microglial cells displayed round morphology, whereas in the presence of 5 microM Gly and 25 microM Ser, which correspond to the concentrations of Gly and Ser in the cerebrospinal fluid, they extended multiple branched processes and formed clusters of rough endoplasmic reticulum. On the other hand, Gly and Ser did not affect morphology of astrocytes. The viability of microglia was not affected by the changes in the concentrations of Gly and Ser. Metabolic activity, activities of acid phosphatase and inducible nitric oxide synthase, and superoxide anion (O2-) generation were all strongly suppressed in Gly/Ser-free medium or in medium containing physiological concentrations of both amino acids. Such activities were all enhanced in harmony with increases in the concentrations of Gly and Ser. Thus, microglial cells cultured in Gly/Ser-free medium, even though exhibiting ameboid morphology, appears to be in the functionally resting state. Furthermore, once the resting state was achieved, the microglial cells remained inactive even after the subsequent 24 h culture in serum-supplemented medium containing 400 microM of both amino acids. The medium conditioned by microglial cells that were cultured in the presence of 400 microM of Gly and Ser was toxic to cortical neurons, whereas the microglia-conditioned medium obtained in the absence of both amino acids facilitated the survival of cortical neurons. Therefore, microglial cells in the resting state, which was induced in the Gly/Ser-free condition, are likely to support neurons. Microglial cells could ramify on glass coverslips coated with astrocyte-derived extracellular matrix or on coverslips coated thinly with fibronectin and/or laminin even under the Gly/Ser-free condition. The ramified cells as induced in this way kept suppressed O2- generating activity. These findings suggest that resting ramified microglial cells with a neurotrophic activity can be induced with the combination of Gly/Ser-free medium and small amounts of extracellular matrix proteins, and that the resting state is rather stable.     

A uniform molecular model of delta opioid agonist and antagonist pharmacophore conformations

Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code.     

Isolation, crystallization, and primary amino acid sequence of human platelet factor 4

Human platelet factor 4 was purified by a method employing affinity chromatography on heparin/agarose. The amino acid sequence of the protein was determined by automatic Edman degradations and carboxypeptidase Y digestion. There are 70 amino acids in the protein with 5 of the 8 negatively charged residues clustered near the NH2 terminus and 10 of the 13 positively charged residues in clusters of 3 and 4 elsewhere in the protein. Small crystals have been obtained from ammonium sulfate solutions which give a promising preliminary x-ray diffraction pattern.     

Representation of amino acid sequences as two-dimensional point patterns

An algorithm for the representation of amino acid sequences as two-dimensional point patterns (2-D plot) is described. The algorithm is based on chaos game representation (CGR) for DNA sequences and was extended for amino acid sequences. The 2-D plot depicts the sequentiality of amino acids and the amino acid composition of a protein. Changes in a protein sequence as insertion, deletion and repeats of amino acids are characterized by specific geometrical properties and changes in the 2-D plots. The 2-D plot may be considered as a two-dimensional "fingerprint" of a protein. The properties of the algorithm are explained by user-defined amino acid sequences. As an example the 2-D plots of two selected heart proteins are generated. The sequences of these proteins are obtained from the protein sequence database SWISS-PROT.     

Prolactin induction of the alpha 2-Macroglobulin gene in rat ovarian granulosa cells: stat 5 activation and binding to the interleukin-6 response element

Lantibiotics form a group of modified peptides with unique structures, containing post-translationally modified amino acids such as dehydrated and lanthionine residues. In the gram-positive bacteria that secrete these lantibiotics, the gene clusters flanking the structural genes for various linear (type A) lantibiotics have recently been characterized. The best studied representatives are those of nisin (nis), subtilin (spa), epidermin (epi), Pep5 (pep), cytolysin (cyl), lactocin S (las) and lacticin 481 (lct). Comparison of the lantibiotic gene clusters shows that they contain conserved genes that probably encode similar functions. The nis, spa, epi and pep clusters contain lanB and lanC genes that are presumed to code for two types of enzymes that have been implicated in the modification reactions characteristic of all lantibiotics, i.e. dehydration and thio-ether ring formation. The cyl, las and lct gene clusters have no homologue of the lanB gene, but they do contain a much larger lanM gene that is the lanC gene homologue. Most lantibiotic gene clusters contain a lanP gene encoding a serine protease that is presumably involved in the proteolytic processing of the prelantibiotics. All clusters contain a lanT gene encoding an ABC transporter likely to be involved in the export of (precursors of) the lantibiotics. The lanE, lanF and lanG genes in the nis, spa and epi clusters encode another transport system that is possibly involved in self-protection. In the nisin and subtilin gene clusters two tandem genes, lanR and lanK, have been located that code for a two-component regulatory system. Finally, non-homologous genes are found in some lantibiotic gene clusters. The nisI and spaI genes encode lipoproteins that are involved in immunity, the pepI gene encodes a membrane-located immunity protein, and epiD encodes an enzyme involved in a post-translational modification found only in the C-terminus of epidermin. Several genes of unknown function are also found in the las gene cluster. A database has been assembled for all putative gene products of type A lantibiotic gene clusters. Database searches, multiple sequence alignment and secondary structure prediction have been used to identify conserved sequence segments in the LanB, LanC, LanE, LanF, LanG, LanK, LanM, LanP, LanR and LanT gene products that may be essential for structure and function. This database allows for a rapid screening of newly determined sequences in lantibiotic gene clusters.     

The Azotobacter vinelandii NifEN complex contains two identical [4Fe-4S] clusters

The nifE and nifN gene products from Azotobacter vinelandii form an alpha2beta2 tetramer (NifEN complex) that is required for the biosynthesis of the nitrogenase FeMo cofactor. In the current model for NifEN complex organization and function, the complex is structurally analogous to the nitrogenase MoFe protein and provides an assembly site for a portion of FeMo cofactor biosynthesis. In this work, gene fusion and immobilized metal-affinity chromatography strategies were used to elevate the in vivo production of the NifEN complex and to facilitate its rapid and efficient purification. The NifEN complex produced and purified in this way exhibits an FeMo cofactor biosynthetic activity similar to that previously described for the NifEN complex purified by traditional chromatography methods. UV-visible, EPR, variable-temperature magnetic circular dichroism, and resonance Raman spectroscopies were used to show that the NifEN complex contains two identical [4Fe-4S]2+ clusters. These clusters have a predominantly S = 1/2 ground state in the reduced form, exhibit a reduction potential of -350 mV, and are likely to be coordinated entirely by cysteinyl residues on the basis of spectroscopic properties and sequence comparisons. A model is proposed where each NifEN complex [4Fe-4S] cluster is bridged between a NifE-NifN subunit interface at a position analogous to that occupied by the P clusters in the nitrogenase MoFe protein. In contrast to the MoFe protein P clusters, the NifEN complex [4Fe-4S] clusters are proposed to be asymmetrically coordinated to the NifEN complex where NifE cysteines-37, -62, and -124 and NifN cysteine-44 are the coordinating ligands. On the basis of a homology model of the three-dimensional structure of the NifEN complex, the [4Fe-4S] cluster sites are likely to be remote from the proposed FeMo cofactor assembly site and are unlikely to become incorporated into the FeMo cofactor during its assembly.     

Regulation of Schizosaccharomyces pombe Wee1 tyrosine kinase

Wee1 tyrosine kinase regulates mitosis by carrying out the inhibitory tyrosine 15 phosphorylation of Cdc2 M-phase inducing kinase. Schizosaccharomyces pombe Wee1 is a large protein, consisting of a C-terminal catalytic domain of approximately 350 amino acids preceded by a N-terminal domain of approximately 550 residues. The functional properties of the Wee1 N-terminal domain were investigated by expressing truncated forms of Wee1 in S. pombe. Both positive and negative regulatory domains were identified. Sequences important for Wee1 function were mapped to a central region (residues 363-408). This region is not required for kinase activity or nuclear localization, suggesting it may be involved in substrate recognition. The negative regulatory domain resides in the N-terminal third of Wee1, Wee1 constructs lacking this domain are more effective at delaying mitosis than wild-type Wee1. The negative regulatory domain contains clusters of potential Cdc2 phosphorylation sites. Investigations to monitor the abundance of Wee1 mRNA and protein during the cell cycle were also carried out.     

A technique for identifying the subgroup membership of certain misarticulating children

Cluster analysis was used to identify two homogeneous clusters of 8-9 1/2-year-old children who misarticulated /s/, /r/, or both. The analysis was based on the children's scores on 40 measures of language, reading, auditory processing, and other variables. Discriminant function analysis was then used to identify a subset of five measures and a means of computing classification scores. These measures and the classification scores can be used to identify the cluster membership of new subjects. The use of classification scores for identifying cluster membership was cross-validated against cluster analysis of a second group of children. The two clusters are described in terms of their performance on language and reading measures.     

Simultaneous over- and underconfidence: The role of error in judgment processes.

Two empirical judgment phenomena appear to contradict each other. In the revision-of-opinion literature, subjective probability (SP) judgments have been analyzed as a function of objective probability (OP) and generally have been found to be conservative, that is, to represent underconfidence. In the calibration literature, analyses of OP (operationalized as relative frequency correct) as a function of SP have led to the opposite conclusion, that judgment is generally overconfident. Reanalysis of 3 studies shows that both results can be obtained from the same set of data, depending on the method of analysis. The simultaneous effects are then generated and factors influencing them are explored by means of a model that instantiates a very general theory of how SP estimates arise from true judgments perturbed by random error. Theoretical and practical implications of the work are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)