Microstructural degeneracy associated with a two-point correlation function and its information content

A two-point correlation function provides a crucial yet an incomplete characterization of a microstructure because distinctly different microstructures may have the same correlation function. In an earlier Letter [Gommes, Jiao, and Torquato, Phys. Rev. Lett. 108, 080601 (2012)], we addressed the microstructural degeneracy question: What is the number of microstructures compatible with a specified correlation function? We computed this degeneracy, i.e., configurational entropy, in the framework of reconstruction methods, which enabled us to map the problem to the determination of ground-state degeneracies. Here, we provide a more comprehensive presentation of the methodology and analyses, as well as additional results. Since the configuration space of a reconstruction problem is a hypercube on which a Hamming distance is defined, we can calculate analytically the energy profile of any reconstruction problem, corresponding to the average energy of all microstructures at a given Hamming distance from a ground state. The steepness of the energy profile is a measure of the roughness of the energy landscape associated with the reconstruction problem, which can be used as a proxy for the ground-state degeneracy. The relationship between this roughness metric and the ground-state degeneracy is calibrated using a Monte Carlo algorithm for determining the ground-state degeneracy of a variety of microstructures, including realizations of hard disks and Poisson point processes at various densities as well as those with known degeneracies (e.g., single disks of various sizes and a particular crystalline microstructure). We show that our results can be expressed in terms of the information content of the two-point correlation functions. From this perspective, the a priori condition for a reconstruction to be accurate is that the information content, expressed in bits, should be comparable to the number of pixels in the unknown microstructure. We provide a formula to calculate the information content of any two-point correlation function, which makes our results broadly applicable to any field in which correlation functions are employed.

Long-lasting transcriptional refractoriness triggered by a single exposure to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrimidine

Parkinson's disease (PD) is a progressive neurodegenerative disorder whose etiology is thought to have environmental (toxin) and genetic contributions. The neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrimidine (MPTP) induces pathological features of PD including loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and striatal dopamine (DA) depletion. We previously described the striatal transcriptional response following acute MPTP administration in MPTP-sensitive C57BL/6J mice. We identified three distinct phases: early (5h), intermediate (24h) and late (72h) and reported that the intermediate and late responses were absent in MPTP-resistant Swiss-Webster (SWR) mice. Here we show that C57BL/6J mice pre-treated with a single 40 mg/kg dose of MPTP and treated 9 days later with 4×20 mg/kg MPTP, display a striatal transcriptional response similar to that of MPTP-resistant SWR mice, i.e. a robust acute response but no intermediate or late response. Transcriptional refractoriness is dependent upon the dose of the priming challenge with as little as 10mg/kg MPTP being effective and can persist for more than 28 days. Priming of SWR mice has no effect on their response to subsequent challenge with MPTP. We also report that paraquat, another free radical producer, also elicits striatal transcriptional alterations but these are largely distinct from those triggered by MPTP. Paraquat-induced changes are also refractory to priming with paraquat. However neither paraquat nor MPTP elicits cross-attenuation. Thus exposure to specific toxins triggers distinct transcriptional responses in striatum that are influenced by prior exposure to the same toxin. The prolonged refractory period described here for MPTP could explain at the molecular level the reported discrepancies between different MPTP administration regimens and may have implications for our understanding of the relationship between environmental toxin exposure and PD.

Density of States for a specified correlation function and the energy landscape

The degeneracy of two-phase disordered microstructures consistent with a specified correlation function is analyzed by mapping it to a ground-state degeneracy. We determine for the first time the associated density of states via a Monte Carlo algorithm. Our results are explained in terms of the roughness of an energy landscape, defined on a hypercubic configuration space. The use of a Hamming distance in this space enables us to define a roughness metric, which is calculated from the correlation function alone and related quantitatively to the structural degeneracy. This relation is validated for a wide variety of disordered structures.

Molecular characterization, polymorphism of the ACOX1 gene and association with ultrasound traits in Bos taurus

Acyl-coenzyme A oxidase 1 (ACOX1) is the first enzyme in peroxisomal fatty acid β-oxidation; it is rate-limiting and plays a key role in fatty acid metabolism and fat deposition. ACOX1 is an important candidate gene for meat quality selection through marker-assisted selection. Genomic structural analysis showed that bovine ACOX1 shares 86% identity with human ACOX1. Using PCR-SSCP technology, we discovered a single nucleotide polymorphism (SNP) (A1865C) in exon 13 of the ACOX1 gene. Allele frequencies of this SNP were investigated and evaluated with the χ(2) test in 641 cattle populations; only the Jiaxian red population was not in Hardy-Weinberg equilibrium. Gene heterozygosity, effective allele numbers and polymorphism information content of the bovine ACOX1 locus in seven populations varied from 0.2778 to 0.4954, 1.3846 to 1.9817 and 0.2392 to 0.3727, respectively. We also looked for a potential association of this SNP with ultrasound traits in 327 individuals and found a significant effect on ultrasound backfat thickness and ultrasound marbling score (P < 0.05). Meat quality traits were analyzed in another 71 Qinchuan individuals to determine associations with genotype. Animals with genotype AA had higher mean values of backfat thickness than those with genotypes AC and CC. A represents the base before mutation and C represents the base after mutation. We conclude that this SNP of the ACOX1 gene has potential as a genetic marker for meat quality traits in cattle reproduction and breeding.

Robust algorithm to generate a diverse class of dense disordered and ordered sphere packings via linear programming

We have formulated the problem of generating dense packings of nonoverlapping, nontiling nonspherical particles within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem called the adaptive-shrinking cell (ASC) formulation [S. Torquato and Y. Jiao, Phys. Rev. E 80, 041104 (2009)]. Because the objective function and impenetrability constraints can be exactly linearized for sphere packings with a size distribution in d-dimensional Euclidean space R(d), it is most suitable and natural to solve the corresponding ASC optimization problem using sequential-linear-programming (SLP) techniques. We implement an SLP solution to produce robustly a wide spectrum of jammed sphere packings in R(d) for d=2, 3, 4, 5, and 6 with a diversity of disorder and densities up to the respective maximal densities. A novel feature of this deterministic algorithm is that it can produce a broad range of inherent structures (locally maximally dense and mechanically stable packings), besides the usual disordered ones (such as the maximally random jammed state), with very small computational cost compared to that of the best known packing algorithms by tuning the radius of the influence sphere. For example, in three dimensions, we show that it can produce with high probability a variety of strictly jammed packings with a packing density anywhere in the wide range [0.6, 0.7408...], where π/√18 = 0.7408... corresponds to the density of the densest packing. We also apply the algorithm to generate various disordered packings as well as the maximally dense packings for d=2, 4, 5, and 6. Our jammed sphere packings are characterized and compared to the corresponding packings generated by the well-known Lubachevsky-Stillinger (LS) molecular-dynamics packing algorithm. Compared to the LS procedure, our SLP protocol is able to ensure that the final packings are truly jammed, produces disordered jammed packings with anomalously low densities, and is appreciably more robust and computationally faster at generating maximally dense packings, especially as the space dimension increases.

A novel polymorphism of the lactoferrin gene and its association with milk composition and body traits in dairy goats

Milk composition and body measurement traits, influenced by genes and environmental factors, play important roles in value assessments of efficiency and productivity in dairy goats. Lactoferrin (LF), involved in the efficient expression of protein in milk, is also an anabolic factor in skeletal tissue and a potent osteoblast survival factor. Therefore, it is an important candidate gene for milk composition and body measurement trait selection in marker-assisted selection. We employed PCR-SSCP and DNA sequencing to screen the genetic variations of the LF gene in 549 Chinese dairy goats. A novel single-nucleotide polymorphism (SNP) (G198A in exon II) of the LF gene was detected. The frequencies of the AA genotype were 0.0285 and 0.0261 in GZ and SN populations, respectively. Both populations were found to have low levels of polymorphism and were in Hardy-Weinberg disequilibrium (P < 0.05). We found significant (P < 0.05) associations of the SNP marker with milk protein and acidity in the total population; animals with the AA genotype had higher mean values for milk protein than those with the GA genotype. Animals with genotype AA had higher mean values for withers height than those with genotype GG (P < 0.05). We concluded that this SNP of the LF gene has potential as a genetic marker for milk composition and body traits in dairy goat breeding.

Distinctive features arising in maximally random jammed packings of superballs

Dense random packings of hard particles are useful models of granular media and are closely related to the structure of nonequilibrium low-temperature amorphous phases of matter. Most work has been done for random jammed packings of spheres and it is only recently that corresponding packings of nonspherical particles (e.g., ellipsoids) have received attention. Here we report a study of the maximally random jammed (MRJ) packings of binary superdisks and monodispersed superballs whose shapes are defined by |x1|2p+...+|xd|2p<or=1 with d=2 and 3, respectively, where p is the deformation parameter with values in the interval (0,infinity). As p increases from zero, one can get a family of both concave (0<p<0.5) and convex (p>or=0.5) particles with square symmetry (d=2), or octahedral and cubic symmetry (d=3). In particular, for p=1 the particle is a perfect sphere (circular disk) and for p-->infinity the particle is a perfect cube (square). We find that the MRJ densities of such packings increase dramatically and nonanalytically as one moves away from the circular-disk and sphere point (p=1). Moreover, the disordered packings are hypostatic, i.e., the average number of contacting neighbors is less than twice the total number of degrees of freedom per particle, and yet the packings are mechanically stable. As a result, the local arrangements of particles are necessarily nontrivially correlated to achieve jamming. We term such correlated structures "nongeneric." The degree of "nongenericity" of the packings is quantitatively characterized by determining the fraction of local coordination structures in which the central particles have fewer contacting neighbors than average. We also show that such seemingly "special" packing configurations are counterintuitively not rare. As the anisotropy of the particles increases, the fraction of rattlers decreases while the minimal orientational order as measured by the tetratic and cubatic order parameters increases. These characteristics result from the unique manner in which superballs break their rotational symmetry, which also makes the superdisk and superball packings distinctly different from other known nonspherical hard-particle packings.

Exact constructions of a family of dense periodic packings of tetrahedra

The determination of the densest packings of regular tetrahedra (one of the five Platonic solids) is attracting great attention as evidenced by the rapid pace at which packing records are being broken and the fascinating packing structures that have emerged. Here we provide the most general analytical formulation to date to construct dense periodic packings of tetrahedra with four particles per fundamental cell. This analysis results in six-parameter family of dense tetrahedron packings that includes as special cases recently discovered "dimer" packings of tetrahedra, including the densest known packings with density phi=4000/4671=0.856347... . This study strongly suggests that the latter set of packings are the densest among all packings with a four-particle basis. Whether they are the densest packings of tetrahedra among all packings is an open question, but we offer remarks about this issue. Moreover, we describe a procedure that provides estimates of upper bounds on the maximal density of tetrahedron packings, which could aid in assessing the packing efficiency of candidate dense packings.

Geometrical ambiguity of pair statistics: point configurations

Point configurations have been widely used as model systems in condensed-matter physics, materials science, and biology. Statistical descriptors, such as the n -body distribution function g(n), are usually employed to characterize point configurations, among which the most extensively used is the pair distribution function g(2). An intriguing inverse problem of practical importance that has been receiving considerable attention is the degree to which a point configuration can be reconstructed from the pair distribution function of a target configuration. Although it is known that the pair-distance information contained in g(2) is, in general, insufficient to uniquely determine a point configuration, this concept does not seem to be widely appreciated and general claims of uniqueness of the reconstructions using pair information have been made based on numerical studies. In this paper, we present the idea of the distance space called the D space. The pair distances of a specific point configuration are then represented by a single point in the D space. We derive the conditions on the pair distances that can be associated with a point configuration, which are equivalent to the realizability conditions of the pair distribution function g(2). Moreover, we derive the conditions on the pair distances that can be assembled into distinct configurations, i.e., with structural degeneracy. These conditions define a bounded region in the D space. By explicitly constructing a variety of degenerate point configurations using the D space, we show that pair information is indeed insufficient to uniquely determine the configuration in general. We also discuss several important problems in statistical physics based on the D space, including the reconstruction of atomic structures from experimentally obtained g(2) and a recently proposed "decorrelation" principle. The degenerate configurations have relevance to open questions involving the famous traveling salesman problem.

Mir-128 Regulates the Self-Renewal of Breast Tumor-Initiating Cells through HTERT

Background: hTERT (human telomerase reverse transcriptase), which maintains telomere ends by addittion of the telomere repeat sequence TTAGGG, is increased in cancer cells and embryonic stem cells. However, whether hTERT has a role in regulating breast tumor-initiating cells remains unknown. Therefore, the regulation of hTERT in breast tumor initiating cells (BT-IC) would potentially facilitate our understanding of the etiology of breast cancer.Material and Methods: Enrichment for BT-ICs was performed by mammospheres from suspension cultures. The capacity of self-renewal and differentiation of BT-ICs were determined by mammosphere formation, immunohistochemical analysis of epithelial markers and FACS, respectively. TRAP assay was used to detect telomerase activity. The expression levels of hTERT in BT-ICs, with or without lentivirus-mediated mir-128 transduction, were determined by qRT-PCR and western blot. hTERT siRNA or lentivirus-shTERT were used to silence the expression of hTERT in BT-ICs. Differentially expressed mir-128 in BT-ICs was quantified by qRT-PCR and Northern Blot. The expression of BMI1 was determined by Western Blot.Results: hTERT, as well as telomerase activity, had a higher expression in BT-ICs, compared to the differentiated breast cancer cells. BMI1, the target of mir-128, is increased in BT-ICs. Conversely, the expression level of mir-128 is lower in BT-ICs, compared to the differentiated cells. Mir-128 over-expressing reduced the level of BMI1,as well as hTERT, in BT-ICs. Silencing BMI1 by lentivirus-shRNA transfection in BT-ICs leads to the decrease of hTERT protein level. Furthermore, BT-ICs, with hTERT knockdown, lost its ability to form mammospheres and proliferated poorly under differentiating conditions.Conclutions: mir-128 miRNA is reduced in mammospheric BT-ICs, resulting in up-regulation of BMI1, which further brought on the up-regulation of hTERT. And hTERT promotes self-renewal and blocks epithelial differentiation of BT-ICs. Therefore, mir-128 regulates BT-IC stem-cell like properties by BMI1 and hTERT.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5157.

Human airway smooth muscle is structurally and mechanically similar to that of other species

Airway smooth muscle (ASM) plays a vital role in the exaggerated airway narrowing seen in asthma. However, whether asthmatic ASM is mechanically different from nonasthmatic ASM is unclear. Much of our current understanding about ASM mechanics comes from measurements made in other species. Limited data on human ASM mechanics prevents proper comparisons between healthy and asthmatic tissues, as well as human and animal tissues. In the current study, we sought to define the mechanical properties of healthy human ASM using tissue from intact lungs and compare these properties to measurements in other species. The mechanical properties measured included: maximal stress generation, force-length properties, the ability of the muscle to undergo length adaptation, the ability of the muscle to recover from an oscillatory strain, shortening velocity and maximal shortening. The ultrastructure of the cells was also examined. Healthy human ASM was found to be mechanically and ultrastructurally similar to that of other species. It is capable of undergoing length adaptation and responds to mechanical perturbation like ASM from other species. Force generation, shortening capacity and velocity were all similar to other mammalian ASM. These results suggest that human ASM shares similar contractile mechanisms with other animal species and provides an important dataset for comparisons with animal models of disease and asthmatic ASM.

Dense packings of polyhedra: Platonic and Archimedean solids

Understanding the nature of dense particle packings is a subject of intense research in the physical, mathematical, and biological sciences. The preponderance of previous work has focused on spherical particles and very little is known about dense polyhedral packings. We formulate the problem of generating dense packings of nonoverlapping, nontiling polyhedra within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem, which we call the adaptive shrinking cell (ASC) scheme. This optimization problem is solved here (using a variety of multiparticle initial configurations) to find the dense packings of each of the Platonic solids in three-dimensional Euclidean space R3 , except for the cube, which is the only Platonic solid that tiles space. We find the densest known packings of tetrahedra, icosahedra, dodecahedra, and octahedra with densities 0.823..., 0.836..., 0.904..., and 0.947..., respectively. It is noteworthy that the densest tetrahedral packing possesses no long-range order. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other nontiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. We also derive a simple upper bound on the maximal density of packings of congruent nonspherical particles and apply it to Platonic solids, Archimedean solids, superballs, and ellipsoids. Provided that what we term the "asphericity" (ratio of the circumradius to inradius) is sufficiently small, the upper bounds are relatively tight and thus close to the corresponding densities of the optimal lattice packings of the centrally symmetric Platonic and Archimedean solids. Our simulation results, rigorous upper bounds, and other theoretical arguments lead us to the conjecture that the densest packings of Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This can be regarded to be the analog of Kepler's sphere conjecture for these solids.The truncated tetrahedron is the only nonchiral Archimedean solid that is not centrally symmetric [corrected], the densest known packing of which is a non-lattice packing with density at least as high as 23/24=0.958 333... . We discuss the validity of our conjecture to packings of superballs, prisms, and antiprisms as well as to high-dimensional analogs of the Platonic solids. In addition, we conjecture that the optimal packing of any convex, congruent polyhedron without central symmetry generally is not a lattice packing. Finally, we discuss the possible applications and generalizations of the ASC scheme in predicting the crystal structures of polyhedral nanoparticles and the study of random packings of hard polyhedra.

Dense packings of the Platonic and Archimedean solids

Dense particle packings have served as useful models of the structures of liquid, glassy and crystalline states of matter, granular media, heterogeneous materials and biological systems. Probing the symmetries and other mathematical properties of the densest packings is a problem of interest in discrete geometry and number theory. Previous work has focused mainly on spherical particles-very little is known about dense polyhedral packings. Here we formulate the generation of dense packings of polyhedra as an optimization problem, using an adaptive fundamental cell subject to periodic boundary conditions (we term this the 'adaptive shrinking cell' scheme). Using a variety of multi-particle initial configurations, we find the densest known packings of the four non-tiling Platonic solids (the tetrahedron, octahedron, dodecahedron and icosahedron) in three-dimensional Euclidean space. The densities are 0.782..., 0.947..., 0.904... and 0.836..., respectively. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other non-tiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. Combining our simulation results with derived rigorous upper bounds and theoretical arguments leads us to the conjecture that the densest packings of the Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This is the analogue of Kepler's sphere conjecture for these solids.

Optimal control policy for probabilistic Boolean networks with hard constraints

It is well known that the control/intervention of some genes in a genetic regulatory network is useful for avoiding undesirable states associated with some diseases like cancer. For this purpose, both optimal finite-horizon control and infinite-horizon control policies have been proposed. Boolean networks (BNs) and its extension probabilistic Boolean networks (PBNs) as useful and effective tools for modelling gene regulatory systems have received much attention in the biophysics community. The control problem for these models has been studied widely. The optimal control problem in a PBN can be formulated as a probabilistic dynamic programming problem. In the previous studies, the optimal control problems did not take into account the hard constraints, i.e. to include an upper bound for the number of controls that can be applied to the captured PBN. This is important as more treatments may bring more side effects and the patients may not bear too many treatments. A formulation for the optimal finite-horizon control problem with hard constraints introduced by the authors. This model is state independent and the objective function is only dependent on the distance between the desirable states and the terminal states. An approximation method is also given to reduce the computational cost in solving the problem. Experimental results are given to demonstrate the efficiency of our proposed formulations and methods.

Optimal packings of superballs

Dense hard-particle packings are intimately related to the structure of low-temperature phases of matter and are useful models of heterogeneous materials and granular media. Most studies of the densest packings in three dimensions have considered spherical shapes, and it is only more recently that nonspherical shapes (e.g., ellipsoids) have been investigated. Superballs (whose shapes are defined by |x1|2p+|x2|2p+|x3|2p<or=1) provide a versatile family of convex particles (p>or=0.5) with both cubic-like and octahedral-like shapes as well as concave particles (0<p<0.5) with octahedral-like shapes. In this paper, we provide analytical constructions for the densest known superball packings for all convex and concave cases. The candidate maximally dense packings are certain families of Bravais lattice packings (in which each particle has 12 contacting neighbors) possessing the global symmetries that are consistent with certain symmetries of a superball. We also provide strong evidence that our packings for convex superballs (p>or=0.5) are most likely the optimal ones. The maximal packing density as a function of p is nonanalytic at the sphere point (p=1) and increases dramatically as p moves away from unity. Two more nontrivial nonanalytic behaviors occur at pc*=1.150 9... and po*=ln 3/ln 4=0.792 4... for "cubic" and "octahedral" superballs, respectively, where different Bravais lattice packings possess the same densities. The packing characteristics determined by the broken rotational symmetry of superballs are similar to but richer than their two-dimensional "superdisk" counterparts [Y. Jiao, Phys. Rev. Lett. 100, 245504 (2008)] and are distinctly different from that of ellipsoid packings. Our candidate optimal superball packings provide a starting point to quantify the equilibrium phase behavior of superball systems, which should deepen our understanding of the statistical thermodynamics of nonspherical-particle systems.

Liposome-mediated transfer can improve the efficacy of islet labeling with superparamagnetic iron oxide

An in vivo method for islet visualization using magnetic resonance imaging (MRI), using superparamagnetic iron oxide (SPIO), has been described. Herein we have developed a protocol that uses cationic liposomes to increase the efficiency of islet cell labeling by SPIO in vitro. Fresh islet cells were incubated in RPMI-1640 medium, to which had been added a range of concentrations of ferucarbotran, a SPIO contrast agent. At each SPIO concentration, duplicate samples were incubated with versus without addition of cationic liposomes. We measured intracellular iron concentration, cell viability, and insulin-release function after labeling. We observed that the amount of iron bound to islet cells increased as the concentration of added SPIO increased. The presence of liposomes increased labeling efficiency at each SPIO concentration. In vitro MRI confirmed the effect of liposomes to improve labeling efficiency of islet cells by SPIO.

Phototrophic Fe(II) oxidation in an atmosphere of H2: implications for Archean banded iron formations

The effect of hydrogen on the rate of phototrophic Fe(II) oxidation by two species of purple bacteria was measured at two different bicarbonate concentrations. Hydrogen slowed Fe(II) oxidation to varying degrees depending on the bicarbonate concentration, but even the slowest rate of Fe(II) oxidation remained on the same order of magnitude as that estimated to have been necessary to deposit the Hamersley banded iron formations. Given the hydrogen and bicarbonate concentrations inferred for the Archean, our data suggest that Fe(II) phototrophy could have been a viable process at this time.

Transformation of nitrogen and distribution of nitrogen-related bacteria in a polluted urban stream

Most researchers focused on either nitrogen species or microbial community for polluted urban stream while ignoring the interaction between them and its effect on nitrogen transformation, which restricted the rational selection of an effective and feasible remediation technology. Taking Buji stream in Shenzhen (China) as target stream, the distribution of nitrogen-related bacteria was investigated by most probable number (MPN) besides analysis of nitrogen species etc. The nitrogen-related bacteria in sediment were 10(2) times richer than those in water. Owing to their faster growth, the MPN of ammonifying bacteria and denitrifying bacteria were 10(5) and 10(2) times higher than those of nitrifying bacteria, respectively. The ammonifying bacteria numbers were significantly related to BOD5 in water, while nitrifying bacteria in sediment correlated well with nitrate in water. Thus, nitrification occurred mainly in sediment surface and was limited by low proportion of nitrifying bacteria. The denitrifying bacteria in sediment had good relationship with BOD5 and nitrite and nitrate in water. Low DO and rich organic compounds were beneficial to denitrification but unfavourable to nitrification. Denitrification was restricted by low nitrite and nitrate concentration. These results could be served as a reference for implementing the remediation scheme of nitrogen polluted urban stream.

Optimal packings of superdisks and the role of symmetry

Almost all studies of the densest particle packings consider convex particles. Here, we provide exact constructions for the densest known two-dimensional packings of superdisks whose shapes are defined by |x{1}|{2p}+|x{2}|{2p}<or=1 and thus contain a large family of both convex (p>or=0.5) and concave (0<p<0.5) particles. Our candidate maximal packing arrangements are achieved by certain families of Bravais lattice packings, and the maximal density is nonanalytic at the "circular-disk" point (p=1) and increases dramatically as p moves away from unity. Moreover, we show that the broken rotational symmetry of superdisks influences the packing characteristics in a nontrivial way.

Modeling heterogeneous materials via two-point correlation functions. II. Algorithmic details and applications

In the first part of this series of two papers, we proposed a theoretical formalism that enables one to model and categorize heterogeneous materials (media) via two-point correlation functions S(2) and introduced an efficient heterogeneous-medium (re)construction algorithm called the "lattice-point" algorithm. Here we discuss the algorithmic details of the lattice-point procedure and an algorithm modification using surface optimization to further speed up the (re)construction process. The importance of the error tolerance, which indicates to what accuracy the media are (re)constructed, is also emphasized and discussed. We apply the algorithm to generate three-dimensional digitized realizations of a Fontainebleau sandstone and a boron-carbide/aluminum composite from the two-dimensional tomographic images of their slices through the materials. To ascertain whether the information contained in S(2) is sufficient to capture the salient structural features, we compute the two-point cluster functions of the media, which are superior signatures of the microstructure because they incorporate topological connectedness information. We also study the reconstruction of a binary laser-speckle pattern in two dimensions, in which the algorithm fails to reproduce the pattern accurately. We conclude that in general reconstructions using S(2) only work well for heterogeneous materials with single-scale structures. However, two-point information via S(2) is not sufficient to accurately model multiscale random media. Moreover, we construct realizations of hypothetical materials with desired structural characteristics obtained by manipulating their two-point correlation functions.

Rare earth doped zinc oxide nanowires

Zinc oxide (ZnO) nanowires were grown via thermal transport and subsequently doped with different concentrations of Tm, Yb, and Eu using ion implantation and post annealing. High ion fluences lead to morphology changes due to sputtering; however, freestanding nanowires become less damaged compared to those attached to substrates. No other phases like rare earth (RE) oxides were detected, no amorphization occurs in any sample, and homogeneous doping with the desired concentrations was achieved. Photoluminescence measurements demonstrate the optical activation of trivalent RE-elements and the emission of the characteristic intra-4f-luminescence of the respective RE atoms, which could be assigned according to the Dieke-diagram. An increasing RE concentration results into decreasing luminescence intensity caused by energy transfer mechanisms to non-radiative remaining implantation defect sites. Furthermore, low thermal quenching was observed due to the considerable wide band gap of ZnO.

Modeling heterogeneous materials via two-point correlation functions: basic principles

Heterogeneous materials abound in nature and man-made situations. Examples include porous media, biological materials, and composite materials. Diverse and interesting properties exhibited by these materials result from their complex microstructures, which also make it difficult to model the materials. Yeong and Torquato [Phys. Rev. E 57, 495 (1998)] introduced a stochastic optimization technique that enables one to generate realizations of heterogeneous materials from a prescribed set of correlation functions. In this first part of a series of two papers, we collect the known necessary conditions on the standard two-point correlation function S2(r) and formulate a conjecture. In particular, we argue that given a complete two-point correlation function space, S2(r) of any statistically homogeneous material can be expressed through a map on a selected set of bases of the function space. We provide examples of realizable two-point correlation functions and suggest a set of analytical basis functions. We also discuss an exact mathematical formulation of the (re)construction problem and prove that S2(r) cannot completely specify a two-phase heterogeneous material alone. Moreover, we devise an efficient and isotropy-preserving construction algorithm, namely, the lattice-point algorithm to generate realizations of materials from their two-point correlation functions based on the Yeong-Torquato technique. Subsequent analysis can be performed on the generated images to obtain desired macroscopic properties. These developments are integrated here into a general scheme that enables one to model and categorize heterogeneous materials via two-point correlation functions. We will mainly focus on basic principles in this paper. The algorithmic details and applications of the general scheme are given in the second part of this series of two papers.

Production of gamma-aminobutyric acid by Streptococcus salivarius subsp. thermophilus Y2 under submerged fermentation

Gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the central nervous system, has several well-known physiological functions and has been applied to the production of many drugs and functional foods. The technology of GABA production via submerged fermentation by Streptococcus salivarius subsp. thermophilus Y2 was investigated in this paper. It indicated that the GABA production was related to the biochemical characteristics of glutamate decarboxylase (GAD) of S. salivarius subsp. thermophilus Y2. After 24 h of fermentation at 37 degrees C, which is the suitable culture conditions for GAD-production, then the culture condition were adjusted to the optimal temperature (40 degrees C) and pH (4.5) for the GAD reaction activity in biotransformation of cells and pyridoxal 5'-phosphate (0.02 mmol/l) were added to the broth at the 48 h, the GABA production was increased up to 1.76-fold, reaching 7984.75 +/- 293.33 mg/l. The strain shows great potential use as a starter for GABA-containing yoghurt, cheese and other functional fermented food productions.

Neuropeptide Y regulates recurrent mossy fiber synaptic transmission less effectively in mice than in rats: Correlation with Y2 receptor plasticity

A unique feature of temporal lobe epilepsy is the formation of recurrent excitatory connections among granule cells of the dentate gyrus as a result of mossy fiber sprouting. This novel circuit contributes to a reduced threshold for granule cell synchronization. In the rat, activity of the recurrent mossy fiber pathway is restrained by the neoexpression and spontaneous release of neuropeptide Y (NPY). NPY inhibits glutamate release tonically through activation of presynaptic Y2 receptors. In the present study, the effects of endogenous and applied NPY were investigated in C57Bl/6 mice that had experienced pilocarpine-induced status epilepticus and subsequently developed a robust recurrent mossy fiber pathway. Whole cell patch clamp recordings made from dentate granule cells in hippocampal slices demonstrated that, as in rats, applied NPY inhibits recurrent mossy fiber synaptic transmission, the Y2 receptor antagonist (S)-N2-[[1-[2-[4-[(R,S)-5,11-dihydro-6(6H)-oxodibenz[b,e]azepin-11-yl]-1-piperazinyl]-2-oxoethyl]cyclopentyl]acetyl]-N-[2-[1,2-dihydro-3,5(4H)-dioxo-1,2-diphenyl-3H-1,2,4-triazol-4-yl]ethyl]-argininamide (BIIE0246) blocks its action and BIIE0246 enhances synaptic transmission when applied by itself. Y5 receptor agonists had no significant effect. Thus spontaneous release of NPY tonically inhibits synaptic transmission in mice and its effects are mediated by Y2 receptor activation. However, both NPY and BIIE0246 were much less effective in mice than in rats, despite apparently equivalent expression of NPY in the recurrent mossy fibers. Immunohistochemistry indicated greater expression of Y2 receptors in the mossy fiber pathway of normal mice than of normal rats. Pilocarpine-induced status epilepticus markedly reduced the immunoreactivity of mouse mossy fibers, but increased the immunoreactivity of rat mossy fibers. Mossy fiber growth into the inner portion of the dentate molecular layer was associated with increased Y2 receptor immunoreactivity in rat, but not in mouse. These contrasting receptor changes can explain the quantitatively different effects of endogenously released and applied NPY on recurrent mossy fiber transmission in mice and rats.

Single-cell RT-PCR, in situ hybridization histochemical, and immunohistochemical studies of substance P and enkephalin co-occurrence in striatal projection neurons in rats

Single-cell RT-PCR studies in 3-4-week-old rats have raised the possibility that as many as 20% of striatal projection neurons may be a unique type that contains both substance P (SP) and enkephalin (ENK). We used single-cell RT-PCR, retrograde labeling, in situ hybridization histochemistry, and immunolabeling to characterize the abundance of this cell type, its projection target(s), and any developmental changes in its frequency. We found by RT-PCR that 11% of neurons containing either SP or ENK contained both in 4-week-old rats, while in 4-month-old rats SP/ENK colocalization was only 3%. SP-only neurons tended to co-contain dynorphin and ENK-only neurons neurotensin, while SP/ENK neurons tended to contain dynorphin. Single-cell RT-PCR showed SP/ENK co-occurrence in 4-week-old rats to be no more common among striatal neurons retrogradely labeled from the substantia nigra than among those retrogradely labeled from globus pallidus. Double-label in situ hybridization showed SP/ENK perikarya to be scattered throughout striatum, making up 8% of neurons containing either SP or ENK at 4 weeks, but only 4% at 4 months. Immunolabeling showed that presumptive striatal terminals in globus pallidus externus, globus pallidus internus and substantia nigra pars reticulata that colocalized SP and ENK were scarce. Terminals colocalizing SP and ENK were, however, abundant in the substantia nigra pars compacta. Thus, SP-only and ENK-only neurons make up the vast majority of striatal projection neurons in rats, the frequency of SP/ENK colocalizing striatal neurons is low in adult rats (3-4%), and SP/ENK colocalizing neurons primarily project to SNc but do not appear to be confined to striosomes.

Dynamic interactions of p53 with DNA in solution by time-lapse atomic force microscopy

Dynamic interactions of the tumor suppressor protein p53 with a DNA fragment containing a p53-specific recognition sequence were directly observed by time-lapse tapping mode atomic force microscopy (AFM) in liquid. The divalent cation Mg(2+) was used to loosely attach both DNA and p53 to a mica surface so they could be imaged by the AFM while interacting with each other. Various interactions of p53 with DNA were observed, including dissociation/re-association, sliding and possibly direct binding to the specific sequence. Two modes of target recognition of p53 were detected: (a) direct binding, and (b) initial non-specific binding with subsequent translocation by one-dimensional diffusion of the protein along the DNA to the specific site.

[Culture and cryopreservation of human mandibular condylar cartilage cells]

OBJECTIVE

To establish an effective way in cryopreserving mandibular condylar cartilage cells.

METHODS

Human mandibular condylar cartilage (MCC) cells were harvested and amplified by microcarrier culture technique. MCC cells were preserve in liquid nitrogen. The biological properties of cryopreserved MCC cells were investigated.

RESULTS

Cells from liquid nitrogen preservation kept their phenotypic, proliferative an metabolic characteristics of MCC cells in vivo.

CONCLUSIONS

Cryopreservation of MCC cells can supply adequate qualified cells for repairing the defects of mandibular condyle cartilage and temporomandibular joint disk.

[Interleukin-1 increase nitric oxide synthesis through up-regulation of inducible nitric-oxide synthase by rabbit mandibular condylar cartilage cells in vitro]

OBJECTIVE

To investigate the influence of IL-1 on the biosynthesis of nitric oxide by rabbit mandibular condylar cartilage (MCC) cells.

METHODS

MCC cells of white rabbits were harvested enzymatically and cultured in DMEM supplemented with 0.4% newborn calf serum. In the experiment, a variety of concentrations of IL-1 were added to the medium. NO production was determined as nitrite accumulation in the medium. The effects of IL-1 on the mRNA levels of inducible nitric-oxide synthase (iNOS) were assessed by mRNA in situ hybridization method.

RESULTS

IL-1 can significantly increase nitric oxide synthesis by MCC cells in a concentration-dependent manner. In addition, normal MCC cells had light expression of iNOS expression and IL-1 (10-100 micrograms/L) promoted the expression of iNOS.

CONCLUSIONS

IL-1 can inhibit the chondrocytes proliferation and induce apoptosis that might be through the way of up-regulation of iNOS expression.

[Significance of her2 oncogene expression in primary nasopharyngeal carcinoma]

OBJECTIVE

To investigate the status of her2 oncogene at DNA level and the molecular mechanism of overexpression of her2 oncoprotein in part of patients with nasopharyngeal carcinoma (NPC).

METHODS

Forty-five cases of PNC tissue and fifteen cases of normal epithelial tissue adjacent to tumor tissue were examined for her 2 signal and centromere 17 signal. Interphase fluorescence in situ hybridization (FISH) was used to examine the copy number of her 2 and immunohistochemical (IHC) staining were used to analyze the copy number and protein expression of her2.

RESULTS

There were 1.92% +/- 0.10% her2 signals per nucleus in normal epithelial tissue adjacent to tumor. 75.52 +/- 9.33% of the nuclei contained 2 her2 signals and 2 centromere 17 signals. No alteration in gene copy number was found in cancerous nuclei. However, IHC staining of the 45 tumors with antibody against her2 showed that overexpression of her2 oncoprotein occurred in 33% (15/45) of NPC. However, there was no significant correlation between her2 expression and sex, age, clinical staging, and clinical outcome of patients.

CONCLUSION

The overexpression of her2 in NPC does not relate to her2 gene amplification. Immunohistochemistry may not be a good measure to examine her2 expression. The mechanism of her2 oncoprotein overexpression and its biological significance in the development of NPC remain to be elucidated.

A new glycogen synthase activity ratio in skeletal muscle: effects of exercise and insulin

It was recently reported that MnSO4 stimulates glycogen synthase-dependent glucose transfer from UDPglucose into trichloroacetic acid precipitable endogenous glycoproteins (GSMn(T)) in human muscle extracts. To determine the physiologic significance of this reaction, we compared a new GS activity ratio, GSMn(T)/GSH(E) (where GSH(E) represents the usual glucose transfer to ethanol precipitable exogenous glycogen by GS at 7.2 mM glucose 6-phosphate), with the generally used GSL(E)/GSH(E) ratio (where GSL(E) represents glucose transfer at 0.17 mM glucose 6-P concentration). Biopsies were obtained from the quadriceps femoris muscle of healthy subjects at rest, after 40 min of bicycle exercise at approximately 65% of maximal oxygen uptake and after isometric contraction at 2/3 maximal force to fatigue (approximately 1 min). GSMn(T)/GSH(E) increased from 0.012+/-0.002 at rest to 0.054+/-0.008 (P<0.01) after 40 min of bicycle exercise and the increase in GSMn(T) activity was strongly related to the decrease in endogenous glycogen (i.e.. increase in short-chain endogenous glycoproteins) (r=0.90; P<0.05). On the other hand, GSL(E)/GSH(E) did not change significantly after bicycle exercise (rest = 0.49+/-0.04; exercise = 0.58+/-0.08, P>0.05). GSMn(T)/GSH(E) increased from 0.010+/-0.001 at rest to 0.016+/-0.002 (P<0.05) after isometric exercise, whereas GSL(E)/GSH(E) decreased from 0.27+/-0.04 to 0.20+/-0.02 (P<0.05) under corresponding conditions. Last, insulin, which stimulates glycogen synthesis, also increased GSMn(T)/GSH(E) (1.8-fold, P<0.05), as well as GSL(E)/GSH(E) (1.4-fold, P<0.05), in isolated rat soleus muscle. These data indicate that GSMn(T)/GSH(E) is influenced by endogenous substrate availability and covalent modification. Therefore, GSMn(T)/GSH(E) ratio may prove to be a useful alternative to other GS activity ratios that only reflect changes in the phosphorylation state of GS.

Functional receptor-channel coupling compared in contractile and proliferative human vascular smooth muscle

We have previously identified a human vascular smooth muscle clone that can reversibly convert between proliferative and contractile phenotypes. Here we compared receptor-channel coupling in these cells using fura-2 to monitor [Ca(2+)](i) and patch-clamp to record currents. Histamine elevated [Ca(2+)](i) in all cells and caused contraction of cells exhibiting the contractile phenotype. The rise of [Ca(2+)](i) persisted in Ca(2+)-free solution and was abolished by thapsigargin, indicating involvement of stores. Whole cell electrophysiological recording revealed that histamine evoked transient outward K(+) current, indicating functional receptor-channel coupling. The time-course and amplitude of the histamine-activated current were similar in cells of the proliferative and contractile phenotypes. Moreover, a large conductance K(+) channel was recorded in cell-attached patches and was activated by histamine as well as the Ca(2+) ionophore A-23187, identifying it as the large conductance Ca(2+)-dependent K(+) channel. This K(+) channel showed similar characteristics and activation in both proliferative and contractile phenotypes, indicating that expression was independent of phenotype. In contrast, histamine also elicited an inward Cl(-) current in some contractile cells, suggesting differential regulation of this current depending on phenotype. These studies demonstrate the usefulness of this human vascular cell clone for studying functional plasticity of smooth muscle, while avoiding complications arising from extended times in culture.

[Study on nuclear DNA content and image cytometry in cervical cancer and precursor lesions]

OBJECTIVE

The aim of this research was to study the biological and clinical features of cervical cancer and precursor lesions.

METHODS

Nuclear DNA was analyzed by image cytometry (ICM) in 125 embedded tissue 5 microns sections stained with Feulgen stain. Samples included normal cervical squamous epithelium (n = 11), cervical intraepithelial neoplasia I (CIN I) (n = 22), CINII (n = 17) and CINIII (n = 13), cervical neoplasm (n = 62).

RESULTS

The mean DNA content, nuclear area increased progressively from normal cervical epithelium, CINI, CINII, CINIII to invasive squamous carcinoma. Statistical analysis revealed significant difference (P < 0.05, < 0.01). Histograms of cellular DNA ploidy distribution showed different pattern, where 9 components (9C) cells were observed in cervical cancer and CINIII. No differences in DNA mean ploidy (DMP), DNA index (DI) and nuclear area were observed between cervical neoplasm.

CONCLUSIONS

It is increased progressively from normal cervical epithelium to cancer, in which CINIII is turning point.

Altered glycogen synthase and phosphorylase activities in skeletal muscle of tetraplegic patients

Despite marked differences in both the extent of physical activity and in muscle metabolism and structure between tetraplegic and control subjects, the glycogen content in the skeletal muscle of both groups is similar. We determined whether this similarity could be explained by the activities of key enzymes of glycogen metabolism. Muscle biopsies were analysed for glycogen synthase (GS) and glycogen phosphorylase (GP) activities, as well as for metabolites. Glycogen content did not differ significantly between the two groups. Total glycogen synthase activity was reduced by almost 60 % in tetraplegics (P < 0.01), whereas total phosphorylase activity did not differ between groups. GS fractional activity did not differ between groups, whereas phosphorylase fractional activity (-/+ AMP) was significantly higher in the tetraplegics (0.08 +/- 0.01, control; 0.25 +/- 0.02, tetraplegics; P < 0.001). Neither uridine diphosphate (UDP)-glucose nor glucose 6-phosphate (G-6-P) content in muscle differed significantly between groups. These data demonstrate that, in tetraplegics, muscle glycogen content is preserved despite decreases in GS activity and increases in phosphorylase fractional activity. Muscle paralysis has differential effects on the activities of GS and GP. Experimental Physiology (2001) 86.2, 205-209.

Genetic alterations in DNA diploid, aneuploid and multiploid colorectal carcinomas identified by the crypt isolation technique

Loss of heterozygosity (LOH) and microsatellite instability (MSI) commonly occur in colorectal carcinomas. However, the role of these genetic alterations in determining DNA ploidy status of tumors (diploid, aneuploid and multiploid) remains unclear. In the present study, we attempted to clarify the relationship between genetic alterations and DNA ploidy status. Crypt isolation coupled with DNA cytometric sorting and polymerase chain reaction assay (17 microsatellite markers) were used to study allelic losses and MSI in 59 colorectal carcinomas (diploid, 15; aneuploid, 10 and multiploid, 34). Of the 15 diploid carcinomas, 6 exhibited MSI in which allelic losses were rarely found. The other 9 diploid tumors mostly exhibited allelic losses, but none displayed MSI status. Whereas allelic losses frequently occurred in the aneuploid carcinomas and the aneuploid populations of multiploid carcinomas, they were rarely detected in the diploid populations of multiploid carcinomas. MSI status was not observed in aneuploid carcinomas nor in either population of multiploid carcinomas. Although multiploid carcinomas genetically resemble aneuploid carcinomas in the expression of the severe LOH phenotype, the genetic alterations seen in the diploid populations of multiploid carcinomas may differ from those of diploid carcinomas. Furthermore, all diploid, aneuploid and both the diploid and aneuploid fractions of the multiploid tumors that were non-MSI exhibited a high rate of LOH, suggesting that LOH is independent of the tumor's ploidy status.

Pathway tracing using biotinylated dextran amines

Biotinylated dextran amines (BDA) are highly sensitive tools for anterograde and retrograde pathway tracing studies of the nervous system. BDA can be reliably delivered into the nervous system by iontophoretic or pressure injection and visualized with an avidin-biotinylated HRP (ABC) procedure, followed by a standard or metal-enhanced diaminobenzidine (DAB) reaction. High molecular weight BDA (10 k) yields sensitive and exquisitely detailed labeling of axons and terminals, while low molecular weight BDA (3 k) yields sensitive and detailed retrograde labeling of neuronal cell bodies. The detail of neuronal cell body labeling can be Golgi-like. BDA tolerates EM fixation and processing well and can, therefore, be readily used in ultrastructural studies. Additionally, BDA can be combined with other anterograde or retrograde tracers (e.g. PHA-L or cholera toxin B fragment) and visualized either by multi-color DAB multiple-labeling - if permanent labels are desired, or by using multiple simultaneous immunofluorescence - if fluorescence viewing is desired. In the same manner, BDA pathway tracing and neurotransmitter immunolabeling can be combined. Note that BDA pathway tracing can also be combined with anterograde or retrograde labeling with fluorescent dextran amines, if one wishes to exclusively use tracers with the favorable transport properties and sensitivities of dextran amines. In this case, the BDA can be visualized together with the fluorescent dextran amines using fluorescence labeling for the BDA, or the fluorescent dextran amines can be visualized together with the BDA by multicolor DAB labeling via immunolabeling of the fluorescent dextran amines using anti-fluorophore antisera. BDA is, thus, a flexible and valuable pathway tracing tool that has gained widespread popularity in recent years.