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PubMed2006

Synthesis and characterization of the octahydrotriborate complexes Cp*V(B3H8)2 and Cp*Cr(B3H8)2 and the unusual cobaltaborane cluster Cp*2Co2(B6H14).

The new compounds CpV(B(3)H(8))(2), CpCr(B(3)H(8))(2), and Cp(2)Co(2)(B(6)H(14)) have been synthesized by treating the pentamethylcyclopentadienyl complexes [CpVCl(2)](3), [CpCrCl(2)](2), and [CpCoCl](2) with NaB(3)H(8). X-ray crystallography shows that CpV(B(3)H(8))(2) and CpCr(B(3)H(8))(2) have the same ligand sets but different molecular structures: the vanadium compound contains two bidentate B(3)H(8) ligands (i.e., bound to the metal center via two vicinal hydrogen atoms), whereas the chromium compound has one bidentate B(3)H(8) ligand and one B(3)H(8) ligand bound in an unprecedented fashion via two geminal hydrogen atoms. The "gem-bound" B(3)H(8) group itself has an atypical structure consisting of a BH(2)-BH(2)-BH(3) triangle with one additional hydrogen atom bridging the unique BH(2)-BH(2) edge. The B-B distances are nearly identical within experimental error at 1.790(5), 1.792(5), and 1.786(6) Angstrom. The relationship between the electronic and molecular structures of the V and Cr compounds is briefly discussed. The structure of Cp(2)Co(2)(B(6)H(14)) can be viewed in two different ways: as a dicobalt complex in which two CpCo units are each bound to four adjacent boron atoms of an S-shaped B(6)H(14) ligand, or as an eight-vertex hypho cluster compound. In the former case, the B(6)H(14) ligand is best regarded as a dianionic bi-borallyl group H(3)B(mu-H)BH(mu-H)BHBH(mu-H)BH(mu-H)BH(3) in which one hydrogen at each end of the chain is involved in an agostic interaction. From a cluster point of view, the structure of Cp(2)Co(2)(B(6)H(14)) can be generated by removing three adjacent high-connectivity vertices from the eleven-vertex closo polyhedron. The Co-B distances vary from 2.008(5) to 2.183(4) Angstrom, and the B-B distances within in the S-shaped chain range from 1.734(8) to 1.889(6) Angstrom. Finally, a new synthesis of the known molybdenum compound Cp(2)Mo(2)(B(5)H(9)) is described; its structure as established by X-ray crystallography closely resembles that of the previously described (C(5)H(4)Me) analogue.

Journal Article↗
PubMed2003

Universal scaling relations in food webs.

The structure of ecological communities is usually represented by food webs. In these webs, we describe species by means of vertices connected by links representing the predations. We can therefore study different webs by considering the shape (topology) of these networks. Comparing food webs by searching for regularities is of fundamental importance, because universal patterns would reveal common principles underlying the organization of different ecosystems. However, features observed in small food webs are different from those found in large ones. Furthermore, food webs (except in isolated cases) do not share general features with other types of network (including the Internet, the World Wide Web and biological webs). These features are a small-world character and a scale-free (power-law) distribution of the degree (the number of links per vertex). Here we propose to describe food webs as transportation networks by extending to them the concept of allometric scaling (how branching properties change with network size). We then decompose food webs in spanning trees and loop-forming links. We show that, whereas the number of loops varies significantly across real webs, spanning trees are characterized by universal scaling relations.

Animals↗
PubMed1992

A lattice model for protein structure prediction at low resolution.

The prediction of the folded structure of a protein from its sequence has proven to be a very difficult computational problem. We have developed an exceptionally simple representation of a polypeptide chain, with which we can enumerate all possible backbone conformations of small proteins. A protein is represented by a self-avoiding path of connected vertices on a tetrahedral lattice, with several amino acid residues assigned to each lattice vertex. For five small structurally dissimilar proteins, we find that we can separate native-like structures from the vast majority of non-native folds by using only simple structural and energetic criteria. This method demonstrates significant generality and predictive power without requiring foreknowledge of any native structural details.

Amino Acid Sequence↗
PubMed2000

PTGF-beta, a type beta transforming growth factor (TGF-beta) superfamily member, is a p53 target gene that inhibits tumor cell growth via TGF-beta signaling pathway.

Identification and characterization of p53 target genes would lead to a better understanding of p53 functions and p53-mediated signaling pathways. Two putative p53 binding sites were identified in the promoter of a gene encoding PTGF-beta, a type beta transforming growth factor (TGF-beta) superfamily member. Gel shift assay showed that p53 bound to both sites. Luciferase-coupled transactivation assay revealed that the gene promoter was activated in a p53 dose- as well as p53 binding site-dependent manner by wild-type p53 but not by several p53 mutants. The p53 binding and transactivation of the PTGF-beta promoter was enhanced by etoposide, a p53 activator, and was largely blocked by a dominant negative p53 mutant. Furthermore, expression of endogenous PTGF-beta was remarkably induced by etoposide in p53-positive, but not in p53-negative, cell lines. Finally, the conditioned medium collected from PTGF-beta-overexpressing cells, but not from the control cells, suppressed tumor cell growth. Growth suppression was not, however, seen in cells that lack functional TGF-beta receptors or Smad4, suggesting that PTGF-beta acts through the TGF-beta signaling pathway. Thus, PTGF-beta, a secretory protein, is a p53 target that could mediate p53-induced growth suppression in autocrinal as well as paracrinal fashions. The finding made a vertical connection between p53 and TGF-beta signaling pathways in controlling cell growth and implied a potential important role of p53 in inflammation regulation via PTGF-beta.

Binding Sites↗
PubMed2006

Characteristics of Asian dust transport based on synoptic meteorological analysis over Korea.

Classification of synoptic patterns and their correlation with dust events over East Asia were performed by means of cluster analysis. The average linkage and K-means clustering techniques were used to identify two major weather types during Asian dust events (ADEs; total 26 ADEs with 47 dusty days) of six spring seasons from 1996 to 2001. The first weather type mainly influenced neighboring Asian countries and frequently occurred with ADEs (approximately 23% of ADE cases). It mostly occurred under a surface high (low)-pressure system over the west (east) of the Korean peninsula coupled with an upper-level trough and cutoff low passage over the center of the Korean peninsula. It showed strong advection in the middle/ upper troposphere with both a high aerosol index and enhanced coarse particulate matter (PM) loading over Korea. In contrast, the second weather type was mostly associated with long distance or continental-scale transport and occurred less frequently with ADEs (approximately 15%). It appeared with an upper-level trough and a cutoff low vertically connected with a surface low system that was formed by a strong cyclonic vortex over the north of the Korean peninsula. There were weak advection, low aerosol index, and low coarse PM concentration over the Korean peninsula during the second weather type. In addition, it was found to be mostly associated with the trans-Pacific transport of Asian dust to the western coast of North America.

Aerosols↗
PubMed2001

The small world of human language.

Words in human language interact in sentences in non-random ways, and allow humans to construct an astronomic variety of sentences from a limited number of discrete units. This construction process is extremely fast and robust. The co-occurrence of words in sentences reflects language organization in a subtle manner that can be described in terms of a graph of word interactions. Here, we show that such graphs display two important features recently found in a disparate number of complex systems. (i) The so called small-world effect. In particular, the average distance between two words, d (i.e. the average minimum number of links to be crossed from an arbitrary word to another), is shown to be d approximately equal to 2-3, even though the human brain can store many thousands. (ii) A scale-free distribution of degrees. The known pronounced effects of disconnecting the most connected vertices in such networks can be identified in some language disorders. These observations indicate some unexpected features of language organization that might reflect the evolutionary and social history of lexicons and the origins of their flexibility and combinatorial nature.

Biological Evolution↗
PubMed2005

Distance-d covering problems in scale-free networks with degree correlations.

A number of problems in communication systems demand the distributed allocation of network resources in order to provide better services, sampling, and distribution methods. The solution to these issues is becoming more challenging due to the increasing size and complexity of communication networks. We report here on a heuristic method to find near-optimal solutions to the covering problem in real communication networks, demonstrating that whether a centralized or a distributed design is to be used relies upon the degree correlations between connected vertices. We also show that the general belief that by targeting the hubs one can efficiently solve most problems on networks with a power-law degree distribution is not valid for assortative networks.

Journal Article↗
PubMed2002

Extreme self-organization in networks constructed from gene expression data.

We study networks constructed from gene expression data obtained from many types of cancers. The networks are constructed by connecting vertices that belong to each others' list of K nearest neighbors, with K being an a priori selected non-negative integer. We introduce an order parameter for characterizing the homogeneity of the networks. On minimizing the order parameter with respect to K, degree distribution of the networks shows power-law behavior in the tails with an exponent of unity. Analysis of the eigenvalue spectrum of the networks confirms the presence of the power-law and small-world behavior. We discuss the significance of these findings in the context of evolutionary biological processes.

Adenocarcinoma↗
PubMed2002

Propagation of action potentials from the soma to individual dendrite of cultured rat amacrine cells is regulated by local GABA input.

Retinal amacrine cells are interneurons that make lateral and vertical connections in the inner plexiform layer of the retina. Amacrine cells do not possess a long axon, and this morphological feature is the origin of their naming. Their dendrites function as both presynaptic and postsynaptic sites. Half of all amacrine cells are GABAergic inhibitory neurons that mediate lateral inhibition, and their light-evoked response consists of graded voltage changes and regenerative action potentials. There is evidence that the amount of neurotransmitter release from presynaptic sites is increased by spike propagation into the dendrite. Thus understanding of how action potentials propagate in dendrites is important to elucidating the extent and strength of lateral inhibition. In the present study, we used the dual whole cell patch-clamp technique on the soma and the dendrite of cultured rat amacrine cells and directly demonstrated that the action potentials propagate into the dendrites. The action potential in the dendrite was TTX sensitive and was affected by the local membrane potential of the dendrite. Propagation of the action potential was suppressed by local application of GABA to the dendrite. Dual dendrite whole cell patch-clamp recordings showed that GABA suppresses the propagation of action potentials in one dendrite of an amacrine cell, while the action potentials propagate in the other dendrites. It is likely that the action potentials in the dendrites are susceptible to various external factors resulting in the nonuniform propagation of the action potential from the soma of an amacrine cell.

Action Potentials↗
PubMed1997

Formation of actin filament networks in cultured rat hepatocytes treated with DMSO and glucagon.

Actin filament organization may play an important role in the maintenance of differentiated functions in epithelial cells. We previously reported our success in inducing and maintaining gap junctions, which are two kinds of differentiated function, in primary rat hepatocytes cultured with 2% DMSO and 10-7 M glucagon. In the present study, we demonstrated the formation of actin filament networks in the hepatocytes cultured with 2% DMSO and 10-7 M glucagon. Actin filaments in hepatocytes cultured in medium with only 2% DMSO added from 96 h after plating were concentrated under the plasma membrane and were observed to be circumferential. In hepatocytes cultured in the medium with both 2% DMSO and 10-7 M glucagon added from 96 h, not only the circumferential actin filaments but also the formation of actin filament networks were observed and the networks developed well with time in culture. The networks were observed as a dome-like structure under the cell face and terminated at the circumferential actin filaments. They were composed of electron-dense star-like vertices connected by microfilament bundles of varying length and were also very sensitive to the actin disruptor cytochalasin B. However, during the network formation, there were no significant increases in the amounts of actin protein and mRNA. The actin filament networks of the hepatocytes in this culture system might be closely related to the maintenance of differentiated functions.

Actins↗
PubMed2004

Tending and befriending: the intertwined relationships of quilters.

Using the convoy model of social relations, we explored the contributions of quilting activities to the relationships of middle- and older-aged women in three distinct groups: Amish, Appalachian, and Latter Day Saints. Semi-structured interviews were conducted with ten women from each group and analyzed qualitatively using McCracken's five-step method for analysis of long interviews. We found that these women had considerable horizontal and vertical connections to others. Specifically, they exhibited generativity by teaching their skills to others, building bonds with grandchildren through quilting, and leaving legacies through their quilts. Many developed friendships with other quilters that provided social support to deal with life challenges. Additional study of the contributions of mid-late life women's leisure activities to their social milieu, personal development, and well-being is needed.

Adult↗
PubMed1978

The computerized medical record in gastroenterology: part 4. Health curriculum vitae.

The health curriculum vitae consists mainly of a chronological sequence of diagnoses, which are the mainstays of the medical record. Each diagnosis is connected vertically in the health curriculum vitae with its aetiological factors and its medical or surgical treatments in a casual concatenation; and horizontally throughout the other three parts of the record with its relevant functional, morphological (descriptive) and numerical laboratory data in a diagnostic association. The health curriculum vitae uses the Systematized Nomenclature of Medicine (SNOMED), the International Nomenclature of the Diseases of the Gastrointestinal Tract (CIOMS) and the International Standard Classification of Occupations of the Internationl Labour Office.

Computers↗
PubMed1994

[Dental curriculum in Nijmegen].

The dental curriculum at the University of Nijmegen is based on what the dentist should know and be able to do after his graduation. The programme is divided up into cognitive, behavioural and motoric modules. These modules are vertically connected through subsequent course years by thematically related lines. For every module, the general objectives and general contents have been formulated. Moreover, all subcomponents have been specified as instructional objectives. Half of the study hours is reserved for practical dentistry, by means of preclinically laboratory courses or patient treatment. The curriculum is based on a scientific approach of dentistry and emphasis is placed on patient related instructional situations.

Curriculum↗
PubMed1998

The development of local, layer-specific visual cortical axons in the absence of extrinsic influences and intrinsic activity.

The laminar specificity of vertical connections in the primary visual cortex (area 17) develops precisely from the outset, leading to the hypothesis that layer-specific axonal targeting is attributable to molecular cues intrinsic to the cortex (Lund et al., 1977; Katz and Callaway, 1992). However, alternative factors that could influence axonal development have not been investigated. This study examines the roles of intrinsic cortical activity and extrinsic influences that could arise from earlier-formed connections with outside cortical and subcortical areas. Organotypic slice cultures were prepared from ferret area 17 before the formation of local axonal connections and were incubated for 5-7 d to allow initial, local axonal arbors to form in the absence of extrinsic influences. Additionally, some slices were cultured in the presence of the Na+ channel blocker tetrodotoxin to block spontaneous action potentials within the slice. Individual neurons were labeled intracellularly with biocytin, and their patterns of local axonal arborizations were reconstructed. This study focuses on the development of layer 6 pyramidal neurons, the axons of which in vivo bypass an incorrect target, layer 5, before specifically arborizing in their local target, layer 4. We found that axonal arbors developing in vitro preferentially arborized in layer 4 versus layer 5. However, inhibition of spontaneous activity within the cortical slice decreased this specificity, resulting in similar numbers of axonal branches in layers 4 and 5. Thus, although cortical axons do not require influences from outside areas, intrinsic spontaneous activity is required for specific axonal arborization in correct laminar targets.

Animals↗
PubMed1983

Morphometric study of the development of Purkinje cell dendritic trees in the mouse using vertex analysis.

Vertices are the points in an arborescence which interconnect segments and comprise terminal or pendant vertices (Vp), nodal or branching points and the root point. Branching points may be dichotomous (Vd) or trichomtomous (Vt), etc., and are subdivided into distinct two-dimensional topological entities according to the number of terminal vertices they drain, i.e. Vds comprise primary vertices (Va), connecting two Vps; secondary vertices (Vb), connecting one Vp and one Vd or one Vt; and tertiary vertices (Vc), connecting either two Vds, two Vts or one Vt and one Vd. The four types of Vt (Va', Vb', Vc', Vd') similarly connect three, two, one and zero Vps respectively. Each Vt may be transformed into two Vds thus, Va' = Va + Vb; Vb' = Va/3 + 4Vb/3 + Vc/3; Vc' = Vb + Vc and Vd' = 2Vc. Analysis proceeds by transforming mixed trees containing varying proportions of Vds and Vts into entirely dichotomous branching structures. The topology is then defined by the Va/Vb ratio which has a unique value according to the mode of growth and the frequency of Vts. Vertices are ordered by a centrifugal technique. The frequency distribution of vertices of different order allow the changes in growth characteristics and in remodelling to be detected within particular regions of the tree. Metrical parameters are readily incorporated into the analysis since all vertices are interconnected by segments of finite length and are given the same order magnitude as the vertex they drain. The analytical capabilities of the method are exemplified by its application to the study of growth and plasticity in the dendritic trees of Purkinje cells in the mouse. Growth is defined in metrical and topological terms and sites of reorganization within the mature tree are identified.

Aging↗
PubMed1999

Connectivity in the somatosensory cortex of the adolescent rat: an in vitro biocytin study.

A promising way to elucidate neuronal information processing is to establish detailed structure-function relationships of identified single neurons or populations of nerve cells, especially their synaptic connectivity. This has been greatly improved by the development of acute brain slice preparations. The cellular physiology of the rodent primary somatosensory (barrel) cortex has been extensively studied. However, for a meaningful interpretation of physiological experiments the degree and pattern of connectivity has to be known for the particular preparation. Since such studies are not available for rat (P15-25) barrel cortex in vitro, we have traced the cortico-cortical and thalamo-cortical connections in 400-microm-thick slices with biocytin. In coronal slices, a wealth of axonal connections in retrograde and anterograde directions were heavily labeled, resembling the full pattern of cortico-cortical projections described in vivo. The most striking connections were vertical and horizontal connections within the primary somatosensory cortex, as well as a columnar projection to the secondary somatosensory cortex and beyond (mainly the parietal ventral area). Electron microscopic extensions of the study indicated that the full possible set of synaptic contacts with an adult-like appearance was already established in these connections. In thalamo-cortical slices, strong reciprocal connections with the ventrobasal (and to a much lesser extent also the posterior) thalamic nucleus were always observed, together with an intensive ramification of fibers in the reticular nucleus. A striatal terminal field was also consistently found. We conclude that all major intracortical and thalamo-cortical connection are richly preserved in the in vitro slice preparations of rats. Thus, these preparations are suitable for elucidation of the functional interaction of the most crucial brain structures involved in somatosensory information processing combining an in vivo-like anatomical structure with the controlled environment of an in vitro slice.

Animals↗
PubMed2002

Small-world view of the amino acids that play a key role in protein folding.

We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called "key residues," act as nucleation centers for protein folding. By constructing graphs corresponding to protein structures we show that they have the "small-world" feature of having a limited set of vertices with large connectivity. These vertices correspond to the key residues that play the role of "hubs" in the network of interactions that stabilize the structure of the transition state.

Amino Acids↗
PubMed2004

Automatic segmentation of thalamus from brain MRI integrating fuzzy clustering and dynamic contours.

Thalamus is an important neuro-anatomic structure in the brain. In this paper, an automated method is presented to segment thalamus from magnetic resonance images (MRI). The method is based on a discrete dynamic contour model that consists of vertices and edges connecting adjacent vertices. The model starts from an initial contour and deforms by external and internal forces. Internal forces are calculated from local geometry of the model and external forces are estimated from desired image features such as edges. However, thalamus has low contrast and discontinues edges on MRI, making external force estimation a challenge. The problem is solved using a new algorithm based on fuzzy C-means (FCM) unsupervised clustering, Prewitt edge-finding filter, and morphological operators. In addition, manual definition of the initial contour for the model makes the final segmentation operator-dependent. To eliminate this dependency, new methods are developed for generating the initial contour automatically. The proposed approaches are evaluated and validated by comparing automatic and radiologist's segmentation results and illustrating their agreement.

Algorithms↗