bluuebunny/crossref_metadata_2025 huggingface dataset:
Enterococcus faecalis
Constitutes an Unusual Bacterial Model in Lysozyme Resistance
Authors: Hébert Laurent , Courtin Pascal , Torelli Riccardo , Sanguinetti Maurizio , Chapot-Chartier Marie-Pierre , Auffray Yanick , Benachour Abdellah
Published: September 2007

Lysozyme is an important and widespread compound of the host constitutive defense system, and it is assumed that
Enterococcus faecalis
is one of the few bacteria that are almost completely lysozyme resistant. On the basis of the sequence analysis of the whole genome of
E. faecalis
V583 strain, we identified two genes that are potentially involved in lysozyme resistance, EF_0783 and EF_1843. Protein products of these two genes share significant homology with
Staphylococcus aureus
peptidoglycan
O
-acetyltransferase (OatA) and
Streptococcus pneumoniae N
-acetylglucosamine deacetylase (PgdA), respectively. In order to determine whether EF_0783 and EF_1843 are involved in lysozyme resistance, we constructed their corresponding mutants and a double mutant. The ΔEF_0783 mutant and ΔEF_0783 ΔEF_1843 double mutant were shown to be more sensitive to lysozyme than the parental
E. faecalis
JH2-2 strain and ΔEF_1843 mutant were. However, compared to other bacteria, such as
Listeria monocytogenes
or
S. pneumoniae
, the tolerance of ΔEF_0783 and ΔEF_0783 ΔEF_1843 mutants towards lysozyme remains very high. Peptidoglycan structure analysis showed that EF_0783 modifies the peptidoglycan by O acetylation of
N
-acetyl muramic acid, while the EF_1843 deletion has no obvious effect on peptidoglycan structure under the same conditions. Moreover, the EF_0783 and EF_1843 deletions seem to significantly affect the ability of
E. faecalis
to survive within murine macrophages. In all, while EF_0783 is currently involved in the lysozyme resistance of
E. faecalis
, peptidoglycan O acetylation and de-N-acetylation are not the main mechanisms conferring high levels of lysozyme resistance to
E. faecalis
.
Characterization of a New Variant of IS
257
That Has Displaced the Capsule Genes within Bovine Isolates of
Staphylococcus aureus
Authors: Tuchscherr L. P. N. , Gomez M. I. , Buzzola F. R. , Calvinho L. F. , Lee J. C. , Sordelli D. O.
Published: September 2007

Many bovine
Staphylococcus aureus
isolates from Argentina are nontypeable (NT), i.e., they do not produce serotype 5 or 8 capsular polysaccharides (CPs). Some of these NT strains have a deletion of the
cap5
(
8
) gene cluster mediated by a variant of IS
257
, now designated IS
cap
. IS
cap
showed 93% amino acid identity to
S. aureus
ORF49 but only 85% identity to IS
431
from
S. aureus
N315 and 88% identity to an IS
257
-like element from bovine strain RF122. Thirty-six (53%) of 68 bovine isolates, drawn from a previously described
S. aureus
strain collection, carried some variant of IS
257
, including IS
cap.
Of these 36 IS
+
isolates, 6 were CP5
+
, 1 was CP8
+
, and 29 were NT. Forty-four of the 68 isolates were NT, and 24 of these 44 NT isolates (55%) exhibited IS
cap
-mediated deletion of the
cap5
(
8
) gene cluster. IS
cap
was not found among 20 human NT
S. aureus
isolates bearing the
cap5HIJK
genes, which suggests that IS
cap
-mediated deletion of the capsule locus is restricted to bovine strains of
S. aureus
. We were unable to identify a precursor strain in which IS
cap
flanked the
cap5
(
8
) capsule locus, nor were we able to select for deletion of the
cap5
(
8
) locus in vitro. Our results support the hypothesis that deletion of the
cap5
locus occurred in the distant past and that the relative abundance of these NT strains may be a result of their ability to persist in subclinical mastitis infection in cows.
Maintenance of Antibody to Pathogen Epitopes Generated by Segmental Gene Conversion Is Highly Dynamic during Long-Term Persistent Infection
Authors: Zhuang Yan , Futse James E. , Brown Wendy C. , Brayton Kelly A. , Palmer Guy H.
Published: September 2007

Multiple bacterial and protozoal pathogens utilize gene conversion to generate rapid intrahost antigenic variation. Both large- and small-genome pathogens expand the size of the variant pool via a combinatorial process in which oligonucleotide segments from distinct donor loci are recombined in various combinations into expression sites. Although the potential combinatorial diversity generated by this segmental gene conversion mechanism is quite large, the functional variant pool depends on whether immune responses against the recombined segments are generated and maintained, regardless of their specific combinatorial context. This question was addressed by tracking the
Anaplasma marginale
variant population and corresponding segment-specific immunoglobulin G (IgG) antibody responses during long-term infection. Antibody was induced early in
A. marginale
infection, predominately against the surface-exposed hypervariable region (HVR) rather than against the invariant conserved flanking domains, and these HVR oligopeptides were most immunogenic at the time of acute bacteremia, when the variant population is derived via recombination from a single donor locus. However antibody to HVR oligopeptides was not consistently maintained during persistent infection, despite reexpression of the same segment, although in a different combinatorial context. This dynamic antibody recognition over time was not attributable to the major histocompatibility complex haplotype of individual animals or use of specific
msp2
donor alleles. In contrast, the position and context of an individual oligopeptide segment within the HVR were significant determinants of antibody recognition. The results unify the genetic potential of segmental gene conversion with escape from antibody recognition and identify immunological effects of variant mosaic structure.
Siderophore-Based Iron Acquisition and Pathogen Control
Authors: Miethke Marcus , Marahiel Mohamed A.
Published: September 2007

High-affinity iron acquisition is mediated by siderophore-dependent pathways in the majority of pathogenic and nonpathogenic bacteria and fungi. Considerable progress has been made in characterizing and understanding mechanisms of siderophore synthesis, secretion, iron scavenging, and siderophore-delivered iron uptake and its release. The regulation of siderophore pathways reveals multilayer networks at the transcriptional and posttranscriptional levels. Due to the key role of many siderophores during virulence, coevolution led to sophisticated strategies of siderophore neutralization by mammals and (re)utilization by bacterial pathogens. Surprisingly, hosts also developed essential siderophore-based iron delivery and cell conversion pathways, which are of interest for diagnostic and therapeutic studies. In the last decades, natural and synthetic compounds have gained attention as potential therapeutics for iron-dependent treatment of infections and further diseases. Promising results for pathogen inhibition were obtained with various siderophore-antibiotic conjugates acting as “Trojan horse” toxins and siderophore pathway inhibitors. In this article, general aspects of siderophore-mediated iron acquisition, recent findings regarding iron-related pathogen-host interactions, and current strategies for iron-dependent pathogen control will be reviewed. Further concepts including the inhibition of novel siderophore pathway targets are discussed.
USING GRAPH CONCEPTS TO UNDERSTAND THE ORGANIZATION OF COMPLEX SYSTEMS
Authors: CHRISTENSEN CLAIRE , ALBERT RÉKA
Published: September 2007

Complex networks are universal, arising in fields as disparate as sociology, physics and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the topologies of different systems. Attempts to explain these similarities have led to the ongoing development and refinement of network models and graph-theoretical analysis techniques with which to characterize and understand complexity. In this tutorial, we demonstrate through illustrative examples, how network measures and models have contributed to the elucidation of the organization of complex systems.
NEOCORTEX'S ARCHITECTURE OPTIMIZES COMPUTATION, INFORMATION TRANSFER AND SYNCHRONIZABILITY, AT GIVEN TOTAL CONNECTION LENGTH
Authors: STOOP R. , WAGNER C.
Published: September 2007

It is experimental evidence that biological neocortical neurons are arranged in a columnar clustered architecture and coupled according to a bi-power law connection probability function. We propose a computational framework that relies on recurrent connectivity and work out associated computational properties. Taking the columns as the basic computational elements, we investigate a bi-power connection probability function paradigm, in order to scan a wide range of network types, for which we measure the speed of information propagation and synchronizability. Whereas the speed of information propagation increases linearly in the neighbor order n for n-nearest neighbor coupled networks, for close-to-biology bi-power models of the cortex it quickly saturates at high values, expressing the superiority of this network type. Our results reveal that these networks optimize information propagation and synchronizability at a minimal total connection length.
EFFICIENCY, VULNERABILITY AND COST: AN OVERVIEW WITH APPLICATIONS TO SUBWAY NETWORKS WORLDWIDE
Authors: CRIADO R. , HERNÁNDEZ-BERMEJO B. , ROMANCE M.
Published: September 2007

Some of the main known results about efficiency, vulnerability and cost for complex networks are reviewed from a mathematical perspective. Such presentation is then completed by including new results that expand the domain of the theory to the realm of directed networks. This mathematical framework is subsequently used to perform a comparative analysis of those performance measures over a significant sample of subway networks worldwide.
EXISTENCE, COST AND ROBUSTNESS OF SPATIAL SMALL-WORLD NETWORKS
Authors: DE LOS RIOS P. , PETERMANN T.
Published: September 2007

Small-world networks embedded in Euclidean space represent useful cartoon models for a number of real systems such as electronic circuits, communication systems, the large-scale brain architecture and others. Since the small-world behavior relies on the presence of long-range connections that are likely to have a cost which is a growing function of the length, we explore whether it is possible to choose suitable probability distributions for the shortcut lengths so as to preserve the small-world feature and, at the same time, to minimize the network cost. The flow distribution for such networks, and their robustness, are also investigated.
TRANSPORT ON COMPLEX NETWORKS: FLOW, JAMMING AND OPTIMIZATION
Authors: TADIĆ BOSILJKA , RODGERS G. J. , THURNER STEFAN
Published: September 2007

Many transport processes on networks depend crucially on the underlying network geometry, although the exact relationship between the structure of the network and the properties of transport processes remain elusive. In this paper, we address this question by using numerical models in which both structure and dynamics are controlled systematically. We consider the traffic of information packets that include driving, searching and queuing. We present the results of extensive simulations on two classes of networks; a correlated cyclic scale-free network and an uncorrelated homogeneous weakly clustered network. By measuring different dynamical variables in the free flow regime we show how the global statistical properties of the transport are related to the temporal fluctuations at individual nodes (the traffic noise) and the links (the traffic flow). We then demonstrate that these two network classes appear as representative topologies for optimal traffic flow in the regimes of low density and high density traffic, respectively. We also determine statistical indicators of the pre-jamming regime on different network geometries and discuss the role of queuing and dynamical betweenness for the traffic congestion. The transition to the jammed traffic regime at a critical posting rate on different network topologies is studied as a phase transition with an appropriate order parameter. We also address several open theoretical problems related to the network dynamics.
DIVERSITY OF CORTICAL STATES AT NONEQUILIBRIUM SIMULATED BY THE ANTI-FERROMAGNETIC ISING MODEL UNDER METROPOLIS DYNAMICS
Authors: COSTA LUCIANO DA FONTOURA , SPORNS OLAF
Published: September 2007

This article investigates the relationship between the interconnectivity and simulated dynamics of the thalamocortical system from the specific perspective of attempting to maximize the diversity of cortical states. This is achieved by designing the dynamics such that they favor opposing activity between adjacent regions, thus promoting dynamic diversity while avoiding widespread activation or de-activation. The anti-ferromagnetic Ising model with Metropolis dynamics is adopted and applied to four variations of the large-scale connectivity of the cat thalamocortical system: (a) considering only cortical regions and connections; (b) considering the entire thalamocortical system; (c) the same as in (b) but with the thalamic connections rewired so as to maintain the statistics of node degree and node degree correlations; and (d) as in (b) but with attenuated weights of the connections between cortical and thalamic nodes. A series of interesting findings are obtained, including the identification of specific substructures revealed by correlations between the activity of adjacent regions in case (a) and a pronounced effect of the thalamic connections in splitting the thalamocortical regions into two large groups of nearly homogenous opposite activation (i.e. cortical regions and thalamic nuclei, respectively) in cases (b) and (c). The latter effect is due to the existence of dense connections between cortical and thalamic regions and the lack of interconnectivity between the latter. Another interesting result regarding case (d) is the fact that the pattern of thalamic correlations tend to mirror that of the cortical regions. The possibility to control the level of correlation between the cortical regions by varying the strength of thalamocortical connections is also identified and discussed.
DYNAMICS OF NETWORKS AND OPINIONS
Authors: SCHNEGG MICHAEL , STAUFFER DIETRICH
Published: September 2007

Social relations between people seldom follow regular lattice structures. In the Barabási–Albert model nodes link to the existing network structure with a probability proportional to the number of nodes previously attached. Here, we present an anthropologically motivated interpolation between Erdös–Rényi and Barabási–Albert rules, where people also prefer to help those who helped them in the past and explore some of its properties. The second part of the paper tackles the question how opinions spread through social networks. We restrict our analysis to one end of the spectrum: scale-free networks. We show for two different models how fast and how sustainable single individuals can influence an appreciable fraction of the population through social contacts.
SYNCHRONIZABILITY AND SYNCHRONIZATION DYNAMICS OF WEIGHED AND UNWEIGHED SCALE FREE NETWORKS WITH DEGREE MIXING
Authors: SORRENTINO FRANCESCO , DI BERNARDO MARIO , GAROFALO FRANCO
Published: September 2007

We study the synchronizability and the synchronization dynamics of networks of nonlinear oscillators. We investigate how the synchronization of the network is influenced by some of its topological features such as variations of the power law degree distribution exponent γ and the degree correlation coefficient r. Using an appropriate construction algorithm based on clustering the network vertices in p classes according to their degrees, we construct networks with an assigned power law distribution but changing degree correlation properties. We find that the network synchronizability improves when the network becomes disassortative, i.e. when nodes with low degree are more likely to be connected to nodes with higher degree. We consider the case of both weighed and unweighed networks. The analytical results reported in the paper are then confirmed by a set of numerical observations obtained on weighed and unweighed networks of nonlinear Rössler oscillators. Using a nonlinear optimization strategy we also show that negative degree correlation is an emerging property of networks when synchronizability is to be optimized. This suggests that negative degree correlation observed experimentally in a number of physical and biological networks might be motivated by their need to synchronize better.
GROWING HIERARCHICAL SCALE-FREE NETWORKS BY MEANS OF NONHIERARCHICAL PROCESSES
Authors: BOCCALETTI S. , HWANG D.-U. , LATORA V.
Published: September 2007

We introduce a fully nonhierarchical network growing mechanism, that furthermore does not impose explicit preferential attachment rules. The growing procedure produces a graph featuring power-law degree and clustering distributions, and manifesting slightly disassortative degree-degree correlations. The rigorous rate equations for the evolution of the degree distribution and for the conditional degree-degree probability are derived.
SPECTRAL METHODS CLUSTER WORDS OF THE SAME CLASS IN A SYNTACTIC DEPENDENCY NETWORK
Authors: FERRER I CANCHO RAMON , CAPOCCI ANDREA , CALDARELLI GUIDO
Published: September 2007

We analyze here a particular kind of linguistic network where vertices represent words and edges stand for syntactic relationships between words. The statistical properties of these networks have been recently studied and various features such as the small-world phenomenon and a scale-free distribution of degrees have been found. Our work focuses on four classes of words: verbs, nouns, adverbs and adjectives. Here, we use spectral methods sorting vertices. We show that the ordering clusters words of the same class. For nouns and verbs, the cluster size distribution clearly follows a power-law distribution that cannot be explained by a null hypothesis. Long-range correlations are found between vertices in the ordering provided by the spectral method. The findings support the use of spectral methods for detecting community structure.
NETWORKS FROM GENE EXPRESSION TIME SERIES: CHARACTERIZATION OF CORRELATION PATTERNS
Authors: REMONDINI D. , NERETTI N. , FRANCESCHI C. , TIERI P. , SEDIVY J. M. , MILANESI L. , CASTELLANI G. C.
Published: September 2007

We address the problem of finding large-scale functional and structural relationships between genes, given a time series of gene expression data, namely mRNA concentration values measured from genetically engineered rat fibroblasts cell lines responding to conditional cMyc proto-oncogene activation. We show how it is possible to retrieve suitable information about molecular mechanisms governing the cell response to conditional perturbations. This task is complex because typical high-throughput genomics experiments are performed with high number of probesets (103–104 genes) and a limited number of observations (< 102 time points). In this paper, we develop a deepest analysis of our previous work [Remondini et al., 2005] in which we characterized some of the main features of a gene-gene interaction network reconstructed from temporal correlation of gene expression time series. One first advancement is based on the comparison of the reconstructed network with networks obtained from randomly generated data, in order to characterize which features retrieve real biological information, and which are instead due to the characteristics of the network reconstruction method. The second and perhaps more relevant advancement is the characterization of the global change in co-expression pattern following cMyc activation as compared to a basal unperturbed state. We propose an analogy with a physical system in a critical state close to a phase transition (e.g. Potts ferromagnet), since the cell responds to the stimulus with high susceptibility, such that a single gene activation propagates to almost the entire genome. Our result is relative to temporal properties of gene network dynamics, and there are experimental evidence that this can be related to spatial properties regarding the global organization of chromatine structure [Knoepfler et al., 2006].
EPIDEMIC PREDICTABILITY IN META-POPULATION MODELS WITH HETEROGENEOUS COUPLINGS: THE IMPACT OF DISEASE PARAMETER VALUES
Authors: COLIZZA V. , BARRAT A. , BARTHÉLEMY M. , VESPIGNANI A.
Published: September 2007

We study the predictability of epidemic forecasts in a data-driven meta-population model considering the complete air transportation system and the associated urban areas. We define the predictability as the robustness of the system evolution with respect to the stochastic fluctuations. As a quantitative measure of predictability we consider the information similarity of the time series characterizing different epidemic outbreaks with the same initial conditions. We study the predictability as a function of the parameters describing the basic susceptible-latent-infected and recovered disease dynamics. We find that the overall predictability is determined by the level of sampling of the underlying travel pattern by infected and latent individuals.
DOCUMENT RETRIEVAL BY PROJECTION BASED FREQUENCY DISTRIBUTION
Authors: SHIOYA ISAMU , OH'UCHI HIROHITO , MIURA TAKAO
Published: September 2007

In document retrieval task, random projection (RP) is a useful technique of dimension reduction. It can be obtained very quickly yet the recalculation is not necessary to any changes. However, in lower dimension, random projection has instability by randomness in itself. In this investigation, we propose a new technique, called skewed projection (SP), for dimension reduction based on term frequency distribution. By our experiments, we show that we can take advantages of local independence thus we can obtain efficient retrieval for documents which belong to specific application area. Also we examine document size by which we can determine term distribution.
SUBGOAL ORDERING AND GRANULARITY CONTROL FOR INCREMENTAL PLANNING
Authors: HSU CHIH-WEI , CHEN YIXIN , WAH BENJAMIN W.
Published: September 2007

In this paper, we study strategies in incremental planning for ordering and grouping subproblems partitioned by the subgoals of a planning problem. To generate a rich set of partial orders for ordering subproblems, we propose an algorithm based on a relaxed plan that ignores the delete lists. The new algorithm considers both the initial and the goal states and can effectively order subgoals in such a way that greatly reduces the number of invalidations during incremental planning. We have also considered trade-offs between the granularity of the subgoal sets and the complexity of solving the overall planning problem. We propose an efficient strategy for dynamically adjusting the grain size in partitioning in order to minimize the total complexity. We further evaluate a redundant-ordering scheme that uses two different subgoal orders to improve the solution quality, without greatly sacrificing run-time efficiency. Experimental results on using Metric-FF, YAHSP, and LPG-TD-speed as the embedded planners in incremental planning show that our strategies are general for improving the time and quality of these planners across various benchmarks. Finally, we compare the performance of the three planners, the incremental versions using these planners as embedded planners, and SGPlan4.1.
REACHABILITY ANALYSIS FOR UNCERTAIN SSPs
Authors: BUFFET OLIVIER
Published: September 2007

Stochastic Shortest Path problems (SSPs) can be efficiently dealt with by the Real-Time Dynamic Programming algorithm (RTDP). Yet, RTDP requires that a goal state is always reachable. This article presents an algorithm checking for goal reachability, especially in the complex case of an uncertain SSP where only a possible interval is known for each transition probability. This gives an analysis method for determining if SSP algorithms such as RTDP are applicable, even if the exact model is not known. As this is a time-consuming algorithm, we also present a simple process that often speeds it up dramatically. Yet, the main improvement still needed is to turn to a symbolic analysis in order to avoid a complete state-space enumeration.
Plasma obestatin is lower at fasting and not suppressed by insulin in insulin-resistant humans
Authors: Anderwald-Stadler Marietta , Krebs Michael , Promintzer Miriam , Mandl Martina , Bischof Martin G. , Nowotny Peter , Kästenbauer Thomas , Luger Anton , Prager Rudolf , Anderwald Christian
Published: September 2007

Obestatin, a recently discovered 23-amino acid peptide, is involved in the regulation of appetite and body weight in antagonistic fashion to ghrelin, both deriving from a common precursor peptide. Ghrelin was shown to be associated with insulin resistance, which may also affect obestatin. We investigated the association between insulin resistance and plasma concentrations of obestatin and ghrelin in nondiabetic individuals with high (IS; n = 18, 13 females and 5 males, age 47 ± 2 yr, BMI = 25.5 ± 0.9 kg/m2) and low (IR; n = 18, 12 females and 6 males, age 45 ± 2 yr, P = 0.49, BMI = 27.5 ± 1.1 kg/m2, P = 0.17) insulin-stimulated glucose disposal (M), measured by 2-h hyperinsulinemic (40 mU·min−1·m−2) isoglycemic clamp tests. M100–120 min was higher in IS (10.7 ± 0.7) than in IR (4.4 ± 0.2 mg·min−1·kg−1, P < 10−9), whereas insulin-dependent suppression of free fatty acids (FFA) in plasma was reduced in IR (71 ± 6% vs. IS: 82 ± 5%, P < 0.02). In both groups, plasma ghrelin concentrations were comparable at fasting and similarly reduced by 24–28% during insulin infusion. IR had lower fasting plasma obestatin levels (383 ± 26 pg/ml vs. IS: 469 ± 23 pg/ml, P < 0.02). Clamp insulin infusion reduced plasma obestatin to ∼81% of basal values in IS ( P < 0.00002), but not in IR. Fasting plasma obestatin was correlated positively with M ( r = 0.34, P = 0.04), HDL cholesterol ( r = 0.45, P = 0.01), and plasma ghrelin concentrations ( r = 0.80, P < 0.000001) and negatively with measures of adiposity, plasma FFA during clamp ( r = −0.42, P < 0.01), and systolic blood pressure ( r = −0.33, P < 0.05). In conclusion, fasting plasma concentrations of obestatin, but not of ghrelin, are reduced in insulin resistance and are positively associated with whole body insulin sensitivity in nondiabetic humans. Furthermore, plasma obestatin is reduced by insulin in insulin-sensitive but not in insulin-resistant persons.
Secretion of neuropeptide Y in human adipose tissue and its role in maintenance of adipose tissue mass
Authors: Kos Katarina , Harte Alison L. , James Sean , Snead David R. , O'Hare Joseph P. , McTernan Philip G. , Kumar Sudhesh
Published: September 2007

NPY is an important central orexigenic hormone, but little is known about its peripheral actions in human adipose tissue (AT) or its potential paracrine effects. Our objective was to examine NPY's role in AT, specifically addressing NPY protein expression, the effect of NPY on adipokine secretion, and the influence of insulin and rosiglitazone (RSG) on adipocyte-derived NPY in vitro. Ex vivo human AT was obtained from women undergoing elective surgery [age: 42.7 ± 1.5 yr (mean ± SE), BMI: 26.2 ± 0.7 kg/m2; n = 38]. Western blot analysis was used to determine NPY protein expression in AT depots. Abdominal subcutaneous (AbSc) adipocytes were isolated and treated with recombinant (rh) NPY, insulin, and RSG. NPY and adipokine levels were measured by ELISA. Our results were that NPY was localized in human AT and adipocytes and confirmed by immunohistochemistry. Depot-specific NPY expression was noted as highest in AbSc AT (1.87 ± 0.23 ODU) compared with omental (Om; 1.03 ± 0.15 ODU, P = 0.029) or thigh AT (Th; 1.0 ± 0.29 ODU, P = 0.035). Insulin increased NPY secretion (control: 0.22 ± 0.024 ng/ml; 1 nM insulin: 0.26 ± 0.05 ng/ml; 100 nM insulin: 0.29 ± 0.04 ng/ml; 1,000 nM insulin: 0.3 ± 0.04 ng/ml; P < 0.05, n = 13), but cotreatment of RSG (10 nM) with insulin (100 nM) had no effect on NPY secretion. Furthermore, adipocyte treatment with rh-NPY downregulated leptin secretion (control: 6.99 ± 0.89 ng/ml; 1 nmol/l rh-NPY: 4.4 ± 0.64 ng/ml; 10 nmol/l rh-NPY: 4.3 ± 0.61 ng/ml, 100 nmol/l rh-NPY: 4.2 ± 0.67 ng/ml; P < 0.05, n = 10) but had no effect on adiponectin or TNF-α secretion. We conclude that NPY is expressed and secreted by human adipocytes. NPY secretion is stimulated by insulin, but this increment was limited by cotreatment with RSG. NPY's antilipolytic action may promote an increase in adipocyte size in hyperinsulinemic conditions. Adipose-derived NPY mediates reduction of leptin secretion and may have implications for central feedback of adiposity signals.
Differential baroreflex control of sympathetic drive by angiotensin II in the nucleus tractus solitarii
Authors: Polson J. W. , Dampney R. A. L. , Boscan P. , Pickering A. E. , Paton J. F. R.
Published: September 2007

Microinjection of angiotensin II into the nucleus tractus solitarii attenuates the baroreceptor reflex-mediated bradycardia by inhibiting both vagal and cardiac sympathetic components. However, it is not known whether the baroreflex modulation of other sympathetic outputs (i.e., noncardiac) also are inhibited by exogenous angiotensin II (ANG II) in nucleus tractus solitarii (NTS). In this study, we determined whether there was a difference in the baroreflex sensitivity of sympathetic outflows at the thoracic and lumbar levels of the sympathetic chain following exogenous delivery of ANG II into the NTS. Experiments were performed in two types of in situ arterially perfused decerebrate rat preparations. Sympathetic nerve activity was recorded from the inferior cardiac nerve, the midthoracic sympathetic chain, or the lower thoracic-lumbar sympathetic chain. Increases in perfusion pressure produced a reflex bradycardia and sympathoinhibition. Microinjection of ANG II (500 fmol) into the NTS attenuated the reflex bradycardia (57% attenuation, P < 0.01) and sympathoinhibition of both the inferior cardiac nerve (26% attenuation, P < 0.05) and midthoracic sympathetic chain (37% attenuation, P < 0.05) but not the lower thoracic-lumbar chain ( P = 0.56). We conclude that ANG II in the nucleus tractus solitarii selectively inhibits baroreflex responses in specific sympathetic outflows, possibly dependent on the target organ innervated.
Electrophysiological Diversity of Layer 5 Pyramidal Cells in the Prefrontal Cortex of the Rhesus Monkey: In Vitro Slice Studies
Authors: Chang Yu-Ming , Luebke Jennifer I.
Published: September 2007

Whole cell patch-clamp recordings were employed to characterize the electrophysiological properties of layer 5 pyramidal cells in slices of the prefrontal cortex (Area 46) of the rhesus monkey. Four electrophysiologically distinct cell types were discriminated based on distinctive repetitive action potential (AP) firing patterns and single AP characteristics: regular-spiking slowly adapting type-1 cells (RS1; 62%), regular-spiking slowly adapting type-2 cells (RS2; 18%), regular-spiking fast-adapting cells (FA; 15%), and intrinsically bursting cells (IB; 5%). These cells did not differ with regard to their location in layer 5 nor in their dendritic morphology. In RS1 cells, AP threshold and amplitude did not change significantly during a 2-s spike train, whereas in RS2 and FA cells, AP threshold increased significantly and AP amplitude decreased significantly during the train. In FA cells, complete adaptation of AP firing was observed within 600 ms. IB cells displayed an all-or-none burst of three to six APs, followed by RS1-type firing behavior. RS1 cells could be further subdivided into three subtypes. Low-threshold spiking (LTS) RS1 cells exhibited an initial doublet riding on a depolarizing potential at the onset of a spike train and a prominent depolarizing afterpotential (DAP); intermediate RS1 cells (IM) exhibited a DAP, but no initial doublet, and non-LTS RS1 cells exhibited neither a DAP nor an initial doublet. RS2 and FA cells did not exhibit a DAP or initial doublets. The distinctive firing patterns of these diverse layer 5 pyramidal cells may reflect different roles played by these cells in the mediation of subcortical neuronal activity by the dorsolateral PFC.
Adrenergic Facilitation of GABAergic Transmission in Rat Entorhinal Cortex
Authors: Lei Saobo , Deng Pan-Yue , Porter James E. , Shin Hee-Sup
Published: September 2007

Whereas the entorhinal cortex (EC) receives noradrenergic innervations from the locus coeruleus of the pons and expresses adrenergic receptors, the function of norepinephrine (NE) in the EC is still elusive. We examined the effects of NE on GABAA receptor–mediated synaptic transmission in the superficial layers of the EC. Application of NE dose-dependently increased the frequency and amplitude of spontaneous inhibitory postsynaptic currents (IPSCs) recorded from the principal neurons in layer II/III through activation of α1 adrenergic receptors. NE increased the frequency and not the amplitude of miniature IPSCs (mIPSCs) recorded in the presence of TTX, suggesting that NE increases presynaptic GABA release with no effects on postsynaptic GABAA receptors. Application of Ca2+ channel blockers (Cd2+ and Ni2+), omission of Ca2+ in the extracellular solution, or replacement of extracellular Na+ with N-methyl-d-glucamine (NMDG) failed to alter NE-induced increase in mIPSC frequency, suggesting that Ca2+ influx through voltage-gated Ca2+ or other cationic channels is not required. Application of BAPTA-AM, thapsigargin, and ryanodine did not change NE-induced increase in mIPSC frequency, suggesting that Ca2+ release from intracellular stores is not necessary for NE-induced increase in GABA release. Whereas α1 receptors are coupled to Gq/11 resulting in activation of the phospholipase C (PLC) pathway, NE-mediated facilitation of GABAergic transmission was independent of PLC, protein kinase C, and tyrosine kinase activities. Our results suggest that NE-mediated facilitation of GABAergic function contributes to its antiepileptic effects in the EC.
A Network Model for Parallel Line Balancing Problem
Authors: Benzer Recep , Gökçen Hadi , Çetinyokus Tahsin , Çerçioglu Hakan
Published: September 2007

Gökçen et al. (2006) have proposed several procedures and a mathematical model on single-model (product) assembly line balancing (ALB) problem with parallel lines. In parallel ALB problem, the goal is to balance more than one assembly line together. In this paper, a network model for parallel ALB problem has been proposed and illustrated on a numerical example. This model is a new approach for parallel ALB and it provides a different point of view for interested researchers.
Concerning Cut Point Spaces of Order Three
Authors: Daniel D. , Mahavier William S.
Published: September 2007

A pointpof a topological spaceXis a cut point ofXifX−{p}is disconnected. Further, ifX−{p}has preciselymcomponents for some natural numberm≥2we will say thatphas cut point orderm. If each pointyof a connected spaceYis a cut point ofY, we will say thatYis a cut point space. Herein we construct a spaceSso thatSis a connected Hausdorff space and each point ofSis a cut point of order three. We also note that there is no uncountable separable cut point space with each point a cut point of order three and therefore no such space may be embedded in a Euclidean space.
PPARs in Alveolar Macrophage Biology
Authors: Smith Monica R. , Standiford Theodore J. , Reddy Raju C.
Published: September 2007

PPARs, most notably PPAR-γ, play a crucial role in regulating the activation of alveolar macrophages, which in turn occupy a pivotal place in the immune response to pathogens and particulates drawn in with inspired air. In this review, we describe the dual role of the alveolar macrophage as both a first-line defender through its phagocytotic activity and a regulator of the immune response. Depending on its state of activation, the alveolar macrophage may either enhance or suppress different aspects of immune function in the lung. We then review the role of PPAR-γand its ligands in deactivating alveolar macrophages—thus limiting the inflammatory response that, if unchecked, could threaten the essential respiratory function of the alveolus—while upregulating the cell's phagocytotic activity. Finally, we examine the role that inadequate or inappropriate PPAR-γresponses play in specific lung diseases.
Effects of Methamphetamine on Single Unit Activity in Rat Medial Prefrontal Cortex In Vivo
Authors: Jang Jinhwa , Ha Hee-Jin , Kim Yun Bok , Chung Young-Ki , Jung Min Whan
Published: September 2007

To investigate how neuronal activity in the prefrontal cortex changes in an animal model of schizophrenia, we recorded single unit activity in the medial prefrontal cortex of urethane-anesthetized and awake rats following methamphetamine (MA) administration. Systemic MA injection (4 mg/kg, IP) induced inconsistent changes, that is, both enhancement and reduction, in unit discharge rate, with a subset of neurons transiently (<30 min) elevating their activities. The direction of firing rate change was poorly predicted by the mean firing rate or the degree of burst firing during the baseline period. Also, simultaneously recorded units showed opposite directions of firing rate change, indicating that recording location is a poor predictor of the direction of firing rate change. These results raise the possibility that systemic MA injection induces random bidirectional changes in prefrontal cortical unit activity, which may underlie some of MA-induced psychotic symptoms.
Anisotropic Vanadium Oxide Nanostructured Host Matrices for Lithium Ion Intercalation
Authors: O'Dwyer C. , Lavayen V. , Santa Ana M. A. , Benavente E. , González G. , Sotomayor Torres C. M.
Published: September 2007

We report on unique high-volume low-dimensional V2O5-based turbostratic nanostructures, prepared using sol-gel synthetic methods from V2O5⋅nH2O xerogels. Electrochemical intercalation of Li+ to form Li0.65V2O5 resulted in a maximum measured charge capacity of 1225 mAh g−1 as the β-LixV2O5 phase. Conductivities of the
order of 10−3 S cm−1 were found on compressed-nanotube parallelepipedal samples, which exhibit an anisotropy factor of 70 at room temperature by preferential alignment of the nanotubes. The improved electrochemical properties observed in novel vanadium oxide nanostructured arrays are attributed to the increased volumetric density for ion intercalation, shorter diffusion paths to the intercalation sites, and a high degree of crystallinity of
the individual nanotubular host structures.
Activating Effect of Benzbromarone, a Uricosuric Drug, on Peroxisome Proliferator-Activated Receptors
Authors: Kunishima Chiyoko , Inoue Ikuo , Oikawa Toshihiro , Nakajima Hiromu , Komoda Tsugikazu , Katayama Shigehiro
Published: September 2007

Benzbromarone, a uricosuric drug, reportedly causes hepatic hypertrophy accompanied by proliferation of peroxisomes in rats. To elucidate the mechanisms underlying induction of peroxisome proliferation by benzbromarone, we examined binding affinity for peroxisome proliferator-activated receptorα(PPARα) andγ(PPARγ), and effects on the binding activity of PPARs with peroxisome proliferation-responsive element (PPRE) and expression of the PPARs target protein. Binding affinity of benzbromarone forPPARαandPPARγwas examined by reporter gene assay. Binding activity of PPARs with PPRE was determined by electric mobility shift assay, and expression of lipoprotein lipase (LPL) and acyl-CoA synthetase (ACS) by Western blot method. Benzbromarone displayed affinity forPPARαandPPARγ, and promoted binding of PPARs to PPRE. Furthermore, cultured cells with benzbromarone added showed upregulated expression of LPL and ACS. These results suggest that benzbromarone induces peroxisome proliferation in hepatocytes by binding to PPARs, and controls expression of proteins related to lipid metabolism.
Temporal and Spatial Features of Single-Trial EEG for Brain-Computer Interface
Authors: Zhao Qibin , Zhang Liqing
Published: September 2007

Brain-computer interface (BCI) systems create a novel communication channel from the brain to an output device bypassing conventional motor output pathways of nerves and muscles. Modern BCI technology is essentially based on techniques for the classification of single-trial brain signals. With respect to the topographic patterns of brain rhythm modulations, the common spatial patterns (CSPs) algorithm has been proven to be very useful to produce subject-specific and discriminative spatial filters; but it didn't consider temporal structures of event-related potentials which may be very important for single-trial EEG classification. In this paper, we propose a new framework of feature extraction for classification of hand movement imagery EEG. Computer simulations on real experimental data indicate that independent residual analysis (IRA) method can provide efficient temporal features. Combining IRA features with the CSP method, we obtain the optimal spatial and temporal features with which we achieve the best classification rate. The high classification rate indicates that the proposed method is promising for an EEG-based brain-computer interface.
Improving the Accuracy of the Diffusion Model in Highly Absorbing Media
Authors: Cong Alexander X. , Shen Haiou , Cong Wenxiang , Wang Ge
Published: September 2007

The diffusion approximation of the Boltzmann transport equation is most commonly used for describing the photon propagation in turbid media. It produces satisfactory results in weakly absorbing and highly scattering media, but the accuracy lessens with the decreasing albedo. In this paper, we presented a method to improve the accuracy of the diffusion model in strongly absorbing media by adjusting the optical parameters. Genetic algorithm‐based optimization tool is used to find the optimal optical parameters. The diffusion model behaves more closely to the physical model with the actual optical parameters substituted by the optimized optical parameters. The effectiveness of the proposed technique was demonstrated by the numerical experiments using the Monte Carlo
simulation data as measurements.
Vibrotactile Feedback for Brain-Computer Interface Operation
Authors: Cincotti Febo , Kauhanen Laura , Aloise Fabio , Palomäki Tapio , Caporusso Nicholas , Jylänki Pasi , Mattia Donatella , Babiloni Fabio , Vanacker Gerolf , Nuttin Marnix , Marciani Maria Grazia , Millán José del R.
Published: September 2007

To be correctly mastered, brain-computer interfaces (BCIs) need an uninterrupted flow of feedback to the user. This feedback is usually delivered through the visual channel. Our aim was to explore the benefits of vibrotactile feedback during users' training and control of EEG-based BCI applications. A protocol for delivering vibrotactile feedback, including specific hardware and software arrangements, was specified. In three studies with 33 subjects (including 3 with spinal cord injury), we compared vibrotactile and visual feedback, addressing: (I) the feasibility of subjects' training to master their EEG rhythms using tactile feedback; (II) the compatibility of this form of feedback in presence of a visual distracter; (III) the performance in presence of a complex visual task on the same (visual) or different (tactile) sensory channel. The stimulation protocol we developed supports a general usage of the tactors; preliminary experimentations. All studies indicated that the vibrotactile channel can function as a valuable feedback modality with reliability comparable to the classical visual feedback. Advantages of using a vibrotactile feedback emerged when the visual channel was highly loaded by a complex task. In all experiments, vibrotactile feedback felt, after some training, more natural for both controls and SCI users.
Inferring Functional Brain States Using Temporal Evolution of Regularized Classifiers
Authors: Zhdanov Andrey , Hendler Talma , Ungerleider Leslie , Intrator Nathan
Published: September 2007

We present a framework for inferring functional brain state from electrophysiological (MEG or EEG) brain signals. Our approach is adapted to the needs of functional brain imaging rather than EEG-based brain-computer interface (BCI). This choice leads to a different set of requirements, in particular to the demand for more robust inference methods and more sophisticated model validation techniques. We approach the problem from a machine learning perspective, by constructing a classifier from a set of labeled signal examples. We propose a framework that focuses on temporal evolution of regularized classifiers, with cross-validation for optimal regularization parameter at each time frame. We demonstrate the inference obtained by this method on MEG data recorded from 10 subjects in a simple visual classification experiment, and provide comparison to the classical nonregularized approach.
Nuclear Receptors in Regulation of Mouse ES Cell Pluripotency and Differentiation
Authors: Mullen Eimear M. , Gu Peili , Cooney Austin J.
Published: September 2007

Embryonic stem (ES) cells have great therapeutic potential because they are capable of indefinite self-renewal and have the potential to differentiate into over 200 different cell types that compose the human body. The switch from the pluripotent phenotype to a differentiated cell involves many complex signaling pathways including those involving LIF/Stat3 and the transcription factors Sox2, Nanog and Oct-4. Many nuclear receptors play an important role in the maintenance of pluripotence (ERRβ, SF-1, LRH-1, DAX-1) repression of the ES cell phenotype (RAR, RXR, GCNF) and also the differentiation of ES cells (PPARγ). Here we review the roles of the nuclear receptors involved in regulating these important processes in ES cells.
Development of a Confocal Optical System Design for Molecular Imaging Applications of Biochip
Authors: Huang Guoliang , Xu Shukuan , Zhu Jiang , Deng Cheng , Dong Zhonghua , Yang Yang , Yang Xiaoyong , Wang Xianhua , Jin Guofan
Published: September 2007

A novel confocal optical system design and a dual laser confocal scanner have been developed to meet the requirements of highly sensitive detection of biomolecules on microarray chips, which is characterized by a long working distance (wd > 3.0 mm), high numerical aperture (NA = 0.72), and only 3 materials and 7 lenses used. This confocal optical system has a high scanning resolution, an excellent contrast and signal‐to‐noise ratio, and an efficiency of collected fluorescence of more than 2‐fold better than that of other commercial confocal biochip scanners. The scanner is as equally good for the molecular imaging detection of enclosed biochips as for the detection of biological samples on a slide surface covered with a cover‐slip glass. Some applications of gene and protein imagings using the dual laser confocal scanner are described.
The Self-Paced Graz Brain-Computer Interface: Methods and Applications
Authors: Scherer Reinhold , Schloegl Alois , Lee Felix , Bischof Horst , Janša Janez , Pfurtscheller Gert
Published: September 2007

We present the self-paced 3-class Graz brain-computer interface (BCI) which is based on the detection of sensorimotor electroencephalogram (EEG) rhythms induced by motor imagery. Self-paced operation means that the BCI is able to determine whether the ongoing brain activity is intended as control signal (intentional control) or not (non-control state). The presented system is able to automatically reduce electrooculogram (EOG) artifacts, to detect electromyographic (EMG) activity, and uses only three bipolar EEG channels. Two applications are presented: the freeSpace virtual environment (VE) and the Brainloop interface. The freeSpace is a computer-game-like application where subjects have to navigate through the environment and collect coins by autonomously selecting navigation commands. Three subjects participated in these feedback experiments and each learned to navigate through the VE and collect coins. Two out of the three succeeded in collecting all three coins. The Brainloop interface provides an interface between the Graz-BCI and Google Earth.