bluuebunny/crossref_metadata_2025 huggingface dataset:
Signal transduction pathway of TonB-dependent transporters
Authors: Ferguson Andrew D. , Amezcua Carlos A. , Halabi Najeeb M. , Chelliah Yogarany , Rosen Michael K. , Ranganathan Rama , Deisenhofer Johann
Published: December 2006

Transcription of the ferric citrate import system is regulated by ferric citrate binding to the outer membrane transporter FecA. A signal indicating transporter occupancy is relayed across the outer membrane to energy-transducing and regulatory proteins embedded in the cytoplasmic membrane. Because transcriptional activation is not coupled to ferric citrate import, an allosteric mechanism underlies this complex signaling mechanism. Using evolution-based statistical analysis we have identified a sparse but structurally connected network of residues that links distant functional sites in FecA. Functional analyses of these positions confirm their involvement in the mechanism that regulates transcriptional activation in response to ferric citrate binding at the cell surface. This mechanism appears to be conserved and provides the structural basis for the allosteric signaling of TonB-dependent transporters.
Precise physical models of protein–DNA interaction from high-throughput data
Authors: Kinney Justin B. , Tkačik Gašper , Callan Curtis G.
Published: December 2006

A cell's ability to regulate gene transcription depends in large part on the energy with which transcription factors (TFs) bind their DNA regulatory sites. Obtaining accurate models of this binding energy is therefore an important goal for quantitative biology. In this article, we present a principled likelihood-based approach for inferring physical models of TF–DNA binding energy from the data produced by modern high-throughput binding assays. Central to our analysis is the ability to assess the relative likelihood of different model parameters given experimental observations. We take a unique approach to this problem and show how to compute likelihood without any explicit assumptions about the noise that inevitably corrupts such measurements. Sampling possible choices for model parameters according to this likelihood function, we can then make probabilistic predictions for the identities of binding sites and their physical binding energies. Applying this procedure to previously published data on the
Saccharomyces cerevisiae
TF Abf1p, we find models of TF binding whose parameters are determined with remarkable precision. Evidence for the accuracy of these models is provided by an astonishing level of phylogenetic conservation in the predicted energies of putative binding sites. Results from
in vivo
and
in vitro
experiments also provide highly consistent characterizations of Abf1p, a result that contrasts with a previous analysis of the same data.
Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase
Authors: Forouhar Farhad , Anderson J. L. Ross , Mowat Christopher G. , Vorobiev Sergey M. , Hussain Arif , Abashidze Mariam , Bruckmann Chiara , Thackray Sarah J. , Seetharaman Jayaraman , Tucker Todd , Xiao Rong , Ma Li-Chung , Zhao Li , Acton Thomas B. , Montelione Gaetano T. , Chapman Stephen K. , Tong Liang
Published: December 2006

Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive structural and biochemical studies of the
Xanthomonas campestris
TDO and a related protein SO4414 from
Shewanella oneidensis
, including the structure at 1.6-Å resolution of the catalytically active, ferrous form of TDO in a binary complex with the substrate
l
-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by electrostatic and hydrogen-bonding interactions with the enzyme and a propionate group of the heme, thus defining the
l
-stereospecificity. A second, possibly allosteric,
l
-Trp-binding site is present at the tetramer interface. The sixth coordination site of the heme-iron is vacant, providing a dioxygen-binding site that would also involve interactions with the ammonium moiety of
l
-Trp and the amide nitrogen of a glycine residue. The indole ring is positioned correctly for oxygenation at the C2 and C3 atoms. The active site is fully formed only in the binary complex, and biochemical experiments confirm this induced-fit behavior of the enzyme. The active site is completely devoid of water during catalysis, which is supported by our electrochemical studies showing significant stabilization of the enzyme upon substrate binding.
Signatures of strong population differentiation shape extended haplotypes across the human
CD28
,
CTLA4
, and
ICOS
costimulatory genes
Authors: Butty Vincent , Roy Matt , Sabeti Pardis , Besse Whitney , Benoist Christophe , Mathis Diane
Published: December 2006

The three members of the costimulatory receptor family, CD28, CTLA-4, and ICOS, have complementary effects on T cell activation, and their balance controls the overall outcome of immune and autoimmune responses. They are encoded in a short genomic interval, and overall activity may result from interplay between allelic variants at each locus. With multiethnic DNA panels that represent a wide spectrum of human populations, we demonstrate long-range linkage disequilibrium among the three genes. A large fraction of the variation found in the locus can be explained by the presence of extended haplotypes encompassing variants at
CD28
,
CTLA4
, and the
ICOS
promoter. There are unusual differences in the distribution of some variants and haplotypes between geographic regions. The differences may reflect demographic events and/or the adaptation to diverse environmental and microbial challenges encountered in the course of human migrations and will be important to consider when interpreting association to immune/autoimmune responsiveness.
Lack of Adenomatous Polyposis Coli Protein Correlates with a Decrease in Cell Migration and Overall Changes in Microtubule Stability
Authors: Kroboth Karin , Newton Ian P. , Kita Katsuhiro , Dikovskaya Dina , Zumbrunn Jürg , Waterman-Storer Clare M. , Näthke Inke S.
Published: December 2006

Most sporadic colorectal tumors carry truncation mutations in the adenomatous polyposis coli (APC) gene. The APC protein is involved in many processes that govern gut tissue. In addition to its involvement in the regulation of β-catenin, APC is a cytoskeletal regulator with direct and indirect effects on microtubules. Cancer-related truncation mutations lack direct and indirect binding sites for microtubules in APC, suggesting that loss of this function contributes to defects in APC-mutant cells. In this study, we show that loss of APC results in disappearance of cellular protrusions and decreased cell migration. These changes are accompanied by a decrease in overall microtubule stability and also by a decrease in posttranslationally modified microtubules in the cell periphery particularly the migrating edge. Consistent with the ability of APC to affect cell shape, the overexpression of APC in cells can induce cellular protrusions. These data demonstrate that cell migration and microtubule stability are linked to APC status, thereby revealing a weakness in APC-deficient cells with potential therapeutic implications.
Atg19 Mediates a Dual Interaction Cargo Sorting Mechanism in Selective Autophagy
Authors: Chang Chiung-Ying , Huang Wei-Pang
Published: December 2006

Autophagy is a catabolic membrane-trafficking mechanism conserved in all eukaryotic cells. In addition to the nonselective transport of bulk cytosol, autophagy is responsible for efficient delivery of the vacuolar enzyme Ape1 precursor (prApe1) in the budding yeast Saccharomyces cerevisiae, suggesting the presence of a prApe1 sorting machinery. Sequential interactions between Atg19-Atg11 and Atg19-Atg8 pairs are thought responsible for targeting prApe1 to the vesicle formation site, the preautophagosomal structure (PAS), and loading it into transport vesicles, respectively. However, the different patterns of prApe1 transport defect seen in the atg11Δ and atg19Δ strains seem to be incompatible with this model. Here we report that prApe1 could not be targeted to the PAS and failed to be delivered into the vacuole in atg8Δ atg11Δ double knockout cells regardless of the nutrient conditions. We postulate that Atg19 mediates a dual interaction prApe1-sorting mechanism through independent, instead of sequential, interactions with Atg11 and Atg8. In addition, to efficiently deliver prApe1 to the vacuole, a proper interaction between Atg11 and Atg9 is indispensable. We speculate that Atg11 may elicit a cargo-loading signal and induce Atg9 shuttling to a specific PAS site, where Atg9 relays the signal and recruits other Atg proteins to induce vesicle formation.
Mutagenesis of the DNA binding residues in bovine pancreatic DNase1: an investigation into the mechanism of sequence discrimination by a sequence selective nuclease
Authors: Doherty Aidan J. , Worrall Andrew F. , Connolly Bernard A.
Published: January 2007

The sequence selectivity of DNasei cleavage has been investigated by site-directed mutagenesis of a chemically synthesised gene. Two key DNA binding residues have been conservatively altered (Y76F and R41K) or have had their side-chains truncated (Y76A and R41A) and the effect on the cleavage of tyr T promoter DNA has been noted. It would appear from these studies that DNasei is not sensitive to minor groove width via these DNA-contacting residues, and it is suggested that DNA helical stiffness is a controlling parameter in determining DNasei sequence selectivity.
Analysis and prediction of functionally important sites in proteins
Authors: Chakrabarti Saikat , Lanczycki Christopher J.
Published: December 2006

The rapidly increasing volume of sequence and structure information available for proteins poses the daunting task of determining their functional importance. Computational methods can prove to be very useful in understanding and characterizing the biochemical and evolutionary information contained in this wealth of data, particularly at functionally important sites. Therefore, we perform a detailed survey of compositional and evolutionary constraints at the molecular and biological function level for a large set of known functionally important sites extracted from a wide range of protein families. We compare the degree of conservation across different functional categories and provide detailed statistical insight to decipher the varying evolutionary constraints at functionally important sites. The compositional and evolutionary information at functionally important sites has been compiled into a library of functional templates. We developed a module that predicts functionally important columns (FIC) of an alignment based on the detection of a significant “template match score” to a library template. Our template match score measures an alignment column's similarity to a library template and combines a term explicitly representing a column's residue composition with various evolutionary conservation scores (information content and position‐specific scoring matrix‐derived statistics). Our benchmarking studies show good sensitivity/specificity for the prediction of functional sites and high accuracy in attributing correct molecular function type to the predicted sites. This prediction method is based on information derived from homologous sequences and no structural information is required. Therefore, this method could be extremely useful for large‐scale functional annotation.
P‐glycoprotein‐mediated transport of oxytetracycline in the Caco‐2 cell model
Authors: SCHRICKX J. , FINK‐GREMMELS J.
Published: January 2007

ATP‐dependent drug transporters such as P‐glycoprotein (P‐gp), multi‐drug resistance associated protein (MRP2) and breast cancer resistant protein (BCRP) are expressed at the brush border membrane of enterocytes. These efflux transporters excrete their substrates, among other various classes of antibiotics, into the lumen thus reducing net absorption as indicated by a low bioavailability after oral administration. Oxytetracycline (OTC) has been used for decennia in veterinary medicine for its extensive spectrum of antimicrobial activity. A major limitation has been, and still remains, its low bioavailability following oral administration. The present study aimed to investigate to what extent this low bioavailability is attributable to the fact that OTC is a substrate for one or more efflux transporters. As an experimental model to study the transmembrane transport of OTC, differentiated Caco‐2 cells grown as monolayers on permeable supports were used. With this model it was shown that the secretion of OTC is slightly higher than its absorption. PSC833, a potent inhibitor of P‐gp, decreased the secretion of OTC without affecting its absorption, while the MRP‐inhibitor MK571 did not exert any effect. These data indicate that OTC is a substrate for P‐gp. The affinity of OTC to these transporters seems to be rather low, as suggested by the low efflux ratio of 1:1.3. In competition experiments, OTC decreased the effluxes of other P‐gp substrates such as Rhodamine123 and ivermectin. These findings are of clinical relevance, as they clearly indicate potential drug–drug interactions at the level of P‐gp‐mediated drug transport.
Pharmacokinetics of florfenicol and its major metabolite, florfenicol amine, in rabbits
Authors: PARK B.‐K. , LIM J.‐H. , KIM M.‐S. , HWANG Y.‐H. , YUN H.‐I.
Published: January 2007

The pharmacokinetics of florfenicol and its active metabolite florfenicol amine were investigated in rabbits after a single intravenous (i.v.) and oral (p.o.) administration of florfenicol at 20 mg/kg bodyweight. The plasma concentrations of florfenicol and florfenicol amine were determined simultaneously by an LC/MS method. After i.v. injection, the terminal half‐life (t1/2λz), steady‐state volume of distribution, total body clearance and mean residence time of florfenicol were 0.90 ± 0.20 h, 0.94 ± 0.19 L/kg, 0.63 ± 0.06 L/h/kg and 1.50 ± 0.34 h respectively. The peak concentrations (Cmax) of florfenicol (7.96 ± 2.75 μg/mL) after p.o. administration were observed at 0.90 ± 0.38 h. The t1/2λz and p.o. bioavailability of florfenicol were 1.42 ± 0.56 h and 76.23 ± 12.02% respectively. Florfenicol amine was detected in all rabbits after i.v. and p.o. administration. After i.v. and p.o. administration of florfenicol, the observed Cmax values of florfenicol amine (5.06 ± 1.79 and 3.38 ± 0.97 μg/mL) were reached at 0.88 ± 0.78 and 2.10 ± 1.08 h respectively. Florfenicol amine was eliminated with an elimination half‐life of 1.84 ± 0.17 and 2.35 ± 0.94 h after i.v. and p.o. administration respectively.
Lack of inhibitory effects of several fluoroquinolones on cytochrome P‐450 3A activities at clinical dosage in dogs
Authors: REGMI N. L. , ABD EL‐ATY A. M. , KUBOTA R. , SHAH S. S. , SHIMODA M.
Published: January 2007

Inhibitory effects of several fluoroquinolones (FQs) on liver CYP3A activities were examined by in vitro and in vivo tests in dogs. Midazolam (MDZ) hydroxylation rate was used to determine the CYP3A activities in liver microsomes. Enrofloxacin (EFX), ofloxacin (OFX) orbifloxacin (OBFX) and ciprofloxacin (CFX) were tested. None of the FQs changed Vmax, Km or intrinsic clearance (Vmax/Km) of MDZ. For in vivo test, we examined the effects of oral administration of EFX and OFX on the pharmacokinetics of quinidine (QN), a CYP3A substrate. EFX or OFX (10 mg/kg) was administered once a day for 3 days. QN (2 mg/kg) was intravenously injected at 2 h after the final dose of FQs administration. The same dose of QN was intravenously injected 3 weeks before the start of FQs administration for control. Neither EFX nor OFX changed the pharmacokinetic parameters of QN. These in vitro and in vivo consisted results suggest that these FQs lack the inhibitory effects on CYP3A activities in dogs. Hence, given these results, the risk of drug–drug interaction is unlikely to occur between FQs and CYP3A substrates in clinical situation in dogs.
Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata
Authors: KIVIMÄKI MAARIT , KÄRKKÄINEN KATRI , GAUDEUL MYRIAM , LØE GEIR , ÅGREN JON
Published: January 2007

The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.
Characterization of a
higBA
Toxin-Antitoxin Locus in
Vibrio cholerae
Authors: Budde Priya Prakash , Davis Brigid M. , Yuan Jie , Waldor Matthew K.
Published: December 2006

Toxin-antitoxin (TA) loci, which were initially characterized as plasmid stabilization agents, have in recent years been detected on the chromosomes of numerous free-living bacteria.
Vibrio cholerae
, the causative agent of cholera, contains 13 putative TA loci, all of which are clustered within the superintegron on chromosome II. Here we report the characterization of the
V. cholerae higBA
locus, also known as VCA0391/2. Deletion of
higA
alone was not possible, consistent with predictions that it encodes an antitoxin, and biochemical analyses confirmed that HigA interacts with HigB. Transient exogenous expression of the toxin HigB dramatically slowed growth of
V. cholerae
and
Escherichia coli
and reduced the numbers of CFU by several orders of magnitude. HigB toxicity could be counteracted by simultaneous or delayed production of HigA, although HigA's effect diminished as the delay lengthened. Transcripts from endogenous
higBA
increased following treatment of
V. cholerae
with translational inhibitors, presumably due to reduced levels of HigA, which represses the
higBA
locus. However, no
higBA
-dependent cell death was observed in response to such stimuli. Thus, at least under the conditions tested, activation of endogenous HigB does not appear to be bactericidal.
Inactivation of Lgt Allows Systematic Characterization of Lipoproteins fromListeria monocytogenes
Authors: Baumgärtner Maja , Kärst Uwe , Gerstel Birgit , Loessner Martin , Wehland Jürgen , Jänsch Lothar
Published: December 2006

Lipoprotein anchoring in bacteria is mediated by the prolipoprotein diacylglyceryl transferase (Lgt), which catalyzes the transfer of a diacylglyceryl moiety to the prospective N-terminal cysteine of the mature lipoprotein. Deletion of thelgtgene in the gram-positive pathogenListeria monocytogenes(i) impairs intracellular growth of the bacterium in different eukaryotic cell lines and (ii) leads to increased release of lipoproteins into the culture supernatant. Comparative extracellular proteome analyses of the EGDe wild-type strain and the Δlgtmutant provided systematic insight into the relative expression of lipoproteins. Twenty-six of the 68 predicted lipoproteins were specifically released into the extracellular proteome of the Δlgtstrain, and this proved that deletion oflgtis an excellent approach for experimental verification of listerial lipoproteins. Consequently, we generated ΔlgtΔprfAdouble mutants to detect lipoproteins belonging to the main virulence regulon that is controlled by PrfA. Overall, we identified three lipoproteins whose extracellular levels are regulated and one lipoprotein that is posttranslationally modified depending on PrfA. It is noteworthy that in contrast to previous studies ofEscherichia coli, we unambiguously demonstrated that lipidation by Lgt is not a prerequisite for activity of the lipoprotein-specific signal peptidase II (Lsp) inListeria.
Mutants, Suppressors, and Wrinkled Colonies: Mutant Alleles of the Cell Division GeneftsQPoint to Functional Domains in FtsQ and a Role for Domain 1C of FtsA in Divisome Assembly
Authors: Goehring Nathan W. , Petrovska Ivana , Boyd Dana , Beckwith Jon
Published: December 2006

Cell division inEscherichia colirequires the concerted action of at least 10 essential proteins. One of these proteins, FtsQ, is physically associated with multiple essential division proteins, including FtsK, FtsL, FtsB, FtsW, and FtsI. In this work we performed a genetic analysis of theftsQgene. Our studies identified C-terminal residues essential for FtsQ's interaction with two downstream proteins, FtsL and FtsB. Here we also describe a novel screen for cell division mutants based on a wrinkled-colony morphology, which yielded several new point mutations inftsQ. Two of these mutations affect localization of FtsQ to midcell and together define a targeting role for FtsQ's α domain. Further characterization of one localization-defective mutant protein [FtsQ(V92D)] revealed an unexpected role in localization for the first 49 amino acids of FtsQ. Finally, we found a suppressor of FtsQ(V92D) that was due to a point mutation in domain 1C of FtsA, a domain previously implicated in the recruitment of divisome proteins. However, despite reports of a potential interaction between FtsA and FtsQ, suppression by FtsA(I143L) is not mediated via direct contact with FtsQ. Rather, this mutation acts as a general suppressor of division defects, which include deletions of the normally essential geneszipAandftsKand mutations in FtsQ that affect both localization and recruitment. Together, these results reveal increasingly complex connections within the bacterial divisome.
Minimum Length Requirement of the Flexible N-Terminal Translocation Subdomain of Colicin E3
Authors: Sharma Onkar , Cramer William A.
Published: December 2006

The 315-residue N-terminal T domain of colicin E3 functions in translocation of the colicin across the outer membrane through its interaction with outer membrane proteins including the OmpF porin. The first 83 residues of the T domain are known from structure studies to be disordered. This flexible translocation subdomain contains the TolB box (residues 34 to 46) that must cross the outer membrane in an early translocation event, allowing the colicin to bind to the TolB protein in the periplasm. In the present study, it was found that cytotoxicity of the colicin requires a minimum length of 19 to 23 residues between the C terminus (residue 46) of the TolB box and the end of the flexible subdomain (residue 83). Colicin E3 molecules of sufficient length display normal binding to TolB and occlusion of OmpF channels in vitro. The length of the N-terminal subdomain is critical because it allows the TolB box to cross the outer membrane and interact with TolB. It is proposed that the length constraint is a consequence of ordered structure in the downstream segment of the T domain (residues 84 to 315) that prevents its insertion through the outer membrane via a translocation pore that includes OmpF.
Distinct Antimicrobial Resistance Patterns and Antimicrobial Resistance-Harboring Genes According to Genomic Species of
Acinetobacter
Isolates
Authors: Lim Yu Mi , Shin Kyeong Seob , Kim Jungmin
Published: December 2006

Using 58 isolates of
Acinetobacter
species recovered from a university hospital between August 2004 and March 2005, we performed genomic identification by amplified rRNA gene restriction analysis (ARDRA) and investigated the existence of metallo-β-lactamase (MBL) producers and extended-spectrum β-lactamase (ESBL) producers. Genomic species identification of
Acinetobacter
strains using ARDRA showed that 40 strains were genomic species 2 (
Acinetobacter baumannii
), 9 were 13 sensu Tjernberg and Ursing (13TU), 5 were
Acinetobacter
phenon 6/ct 13TU, and 4 were
Acinetobacter
genospecies 3. Among 58 strains, 13 isolates were MBL producers carrying
bla
IMP-1
or
bla
VIM-2
and 13 isolates were ESBL producers carrying
bla
PER-1
. Notably, the MBL producers were mostly 13TU,
Acinetobacter
phenon 6/ct 13TU, and
Acinetobacter
genospecies 3, which showed susceptibility to ciprofloxacin and ampicillin-sulbactam. However, 12 of 13 strains carrying
bla
PER-1
were
A. baumannii
, showing multidrug resistance. The data revealed that the antimicrobial resistance patterns and resistance-harboring genes of
Acinetobacter
species are remarkably distinct according to the genomic species of
Acinetobacter
isolates.
Tropism Modification of Adenovirus Vectors by Peptide Ligand Insertion into Various Positions of the Adenovirus Serotype 41 Short-Fiber Knob Domain
Authors: Hesse Andrea , Kosmides Daniela , Kontermann Roland E. , Nettelbeck Dirk M.
Published: December 2006

Recombinant adenoviruses have emerged as promising agents in therapeutic gene transfer, genetic vaccination, and viral oncolysis. Therapeutic applications of adenoviruses, however, would benefit substantially from targeted virus cell entry, for example, into cancer or immune cells, as opposed to the broad tropism that adenoviruses naturally possess. Such tropism modification of adenoviruses requires the deletion of their natural cell binding properties and the incorporation of cell binding ligands. The short fibers of subgroup F adenoviruses have recently been suggested as a tool for genetic adenovirus detargeting based on the reduced infectivity of corresponding adenovectors with chimeric fibers in vitro and in vivo. The goal of our study was to determine functional insertion sites for peptide ligands in the adenovirus serotype 41 (Ad41) short fiber knob. With a model peptide, CDCRGDCFC, we could demonstrate that ligand incorporation into three of five analyzed loops of the knob, namely, EG, HI, and IJ, is feasible without a loss of fiber trimerization. The resulting adenovectors showed enhanced infectivity for various cell types, which was superior to that of viruses with the same peptide fused to the fiber C terminus. Strategies to further augment gene transfer efficacy by extension of the fiber shaft, insertion of tandem copies of the ligand peptide, or extension of the ligand-flanking linkers failed, indicating that precise ligand positioning is pivotal. Our study establishes that internal ligand incorporation into a short-shafted adenovirus fiber is feasible and suggests the Ad41 short fiber with ligand insertion into the top (IJ loop) or side (EG and HI loops) of the knob domain as a novel platform for genetic targeting of therapeutic adenoviruses.
High hopes and automatic escalators: a critique of some new arguments in bioethics
Authors: Holm S , Takala T
Published: January 2007

Two protechnology arguments, the “hopeful principle” and the “automatic escalator”, often used in bioethics, are identified and critically analysed in this paper. It is shown that the hopeful principle is closely related to the problematic precautionary principle, and the automatic escalator argument has close affinities to the often criticised empirical slippery slope argument. The hopeful principle is shown to be really hopeless as an argument, and automatic escalator arguments often lead nowhere when critically analysed. These arguments should therefore only be used with great caution.
GENERIC q-MARKOV SEMIGROUPS AND SPEED OF CONVERGENCE OF q-ALGORITHMS
Authors: ACCARDI LUIGI , FAGNOLA FRANCO , HACHICHA SKANDER
Published: December 2006

We study a special class of generic quantum Markov semigroups, on the algebra of all bounded operators on a Hilbert space [Formula: see text], arising in the stochastic limit of a generic system interacting with a boson–Fock reservoir. This class depends on an orthonormal basis of [Formula: see text]. We obtain a new estimate for the trace distance of a state from a pure state and use this estimate to prove that, under the action of a semigroup of this class, states with finite support with respect to the given basis converge to equilibrium with a speed which is exponential, but with a polynomial correction which makes the convergence increasingly worse as the dimension of the support increases (Theorem 5.1). We interpret the semigroup as an algorithm, its initial state as input and, following Belavkin and Ohya,10 the dimension of the support of a state as a measure of complexity of the input. With this interpretation, the above results mean that the complexity of the input "slows down" the convergence of the algorithm. Even if the convergence is exponential and the slow down the polynomial, the constants involved may be such that the convergence times become unacceptable from a computational standpoint. This suggests that, in the absence of estimates of the constants involved, distinctions such as "exponentially fast" and "polynomially slow" may become meaningless from a constructive point of view.

We also show that, for arbitray states, the speed of convergence to equilibrium is controlled by the rate of decoherence and the rate of purification (i.e. of concentration of the probability on a single pure state). We construct examples showing that the order of magnitude of these two decays can be quite different.
UNIQUENESS OF INTEGRANDS IN QUANTUM STOCHASTIC INTEGRAL
Authors: JI UN CIG , SINHA KALYAN B.
Published: December 2006

As a general study for uniqueness of integrands in quantum martingale representation, we present a necessary and sufficient condition for uniqueness of integrands in a quantum stochastic integral. Also, several equivalent conditions to the necessary and sufficient condition are studied.
Measuring Firm-Specific Organizational Capital and its Impact on Value and Productivity: Evidence From Japan
Authors: Ramirez Pablo Gonzalo , Hachiya Toyohiko
Published: December 2006

In this study we used Japanese firm-level data in order to explore the productive impact of organizational capital by isolating the effect of other intangibles like R&D, brand, human and social capital. Fixed-effect and random-effect panel methodology are proposed to assess specific-organizational capital at firm level. Our results suggest that in monetary terms the value of firm-specific organizational capital stock is significant when compared to traditional assets. Findings suggest that firms building up higher stocks of organizational capital not only increase their productivity but also their value.
Volatility–Volume Relationships Among Types of Traders Considering the Investment Limitation to Foreign Investors
Authors: Huang Ching-Mann , Lin Tsai-Yin , Yu Chih-Hsien , Hoe Si-Ying
Published: December 2006

This paper examines the volatility–volume relationship in Taiwan stock market, using volume data categorized by type of trader. We consider before and after our event period of lifting the investment restrictions for foreign investors. We partition trading volume into expected and unexpected volume and find that the unexpected volume shocks for individual investors are more important than the expected volume shocks in explaining volatility before lifting the investment restrictions for the foreign investors. We find that the positive volatility–volume relationship is driven by the individual investors even during the period of the lifting of investment restrictions for foreign investors. However, with respect to institutional investors, before the removal of investment restrictions for foreign investors, the unexpected volume of trading of the domestic dealers exhibit positive volatility–volume relationship. Further, after the removal of investment restrictions, the unexpected volume of the foreign investors has a positive volatility–volume relationship.
TEMPERATURE AND MAGNETIC FIELD DEPENDENCE OF CONDUCTION NOISE IN DOUBLE LAYERED La1.4Ca1.6Mn2O7 MANGANITE
Authors: GUPTA AJAI K. , BHALLA G. L. , KHARE NEERAJ
Published: December 2006

Bulk samples of double layered manganite La 1.4 Ca 1.6 Mn 2 O 7 were prepared by solid-state reaction method. Study of magnetotransport properties revealed a metal to insulator transition at 160 K, a ferromagnetic transition at 164 K and appearance of two-dimensional short range ferromagnetic correlations around 235 K. The temperature dependence of conduction noise showed three peaks at 114 K, 165 K and 235 K which are attributed to excess noise generated due to setting up of three-dimensional out-of-plane ferromagnetic transition, two-dimensional out-of-plane ferromagnetic transition temperatures and appearance of two-dimensional short range ferromagnetic correlations respectively. In the temperature region ~ 160 K, excess noise was also generated due to the metal-insulator transition. In the paramagnetic region, conduction noise was found to remain unchanged with the applied magnetic field whereas in the ferromagnetic regions, the peaks at 114 K and 235 K got disappeared. The latter is attributed to the suppression of spin fluctuations.
GLOBAL DISSIPATIVE SOLUTIONS OF THE CAMASSA–HOLM EQUATION
Authors: BRESSAN ALBERTO , CONSTANTIN ADRIAN
Published: December 2006

This paper is devoted to the continuation of solutions to the Camassa–Holm equation after wave breaking. By introducing a new set of independent and dependent variables, the evolution problem is rewritten as a semilinear hyperbolic system in an L∞space, containing a non-local source term which is discontinuous but has bounded directional variation. For a given initial condition, the Cauchy problem has a unique solution obtained as fixed point of a contractive integral transformation. Returning to the original variables, we obtain a semigroup of global dissipative solutions, defined for every initial data [Formula: see text], and continuously depending on the initial data. The new variables resolve all singularities due to possible wave breaking and ensure that energy loss occurs only through wave breaking.
AN APPLICATION OF MELLIN TRANSFORM TECHNIQUES TO A BLACK–SCHOLES EQUATION PROBLEM
Authors: RODRIGO MARIANITO R. , MAMON ROGEMAR S.
Published: December 2006

In this article, we use a Mellin transform approach to prove the existence and uniqueness of the price of a European option under the framework of a Black–Scholes model with time-dependent coefficients. The formal solution is rigorously shown to be a classical solution under quite general European contingent claims. Specifically, these include claims that are bounded and continuous, and claims whose difference with some given but arbitrary polynomial is bounded and continuous. We derive a maximum principle and use it to prove uniqueness of the option price. An extension of the put-call parity which relates the aforementioned two classes of claims is also given.
LONG-RANGE-CORRECTED TIME-DEPENDENT DENSITY FUNCTIONAL STUDY ON ELECTRONIC SPECTRA OF FIVE-MEMBERED RING COMPOUNDS AND FREE-BASE PORPHYRIN
Authors: TOKURA SEIKEN , TSUNEDA TAKAO , HIRAO KIMIHIKO
Published: December 2006

Long-range-corrected time-dependent density functional theory (LC-TDDFT) was applied to five-membered ring compounds (cyclopentadiene, pyrrole, and furan molecules) and free-base porphyrin. The vertical π-π* and Rydberg excitation energies and corresponding oscillator strengths were calculated by LC-TDDFT. The LC scheme obviously improved the Rydberg excitation energies and oscillator strengths of these systems, which have been fairly underestimated by TDDFT with conventional pure and hybrid B3LYP functionals. On the whole, LC-TDDFT results were very close to the results of the ab initio symmetry-adapted cluster configuration interaction (SAC-CI) method for most excitations. However, LC-TDDFT is poor in describing doubly excited states such as the 1 1A1 state of five-membered ring compounds.
Effect of two different intense training regimens on skeletal muscle ion transport proteins and fatigue development
Authors: Mohr Magni , Krustrup Peter , Nielsen Jens Jung , Nybo Lars , Rasmussen Martin Krøyer , Juel Carsten , Bangsbo Jens
Published: December 2006

This study examined the effect of two different intense exercise training regimens on skeletal muscle ion transport systems, performance, and metabolic response to exercise. Thirteen subjects performed either sprint training [ST; 6-s sprints ( n = 6)], or speed endurance training [SET; 30-s runs ∼130% V̇o2 max, n = 7]. Training in the SET group provoked higher ( P < 0.05) plasma K+ levels and muscle lactate/H+ accumulation. Only in the SET group was the amount of the Na+/H+ exchanger isoform 1 (31%) and Na+-K+-ATPase isoform α2 (68%) elevated ( P < 0.05) after training. Both groups had higher ( P < 0.05) levels of Na+-K+-ATPase β1-isoform and monocarboxylate transporter 1 (MCT1), but no change in MCT4 and Na+-K+-ATPase α1-isoform. Both groups had greater ( P < 0.05) accumulation of lactate during exhaustive exercise and higher ( P < 0.05) rates of muscle lactate decrease after exercise. The ST group improved ( P < 0.05) sprint performance, whereas the SET group elevated ( P < 0.05) performance during exhaustive continuous treadmill running. Improvement in the Yo-Yo intermittent recovery test was larger ( P < 0.05) in the SET than ST group (29% vs. 10%). Only the SET group had a decrease ( P < 0.05) in fatigue index during a repeated sprint test. In conclusion, turnover of lactate/H+ and K+ in muscle during exercise does affect the adaptations of some but not all related muscle ion transport proteins with training. Adaptations with training do have an effect on the metabolic response to exercise and specific improvement in work capacity.
Vinblastine, a Chemotherapeutic Drug, Inhibits Palmitoylation of Tubulin in Human Leukemic Lymphocytes
Authors: Caron Joan M. , Herwood Margot
Published: January 2007

Background: We have previously shown that tubulin, the major protein of microtubules, is posttranslationally modified by palmitoylation. In addition, we demonstrated that palmitoylation of tubulin is inhibited in vitro by stoichiometric levels of the chemotherapeutic drug, vinblastine. Here, we sought to determine whether a clinically relevant dose of vinblastine inhibits palmitoylation of tubulin in vivo. Methods: Human CEM leukemic lymphocytes were incubated with [3H]palmitate in the presence and absence of a low, clinically relevant dose of vinblastine. [3H]palmitoylated tubulin was identified by two-dimensional PAGE and autoradiography. Results: We found, first, that tubulin was palmitoylated in CEM cells. Second, the clinically relevant dose of vinblastine inhibited palmitoylation of tubulin in vivo in CEM cells. In addition, microtubules were disassembled and cells became apoptotic. Conclusion: This study identifies a previously unknown mechanism of action of vinblastine, the depalmitoylation of tubulin, and suggests that depalmitoylation of tubulin may be a target for new chemotherapeutic drugs.
Two Tales: Hemorrhagic Transformation but Not Parenchymal Hemorrhage After Thrombolysis Is Related to Severity and Duration of Ischemia
Authors: Thomalla Götz , Sobesky Jan , Köhrmann Martin , Fiebach Jochen B. , Fiehler Jens , Zaro Weber Olivier , Kruetzelmann Anna , Kucinski Thomas , Rosenkranz Michael , Röther Joachim , Schellinger Peter D.
Published: January 2007

Background and Purpose—

Intracerebral hemorrhage represents the most feared complication of treatment with intravenous tissue plasminogen activator. We studied whether perfusion-weighted imaging and diffusion-weighted imaging has the potential to identify patients at risk of severe intracerebral hemorrhage after treatment with intravenous tissue plasminogen activator.

Methods—

We analyzed data of prospectively studied MRI selected acute ischemic stroke patients treated with intravenous tissue plasminogen activator within 6 hours. All patients were examined by perfusion- and diffusion-weighted imaging ≤6 hours. Perfusion- and diffusion-weighted imaging lesion volumes were calculated. Hemorrhagic transformation was assessed on follow-up CT or MRI and diagnosed as hemorrhagic transformation, parenchymal hemorrhage, or symptomatic intracerebral hemorrhage according to ECASS II criteria.

Results—

Of 152 patients, hemorrhagic transformation was seen in 60 (39.5%), parenchymal hemorrhage in 15 (9.9%), and symptomatic intracerebral hemorrhage in 4 (2.6%). Multiple logistic regression analysis identified onset to treatment time after 3 to 6 hours (
P
<0.001), a larger perfusion-weighted imaging lesion volume (
P
=0.002), and, as a tendency, a higher score on the National Institutes of Health Stroke Scale on admission (
P
=0.068) as independent predictors of hemorrhagic transformation. Neither MRI lesion volumes nor severity of symptoms, but rather only an older age tended to be associated with parenchymal hemorrhage (
P
=0.087).

Conclusion—

Our results further support the concept of a different pathogenesis for hemorrhagic transformation and parenchymal hemorrhage. Whereas hemorrhagic transformation should be regarded as a clinically irrelevant epiphenomenon of ischemic damage and reperfusion, parenchymal hemorrhage appears to be related to biologic effects of tissue plasminogen activator and other pre-existing pathologic conditions, which deserve further investigation.
Effects of Locomotion Training With Assistance of a Robot-Driven Gait Orthosis in Hemiparetic Patients After Stroke
Authors: Husemann Britta , Müller Friedemann , Krewer Carmen , Heller Silke , Koenig Eberhardt
Published: January 2007

Background and Purpose—

The success of gait rehabilitation after stroke depends on active walking exercises. However, the disabling after-effects of stroke often make such exercises impossible at the onset of therapy. To facilitate treadmill training of paraparetic patients, a robot-driven gait orthosis (Lokomat) was developed. We investigated the effects of the Lokomat when used with hemiparetic patients.

Methods—

The authors conducted a randomized, controlled pilot study of 30 acute stroke survivors. The treatment group received 30 minutes of robotic training daily and the control group 30 minutes of conventional physiotherapy daily in addition to 30 minutes of conventional physiotherapy for each group. Outcome measures were independence of gait, gait speed, gait parameters, and body tissue composition.

Results—

After 4 weeks of therapy, the walking ability of the Lokomat group and the control group expressed as the functional ambulation classification was significantly improved. The functional ambulation category (median± interquartile range) was at baseline 0±0 in control and 0±1 in the therapy group and increased after therapy to 1±3 in both groups significantly (
P
=0.01). There was no significant difference in gain of these parameters between the groups. The Lokomat group had a significantly longer single stance phase (sec; mean±SEM) on the paretic leg when walking on the floor. At baseline, it was 0.19±0.17 and after therapy 0.49±0.07 (
P
=0.014). The control group had increased their body weight approximately 1.33±1.40 kg (mean±SEM;
P
=0.046), mostly as fat mass, whereas the Lokomat group had lost fat mass approximately −2.9±1.0 kg (mean±SEM;
P
=0.016) and increased their muscle mass approximately 3.36±1.4 kg (mean± SEM;
P
=0.031).

Conclusions—

This pilot study indicates that Lokomat therapy is a promising intervention for gait rehabilitation. Although there was no difference between groups in gain of functional scores, the Lokomat group showed an advantage of robotic training over conventional physiotherapy in improvement of gait abnormality and body tissue composition.
Temperament-Based Learning Styles of Identified Gifted and Nongifted Students
Authors: Oakland Thomas , Joyce Diana , Horton Connie , Glutting Joseph
Published: January 2007

Learning style preferences of 1,554 students identified as gifted and nongifted students, ages 8 to 17, were measured using the Student Styles Questionnaire (SSQ). Students identified as gifted and nongifted students did not differ significantly on extroverted-introverted, organlzed-flexible, and thinking-feeling styles. Students identified as gifted displayed a stronger preference for imagnative styles, while nongifted children displayed a stronger preference for practical styles. Gender differences were significant. Boys displayed a stronger preference for flexible and thinking styles while girls displayed a stronger preference for organized and feeling styles. Two gifted-by-gendcr interactions also were significant. Compared with boys identified as gifted, girls identified as gifted were more likely to prefer imaginative styles. Furthermore, although boys generally expressed a stronger preference for thinking than feeling, nongifted boys expressed a stronger preference for thinking than did boys identified as gifted.
Gifted Dropouts: The Who and the Why
Authors: Renzulli Joseph S. , Park Sunghee
Published: January 2007

Two studies were conducted to obtain comprehensive information about ifted high school dropouts and to examine factors that are related to their dropout behavior using the Dropout and Student questionnaires of the National Education Longitudinal Study of 1988 (NELS:88). The results indicated that mwny gifted dropouts were from low socioeconomic-status families and racial minority groups; had parents with low levels of education; and participated less in extracurricular activities. Also, reasons for gifted male dropouts were More related to econornic issues, while reasons for gifted teniale dropouts were more related to personal issues, although both males and femiales were likely to offer school-related reasons. The logistic regression analysis results indicated that dropout behavior for gifted students was significantly related to students' educational aspirations. pregnancy or child-rearing, gender, father's highest level of education, and mother's highest level of education.
Gifted Students' Perceptions of Their Class Activities: Differences Among Rural, Urban, and Suburban Student Attitudes
Authors: Gentry Marcia , Rizza Mary G. , Gable Robert K.
Published: January 2007

The purpose of this study was to investigate differences in attitudes toward classroom activities among rural, urban, and suburban gifted students. More specifically, the instrument My Class Activities designed to assess students' attitudes toward, their class activities with respect to Interest, Challenge, Choice, and Enjoyment, was used to show how gifted students from rural schools differed from their counterparts in urban and suburban schools. Rural elementary students found their classrooms less frequently interesting and challenging, but found the more frequently enjoyable than their urban and suburban peers. Rural middle school students reported less challenge and less enjoyment than their suburban peers. Implications of the findings for gifted students in rural settings are discussed and suggestions for addressing these dimensions for gifted students in rural areas provided. Additionally, validity and reliability evidence is provided for My Class Activities.
Global and Domain-Specific Self-Concepts in Academically Talented Asian American and White Adolescents
Authors: Worrell Frank C.
Published: January 2007

Previous research has suggested that ethnic groups may not only differ on self-concept, but that self-concept variables may be of different importance to different ethnic groups. This study examined these questions in a sample of academically talented White and Asian American students. White students obtained significantly higher scores than Asian Armericans on scholastic and job self-concepts, but the effect sizes were small. No domain-specific self-concept was a strong predictor of global self-concept for Asian American students, whereas self-concept related to appearance was a strong predictor of global self-concept for White students.