bluuebunny/crossref_metadata_2025 huggingface dataset:
Drug-Lipid A Interactions on the
Escherichia coli
ABC Transporter MsbA
Authors: Woebking Barbara , Reuter Galya , Shilling Richard A. , Velamakanni Saroj , Shahi Sanjay , Venter Henrietta , Balakrishnan Lekshmy , van Veen Hendrik W.
Published: September 2005

MsbA is an essential ATP-binding cassette half-transporter in the cytoplasmic membrane of the gram-negative
Escherichia coli
and is required for the export of lipopolysaccharides (LPS) to the outer membrane, most likely by transporting the lipid A core moiety. Consistent with the homology of MsbA to the multidrug transporter LmrA in the gram-positive
Lactococcus lactis
, our recent work in
E. coli
suggested that MsbA might interact with multiple drugs. To enable a more detailed analysis of multidrug transport by MsbA in an environment deficient in LPS, we functionally expressed MsbA in
L. lactis
. MsbA expression conferred an 86-fold increase in resistance to the macrolide erythromycin. A kinetic characterization of MsbA-mediated ethidium and Hoechst 33342 transport revealed apparent single-site kinetics and competitive inhibition of these transport reactions by vinblastine with

K
i

values of 16 and 11 μM, respectively. We also detected a simple noncompetitive inhibition of Hoechst 33342 transport by free lipid A with a

K
i

of 57 μM, in a similar range as the

K
i

for vinblastine, underscoring the relevance of our LPS-less lactococcal model for studies on MsbA-mediated drug transport. These observations demonstrate the ability of heterologously expressed MsbA to interact with free lipid A and multiple drugs in the absence of auxiliary
E. coli
proteins. Our transport data provide further functional support for direct LPS-MsbA interactions as observed in a recent crystal structure for MsbA from
Salmonella enterica
serovar Typhimurium (C. L. Reyes and G. Chang, Science 308:1028-1031, 2005).
Bacterial Cyanide Oxygenase Is a Suite of Enzymes Catalyzing the Scavenging and Adventitious Utilization of Cyanide as a Nitrogenous Growth Substrate
Authors: Fernandez Ruby F. , Kunz Daniel A.
Published: September 2005

Cyanide oxygenase (CNO) from
Pseudomonas fluorescens
NCIMB 11764 catalyzes the pterin-dependent oxygenolytic cleavage of cyanide (CN) to formic acid and ammonia. CNO was resolved into four protein components (P1 to P4), each of which along with a source of pterin cofactor was obligately required for CNO activity. Component P1 was characterized as a multimeric 230-kDa flavoprotein exhibiting the properties of a peroxide-forming NADH oxidase (oxidoreductase) (Nox). P2 consisted of a 49.7-kDa homodimer that showed 100% amino acid identity at its N terminus to NADH peroxidase (Npx) from
Enterococcus faecali
s. Enzyme assays further confirmed the identities of both Nox and Npx enzymes (specific activity, 1 U/mg). P3 was characterized as a large oligomeric protein (∼300 kDa) that exhibited cyanide dihydratase (CynD) activity (specific activity, 100 U/mg). Two polypeptides of 38 kDa and 43 kDa were each detected in the isolated enzyme, the former believed to confer catalytic activity based on its similar size to other CynD enzymes. The amino acid sequence of an internal peptide of the 43-kDa protein was 100% identical to bacterial elongation factor Tu, suggesting a role as a possible chaperone in the assembly of CynD or a multienzyme CNO complex. The remaining P4 component consisted of a 28.9-kDa homodimer and was identified as carbonic anhydrase (specific activity, 2,000 U/mg). While the function of participating pterin and the roles of Nox, Npx, CynD, and CA in the CNO-catalyzed scavenging of CN remain to be determined, this is the first report describing the collective involvement of these four enzymes in the metabolic detoxification and utilization of CN as a bacterial nitrogenous growth substrate.
Nitrate-Dependent Activation of the Dif Signaling Pathway ofMyxococcus xanthusMediated by a NarX-DifA Interspecies Chimera
Authors: Xu Qian , Black Wesley P. , Ward Scott M. , Yang Zhaomin
Published: September 2005

Myxococcus xanthusfibril exopolysaccharide (EPS), essential for the social gliding motility and development of this bacterium, is regulated by the Dif chemotaxis-like pathway. DifA, an MCP homolog, is proposed to mediate signal input to the Dif pathway. However, DifA lacks a prominent periplasmic domain, which in classical chemoreceptors is responsible for signal perception and for initiating transmembrane signaling. To investigate the signaling properties of DifA, we constructed a NarX-DifA (NafA) chimera from the sensory module ofEscherichia coliNarX and the signaling module ofM. xanthusDifA. We report here the first functional chimeric signal transducer constructed using genes from organisms in two different phylogenetic subdivisions. When expressed inM. xanthus, NafA restored fruiting body formation, EPS production, and S-motility todifAmutants in the presence of nitrate. Studies with various double mutants indicate that NafA requires the downstream Dif proteins to function. We propose that signal inputs to the Dif pathway and transmembrane signaling by DifA are essential for the regulation of EPS production inM. xanthus. Despite the apparent structural differences, DifA appears to share similar transmembrane signaling mechanisms with enteric sensor kinases and chemoreceptors.
Regulation of Tryptophan Operon Expression in the Archaeon
Methanothermobacter thermautotrophicus
Authors: Xie Yunwei , Reeve John N.
Published: September 2005

Conserved
trp
genes encode enzymes that catalyze tryptophan biosynthesis in all three biological domains, and studies of their expression in
Bacteria
and eukaryotes have revealed a variety of different regulatory mechanisms. The results reported here provide the first detailed description of an archaeal
trp
gene regulatory system. We have established that the
trpEGCFBAD
operon in
Methanothermobacter thermautotrophicus
is transcribed divergently from a gene (designated
trpY
) that encodes a tryptophan-sensitive transcription regulator. TrpY binds to TRP box sequences (consensus, TGTACA) located in the overlapping promoter regions between
trpY
and
trpE
, inhibiting
trpY
transcription in the absence of tryptophan and both
trpY
and
trpEGCFBAD
transcription in the presence of tryptophan. TrpY apparently inhibits
trpY
transcription by blocking RNA polymerase access to the site of
trpY
transcription initiation and represses
trpEGCFBAD
transcription by preventing TATA box binding protein (TBP) binding to the TATA box sequence. Given that residue 2 (W2) is the only tryptophan in TrpY and in TrpY homologues in other
Euryarchaea
and that there is only one tryptophan codon in the entire
trpEGCFBAD
operon (
trpB
encodes W175), expression of the
trp
operon may also be regulated in vivo by the supply of charged tRNA
Trp
available to translate the second codon of the
trpY
mRNA.
Positive Autoregulation of
c
I Is a Dispensable Feature of the Phage λ Gene Regulatory Circuitry
Authors: Michalowski Christine B. , Little John W.
Published: September 2005

Complex gene regulatory circuits contain many features that are likely to contribute to their operation. It is unclear, however, whether all these features are necessary for proper circuit behavior or whether certain ones are refinements that make the circuit work better but are dispensable for qualitatively normal behavior. We have addressed this question using the phage λ regulatory circuit, which can persist in two stable states, the lytic state and the lysogenic state. In the lysogenic state, the CI repressor positively regulates its own expression by stimulating transcription from the
P
RM
promoter. We tested whether this feature is an essential part of the regulatory circuitry. Several phages with a
c
I mutation preventing positive autoregulation and an up mutation in the
P
RM
promoter showed near-normal behavior. We conclude that positive autoregulation is not necessary for proper operation of the λ circuitry and speculate that it serves a partially redundant function of stabilizing a bistable circuit, a form of redundancy we term “circuit-level redundancy.” We discuss our findings in the context of a two-stage model for evolution and elaboration of regulatory circuits from simpler to more complex forms.
Analysis of PutativeChlamydia trachomatisChaperones Scc2 and Scc3 and Their Use in the Identification of Type III Secretion Substrates
Authors: Fields Kenneth A. , Fischer Elizabeth R. , Mead David J. , Hackstadt Ted
Published: September 2005

The obligate intracellular pathogenChlamydia trachomatisexpresses a type III secretion system (T3SS) which has the potential to contribute significantly to pathogenesis. Based on a demonstrated role of type III secretion (T3S)-specific chaperones in the secretion of antihost proteins by gram-negative pathogens, we initiated a study of selected putativeChlamydiaT3S chaperones in an effort to gain mechanistic insight into theChlamydiaT3SS and to potentially identifyChlamydia-specific secreted products.C. trachomatisScc2 and Scc3 are homologous to SycD ofYersiniaspp. Functional studies of the heterologousYersiniaT3SS indicated that although neither Scc2 nor Scc3 was able to fully complement asycDnull mutant, both have SycD-like characteristics. Both were able to associate with the translocator protein YopD, and Scc3 expression restored limited secretion of YopD in in vitro studies of T3S. CopB (CT578) and CopB2 (CT861) are encoded adjacent toscc2andscc3, respectively, and have structural similarities with the YopB family of T3S translocators. Either Scc2 or Scc3 coprecipitates with CopB fromC. trachomatisextracts. Expression of CopB or CopB2 inYersiniaresulted in their type III-dependent secretion, and localization studies withC. trachomatis-infected cells indicated that both were secreted byChlamydia.
Structural Characterization of a Flavonoid-Inducible
Pseudomonas aeruginosa
A-Band-Like O Antigen of
Rhizobium
sp. Strain NGR234, Required for the Formation of Nitrogen-Fixing Nodules
Authors: Reuhs Bradley L. , Relić Biserka , Forsberg L. Scott , Marie Corinne , Ojanen-Reuhs Tuula , Stephens Samuel B. , Wong Chee-Hoong , Jabbouri Saïd , Broughton William J.
Published: September 2005

Rhizobium
(
Sinorhizobium
) sp. strain NGR234 contains three replicons, the smallest of which (pNGR234
a
) carries most symbiotic genes, including those required for nodulation and lipo-chito-oligosaccharide (Nod factor) biosynthesis. Activation of
nod
gene expression depends on plant-derived flavonoids, NodD transcriptional activators, and
nod
box promoter elements. Nod boxes NB6 and NB7 delimit six different types of genes, one of which (
fixF
) is essential for the formation of effective nodules on
Vigna unguiculata
. In vegetative culture, wild-type NGR234 produces a distinct, flavonoid-inducible lipopolysaccharide (LPS) that is not produced by the mutant (NGRΩ
fixF
); this LPS is also found in nitrogen-fixing bacteroids isolated from
V. unguiculata
infected with NGR234. Electron microscopy showed that peribacteroid membrane formation is perturbed in nodule cells infected by the
fixF
mutant. LPSs were purified from free-living NGR234 cultured in the presence of apigenin. Structural analyses showed that the polysaccharide portions of these LPSs are specialized, rhamnose-containing O antigens attached to a modified core-lipid A carrier. The primary sequence of the O antigen is [-3)-α-
l
-Rha
p
-(1,3)-α-
l
-Rha
p
-(1,2)-α-
l
-Rha
p
-(1-]
n
, and the LPS core region lacks the acidic sugars commonly associated with the antigenic outer core of LPS from noninduced cells. This rhamnan O antigen, which is absent from noninduced cells, has the same primary sequence as the A-band O antigen of
Pseudomonas aeruginosa
, except that it is composed of
l
-rhamnose rather than the
d
-rhamnose characteristic of the latter. It is noteworthy that A-band LPS is selectively maintained on the
P. aeruginosa
cell surface during chronic cystic fibrosis lung infection, where it is associated with an increased duration of infection.
Whole-Genome Sequence Analysis of
Pseudomonas syringae
pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition
Authors: Joardar Vinita , Lindeberg Magdalen , Jackson Robert W. , Selengut Jeremy , Dodson Robert , Brinkac Lauren M. , Daugherty Sean C. , DeBoy Robert , Durkin A. Scott , Giglio Michelle Gwinn , Madupu Ramana , Nelson William C. , Rosovitz M. J. , Sullivan Steven , Crabtree Jonathan , Creasy Todd , Davidsen Tanja , Haft Dan H. , Zafar Nikhat , Zhou Liwei , Halpin Rebecca , Holley Tara , Khouri Hoda , Feldblyum Tamara , White Owen , Fraser Claire M. , Chatterjee Arun K. , Cartinhour Sam , Schneider David J. , Mansfield John , Collmer Alan , Buell C. Robin
Published: September 2005

Pseudomonas syringae
pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of
P. syringae
pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar,
P. syringae
pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and
Arabidopsis
. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core
Pseudomonas
genome and 365 ORFs that are
P. syringae
specific.
TP0453, a Concealed Outer Membrane Protein of
Treponema pallidum
, Enhances Membrane Permeability
Authors: Hazlett Karsten R. O. , Cox David L. , Decaffmeyer Marc , Bennett Michael P. , Desrosiers Daniel C. , La Vake Carson J. , La Vake Morgan E. , Bourell Kenneth W. , Robinson Esther J. , Brasseur Robert , Radolf Justin D.
Published: September 2005

The outer membrane of
Treponema pallidum
, the noncultivable agent of venereal syphilis, contains a paucity of protein(s) which has yet to be definitively identified. In contrast, the outer membranes of gram-negative bacteria contain abundant immunogenic membrane-spanning β-barrel proteins mainly involved in nutrient transport. The absence of orthologs of gram-negative porins and outer membrane nutrient-specific transporters in the
T. pallidum
genome predicts that nutrient transport across the outer membrane must differ fundamentally in
T. pallidum
and gram-negative bacteria. Here we describe a
T. pallidum
outer membrane protein (TP0453) that, in contrast to all integral outer membrane proteins of known structure, lacks extensive β-sheet structure and does not traverse the outer membrane to become surface exposed. TP0453 is a lipoprotein with an amphiphilic polypeptide containing multiple membrane-inserting, amphipathic α-helices. Insertion of the recombinant, nonlipidated protein into artificial membranes results in bilayer destabilization and enhanced permeability. Our findings lead us to hypothesize that TP0453 is a novel type of bacterial outer membrane protein which may render the
T. pallidum
outer membrane permeable to nutrients while remaining inaccessible to antibody.
Characterization of a Novel Porin Protein from
Moraxella catarrhalis
and Identification of an Immunodominant Surface Loop
Authors: Easton Donna M. , Smith Adam , Gallego Sara Gomez , Foxwell A. Ruth , Cripps Allan W. , Kyd Jennelle M.
Published: September 2005

Moraxella catarrhalis
is a gram-negative bacterium that is mainly responsible for respiratory tract infections. In this study we report a novel outer membrane protein (OMP), designated M35, with a molecular mass of 36.1 kDa. This protein was structurally homologous to classic gram-negative porins, such as OMP C from
Escherichia coli
and OMP K36 from
Klebsiella pneumoniae
, with a predicted structure of 8 surface loops and 16 antiparallel β-sheets. The DNA sequences of the genes from 18 diverse clinical isolates showed that the gene was highly conserved (99.6 to 100% of nucleotides), with only one isolate (ID78LN266) having base variations that resulted in amino acid substitutions. Electrophoresis and analysis of recognition of the protein using mouse anti-M35 sera showed that M35 was expressed on the bacterial surface and constitutively expressed across
M. catarrhalis
isolates, with only ID78LN266 showing poor antibody recognition. Our results showed that the single amino acid mutation in loop 3 significantly affected antibody recognition, indicating that loop 3 appeared to contain an immunodominant B-cell epitope. The antibody specificity to loop 3 may be a potential mechanism for evasion of host immune responses targeted to M35, since loop 3 should theoretically orientate into the porin channel. Thus, M35 is a highly conserved, surface-expressed protein that is of significance for its potential functional role as an
M. catarrhalis
porin and is of interest as a vaccine candidate.
Cell Division inBacillus subtilis: FtsZ and FtsA Association Is Z-Ring Independent, and FtsA Is Required for Efficient Midcell Z-Ring Assembly
Authors: Jensen S. O. , Thompson L. S. , Harry E. J.
Published: September 2005

The earliest stage in cell division in bacteria is the assembly of a Z ring at the division site at midcell. Other division proteins are also recruited to this site to orchestrate the septation process. FtsA is a cytosolic division protein that interacts directly with FtsZ. Its function remains unknown. It is generally believed that FtsA localization to the division site occurs immediately after Z-ring formation or concomitantly with it and that FtsA is responsible for recruiting the later-assembling membrane-bound division proteins to the division site. Here, we report the development of an in vivo chemical cross-linking assay to examine the association between FtsZ and FtsA inBacillus subtiliscells. We subsequently use this assay in a synchronous cell cycle to show that these two proteins can interact prior to Z-ring formation. We further show that in aB. subtilisstrain containing anftsAdeletion, FtsZ localized at regular intervals along the filament but the majority of Z rings were abnormal. FtsA in this organism is therefore critical for the efficient formation of functional Z rings. This is the first report of abnormal Z-ring formation resulting from the loss of a single septation protein. These results suggest that in this organism, and perhaps others, FtsA ensures recruitment of the membrane-bound division proteins by ensuring correct formation of the Z ring.
Differences in Gene Content betweenSalmonella entericaSerovar Enteritidis Isolates and Comparison to Closely Related Serovars Gallinarum and Dublin
Authors: Porwollik S. , Santiviago C. A. , Cheng P. , Florea L. , McClelland M.
Published: September 2005

Salmonella entericaserovar Enteritidis is often transmitted into the human food supply through eggs of hens that appear healthy. This pathogen became far more prevalent in poultry following eradication of the fowl pathogenS. entericaserovar Gallinarum in the mid-20th century. To investigate whether changes in serovar Enteritidis gene content contributed to this increased prevalence, and to evaluate genetic heterogeneity within the serovar, comparative genomic hybridization was performed on eight 60-year-old and nineteen 10- to 20-year-old serovar Enteritidis strains from various hosts, using aSalmonella-specific microarray. Overall, almost all the serovar Enteritidis genomes were very similar to each other. Excluding two rare strains classified as serovar Enteritidis in theSalmonellareference collection B, only eleven regions of the serovar Enteritidis phage type 4 (PT4) chromosome (sequenced at the Sanger Center) were absent or divergent in any of the other serovar Enteritidis strains tested. The more recent isolates did not have consistent differences from 60-year-old field isolates, suggesting that no large genomic additions on a whole-gene scale were needed for serovar Enteritidis to become more prevalent in domestic fowl. Cross-hybridization of phage genes on the array with related genes in the examined genomes grouped the serovar Enteritidis isolates into two major lineages. Microarray comparisons of the sequenced serovar Enteritidis PT4 to isolates of the closely related serovars Dublin and Gallinarum (biovars Gallinarum and Pullorum) revealed several genomic areas that distinguished them from serovar Enteritidis and from each other. These differences in gene content could be useful in DNA-based typing and in understanding the different phenotypes of these related serovars.
Evolutionary and Diagnostic Implications of Intragenomic Heterogeneity in the 16S rRNA Gene inAeromonasStrains
Authors: Morandi Alessia , Zhaxybayeva Olga , Gogarten J. Peter , Graf Joerg
Published: September 2005

Sequencing 16S rRNA genes (SSU) cloned fromAeromonasstrains revealed that strains contained up to six copies differing by ≤1.5%. The SSU copies fromAeromonas veroniiLMG13695 clustered with sequences from fourAeromonasspecies. These results demonstrate intragenomic heterogeneity of SSU and suggest caution when using SSU to identify aeromonads.
Transcriptome Analysis ofPseudomonas aeruginosaGrowth: Comparison of Gene Expression in Planktonic Cultures and Developing and Mature Biofilms
Authors: Waite Richard D. , Papakonstantinopoulou Anastasia , Littler Eddie , Curtis Michael A.
Published: September 2005

The transcriptomes of logarithmic- and stationary-phasePseudomonas aeruginosaplanktonic cultures and static biofilms of different stages of development were compared. Developing and confluent biofilm transcriptomes were found to be related to those of logarithmic- and stationary-phase planktonic cultures, respectively. In addition, a number of novel genes were up-regulated in developing and confluent biofilms, including genes encoding putative solute transport proteins and transcriptional regulators, respectively.
Extended −10 Motif Is Critical for Activity of thecspAPromoter but Does Not Contribute to Low-Temperature Transcription
Authors: Phadtare Sangita , Severinov Konstantin
Published: September 2005

Bacterial promoters belonging to the extended −10 class contain a conserved TGn motif upstream of the −10 promoter consensus element. Open promoter complexes can be formed on some extended −10Escherichia colipromoters at temperatures as low as 6°C, when complexes on most promoters are closed. The promoter ofcspA, a gene that codes for the major cold shock protein CspA ofE. coli, contains an extended −10 motif. CspA is dramatically induced upon temperature downshift from 37 to 15°C, and its cold shock induction has been attributed to transcription, translation, and mRNA stabilization effects. Here, we show that though the extended −10 motif is critical for high-level expression ofcspA, it does not contribute to low-temperature expression. In fact, transcription from the wild-typecspApromoter is cold sensitive in vitro and in vivo. Thus, transcription appears to play little or no role in low-temperature induction ofcspAexpression.
Surgical correction of unilateral and bilateral facial palsy
Authors: Harrison D H
Published: September 2005

Unilateral and bilateral facial palsies are debilitating and depressing conditions for the patient. For the past 30 years attempts have been made to improve the reanimation of these patients. The ability to transfer axons over significant distances with nerve grafts and the transfer of muscle that can be revascularised by microvascular surgery greatly improves results of this surgery. The revascularisation of muscle has been the important step forward but the re-focusing of interest in this condition has brought about a number of peripheral advances.
Gastrointestinal involvement in POEMS syndrome: a novel clinical manifestation
Authors: Dogan S , Beyazit Y , Shorbagi A , Köklü S , Ustunel S , Guler N , Uner A
Published: September 2005

POEMS syndrome (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes) is characterised by a rare multisystem disorder of unknown pathogenesis. Although its pathophysiology is not well understood, overexpression of proinflammatory cytokines has been implicated. Gastrointestinal system disorders have not been reported among the components of the syndrome. A case is reported of POEMS syndrome with gastrointestinal involvement shown by gastrointestinal endoscopy.
Early diffusion weighted imaging and expression of heat shock protein 70 in newborn pigs with hypoxic ischaemic encephalopathy
Authors: Cheng Y , Liu G R , Guan J T , Guo Y L , Li Y K , Wu R H
Published: September 2005

Objective

To establish a cerebral hypoxia ischaemic model in piglets and to explore the early diffusion weighted imaging (DWI) as well as the expression of heat shock protein 70 (HSP70) with hypoxic ischaemic encephalopathy (HIE).

Methods

Twenty four 3 day old piglets were permanently ligated common carotid arteries bilaterally and ventilated with 3% oxygen for 30 minutes, and their brains were examined at three hours, six hours, and 24 hours after hypoxic ischaemia with T2 weighted images and diffusion weighted images. Apparent diffusion coefficient (ADC) values were measured and HSP70 expression was detected in the central and peripheral regions of lesions.

Results

Abnormal signal intensity was detected on DWI and ADC maps in three hypoxic ischaemic groups. ADC values in the central lesions rapidly decreased, whereas ADC values in the peripheral regions reduced prominently at 24 hours after hypoxic ischaemia. There were significant differences (p<0.01) between ADC values of the central regions and the peripheral regions of lesions. The number of HSP70 positive cells was low at three hours, raised at the highest peak at six hours, and then rapidly decreased. There was statistical difference between HSP70 positive cells in the central regions and those in peripheral regions (p<0.01).

Conclusion

DWI may identify more early lesions, and improve conspicuity in the acute setting. ADC values can be used as an objective measure for hypoxic ischaemic injury. Tissue reversibility can be further reflected according to the information of ADC values and HSP70 immunohistochemical staining.
Use of the single subject design for practice based primary care research
Authors: Janosky J E
Published: September 2005

The use of a single subject research design is proposed for practice based primary care research. An overview of the rationale of the design, an introduction to the methodology, strengths, limitations, a sample of recent literature citations, a working example, and possible clinical applications are presented.
Diagnosis and disease modifying treatments in multiple sclerosis
Authors: Zajicek J
Published: September 2005

Multiple sclerosis (MS) refers to scattered areas of hardening found on sectioning central nervous system tissue of affected people, usually after many years of illness. It rarely causes early death but is the commonest cause of neurological disability among young people. Overall results from controlled trials over the past 50 years have been rather disappointing but the comparatively recent licensing of drugs such as interferon beta and glatiramer acetate has led to a reappraisal of many aspects of MS. There are now new diagnostic criteria, which encompass developments in magnetic resonance imaging. Older clinical methods of measuring disease impact are now being re-evaluated to facilitate clinical trials of the approximate 150 new products currently being developed as potential disease modifying agents. The success and failure of agents that should be effective on theoretical grounds, together with advances in neuropathology, have led to fundamental questions regarding our basic understanding of disease pathogenesis being re-addressed.
Important cutaneous manifestations of inflammatory bowel disease
Authors: Trost L B , McDonnell J K
Published: September 2005

Inflammatory bowel disease (IBD) has many extraintestinal manifestations. Cutaneous manifestations are usually related to the activity of the bowel disease but may have an independent course. Anyone presenting with IBD should be examined for cutaneous manifestations. Pyoderma gangrenosum is a severe painful ulcerating disease that requires moist wound management and, in the absence of secondary infection, systemic corticosteroids, cyclosporine, or both. Infliximab may also be used. Erythema nodosum is a common cause of tender red nodules of the shins. Management includes leg elevation, NSAIDs, and potassium iodide. Oral manifestations of IBD include aphthous stomatitis, mucosal nodularity (cobblestoning), and pyostomatitis vegetans. Treatment should be directed both at the cutaneous lesions and at the underlying systemic condition.
Comparative study of enema retention and preference in ulcerative colitis
Authors: Ingram J R , Rhodes J , Evans B K , Newcombe R G , Thomas G A O
Published: September 2005

Background

Therapeutic enemas are often used to treat active colitis but their retention may be limited because of urgency to defecate. Some preparations may be better retained and tolerated than others because of their physical properties.

Aim

To compare patient preference and retention of four therapeutic enemas, including a nicotine enema, in patients with ulcerative colitis (UC).

Methods

Twenty four patients with active UC received the four trial enemas—corticosteroid, 5-amino salicylate (5-ASA), and nicotine liquid enemas and a corticosteroid foam, in a randomised order, taking one enema on each of four successive nights. Patients scored them 1 to 4 for ease of administration and retention, degree of abdominal bloating, and for their overall preference.

Results

Fifteen patients rated nicotine their overall favourite or second favourite, compared with 14 for corticosteroid foam and 11 for 5-ASA and corticosteroid liquids, but this was not significant (p = 0.302). Overall, there was no significant difference in overnight retention. However, the nicotine enema tended to be less well retained in patients with milder urgency but a higher proportion retained it overnight with more severe urgency (p = 0.031 compared with 5-ASA enema).

Conclusion

There was no significant difference in patient preference or overall duration of retention for the four enemas.
Implications of the new definition of myocardial infarction
Authors: Wong C-K , White H D
Published: September 2005

The new definition of acute myocardial infarction is based primarily on raised troponin levels because of the sensitivity and specificity of these markers and their correlation with the pathophysiology of acute coronary syndromes with plaque fissuring or rupture and embolisation of platelets causing myocyte necrosis. Raised troponin levels are associated with increased risks of death and recurrent myocardial infarction. Greater treatment benefit with low molecular weight heparin, IIb/IIIa antagonists and revascularisation is seen when troponin levels are raised. There are many implications for patients and society of the new definition including changes in insurability and ability to continue certain occupations. Many more patients, who would previously been diagnosed as having unstable angina, will now be diagnosed as having had an acute myocardial infarction. In addition case fatality rates will fall and comparison with previous epidemiological studies using the old definition will be problematic. However, the new definition may result in greater use of evidence based therapies with improved patient outcomes and decreased community death rates.
THE CASIMIR EFFECT BETWEEN NON-PARALLEL PLATES BY GEOMETRIC OPTICS
Authors: GUILFOYLE BRENDAN , KLINGENBERG WILHELM , SEN SIDDHARTHA
Published: September 2005

The first two authors have developed a technique which uses the complex geometry of the space of oriented affine lines in ℝ3 to describe the reflection of rays off a surface. This can be viewed as a parametric approach to geometric optics which has many possible applications. Recently, Jaffe and Scardicchio have developed a geometric optics approximation to the Casimir effect and the main purpose of this paper is to show that the quantities involved can be easily computed by this complex formalism. To illustrate this, we determine explicitly and in closed form the geometric optics approximation of the Casimir force between two non-parallel plates. By making one of the plates finite, we regularize the divergence that is caused by the intersection of the planes. In the parallel plate limit, we prove that our expression reduces to Casimir's original result.
COMBINATORIAL HOPF ALGEBRAS IN QUANTUM FIELD THEORY I
Authors: FIGUEROA HÉCTOR , GRACIA-BONDÍA JOSÉ M.
Published: September 2005

This paper stands at the interface between combinatorial Hopf algebra theory and renormalization theory. Its plan is as follows: Sec. 1.1 is the introduction, and contains an elementary invitation to the subject as well. The rest of Sec. 1 is devoted to the basics of Hopf algebra theory and examples in ascending level of complexity. Section 2 turns around the all-important Faà di Bruno Hopf algebra. Section 2.1 contains a first, direct approach to it. Section 2.2 gives applications of the Faà di Bruno algebra to quantum field theory and Lagrange reversion. Section 2.3 rederives the related Connes–Moscovici algebras. In Sec. 3, we turn to the Connes–Kreimer Hopf algebras of Feynman graphs and, more generally, to incidence bialgebras. In Sec. 3.1, we describe the first. Then in Sec. 3.2, we give a simple derivation of (the properly combinatorial part of) Zimmermann's cancellation-free method, in its original diagrammatic form. In Sec. 3.3, general incidence algebras are introduced, and the Faà di Bruno bialgebras are described as incidence bialgebras. In Sec. 3.4, deeper lore on Rota's incidence algebras allows us to reinterpret Connes–Kreimer algebras in terms of distributive lattices. Next, the general algebraic-combinatorial proof of the cancellation-free formula for antipodes is ascertained. The structure results for commutative Hopf algebras are found in Sec. 4. An outlook section very briefly reviews the coalgebraic aspects of quantization and the Rota–Baxter map in renormalization.
PHYSICS AT B-FACTORIES: TIME-DEPENDENT CP VIOLATION IN b→s TRANSITIONS AND DOUBLE CHARMONIUM PRODUCTION IN e+e-ANNIHILATIONS
Authors: ZIEGLER THOMAS
Published: September 2005

By reviewing the status of time-dependent CP-violation in b →s transitions and double charmonium production in e+e-collisions, two examples of the rich and exciting physics outcome from the B-factories are presented. Both analyses exhibited significant differences in measurement and standard model calculations in the last two years and therefore received particular interest. After a short introduction into the subjects, the results from BaBar and Belle are presented and discussed.
COMBINATIONAL APPROACH AND A LOOK INTO THE PARTICLE PRODUCTION DATA AT 530 and 800 GeV/c
Authors: DE BHASKAR , BISWAS S. K. , BHATTACHARYYA S.
Published: September 2005

In the light of the combinational approach that has been recently utilized to accommodate data from high energy nuclear collisions, we attempt here to interpret the nature of the latest data obtained by E706 collaboration of FERMILAB on neutral mesons produced in both proton–proton (PP) and proton–beryllium (P Be ) collisions. The study demonstrates that the approach can be useful for analyzing data on particle production in collisions involving both heavy and relatively much light nuclei such as beryllium.
SEMILEPTONIC B DECAYS AND DETERMINATION OF |Vub|
Authors: MORII MASAHIRO
Published: September 2005

Semileptonic decays of the B mesons provide an excellent probe for the weak and strong interactions of the bottom quark. The large data samples collected at the B Factories have pushed the experimental studies of the semileptonic B decays to a new height and stimulated significant theoretical developments. We review recent progresses in this fast-evolving field, with an emphasis on the determination of the magnitude of the Cabibbo–Kobayashi–Maskawa matrix element |Vub|.
QCD PHASE DIAGRAM AND THE CRITICAL POINT
Authors: Stephanov M. A.
Published: September 2005

The properties of the QCD phase diagram and the physics of the QCD critical point are reviewed.
QGP SIGNALS AND THE DUAL PARTON MODEL: IS THERMAL EQUILIBRIUM REACHED IN HEAVY ION COLLISIONS?
Authors: CAPELLA A.
Published: September 2005

Some of the so-called signals of Quark Gluon Plasma (QGP) formation are examined in the framework of a string model, the Dual Parton Model, supplemented with final state interaction. The aim is to determine the strength and duration time of the final state interaction required to describe the data, in order to gain some insight on whether or not the system reaches thermal equilibrium.
SPONTANEOUS BREAKING OF SCALE INVARIANCE AND SUPERSYMMETRIC MODELS AT FINITE TEMPERATURE
Authors: Feinberg Joshua , Moshe Moshe , Smolkin Michael , Zinn-Justin Jean
Published: September 2005

The phase structure of a supersymmetric, vector O(N) symmetric model at Large N in three dimension is presented. At zero temperature it reveals spontaneous breaking of scale invariance with no explicit breaking. When the attracting force between the massive quanta, bosons and fermions, is tuned to a certain critical value one finds massless bound states, a Goldstone boson and a Goldstone fermion, associated with the spontaneous breaking of scale invariance (massless dilaton and dilatino). The effect of finite temperature on this phenomenon is elucidated. Expectation values of the energy momentum tensor are calculated at zero and finite temperatures. The phase structure is unveiled in the limit N → ∞. We point out that at a certain critical value of the coupling constant the trace of the energy momentum tensor vanishes at all temperatures.
GLUEBALL SPECTRUM AND REGGE TRAJECTORY FROM SUPERGRAVITY
Authors: CACERES ELENA
Published: September 2005

Brief review of the status of the glueball spectrum in the deformed conifold background. Talk based on work done in collaboration with R. Herández and X. Amador.
Implications of a generalized heat kernel expansion for an effective QCD chiral Lagrangian with SU(3) and UA(1) breaking
Authors: HANSEN H. , OSIPOV A. A. , HILLER B.
Published: September 2005

This work is a follow up of recent investigations where the implications of a generalized heat kernel expansion is studied, constructed to incorporate non-perturbatively the effects of a non-commutative quark mass matrix in a fully covariant way at each order of the expansion. As underlying Lagrangian we use the Nambu – Jona-Lasinio (NJL) model of QCD, with SUf(3) and UA(1) breaking, the latter generated by the 't Hooft flavor determinant interaction. The associated bosonized Lagrangian is derived in leading stationary phase approximation (SPA) and up to second order in the generalized heat kernel expansion. Its symmetry breaking pattern is shown to have a complex structure, involving all powers of the mesonic fields allowed by symmetry. The considered Lagrangian yields a reliable playground for the study of the implications of symmetry and vacuum structure on the mesonic spectra, which we evaluate for the scalar and pseudoscalar meson nonets and compare with other approaches and experiment.
Magnetic condensation, Abelian dominance, and instability of Savvidy vacuum in Yang-Mills theory
Authors: KONDO Kei-Ichi
Published: September 2005

We propose a novel type of color magnetic condensation originating from magnetic monopoles so that it provides the mass of off-diagonal gluons in the Yang-Mills theory. This dynamical mass generation enables us to explain the infrared Abelian dominance and monopole dominance by way of a non-Abelian Stokes theorem, which supports the dual superconductivity picture of quark confinement. Moreover, we show that the instability of Savvidy vacuum disappears by sufficiently large color magnetic condensation.
GRAVITATIONAL INSTABILITY OF THE VACUUM AND THE COSMOLOGICAL CONSTANT PROBLEM
Authors: MOFFAT J. W.
Published: September 2005

A mechanism for suppressing the cosmological constant is described, using a superconducting analogy in which fermions coupled perturbatively to gravitons are in an unstable false vacuum. The coupling of the fermions to gravitons and a screened attractive interaction among pairs of fermions generates fermion condensates with zero momentum and a phase transition induces a non-perturbative transition to a true vacuum state. This produces a positive energy gap Δ in the vacuum energy identified with [Formula: see text] where Λ is the cosmological constant. In the strong coupling limit, a large cosmological constant induces a period of inflation in the early universe, followed by a weak coupling limit in which [Formula: see text] vanishes exponentially fast as the universe expands due to the dependence of the energy gap on the density of Fermi surface fermions, predicting a small cosmological constant in the early universe.
AN ACCURATE FIR APPROXIMATION OF IDEAL FRACTIONAL DELAY FILTER WITH COMPLEX COEFFICIENTS IN HILBERT SPACE
Authors: RIZVANDI N. BABAII , NABAVI A. , HESSABI SH.
Published: September 2005

This paper presents a low-order and accurate method for the design of FIR fractional delay (FD) filters with complex coefficients. This method employs least square technique in Hilbert space to approximate the ideal FD transfer function with a FIR filter and to calculate its coefficients. The main advantages of the resulting filter are: very good response at all frequencies compared to other FD filter design methods and a good method to create very small delay. Design examples are presented to illustrate the effectiveness of this new design approach.
MINIMIZATION OF CIRCUIT DESIGN USING PERMUTATION OF HAAR WAVELET SERIES
Authors: FALKOWSKI BOGDAN J. , STANKOVIĆ RADOMIR S. , JANKOVIĆ DRAGAN
Published: September 2005

The paper discusses complexity of circuit realization through Haar wavelet series. The efficiency in circuit synthesis using a method for minimization of the number of non-zero Haar coefficients by permutation of binary coordinates of indices of Haar functions is considered. Some applications of Haar wavelet transform and efficient ways of its calculation for logic domain are also discussed.
EXPERIMENTAL REALIZATION OF BINARY SIGNALS TRANSMISSION USING CHAOS
Authors: CRUZ-HERNÁNDEZ C. , LÓPEZ-MANCILLA D. , GARCÍA-GRADILLA V. , SERRANO-GUERRERO H. , NÚÑEZ-PÉREZ R.
Published: September 2005

In this paper, an experimental study of practical realization to transmit private binary signals using chaos is presented. In particular, we use a Generalized Hamiltonian forms approach to synchronize two unidirectionally coupled Chua's circuits with the receiver being given by an observer. Experimental results are in close accordance with the numerical simulations.
SIZE EFFECTS ON EFFECTIVE YOUNG'S MODULUS OF NANO CRYSTAL COPPER WIRES
Authors: WANG LIFENG , HU HAIYAN
Published: September 2005

In this paper, a study is made for the size effects on the effective Young's modulus of nano crystal copper wires. On the basis of numerical results of molecular dynamics simulation, the inhomogeneous property of the nano wires is taken into account so that the continuum model of either a rod or a beam is constructed to predict the size dependence of the effective Young's modulus. The comparison with molecular dynamics simulation based on embedded atom method shows that the new rod model enables one to predict the effective Young's modulus as accurately as existing models for the nano wires of different sizes of cross sections under axial load. Furthermore, the beam model gives better prediction than the current model for the nano wires subject to pure bending. The size effect on the elastic property can also be observed from the longitudinal and transverse natural vibration of the nano wires. In this case, the effective Young's modulus is nearly the same as that obtained through axial deformation and pure bending respectively.
MODELING OF COMBINED RADIATIVE AND CONVECTIVE HEAT TRANSFER IN AN ENCLOSURE WITH A HEAT-GENERATING CONDUCTING BODY
Authors: MEZRHAB A. , BOUALI H. , ABID C.
Published: September 2005

In this paper, we present a numerical study of the radiation-natural convection interactions in a differentially heated enclosure, within which a centered, squared, heat-conducting body generates heat. A specifically developed numerical model based on the finite-volume method and the SIMPLER algorithm is used for the solution of the governing equations. The working fluid (air) is perfectly transparent to the radiation. The Rayleigh number Ra and the temperature-difference ratio ΔT* were varied parametrically. For Pr = 0.71, the results obtained show that: (i) The isotherms and streamlines are strongly affected by the radiation exchange at high Rayleigh numbers (Ra ≥ 106), (ii) the temperature of the inner body decreases under the radiation exchange effect, (iii) for a constant Ra, the average Nusselt number at the hot and cold walls (Nuh and Nuc) vary linearly with increasing ΔT*: Nuh decreases with ΔT* while Nuc increases with ΔT*. Furthermore, the radiation exchange increases both average Nusselt numbers Nuh and Nuc, especially at Ra ≥ 105, and consequently, [Formula: see text] increases.
Assessment of intraluminal impedance for the detection of pharyngeal bolus flow during swallowing in healthy adults
Authors: Omari Taher I. , Rommel Nathalie , Szczesniak Michal M. , Fuentealba Sergio , Dinning Philip G. , Davidson Geoffrey P. , Cook Ian J.
Published: September 2005

Intraluminal impedance, a nonradiological method for assessing bolus flow within the gut, may be suitable for investigating pharyngeal disorders. This study evaluated an impedance technique for the detection of pharyngeal bolus flow during swallowing. Patterns of pharyngoesophageal pressure and impedance were simultaneously recorded with videofluoroscopy in 10 healthy volunteers during swallowing of liquid, semisolid, and solid boluses. The timing of bolus head and tail passage recorded by fluoroscopy was correlated with the timing of impedance drop and recovery at each recording site. Bolus swallowing produced a drop in impedance from baseline followed by a recovery to at least 50% of baseline. The timing of the pharyngeal and esophageal impedance drop correlated with the timing of the arrival of the bolus head. In the pharynx, the timing of impedance recovery was delayed relative to the timing of clearance of the bolus tail. In contrast, in the upper esophageal sphincter (UES) and proximal esophagus, the timing of impedance recovery correlated well with the timing of clearance of the bolus tail. Impedance-based estimates of pharyngoesophageal bolus clearance time correlated with true pharyngoesophageal bolus clearance time. Patterns of intraluminal impedance recorded in the pharynx during bolus swallowing are therefore more complex than those in the esophagus. During swallowing, mucosal contact between the tongue base and posterior pharyngeal wall prolongs the duration of pharyngeal impedance drop, leading to overestimation of bolus tail timing. Therefore, we conclude that intraluminal impedance measurement does not accurately reflect the bolus transit in the pharynx but does accurately reflect bolus transit across the UES and below.