bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of an implantable dosimeter for single‐point water equivalent path length verification in proton therapy
Authors: Lu Hsiao‐Ming , Mann Greg , Cascio Ethan
Published: November 2010

Purpose:

In vivo range verification in proton therapy is highly desirable. A recent study suggested that it was feasible to use point dose measurement for in vivo beam range verification in proton therapy, provided that the spread‐out Bragg peak dose distribution is delivered in a different and rather unconventional manner. In this work, the authors investigate the possibility of using a commercial implantable dosimeter with wireless reading for this particular application.

Methods:

The traditional proton treatment technique delivers all the Bragg peaks required for a SOBP field in a single sequence, producing a constant dose plateau across the target volume. As a result, a point dose measurement anywhere in the target volume will produce the same value, thus providing no information regarding the water equivalent path length to the point of measurement. However, the same constant dose distribution can be achieved by splitting the field into a complementary pair of subfields, producing two oppositely “sloped” depth‐dose distributions, respectively. The ratio between the two distributions can be a sensitive function of depth and measuring this ratio at a point inside the target volume can provide the water equivalent path length to the dosimeter location. Two types of field splits were used in the experiment, one achieved by the technique of beam current modulation and the other by manipulating the location and width of the beam pulse relative to the range modulator track. Eight MOSFET‐based implantable dosimeters at four different depths in a water tank were used to measure the dose ratios for these field pairs. A method was developed to correct the effect of the well‐known LET dependence of the MOSFET detectors on the depth‐dose distributions using the columnar recombination model. The LET‐corrected dose ratios were used to derive the water equivalent path lengths to the dosimeter locations to be compared to physical measurements.

Results:

The implantable dosimeters measured the dose ratios with a reasonable relative uncertainty of 1%–3% at all depths, except when the ratio itself becomes very small. In total, 55% of the individual measurements reproduced the water equivalent path lengths to the dosimeters within 1 mm. For three dosimeters, the difference was consistently less than 1 mm. Half of the standard deviations over the repeated measurements were equal or less than 1 mm.

Conclusions:

With a single fitting parameter, the LET‐correction method worked remarkably well for the MOSFET detectors. The overall results were very encouraging for a potential method ofin vivo beam range verification with millimeter accuracy. This is sufficient accuracy to expand range of clinical applications in which the authors could use the distal fall off of the proton depth dose for tight margins.
Sinogram preprocessing and binary reconstruction for determination of the shape and location of metal objects in computed tomography (CT)
Authors: Meng Bowen , Wang Jing , Xing Lei
Published: November 2010

Purpose:

To develop a binary image reconstruction method for the autolocalization of metallic object(s) in CT with sparse projections.

Methods:

The authors divide the system into two types of contents: Metal(s) and nonmetal(s). The boundaries of metallic objects are obtained by using a penalized weighted least‐squares algorithm with the adequate intensity gradient‐controlled. A novel mechanism of “amplifying” the difference between metal(s) and nonmetallic substances is introduced by preprocessing the sinogram data, which is shown to be necessary in dealing with a case with sparse projection data. A series of experimental studies are performed to evaluate the proposed approach.

Results:

A novel binary CT image reconstruction formalism is established for the autodetermination of the shape and location of metallic objects in the presence of limited number of projections. Experimental studies reveal that the presented algorithm works well even when the embedded metal object(s) has different shape(s). It is also shown that when the projection data are sparse, a differential manipulation of projection data can greatly facilitate the binary reconstruction process and allow the authors to obtain accurate binary CT images that would otherwise be unattainable.

Conclusions:

Binary CT reconstruction provides a viable method for determining the geometric distribution information of the implanted metal objects in CT imaging.
Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators
Authors: Bhardwaj Nitin , Kim Philip M. , Gerstein Mark B.
Published: November 2010

Transcriptional regulatory networks appear to have an organization similar to a corporation, with top-level managers having the most influence.
DNMT1 Stability Is Regulated by Proteins Coordinating Deubiquitination and Acetylation-Driven Ubiquitination
Authors: Du Zhanwen , Song Jing , Wang Yong , Zhao Yiqing , Guda Kishore , Yang Shuming , Kao Hung-Ying , Xu Yan , Willis Joseph , Markowitz Sanford D. , Sedwick David , Ewing Robert M. , Wang Zhenghe
Published: November 2010

Degradation of a DNA methyltransferase implicated in cancer is determined by its acetylation status.
Eau de Rotting Fruit
Authors: Wong Wei
Published: November 2010

The Solomon’s lily targets odorant receptors that enable drosophilids to detect odors from their food source.
Multifarious Meristem Maintenance
Authors: VanHook Annalisa M.
Published: November 2010

A mutant screen identifies a third pathway through which CLAVATA3 regulates stem cell proliferation.
Focus Issue: Signals for Gene Expression
Authors: Wong Wei
Published: November 2010

Signaling pathways can regulate gene expression—and vice versa.
Posttranscriptional Regulation of PTEN Dosage by Noncoding RNAs
Authors: He Lin
Published: November 2010

The abundance of the tumor suppressor PTEN is modulated by microRNAs and pseudogenes.
Intracellular Delivery Strategies for MicroRNAs and Potential Therapies for Human Cardiovascular Diseases
Authors: Shi Michael A. , Shi Guo-Ping
Published: November 2010

MicroRNAs can help maintain healthy cardiovascular systems or contribute to the pathogenesis of cardiovascular diseases.
Sensitive
In Vitro
System To Assess Morphological and Biochemical Effects of Praziquantel and Albendazole on
Taenia solium
Cysts
Authors: Mahanty S. , Paredes A. , Marzal M. , Gonzalez E. , Rodriguez S. , Dorny P. , Guerra-Giraldez C. , Garcia H. H. , Nash T.
Published: November 2010

Neurocysticercosis resulting from
Taenia solium
infections is a major cause of adult-acquired seizures worldwide. Disease is caused by larval cysts, and treatment consists of the anthelmintic drugs albendazole or praziquantel. There are no standard methods to assess drug activity to
T. solium
cysts
in vitro
. Morphological, functional, and biochemical changes that might reflect damaging (inhibiting, cytotoxic) drug effects were analyzed after exposure of cysts to albendazole sulfoxide (ABZ-SO), the major active metabolite of the drug
in vivo
, praziquantel (PZQ), or combinations of both. PZQ exposure led to a decrease in cyst size and inhibition of evagination, whereas ABZ-SO exposure resulted in minimal changes. Alkaline phosphatase (AP) is normally secreted by cysts, and both drugs inhibited AP secretion at concentrations of 5 and 50 ng/ml for PZQ and ABZ-SO, respectively. Some combinations of both drugs resulted in additive and/or synergistic activities. Parasite-specific antigen, detected in the cerebrospinal fluid and blood of infected patients, is also normally secreted by
T. solium
cysts. Antigen secretion was similarly inhibited by ABZ-SO and PZQ and a combination of both drugs, suggesting that inhibition of secretion is a common downstream consequence of the activities of both drugs. These studies establish quantitative methods to measure
in vitro
anthelmintic activity and suggest combination therapy with ABZ-SO and PZQ may have clinical benefit.
Genetic Context and Biochemical Characterization of the IMP-18 Metallo-β-Lactamase Identified in a
Pseudomonas aeruginosa
Isolate from the United States
Authors: Borgianni Luisa , Prandi Silvia , Salden Laurie , Santella Gisela , Hanson Nancy D. , Rossolini Gian Maria , Docquier Jean-Denis
Published: November 2010

The production of metallo-β-lactamase (MBL) is an important mechanism of resistance to β-lactam antibiotics, including carbapenems. Despite the discovery and emergence of many acquired metallo-β-lactamases, IMP-type determinants (now counting at least 27 variants) remain the most prevalent in some geographical areas. In Asian countries, and notably Japan, IMP-1 and its closely related variants are most widespread. Some other variants have been detected in other countries and show either an endemic (e.g., IMP-13 in Italy) or sporadic (e.g., IMP-12 in Italy or IMP-18 in the United States) occurrence. The IMP-18-producing
Pseudomonas aeruginosa
strain PS 297 from the southwestern United States carried at least two class 1 integrons. One was identical to In
51
, while the other, named In
133
and carrying the
bla
IMP-18
gene cassette in the third position, showed an original array of five gene cassettes, including
aacA7
,
qacF
,
aadA1
, and an unknown open reading frame (ORF). Interestingly. In
133
differed significantly from In
96
, the
bla
IMP-18
-carrying integron identified in a
P. aeruginosa
isolate from Mexico. The meropenem and ertapenem MIC values were much lower for
Escherichia coli
strains producing IMP-18 (0.06 and 0.12 μg/ml, respectively) than for strains producing IMP-1 (2 μg/ml for each). Kinetic data obtained with the purified enzyme revealed lower turnover rates of IMP-18 than of other IMP-type enzymes with most substrates.
Polymyxin-Resistant Clinical Isolates of
Escherichia
coli
Authors: Urban Carl , Tiruvury Hemavarna , Mariano Noriel , Colon-Urban Rita , Rahal James J.
Published: November 2010

A surveillance study to identify patients from the community with
Escherichia
coli
resistant to broad-spectrum cephalosporins discovered two isolates that were also resistant to polymyxin B and colistin. One isolate from a patient in the community and a second from a patient who received multiple courses of polymyxin B also possessed a CTX-M-15 enzyme. Resistance to cationic peptides in
E
.
coli
is unusual, and testing for susceptibility to these agents should be performed.
Simultaneous Presence of PrtH and PrtH2 Proteinases in
Lactobacillus helveticus
Strains Improves Breakdown of the Pure α
s1
-Casein
Authors: Sadat-Mekmene L. , Jardin J. , Corre C. , Mollé D. , Richoux R. , Delage M.-M. , Lortal S. , Gagnaire V.
Published: October 2010

Lactobacillus helveticus
can possess one or two cell envelope proteinases (CEPs), called PrtH2 and PrtH. The aim of this work was to explore the diversity of 15 strains of
L. helveticus
, isolated from various origins, in terms of their proteolytic activities and specificities on pure caseins or on milk casein micelles. CEP activity differed 14-fold when the strains were assayed on a synthetic substrate, but no significant differences were detected between strains possessing one or two CEPs. No correlation was observed between the proteolytic activities of the strains and their rates of acidification in milk. The kinetics of hydrolysis of purified α
s1
- and β-casein by
L. helveticus
whole cells was monitored using Tris-Tricine sodium dodecyl sulfate (SDS) electrophoresis, and for four strains, the peptides released were identified using mass spectrometry. While rapid hydrolysis of pure β-casein was observed for all strains, the hydrolysis kinetics of α
s1
-casein was the only criterion capable of distinguishing between the strains based on the number of CEPs. Fifty-four to 74 peptides were identified for each strain. When only PrtH2 was present, 22 to 30% of the peptides originated from α
s1
-casein. The percentage increased to 41 to 49% for strains in which both CEPs were expressed. The peptide size ranged from 6 to 33 amino acids, revealing a broad range of cleavage specificities, involving all classes of amino acids (Leu, Val, Ala, Ile, Glu, Gln, Lys, Arg, Met, and Pro). Regions resistant to proteolysis were identified in both caseins. When strains were grown in milk, a drastic reduction in the number of peptides was observed, reflecting changes in accessibility and/or peptide assimilation during growth.
Development of an Efficient Real-Time Quantitative PCR Protocol for Detection ofXanthomonas arboricolapv. pruni inPrunusSpecies
Authors: Palacio-Bielsa Ana , Cubero Jaime , Cambra Miguel A. , Collados Raquel , Berruete Isabel M. , López María M.
Published: October 2010

Xanthomonas arboricolapv. pruni, the causal agent of bacterial spot disease of stone fruit, is considered a quarantine organism by the European Union and the European and Mediterranean Plant Protection Organization (EPPO). The bacterium can undergo an epiphytic phase and/or be latent and can be transmitted by plant material, but currently, only visual inspections are used to certify plants as beingX. arboricolapv. pruni free. A novel and highly sensitive real-time TaqMan PCR detection protocol was designed based on a sequence of a gene for a putative protein related to an ABC transporter ATP-binding system inX. arboricolapv. pruni. Pathogen detection can be completed within a few hours with a sensitivity of 102CFU ml−1, thus surpassing the sensitivity of the existing conventional PCR. Specificity was assessed forX. arboricolapv. pruni strains from different origins as well as for closely relatedXanthomonasspecies, non-Xanthomonasspecies, saprophytic bacteria, and healthyPrunussamples. The efficiency of the developed protocol was evaluated with field samples of 14Prunusspecies and rootstocks. For symptomatic leaf samples, the protocol was very efficient even when washed tissues of the leaves were directly amplified without any previous DNA extraction. For samples of 117 asymptomatic leaves and 285 buds, the protocol was more efficient after a simple DNA extraction, andX. arboricolapv. pruni was detected in 9.4% and 9.1% of the 402 samples analyzed, respectively, demonstrating its frequent epiphytic or endophytic phase. This newly developed real-time PCR protocol can be used as a quantitative assay, offers a reliable and sensitive test forX. arboricolapv. pruni, and is suitable as a screening test for symptomatic as well as asymptomatic plant material.
Cadherin, Alkaline Phosphatase, and Aminopeptidase N as Receptors of Cry11Ba Toxin from
Bacillus thuringiensis
subsp.
jegathesan
in
Aedes aegypti
Authors: Likitvivatanavong Supaporn , Chen Jianwu , Bravo Alejandra , Soberón Mario , Gill Sarjeet S.
Published: October 2010

Cry11Ba is one of the most toxic proteins to mosquito larvae produced by
Bacillus thuringiensis
. It binds
Aedes aegypti
brush border membrane vesicles (BBMV) with high affinity, showing an apparent dissociation constant (

K
d

) of 8.2 nM. We previously reported that an anticadherin antibody competes with Cry11Ba binding to BBMV, suggesting a possible role of cadherin as a toxin receptor. Here we provide evidence of specific cadherin repeat regions involved in this interaction. Using cadherin fragments as competitors, a C-terminal fragment which contains cadherin repeat 7 (CR7) to CR11 competed with Cry11Ba binding to BBMV. This binding was also efficiently competed by the CR9, CR10, and CR11 peptide fragments. Moreover, we show CR11 to be an important region of interaction with Cry11Ba toxin. An alkaline phosphatase (AaeALP1) and an aminopeptidase-N (AaeAPN1) also competed with Cry11Ba binding to
Ae. aegypti
BBMV. Finally, we found that Cry11Ba and Cry4Ba share binding sites. Synthetic peptides corresponding to loops α8, β2-β3 (loop 1), β8-β9, and β10-β11 (loop 3) of Cry4Ba compete with Cry11Ba binding to BBMV, suggesting Cry11Ba and Cry4Ba have common sites involved in binding
Ae. aegypti
BBMV. The data suggest that three different
Ae. aegypti
midgut proteins, i.e., cadherin, AaeALP1, and AaeAPN1, are involved in Cry11Ba binding to
Ae. aegypti
midgut brush border membranes.
Detection of Clonal Group A
Escherichia coli
Isolates from Broiler Chickens, Broiler Chicken Meat, Community-Dwelling Humans, and Urinary Tract Infection (UTI) Patients and Their Virulence in a Mouse UTI Model
Authors: Jakobsen Lotte , Hammerum Anette M. , Frimodt-Møller Niels
Published: October 2010

Escherichia coli
clonal group A isolates cause infections in people. We investigated 158 phylogroup D
E. coli
isolates from animals, meat, and humans. Twenty-five of these isolates were of clonal group A, and 15 isolates were shown to cause infection in a mouse urinary tract infection (UTI) model. We conclude that clonal group A isolates are found in both broiler chickens and broiler chicken meat and may cause UTI in humans.
Structural Dissection and
In Vivo
Effectiveness of a Peptide Inhibitor of
Porphyromonas gingivalis
Adherence to
Streptococcus gordonii
Authors: Daep Carlo Amorin , Novak Elizabeth A. , Lamont Richard J. , Demuth Donald R.
Published: November 2010

The interaction of the minor fimbrial antigen (Mfa) with streptococcal antigen I/II (e.g., SspB) facilitates colonization of the dental biofilm by
Porphyromonas gingivalis.
We previously showed that a 27-mer peptide derived from SspB (designated BAR) resembles the nuclear receptor (NR) box protein-protein interacting domain and potently inhibits this interaction
in vitro
. Here, we show that the EXXP motif upstream of the NR core α-helix contributes to the Mfa-SspB interaction and that BAR reduces
P. gingivalis
colonization and alveolar bone loss
in vivo
in a murine model of periodontitis. Substitution of Gln for Pro
1171
or Glu
1168
increased the α-helicity of BAR and reduced its inhibitory activity
in vitro
by 10-fold and 2-fold, respectively. To determine if BAR prevents
P. gingivalis
infection
in vivo
, mice were first infected with
Streptococcus gordonii
and then challenged with
P. gingivalis
in the absence and presence of BAR. Animals that were infected with either 10
9
CFU of
S. gordonii
DL-1 or 10
7
CFU of
P. gingivalis
33277 did not show a statistically significant increase in alveolar bone resorption over sham-infected controls. However, infection with 10
9
CFU of
S. gordonii
followed by 10
7
CFU of
P. gingivalis
induced significantly greater bone loss (
P
< 0.01) than sham infection or infection of mice with either organism alone.
S. gordonii
-infected mice that were subsequently challenged with 10
7
CFU of
P. gingivalis
in the presence of BAR exhibited levels of bone resorption similar to those of sham-infected animals. Together, these results indicate that both EXXP and the NR box are important for the Mfa-SspB interaction and that BAR peptide represents a potential therapeutic that may limit colonization of the oral cavity by
P. gingivalis
.
Modifications to the Peptidoglycan Backbone Help Bacteria To Establish Infection
Authors: Davis Kimberly M. , Weiser Jeffrey N.
Published: November 2010

Bacterial pathogens that colonize mucosal surfaces have acquired resistance to antimicrobials that are abundant at these sites. One of the main antimicrobials present on mucosal surfaces is lysozyme, a muramidase that hydrolyzes the peptidoglycan backbone of bacteria. Cleavage of the peptidoglycan backbone leads to bacterial cell death and lysis, which releases bacterial fragments, including peptidoglycan, at the site of infection. Peptidoglycan fragments can be recognized by host receptors and initiate an immune response that will aid in clearing infection. Many mucosal pathogens modify the peptidoglycan residues surrounding the cleavage site for lysozyme to avoid peptidoglycan degradation and the release of these proinflammatory fragments. This review will focus specifically on peptidoglycan modifications, their role in lysozyme resistance, and downstream effects on the host immune response to infection.
A
fadD
mutant of
Vibrio cholerae
Is Impaired in the Production of Virulence Factors and Membrane Localization of the Virulence Regulatory Protein TcpP
Authors: Ray Sreejana , Chatterjee Epshita , Chatterjee Arpita , Paul Kalidas , Chowdhury Rukhsana
Published: November 2010

In the enteric pathogen
Vibrio cholerae
, expression of the major virulence factors is controlled by the hierarchical expression of several regulatory proteins comprising the ToxR regulon. In this study, we demonstrate that disruption of the
fadD
gene encoding a long-chain fatty acyl coenzyme A ligase has marked effects on expression of the ToxR virulence regulon, motility, and
in vivo
lethality of
V. cholerae
. In the
V. cholerae fadD
mutant, expression of the major virulence genes
ctxAB
and
tcpA
, encoding cholera toxin (CT), and the major subunit of the toxin-coregulated pilus (TCP) was drastically repressed and a growth-phase-dependent reduction in the expression of
toxT
, encoding the transcriptional activator of
ctxAB
and
tcpA
, was observed. Expression of
toxT
from an inducible promoter completely restored CT to wild-type levels in the
V. cholerae fadD
mutant, suggesting that FadD probably acts upstream of
toxT
expression. Expression of
toxT
is activated by the synergistic effect of two transcriptional regulators, TcpP and ToxR. Reverse transcription-PCR and Western blot analysis indicated that although gene expression and production of both TcpP and ToxR are unaffected in the
fadD
mutant strain, membrane localization of TcpP, but not ToxR, is severely impaired in the
fadD
mutant strain from the mid-logarithmic phase of growth. Since the decrease in
toxT
expression occurred concomitantly with the reduction in membrane localization of TcpP, a direct correlation between the defect in membrane localization of TcpP and reduced
toxT
expression in the
fadD
mutant strain is suggested.
Strain-Specific Polymorphisms in Paneth Cell α-Defensins of C57BL/6 Mice and Evidence of Vestigial Myeloid α-Defensin Pseudogenes
Authors: Shanahan Michael T. , Tanabe Hiroki , Ouellette André J.
Published: November 2010

Paneth cells at the base of small intestinal crypts secrete microbicidal α-defensins, termed cryptdins (Crps) in mice, as mediators of innate immunity. Proteomic studies show that five abundant Paneth cell α-defensins in C57BL/6 mice are strain specific in that they have not been identified in other inbred strains of mice. Two C57BL/6-specific peptides are coded for by theDefcr20and -21genes evident in the NIH C57BL/6 genome but absent from the Celera mixed-strain assembly, which excludes C57BL/6 data and differs from the NIH build with respect to the organization of the α-defensin gene locus. Conversely, C57BL/6 mice lack the Crp1, -2, -4, and -6 peptides and their correspondingDefcr1, -2, -4, and -6genes, which are common to several mouse strains, including those of the Celera assembly. In C57BL/6 mice, α-defensin gene diversification appears to have occurred by tandem duplication of a multigene cassette that was not found in the mixed-strain assembly. Both mouse genome assemblies contain conserved α-defensin pseudogenes that are closely related to functional myeloid α-defensin genes in the rat, suggesting that the neutrophil α-defensin defect in mice resulted from progressive gene loss. Given the role of α-defensins in shaping the composition of the enteric microflora, such polymorphisms may influence outcomes in mouse models of disease or infection.
Cooperation between LepA and PlcH Contributes to theIn VivoVirulence and Growth ofPseudomonas aeruginosain Mice
Authors: Kida Yutaka , Shimizu Takashi , Kuwano Koichi
Published: November 2010

Pseudomonas aeruginosa-derived large extracellular protease (LepA) and hemolytic phospholipase C (PlcH) are considered to play an important role in the pathogenicity of this organism. Although bacterial growth appears to be closely related to virulence, little is known about whether LepA and PlcH participate in the growth and virulence ofP. aeruginosa. In this study, we investigated whether LepA and PlcH contribute to the virulence and growth ofP. aeruginosausing a wild-type strain and mutants. The growth rate of the isogeniclepAsingle mutant was lower than that of the wild-type strain in a minimal medium containing serum albumin or hemoglobin as the sole carbon and nitrogen source. Furthermore, the growth rate of thelepA plcHdouble mutant decreased greatly compared with that of the wild-type strain in a minimal medium containing erythrocytes as a sole nutrient source for growth. Thus, these results indicate that cooperation between LepA and PlcH would contribute to the utilization of erythrocytes as a sole nutrient source for the growth ofP. aeruginosa. In addition, mouse infection experiments demonstrated that the virulence of thelepAandplcHsingle mutants was attenuated, and the numbers of the mutants were lower than the numbers of the wild-type strain in peritoneal lavage fluid and whole-blood specimens. In particular, the virulence and growth rate of thelepA plcHdouble mutant were markedly lower than those of the wild-type strain. Collectively, these results suggest that LepA and PlcH contribute to thein vivovirulence and growth ofP. aeruginosa.
Parallel Evolution in Pseudomonas aeruginosa over 39,000 Generations
In Vivo
Authors: Huse Holly K. , Kwon Taejoon , Zlosnik James E. A. , Speert David P. , Marcotte Edward M. , Whiteley Marvin
Published: November 2010

The Gram-negative bacterium
Pseudomonas aeruginosa
is a common cause of chronic airway infections in individuals with the heritable disease cystic fibrosis (CF). After prolonged colonization of the CF lung,
P. aeruginosa
becomes highly resistant to host clearance and antibiotic treatment; therefore, understanding how this bacterium evolves during chronic infection is important for identifying beneficial adaptations that could be targeted therapeutically. To identify potential adaptive traits of
P. aeruginosa
during chronic infection, we carried out global transcriptomic profiling of chronological clonal isolates obtained from 3 individuals with CF. Isolates were collected sequentially over periods ranging from 3 months to 8 years, representing up to 39,000
in vivo
generations. We identified 24 genes that were commonly regulated by all 3
P. aeruginosa
lineages, including several genes encoding traits previously shown to be important for
in vivo
growth. Our results reveal that parallel evolution occurs in the CF lung and that at least a proportion of the traits identified are beneficial for
P. aeruginosa
chronic colonization of the CF lung.

IMPORTANCE
Deadly diseases like AIDS, malaria, and tuberculosis are the result of long-term chronic infections. Pathogens that cause chronic infections adapt to the host environment, avoiding the immune response and resisting antimicrobial agents. Studies of pathogen adaptation are therefore important for understanding how the efficacy of current therapeutics may change upon prolonged infection. One notorious chronic pathogen is
Pseudomonas aeruginosa
, a bacterium that causes long-term infections in individuals with the heritable disease cystic fibrosis (CF). We used gene expression profiles to identify 24 genes that commonly changed expression over time in 3
P. aeruginosa
lineages, indicating that these changes occur in parallel in the lungs of individuals with CF. Several of these genes have previously been shown to encode traits critical for
in vivo
-relevant processes, suggesting that they are likely beneficial adaptations important for chronic colonization of the CF lung.
PARAMETER CHARACTERISTICS FOR STABLE AND UNSTABLE SOLUTIONS IN NONLINEAR DISCRETE DYNAMICAL SYSTEMS
Authors: LUO ALBERT C. J. , GUO YU
Published: November 2010

This paper studies complete stable and unstable periodic solutions for n-dimensional nonlinear discrete dynamical systems. The positive and negative iterative mappings of discrete systems are used to develop mapping structures of the stable and unstable periodic solutions. The complete bifurcation and stability analysis are presented for the stable and unstable periodic solutions which are based on the positive and negative mapping structures. A comprehensive investigation on the Henon map is carried out for a better understanding of complexity in nonlinear discrete systems. Given is the bifurcation scenario based on positive and negative mappings of the Henon map, and the analytical predictions of the corresponding periodic solutions are achieved. The corresponding eigenvalue analysis of the periodic solutions is presented. The Poincare mapping sections relative to the Neimark bifurcations of periodic solutions are presented. A parameter map for periodic and chaotic solutions is developed. The complete unstable and stable periodic solutions in nonlinear discrete systems are presented for the first time. The results presented in this paper provide a new idea for one to rethink the current existing theories.
MODELING CROSS-CORRELATIONS OF TRAFFIC FLOW
Authors: SHANG PENGJIAN , DONG KEQIANG , KAMAE SANTI
Published: November 2010

The study of diverse natural and nonstationary signals has recently become an area of active research for physicists. This is because these signals exhibit interesting dynamical properties such as scale invariance, volatility correlation, heavy tails and fractality. The focus of the present paper is on the intriguing power-law autocorrelations and cross-correlations in traffic series. Detrended Cross-Correlation Analysis (DCCA) is used to study the traffic flow fluctuations. It is demonstrated that the time series, observed on the Anhua-Bridge highway in the Beijing Third Ring Road (BTRR), may exhibit power-law cross-correlations when they come from two adjacent sections or lanes. This indicates that a large increment in one traffic variable is more likely to be followed by large increment in the other traffic variable. However, for traffic time series derived from nonadjacent sections or lanes, we find that even though they are power-law autocorrelated, there is no cross-correlation between them with a unique exponent. Our results show that DCCA techniques based on Detrended Fluctuation Analysis (DFA) can be used to analyze and interpret the traffic flow.
BIFURCATIONS OF PERIODIC ORBITS AND INTEGRABILITY OF DYNAMICAL SYSTEMS
Authors: KASPERCZUK STANISŁAW P.
Published: November 2010

In this paper, we study the problem of transition from integrable (regular) to nonintegrable (chaotic) dynamics in a family of Hamiltonian systems [Formula: see text]. We show that this transition happens exactly at bifurcation of the periodic orbit of the Hamiltonian system, when its stability discriminant Δ(ε) = +2. As an example, we investigate the system [Formula: see text].
A UNIFIED APPROACH FOR SHEWHART-TYPE PHASE I CONTROL CHARTS FOR THE MEAN
Authors: HUMAN S. W. , CHAKRABORTI S.
Published: November 2010

The false alarm probability (FAP) is the metric typically used to design and evaluate the performance of Phase I control charts. It is shown that in situations where the exact or the asymptotic joint p.d.f. of the standardized charting statistics follows a singular standard multivariate normal distribution with a common negative correlation, the FAP of some Shewhart-type Phase I charts for the mean can be expressed as a multiple integral of the joint p.d.f. Hence the required charting constants can be calculated (and the control chart can be implemented) by evaluating this integral. A table with the charting constants is provided for some popular choices of the nominal FAP (denoted FAP0) and the number of Phase I samples, m. The proposed methodology is useful to unify some existing Phase I charts and is illustrated with two charts from the literature: the p chart for the fraction nonconforming and the [Formula: see text] chart for the mean. A summary and some conclusions are provided.
SELECTION OF MAINTENANCE STRATEGY FOR AIRCRAFT SYSTEMS USING MULTI-CRITERIA DECISION MAKING METHODOLOGIES
Authors: AHMADI ALIREZA , GUPTA SUPRAKASH , KARIM RAMIN , KUMAR UDAY
Published: November 2010

This paper, proposes the Multi-Criteria Decision Making (MCDM) methodology for selection of a maintenance strategy to assure the consistency and effectiveness of maintenance decisions. The methodology is based on an AHP-enhanced TOPSIS, VIKOR and benefit-cost ratio, in which the importance of the effectiveness appraisal criteria of a maintenance strategy is determined by the use of AHP. Furthermore, in the proposed methodology the different maintenance policies are ranked using the benefit-cost ratio, TOPSIS and VIKOR. The method provides a basis for consideration of different priority factors governing decisions, which may include the rate of return, total profit, or lowest investment. When the preference is the rate of return, the benefit-cost ratio is used, and for the total profit TOPSIS is applied. In cases where the decision maker has specific preferences, such as the lowest investment, VIKOR is adopted. The proposed method has been tested through a case study within the aviation context for an aircraft system. It has been found that using the methodology presented in the paper, the relative advantage and disadvantage of each maintenance strategy can be identified in consideration of different aspects, which contributes to the consistent and rationalized justification of the maintenance task selection. The study shows that application of the combined AHP, TOPSIS, and VIKOR methodologies is an applicable and effective way to implement a rigorous approach for identifying the most effective maintenance alternative.
RELIABILITY MANAGEMENT AND IMPROVEMENT FOR PLANNING AND OPERATIONAL PROCESS ENHANCEMENT MEASURES IN DEREGULATED POWER SYSTEMS USING ATC
Authors: VENU V. VIJAY , VERMA A. K.
Published: November 2010

In this paper, beginning with a concise overview of the Available Transfer Capability (ATC) evaluation methods, we make a proposition for reliability management in the planning horizon of deregulated power systems through the concept of Adequacy Resiliency. The derived indices are meant as indicators of adaptability of power systems to ensure the required reliability levels. Improvements to this conceptualization upon the deployment of Flexible AC Transmission System (FACTS) devices are then put forward. We also explore the option of employing the created indices to the operational horizon of power systems, explaining the means of market enhancement. Core reliability issues arising out of the usage of FACTS are then discussed.
MULTISCALE COMPARISON AND CLUSTERING OF THREE-DIMENSIONAL TRAJECTORIES BASED ON CURVATURE MAXIMA
Authors: HIRANO SHOJI , TSUMOTO SHUSAKU
Published: November 2010

This paper presents a multiscale comparison method for three-dimensional trajectories. In order to deal with the problem that zero-crossings of curvature cannot be determined for space curve, we utilize the maxima of curvature. The method first traces the positions of curvature maxima across scales for recognizing the hierarchy of partial trajectories. Then it performs cross-scale matching of partial trajectories derived from two input trajectories, and obtains the structurally best matches. Finally, it calculates the value-based dissimilarity for each pair of the matched partial trajectories and output as the final dissimilarity between trajectories that can be further used for clustering or classification tasks. In experiments on the UCI character trajectory dataset we demonstrate that reasonable correspondences were captured successfully and the derived dissimilarity yielded good clustering results comparable to DTW. We also demonstrate using real medical data that the method could generate interesting clusters that might reflect distribution of fibrotic stages.
FUZZY, DISTRIBUTED, INSTANCE COUNTING, AND DEFAULT ARTMAP NEURAL NETWORKS FOR FINANCIAL DIAGNOSIS
Authors: NACHEV ANATOLI , HILL SEAMUS , BARRY CHRIS , STOYANOV BORISLAV
Published: November 2010

This paper shows the potential of neural networks based on the Adaptive Resonance Theory as tools that generate warning signals when bankruptcy of a company is expected (bankruptcy prediction problem). Using that class of neural networks is still unexplored to date. We examined four of the most popular networks of the class — fuzzy, distributed, instance counting, and default ARTMAP. In order to illustrate their performance and to compare with other techniques, we used data, financial ratios, and experimental conditions identical to those published in previous studies. Our experiments show that two financial ratios provide highest discriminatory power of the model and ensure best prediction accuracy. We examined performance and validated results by exhaustive search of input variables, cross-validation, receiver operating characteristic analysis, and area under curve metric. We also did application-specific cost analysis. Our results show that distributed ARTMAP outperforms the other three models in general, but the fuzzy model is best performer for certain vigilance values and in the application-specific context. We also found that ARTMAP outperforms the most popular neural networks — multi-layer perceptrons and other statistical techniques applied to the same data.
PROVIDING TIMELY UPDATED SEQUENTIAL PATTERNS IN DECISION MAKING
Authors: HONG TZUNG-PEI , WANG CHING-YAO , LIN CHUN-WEI
Published: November 2010

Mining knowledge from large databases has become a critical task for organizations. Managers commonly use the obtained sequential patterns to make decisions. In the past, databases were usually assumed to be static. In real-world applications, however, transactions may be updated. In this paper, a maintenance algorithm for rapidly updating sequential patterns for real-time decision making is proposed. The proposed algorithm utilizes previously discovered large sequences in the maintenance process, thus greatly reducing the number of database rescans and improving performance. Experimental results verify the performance of the proposed approach. The proposed algorithm provides real-time knowledge that can be used for decision making.
HIGH UTILITY ITEMSETS MINING
Authors: LIU YING , LI JIANWEI , LIAO WEI-KENG , CHOUDHARY ALOK , SHI YONG
Published: November 2010

High utility itemsets mining identifies itemsets whose utility satisfies a given threshold. It allows users to quantify the usefulness or preferences of items using different values. Thus, it reflects the impact of different items. High utility itemsets mining is useful in decision-making process of many applications, such as retail marketing and Web service, since items are actually different in many aspects in real applications. However, due to the lack of "downward closure property", the cost of candidate generation of high utility itemsets mining is intolerable in terms of time and memory space. This paper presents a Two-Phase algorithm which can efficiently prune down the number of candidates and precisely obtain the complete set of high utility itemsets. The performance of our algorithm is evaluated by applying it to synthetic databases and two real-world applications. It performs very efficiently in terms of speed and memory cost on large databases composed of short transactions, which are difficult for existing high utility itemsets mining algorithms to handle. Experiments on real-world applications demonstrate the significance of high utility itemsets in business decision-making, as well as the difference between frequent itemsets and high utility itemsets.
AUDIO QUALITY IMPROVEMENT OF VEHICULAR HANDS-FREE COMMUNICATION USING VARIABLE STEP-SIZE AFFINE-PROJECTION ALGORITHM
Authors: WU JIAN-DA , LIN SHIH-LIN
Published: November 2010

For a vehicular hands-free communication system, the sound quality of communication is usually degraded by noise which is known to be detrimental to system performance. In this paper, a novel adaptive filtering algorithm and an integrated system for acoustic echo and noise cancellation are presented. The proposed system includes adaptive noise cancellation, line enhancer, and echo cancellation which are based on a variable step-size affine-projection algorithm (VSS APA). The proposed VSS APA filtering algorithm is a combination of a variable step-size least-mean-square (VSS LMS) and an affine-projection algorithm (APA). The matrix of the APA allows more accurate, thorough input data and transforms the data into the structure of orthogonality, thus making the estimate of the weight vector faster and more accurate. To understand and verify the effectiveness of the proposed system, performance evaluation and comparison were conducted to compare the proposed algorithm and various traditional adaptive filtering algorithms in this application. The results demonstrated that the VSS APA has an effective performance and convergence in sound quality improvement of hands-free communication systems.
WAVELET SUB-BAND BASED TEMPORAL FEATURES FOR ROBUST HINDI PHONEME RECOGNITION
Authors: FAROOQ O. , DATTA S. , SHROTRIYA M. C.
Published: November 2010

This paper proposes the use of wavelet transform-based feature extraction technique for Hindi speech recognition application. The new proposed features take into account temporal as well as frequency band energy variations for the task of Hindi phoneme recognition. The recognition performance achieved by the proposed features is compared with the standard MFCC and 24-band admissible wavelet packet-based features using a linear discriminant function based classifier. To evaluate robustness of these features, the NOISEX database is used to add different types of noise into phonemes to achieve signal-to-noise ratios in the range of 20 dB to -5 dB. The recognition results show that under noisy background the proposed technique always achieves a better performance over MFCC-based features.
CONSTRUCTION OF COMPACTLY SUPPORTED CONJUGATE SYMMETRIC COMPLEX TIGHT WAVELET FRAMES
Authors: YANG SHOUZHI , XUE YANMEI
Published: November 2010

Two algorithms for constructing a class of compactly supported complex tight wavelet frames with conjugate symmetry are provided. Firstly, based on a given complex refinable function ϕ, an explicit formula for constructing complex tight wavelet frames is presented. If the given complex refinable function ϕ is compactly supported conjugate symmetric, then we prove that there exists a compactly supported conjugate symmetric/anti-symmetric complex tight wavelet frame Ψ = {ψ1, ψ2, ψ3} associated with ϕ. Secondly, under the conditions that both the low-pass filters and high-pass filters are unknown, we give a parametric formula for constructing a class of smooth conjugate symmetric/anti-symmetric complex tight wavelet frames. Free parameters in the algorithm are explicitly identified, and can be used to optimize the result with respect to other criteria. Finally, two examples are given to illustrate how to use our method to construct conjugate symmetric complex tight wavelet frames.
ROBUST WATERMARKING SCHEMES USING SELECTIVE CURVELET COEFFICIENTS BASED ON A HVS MODEL
Authors: LEUNG H. Y. , CHENG L. M. , CHENG L. L.
Published: November 2010

In this paper, six robust non-blind watermarking schemes based on curvelet transform are proposed. Single band watermarking method was proposed in Ref. 1. This paper develops the single band watermarking method and adds Human Vision System (HVS) to form six different multi-bands watermarking methods. With the increasing redundancy of watermark, the robustness of the algorithm will be investigated and comparative studies with the single band watermarking will be shown. The experimental results demonstrate that the proposed algorithms have great robustness against various imaging attacks.
A COMPACTLY SUPPORTED, SYMMETRICAL AND QUASI-ORTHOGONAL WAVELET
Authors: HOU YU
Published: November 2010

Based on the wavelet theory and optimization method, a class of single wavelets with compact support, symmetry and quasi-orthogonality are designed and constructed. Some mathematical properties of the wavelets, such as orthogonality, linear phase property and vanishing moments and so on, are studied. A speech compression experiment is implemented in order to investigate the performance of signal reconstruction and speech compression for the proposed wavelets. Comparison with some conventional wavelets shows that the proposed wavelets have a very good performance of signal reconstruction and speech compression.
THEORETICAL INVESTIGATION OF THE EFFECT OF FLUTE PROFILE ON FLAT CRUSH STRENGTH OF CORRUGATED BOARD
Authors: MAHAJERIN ENAYAT , BURGESS GARY
Published: November 2010

Curved beam theory is used to investigate the buckling failure of corrugated boards. The corresponding governing differential equation is developed from the geometry of the flute and the equilibrium equations. The resulting differential equation is highly nonlinear for which an iterative algorithm is presented. The method can be used to study buckling of the CB and measure the flat crush test (FCT) of a variety of flute shapes. It is shown that for a given amount of medium, there exists an optimum flute shape that gives the highest FCT. Because a low FCT means poor performance in printing operations and cushioning, the method can help manufacturers to select appropriate board. The corresponding algorithm and examples are presented.
HEMODYNAMICS IN STENOSED ARTERIES — EFFECTS OF STENOSIS SHAPES
Authors: BANERJEE MOLOY K. , NAG DEBABRATA , GANGULY RANJAN , DATTA AMITAVA
Published: November 2010

A numerical analysis has been carried out to investigate the hemodynamic flow through stenosed arteries having mild (S = 25%) to severe (S = 65%) occlusions and under different regimes of flow Reynolds numbers ( Re ) ranging from 50 to 400. Influence of different stenosis shapes (rectangular, trapezoidal, cosine, and Gaussian) on key hemodynamic parameters e.g., recirculation length, wall shear stress (WSS), pressure drop, and irreversible pressure loss coefficient (C I ) are studied. It has been observed that for S = 25%, no flow separation takes place with cosine and Gaussian shaped stenoses for all the Re values considered, while for rectangular or trapezoidal shapes the flow begins to separate at Re = 400. At higher degrees of stenosis, post-stenotic recirculation is noticed for all the shapes considered — the largest recirculation length being observed with the rectangular shape. The peak centerline velocity in the stenosed region is more sensitive to a change in the degree of occlusion for rectangular stenosis than the other shapes. From the study, it is also revealed that the irreversible pressure loss coefficient (C I ) is the maximum for rectangular shaped stenosis, while it is the least for Gaussian shape. It is observed that at high Re regime, C I becomes insensitive to Re values and can be approximated to be a function of the degree of stenosis (S) and the stenosis shape only.
ADAPTIVE METHOD OF PARTICULAR SOLUTION FOR SOLVING 3D INHOMOGENEOUS ELLIPTIC EQUATIONS
Authors: CHEN C. S. , KWOK T. O. , LING L.
Published: November 2010

Recently, particular solutions using radial basis functions have been used as a basis for solving inhomogeneous partial differential equations as a one-stage approach without the need of finding homogeneous solutions. In this paper, we adopt a newly developed adaptive greedy algorithm to enhance the performance of the one-stage method and alleviate the difficulty of ill-conditioning of the resultant matrix. To demonstrate the effectiveness of coupling these two methods, we give two 3D examples with excellent numerical results.