bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Imaging of Epithelial Cell Scattering Identifies Specific Inhibitors of Cell Motility and Cell-Cell Dissociation
Authors: Loerke Dinah , le Duc Quint , Blonk Iris , Kerstens Andre , Spanjaard Emma , Machacek Matthias , Danuser Gaudenz , de Rooij Johan
Published: July 2012

Imaging analysis tools identify drugs that inhibit different aspects of cell scattering, which occurs in cancer cells.
Perinuclear Mitochondrial Clustering Creates an Oxidant-Rich Nuclear Domain Required for Hypoxia-Induced Transcription
Authors: Al-Mehdi Abu-Bakr , Pastukh Viktor M. , Swiger Brad M. , Reed Darla J. , Patel Mita R. , Bardwell Gina C. , Pastukh Viktoriya V. , Alexeyev Mikhail F. , Gillespie Mark N.
Published: July 2012

Reactive oxygen species generated by mitochondria that redistribute near the nucleus promote transcriptional responses to hypoxia.
Plant Hormone Modulators
Authors: Hines Pamela J.
Published: July 2012

Crystal structures of plant GH3 proteins reveal how these enzymes accommodate jasmonates, auxins, and benzoates.
Stable, But Transcriptionally Inactive
Authors: Gough Nancy R.
Published: July 2012

Phosphorylation-stimulated SUMOylation of the estrogen receptor β prevents receptor degradation but also reduces promoter binding.
The Presence of an
FKS
Mutation Rather than MIC Is an Independent Risk Factor for Failure of Echinocandin Therapy among Patients with Invasive Candidiasis Due to Candida glabrata
Authors: Shields Ryan K. , Nguyen M. Hong , Press Ellen G. , Kwa Andrea L. , Cheng Shaoji , Du Chen , Clancy Cornelius J.
Published: July 2012

Echinocandins are frontline agents against invasive candidiasis (IC), but predictors for echinocandin therapeutic failure have not been well defined. Mutations in
Candida FKS
genes, which encode the enzyme targeted by echinocandins, result in elevated MICs and have been linked to therapeutic failures. In this study, echinocandin MICs by broth microdilution and
FKS1
and
FKS2
mutations among
C. glabrata
isolates recovered from patients with IC at our center were correlated retrospectively with echinocandin therapeutic responses. Thirty-five patients with candidemia and 4 with intra-abdominal abscesses were included, 92% (36/39) of whom received caspofungin. Twenty-six percent (10) and 74% (29) failed and responded to echinocandin therapy, respectively. Caspofungin, anidulafungin, and micafungin MICs ranged from 0.5 to 8, 0.03 to 1, and 0.015 to 0.5 μg/ml, respectively.
FKS
mutations were detected in 18% (7/39) of
C. glabrata
isolates (
FKS1
,
n
= 2;
FKS2
,
n
= 5). Median caspofungin and anidulafungin MICs were higher for patients who failed therapy (
P
= 0.04 and 0.006, respectively). By receiver operating characteristic (ROC) analyses, MIC cutoffs that best predicted failure were >0.5 (caspofungin), >0.06 (anidulafungin), and >0.03 μg/ml (micafungin), for which sensitivity/specificity were 60%/86%, 50%/97%, and 40%/90%, respectively. Sensitivity/specificity of an
FKS
mutation in predicting failure were 60%/97%. By univariate analysis, recent gastrointestinal surgery, prior echinocandin exposure, anidulafungin MIC of >0.06 μg/ml, caspofungin MIC of >0.5 μg/ml, and an
FKS
mutation were significantly associated with failure. The presence of an
FKS
mutation was the only independent risk factor by multivariate analysis (
P
= 0.002). In conclusion, detection of
C. glabrata FKS
mutations was superior to MICs in predicting echinocandin therapeutic responses among patients with IC.
Correlation between Triazole Treatment History and Susceptibility in Clinically Isolated Aspergillus fumigatus
Authors: Tashiro Masato , Izumikawa Koichi , Hirano Katsuji , Ide Shotaro , Mihara Tomo , Hosogaya Naoki , Takazono Takahiro , Morinaga Yoshitomo , Nakamura Shigeki , Kurihara Shintaro , Imamura Yoshifumi , Miyazaki Taiga , Nishino Tomoya , Tsukamoto Misuzu , Kakeya Hiroshi , Yamamoto Yoshihiro , Yanagihara Katsunori , Yasuoka Akira , Tashiro Takayoshi , Kohno Shigeru
Published: July 2012

This is the first report of a detailed relationship between triazole treatment history and triazole MICs for 154
Aspergillus fumigatus
clinical isolates. The duration of itraconazole dosage increased as the itraconazole MIC increased, and a positive correlation was observed (
r
= 0.5700,
P
< 0.0001). The number of itraconazole-naïve isolates dramatically decreased as the itraconazole MIC increased, particularly for MICs exceeding 2 μg/ml (0.5 μg/ml versus 2 μg/ml,
P
= 0.03). We also examined the relationship between cumulative itraconazole usage and the MICs of other azoles. A positive correlation existed between itraconazole dosage period and posaconazole MIC (
r
= 0.5237,
P
< 0.0001). The number of itraconazole-naïve isolates also decreased as the posaconazole MIC increased, particularly for MICs exceeding 0.5 μg/ml (0.25 μg/ml versus 0.5 μg/ml,
P
= 0.004). Conversely, the correlation coefficient obtained from the scattergram of itraconazole usage and voriconazole MICs was small (
r
= −0.2627,
P
= 0.001). Susceptibility to three triazole agents did not change as the duration of voriconazole exposure changed. In addition, we carried out detailed analysis, including microsatellite genotyping, for isolates obtained from patients infected with azole-resistant
A. fumigatus
. We confirmed the presence of acquired resistance to itraconazole and posaconazole due to a G54 substitution in the
cyp51A
gene for a patient with chronic pulmonary aspergillosis after oral itraconazole therapy. We should consider the possible appearance of azole-resistant
A. fumigatus
if itraconazole is used for extended periods.
Multicenter Study of Voriconazole Pharmacokinetics and Therapeutic Drug Monitoring
Authors: Dolton Michael J. , Ray John E. , Chen Sharon C.-A. , Ng Kingsley , Pont Lisa G. , McLachlan Andrew J.
Published: July 2012

Voriconazole is a first-line agent in the treatment of many invasive fungal infections and is known to display highly variable pharmacokinetics. Previous studies of voriconazole therapeutic drug monitoring (TDM) have suggested concentration monitoring to be clinically useful but have been limited by small patient samples at a single institution. This multicenter retrospective study aimed to investigate relationships between voriconazole concentration and clinical outcomes and adverse events and to assess clinical factors and drug interactions that may affect voriconazole concentration. Medical records were reviewed for patients who received voriconazole and had at least 1 concentration measured at seven hospitals in Australia. The study included 201 patients with 783 voriconazole trough concentrations. Voriconazole concentrations of <1.7 mg/liter were associated with a significantly greater incidence of treatment failure (19/74 patients [26%]) than concentrations of ≥1.7 mg/liter (6/89 patients [7%]) (
P
< 0.01). Neurotoxic adverse events (visual and auditory hallucinations) occurred more frequently at voriconazole concentrations of >5 mg/liter (10/31 patients [32%]) than at concentrations of ≤5 mg/liter (2/170 patients [1.2%]) (
P
< 0.01). Multiple regression analysis of voriconazole concentration identified associations between increasing patient weight, oral administration of voriconazole, and coadministration of phenytoin or rifampin and significantly reduced concentrations, and associations between increasing patient age and coadministration of proton pump inhibitors and increased concentrations. Coadministration of glucocorticoids was found to significantly reduce voriconazole concentrations, inferring a previously unreported drug interaction between glucocorticoids and voriconazole.
Optimal Control Strategies for Disinfection of Bacterial Populations with Persister and Susceptible Dynamics
Authors: Cogan N. G. , Brown Jason , Darres Kyle , Petty Katherine
Published: July 2012

It is increasingly clear that bacteria manage to evade killing by antibiotics and antimicrobials in a variety of ways, including mutation, phenotypic variations, and formation of biofilms. With recent advances in understanding the dynamics of the tolerance mechanisms, there have been subsequent advances in understanding how to manipulate the bacterial environments to eradicate the bacteria. This study focuses on using mathematical techniques to find the optimal disinfection strategy to eliminate the bacteria while managing the load of antibiotic that is applied. In this model, the bacterial population is separated into those that are tolerant to the antibiotic and those that are susceptible to disinfection. There are transitions between the two populations whose rates depend on the chemical environment. Our results extend previous mathematical studies to include more realistic methods of applying the disinfectant. The goal is to provide experimentally testable predictions that have been lacking in previous mathematical studies. In particular, we provide the optimal disinfection protocol under a variety of assumptions within the model that can be used to validate or invalidate our simplifying assumptions and the experimental hypotheses that we used to develop the model. We find that constant dosing is not the optimal method for disinfection. Rather, cycling between application and withdrawal of the antibiotic yields the fastest killing of the bacteria.
Influence of Multidrug Resistance and Appropriate Empirical Therapy on the 30-Day Mortality Rate of Pseudomonas aeruginosa Bacteremia
Authors: Morata Laura , Cobos-Trigueros Nazaret , Martínez José A. , Soriano Álex , Almela Manel , Marco Francesc , Sterzik Holguer , Núñez Raquel , Hernández Cristina , Mensa José
Published: July 2012

Infections due to multidrug-resistant (MDR)
Pseudomonas aeruginosa
are increasing. The aim of our study was to evaluate the influences of appropriate empirical antibiotic therapy and multidrug resistance on mortality in patients with bacteremia due to
P. aeruginosa
(PAB). Episodes of PAB were prospectively registered from 2000 to 2008. MDR was considered when the strain was resistant to ≥3 antipseudomonal antibiotics. Univariate and multivariate analyses were performed. A total of 709 episodes of PAB were studied. MDR PAB (
n
= 127 [17.9%]) was more frequently nosocomial and associated with longer hospitalization, bladder catheter use, steroid and antibiotic therapy, receipt of inappropriate empirical antibiotic therapy, and a higher mortality. Factors independently associated with mortality were age (odds ratio [OR], 1.02; 95% confidence interval [CI], 1.002 to 1.033), shock (OR, 6.6; 95% CI, 4 to 10.8), cirrhosis (OR, 3.3; 95% CI, 1.4 to 7.6), intermediate-risk sources (OR, 2.5; 95% CI, 1.4 to 4.3) or high-risk sources (OR, 7.3; 95% CI, 4.1 to 12.9), and inappropriate empirical therapy (OR, 2.1; 95% CI, 1.3 to 3.5). To analyze the interaction between empirical therapy and MDR, a variable combining both was introduced in the multivariate analysis. Inappropriate therapy was significantly associated with higher mortality regardless of the susceptibility pattern, and there was a trend toward higher mortality in patients receiving appropriate therapy for MDR than in those appropriately treated for non-MDR strains (OR, 2.2; 95% CI, 0.9 to 5.4). In 47.9% of MDR PAB episodes, appropriate therapy consisted of monotherapy with amikacin. In conclusion, MDR PAB is associated with a higher mortality than non-MDR PAB. This may be related to a higher rate of inappropriate empirical therapy and probably also to amikacin as frequently the only appropriate empirical therapy given to patients with MDR PAB.
In Vitro
Synergy of Colistin Combinations against Colistin-Resistant Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae Isolates
Authors: Vidaillac Céline , Benichou Lothaire , Duval Raphaël E.
Published: July 2012

Colistin resistance, although uncommon, is increasingly being reported among Gram-negative clinical pathogens, and an understanding of its impact on the activity of antimicrobials is now evolving. We evaluated the potential for synergy of colistin plus trimethoprim, trimethoprim-sulfamethoxazole (1/19 ratio), or vancomycin against 12 isolates of
Acinetobacter baumannii
(
n
= 4),
Pseudomonas aeruginosa
(
n
= 4), and
Klebsiella pneumoniae
(
n
= 4). The strains included six multidrug-resistant clinical isolates,
K. pneumoniae
ATCC 700603,
A. baumannii
ATCC 19606,
P. aeruginosa
ATCC 27853, and their colistin-resistant derivatives (KPm1, ABm1, and PAm1, respectively). Antimicrobial susceptibilities were assessed by broth microdilution and population analysis profiles. The potential for synergy of colistin combinations was evaluated using a checkerboard assay, as well as static time-kill experiments at 0.5× and 0.25× MIC. The MIC ranges of vancomycin, trimethoprim, and trimethoprim-sulfamethoxazole (1/19) were ≥128, 4 to ≥128, and 2/38 to >128/2,432 μg/ml, respectively. Colistin resistance demonstrated little impact on vancomycin, trimethoprim, or trimethoprim-sulfamethoxazole MIC values. Isolates with subpopulations heterogeneously resistant to colistin were observed to various degrees in all tested isolates. In time-kill assays, all tested combinations were synergistic against KPm1 at 0.25× MIC and 0.5× MIC and ABm1 and PAm1 at 0.5× MIC. In contrast, none of the tested combinations demonstrated synergy against any colistin-susceptible
P. aeruginosa
isolates and clinical strains of
K. pneumoniae
isolates. Only colistin plus trimethoprim or trimethoprim-sulfamethoxazole was synergistic and bactericidal at 0.5× MIC against
K. pneumoniae
ATCC 700603. Colistin resistance seems to promote the
in vitro
activity of unconventional colistin combinations. Additional experiments are warranted to understand the clinical significance of these observations.
Mlp24 (McpX) of Vibrio cholerae Implicated in Pathogenicity Functions as a Chemoreceptor for Multiple Amino Acids
Authors: Nishiyama So-ichiro , Suzuki Daisuke , Itoh Yasuaki , Suzuki Kazuho , Tajima Hirotaka , Hyakutake Akihiro , Homma Michio , Butler-Wu Susan M. , Camilli Andrew , Kawagishi Ikuro
Published: July 2012

The chemotaxis of
Vibrio cholerae
, the causative agent of cholera, has been implicated in pathogenicity. The bacterium has more than 40 genes for methyl-accepting chemotaxis protein (MCP)-like proteins (MLPs). In this study, we found that glycine and at least 18
l
-amino acids, including serine, arginine, asparagine, and proline, serve as attractants to the classical biotype strain O395N1. Based on the sequence comparison with
Vibrio parahaemolyticus
, we speculated that at least 17 MLPs of
V. cholerae
may mediate chemotactic responses. Among them, Mlp24 (previously named McpX) is required for the production of cholera toxin upon mouse infection.
mlp24
deletion strains of both classical and El Tor biotypes showed defects in taxis toward several amino acids, which were complemented by the expression of Mlp24. These amino acids enhanced methylation of Mlp24. Serine, arginine, asparagine, and proline were shown to bind directly to the periplasmic fragment of Mlp24. The structural information of its closest homolog, Mlp37, predicts that Mlp24 has two potential ligand-binding pockets per subunit, the membrane distal of which was suggested, by mutational analyses, to be involved in sensing of amino acids. These results suggest that Mlp24 is a chemoreceptor for multiple amino acids, including serine, arginine, and asparagine, which were previously shown to stimulate the expression of several virulence factors, implying that taxis toward a set of amino acids plays critical roles in pathogenicity of
V. cholerae
.
Phosphate Groups of Lipid A Are Essential for Salmonella enterica Serovar Typhimurium Virulence and Affect Innate and Adaptive Immunity
Authors: Kong Qingke , Six David A. , Liu Qing , Gu Lillian , Wang Shifeng , Alamuri Praveen , Raetz Christian R. H. , Curtiss Roy
Published: July 2012

Lipid A is a key component of the outer membrane of Gram-negative bacteria and stimulates proinflammatory responses via the Toll-like receptor 4 (TLR4)-MD2-CD14 pathway. Its endotoxic activity depends on the number and length of acyl chains and its phosphorylation state. In
Salmonella enterica
serovar Typhimurium, removal of the secondary laurate or myristate chain in lipid A results in bacterial attenuation and growth defects
in vitro
. However, the roles of the two lipid A phosphate groups in bacterial virulence and immunogenicity remain unknown. Here, we used an
S
. Typhimurium
msbB pagL pagP lpxR
mutant, carrying penta-acylated lipid A, as the parent strain to construct a series of mutants synthesizing 1-dephosphorylated, 4′-dephosphorylated, or nonphosphorylated penta-acylated lipid A. Dephosphorylated mutants exhibited increased sensitivity to deoxycholate and showed increased resistance to polymyxin B. Removal of both phosphate groups severely attenuated the mutants when administered orally to BALB/c mice, but the mutants colonized the lymphatic tissues and were sufficiently immunogenic to protect the host from challenge with wild-type
S
. Typhimurium. Mice receiving
S
. Typhimurium with 1-dephosphorylated or nonphosphorylated penta-acylated lipid A exhibited reduced levels of cytokines. Attenuated and dephosphorylated
Salmonella
vaccines were able to induce adaptive immunity against heterologous (PspA of
Streptococcus pneumoniae
) and homologous antigens (lipopolysaccharide [LPS] and outer membrane proteins [OMPs]).
A Novel Phage Element of Salmonella enterica Serovar Enteritidis P125109 Contributes to Accelerated Type III Secretion System 2-Dependent Early Inflammation Kinetics in a Mouse Colitis Model
Authors: Vishwakarma Vikalp , Periaswamy Balamurugan , Bhusan Pati Niladri , Slack Emma , Hardt Wolf-Dietrich , Suar Mrutyunjay
Published: July 2012

Salmonella enterica
subsp. I serovar Enteritidis exhibits type III secretion system 2 (TTSS2)-dependent early colonization and inflammation kinetics faster than those of closely related
S. enterica
serovar Typhimurium. To investigate the accelerated TTSS-2-dependent pathogenic potential of
S
. Enteritidis, we focused on its genome. Results of a previously published comparative genomic study revealed the presence of mutually exclusive genes in both serovars. In this study, we investigated the roles of six
S
. Enteritidis-specific genes
in vivo
by using differential fluorescence induction (DFI) through putative gene-specific promoters. The promoter construct associated with the gene locus
SEN1140
induced green fluorescent protein (GFP) expression in the gut lumen, lamina propria, mesenteric lymph nodes, and related systemic organs. To further investigate the potential role of
SEN1140
, we compared a
SEN1140
deletion mutant with
S
. Typhimurium in a TTSS1-deficient background. Interestingly, the
S
. Enteritidis mutant lacking
SEN1140
did not show the unique TTSS-2-dependent early colonization and inflammation kinetic phenotype of
S
. Typhimurium. Consistent with this result, complementation of
SEN1140
restored the TTSS-2-dependent accelerated inflammatory potential of
S
. Enteritidis. This report presents a suitable screening strategy that uses a combination of DFI, fluorescence-activated cell sorting, quantitative PCR, and wild-type isogenic tagged-strain techniques to explore the unique roles of
S
. Enteritidis-specific genes in bacterial pathogenesis.
Dissemination Bottleneck in a Murine Model of Inhalational Anthrax
Authors: Plaut Roger D. , Kelly Vanessa K. , Lee Gloria M. , Stibitz Scott , Merkel Tod J.
Published: July 2012

Inhalational anthrax is caused by the sporulating bacterium
Bacillus anthracis
. A current model for progression in mammalian hosts includes inhalation of bacterial spores, phagocytosis of spores in the nasal mucosa-associated lymphoid tissue (NALT) and lungs by macrophages and dendritic cells, trafficking of phagocytes to draining lymph nodes, germination of spores and multiplication of vegetative bacteria in the NALT and lymph nodes, and dissemination of bacteria via the bloodstream to multiple organs. In previous studies, the kinetics of infection varied greatly among mice, leading us to hypothesize the existence of a bottleneck past which very few spores (perhaps only one) progress to allow the infection to proceed. To test this hypothesis, we engineered three strains of
B. anthracis
Sterne, each marked with a different fluorescent protein, enabling visual differentiation of strains grown on plates. Mice were infected with a mixture of the three strains, the infection was allowed to proceed, and the strains colonizing the organs were identified. Although the inoculum consisted of approximately equal numbers of each of the three strains, the distal organs were consistently colonized by a majority of only one of the three strains, with the dominant strain varying among animals. Such dominance of one strain over the other two was also found at early time points in the cervical lymph nodes but not in the mediastinal lymph nodes. These results support the existence of a bottleneck in the infectious process.
An unusual radiological presentation of pulmonary Langerhans’ cell histiocytosis
Authors: Burr Lucy , Fanning Steven , Wong David , Bowler Simon
Published: July 2012

Langerhans’ cell histiocytosis is a proliferative disease of the dendritic cell lineage. It usually has a characteristic radiological presentation of apical nodules and small cysts occurring predominantly in young adult smokers. Here we report a case of multisystem Langerhans cell histiocytosis in a 75-year-old woman with unusual chest radiology.
Environmental pathways of potential impacts to human health from oil and gas development in northeast British Columbia, Canada
Authors: Krzyzanowski Judi
Published: July 2012

Concerns have arisen recently as to whether the upstream oil and gas (UOG) sector — responsible for exploration, production, and some processing of raw fossil fuels — is negatively impacting human (and environmental) health in northeast British Columbia (NEBC). The region has experienced increased rates of cancers and other illnesses that have been linked to the contaminants and stressors associated with UOG. Contaminants reach human receptors through environmental pathways, namely air, soil, water, and food. Each contaminant or stressor has specific sources, transport, exposure mechanisms, and biochemistry; and each can impact health both directly and indirectly. Of particular concern are airborne sulphur and nitrogen oxides, hazardous volatile organic compounds, hydrogen sulphide, ozone, noise, and radiation; as well as soil- or water-borne hydrocarbons, heavy metals, and radiation — some of which can also impact human health through food pathways. It has been determined that UOG is negatively impacting human health in NEBC; however, further information, such as environmental monitoring, is required before the actual health risks and impacts posed by UOG can be quantified.
Singing sands, booming dune sands, and the stick–slip effect
Authors: Patitsas A.J.
Published: July 2012

The origin of the acoustic and seismic emissions from impacted singing grains and from avalanching dune sand grains is sought in modes of vibration in discreet grain columns. It is postulated that when the grains in a column are pressed together and forced to slide over one another, elastic shear bands are formed at the contact areas with distinct elastic moduli. Such contact shear bands would have implications in the formulation of the Hertz–Mindlin contact theory. The assembly of all grain columns below the impacting pestle forms the slip (slide) shear band. The transfer of energy from the pestle to the modes of vibration in such columns is effected by the stick–slip effect. The intense collective vibration of all columns in the slip shear band results in the familiar musical sound. The concept of grain flowability is used to justify the disparity between the acoustic emissions from impacted singing grains and from avalanching booming dune sand grains. The concept of grain columns is assumed to apply in the freely avalanching sand band, but with longer length to justify the lower frequencies. This approach predicts frequency spectra comprising a low-frequency content and a dominant frequency with its harmonics in agreement with the experimental evidence. Additionally, it can account for the low-frequency vibration evoked when booming sand flows through a funnel, with implications in the understanding of grain silo vibrations. It is argued that sand grains do not sing or boom because the stick–slip effect in not applicable in the contact shear bands.
Electric field induced crossings of energy terms of a Rydberg quasi molecule enhancing charge exchange and ionization
Authors: Kryukov N. , Oks E.
Published: July 2012

Charge exchange is one of the most important atomic processes in plasmas. Charge exchange and crossings of corresponding energy levels that enhance charge exchange are strongly connected with problems of energy losses and of diagnostics in high temperature plasmas. Charge exchange was also proposed as an effective mechanism for population inversion in the soft X-ray and vacuum ultraviolet ranges. One of the most fundamental theoretical domains for studying charge exchange is the problem of electron terms in the field of two stationary Coulomb centers (TCC) of charges Z and Z′ separated by a distance R. It presents an intriguing atomic physics: the terms can have crossings and quasi crossings. These intrinsic features of the TCC problem also manifest in different areas of physics, such as plasma spectroscopy: a quasi crossing of the TCC terms, by enhancing charge exchange, can result in an unusual structure (a dip) in the spectral line profile emitted by a Z-ion from a plasma consisting of both Z- and Z′-ions, as was shown theoretically and experimentally. Before the year 2000, the paradigm was that the preceding sophisticated features of the TCC problem and its flourishing applications were inherently quantum phenomena. In 2000, a purely classical description of the crossings of energy terms was presented. In the present paper we study the effect of an electric field (along the internuclear axis) on circular Rydberg states of the TCC system. We provide analytical results for strong fields, as well as numerical results for moderate fields. We show that the electric field has several effects. First, it leads to the appearance of an extra energy term: the fourth classical energy term — in addition to the three classical energy terms at zero field. Second, but more importantly, the electric field creates additional crossings of these energy terms. We show that some of these crossings significantly enhance charge exchange, while other crossings enhance the ionization of the Rydberg quasi molecule.
SELF-STABILIZING MASTER–SLAVE TOKEN CIRCULATION AND EFFICIENT SIZE-COMPUTATION IN A UNIDIRECTIONAL RING OF ARBITRARY SIZE
Authors: GODDARD WAYNE , SRIMANI PRADIP K.
Published: July 2012

Self-stabilizing algorithms represent an extension of distributed algorithms in which nodes of the network have neither coordination, synchronization, nor initialization. We consider the model where there is one designated master node and all other nodes are anonymous and have constant space. Recently, Lee et al. obtained such an algorithm for determining the size of a unidirectional ring. We provide a new algorithm that converges much quicker. This algorithm exploits a token-circulation idea due to Afek and Brown. Disregarding the time for stabilization, our algorithm computes the size of the ring at the master node in O(n log n) time compared to O(n3) steps used in the algorithm by Lee et al. We have also shown that the master node, after determining the size of the ring, can compute the average of observations made at each node in O(n) rounds or O(n2) steps. It seems likely that one should be able to obtain master–slave algorithms for other problems in networks.
PERFORMANCE ANALYSIS AND EVALUATION OF RANDOM WALK ALGORITHMS ON WIRELESS NETWORKS
Authors: LI KEQIN
Published: July 2012

We propose a model of dynamically evolving random networks and give an analytical result of the cover time of the simple random walk algorithm on a dynamic random symmetric planar point graph. Our dynamic network model considers random node distribution and random node mobility. We analyze the cover time of the parallel random walk algorithm on a complete network and show by numerical data that k parallel random walks reduce the cover time by almost a factor of k. We present simulation results for four random walk algorithms on random asymmetric planar point graphs. These algorithms include the simple random walk algorithm, the intelligent random walk algorithm, the parallel random walk algorithm, and the parallel intelligent random walk algorithm. Our random network model considers random node distribution and random battery transmission power. Performance measures include normalized cover time, probability distribution of the length of random walks, and load distribution.
AN ADAPTIVE RANDOM WALK BASED DISTRIBUTED CLUSTERING ALGORITHM
Authors: BUI ALAIN , KUDIRETI ABDURUSUL , SOHIER DEVAN
Published: July 2012

In this paper, we present a fully distributed random walk based clustering algorithm intended to work on dynamic networks of arbitrary topologies.

A bounded-size core is built through a random walks based procedure. Its neighboring nodes that do not belong to any cluster are recruited by the core as ordinary nodes. Using cores allow us to formulate constraints on the clustering and fulfill them on any topology.

The correctness and termination of our algorithm are proven. We also prove that when two clusters are adjacent, at least one of them has a complete core (i.e. a core with the maximum size allowed by the parameter).

One of the important advantages of our mobility-adaptive algorithm is that the re-clustering is local: the management of the connections or disconnections of links and reorganization of nodes affect only the clusters in which they are, possibly adjacent clusters, and at worst, the ordinary nodes of the clusters adjacent to the neighboring clusters. This allows us to bound the diameter of the portion of the network that is affected by a topological change.
MODELING AND ANALYSIS OF REAL-TIME SYSTEMS WITH MUTEX COMPONENTS
Authors: LI GUOQIANG , CAI XIAOJUAN , YUEN SHOJI
Published: July 2012

Timed automata are commonly recognized as a formal behavioral model for real-time systems. For compositional system design, parallel composition of timed automata as proposed by Larsen et al. [22] is useful. Although parallel composition provides a general method for system construction, in the low level behavior, components often behave sequentially by passing control via communication. This paper proposes a behavioral model, named controller automata, to combine timed automata by focusing on the control passing between components. In a controller automaton, to each state a timed automaton is assigned. A timed automaton at a state may be preempted by the control passing to another state by a global labeled transition. A controller automaton properly extends the expressive power because of the stack, but this can make the reachability problem undecidable. Given a strict partial order over states, we show that this problem can be avoided and a controller automaton can be faithfully translated into a timed automaton.
A PARALLEL ALGORITHM FOR THE CONSTRAINED MULTIPLE SEQUENCE ALIGNMENT PROBLEM DESIGNED FOR GPUs
Authors: GUDYŚ ADAM , DEOROWICZ SEBASTIAN
Published: July 2012

Multiple sequence alignment (MSA) is one of the most important problems in computational biology. As availability of genomic and proteomic data constantly increases, new tools for processing this data in reasonable time are needed. One method of addressing this issue is parallelization. Nowadays, graphical processing units offer much more computational power than central processors, hence GPUs become more and more popular in computational-intensive tasks, including sequence alignment. We investigate the constrained multiple sequence alignment problem (CMSA) which allows some prior knowledge to be introduced to a final alignment. As a result we propose a GPU-parallel version of the Center Star algorithm which overtakes vastly its CPU-serial equivalent as well as the parallel version run on the quad-core processor. The speedups over CPU-serial algorithm were from 30 to 110 in the case of synthetic sets and from 55 to 75 for the real sequences obtained from the Pfam database.
TIME-SHIFT IN THE OPERA SETUP: PROOF AGAINST SUPERLUMINAL NEUTRINOS WITHOUT THE NEED OF KNOWING THE CERN–LNGS DISTANCE AND REMINISCENCES ON THE ORIGIN OF THE GRAN SASSO LAB, OF THE THIRD NEUTRINO AND OF THE "TERAMO ANOMALY"
Authors: ZICHICHI ANTONINO
Published: July 2012

The LVD time stability allows one to establish a time-shift in the OPERA experiment, thus providing the first proof against superluminal neutrinos, using the horizontal muons of the "Teramo Anomaly." This proof is particularly interesting since it does not need the knowledge of the distance between the location at which the neutrinos are produced (CERN) and the location they are detected (LNGS). Since the superluminal neutrinos generated in the physics community a vivid interest in good and bad behavior in physics research, the author thought it was appropriate to recall the origin of the Gran Sasso Lab, of the third neutrino, of the horizontal muons due to the "Teramo Anomaly" and of the oscillation between leptonic flavors, when the CERN–Gran Sasso neutrino beam was included in the project for the most powerful underground laboratory in the world.
DYNAMIC MANAGEMENT OF MULTIPLE CLASSIFIERS IN COMPLEX RECOGNITION SYSTEM
Authors: LIU HUI-MIN , WANG PATRICK , WANG HONG-QIANG , LI XIANG
Published: July 2012

There are different kinds of multiple classifiers in complex recognition systems in pursuit of better recognition capabilities. To exploit the classifiers' potential as individual ones sufficiently and enable them to work cooperatively for the best classification results, they need to be considered as a whole and be dynamically managed according to the changing recognition occasions. In this paper, we present the conception of distributed Multiple Classifiers Management (MCM) and a self-adaptive recursive MCM model based on Mixture-of-Experts (ME). A control subsystem is consisted in the model, which allows the classification progress to be controlled by the systems' priori information when necessary. The model adjusts its parameters dynamically according to the current recognition state and gives the recognition results by combining the current individual classifiers' results with the previous combination result under priori information's control. An algorithm based on one step error correction is presented to acquire the model's parameters dynamically. It takes the previous times' ensemble classification results as true and corrects the current weights of the classifiers. At last, an experiment on the recognition of space objects is simulated. The experiment results show that the MCM model in this paper is effective for complex recognition system containing heterogeneous classifiers on improving the recognition rate and robustness.
DESIGN AND OPTIMIZATION OF SINGLE AND MULTIPLE-LOOP REVERSIBLE AND QUANTUM FEEDBACK CIRCUITS
Authors: MOHAMMADI MAJID , NIKNAFS ALIAKBAR , ESHGHI MOHAMMAD , DUECK GERHARD W.
Published: July 2012

The majority of work in reversible logic circuits has been limited to combinational logic. Researchers are now beginning to suggest designs for sequential circuits. In this paper we propose a new method to design and optimize feedback reversible logic circuits and a specific group of quantum logic circuits based on the reversible state transition table and genetic algorithms (GA). To show the efficiency of the proposed method, some reversible sequential elements such as D and T flip-flops (FFs), with and without clock and reset, and edge triggered FFs are designed. We have also extended our method to multiple loop feedback circuits. The proposed circuits are highly optimized using a GA synthesis tool that allows don't care values. Some of the designs in this paper are presented in other papers; however, the comparisons show that the quantum cost and number of garbage inputs/outputs are reduced efficiently by our method.
HANDLING EDGE LISTS IN 2D VECTOR GRAPHICS HARDWARE
Authors: SEO SANG-WOO , SHEN YONG-LUO , KIM KWAN-YOUNG , OH HYEONG-CHEOL
Published: July 2012

In rendering two-dimensional (2D) vector graphics, edge lists are often so large that their handling hinders the desired operation of portable devices. This paper proposes and evaluates an efficient edge-list handling method for a 2D vector graphics hardware accelerator. The proposed method selects edges that span the next scanline from among those spanning the current scanline and stores them in a small list in the internal memory. An edge list is assigned to each scanline and it stores only those edges that have not appeared in previous edge lists. Given that most active edges span only a few scanlines, the internal list can be small and implemented in the accelerator, whereas the edge lists are held in the external memory. Experimental results show that the proposed method can reduce external memory access by 23.4%–76.6% for the benchmark images considered compared to the prior methods.
HIGH-GAIN/EFFICIENCY MULTISTAGE SWITCHED-CAPACITOR-VOLTAGE-MULTIPLIER DC–DC CONVERTER
Authors: CHANG YUEN-HAW
Published: July 2012

A closed-loop interleaved multistage switched-capacitor-voltage-multiplier (mc × nc-stage SCVM) dc–dc converter is proposed by combining a variable-conversion-ratio (VCR) and pulse-width-modulation (PWM) control for low-power step-up conversion and high-efficiency regulation. In this SCVM, the power part is composed of two mc-stage SC cells (front) and two nc-stage SC cells (rear) in cascade, and these cells are operated by two-phase nonoverlapping clocks for an interleaved operation with voltage gain of mc × nc at most. This paper presents the VCR control to change the running stage number m,n and topological path for a more flexible and suitable gain level m × n (1 × 1, 2 × 1, 2 × 2, 3 × 1, 3 × 2, 3 × 3,…, mc × nc) according to the desired output so as to improve power efficiency, especially for the lower output. Besides, PWM is adopted not only to enhance output regulation for different outputs, but also to reinforce output robustness to source/loading variation. Further, some theoretical analysis and design include: SCVM model, steady-state analysis, conversion ratio, power efficiency, output ripple, stability, capacitance selection, and control design. Finally, the closed-loop SCVM is simulated, and the hardware is implemented and tested. All the results are illustrated to show the efficacy of the proposed scheme.
FLIPPED VOLTAGE FOLLOWER ANALOG NONLINEAR CIRCUITS
Authors: SAKUL CHAIWAT , DEJHAN KOBCHAI
Published: July 2012

This paper describes squaring and square-rooting circuits operable on low voltage supplies, with their application proposed hereby as vector-summation and four-quadrant multiplier circuits. These circuits make use of a flipped voltage follower (FVF) as fundamental circuit. A detail classification of basic topologies derived from the FVF is given. The proposed circuits have simple structure, wide input range and low power consumption as well as small number of devices. All circuits are also examined and supported by a set of simulations with PSpice program. The circuits can operate at power supply of ±0.7 volts, the input voltage range of the squaring circuit is ±0.8 volts with 1.59% relative error and 1.78 μW power dispersion, the input current of the square-rooting circuit is about 50 μA with 0.55% relative error and 1.4 μW power dispersion and the vector-summation circuit have linearity error of 0.23% and 2.92 μW power dispersion. As in four-quadrant multiplier circuit, the total harmonic distortion of the multiplier is less than 1.2% for 0.8 VP-P input signal at 1 MHz fundamental frequency. Experimental result is carried out to confirm the operation by using commercial CMOS transistor arrays (CD4007). These circuits are highly expected to be effective in further application of the low voltage analog signal processing.
PATHOLOGICAL REALIZATIONS OF BOTA AND FDDTA USING GROUNDED RESISTORS
Authors: SOLIMAN AHMED M.
Published: July 2012

Sixteen pathological realizations of the balanced output transconductance amplifier (BOTA) using four grounded G are generated. Each of these circuits is realizable using four current conveyors (CCII) or four inverting current conveyors (ICCII) or a combination of four CCII and ICCII. Six new pathological realizations of the BOTA using two grounded G based on current subtraction are introduced. Four new pathological realizations of the BOTA using two grounded G based on voltage subtraction are introduced. Several new pathological realizations of the FDDTA as a voltage subtraction stage and a BOTA stage are also given. Simulation results are included.
THERMODYNAMICS OF A SCHWARZSCHILD BLACK HOLE IN PHANTOM COSMOLOGY WITH ENTROPY CORRECTIONS
Authors: JAMIL MUBASHER , MOMENI D. , BAMBA KAZUHARU , MYRZAKULOV RATBAY
Published: July 2012

Motivated by some earlier works [G. Izquierdo and D. Pavon, Phys. Lett. B 639 (2006) 1; H. M. Sadjadi, Phys. Lett. B 645 (2007) 108.] dealing with the study of generalized second law (GSL) of thermodynamics for a system comprising of a Schwarzschild black hole accreting a test nonself-gravitating fluid namely phantom energy in FRW universe, we extend them when the entropy of horizons of black hole and the cosmological undergo quantum corrections. Two types of such corrections are relevant here including logarithmic and power-law, while both are motivated from different theoretical backgrounds. We obtain general mathematical conditions for the validity of GSL in each case. Further we find that GSL restricts the mass of black hole for accretion of phantom energy. As such we obtain upper bounds on the mass of black hole above which the black hole cannot accrete the phantom fluid, otherwise the GSL is violated.
INFLUENCE OF SURFACTANTS ON THE CORROSION PROPERTIES OF CHROMIUM-FREE ELECTROLESS NICKEL DEPOSIT ON MAGNESIUM ALLOY
Authors: SUDAGAR JOTHI , DEWEN RUAN , LIANG YAQIN , ELANSEZHIAN RASU , LIAN JIANSHE
Published: July 2012

Influence of surfactants on the corrosion properties of chromium-free electroless nickel deposit were investigated on AZ91D magnesium alloy. The corrosion tests were carried out by immersion test (1 M HCl) and electrochemical polarization test (3.5 wt% NaCl ). The surfactants in the electroless nickel bath increases the corrosion resistance properties of the deposit on the magnesium alloy. In addition, smoothness and amorphous plus nano-crystalline phase were increased and accounted for the significant corrosion resistance. As a consequence, the corrosion potential moved towards the positive direction and the corrosion current density decreased. The immersion tests also provided the same trend as that of electrochemical polarization test. On the whole, the study concluded that corrosion resistance was enhanced by including a surfactant in the electroless deposits on magnesium alloy.
GROWTH MECHANISM OF RING SHAPED NANOSTRUCTURES SELF-ASSEMBLY UPON DROPLET EPITAXY
Authors: TAN X. , ZHONG J. X. , YANG G. W.
Published: July 2012

A quantitatively kinetic model has been established to address the self-assembly of the ring shaped nanostructures upon the droplet epitaxy via kinetic Monte Carlo simulations. The theoretical predictions about the temperature and As flux dependences of the self-assembly of the ring shaped nanostructures were in well agreement with recent experiments. It was found that the morphological evolution of the ring shaped nanostructures was attributed to the cooperation of the enhanced diffusion barriers of free Ga atoms in the inner ring region and the effects of the surface reconstruction around the Ga droplets during the arsenization step.
STUDY ON IFD CALCULATED THEORY AND NATURE OF TRUE COLOR IMAGE
Authors: LI Y. X. , GAO M. Z. , ZHU Z. M. , QI L.
Published: July 2012

In this paper, a new calculated method of image fractal dimension (IFD) of true color image has been presented in order to solve the problem that laser scanning profilimeter, applied to measuring fractal characteristic of rough surface, has too small scanning field to obtain three-dimensional coordinates of larger area surface. The method can also characterize indirectly surface profile by quantifying roughness of true color surface built in terms of connecting endpoint of the vector with three components of red, green and blue. The correctness and feasibility of the IFD method have been verified by scanning test on rough surface using larger-scale laser profilimeter. Comparison between conventional dimension theory presented in previous study and IFD proposed in the paper has shown that IFD method has the advantage of simplification, convenience and large scanning capacity, and is progressing in the field of surface configuration investigation. Furthermore, fractal characteristic of binary image, grey-scale image as well as true color image is researched to probe their physical nature. Comparison among IFD of three kinds of image implies that, IFD of true color image is largest, IFD of grey-scale image is second largest, and IFD of binary image varying within the range of 1–2 is the smallest. From the phenomena, it is indicated that: (i) IFD of binary image is dimension of curved line; (ii) for IFD of grey-scale image, only effect of luminance is considered; (iii) for IFD of true color image, contribution of hue, saturation and luminance is sufficiently considered, and therefore it is just "complete" IFD.
ON THE NEWTON–KANTOROVICH THEOREM
Authors: CIARLET PHILIPPE G. , MARDARE CRISTINEL
Published: July 2012

The Newton–Kantorovich theorem enjoys a special status, as it is both a fundamental result in Numerical Analysis, e.g., for providing an iterative method for computing the zeros of polynomials or of systems of nonlinear equations, and a fundamental result in Nonlinear Functional Analysis, e.g., for establishing that a nonlinear equation in an infinite-dimensional function space has a solution. Yet its detailed proof in full generality is not easy to locate in the literature.

The purpose of this article, which is partly expository in nature, is to carefully revisit this theorem, by means of a two-tier approach.

First, we give a detailed, and essentially self-contained, account of the classical proof of this theorem, which essentially relies on careful estimates based on the integral form of the mean value theorem for functions of class [Formula: see text] with values in a Banach space, and on the so-called majorant method. Our treatment also includes a careful discussion of the often overlooked uniqueness issue. An example of a nonlinear two-point boundary value problem is also given that illustrates the power of this theorem for establishing an existence theorem when other methods of nonlinear functional analysis cannot be used.

Second, we give a new version of this theorem, the assumptions of which involve only one constant instead of three constants in its classical version and the proof of which is substantially simpler as it altogether avoids the majorant method. For these reasons, this new version, which captures all the basic features of the classical version could be considered as a good alternative to the classical Newton–Kantorovich theorem.