bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative PCR Method for Sensitive Detection of Ruminant Fecal Pollution in Freshwater and Evaluation of This Method in Alpine Karstic Regions
Authors: Reischer Georg H. , Kasper David C. , Steinborn Ralf , Mach Robert L. , Farnleitner Andreas H.
Published: August 2006

A quantitative TaqMan minor-groove binder real-time PCR assay was developed for the sensitive detection of a ruminant-specific genetic marker in fecal members of the phylum
Bacteroidetes
. The qualitative and quantitative detection limits determined were 6 and 20 marker copies per PCR, respectively. Tested ruminant feces contained an average of 4.1 × 10
9
marker equivalents per g, allowing the detection of 1.7 ng of feces per filter in fecal suspensions. The marker was detected in water samples from a karstic catchment area at levels matching a gradient from negligible to considerable ruminant fecal influence (from not detectable to 10
5
marker equivalents per liter).
Identification of a Gene Cluster for Biosynthesis of Mannosylerythritol Lipids in the Basidiomycetous Fungus
Ustilago maydis
Authors: Hewald Sandra , Linne Uwe , Scherer Mario , Marahiel Mohamed A. , Kämper Jörg , Bölker Michael
Published: August 2006

Many microorganisms produce surface-active substances that enhance the availability of water-insoluble substrates. Although many of these biosurfactants have interesting potential applications, very little is known about their biosynthesis. The basidiomycetous fungus
Ustilago maydis
secretes large amounts of mannosylerythritol lipids (MELs) under conditions of nitrogen starvation. We recently described a putative glycosyltransferase, Emt1, which is essential for MEL biosynthesis and whose expression is strongly induced by nitrogen limitation. We used DNA microarray analysis to identify additional genes involved in MEL biosynthesis. Here we show that
emt1
is part of a gene cluster which comprises five open reading frames. Three of the newly identified proteins, Mac1, Mac2, and Mat1, contain short sequence motifs characteristic for acyl- and acetyltransferases. Mutational analysis revealed that Mac1 and Mac2 are essential for MEL production, which suggests that they are involved in the acylation of mannosylerythritol. Deletion of
mat1
resulted in the secretion of completely deacetylated MELs, as determined by mass spectrometry. We overexpressed Mat1 in
Escherichia coli
and demonstrated that this enzyme acts as an acetyl coenzyme A-dependent acetyltransferase. Remarkably, Mat1 displays relaxed regioselectivity and is able to acetylate mannosylerythritol at both the C-4 and C-6 hydroxyl groups. Based on these results, we propose a biosynthesis pathway for the generation of mannosylerythritol lipids in
U. maydis
.
Resolution of Distinct Membrane-Bound Enzymes fromEnterobacter cloacaeSLD1a-1 That Are Responsible for Selective Reduction of Nitrate and Selenate Oxyanions
Authors: Ridley Helen , Watts Carys A. , Richardson David J. , Butler Clive S.
Published: August 2006

Enterobacter cloacaeSLD1a-1 is capable of reductive detoxification of selenate to elemental selenium under aerobic growth conditions. The initial reductive step is the two-electron reduction of selenate to selenite and is catalyzed by a molybdenum-dependent enzyme demonstrated previously to be located in the cytoplasmic membrane, with its active site facing the periplasmic compartment (C. A. Watts, H. Ridley, K. L. Condie, J. T. Leaver, D. J. Richardson, and C. S. Butler, FEMS Microbiol. Lett.228:273-279, 2003). This study describes the purification of two distinct membrane-bound enzymes that reduce either nitrate or selenate oxyanions. The nitrate reductase is typical of the NAR-type family, with α and β subunits of 140 kDa and 58 kDa, respectively. It is expressed predominantly under anaerobic conditions in the presence of nitrate, and while it readily reduces chlorate, it displays no selenate reductase activity in vitro. The selenate reductase is expressed under aerobic conditions and expressed poorly during anaerobic growth on nitrate. The enzyme is a heterotrimeric (αβγ) complex with an apparent molecular mass of ∼600 kDa. The individual subunit sizes are ∼100 kDa (α), ∼55 kDa (β), and ∼36 kDa (γ), with a predicted overall subunit composition of α3β3γ3. The selenate reductase contains molybdenum, heme, and nonheme iron as prosthetic constituents. Electronic absorption spectroscopy reveals the presence of ab-type cytochrome in the active complex. The apparentKmfor selenate was determined to be ∼2 mM, with an observedVmaxof 500 nmol SeO42−min−1mg−1(kcat, ∼5.0 s−1). The enzyme also displays activity towards chlorate and bromate but has no nitrate reductase activity. These studies report the first purification and characterization of a membrane-bound selenate reductase.
Characterization of the β-Ketoadipate Pathway inSinorhizobium meliloti
Authors: MacLean Allyson M. , MacPherson Gordon , Aneja Punita , Finan Turlough M.
Published: August 2006

Aromatic compounds represent an important source of energy for soil-dwelling organisms. The β-ketoadipate pathway is a key metabolic pathway involved in the catabolism of the aromatic compounds protocatechuate and catechol, and here we show through enzymatic analysis and mutant analysis that genes required for growth and catabolism of protocatechuate in the soil-dwelling bacteriumSinorhizobium melilotiare organized on the pSymB megaplasmid in two transcriptional units designatedpcaDCHGBandpcaIJF. ThepcaDpromoter was mapped by primer extension, and expression from this promoter is demonstrated to be regulated by the LysR-type protein PcaQ. β-Ketoadipate succinyl-coenzyme A (CoA) transferase activity inS. melilotiwas shown to be encoded by SMb20587 and SMb20588, and these genes have been renamedpcaIandpcaJ, respectively. These genes are organized in an operon with a putative β-ketoadipyl-CoA thiolase gene (pcaF), and expression of thepcaIJFoperon is shown to be regulated by an IclR-type transcriptional regulator, SMb20586, which we have namedpcaR. We show thatpcaRtranscription is negatively autoregulated and that PcaR is a positive regulator ofpcaIJFexpression and is required for growth ofS. melilotion protocatechuate as the carbon source. The characterization of the protocatechuate catabolic pathway inS. melilotioffers an opportunity for comparison with related species, includingAgrobacterium tumefaciens. Differences observed betweenS. melilotiandA. tumefaciens pcaIJoffer the first evidence ofpcagenes that may have been acquired after speciation in these closely related species.
Molecular Epidemiologic Investigation of
Campylobacter coli
in Swine Production Systems, Using Multilocus Sequence Typing
Authors: Thakur Siddhartha , Morrow W. E. Morgan , Funk Julie A. , Bahnson Peter B. , Gebreyes Wondwossen A.
Published: August 2006

Multilocus sequence typing of 151
Campylobacter coli
isolates from swine reared in conventional (
n
= 74) and antimicrobial-free (
n
= 77) production systems revealed high genotypic diversity. Sequence type (ST) 1413 was predominant and observed among ciprofloxacin-resistant strains. We identified a
C. coli
ST 828 clonal complex consisting of isolates from both production systems.
Improvement of Lactic Acid Production in
Saccharomyces cerevisiae
by Cell Sorting for High Intracellular pH
Authors: Valli Minoska , Sauer Michael , Branduardi Paola , Borth Nicole , Porro Danilo , Mattanovich Diethard
Published: August 2006

Yeast strains expressing heterologous
l
-lactate dehydrogenases can produce lactic acid. Although these microorganisms are tolerant of acidic environments, it is known that at low pH, lactic acid exerts a high level of stress on the cells. In the present study we analyzed intracellular pH (pH
i
) and viability by staining with cSNARF-4F and ethidium bromide, respectively, of two lactic-acid-producing strains of
Saccharomyces cerevisiae
, CEN.PK m850 and CEN.PK RWB876. The results showed that the strain producing more lactic acid, CEN.PK m850, has a higher pH
i
. During batch culture, we observed in both strains a reduction of the mean pH
i
and the appearance of a subpopulation of cells with low pH
i
. Simultaneous analysis of pH
i
and viability proved that the cells with low pH
i
were dead. Based on the observation that the better lactic-acid-producing strain had a higher pH
i
and that the cells with low pH
i
were dead, we hypothesized that we might find better lactic acid producers by screening for cells within the highest pH
i
range. The screening was performed on UV-mutagenized populations through three consecutive rounds of cell sorting in which only the viable cells within the highest pH
i
range were selected. The results showed that lactic acid production was significantly improved in the majority of the mutants obtained compared to the parental strains. The best lactic-acid-producing strain was identified within the screening of CEN.PK m850 mutants.
Isolation, Characterization, and Ecology of Cold-Active, Chemolithotrophic, Sulfur-Oxidizing Bacteria from Perennially Ice-Covered Lake Fryxell, Antarctica
Authors: Sattley W. Matthew , Madigan Michael T.
Published: August 2006

Novel strains of obligately chemolithoautotrophic, sulfur-oxidizing bacteria have been isolated from various depths of Lake Fryxell, Antarctica. Physiological, morphological, and phylogenetic analyses showed these strains to be related to mesophilic
Thiobacillus
species, such as
T. thioparus
. However, the psychrotolerant Antarctic isolates showed an adaptation to cold temperatures and thus should be active in the nearly freezing waters of the lake. Enumeration by most-probable-number analysis in an oxic, thiosulfate-containing medium revealed that the sulfur-oxidizing chemolithotroph population peaks precisely at the oxycline (9.5 m), although viable cells exist well into the anoxic, sulfidic waters of the lake. The sulfur-oxidizing bacteria described here likely play a key role in the biogeochemical cycling of carbon and sulfur in Lake Fryxell.
Unlocking
Streptomyces
spp. for Use as Sustainable Industrial Production Platforms by Morphological Engineering
Authors: van Wezel Gilles P. , Krabben Preben , Traag Bjørn A. , Keijser Bart J. F. , Kerste Rob , Vijgenboom Erik , Heijnen Josef J. , Kraal Barend
Published: August 2006

Filamentous actinomycetes are commercially widely used as producers of natural products (in particular antibiotics) and of industrial enzymes. However, the mycelial lifestyle of actinomycetes, resulting in highly viscous broths and unfavorable pellet formation, has been a major bottleneck in their commercialization. Here we describe the successful morphological engineering of industrially important streptomycetes through controlled expression of the morphogene
ssgA
. This led to improved growth of many industrial and reference streptomycetes, with fragmentation of the mycelial clumps resulting in significantly enhanced growth rates in batch fermentations of
Streptomyces coelicolor
and
Streptomyces lividans
. Product formation was also stimulated, with a twofold increase in yield of enzyme production by
S. lividans
. We anticipate that the use of the presented methodology will make actinomycetes significantly more attractive as industrial and sustainable production hosts.
Temporal Expression of Respiratory Genes in an Enrichment Culture Containing
Dehalococcoides ethenogenes
Authors: Rahm Brian G. , Morris Robert M. , Richardson Ruth E.
Published: August 2006

Multiple reductive dehalogenase (RDase), hydrogenase (H
2
ase), and other respiration-associated (RA) oxidoreductase genes have been identified in cultured representatives of
Dehalococcoides
. Although their products are likely to play key roles in the environmentally important process of reductive dechlorination, very little information is available about their regulation and specific functions. Here we show increased expression and temporal variability in the expression of five RDase genes and in the expression of genes for a putative formate dehydrogenase (Fdh) and two H
2
ases, including a periplasmic [Ni/Fe] H
2
ase (Hup) and a cytoplasmic [Fe] H
2
ase (Vhu). mRNA transcripts extracted from tetrachloroethene-dechlorinating mixed cultures corresponding to Fdh, the H
2
ase Hup, and the RDase targets TceA and DET0162 were expressed most highly, with average levels 34 (± 7.5)-, 23 (± 6.7)-, 16 (± 3.3)-, and 13 (± 3.3)-fold higher, respectively, than that for RNA polymerase (RpoB). H
2
ase and RA transcripts reached their respective expression maxima within the first 2 h after feeding. RDase transcripts, however, were most highly expressed after 3 h and exhibited greater temporal variability than other transcripts. Comparison with
D. ethenogenes
strain 195 pure culture expression levels indicated that RDase DET1545 was more highly expressed in mixed cultures, where, on average, its transcript level was sixfold higher than that of RpoB. While the specific functions of several of these gene products remain elusive, the high expression levels and temporal variability reported here suggest that these groups of enzymes are metabolically important for the respiration of chlorinated ethenes in mixed cultures containing
Dehalococcoides
.
Virus-Bacterium Interactions in Water and Sediment of West African Inland Aquatic Systems
Authors: Bettarel Yvan , Bouvy Marc , Dumont Claire , Sime-Ngando Télesphore
Published: August 2006

The ecology of virioplankton in tropical aquatic ecosystems is poorly documented, and in particular, there are no references concerning African continental waters in the literature. In this study, we examined virus-bacterium interactions in the pelagic and benthic zones of seven contrasting shallow inland waters in Senegal, including one hypersaline lake. SYBR Gold-stained samples revealed that in the surface layers of the sites, the numbers of viruses were in the same range as the numbers of viruses reported previously for productive temperate systems. Despite high bacterial production rates, the percentages of visibly infected cells (as determined by transmission electron microscopy) were similar to the lowest percentages (range, 0.3 to 1.1%; mean, 0.5%) found previously at pelagic freshwater or marine sites, presumably because of the local environmental and climatic conditions. Since the percentages of lysogenic bacteria were consistently less than 8% for pelagic and benthic samples, lysogeny did not appear to be a dominant strategy for virus propagation at these sites. In the benthic samples, viruses were highly concentrated, but paradoxically, no bacteria were visibly infected. This suggests that sediment provides good conditions for virus preservation but ironically is an unfavorable environment for proliferation. In addition, given the comparable size distributions of viruses in the water and sediment samples, our results support the paradigm that aquatic viruses are ubiquitous and may have moved between the two compartments of the shallow systems examined. Overall, this study provides additional information about the relevance of viruses in tropical areas and indicates that the intensity of virus-bacterium interactions in benthic habitats may lower than the intensity in the adjacent bodies of water.
Molecular Biological Detection of Anaerobic Gut Fungi (
Neocallimastigales
) from Landfill Sites
Authors: Lockhart Robert J. , Van Dyke Michele I. , Beadle Ian R. , Humphreys Paul , McCarthy Alan J.
Published: August 2006

Oligonucleotide primers were designed for the 18S rRNA genes of members of the
Neocallimastigales
and used in a nested PCR protocol to amplify 787-bp fragments of DNA from landfill site samples. The specificities of the primers were confirmed by phylogenetic analysis of the environmental clone sequences, and this method can therefore now be used to investigate the ecology of the obligately anaerobic fungi. To our knowledge, this is the first demonstration of the occurrence of members of the
Neocallimastigales
outside the mammalian gut, and their distribution across the landfill samples examined here suggests that they are actively involved in cellulose degradation.
Salt, Alone or in Combination with Sucrose, Can Improve the Survival of
Escherichia coli
O157 (SERL 2) in Model Acidic Sauces
Authors: Chapman B. , Jensen N. , Ross T. , Cole M.
Published: August 2006

The commercial production of microbiologically safe and stable sauces containing acetic acid is guided by the Comité des Industries des Mayonnaises et Sauces Condimentaires de la Communauté Économique Européenne's (CIMSCEE) code. The CIMSCEE safety value is calculated using a linear regression equation combining weighted contributions of pH and aqueous-phase concentrations of undissociated acetic acid, NaCl, and sugars. By implication, the CIMSCEE safety equation predicts that increasing concentrations of hurdles will always increase inactivation of the target pathogen. In this study, the time to achieve a 3-log
10
reduction of an acid-resistant, acid-adapted, Shiga toxin-producing
Escherichia coli
(STEC) O157 isolate was determined experimentally for 81 formulations at various pHs and acetic acid, NaCl, and sucrose concentrations in a broth model. The combinations were intended to simulate the aqueous phase of acidic sauces and dressings. Experimental data were fitted to the log logistic model to estimate the time to 3-log
10
reduction (
t
3D
). Comparison of fitted
t
3D
estimates with CIMSCEE values showed agreement in predicting safety (as defined by CIMSCEE) for the majority of formulations. However, CIMSCEE safety predictions were “fail dangerous” for 13 of 81 formulations. Among these formulations and others, the observed
E. coli t
3D
initially increased and then decreased with increasing osmolalities (NaCl and sucrose). Relative protection increased with exposure time where the protective effect of NaCl predominated. While commercial acidic sauces are not considered high-risk vehicles for STEC, interactions among hurdles that decrease their combined effectiveness are deserving of further investigation because they may reveal mechanisms of broader relevance in the inactivation of pathogens in foods.
Improved In Situ Hybridization Efficiency with Locked-Nucleic-Acid-Incorporated DNA Probes
Authors: Kubota Kengo , Ohashi Akiyoshi , Imachi Hiroyuki , Harada Hideki
Published: August 2006

Low signal intensity due to poor probe hybridization efficiency is one of the major drawbacks of rRNA-targeted in situ hybridization. There are two major factors affecting the hybridization efficiency: probe accessibility and affinity to the targeted rRNA molecules. In this study, we demonstrate remarkable improvement in in situ hybridization efficiency by applying locked-nucleic-acid (LNA)-incorporated oligodeoxynucleotide probes (LNA/DNA probes) without compromising specificity. Fluorescently labeled LNA/DNA probes with two to four LNA substitutions exhibited strong fluorescence intensities equal to or greater than that of probe Eub338, although these probes did not show bright signals when they were synthesized as DNA probes; for example, the fluorescence intensity of probe Eco468 increased by 22-fold after three LNA bases were substituted for DNA bases. Dissociation profiles of the probes revealed that the dissociation temperature was directly related to the number of LNA substitutions and the fluorescence intensity. These results suggest that the introduction of LNA residues in DNA probes will be a useful approach for effectively enhancing probe hybridization efficiency.
Basin-Wide Analysis of the Dynamics of Fecal Contamination and Fecal Source Identification in Tillamook Bay, Oregon
Authors: Shanks Orin C. , Nietch Christopher , Simonich Michael , Younger Melissa , Reynolds Don , Field Katharine G.
Published: August 2006

The objectives of this study were to elucidate spatial and temporal dynamics in source-specific
Bacteroidales
16S rRNA genetic marker data across a watershed; to compare these dynamics to fecal indicator counts, general measurements of water quality, and climatic forces; and to identify geographic areas of intense exposure to specific sources of contamination. Samples were collected during a 2-year period in the Tillamook basin in Oregon at 30 sites along five river tributaries and in Tillamook Bay. We performed
Bacteroidales
PCR assays with general, ruminant-source-specific, and human-source-specific primers to identify fecal sources. We determined the
Escherichia coli
most probable number, temperature, turbidity, and 5-day precipitation. Climate and water quality data collectively supported a rainfall runoff pattern for microbial source input that mirrored the annual precipitation cycle. Fecal sources were statistically linked more closely to ruminants than to humans; there was a 40% greater probability of detecting a ruminant source marker than a human source marker across the basin. On a sample site basis, the addition of fecal source tracking data provided new information linking elevated fecal indicator bacterial loads to specific point and nonpoint sources of fecal pollution in the basin. Inconsistencies in
E. coli
and host-specific marker trends suggested that the factors that control the quantity of fecal indicators in the water column are different than the factors that influence the presence of
Bacteroidales
markers at specific times of the year. This may be important if fecal indicator counts are used as a criterion for source loading potential in receiving waters.
Expression of nuclear insulin receptor substrate 1 in breast cancer
Authors: Sisci Diego , Morelli Catia , Garofalo Cecilia , Romeo Francesco , Morabito Lucio , Casaburi Filomena , Middea Emilia , Cascio Sandra , Brunelli Elvira , Andò Sebastiano , Surmacz Eva
Published: August 2006

Background:Insulin receptor substrate 1 (IRS-1), a cytoplasmic protein transmitting signals from the insulin and insulin-like growth factor 1 receptors, has been implicated in breast cancer. Previously, it was reported that IRS-1 can be translocated to the nucleus and modulate oestrogen receptor α (ERα) activity in vitro. However, the expression of nuclear IRS-1 in breast cancer biopsy specimens has never been examined.

Aims:To assess whether nuclear IRS-1 is present in breast cancer and non-cancer mammary epithelium, and whether it correlates with other markers, especially ERα. Parallel studies were carried out for the expression of cytoplasmatic IRS-1.

Methods:IRS-1 and ERα expression was assessed by immunohistochemical analysis. Data were evaluated using Pearson’s correlation, linear regression and receiver operating characteristic analysis.

Results:Median nuclear IRS-1 expression was found to be low in normal mammary epithelial cells (1.6%) and high in benign tumours (20.5%), ductal grade 2 carcinoma (11.0%) and lobular carcinoma (∼30%). Median ERα expression in normal epithelium, benign tumours, ductal cancer grade 2 and 3, and lobular cancer grade 2 and 3 were 10.5, 20.5, 65.0, 0.0, 80 and 15%, respectively. Nuclear IRS-1 and ERα positively correlated in ductal cancer (p<0.001) and benign tumours (p<0.01), but were not associated in lobular cancer and normal mammary epithelium. In ductal carcinoma, both nuclear IRS-1 and ERα negatively correlated with tumour grade, size, mitotic index and lymph node involvement. Cytoplasmic IRS-1 was expressed in all specimens and positively correlated with ERα in ductal cancer.

Conclusions:A positive association between nuclear IRS-1 and ERα is a characteristic for ductal breast cancer and marks a more differentiated, non-metastatic phenotype.
Immunomodulating Effects of Fractioned Polysaccharides Isolated from Yu-Ping-Feng-Powder in Cyclophosphamide-Treated Mice
Authors: Chen Xiang-Tao , Li Jun , Wang Hui-Li , Cheng Wen-Ming , Zhang Lei , Ge Jin-Fang
Published: August 2006

Yu-Ping-Feng-Powder (YP), a traditional Chinese medicine prescription, is widely applied in China for the cure and prevention of diseases related to immunodeficiency. To test whether the fractioned polysaccharides (YPF-P) isolated from YP have immunomodulating activities, the effects of YPF-P on cyclophosphamide (Cy)-treated mice were studied in relation to phagocytosis of macrophage, splenocyte proliferation, and humoral, and cellular immunity parameters. It was found that YPF-P enhances phagocytic activity, augments ConA- or LPS-stimulated T cell proliferation, increases the quantitative haemolysis of SRBC (QHS) and delayed-type hypersensitivity reaction (DTH) to dinitrofluorobenzene. Hence, YPF-P restored the immuno-competence suppressed by Cy. YPF-P also augmented IL-2 and IFN-γ production, but failed to increase IL-4 production, which indicates that there is high probability that it enhance Th1 function. These results suggested that YPF-P has immunomodulating effects and that the polysaccharides constitute one of the active components of YP.
Effect of 3-Phenyl-2-Propene-1-ol on PGE2Release from Rat Cerebral Microvascular Endothelial Cells Stimulated by IL-1β
Authors: Guo Jian-You , Huo Hai-Ru , Zhao Bao-Sheng , Liu Hong-Bin , Li Lan-Fang , Guo Shu-Ying , Jiang Ting-Liang
Published: August 2006

Fever, an elevation in body temperature, is thought to be terminally mediated by prostaglandin E2(PGE2). Both Guizhi Tang (GZT) and its active fraction A (Fr.A) showed an antipyretic effect in rats. 3-Phenyl-2-propene-1-ol was one of the active compounds isolated from Fr.A. In the present study, we examined the influence of interleukin-1β (IL-1β) on prostaglandin E2(PGE2) release, and the effect of 3-phenyl-2-propene-1-ol on IL-1β-induced PGE2release from rat cerebral endothelial cells (rCMEC). Cultured rCMEC were used in the study. In vitro, cells express typical phenotypic markers of brain endothelium. Using a monoclonal antibody against von Willebrand factor, immunocytochemical analysis revealed positive immunoreactivity in the cytoplasm of cultured cells. rCMEC were incubated in M199 medium containing IL-1β in the presence or absence of 3-phenyl-2-propene-1-ol. After incubation, the conditioned media were collected and the amount of PGE2was measured by enzyme-linked immunosorbent assay (ELISA). IL-1β increased the production of PGE2in a dose- and time-dependent manner. 3-Phenyl-2-propene-1-ol significantly decreased IL-1β-induced PGE2release in a dose-dependent manner. Our results indicate that 3-phenyl-2-propene-1-ol inhibits the PGE2release from rCMEC stimulated by IL-1β, and may have an antipyretic effect.
SALIENCE-ADAPTIVE PAINTERLY RENDERING USING GENETIC SEARCH
Authors: COLLOMOSSE J. P. , HALL P. M.
Published: August 2006

We present a new non-photorealistic rendering (NPR) algorithm for rendering photographs in an impasto painterly style. We observe that most existing image-based NPR algorithms operate in a spatially local manner, typically as non-linear image filters seeking to preserve edges and other high-frequency content. By contrast, we argue that figurative artworks are salience maps, and develop a novel painting algorithm that uses a genetic algorithm (GA) to search the space of possible paintings for a given image, so approaching an "optimal" artwork in which salient detail is conserved and non-salient detail is attenuated. Differential rendering styles are also possible by varying stroke style according to the classification of salient artifacts encountered, for example edges or ridges. We demonstrate the results of our technique on a wide range of images, illustrating both the improved control over level of detail due to our salience adaptive painting approach, and the benefits gained by subsequent relaxation of the painting using the GA.
GENETIC LEARNING FOR BIOLOGICALLY INSPIRED AESTHETIC PROCESSES
Authors: GREENFIELD GARY
Published: August 2006

We investigate the use of the non-interactive genetic algorithm as a tool in evolutionary art for evolving aesthetic images. We consider two problem domains. Our first uses a modification of a model for differential gene expression in order to simulate cell morphology and evolve images consisting of matrices of cells meeting our subjective aesthetic criteria. Our second uses a modification of a model for simulating ants that can deposit and follow scent (in the guise of color trails) in order to evolve ant paintings meeting out subjective aesthetic criteria. In both cases, we focus upon the design of fitness functions that are particularly well suited for ensuring that genetic learning can effectively guide the evolution of cellular or behavioral processes to yield aesthetic results.
THIRD-ORDER NONLINEAR OPTICAL INVESTIGATION OF A NOVEL MATERIAL: (HEXADECYLTRIMETHYLAMMONIUM) BIS(4,5-DITHIOLE-1,3-DITHIOLE-2-THIONE)COPPER
Authors: FENG L. , WANG Y. L. , REN Q. , ZHANG G. H. , YANG H. L. , SUN X. B.
Published: August 2006

A novel dmit2- salt: (hexadecyltrimethylammonium)bis(4,5-dithiolato-1,3-dithiole-2-thione)copper, abbreviated as HTCu , is synthesized and characterized for third-order optical nonlinearity by Z-scan technique at a wavelength of 1064 nm with laser duration of 30 ps. Z-scan spectra reveal a negative Kerr coefficient at 1064 nm and no nonlinear absorption was observed under this condition. The nonlinear refraction coefficient n2 and the second hyperpolarizability γ have been determined to be -1.51 × 10-11 and 1.36 × 10-30 esu , respectively, suggesting HTCu is a promising material for all-optical switching.
Corridors for Conservation: Integrating Pattern and Process
Authors: Chetkiewicz Cheryl-Lesley B. , St. Clair Colleen Cassady , Boyce Mark S.
Published: August 2006

Corridors are commonly used to connect fragments of wildlife habitat, yet the identification of conservation corridors typically neglects processes of habitat selection and movement for target organisms. Instead, corridor designs often are based on binary patterns of habitat suitability. New technologies and analytical tools make it possible to better integrate landscape patterns with behavioral processes. We show how resource selection functions can be used to describe habitat suitability with continuous and multivariable metrics and review methods by which animal movement can be quantified, analyzed, and modeled. We then show how the processes of habitat selection and movement can be integrated with landscape features using least-cost paths, graph theory, and step selection functions. These tools offer new ways to design, implement, and study corridors as landscape linkages more objectively and holistically.
Gene Regulation by Chromatin Structure: Paradigms Established inDrosophila melanogaster
Authors: Schulze Sandra R. , Wallrath Lori L.
Published: August 2006

Studies in Drosophila melanogaster have revealed paradigms for regulating gene expression through chromatin structure, including mechanisms of gene activation and silencing. Regulation occurs at the level of individual genes, chromosomal domains, and entire chromosomes. The chromatin state is dynamic, allowing for changes in gene expression in response to cellular signals and/or environmental cues. Changes in chromatin result from the action of ATP-dependent chromatin-remodeling complexes, reversible epigenetic histone modifications, and the incorporation of histone variants. Many of the chromatin-based transcriptional regulatory mechanisms discovered in D. melanogaster are evolutionarily conserved and therefore serve as a foundation for studies in other organisms.
Metabolically active portion of fat-free mass: a cellular body composition level modeling analysis
Authors: Wang ZiMian , Heshka Stanley , Wang Jack , Gallagher Dympna , Deurenberg Paul , Chen Zhao , Heymsfield Steven B.
Published: August 2006

The proportion of fat-free mass (FFM) as body cell mass (BCM) is highly related to whole body resting energy expenditure. However, the magnitude of BCM/FFM may have been underestimated in previous studies. This is because Moore's equation [BCM (kg) = 0.00833 × total body potassium (in mmol)], which was used to predict BCM, underestimates BCM by ∼11%. The aims of the present study were to develop a theoretical BCM/FFM model at the cellular level and to explore the influences of sex, age, and adiposity on the BCM/FFM. Subjects were 112 adults who had the following measurements: total body water by2H2O or3H2O dilution; extracellular water by NaBr dilution; total body nitrogen by in vivo neutron activation analysis; and bone mineral by dual-energy X-ray absorptiometry. FFM was calculated using a multicomponent model and BCM as the difference between FFM and the sum of extracellular fluid and solids. The developed theoretical model revealed that the proportion of BCM to FFM is mainly determined by water distribution (i.e., E/I, the ratio of extracellular to intracellular water). A significant correlation ( r = 0.90, P < 0.001) was present between measured and model-predicted BCM/FFM for all subjects pooled. Measured BCM/FFM [mean (SD)] was 0.584 ± 0.041 and 0.529 ± 0.041 for adult men and women ( P < 0.001), respectively. A multiple linear regression model showed that there are independent significant associations of sex, age, and fat mass with BCM/FFM.
Incomplete Suppression of Distractor-Related Activity in the Frontal Eye Field Results in Curved Saccades
Authors: McPeek Robert M.
Published: August 2006

Saccades in the presence of distractors show significant trajectory curvature. Based on previous work in the superior colliculus (SC), we speculated that curvature arises when a movement is initiated before competition between the target and distractor goals has been fully resolved. To test this hypothesis, we recorded frontal eye field (FEF) activity for curved and straight saccades in search. In contrast to the SC, activity in FEF is normally poorly correlated with saccade dynamics. However, the FEF, like the SC, is involved in target selection. Thus if curvature is caused by incomplete target selection, we expect to see its neural correlates in the FEF. We found that saccades that curve toward a distractor are accompanied by an increase in perisaccadic activity of FEF neurons coding the distractor location, and saccades that curve away are accompanied by a decrease in activity. In contrast, for FEF neurons coding the target location, there is no significant difference in activity between curved and straight saccades. To establish that the distractor-related activity is causally related to saccade curvature, we applied microstimulation to sites in the FEF before saccades to targets presented without distractors. The stimulation was subthreshold for evoking saccades and the temporal structure of the stimulation train resembled the activity recorded for curved saccades. The resulting movements curved toward the location coded by the stimulation site. These results support the idea that saccade curvature results from incomplete suppression of distractor-related activity during target selection.
Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver
Authors: Lam Siew Hong , Winata Cecilia Lanny , Tong Yan , Korzh Svetlana , Lim Wen San , Korzh Vladimir , Spitsbergen Jan , Mathavan Sinnakarupan , Miller Lance D. , Liu Edison T. , Gong Zhiyuan
Published: August 2006

Arsenic is a prominent environmental toxicant and carcinogen; however, its molecular mechanism of toxicity and carcinogenicity remains poorly understood. In this study, we performed microarray-based expression profiling on liver of zebrafish exposed to 15 parts/million (ppm) arsenic [As(V)] for 8–96 h to identify global transcriptional changes and biological networks involved in arsenic-induced adaptive responses in vivo. We found that there was an increase of transcriptional activity associated with metabolism, especially for biosyntheses, membrane transporter activities, cytoplasm, and endoplasmic reticulum in the 96 h of arsenic treatment, while transcriptional programs for proteins in catabolism, energy derivation, and stress response remained active throughout the arsenic treatment. Many differentially expressed genes encoding proteins involved in heat shock proteins, DNA damage/repair, antioxidant activity, hypoxia induction, iron homeostasis, arsenic metabolism, and ubiquitin-dependent protein degradation were identified, suggesting strongly that DNA and protein damage as a result of arsenic metabolism and oxidative stress caused major cellular injury. These findings were comparable with those reported in mammalian systems, suggesting that the zebrafish liver coupled with the available microarray technology present an excellent in vivo toxicogenomic model for investigating arsenic toxicity. We proposed an in vivo, acute arsenic-induced adaptive response model of the zebrafish liver illustrating the relevance of many transcriptional activities that provide both global and specific information of a coordinated adaptive response to arsenic in the liver.
Robust adaptive tracking for Markovian jump nonlinear systems with unknown nonlinearities
Authors: Zhu Jin , Xi Hong-Sheng , Ji Hai-Bo , Wang Bing
Published: August 2006

Robust adaptive tracking problems for a class of Markovian jump parametric‐strict‐feed‐back systems with both parametric uncertainty and unknown nonlinearity are investigated. The unknown nonlinearities considered herein lie within some “bounding functions,” which are assumed to be partially known. By using a stochastic Lyapunov method and backstepping techniques, a parameter adaptive law and a control law were obtained, which guarantee that the tracking error could be within a small neighborhood around the origin in the sense of the fourth moment. Moreover, all signals of the closed‐loop system could be globally uniformly ultimately bounded.
Existence, uniqueness, and quasilinearization results for nonlinear differential equations arising in viscoelastic fluid flow
Authors: Akyildiz F. Talay , Vajravelu K.
Published: August 2006

Solutions for a class of nonlinear second‐order differential
equations arising in steady Poiseuille flow of an Oldroyd
six‐constant model are obtained using the quasilinearization
technique. Existence, uniqueness, and analyticity results are
established using Schauder theory. Numerical results
are presented graphically and salient features of the solutions
are discussed.
Analytical solutions for the neutron transport using the spectral methods
Authors: Kadem Abdelouahab
Published: August 2006

We present a method for solving the two‐dimensional equation of
transfer. The method can be extended easily to the general linear
transport problem. The used technique allows us to reduce the
two‐dimensional equation to a system of one‐dimensional equations.
The idea of using the spectral method for searching for solutions
to the multidimensional transport problems leads us to a solution
for all values of the independant variables, the proposed method
reduces the solution of the multidimensional problems into a set
of one‐dimensional ones that have well‐established deterministic
solutions. The procedure is based on the development of the
angular flux in truncated series of Chebyshev polynomials which
will permit us to transform the two‐dimensional problem into a set
of one‐dimensional problems.
Modeling nonlinearities with mixtures‐of‐experts of time series models
Authors: Carvalho Alexandre X. , Tanner Martin A.
Published: August 2006

We discuss a class of nonlinear models based on
mixtures‐of‐experts of regressions of exponential family time
series models, where the covariates include functions of lags of
the dependent variable as well as external covariates. The
discussion covers results on model identifiability, stochastic
stability, parameter estimation via maximum likelihood estimation,
and model selection via standard information criteria.
Applications using real and simulated data are presented to
illustrate how mixtures‐of‐experts of time series models can be
employed both for data description, where the usual mixture
structure based on an unobserved latent variable may be
particularly important, as well as for prediction, where only the
mixtures‐of‐experts flexibility matters.
Iterates of Volterra operators and indeterminate forms
Authors: e Silva Pablo Braz , Papa Andrés R. R.
Published: August 2006

We state and prove a theorem showing how iterates of the Volterra
operator can be used to evaluate indeterminate forms of type 0/0. This general result allows one to recover the Boltzmann‐Gibbs entropy as a limit of a wide class of generalized entropies, as considered in an earlier work.
Exact category of hypermodules
Authors: Madanshekaf A.
Published: August 2006

It is shown, among other things, that the category of
hypermodules is an exact category, thus generalizing the
classical case.
Polynomial approach for the most general linear Fredholm integrodifferential‐difference equations using Taylor matrix method
Authors: Sezer Mehmet , Gülsu Mustafa
Published: August 2006

A Taylor matrix method is developed to find an approximate
solution of the most general linear Fredholm
integrodifferential‐difference equations with variable
coefficients under the mixed conditions in terms of Taylor
polynomials. This method transforms the given general linear
Fredholm integrodifferential‐difference equations and the mixed
conditions to matrix equations with unknown Taylor coefficients.
By means of the obtained matrix equations, the Taylor coefficients
can be easily computed. Hence, the finite Taylor series approach
is obtained. Also, examples are presented and the results are
discussed.
Simultaneous approximation for the Phillips operators
Authors: Govil N. K. , Gupta Vijay , Noor Muhammad Aslam
Published: August 2006

We study the simultaneous approximation properties of the
well‐known Phillips operators. We establish the rate of
convergence of the Phillips operators in simultaneous
approximation by means of the decomposition technique for
functions of bounded variation.
Finite rank intermediate Hankel operators and the big Hankel operator
Authors: Osawa Tomoko
Published: August 2006

Let be a Bergman space. We are interested in an
intermediate Hankel operator from to a closed subspace M of L2 which is invariant under the multiplication by the coordinate function z. It is well known that there do not exist any nonzero finite rank big Hankel
operators, but we are studying same types in case is close to big Hankel operator. As a result, we give a necessary and
sufficient condition about M that there does not exist a finite rank except .
A note on irreducible Heegaard diagrams
Authors: Cavicchioli Alberto , Spaggiari Fulvia
Published: August 2006

We construct a Heegaard diagram of genus three for the real
projective 3‐space, which has no waves and pairs of complementary
handles. The first example was given by Im and Kim but our diagram
has smaller complexity. Furthermore the proof presented here is
quite different to that of the quoted authors, and permits also to
obtain a simple alternative proof of their result. Examples of
irreducible Heegaard diagrams of certain connected sums complete
the paper.
The equivalence between the Mann and Ishikawa iterations dealing with generalized contractions
Authors: Rhoades B. E. , Şoltuz Ştefan M.
Published: August 2006

We show that the Mann and Ishikawa iterations are equivalently used to approximate fixed points of generalized contractions.
A nonexistence result for a nonlinear PDE with Robin condition
Authors: Khodja Brahim
Published: August 2006

Under the assumption λ > 0 and f verifying f(x, y, 0) = 0 in D, 2F(x, y, u) − uf(x, y, u) ≥ 0, u ≠ 0, and if Ω = R × D, we show the convexity of function E(t) = ∬D|u(t,x,y)|2dxdy, where u : Ω → ℝ is a solution of problem λ(∂2u/∂t2) − (∂/∂x)(p(x, y)(∂u/∂x)) − (∂/∂y)(q(x, y)(∂u/∂y)) + f(x, y, u) = 0 in Ω, u + ε(∂u/∂n) = 0 on ∂Ω, considered in H2(Ω)∩L∞(Ω), are two nonnull functions on D, ε is a positive real number, and D = ]a1, b1[ × ]a2, b2[, .
Comparison of wavelet approximation order in different smoothness spaces
Authors: Islam M. R. , Ahemmed S. F. , Rahman S. M. A.
Published: August 2006

In linear approximation by wavelet, we approximate a given
function by a finite term from the wavelet series. The
approximation order is improved if the order of smoothness of the
given function is improved, discussed by Cohen
(2003), DeVore (1998), and Siddiqi (2004). But in the case of
nonlinear approximation, the approximation order is improved
quicker than that in linear case. In this
study we proved this assumption only for the Haar wavelet. Haar
function is an example of wavelet and this fundamental example
gives major feature of the general wavelet. A nonlinear space
comes from arbitrary selection of wavelet coefficients, which
represent the target function almost equally. In this case our
computational work will be reduced tremendously in the sense that
approximation error decays more quickly than that in
linear case.
Intuitionistic fuzzy Hv‐ideals
Authors: Davvaz Bijan , Dudek Wieslaw A.
Published: August 2006

The notion of intuitionistic fuzzy sets was introduced by
Atanassov as a generalization of the notion of fuzzy sets. In this
paper, we apply the concept of intuitionistic fuzzy sets to
Hv‐rings. We introduce the notion of an
intuitionistic fuzzy Hv‐ideal of an Hv‐ring and
then some related properties are investigated. We state some
characterizations of intuitionistic fuzzy Hv‐ideals. Also we
investigate some natural equivalence relations on the set of all
intuitionistic fuzzy Hv‐ideals of an Hv‐ring.
(Co)homology of triassociative algebras
Authors: Yau Donald
Published: August 2006

We study homology and cohomology of triassociative algebras with
nontrivial coefficients. The cohomology theory is applied to
study algebraic deformations of triassociative algebras.
Integral means of certain multivalent functions
Authors: Eker S. Sümer , Güney H. Özlem , Owa Shigeyoshi
Published: August 2006

For analytic and multivalent functions f(z) and p(z) in the
open unit disk , a subordination theorem due
to Littlewood (1925) which was called the integral mean
is applied. Some simple examples for our results are also considered.
On λ‐rings and topological realization
Authors: Yau Donald
Published: August 2006

It is shown that most possibly truncated power series rings admit
uncountably many filtered λ‐ring structures. The question
of how many of these filtered λ‐ring structures are
topologically realizable by the K‐theory of torsion‐free spaces
is also considered for truncated polynomial rings.
Biharmonic curves in Minkowski 3‐space. Part II
Authors: Inoguchi Jun-Ichi
Published: August 2006

We give a differential geometric characterization for biharmonic
curves with null principal normal in Minkowski 3‐space.
Reverse convex problems: an approach based on optimality conditions
Authors: Tseveendorj Ider
Published: August 2006

We present some results concerning reverse convex problems. Global optimality conditions for the problems with a nonsmooth reverse convex constraint are established and convergence of an algorithm in the case of linear program with an additional quadratic reverse convex constraint is studied.
Maximizing residual capacity in connection-oriented networks
Authors: Walkowiak Krzysztof
Published: August 2006

The following problem arises in the study of survivable
connection-oriented networks. Given a demand matrix to be routed
between nodes, we want to route all demands, so that the residual
capacity given by the difference between link capacity and link
flow is maximized. Each demand can use only one path. Therefore,
the flow is modeled as nonbifurcated multicommodity flow. We call
the considered problem nonbifurcated congestion (NBC) problem.
Solving NBC problem enables robust restoration of failed
connections in a case of network failure. We propose a new
heuristic algorithm for NBC problem and compare its performance
with existing algorithms.
ACS-TS: train scheduling using ant colony system
Authors: Ghoseiri Keivan , Morshedsolouk Fahimeh
Published: August 2006

This paper develops an algorithm for the train scheduling problem
using the ant colony system metaheuristic called ACS-TS. At first,
a mathematical model for a kind of train scheduling problem is
developed and then the algorithm based on ACS is presented to
solve the problem. The problem is considered as a
traveling salesman problem (TSP) wherein cities represent
the trains. ACS determines the sequence of trains dispatched on
the graph of the TSP. Using the sequences obtained and removing
the collisions incurred, train scheduling is determined.
Numerical examples in small and medium sizes are solved using
ACS-TS and compared to exact optimum solutions to check for
quality and accuracy. Comparison of the solutions shows that
ACS-TS results in good quality and time savings. A case study is
presented to illustrate the solution.