bluuebunny/crossref_metadata_2025 huggingface dataset:
Masker-first advantage for cues in informational masking
Authors: Richards Virginia M. , Huang Rong , Kidd Gerald
Published: October 2004

The detectability of a pure-tone signal may be reduced by adding a small number of randomly drawn masker tones remote from the signal frequency, an effect attributed to informational masking. A pretrial cue consisting of either the upcoming signal or masker releases informational masking, but a pretrial cue of the signal-plus-masker stimulus does not. In these experiments the relative potency of pre- and posttrial cues in releasing informational masking was examined. In separate conditions the masker-alone and signal-plus-masker stimuli were cues. The results indicated a masker-first advantage, i.e., sensitivity was superior when a masker cue preceded a yes/no trial interval compared to (a) when a signal-plus-masker preceded the trial, and (b) when either cue type followed the yes/no trial interval. A masker-first advantage was also obtained when the results from a two-interval forced-choice same/different task were examined. In contrast, a masker-first advantage was not obtained when the frequency of the signal to be detected was random. For detection tasks using random multi-tone maskers there may be differences in processing efficiency depending on the order in which stimuli are presented. The “masker-first advantage” may depend, in part, on observers maintaining their attention at the signal frequency.
Acoustic imaging in enclosed spaces: Analysis of room geometry modifications on the impulse response
Authors: Kuster M. , de Vries D. , Hulsebos E. M. , Gisolf A.
Published: October 2004

Sound propagation in enclosed spaces is characterized by reflections at the boundaries of the enclosure. Reflections can be wanted in the case when they support the direct sound or give a feeling of envelopment or they can be unwanted when they lead to echoes and colouration. When measuring multiple impulse responses in an enclosed space along an array the reflections can be mapped to the reflecting objects. Similar to seismic exploration, medical diagnostics, and underwater acoustics, an image of the reflecting objects is obtained in terms of reflected energy. The imaging process is based on inverse wave field extrapolation with the Kirchhoff–Helmholtz and Rayleigh integrals. The inverse of the imaging process recreates the measured impulse responses from the image and it allows one to remove or alter reflecting objects in the image and investigate their influence on the wave field in the enclosed space in a physically correct way. This can be verified by reimaging the altered wave field. Preliminary results from listening tests for the perceptual evaluation are presented. They indicate that the influence of a reflecting object can only be perceived in its close proximity.
Enhancing temporal cues to voice pitch in continuous interleaved sampling cochlear implants
Authors: Green Tim , Faulkner Andrew , Rosen Stuart
Published: October 2004

The limited spectral resolution of cochlear implant systems means that voice pitch perception depends on weak temporal envelope cues. Enhancement of such cues was investigated in implant users and in acoustic simulations. Subjects labeled the pitch movement of processed synthetic diphthongal glides. In standard processing, noise carriers (simulations) or pulse trains (implant users) were modulated by 400 Hz low-pass envelopes. In modified processing, carriers were modulated by two components: (1) Slow-rate (<32 Hz) envelope modulations, conveying dynamic spectral shape changes crucial for speech; (2) a simplified waveform (e.g., a sawtooth) matching the periodicity of the input diphthong. In both normal listeners and implant users performance was better with modified processing, though temporal envelope cues were less effective with higher F0. Factors contributing to the advantage for modified processing may include increased modulation depth and use of a modulation waveform featuring a rapid onset in each period, resulting in a clearer representation of F0 in the neural firing pattern. Eliminating slow-rate spectral dynamics, so that within-channel amplitude changes solely reflected F0, showed that dynamic spectral variation obscured temporal pitch cues. Though significant, advantages for modified processing were small, suggesting that the potential for developing strategies delivering enhanced pitch perception is limited.
Acoustic absorption measurements for characterization of gas mixing
Authors: Cottet Aurelien , Neumeier Yedidia , Scarborough David , Bibik Oleksandr , Lieuwen Tim
Published: October 2004

Controlling and/or monitoring the degree of mixing between constituents of a multicomponent media is a key problem in a variety of applications. Monitoring such mixing processes necessarily requires capabilities for quantification of the level of “mixedness.” However, quantification of molecular mixedness levels, as opposed to macroscale mixture uniformity, is difficult. This paper demonstrates the use of acoustic absorption measurements to characterize an average level of molecular mixedness between gases across the wave propagation path. This approach takes advantage of the fact that over a large frequency range, acoustic damping is dominated by vibrational relaxation processes. The vibrational relaxation frequency for a particular gas is often a strong function of the other species it is in molecular contact with. Thus, the relaxation frequency of each species in a multicomponent gas mixture varies with the level of molecular mixedness of the constituent species. This paper presents the results of example calculations and experiments demonstrating the feasibility of this approach and the significant sensitivity of acoustic absorption levels upon gas mixedness; e.g., measurements reported here show acoustic amplitude differences of up to a factor of 10 between identical gas mixtures whose only difference is the level of mixedness of their constituents.
Simultaneous measurement of middle-ear input impedance and forward/reverse transmission in cat
Authors: Voss Susan E. , Shera Christopher A.
Published: October 2004

Reported here is a technique for measuring forward and reverse middle-ear transmission that exploits distortion-product otoacoustic emissions (DPOAEs) to drive the middle ear “in reverse” without opening the inner ear. The technique allows measurement of DPOAEs, middle-ear input impedance, and forward and reverse middle-ear transfer functions in the same animal. Intermodulation distortion in the cochlea generates a DPOAE at frequency 2f1−f2 measurable in both ear-canal pressure and the velocity of the stapes. The forward transfer function is computed from stapes velocities and corresponding ear-canal pressures measured at the two primary frequencies; the reverse transfer function is computed from velocity and pressure measurements at the DPOAE frequency. Middle-ear input impedance is computed from ear-canal pressure measurements and the measured Thévenin equivalent of the sound-delivery system. The technique was applied to measure middle-ear characteristics in anesthetized cats with widely opened middle-ear cavities (0.2–10 kHz). Stapes velocity was measured at the incudo-stapedial joint. Results on five animals are reported and compared with a published middle-ear model. The measured forward transfer functions and input impedances generally agree with previous measurements, and all measurements agree qualitatively with model predictions. The reverse transfer function is shown to depend on the acoustic load in the ear canal, and the measurements are used to compute the round-trip middle-ear gain and delay. Finally, the measurements are used to estimate the parameters of a two-port transfer-matrix description of the cat middle ear.
Searching for the optimal stimulus eliciting auditory brainstem responses in humans
Authors: Fobel Oliver , Dau Torsten
Published: October 2004

This study examines auditory brainstem responses (ABR) elicited by rising frequency chirps. Two chirp stimuli were developed and designed such as to compensate for cochlear travel-time differences across frequency, in order to maximize neural synchrony. One chirp, referred to as the O-chirp, was based on estimates of human basilar membrane (BM) group delays derived from stimulus-frequency otoacoustic emissions (SFOAE) at a sound pressure level of 40 dB [Shera and Guinan, in Recent Developments in Auditory Mechanics (2000)]. The other chirp, referred to as the A-chirp, was derived from latency functions fitted to tone-burst-evoked ABR wave-V data over a wide range of stimulus levels and frequencies [Neely et al., J. Acoust. Soc. Am. 83(2), 652–656 (1988)]. In this case, a set of level-dependent chirps was generated. The chirp-evoked responses, particularly wave-V amplitude and latency, were compared to click responses and to responses obtained with the original chirp as defined in Dau et al. [J. Acoust. Soc. Am. 107(3), 1530–1540 (2000)], referred to here as the M-chirp since it is based on a (linear) cochlea model. The main hypothesis was that, at low and medium stimulation levels, the O- and A-chirps might produce a larger response than the original M-chirp whose parameters were essentially derived from high-level BM data. The main results of the present study are as follows: (i) All chirps evoked a larger wave-V amplitude than the click stimulus indicating that for the chirps a broader range of spectral components contributes effectively to the ABR. (ii) Only small differences were found between the O-chirp and M-chirp responses at low and medium levels. This indicates that SFOAE may not provide a robust estimate of BM group delay, particularly at low frequencies, or that frequency-dependent neural delays exist which are not reflected in the design of these chirps. (iii) The A-chirp produced the largest responses, particularly at low stimulation levels. This chirp might therefore be valuable for clinical applications, particularly in tests where the click stimulus has been used so far.
Sound attenuation in lined bends
Authors: Félix S. , Pagneux V.
Published: October 2004

In the present paper we are concerned with sound propagation and attenuation in two- or three-dimensional lined bends. First it is shown that the effect of locally reacting absorbing materials at the walls of a waveguide can easily be taken into account in the multimodal formulation proposed in earlier papers by the authors, and, for bends, algebraic solutions are carried out for the acoustic field and scattering properties. Then a study of the sound attenuation in lined bends is given using the multimodal formulation and the properties of such waveguides are shown and discussed, in particular, the presence of a plateau of attenuation at high frequencies and a whispering gallery effect that occurs in bends.
Plane-wave decomposition of the sound field on a sphere by spherical convolution
Authors: Rafaely Boaz
Published: October 2004

Spherical microphone arrays have been recently studied for sound analysis and sound recordings, which have the advantage of spherical symmetry facilitating three-dimensional analysis. This paper complements the recent microphone array design studies by presenting a theoretical analysis of plane-wave decomposition given the sound pressure on a sphere. The analysis uses the spherical Fourier transform and the spherical convolution, where it is shown that the amplitudes of the incident plane waves can be calculated as a spherical convolution between the pressure on the sphere and another function which depends on frequency and the sphere radius. The spatial resolution of plane-wave decomposition given limited bandwidth in the spherical Fourier domain is formulated, and ways to improve the computation efficiency of plane-wave decomposition are introduced. The paper concludes with a simulation example of plane-wave decomposition.
Reconstructing Past Climate from Noisy Data
Authors: von Storch Hans , Zorita Eduardo , Jones Julie M. , Dimitriev Yegor , González-Rouco Fidel , Tett Simon F. B.
Published: October 2004

Empirical reconstructions of the Northern Hemisphere (NH) temperature in the past millennium based on multiproxy records depict small-amplitude variations followed by a clear warming trend in the past two centuries. We use a coupled atmosphere-ocean model simulation of the past 1000 years as a surrogate climate to test the skill of these methods, particularly at multidecadal and centennial time scales. Idealized proxy records are represented by simulated grid-point temperature, degraded with statistical noise. The centennial variability of the NH temperature is underestimated by the regression-based methods applied here, suggesting that past variations may have been at least a factor of 2 larger than indicated by empirical reconstructions.
Accumulation of Mn(II) in
Deinococcus radiodurans
Facilitates Gamma-Radiation Resistance
Authors: Daly M. J. , Gaidamakova E. K. , Matrosova V. Y. , Vasilenko A. , Zhai M. , Venkateswaran A. , Hess M. , Omelchenko M. V. , Kostandarithes H. M. , Makarova K. S. , Wackett L. P. , Fredrickson J. K. , Ghosal D.
Published: October 2004

Deinococcus radiodurans
is extremely resistant to ionizing radiation. How this bacterium can grow under chronic γ radiation [50 grays (Gy) per hour] or recover from acute doses greater than 10 kGy is unknown. We show that
D. radiodurans
accumulates very high intracellular manganese and low iron levels compared with radiation-sensitive bacteria and that resistance exhibits a concentration-dependent response to manganous chloride [Mn(II)]. Among the most radiation-resistant bacterial groups reported,
Deinococcus, Enterococcus, Lactobacillus
, and cyanobacteria accumulate Mn(II). In contrast,
Shewanella oneidensis
and
Pseudomonas putida
have high iron but low intracellular manganese concentrations and are very sensitive. We propose that Mn(II) accumulation facilitates recovery from radiation injury.
Anabaena
Sensory Rhodopsin: A Photochromic Color Sensor at 2.0 Å
Authors: Vogeley Lutz , Sineshchekov Oleg A. , Trivedi Vishwa D. , Sasaki Jun , Spudich John L. , Luecke Hartmut
Published: October 2004

Microbial sensory rhodopsins are a family of membrane-embedded photoreceptors in prokaryotic and eukaryotic organisms. Structures of archaeal rhodopsins, which function as light-driven ion pumps or photosensors, have been reported. We present the structure of a eubacterial rhodopsin, which differs from those of previously characterized archaeal rhodopsins in its chromophore and cytoplasmic-side portions.
Anabaena
sensory rhodopsin exhibits light-induced interconversion between stable 13-cis and all-trans states of the retinylidene protein. The ratio of its cis and trans chromophore forms depends on the wavelength of illumination, thus providing a mechanism for a single protein to signal the color of light, for example, to regulate color-sensitive processes such as chromatic adaptation in photosynthesis. Its cytoplasmic half channel, highly hydrophobic in the archaeal rhodopsins, contains numerous hydrophilic residues networked by water molecules, providing a connection from the photoactive site to the cytoplasmic surface believed to interact with the receptor's soluble 14-kilodalton transducer.
RNA Polymerase II Localizes in
Tetrahymena thermophila
Meiotic Micronuclei When Micronuclear Transcription Associated with Genome Rearrangement Occurs
Authors: Mochizuki Kazufumi , Gorovsky Martin A.
Published: October 2004

The germ line micronucleus in
Tetrahymena thermophila
is transcriptionally silent in vegetatively growing cells. However, micronuclear transcription has been observed in the early (“crescent”) stages of the sexual process, conjugation. This transcription is proposed to play a central role in identifying sites for subsequent genome rearrangements that accompany development of the somatic macronucleus from the micronucleus.
RPB3
(
cnjC
), a gene encoding a protein homologous to the third largest subunit of RNA polymerase II (RNAP II), was previously reported to be expressed specifically during conjugation, suggesting a role in micronucleus-specific transcription. Rpb3p localized in the micronucleus only during the meiotic prophase, when micronuclear transcription occurs, and its intranuclear distribution is strikingly similar to that for previously described sites of micronuclear RNA synthesis. By contrast, Rpc5p, the homologous subunit shared by RNAPs I and III, was not detectable in the micronucleus at any stage of the life cycle. However, Rpb3p is not specific to the transcribing micronucleus. Like Rpc5p, it also localizes to macronuclei in all stages of the life cycle. Rpb3p is encoded by a unique, essential gene in
Tetrahymena
. Thus, RNAP II is associated with both somatic transcription and crescent transcription and probably has an important role in genome rearrangement.
A Temperature-Sensitive
dcw1
Mutant of
Saccharomyces cerevisiae
Is Cell Cycle Arrested with Small Buds Which Have Aberrant Cell Walls
Authors: Kitagaki Hiroshi , Ito Kiyoshi , Shimoi Hitoshi
Published: October 2004

Dcw1p and Dfg5p in
Saccharomyces cerevisiae
are homologous proteins that were previously shown to be involved in cell wall biogenesis and to be essential for growth. Dcw1p was found to be a glycosylphosphatidylinositol-anchored membrane protein. To investigate the roles of these proteins in cell wall biogenesis and cell growth, we constructed mutant alleles of
DCW1
by random mutagenesis, introduced them into a Δ
dcw1
Δ
dfg5
background, and isolated a temperature-sensitive mutant, DC61 (
dcw1-3
Δ
dfg5
). When DC61 cells were incubated at 37°C, most cells had small buds, with areas less than 20% of those of the mother cells. This result indicates that DC61 cells arrest growth with small buds at 37°C. At 37°C, fewer DC61 cells had 1N DNA content and most of them still had a single nucleus located apart from the bud neck. In addition, in DC61 cells incubated at 37°C, bipolar spindles were not formed. These results indicate that DC61 cells, when incubated at 37°C, are cell cycle arrested after DNA replication and prior to the separation of spindle pole bodies. The small buds of DC61 accumulated chitin in the bud cortex, and some of them were lysed, which indicates that they had aberrant cell walls. A temperature-sensitive
dfg5
mutant, DF66 (Δ
dcw1 dfg5-29
), showed similar phenotypes.
DCW1
and
DFG5
mRNA levels peaked in the G
1
and S phases, respectively. These results indicate that Dcw1p and Dfg5p are involved in bud formation through their involvement in biogenesis of the bud cell wall.
Rapid Production of Gene Replacement Constructs and Generation of a Green Fluorescent Protein-Tagged Centromeric Marker in
Aspergillus nidulans
Authors: Yang Lin , Ukil Leena , Osmani Aysha , Nahm Francis , Davies Jonathan , De Souza Colin P. C. , Dou Xiaowei , Perez-Balaguer Ariadna , Osmani Stephen A.
Published: October 2004

A method to rapidly generate gene replacement constructs by fusion PCR is described for
Aspergillus nidulans
. The utility of the approach is demonstrated by green fluorescent protein (GFP) tagging of
A. nidulans ndc80
to visualize centromeres through the cell cycle. The methodology makes possible large-scale GFP tagging, promoter swapping, and deletion analysis of
A. nidulans
.
How low can they go? Potential for reduction in work injury rates
Authors: Shannon H S , Vidmar M
Published: October 2004

Background:There is a considerable variability in occupational injury rates across companies, even within the same industry. The aim of this study was to estimate how many injuries could be prevented if all firms could achieve the performance of their better peers.

Method:Data were obtained from the Workplace Safety & Insurance Board of Ontario on all insured firms in the province. Within rate groups (firms in the same type of business) the number of injuries expected if all firms had a lost time injury rate at the 25th percentile of the distribution for the rate group were estimated. The total number of injuries were compared with the expected number, after adjusting for firm size and type of injury.

Results:Overall, using the 25th percentile as a benchmark, 42% of lost time injuries in Ontario could be prevented.

Discussion:There is considerable potential for prevention of work injuries based on currently achieved, non-optimal benchmarks.
A survey of the composition and diversity of bacterial populations in bleached kraft pulp-mill wastewater secondary treatment systems
Authors: Gilbride Kimberley A , Fulthorpe Roberta R
Published: October 2004

Bacterial community compositions from 10 pulp- and paper-mill treatment systems were compared using both traditional and molecular techniques. 16S-RFLP (Random Fragment Length Polymorphisms) analysis was used to examine the genotypic profiles of the whole bacterial community of each treatment system. Although all the communities shared approximately 60% of their DNA band pattern, as determined by computer-assisted cluster analysis, each community displayed a unique profile that was stable over time under normal operating parameters. Reverse Sample Genome Probing (RSGP) and 16S-RFLP were used to compare the culturable bacterial communities of several geographically separated pulp-mill biotreatment system communities. There was little overlap in the composition of the culturable community between mills at the genus level. Furthermore, RSGP variation was almost as high within a mill as between mills. Partial sequences of the 16S rRNA genes from culturable isolates identified Bacillus spp., Pseudomonas spp., and Xanthobacter as some of the dominant species. Finally, several 16S rRNA genes from two whole community 16S RNA gene libraries were partially sequenced and identified as similar to unknown α-, β-, and γ-Proteobacteria, Ralstonia, Alcaligenes, Nitrospira, Firmicutes, and clones representing the new Holophaga/Acidobacterium phylum. These findings suggest that although these pulp- and paper-mill biotreatment communities perform similar functions, they are populated by unique mixtures of species.Key words: biodiversity, 16S-RFLP, secondary treatment, pulp mills.
Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003)
Authors: Bashan Yoav , Holguin Gina , de-Bashan Luz E
Published: October 2004

This review presents a critical and comprehensive documentation and analysis of the developments in agricultural, environmental, molecular, and physiological studies related to Azospirillum cells, and to Azospirillum interactions with plants, based solely on information published between 1997 and 2003. It was designed as an update of previous reviews (Bashan and Levanony 1990; Bashan and Holguin 1997a), with a similar scope of interest. Apart from an update and critical analysis of the current knowledge, this review focuses on the central issues of Azospirillum research today, such as, (i) physiological and molecular studies as a general model for rhizosphere bacteria; (ii) co-inoculation with other microorganisms; (iii) hormonal studies and re-consideration of the nitrogen contribution by the bacteria under specific environmental conditions; (iv) proposed Azospirillum as a non-specific plant-growth-promoting bacterium; (v) re-introduction of the "Additive Hypothesis," which suggests involvement of multiple mechanisms employed by the bacteria to affect plant growth; (vi) comment on the less researched areas, such as inoculant and pesticide research; and (vii) proposes possible avenues for the exploitation of this bacterium in environmental areas other than agriculture.Key words: Azospirillum, plant–bacteria interaction, plant-growth-promoting bacteria, PGPB, PGPR, rhizosphere bacteria.
Isolation and transcriptional regulation of theKluyveromyces lactisFBA1(fructose-1,6-bisphosphate aldolase) gene
Authors: Díaz Prado Silvia M , Cerdán M Esperanza , González Siso M Isabel
Published: October 2004

Cloning and transcriptional regulation of the KlFBA1 gene that codes for the class II fructose-1,6-bisphosphate aldolase of the yeast Kluyveromyces lactis are described. KlFBA1 mRNA diminishes transiently during the shift from hypoxic to fully aerobic conditions and increases in the reversal shift. This regulation is mediated by heme since expression was higher in a mutant defective in heme biosynthesis. KlFBA1 transcription is not induced by calcium-shortage, low temperature, or at stationary phase. These data suggest that KlFBA1 plays a role in the balance between oxidative and fermentative metabolism and that this gene is differentially regulated in K. lactis and Saccharomyces cerevisiae, i.e., a respiratory vs. fermentative yeast.Key words: FBA1, fructose-1,6-bisphosphate aldolase, Kluyveromyces, transcriptional regulation, yeast.
Preservation of in vitro cultures of the mite pathogenic fungusNeozygites tanajoae
Authors: Delalibera Jr. Italo , Humber Richard A , Hajek Ann E
Published: October 2004

Neozygites tanajoae has recently been described as a new fungal pathogen distinct from Neozygites floridana. This pathogen is currently being used as a classical biological control agent against the cassava green mite, Mononychellus tanajoa (Bondar), in Africa. Neozygites tanajoae is a particularly fastidious species, and in vitro cultures of isolates from Brazil and Africa have only recently been established. In this study, the efficacy of several cryoprotectants at different exposure times, cooling rates, and warming rates for protecting hyphal bodies of N. tanajoae during cryopreservation was investigated. A protocol for preservation of cultures of N. tanajoae at ultra-low temperatures of –80 °C or –196 °C, using 1% trehalose + 2% dimethyl sulfoxide as cryoprotective agents, is described in detail. In this study, we demonstrate that N. tanajoae differs remarkably from N. floridana (isolates ARSEF 662 and ARSEF 5376) in the ability to withstand the stress of cold temperature (4 °C) and cryopreservation. In vitro cultures of the 2 N. floridana isolates remained viable at 4 °C for up to 47 d; however, cultures of N. tanajoae did not survive this temperature for 4 d. Cryopreservation methods successful for N. tanajoae isolates are not suitable for N. floridana and are unusual in comparison to those for many fungi.Key words: Neozygites floridana, Mononychellus tanajoa, cryopreservation, fungal storage, Entomophthorales.
Pig slurry reduces the survival ofRalstonia solanacearumbiovar 2 in soil
Authors: Gorissen A , van Overbeek L S , van Elsas J D
Published: October 2004

The effect of added pig slurry and solarization on the survival of Ralstonia solanacearum biovar 2 strain 1609 in soil was analysed in soil microcosms and field plots. In addition, the invasion of potato plants by R. solanacearum and the development of disease symptoms were determined, as measures of induced disease suppressiveness. In untreated soil, R. solanacearum showed slow population declines in both microcosms and the field from, initially, 106–107to 103–104CFU·(g dry soil)–1in about 9 weeks. The suppressiveness assays of these untreated soils after this period revealed that most of the plants that were used developed wilting symptoms and (or) contained the pathogen in their lower stem parts, as shown by immunofluorescence colony staining and PCR. The addition of pig slurry resulted in a significantly lower population size of R. solanacearum as well as reduced numbers of infected and (or) diseased plants in the soil suppressiveness tests. On the other hand, solarization of soil also decreased R. solanacearum survival but did not enhance soil suppressiveness as measured by development of disease symptoms and (or) plant invasion after 9 weeks. Combined soil solarization and pig slurry addition showed an additive effect of both treatments. Healthy-looking plants, primarily from soils treated with pig slurry and solarization, incidentally revealed the latent presence of R. solanacearum in the lower stem parts. The mechanism behind the enhanced population declines and disease suppressiveness induced by pig slurry is unclear but shifts in community profiles were clearly discernible by PCR – denaturing gradient gel electrophoresis 9 weeks after pig slurry addition in the field experiment, indicating induced changes in the bacterial community structure.Key words: soil suppressiveness, organic amendment, solarization, DGGE analysis, immunofluorescence colony staining.
Field and soil microcosm studies on the survival and conjugation of aPseudomonas putidastrain bearing a recombinant plasmid, pADPTel
Authors: Hirkala Danielle L.M , Germida J J
Published: October 2004

Pseudomonas putida CR30RNS (pADPTel) is an antibiotic-resistant strain with a recombinant plasmid that confers resistance to tellurite and the ability to catabolize atrazine. The survival of this strain as well as its ability to transfer genes for atrazine degradation and tellurite resistance to indigenous soil bacteria were tested in both fallow soil and canola (Brassica napus) rhizosphere by the use of parallel field and laboratory releases. Culturable CR30RNS (pADPTel) were enumerated in field and microcosm soils at 7- to 14-day intervals over 49 d. Strain CR30RNS (pADPTel) survived for up to 7 weeks in microcosm soils at a density of 104CFU/g soil, whereas in field soils the population declined to 103CFU/g soil by the fourth week. In contrast, when CR30RNS (pADPTel) was introduced into the soil as a seed coating of canola (B. napus 'Karoo'), the bacterium established at higher cell densities in the rhizosphere (106–105CFU/g fresh root mass), with no subsequent decrease in numbers. The presence of selective pressure (i.e., atrazine) had no significant effect on the survival of CR30RNS (pADPTel) in either field or microcosm soils. One year postinoculation field sites were examined for the presence of CR30RNS (pADPTel) and no evidence of culturable parental cells was observed when samples were plated onto selective media. However, the atzC and telAB gene segments were amplified from the field soils at that time. Under laboratory conditions, indigenous soil bacteria were capable of receiving and expressing the engineered plasmid construct at frequencies ranging from 1 to 10-3transconjugants per donor. However, no plasmid transfer to indigenous soil bacteria was detected in the field or microcosm soils regardless of the presence of canola rhizosphere and (or) the application of atrazine. Our results show that the survival and population size of P. putida CR30RNS (pADPTel) might be sufficient for degradation of environmental pollutants but that the transfer frequency was too low to be detected under the conditions of this study.Key words: Pseudomonas putida CR30RNS (pADPTel), survival, gene transfer, field, microcosm.
Molecular and physiological comparisons betweenSaccharomyces cerevisiaeandSaccharomyces boulardii
Authors: Fietto Juliana L.R , Araújo Raquel S , Valadão Frederico N , Fietto Luciano G , Brandão Rogelio L , Neves Maria J , Gomes Fátima C.O , Nicoli Jacques R , Castro Ieso M
Published: October 2004

In this paper, comparative molecular studies between authentic Saccharomyces cerevisiae strains, related species, and the strain described as Saccharomyces boulardii were performed. The response of a S. boulardii strain and a S. cerevisiae strain (W303) to different stress conditions was also evaluated. The results obtained in this study show that S. boulardii is genetically very close or nearly identical to S. cerevisiae. Metabolically and physiologically, however, it shows a very different behavior, particularly in relation to growth yield and resistance to temperature and acidic stresses, which are important characteristics for a microorganism to be used as a probiotic.Key words: Saccharomyces boulardii, probiotic, stress response, rDNA.
Diversity ofcrygenes and genetic characterization ofBacillus thuringiensisisolated from Brazil
Authors: Vilas-Bôas Gislayne Trindade , Lemos Manoel Victor Franco
Published: October 2004

Two hundred and eighteen Bacillus thuringiensis isolates from Brazil were characterized by the presence of crystal protein genes by PCR with primers specific to different cry and cyt genes. Among these isolates, 95 were selected according to their geographic origin for genetic characterization with the 16S rRNA gene, RAPD, and plasmid profile. Isolates containing cry1 genes were the most abundant (48%) followed by the cry11 and cyt (7%) and cry8 genes (2%). Finally, 40.3% of the isolates did not produce any PCR product. The plasmid profile and RAPD analysis showed a remarkable diversity among the isolates of B. thuringiensis not observed in the 16S rRNA gene. These results suggest that the genetic diversity of B. thuringiensis species results from the influence of different ecological factors and spatial separation between strains generated by the conquest of different habitats.Key words: Bacillus thuringiensis, cry genes, 16S rRNA gene, RAPD, plasmid profile, genetic diversity, ecology.
Determining the environmental fate of a filamentous fungus,Trichoderma reesei, in laboratory-contained intact soil-core microcosms using competitive PCR and viability plating
Authors: Providenti Miguel A , Mautner Selma I , Chaudhry Omar , Bombardier Manon , Scroggins Richard , Gregorich Edward , Smith Myron L
Published: October 2004

Trichoderma spp. are used extensively in industry and are routinely disposed of in landfill sites as spent biomass from fermentation plants. However, little is known regarding the environmental fate of this biomass. We tracked the survival of T. reesei strain QM6A#4 (a derivative of strain QM6A marked with a recombinant construct) over a 6-month period in laboratory-contained, intact soil-core microcosms incubated in a growth chamber. Survival was tested in 3 different soils and the effect of a plant rhizosphere (bush lima beans, Phaseolus limensis) was investigated. Levels and viability of the fungus were determined, respectively, by quantitative competitive polymerase chain reaction analysis of total soil DNA extracts and dilution-plating of soil on a semiselective growth medium. Whereas chemically killed QM6A#4 became undetectable within 3 d, QM6A#4 added as a live inoculum decreased ~4- to ~160-fold over the first 1–3 months and then reached a steady state. After 4 months, soil cores were subjected to a 1.5-month simulated winter period, which did not significantly affect QM6A#4 levels. Throughout the experiment, QM6A#4 remained viable. These results indicate that, following release into the environment, live T. reesei will persist in soil for at least 2 seasons.Key words: competitive PCR, genetically engineered microorganisms (GEMs), genetically modified organism (GMO), survival of microorganisms, microcosm, Trichoderma.
Increased frequency of drug-resistant bacteria and fecal coliforms in an Indiana Creek adjacent to farmland amended with treated sludge
Authors: Selvaratnam Shivi , Kunberger J David
Published: October 2004

Many studies indicate the presence of human pathogens and drug-resistant bacteria in treated sewage sludge. Since one of the main methods of treated sewage disposal is by application to agricultural land, the presence of these organisms is of concern to human health. The goal of this study was to determine whether the frequency of drug-resistant and indicator bacteria in Sugar Creek, which is used for recreational purposes, was influenced by proximity to a farmland routinely amended with treated sludge (site E). Surface water from 3 sites along Sugar Creek (site E, 1 upstream site (site C) and 1 downstream site (site K)) were tested for the presence of ampicillin-resistant (AmpR) bacteria, fecal and total coliforms over a period of 40 d. Site E consistently had higher frequencies of AmpRbacteria and fecal coliforms compared with the other 2 sites. All of the tested AmpRisolates were resistant to at least 1 other antibiotic. However, no isolate was resistant to more than 4 classes of antimicrobials. These results suggest that surface runoff from the farmland is strongly correlated with higher incidence of AmpRand fecal coliforms at site E.Key words: drug-resistant bacteria, indicator bacteria, treated sludge, surface runoff.
SUBFACTORS OF A FACTOR OF TYPE IIIλ WHICH CONTAIN A MAXIMAL CENTRALIZER
Authors: HAAGERUP UFFE , STØRMER ERLING
Published: October 2004

If M is a factor of type IIIλ, 0<λ<1 we classify the subfactors which contain the centralizer of a periodic state or a generalized trace.
GLOBAL NONLINEAR POLYNOMIAL MODELS: STRUCTURE, TERM CLUSTERS AND FIXED POINTS
Authors: AGUIRRE LUIS ANTONIO , MENDES EDUARDO M. A. M.
Published: October 2004

In this paper, it is shown that the number and location of the fixed points of global nonlinear polynomials can be specified in terms of the term clusters and cluster coefficients of the respective models. It is also shown that if the structure (that is, the model basis) of a nonlinear polynomial model of degree ℓ includes all possible terms then such a model will always have ℓ nontrivial fixed points. In modeling problems, where the estimated polynomials are to reproduce fundamental invariants of the original system, this situation will not always be welcome and therefore suggests that the structure of polynomial models should be carefully chosen. Ways of achieving this are briefly mentioned.
BIFURCATIONAL BEHAVIOR OF THE STATE EQUATION FOR AN ASSEMBLY OF INTERACTING RESONATORS
Authors: PEREIRA J. VASSALO
Published: October 2004

We deduce a pde equation governing the evolution in time of the state (i.e., the distribution on the phases) of an ensemble of resonators interacting by means of their own emitting waves. A result due to Rayleigh (concerning the statistical properties of a superposition of a great number of identical waves) is generalized and provides the basic tool of this research. We find a "two mode” equation, whose structure changes for different ranges of the values of the distribution of the phases.
OPTIMAL RECONSTRUCTION SPACE FOR ESTIMATING CORRELATION DIMENSION
Authors: HILBORN ROBERT C. , DING MINGZHOU
Published: October 2004

In this paper we consider the estimation of the correlation dimension from a scalar chaotic time series using delay coordinates. Past work has shown that there appears to be a reconstruction space for which the correlation integral has the longest scaling region. We give a firmer foundation to this idea by developing a theory that estimates the dimension of this “optimal” reconstruction space in terms of dynamical quantities such as the largest Lyapunov exponent.
CENTRIFUGAL DESTABILIZATION AND RESTABILIZATION OF PLANE SHEAR FLOWS
Authors: CONLEY A. J.
Published: October 2004

The flow of an incompressible viscous fluid between parallel plates becomes unstable when the plates are tumbled. As the tumbling rate increases, the flow restabilizes. This phenomenon is elucidated by path-following techniques. The solution of the Navier-Stokes equations is approximated by spectral techniques. The linear stability of these solutions is studied.
CONTROL OF THE ARNOLD CIRCLE MAP
Authors: ARROWSMITH DAVID K. , LANSBURY ALEXIS N. , MONDRAGÓN C RAÚL J.
Published: October 2004

The phenomenon of entrainment is a critical feature of non-linear oscillation theory. In this paper we consider entrainment of the Arnold circle map. Specifically, we show how the map can be modified to produce local entrainment with small perturbations. We can predict the growth in size of the resonance region by which local entrainment can be optimised. We also consider the time-cost of targetting using chaotic regimes and local feedback control as developed by Ott, Grebogi and Yorke.
BIFURCATIONS IN A POWER SYSTEM MODEL
Authors: NAYFEH ALI H. , HARB AHMAD M. , CHIN CHAR-MING
Published: October 2004

Bifurcations are performed for a power system model consisting of two generators feeding a load, which is represented by an induction motor in parallel with a capacitor and a combination of constant power and impedance PQ load. The constant reactive power and the coefficient of the reactive impedance load are used as the control parameters. The response of the system undergoes saddle-node, subcritical and supercritical Hopf, cyclic-fold, and period-doubling bifurcations. The latter culminate in chaos. The chaotic solutions undergo boundary crises. The basin boundaries of the chaotic solutions may consist of the stable manifold of a saddle or an unstable limit-cycle. A nonlinear controller is used to control the subcritical Hopf and the period-doubling bifurcations and hence mitigate voltage collapse.
ENTROPY AND EXTENDED MEMORY IN DISCRETE CHAOTIC DYNAMICS
Authors: EBELING WERNER , FREUND JAN , RATEITSCHAK KATJA
Published: October 2004

We investigate simple one-dimensional maps which allow for exact solutions of their related statistical properties. In addition to the originally refined dynamical description a coarsegrained level of description based on certain partitions of the phase space is selected. The deterministic micropscopic dynamics is shifted to a stochastic symbolic dynamics. The higher order entropies are studied for the logistic map, the tent map, and the shark fin map. Markov sources of any prescribed order are constructed explicitly. In a special case, long memory tails are observed. Systems of this type may be of interest for modelling naturally ocurring phenomena.
A FINITE AUTOMATA MODEL OF SPIKING-BURSTING NEURONS
Authors: HUERTA R.
Published: October 2004

A simple qualitative model of spiking-bursting neurons is proposed. It is mainly built from the qualitative behavior observed in central pattern generators (CPG’s) and pacemaker neurons. It is a finite automata which is convenient for computer modelling even for large neural networks. The number of rules utilized in the finite automata are the minimum necessary to reproduce a great variety of phenomena. The validity of the model is determined using actual experimental measurements between two coupled neurons in CPG’s. We reproduce, in the framework of the model, the dynamic patterns observed in Tritonia’s escape swimming CPG. Finally, we study the dynamics of an open chain of 100 reciprocally coupled “symbolic neurons” and investigate the stable patterns reached with time.
MUTUAL AND SELF-COMPOUNDING OF CHAOTIC SYSTEMS
Authors: SINGH R. , MOHARIR P.S. , MARU V.M.
Published: October 2004

The notion of compounding a chaotic system was introduced earlier. It consisted of varying the parameters of the compoundee system in proportion to the variables of the compounder system, resulting in a compound system which has in general higher Lyapunov exponents. Here, the notion is extended to self-compounding of a system with a real-earth example, and mutual compounding of dynamic systems. In the former, the variables in a system perturb its parameters. In the latter, two systems affect the parameters of each other in proportion to their variables. Examples of systems in such compounding relationships are studied. The existence of self-compounding is indicated in the geodynamics of mantle convection. The effect of mutual compounding is studied in terms of Lyapunov exponent variations.
AN ODE WHOSE SOLUTIONS CONTAIN ALL KNOTS AND LINKS
Authors: GHRIST ROBERT W. , HOLMES PHILIP J.
Published: October 2004

Periodic orbits of a third-order ODE are topological knots. Using results from the theory of branched 2-manifolds, we prove the existence of simple ODEs whose periodic orbit set contains every type of knot and collection of knots (link). The construction depends on the dynamics near certain configurations of Shil'nikov connections, and can be applied to, among other things, a model of a nonlinear electric circuit.
ON DIMENSION OF NON-LOCAL BIFURCATIONAL PROBLEMS
Authors: TURAEV D.
Published: October 2004

An analogue of the center manifold theory is proposed for non-local bifurcations of homo- and heteroclinic contours. In contrast with the local bifurcation theory it is shown that the dimension of non-local bifurcational problems is determined by the three different integers: the geometrical dimension dg which is equal to the dimension of a non-local analogue of the center manifold, the critical dimension dc which is equal to the difference between the dimension of phase space and the sum of dimensions of leaves of associated strong-stable and strong-unstable foliations, and the Lyapunov dimension dL which is equal to the maximal possible number of zero Lyapunov exponents for the orbits arising at the bifurcation. For a wide class of bifurcational problems (the so-called semi-local bifurcations) these three values are shown to be effectively computed. For the orbits arising at the bifurcations, effective restrictions for the maximal and minimal numbers of positive and negative Lyapunov exponents (correspondingly, for the maximal and minimal possible dimensions of the stable and unstable manifolds) are obtained, involving the values dc and dL. A connection with the problem of hyperchaos is discussed.
FROM ALMOST PERIODIC TO CHAOTIC: THE FUNDAMENTAL MAP
Authors: BROWN RAY , CHUA LEON O.
Published: October 2004

In this paper we present a single map that displays an extraordinary range of dynamics that lies between the Bernoulli maps and almost periodic maps. Of central importance is the fact that this map illustrates how almost-periodic dynamics evolves into Bernoulli dynamics. Due to its continuous spectrum of dynamics between Bernoulli and almost periodic, we call this map the fundamental map in contrast to the better known standard map. The range of dynamics found in this map suggests that as order gives way to chaos, both the geometry of the orbit and the sequence of coordinates of the points of the orbit evolve from order to disorder. An interesting point brought out by this map is that the spatial and temporal properties of orbits near each end of the scale bear some striking similarities. Additionally, we show how to derive a Poincaré map from the fundamental map and derive the associated ODE, an equation for an electronic circuit.
A REMARK CONCERNING THE THERMODYNAMICAL LIMIT OF THE LYAPUNOV SPECTRUM
Authors: SINAI Ya. G.
Published: October 2004

We consider dynamical systems of N particles confined in domains of volume V with pair-wise short range interaction. We propose a new definition of the limiting distribution of Lyapunov Spectrum according to which the thermodynamical limit transition is taken before the limit t→∞. The main result proven under rather general conditions gives the existence of this modified limiting distribution of Lyapunov Spectrum.
HOMOCLINIC ORBITS BIFURCATIONS OF ONE- AND TWO-DIMENSIONAL MAPS
Authors: BELYKH V. N.
Published: October 2004

We study the 1D and 2D maps arising in applications. The bifurcation set exhibiting a box-within-a-box structure for the 1D map is discussed from the homoclinic orbits existence point of view. Some theorems on the bifurcations of nonrough Poincaré homoclinic curves are stated for 2D maps. We introduce the transition of the phase pictures from the closed invariant curve to the complicated homoclinic structures. The latter may be interpreted as a version of torus break-down for a corresponding flow of the 3D vector field.
NUMERICAL COMPUTATIONS OF CONNECTING ORBITS IN DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS
Authors: BAI FENGSHAN , LORD GABRIEL J. , SPENCE ALASTAIR
Published: October 2004

The aim of this paper is to present a numerical technique for the computation of connections between periodic orbits in nonautonomous and autonomous systems of ordinary differential equations. First, the existence and computation of connecting orbits between fixed points in discrete dynamical systems is discussed; then it is shown that the problem of finding connections between equilibria and periodic solutions in continuous systems may be reduced to finding connections between fixed points in a discrete system. Implementation of the method is considered: the choice of a linear solver is discussed and phase conditions are suggested for the discrete system. The paper concludes with some numerical examples: connections for equilibria and periodic orbits are computed for discrete systems and for nonautonomous and autonomous systems, including systems arising from the discretization of a partial differential equation.