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Impact of nitrogen and phosphorus on [C]lignocellulose decomposition by stream wood microflora.

Nutritional and physical factors affecting the decomposition of [C]lignocellulose prepared from Douglas fir (Pseudotsuga menziesii) were examined by incubating the labeled substrate with homogenized surface wood scrapings obtained from a Douglas fir log in a Pacific Northwest stream. Incubations were conducted in distilled water, in stream water collected from four different sources, or in a defined mineral salts solution with or without supplemental N (KNO(3)). Decomposition rates of [C]lignocellulose, as measured by CO(2) evolution, were greater in each of the four filter-sterilized sources of stream water than in distilled water alone. Decomposition experiments conducted in stream water media with the addition of defined mineral salts demonstrated that [C]cellulose decomposition was stimulated 50% by the addition of either KNO(3) or KH(2)PO(4)/K(2)HPO(4) and further enhanced (167%) by a combination of both. In contrast, [C]lignin decomposition was stimulated (65%) only by the addition of both N and P. Decomposition of [C]lignocellulose was greatest when supplemental KNO(3) was supplied in concentrations of at least 10.0 mg of N liter but not increased further by higher concentrations. The decomposition of [C]lignocellulose increased as the incubation temperature was raised and NO(3)-N supplementation further increased these rates between three-and sevenfold over the range of temperatures examined (5 to 22 degrees C). Accumulation of NH(4) (2 to 4 mg of N liter) was always observed in culture filtrates of incubations which had been supplemented with KNO(3), the quantity being independent of NO(3) concentrations >/= 10 mg of N liter. The role of supplemental NO(3) in the decomposition of [C]lignocellulose is discussed in relation to wood decomposition and the low concentrations of N found in stream ecosystems of the Pacific Northwest.

Journal Article↗

Cloning and sequencing of an Agrobacterium tumefaciens beta-glucosidase gene involved in modifying a vir-inducing plant signal molecule.

Induction of Agrobacterium tumefaciens virulence genes by plant phenolic compounds is essential for successful T-DNA transfer to a host plant. In Douglas fir needles, the major virulence region inducer is the glycoside coniferin (J. W. Morris and R. O. Morris, Proc. Natl. Acad. Sci. USA 87:3612-3618, 1990). Agrobacterium strains with high beta-glucosidase activity respond to coniferin and infect Douglas fir seedlings, whereas most strains with low beta-glucosidase activity fail to respond to coniferin and are avirulent on this host. We have cloned two beta-glucosidase genes from A. tumefaciens B3/73 and sequenced one of them, cbg1. It appears to be part of a polycistronic unit and shows a high bias for GC-rich codons. When expressed in Escherichia coli, Cbg1 beta-glucosidase hydrolyzes coniferin but not cellobiose. The 88-kDa predicted product of cbg1 is highly similar to one other bacterial beta-glucosidase and several fungal beta-glucosidases. There is little homology between Cbg1 and other bacterial beta-glucosidases, including an Agrobacterium cellobiase.

Agrobacterium tumefaciens↗

FBPs are calibrated molecular tools to adjust gene expression.

The three far-upstream element (FUSE) binding protein (FBP) family members have been ascribed different functions in gene regulation. They were therefore examined with various biochemical, molecular biological, and cell biological tests to evaluate whether their sequence differences reflect functional customization or neutral changes at unselected residues. Each FBP displayed a characteristic profile of intrinsic transcription activation and repression, binding with protein partners, and subcellular trafficking. Although some differences, such as weakened FBP3 nuclear localization, were predictable from primary sequence differences, the unexpected failure of FBP3 to bind the FBP-interacting repressor (FIR) was traced to seemingly conservative substitutions within a small patch of an N-terminal alpha-helix. The transactivation strength and the FIR-binding strength of the FBPs were in the opposite order. Despite their distinguishing features and differential activities, the FBPs traffic to shared subnuclear sites and regulate many common target genes, including c-myc. Though a variety of functions have been attributed to the FBPs, based upon their panel of shared and unique features, we propose that they constitute a molecular regulatory kit that tunes the expression of shared targets through a common mechanism.

Amino Acid Sequence↗

Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci.

Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.

Alleles↗

Sufficient conditions for error backflow convergence in dynamical recurrent neural networks.

This article extends previous analysis of the gradient decay to a class of discrete-time fully recurrent networks, called dynamical recurrent neural networks, obtained by modeling synapses as finite impulse response (FIR) filters instead of multiplicative scalars. Using elementary matrix manipulations, we provide an upper bound on the norm of the weight matrix, ensuring that the gradient vector, when propagated in a reverse manner in time through the error-propagation network, decays exponentially to zero. This bound applies to all recurrent FIR architecture proposals, as well as fixed-point recurrent networks, regardless of delay and connectivity. In addition, we show that the computational overhead of the learning algorithm can be reduced drastically by taking advantage of the exponential decay of the gradient.

Journal Article↗

Adaptive clutter filtering via blind source separation for two-dimensional ultrasonic blood velocity measurement.

A method for adaptive clutter rejection via blind source separation (BSS) using principal and independent component analyses is presented in application to blood velocity measurement in the carotid artery. In particular, the filtering method's efficacy for eliminating clutter and preserving lateral blood flow signal components is presented. The performance of IIR filters is compromised by shorth data ensembles (10 to 20 temporal samples) as implemented for color-flow and high frame-rate imaging due to initialization requirements. Further, the ultrasonic imaging system's transfer function maps axial wall and lateral blood motion to overlapping spectra. As such, frequency domain-based approaches to wall filtering are ineffective for distinguishing wall from blood motion signals. Rather than operating in the frequency domain. BSS performs clutter rejection by decomposing the input data ensemble into N constitutive source signals in time, where N is the ensemble length. Source signal energy coupled with respective signal depth and time course profiles reveal which source signals correspond to blood, noise and clutter components. Clutter components may then be removed without disruption of lateral blood flow information needed for two-dimensional blood velocity measurement. A simplistic data simulation is employed to offer an intuitive understanding of BSS methods for signal separation. The adaptive BSS filter is further demonstrated using a Field II simulation of blood flow through the carotid artery including tissue motion. BSS clutter filter performance is compared to the performance of FIR, IIR and polynomial regression clutter filters. Finally, the filter is employed for clinical application using a Siemens Elegra scanner, carotid artery data with lateral blood flow collected from healthy volunteers, and Speckle Tracking; velocity magnitude and angle profiles are shown. Once again, the BSS clutter filter is contrasted to FIR, IIR and polynomial regression clutter filters using clinical examples. Velocities computed with Speckle Tracking after BSS wall filtering are highest in the center of the artery and diminish to low velocities near the vessel walls, with velocity magnitudes consistent with physiological expectations. These results demonstrate that the BSS adaptive filter sufficiently suppresses wall motion signal for clinical lateral blood velocity measurement using data ensembles suitable for color-flow and high frame-rate imaging.

Blood Flow Velocity↗

Blood flow estimation error with intravascular ultrasound due to in-plane component of flow.

Previously, we presented a real-time method to measure blood flow perpendicular to the image plane of an intravascular ultrasound (IVUS) imaging system using a slow-time FIR (finite impulse response) filter bank. Any in-plane flow introduces error in the flow measurement using the filter bank algorithm. Simulations show that for a flow angle of +/- 10 degrees and velocities between 200 mm/s and 300 mm/s, the energy within the lowest frequency band filter is 6.92 to 7.80 times higher than for perpendicular flow in the worst case. We present a variation of the FIR filter bank algorithm, applying filter coefficients in a tilted fashion to slow-time signals (i.e., combining slow-time and fast-time). An appropriate tilt, which depends on the flow angle and velocity, corrects for the increased energy under the frequency bands. In this case, the energy under the lowest frequency band filter for an angle of +/- 10 degrees and velocities ranging from 200 mm/s to 300 mm/s is 2.09 to 2.94 times higher than for perpendicular flow, yielding greater than a factor of three improvement in the worst case over the original slow-time method. Moreover, the average energy over the vessel determined with the appropriate tilt is within 2-3% of the true value.

Algorithms↗

Modeling acoustic attenuation of soft tissue with a minimum-phase filter.

Soft biological tissue has been observed to exhibit an acoustic attenuation log-magnitude characteristic which increases as an approximately linear function of frequency. This paper describes the implementation of a finite-impulse-response (FIR) digital filter model for simulating this behavior on a digital computer. To insure that the filter is causal, the minimum-phase constraint is imposed. For minimum-phase filters, the log-magnitude and phase characteristics form a Hilbert Transform pair. The discrete-time Hilbert Transform of the linear log-magnitude characteristic was evaluated to determine the phase of the filter. The inverse Fourier Transform of the resulting real and imaginary components of the frequency transform produces the finite-duration unit-sample response of the digital filter model. Experimental results using plexiglas material, which has a linear-with-frequency loss characteristic, indicate that the minimum-phase model is more accurate than the linear-phase model, resulting in a rms error between predicted and observed time waveforms that is 3 times smaller. The effects of varying the sampling period and the size of the FIR filter are discussed. A FORTRAN program to calculate the minimum-phase unit-sample response from the slope of the log-magnitude characteristic is included in the Appendix.

Computers↗

Estimation of hospital emergency room data using OTC pharmaceutical sales and least mean square filters.

BACKGROUND: Surveillance of Over-the-Counter pharmaceutical (OTC) sales as a potential early indicator of developing public health conditions, in particular in cases of interest to Bioterrorism, has been suggested in the literature. The data streams of interest are quite non-stationary and we address this problem from the viewpoint of linear adaptive filter theory: the clinical data is the primary channel which is to be estimated from the OTC data that form the reference channels. METHOD: The OTC data are grouped into a few categories and we estimate the clinical data using each individual category, as well as using a multichannel filter that encompasses all the OTC categories. The estimation (in the least mean square sense) is performed using an FIR (Finite Impulse Response) filter and the normalized LMS algorithm. RESULTS: We show all estimation results and present a table of effectiveness of each OTC category, as well as the effectiveness of the combined filtering operation. Individual group results clearly show the effectiveness of each particular group in estimating the clinical hospital data and serve as a guide as to which groups have sustained correlations with the clinical data. CONCLUSION: Our results indicate that Multichannel adaptive FIR least squares filtering is a viable means of estimating public health conditions from OTC sales, and provide quantitative measures of time dependent correlations between the clinical data and the OTC data channels.

Adolescent↗

Drosophila Hfp negatively regulates dmyc and stg to inhibit cell proliferation.

Mammalian FIR has dual roles in pre-mRNA splicing and in negative transcriptional control of Myc. Here we show that Half pint (Hfp), the Drosophila orthologue of FIR, inhibits cell proliferation in Drosophila. We find that Hfp overexpression potently inhibits G1/S progression, while hfp mutants display ectopic cell cycles. Hfp negatively regulates dmyc expression and function, as reducing the dose of hfp increases levels of dmyc mRNA and rescues defective oogenesis in dmyc hypomorphic flies. The G2-delay in dmyc-overexpressing cells is suppressed by halving the dosage of hfp, indicating that Hfp is also rate-limiting for G2-M progression. Consistent with this, the cycle 14 G2-arrest of stg mutant embryos is rescued by the hfp mutant. Analysis of hfp mutant clones revealed elevated levels of Stg protein, but no change in the level of stg mRNA, suggesting that hfp negatively regulates Stg via a post-transcriptional mechanism. Finally, ectopic activation of the wingless pathway, which is known to negatively regulate dmyc expression in the wing, results in an accumulation of Hfp protein. Our findings indicate that Hfp provides a critical molecular link between the developmental patterning signals induced by the wingless pathway and dMyc-regulated cell growth and proliferation.

Animals↗

Far-infrared laser measurement of the refractive index of polypropylene.

The refractive index of polypropylene in the far infrared (FIR) is measured by means of a suitably modified laser of a FIR spectrometer. When thin polypropylene films of 12.7-microm nominal thickness are introduced in the optical cavity of a laser at the Brewster angle, the radiation ceases because of the change in the optical path of the laser beam. This change is measured from the displacement of one of the laser mirrors, which is necessary to restore the laser resonance. The refractive index of polypropylene is deduced from this measurement and from the film thickness, as obtained from an independent measurement based in pycnometry. The value obtained for the refractive index is 1.492(15) for the wavelengths between 118.834 and 251.140 microm, for a polypropylene film of 12.71(2)-microm thickness and 0.9049(7) g/cm3 density.

Journal Article↗

Particle swarm optimization-based approach for optical finite impulse response filter design.

This study presents what is to our knowledge a new and efficient method for the design of an optical finite impulse response (FIR) filter by employing a particle swarm optimization technique. With the method proposed, the design of an optical FIR filter, which is able to provide an arbitrary spectrum output based on crystal birefringence, could be implemented with good performance and high efficiency. The design procedure is discussed. A typical example of a green/magenta filter used in a liquid crystal on silicon projection display is included to demonstrate the feasibility and efficiency of this method in this design process as compared with simulated annealing.

Journal Article↗

Design of Stark-tuned far-infrared laser with circular hollow waveguide.

A novel design of a Stark-tuned far-infrared laser using a circular hollow dielectric waveguide is proposed, and its characteristics are studied. Supplementary electrodes are inserted inside the circular hollow dielectric tube to suppress charge accumulation while keeping field uniformity. In what is believed to be a new design, the mode property is found to be improved, and the angular dependency of the attenuation loss according to the beam polarization is estimated to be much smaller than that of the conventional rectangular hybrid waveguide design. In this new design, DeltaM=0 far-infrared (FIR) transition as well as DeltaM=+/-1 transition can be observed, and the power enhancement for the DeltaM=0 FIR transition is expected.

Journal Article↗

Coherent multiwave heterodyne frequency measurement of a far-infared laser by means of a femtosecond laser comb.

We demonstrate the possibility of using a femtosecond laser to measure with high accuracy the frequency of a far-infrared (FIR) monochromatic source, such as an optically pumped molecular laser, by generating in a suitable mixer a signal in the radio-frequency region at the frequency difference between n steps of a femtosecond comb and the FIR source. All the couples of modes lying a distance of n steps from one another contribute coherently to the heterodyne signal. The technique has been tested up to 670 GHz.

Journal Article↗

Digital filtering implementations for the detection of broad spectral features by direct analysis of passive Fourier transform infrared interferograms.

Finite impulse response (FIR) filters and finite impulse response matrix (FIRM) filters are evaluated for use in the detection of volatile organic compounds with wide spectral bands by direct analysis of interferogram data obtained from passive Fourier transform infrared (FT-IR) measurements. Short segments of filtered interferogram points are classified by support vector machines (SVMs) to implement the automated detection of heated plumes of the target analyte, ethanol. The interferograms employed in this study were acquired with a downward-looking passive FT-IR spectrometer mounted on a fixed-wing aircraft. Classifiers are trained with data collected on the ground and subsequently used for the airborne detection. The success of the automated detection depends on the effective removal of background contributions from the interferogram segments. Removing the background signature is complicated when the analyte spectral bands are broad because there is significant overlap between the interferogram representations of the analyte and background. Methods to implement the FIR and FIRM filters while excluding background contributions are explored in this work. When properly optimized, both filtering procedures provide satisfactory classification results for the airborne data. Missed detection rates of 8% or smaller for ethanol and false positive rates of at most 0.8% are realized. The optimization of filter design parameters, the starting interferogram point for filtering, and the length of the interferogram segments used in the pattern recognition is discussed.

Journal Article↗

Strategies to enhance the enzymatic hydrolysis of pretreated softwood with high residual lignin content.

Pretreatment of Douglas-fir by steam explosion produces a substrate containing approx 43% lignin. Two strategies were investigated for reducing the effect of this residual lignin on enzymatic hydrolysis of cellulose: mild alkali extraction and protein addition. Extraction with cold 1% NaOH reduced the lignin content by only approx 7%, but cellulose to glucose conversion was enhanced by about 30%. Before alkali extraction, addition of exogenous protein resulted in a significant improvement in cellulose hydrolysis, but this protein effect was substantially diminished after alkali treatment. Lignin appears to reduce cellulose hydrolysis by two distinct mechanisms: by forming a physical barrier that prevents enzyme access and by non-productively binding cellulolytic enzymes. Cold alkali appears to selectively remove a fraction of lignin from steam-exploded Douglas-fir with high affinity for protein. Corresponding data for mixed softwood pretreated by organosolv extraction indicates that the relative importance of the two mechanisms by which residual lignin affects hydrolysis is different according to the pre- and post-treatment method used.

Cell Culture Techniques↗

Thresholds for perception of ripple depth in the passband of a low-pass filter.

Filters are often used in research related to speech and tone perception. Idealized filters with flat pass-bands, flat stop-bands, and infinitely steep rolloff are impossible to implement, thus practical filters often have a frequency response curve that has a certain degree of ripple, and always have finite rolloff. Despite this, there is a dearth of literature concerning the sensitivity of the ear to such artifacts. In the current study we examined the threshold of sensitivity to ripple depth in the pass-band of a digital low pass finite impulse response (FIR) filter. FIR filters are often used due to their lack of phase distortion, and due to the fact that their ripple depth can be closely controlled. Using an adaptive threshold detection paradigm, we found the threshold of noticeable ripple depth to be 2.7 dB (SD = 1.45) for filtered noise, and 4.89 dB (SD = 2.09) for a filtered chirp signal. This is significantly larger than the difference limen in intensity (DLI) for noise or pure tones. Notably, the threshold for filtered noise is significantly lower and more uniform across subjects, compared to the threshold for a filtered chirp signal. We conclude that these issues must be addressed when the necessity for filtering arises, though they cannot be considered independently of the signals themselves.

Acoustic Stimulation↗

Cerebral palsy and fetal inflammatory response syndrome: a review.

Cerebral palsy (CP) is the most common cause of severe physical disability in childhood. The precise etiological factor for the development of the majority of cases of CP has not been identified, however, prematurity is considered to be the leading identifiable risk factor. During the last decade, intrauterine infection/inflammation has been identified as the most common cause of preterm delivery and neonatal complications. When microorganisms or their products gain access to the fetus they stimulate the production of cytokines and a systemic response termed FIRS (Fetal Inflammatory Response Syndrome). Subsequently, FIRS was implicated as a cause of fetal or neonatal injury that leads to CP and chronic lung disease. Several authors found an increase in the risk for CP in infants born to mothers with clinical chorioamnionitis, especially in preterm neonates. A relationship between CP and intra-amniotic inflammation was demonstrated, intrauterine infection may lead to activation of the cytokine network which in turn can cause white matter brain damage and preterm delivery, as well as the future development of CP. This white matter insult is identified clinically as periventricular leucomalacia (PVL) which is associated with the subsequent development of impaired neurological outcomes of variable severity including CP.

Cerebral Palsy↗