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PubMed2003

Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin.

Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.

Bacteriorhodopsins↗
PubMed2003

Developmental regulation of FERM domain including guanine nucleotide exchange factor gene expression in the mouse brain.

FERM domain including Rho GEF (FIR) is one of the guanine nucleotide exchange factors for Rac1. FIR, expressed in hippocampal and cortical neurons in vitro, is suggested to be involved in neurite remodeling. We examine developmental regulation of FIR mRNA expression in the mouse brain using in situ hybridization to get insight into its function. FIR mRNA is expressed in the ventricular zone and the intermediate zone as well as the cortical plate and the preplate in the brain from mice during the embryonic stages 12.5 to 14.5. In the brain during the later embryonic stages and the postnatal stages, the expression was restricted to the cortical plate. These results suggest that FIR may play a role not only in neurogenesis, but also in the asymmetrical cell division and migration of neurons.

Animals↗
PubMed2005

Effect of far-infrared irradiation on the antioxidant activity of defatted sesame meal extracts.

To determine the effect of far-infrared (FIR) irradiation on the antioxidant activities of sesame meal, half of sesame seeds were FIR-irradiated and then oil was extracted from the seeds. The resulting defatted sesame meal (DSM) was extracted with methanol, and the antioxidant activities of methanolic extract were determined. FIR irradiation of sesame seeds for 30 min increased the total phenol content from 34.0 to 59.0 muM and radical scavenging activity of DSM extracts from 26.40 to 68.76%. The induction time of lipid oxidation of oil added to extracts was also retarded from 0.82 to 0.96 h. According to the gas chromatography-mass spectrometry analysis, several low molecular weight phenolic compounds, such as p-hydroxy benzoic acid, vanillic acid, p-coumaric acid, isoferulic acid, and o-coumaric acid, were frequently detected in FIR-irradiated DSM extracts as compared to unirradiated ones. These results indicated that FIR irradiation of sesame seeds increased the antioxidant activity of methanolic extracts of DSM.

Antioxidants↗
PubMed2006

Application of far-infrared irradiation in the manufacturing process of green tea.

Seven kinds of green tea leaves were manufactured with far-infrared (FIR) irradiation, and the physicochemical characteristics of the green tea were determined. Appropriate FIR irradiation during the manufacturing process significantly increased the polyphenolic content of green tea. FIR irradiation at 90 degrees C for 10 min, replacing the roasting step, and of the fully processed green tea leaves (GTP3) increased the total phenol content of green tea from 475.6 to 811.1 mg/g and the total flavanol content from 175.7 to 208.7 mg/g, as compared to the control. Epigallocatechin and epigallocatechin gallate increased from 57.68 and 9.60 mg/g in a nonirradiated control to 89.88 and 16.33 mg/g in GTP3, respectively. Ascorbic acid, caffeine, and nitrite scavenging activities were also increased in GTP3. However, the overall color change of GTP3 was negligible. These results indicate that the chemical properties of green tea are significantly affected by FIR irradiation at specific stages of the manufacturing process of green tea leaves and that this FIR irradiation results in high-quality green tea.

Ascorbic Acid↗
PubMed2004

Habitat-related variation in infestation of lizards and rodents with Ixodes ticks in dense woodlands in Mendocino County, California.

During the spring and early summer of 2002, we examined the relative importance of Borrelia-refractory lizards (Sceloporus occidentalis, Elgaria spp.) versus potential Borrelia burgdorferi sensu lato (s.l.)-reservoirs (rodents) as hosts for Ixodes pacificus immatures in 14 woodland areas (six oak, five mixed oak/Douglas fir, and three redwood/tanoak areas) distributed throughout Mendocino County, California. Lizards were estimated to serve as hosts for 93-98% of all larvae and > or =99.6% of all nymphs infesting lizards or rodents in oak woodlands and oak/Douglas fir sites in the southern part of the county. In redwood/tanoak woodlands and oak/Douglas fir sites in northern Mendocino County, the contribution of rodents to larval feedings reached 36-69% but lizards still accounted for 94-100% of nymphal bloodmeals. From late April to mid-June, I. pacificus larvae were recovered from 95 to 96% of lizards and dusky-footed woodrats (Neotoma fuscipes) and from 59% of Peromyscus spp. mice. In contrast, 99% of lizards but few woodrats (15%) and none of the mice were infested by nymphs. Comparisons of tick loads for 19 lizard-Peromyscus spp. mouse pairings, where the lizard and mouse were captured within 10m of each other, revealed that the lizards harbored 36 times more larvae and >190 times more nymphs than the mice. In oak woodlands, loads of I. pacificus larvae decreased from late April/early May to late June for S. occidentalis lizards but increased for Peromyscus spp. mice. We conclude that the relative utilization of Borrelia-refractory lizards, as compared to rodents, by I. pacificus larvae was far higher in dry oak woodlands than in moister habitats such as redwood/tanoak and oak/Douglas fir woodlands in northern Mendocino County. Non-lizard-infesting potential enzootic vectors of B. burgdorferi s.l. (I. angustus and I. spinipalpis) were recorded from rodents in three of six oak woodland areas, two of five oak/Douglas fir woodland areas, and two of three redwood/tanoak woodland areas.

Animals↗
PubMed2002

Effects of hydroxyapatite in combination with far-infrared rays on spontaneous mammary tumorigenesis in SHN mice.

We have found that the administration of a diet containing 5% hydroxyapatite (HAP) derived from pig and cattle bones, and exposure to far-infrared rays (FIR) markedly inhibited spontaneous mammary tumorigenesis in SHN mice. Thus, the effect of combined treatment with HAP and FIR on mammary tumorigenesis was examined. The significant inhibition of tumor development by individual treatment with HAP or FIR was not enhanced by combined treatment; instead, the decrease in the inhibitory effect of HAP with age was ameliorated. Associated with this, life span was elongated and a decline in ovarian function was prevented by HAP plus FIR. Normal and preneoplastic growth of mammary glands and plasma component levels were not significantly affected by any treatment. The findings indicate that HAP and FIR have characteristics common to most natural products; in combination with other agents, they have little additive effect, when each is highly active.

Animals↗
PubMed2002

Photon absorption in resonant-cavity-enhanced gaas far-infrared detectors.

Interface reflection has been demonstrated to play an important role in GaAs multilayer homojunction far-infrared (FIR) detectors. A transfer matrix method that is able to provide a true optical field distribution within an FIR detector has been employed to optimize photon absorption and structure. The dependence of photon absorption on the reflectivity and the phase shift of the bottom mirror in a resonant-cavity-enhanced GaAs FIR detector has been investigated. Weak wavelength selectivity has been observed for both resonant and off-resonant FIR, which is a unique advantage for detector application. In comparison with the experimental result, a 20.8% increase in quantum efficiency was found in an optimized FIR detector.

Journal Article↗
PubMed2005

Special relationships between fetal inflammatory response syndrome and bronchopulmonary dysplasia in neonates.

OBJECTIVE: To confirm previous known relationships between Fetal Inflammatory Response Syndrome (FIRS) and neonatal bronchopulmonary dysplasia (BPD) and to present information on previously unknown special relationships between inflammatory variables and BPD. STUDY DESIGN: At delivery, we obtained biological specimens including umbilical cord venous blood for plasma interleukin-6 levels, as well as placental histology and bacteriology. Among other neonatal outcomes, we collected prospective information on BPD. RESULTS: Of 141 newborns in the study, 16 had BPD; 79% of these had antecedent FIRS, 27% of those without FIRS had BPD. By multivariable regression, only very low birth weight (adjusted [adj] odds ratio [OR] 32.0, 95% Confidence Interval [CI] 5.0 to positive infinity) and FIRS (adj OR 5.7, 95% CI 1.1 to 42.3) remained significant risk factors. Escherichia coli, perhaps due to its pyogenic nature (strongly elicits inflammatory responses), may have had a special relationship with BPD. CONCLUSIONS: In our data, FIRS and neonatal BPD are highly associated. It is possible that certain pyogenic bacteria in the chorioamnion space may be implicated more often than others. CONDENSATION: Neonates having Fetal Inflammatory Response Syndrome at delivery may later develop BPD. Pyogenic bacteria, such as Escherichia coli, may be implicated more frequently.

Bronchopulmonary Dysplasia↗
PubMed2002

Elution rate and spacing of antiaggregation pheromone dispensers for protecting live trees from Dendroctonus pseudotsugae (Coleoptera: Scolytidae).

The antiaggregation pheromone 3-methylcyclohex-2-en-1-one (MCH) is highly effective in preventing the infestation of high-risk trees by Douglas-fir beetle, Dendroctonus pseudotsugae Hopkins. A large portion of the cost of an MCH treatment is related to the time applicators spend walking through an area dispersing the formulated pheromone. Application of fewer MCH dispensers eluting at a higher rate than those currently registered for operational use could potentially reduce treatment costs. Two higher elution rates, 6 and 18 mg/d per dispenser, were compared with the current standard of 2 mg/d per dispenser and an untreated control on 1-ha circular plots. Dispensers were spaced 5,15, and 44 m apart around the plot perimeters eluting 2, 6, and 18 mg/d, respectively. The nominal dose of MCH was 144 mg/ha/d on all plots. Percentages of Douglas-fir trees > or = 20 cm diameter at breast height mass attacked by Douglas-fir beetle were significantly lower on plots treated with dispensers eluting 2 and 6 mg/d and spaced 5 and 15 m apart, respectively, compared with the untreated control. Infestation rate on plots treated with dispensers eluting 18 mg/d and spaced 44 m apart was not significantly different from the control. Douglas-fir beetle abundance and host tree availability were similar on all plots. These results indicate that MCH dispensers eluting 6 mg/d (three times the current standard rate) and spaced 15 m apart (three times existing standard distance) can effectively prevent Douglas-fir beetle infestations.

Animals↗
PubMed2002

Molecular cloning, identification and characterization of four distinct receptor subtypes for insulin and IGF-I in Japanese flounder, Paralichthys olivaceus.

Insulin receptor (IR) and IGF-I receptor (IGF-IR) are structurally and functionally related and belong to the tyrosine kinase receptor family. In teleosti such as salmonids and turbot, occurrence of multiple IR and IGF-IR members has been reported, but the structures of a complete set of both IR and IGF-IR members in a single teleost species have not yet been characterized. In this study, we cloned and analysed four distinct cDNA clones for IR and IGF-IR members from the liver and kidney of the Japanese flounder (Paralichthys olivaceus). Deduced amino acid sequence analyses and phylogenetic analysis have revealed that two of them (fIR-1 and fIR-2) belong to IR members and the other two (fIGF-IR-1 and fIGF-IR-2) are IGF-IRs. fIR-1 and fIR-2 comprised 1369 and 1368 amino acid residues respectively, and fIGF-IR-1 and fIGF-IR-2 comprised 1412 and 1418 residues respectively. All the receptor proteins contained cysteine-rich domains in their alpha-subunits, and conserved each transmembrane and tyrosine kinase domains in their beta-subunits. The amino acid sequences of fIRs and fIGF-IRs showed more than 90% sequence identity with turbot IR and IGF-IR respectively. When compared with their mammalian homologues, fIGF-IR-1 and fIGF-IR-2 proteins contained large insertions at their C-termini, as was observed in the corresponding region of turbot IGF-IR. Occurrence of multiple species of mRNA for each IR and IGF-IR was suggested by Northern blot analyses. A ribonuclease protection assay revealed diverse expressions of four receptor mRNAs in a wide range of tissues including heart, liver, ovary, testis, brain, gill arch, kidney, skeletal muscle, intestine, stomach, spleen and eye of the flounder.

5' Untranslated Regions↗
PubMedDate not supplied

Evidence that irradiation of far-infrared rays inhibits mammary tumour growth in SHN mice.

To evaluate the effect of irradiation of far infrared rays (FIR), the growth of spontaneous mammary tumours of SHN mice was compared among 3 groups: the control was kept until the end of experiment on the normal rack in the absence of FIR and Experimental group I was constantly exposed to FIR. Experimental group Il was raised as the control followed by movement to the FIR rack after mammary tumour appearance. While there was little difference between the control and Experimental group I in mammary tumour growth for 16 days, Experimental group II was significantly lower than the control in this parameter. Furthermore, the percentage of rapidly growing tumours showing greater than 200% of growth rate was apparently lower in Experimental group II. Associated with this, epidermal growth factor receptor expression in mammary tumours, anterior pituitary weight and serum leptin level were significantly decreased in Experimental group II. The findings suggest that whole-body FIR irradiation at ambient temperature could be a possible way of a hyperthermic therapy for tumours.

Animals↗
PubMedDate not supplied

Effects of far-infrared ray on reproduction, growth, behaviour and some physiological parameters in mice.

The effects of chronic exposure to far-infrared ray (FIR) on reproduction, growth, behaviour, survival time and some related parameters were examined in SHN mice. The reproductive parameters differed slightly between the females on the normal racks and those on the FIR racks, which emitted FIR from the ceiling. The age and body weight on the day of vaginal opening was lower in the experimental mice born and maintained on the FIR rack than in the control on the normal rack. In both sexes, the levels of urinary components in the experimental group was significantly higher than the control at 6-7 months of age. Spontaneous motor activity of females during the light and dark phases were higher and lower, respectively, in the experimental group than the control. The survival rate was significantly higher in the experimental group than the control. These findings suggest that FIR has 'normalization effects' on the organisms.

Animals↗
PubMed1990

Development of a non-linear smoothing filter for the processing of eye-movement signals.

The analysis of eye-movement (EM) signals poses problems for the designer of smoothing filters since many of the interesting types of EMs are bimodal. For example, optokinetic and/or vestibular stimulation results in an EM pattern called nystagmus consisting of alternating fast- and slow-phase components. Also, saccadic (refixation) EMs do not occur continuously, but are interspersed with periods of fixation. Conventional linear, low-pass filters (both finite impulse response (FIR) and infinite impulse response (IIR) types) smear the boundries between the fast- and slow-phases of nystagmus and the fixation and fast components of saccadic EMs. We have adapted a nonlinear smoothing filter (originally designed to optimize edge preservation in image processing applications) for the smoothing of EM signals. This filter is called a Predictive FIR-Median Hybrid (PFMH) filter. The PFMH filter operates on a moving window of data samples centered at the current point of interest. Several predictive FIR filters are applied to the "upper" and "lower" halves of the window and each are designed to predict the sample value at the center of the window. The median of these FIR filter outputs and the actual center data sample are taken as the PFMH filter output for each window position. By properly choosing the length and structure of the FIR subfilters, a PFMH filter can be designed to smooth a bimodal EM signal without blurring the boundries between the two signal components.

Electrooculography↗
PubMed2026

SNP genotyping in Pseudotsuga menziesii and Pinus radiata using targeted genotyping-by-sequencing (GBS): improved Bayesian SNP calling using a beta-binomial distribution and other optimized input parameters.

BACKGROUND: Single-nucleotide polymorphism markers (SNPs) have important applications in gene conservation, breeding, and fundamental genetics research. Our long-term goal is to develop routine approaches for SNP genotyping in forest trees. Ideally, these approaches would be inexpensive, able to accommodate a wide range of samples and SNPs, available through commercial providers, and produce high-quality SNP data. RESULTS: Using targeted genotyping-by-sequencing (GBS), we developed SNP assays for two highly heterozygous tree species, Douglas-fir (Pseudotsuga menziesii) and radiata pine (Pinus radiata). Using Douglas-fir haploid and diploid data, we optimized Bayesian SNP calling by testing four input parameters: (1) allele and genotype prior probabilities, (2) Rho, the beta-binomial dispersion parameter, (3) estimated read error (BayesReadError), and (4) the logPO cutoff used to filter low confidence SNP calls. logPO is the Bayesian posterior odds ratio for a called SNP. Compared to assuming a binomial distribution of read counts (Rho = 0), the beta-binomial distribution (Rho = 0.33) substantially reduced call error and heterozygote undercalling. Compared to the other Bayesian parameters, genotype priors had little effect on genotyping success. For Douglas-fir, we tested 5,360 SNP assays, and then studied the performance of the best 4,000. For radiata pine, we tested 6,000 SNP assays, and then studied the performance of the best 4,570. In Douglas-fir and radiata pine, our Bayesian approach resulted in median call rates of 95% to 98% for the top-ranked SNPs, with an estimated call error of 1.60% for known homozygous genotypes and 2.27% for known heterozygotes. In radiata pine, median and mean call rates were above 91% for GBS and SNP genotyping using an Axiom fixed genotyping array. Additionally, the median correspondence between the GBS and Axiom genotypes was about 98% overall (mean 96%). CONCLUSIONS: By optimizing Bayesian SNP calling, selecting the best 4-5 K SNPs, and excluding samples with low DNA amounts, we substantially reduced call error and heterozygote undercalling, resulting in SNP genotypes that were nearly identical to genotypes obtained using the Axiom array. Furthermore, genotyping performance should increase even further if our SNP rankings were used to develop less complex probe pools that target fewer SNPs.

Pinus↗
PubMed1998

Methanol Laser Line Assignments: Evidence of Four-Level Laser Systems

The "Ritz" computer program, developed for facilitating the assignment of molecular Fourier transform absorption spectra and described in a previous work, determines the energy level values involved in the assigned transitions by the Rydberg-Ritz combination principle. Combining the data obtained from the analyses of high-resolution infrared (IR) and far-infrared (FIR) spectra, it is possible to predict possible FIR laser emissions of molecules. In the present work we have applied this method to the common isotopomer methanol, 12CH3 16OH, and obtained 14 proposed assignments for previously unassigned FIR laser lines. We also predict 15 possible new FIR laser emissions. For the first time, an assignment involving a four-level laser system with collisional population transfer to a slightly higher energy level is reported. Copyright 1998 Academic Press.

Journal Article↗
PubMed1998

Far-Infrared Laser Sideband Spectroscopy of the NH2 Radical.

We have constructed a far-infrared (FIR) laser sideband spectrometer for carrying out pure rotational spectroscopy of fundamental radicals and ions in the FIR or "terahertz" frequency region. The tunable FIR source is obtained by sideband generation of a carbon dioxide laser-pumped FIR laser with a GaAs Schottky barrier diode. The minimum detectable absorption coefficient of the spectrometer achieved so far is 1 x 10(-6) cm-1 at 1600 GHz. Observation of the pure rotational spectrum of the NH2 radical in the 2B1 ground electronic state was demonstrated as the first example. Spectra were measured by utilizing the double modulation technique; i.e., the Zeeman effect was used in addition to the normal frequency modulation technique in order to flatten the baseline and to appreciate full system sensitivity. The radical was generated by a DC glow discharge of a mixture of ammonia and helium. Nine Q- and R-branch rotational transitions were measured in the frequency range between 1300 and 2600 GHz. Zero-field transition frequencies were obtained with an accuracy of around 1 MHz. The line frequencies were analyzed with previous microwave spectroscopic results, and the rotational and spin-rotation constants with their centrifugal correction terms were revised. With the aid of the revised rotational constants, it becomes possible to predict the line frequency of certain low N transitions of the radical to within about 1 MHz for the first time. Copyright 1998 Academic Press.

Journal Article↗
PubMed2000

Global Fit of Torsion-Rotational Transitions in the First Three Torsional States of CH(3)OD.

A global fit of the observed high-resolution microwave (MW), millimeter-wave (MMW), and Fourier transform far-infrared (FIR) spectra for CH(3)OD has been performed using a reduced torsion-rotational Hamiltonian that is obtained from the one-large-amplitude internal-rotation model. The CH(3)OD data set contains 460 MW and MMW transitions with two or fewer quanta in the torsion, v(t) </= 2, and 2348 Fourier transform FIR transitions with v(t) </= 1 and J </= 21. The MW and MMW transitions have been fitted with a root-mean-square (rms) deviation of 0.11 MHz (0.098 MHz for J </= 10) while FIR transitions have a rms deviation of 0.0002 cm(-1). These deviations are approximately equal to the experimental uncertainties, indicating that the MW, MMW, and FIR spectral transitions have been fit to experimental accuracy. Copyright 2000 Academic Press.

Journal Article↗
PubMed1982

Design and application of finite impulse response digital filters.

The finite impulse response (FIR) digital filter is a spatial domain filter with a frequency domain representation. The theory of the FIR filter is presented and techniques are described for designing FIR filters with known frequency response characteristics. Rational design principles are emphasized based on characterization of the imaging system using the modulation transfer function and physical properties of the imaged objects. Bandpass, Wiener, and low-pass filters were designed and applied to 201Tl myocardial images. The bandpass filter eliminates low-frequency image components that represent background activity and high-frequency components due to noise. The Wiener, or minimum mean square error filter 'sharpens' the image while also reducing noise. The Wiener filter illustrates the power of the FIR technique to design filters with any desired frequency response. The low-pass filter, while of relative limited use, is presented to compare it with a popular elementary 'smoothing' filter.

Filtration↗