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We succeeded in extending the decay time of terahertz electromagnetic waves from coherent longitudinal optical (LO) phonons in GaAs epitaxial layers with the use of fast atom bombardment, a treatment method for introducing defects and/or disorders at the surface. The decay time becomes long, up to 4.81 ± 0.15 ps, with the bombardment time of 4.0 min. This value is 2.4-times larger than the decay time of 2.04 ± 0.04 ps of the reference sample (untreated sample). We attribute the origin of the present phenomenon to the fact that the reduction of the photogenerated carrier scattering effect on the coherent LO phonon, which is caused by the presence of the surface defects and disorders formed by the fast atom bombardment, results in the extending of the decay time of the terahertz wave from the coherent LO phonon.

We demonstrate that sensitivity of polariscopy to residual strains is higher than that of the photoluminescence spectroscopy in a (110)-oriented ZnTe single crystal. We carried out x-ray topography and micro θ -2 θ x-ray diffraction measurements in order to thoroughly clarify the crystal quality connecting with the residual strains. The two x-ray analyses revealed that there is misalignment from the [110] direction in some regions of the present sample. We found the following main results: The polariscopic analysis detects the residual strain formed by the misalignment, whereas the photoluminescence measurement cannot detect the residual strain. Thus, we conclude that polariscopy has the sensitivity to the residual strain higher than that of the photoluminescence spectroscopy. We confirmed that the polariscopic analysis can detect the internal strain less than 0.02% in the ZnTe crystal. In addition, we discuss the applicability of polariscopic analysis to other compound semiconductors.

We present the experimental fact that, in a (110)-oriented ZnTe single crystal, polariscopy is highly sensitive to the internal strain, comparing with Raman scattering spectroscopy. We utilized X-ray topography and X-ray diffraction analysis to thoroughly investigate the crystal structure that is intimately associated with the internal strain. The two X-ray structure analyses clarified that the misalignment from the [110] direction is formed in some regions. We obtained the following main result: The polariscopic analysis detects the internal strain formed by the misalignment, whereas the Raman scattering measurement is insensitive to the internal strain. We, therefore, conclude that polariscopy has the strain-detection sensitivity higher than the Raman scattering spectroscopy. We have confirmed that the polariscopic analysis can detect the internal strain less than 0.5% in the ZnTe crystal. (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Damage characteristics of SiC surfaces etched by capacitively coupled radio frequency Ar plasmas at various gas pressures have been studied from the viewpoint of synergy effect of Ar plasma ion and plasma-induced ultraviolet (UV) light irradiations. In the absence of UV light emission at the low gas pressure of 10 mTorr, morphology of the etched SiC surface is similar to that of the as-grown surface regardless of an increase in etching time. In contrast, the experimental Si/C ratio at the surface decreases with an increase in etching time, which agrees with the simulation that Si atoms at the surface are preferentially removed by Ar + ions impinging on the surface. The agreement indicates that the physical etching effect, which originates from the Ar + impact, contributes to the decrease in the Si/C ratio. In the presence of the UV light emission, the surface morphology at the high gas pressure of 50–100 mTorr depends on the etching time. The surface morphology changes as the etching time increases to 200 min. The experimental etch depth at the etching time of 200 min does not agree with that of the simulation. The experimental etch depth is much higher than the simulated one. The difference connecting with the gas pressures can be related to the factor whether the UV light is emitted from the plasma: the result at the high gas pressure suggests the contribution of the synergy effect caused by the following possible phenomenon: Si–C bonding at the surface is weakened.

We demonstrate that, in a GaSb/GaAs epitaxial structure, a coherent longitudinal optical (LO) phonon in a GaAs buffer layer optically covered with a GaSb top layer is observed utilizing terahertz spectroscopy. It is confirmed from Raman scattering measurements that only the optical phonons in the GaSb layer is optically observable. In the terahertz-wave measurement, the Fourier power spectrum of a terahertz waveform exhibits both the coherent GaAs and GaSb LO phonon bands; namely, the coherent LO phonon in the optically covered GaAs buffer layer is observed in the terahertz-wave measurement. This fact demonstrates that the instantaneous surface potential modulation, which originates from the impulsive carrier excitation by the pump beam, reaches the GaAs buffer layer. Consequently, the above-mentioned surface potential modulation generates the coherent GaAs LO phonon that cannot be optically excited. In addition, we perform a time-partitioning Fourier transform analysis in order to investigate the decay dynamics of the coherent GaAs and GaSb LO phonons. The decay times of the coherent GaAs and GaSb LO phonons are estimated to be 2.0 and 3.3 ps, respectively. The longer decay time of the coherent GaSb LO phonon is attributed to the fact that the phonon density of state in a final state of the decay process of GaSb is relatively small in comparison with that of GaAs.

We demonstrate that, in a GaSb/GaAs epitaxial structure, the coherent longitudinal optical (LO) phonon in a GaAs buffer layer optically masked by a GaSb top layer is observed utilizing terahertz spectroscopy. It is confirmed from Raman scattering measurements that only the optical phonons in the GaSb layer is observable. In the terahertz-wave measurement, the Fourier power spectrum of a terahertz waveform exhibits both the coherent GaAs and GaSb LO phonon bands; namely, the coherent LO phonon in the optically masked GaAs buffer layer is observed. This fact demonstrates that the instantaneous surface potential modulation, which originates from the impulsive carrier excitation by a pump beam, reaches the GaAs buffer layer. We perform a time-partitioning Fourier transform analysis in order to investigate the decay dynamics of the coherent GaAs and GaSb LO phonons. (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

The wavenumber of W3 Raman band of Trp ( ν W3 ) is known to be sensitive to the absolute value of the χ 2,1 torsional angle of the Cα Cβ C3 C2 linkage (| χ 2,1 |). In this study, the theoretical basis of the empirical relationship between | χ 2,1 | and ν W3 was examined. By quantum mechanical vibrational analysis, the | χ 2,1 | dependence of ν W3 was found to arise from changes of the stretch force constants of the C2 C3, C3 Cβ, and N1 C2 bonds caused by the change of | χ 2,1 |. The empirical equation proposed previously to describe the | χ 2,1 |– ν W3 relationship was verified to be applicable to Trp residues in proteins beyond the original | χ 2,1 | range of 60–120°, though an equation based on the theoretical vibrational analysis gave a better approximation of the relationship in the | χ 2,1 | region below 60°. This study provides the theoretical basis for the empirical | χ 2,1 |– ν W3 relationship and its extension to a wider range of | χ 2,1 |. It is confirmed that ν W3 is a good marker of | χ 2,1 | not only for small molecules of Trp derivatives but also Trp residues in proteins.

We have explored the effectiveness of applying the circular polariscopic measurement to the mapping of the strains in a ZnO wafer. Initially, monochromatic X-ray topography, which is regarded as a fundamental evaluation technique for wafers, is applied. The measured monochromatic X-ray topograph shows that the image contrast is remarkably inhomogeneous; namely, the bark patterns exist in various regions. In order to clarify the origin of the above-mentioned dark patterns, we apply the circular polariscopic measurement, which is sensitive to strains through the photoelastic effect. The brightness of the circular polariscopic wafer map reveals that the dark pattern in the monochromatic X-ray topograph results from the strain. Thus, we conclude that the circular polariscopic analysis has the ability to compliment the information obtained by the monochromatic X-ray topographic measurement. The presence of the relatively large strains is confirmed from the fact that the forbidden reflection lines are observed in the θ -2θ X-ray diffraction pattern. (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important for designing and fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg(II)-mediated T-T (T-Hg(II)-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of Hg(II). A characteristic Raman marker band at 1586 cm(-1) was observed and assigned to the C4=O4 stretching mode. We confirmed the assignment by the isotopic shift ((18)O-labeling at O4) and density functional theory (DFT) calculations. The unusually low wavenumber of the C4=O4 stretching suggested that the bond order of the C4=O4 bond reduced from its canonical value. This reduction of the bond order can be explained if the enolate-like structure (N3=C4-O4(-)) is involved as a resonance contributor in the thymine ring of the T-Hg(II)-T pair. This resonance includes the N-Hg(II)-bonded state (Hg(II)-N3-C4=O4) and the N-Hg(II)-dissociated state (Hg(II+) N3=C4-O4(-)), and the latter contributor reduced the bond order of N-Hg(II). Consequently, the Hg(II) nucleus in the T-Hg(II)-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.

We demonstrate that, in a GaSb/GaAs epitaxial structure, the coherent longitudinal optical (LO) phonon in the GaAs layer optically covered with the GaSb top layer is observed utilizing terahertz spectroscopy. In the terahertz‐wave measurement, the Fourier power spectrum of the terahertz waveform exhibits both the GaAs and the GaSb LO phonons; namely, the coherent LO phonon in the optically covered GaAs buffer layer is observed in the terahertz‐wave measurement. This fact demonstrates that the instantaneous surface potential modulation originating from the impulsive carrier excitation by the pump pulses reaches the GaAs buffer layer. This surface potential modulation generates the coherent GaAs LO phonon.

We have explored the effectiveness of applying the circular polariscopic measurement to the mapping of the strains in a semi-insulating 6H-SiC wafer. Initially, monochromatic Lang X-ray topography, which is regarded as a fundamental evaluation technique for wafers, is applied. In the monochromatic Lang X-ray topograph, the disappearance of the images is found in various areas, which suggests that the monochromatic Lang X-ray topographic measurement is not almighty. Next, we apply the circular polariscopic measurement, which is sensitive to strains through the photoelastic effect. The brightness of the circular polariscopic wafer map reveals that the inhomogeneous distribution of the strains. The observed phenomenon indicates that the magnitude of the crystal-plane distortion is too strong to apply monochromatic Lang X-ray topography. The presence of the relatively large strains is confirmed from the fact that the forbidden reflection lines are observed in the θ -2θ X-ray diffraction pattern. We also measure the Raman spectra of the several region of the wafer to evaluate the stress from the phonon frequency shift. The maximum stress is estimated to be ∼490 MPa. (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Cu,Zn-superoxide dismutase (SOD1) is a cytosolic antioxidant enzyme, and its mutation has been implicated in amyotrophic lateral sclerosis (ALS), a disease causing a progressive loss of motor neurons. Although the pathogenic mechanism of ALS remains unclear, it is hypothesized that some toxic properties acquired by mutant SOD1 play a role in the development of ALS. We have examined the structural and catalytic properties of an ALS-linked mutant of human SOD1, His43Arg (H43R), which is characterized by rapid disease progression. As revealed by circular dichroism spectroscopy, H43R assumes a stable β-barrel structure in the Cu(2+),Zn(2+)-bound holo form, but its metal-depleted apo form is highly unstable and readily unfolds or misfolds into an irregular structure at physiological temperature. The conformational change occurs as a two-state transition from a nativelike apo form to a denatured apo form with a half-life of ∼0.5 h. At the same time as the denaturation, the apo form of H43R acquires pro-oxidant potential, which is fully expressed in the presence of Cu(2+) and H(2)O(2), as monitored with a fluorogenic probe for detecting pro-oxidant activity. Comparison of d-d absorption bands suggests that the Cu(2+) binding mode of the denatured apo form is different from that of the native holo form. The denatured apo form of H43R is likely to provide non-native Cu(2+) binding sites where the Cu(2+) ion is activated to catalyze harmful oxidation reactions. This study raises the possibility that the structural instability and the resultant Cu-dependent pro-oxidant activity of the apo form of mutant SOD1 may be one of the pathogenic mechanisms of ALS.

We have investigated sub-picosecond-range carrier-transport processes in undoped GaAs/n-type GaAs (i-GaAs/n-GaAs) epitaxial layer structures with various i-GaAs-layer thicknesses d ranging from 200 to 2000 nm, focusing on the relation between carrier-transport processes and terahertz electromagnetic wave frequency. Initially, using numerical simulation and photoreflectance measurement, we confirm that a decrease in d enhances the built-in electric field in the i-GaAs layer. In the time-domain terahertz waveform, it is observed that the intense monocycle oscillation induced by the surge current of photogenerated carriers, the so-called first burst, is followed by the oscillation patterns originating from the coherent GaAs longitudinal optical (LO) phonon. From the Fourier power spectra of the terahertz waveforms, it is clarified that the decrease in d causes a high frequency shift of the band of the first burst. Consequently, we conclude that, in the sub-picosecond time range, the photogenerated carriers are monotonously accelerated by the built-in electric field without being affected by intervalley scattering. The present conclusion signifies that the frequency-tunable terahertz emitters are realized by controlling i-GaAs-layer thickness. We also find the intensity of the coherent LO phonon band is enhanced by a decrease in d.

The biological activity of endothelin-1 (ET-1), a 21-residue vasoconstrictive peptide hormone, has been reported to largely increase upon substitution of Ala for His16. We have investigated possible differences in structural properties between wild type ET-1 and its H16A mutant by using circular dichroism, ultraviolet resonance Raman, visible Raman, and infrared absorption spectroscopy. The C-terminal region of ET-1 spanning from His16 to Trp21 is found to be sensitive to the environment and folds into an α-helical structure under hydrophobic conditions. The environmental sensitivity is elevated in the H16A mutant. A pH decrease from 7.0 to 5.5 does not affect the secondary structure of WT ET-1 but induces an α-helical structure in the H16A mutant. These observations indicate that the mutation of His16 to Ala significantly increases the flexibility of the C-terminal region. The increased flexibility of the H16A mutant may be advantageous for efficient but not for specific binding to receptors. His16 may play an important role in maintaining the structural flexibility of the C-terminal region at an appropriate level and keeping a high specificity to the endothelin receptors.

Histidine is an important and versatile amino acid residue that plays a variety of structural and functional roles in proteins. Although the Raman bands of histidine are generally weak, histidine in the N-deuterated cationic form with imidazole NπD and NτD bonds (N-deuterated histidinium) gives two strong Raman bands assignable to the C4C5 stretch (νCC) and the NπC2Nτ symmetric stretch (νNCN) of the imidazole ring. We examined the Raman spectra of N-deuterated histidinium in 12 crystals with known structures. The observed νCC and νNCN wavenumbers were analyzed to find empirical correlations with the conformation and hydrogen bonding. The effect of conformation on the vibrational wavenumber was expressed as a threefold cosine function of the CαCβC4C5 torsional angle. The effect of hydrogen bonding at Nπ or Nτ was assumed to be proportional to the inverse sixth power of the distance between the hydrogen and acceptor atoms. Multiple linear regression analysis clearly shows that the conformational effect on the vibrational wavenumber is comparable for νCC and νNCN. The hydrogen bond at Nπ weakly lowers the νCC wavenumber and substantially raises the νNCN wavenumber. On the other hand, the hydrogen bond at Nτ strongly raises the νCC wavenumber but does not affect the νNCN wavenumber. These empirical correlations may be useful in Raman spectral analysis of the conformation and hydrogen bonding states of histidine residues in proteins. Copyright © 2010 John Wiley & Sons, Ltd.

Lactoperoxidase (LPO), a mammalian secretory heme peroxidase, catalyzes the oxidation of thiocyanate by hydrogen peroxide to produce hypothiocyanate, an antibacterial agent. Although LPO is known to be activated at acidic pH and in the presence of iodide, the structural basis of the activation is not well understood. We have examined the effects of pH and iodide concentration on the catalytic activity and the structure of LPO. Electrochemical and colorimetric assays have shown that the catalytic activity is maximized at pH 4.5. The heme Soret absorption band exhibits a small red-shift at pH 5.0 upon acidification, which is ascribable to a structural transition from a neutral to an acidic form. Resonance Raman spectra suggest that the heme porphyrin core is slightly contracted and the Fe-His bond is strengthened in the acidic form compared to the neutral form. The structural change of LPO upon activation at acidic pH is similar to that observed for myeloperoxidase, another mammalian heme peroxidase, upon activation at neutral pH. Binding of iodide enhances the catalytic activity of LPO without affecting either the optimum pH of activity or the heme structure, implying that the iodide binding occurs at a protein site away from the heme-linked protonation site.

We have investigated the emission of the terahertz (THz) electromagnetic wave from an undoped GaAs (200 nm)/n -type GaAs (3 μm) epitaxial layer structure (i -GaAs/n -GaAs structure), where the doping concentration of the n -GaAs layer is 3 × 1018cm-3. It is found that the first-burst amplitude of THz wave of the i -GaAs/n -GaAs structure is considerably stronger than that of an n -GaAs crystal, which means that the i -GaAs layer enhances the THz emission intensity. The first-burst amplitude of the i -GaAs/n -GaAs structure, by tuning the pump-beam energy to the higher energy side, exceeds that of an i -InAs crystal known as one of the most intense THz emitters. We, therefore, conclude that the i -GaAs/n -GaAs structure is useful to obtain intense THz emission. From the pump-beam energy dependence of the first-burst amplitude, the THz-emission mechanism of the i -GaAs/n -GaAs structure is attributed to the surge current of the photogenerated carriers flowing through the i -GaAs layer. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

We demonstrate that photoluminescence-excitation (PLE) spectroscopy is applicable to probe effects of the surface damages on the carrier transport in AlxGa1–xN/GaN heterostructures by systematically characterizing as-grown and plasma-exposed samples. The characterization of the surface morphology with atomic force microscopy clarifies that the plasma exposure modifies the atomic steps and pits on the AlxGa1–xN surface. The PLE spectrum of the as-grown sample measured at the energy of the photoluminescence from the GaN layer shows a step rising from the AlxGa1–xN fundamental transition energy, which reflects the photogenerated-carrier injection from the AlxGa1–xN layer to the GaN layer, while the rising step disappears in the plasma-exposed sample. In contrast, the reflectance spectra are the same in the two samples; namely, the excitonic transition is hardly changed. Thus, it is concluded that PLE spectroscopy is highly sensitive to probe the carrier-transport characteristics in the AlxGa1–xN/GaN heterostructure. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

We demonstrate that Franz-Keldysh oscillations (FKOs) observed by photoreflectance (PR) spectroscopy are highly sensitive to the surface morphology of Al x Ga 1− x N layers in Al x Ga 1− x N heterostructures. Three Al 0.2 Ga 0.8 N/GaN heterostructures with different surface-morphology profiles, which are confirmed with atomic force microscopy, have been investigated. The X-ray-diffraction patterns are hardly affected by the Al 0.2 Ga 0.8 N/GaN-layer morphology. In contrast, it is revealed that cracks and pits dominating the morphology remarkably reduce the amplitude of the FKOs from the Al 0.2 Ga 0.8 N/GaN layer, which is attributed to the following two mechanisms related to the cracks and pits. One is lifetime broadening due to carrier scattering, and the other is the suppression of the modulation magnitude for the built-in electric field, which is caused by the trapping and recombination of photogenerated carriers at the surface.

We have investigated longitudinal optical phonons (LO) characteristics in i-GaAs/n-GaAs epitaxial structures. The LO phonons and LO phonon-plasmon coupled modes were observed in the Raman scattering spectra, whereas only the coherent LO phonon was detected in terahertz spectroscopy. We conclude that the initial polarization is responsible for emission of the co-herent-LO-phonon terahertz wave.

We have investigated the dynamical properties of terahertz radiation from coherent longitudinal optical pho-non-plasmon coupled (LOPC) modes in an undoped GaAs/n-type GaAs epitaxial structure using time-domain terahertz spectros-copy. It was confirmed that the frequencies of the lower and upper LOPC modes are dominated by a photogenerated carrier density. The dynamical properties of the LOPC modes, the lifetimes of which are about 0.2 ps, were examined by time-partitioning Fourier transformed spectra of the time-domain terahertz signals. It was found that the lifetimes of the LOPC modes depend on their frequencies.

We have investigated electric field strengths in the AlxGa1-xN layer, FAlGaN's, of AlxGa1-xN/GaN heterostructures with and without a GaN cap layer using photoreflectance (PR) spectroscopy. Franz-Keldysh oscillations (FKOs) from the AlxGa1-xN layer are clearly observed in the PR spectra. It is found from analysis of the FKOs that stacking of the cap layer causes a remarkable enhancement of FAlGaN. This fact demonstrates that the FKO profile is a non-destructive probe for a change of built-in electric field strength induced by a cap layer. Numerical calculations of FAlGaN based on a Schrodinger-Poisson equation clarify that the magnitude of the enhancement of FAlGaN is dominated by the cap-layer thickness.

The physiological function of the prion protein (PrP) remains enigmatic despite its established involvement in the pathogenesis of spongiform encephalopathies. PrP is a glycolipid-anchored membrane protein, which constitutively recycles between the cell surface and an endosomal compartment. The N-terminal region of PrP contains a four tandem repeat (OP4) of the octapeptide PHGGGWGQ (OP) that binds and reduces Cu(II) ions. We have examined the kinetic properties of the OP4-mediated Cu(II) reduction and found that OP4 exhibits the highest reduction activity around pH 6.5, close to the pH in early endosomes. All four OP units and at least one tryptophan side chain are essential for Cu(II) reduction. The reaction is described by an uncompetitive substrate inhibition mechanism involving a 1:1 Cu(II)-OP4 active intermediate. Structural analysis by Raman spectroscopy has revealed that the Cu(II) ion is coordinated by four histidine Ntau atoms in the active intermediate and the feasibility of formation of this intermediate correlates with the Cu(II) reduction over a pH range from 5.0 to 8.2. Molecular mechanics calculations suggest that two tryptophan residues of OP4 are located near the Cu(II) site, being consistent with the importance of redox-active tryptophan in the Cu(II) reduction. PrP has been proposed to capture Cu(II) ions in the extracellular space and release them in the endosome. The results of this study strongly suggest that PrP also plays a role in the reduction of captured Cu(II) ions prior to their transfer to Cu(I)-specific intracellular copper trafficking proteins.

The absorption and UV resonance Raman spectra of 2′,3′,5′-tri- O -acetyladenosine (AcAdo) were investigated in two non-hydrogen-bonding, three proton acceptor, and four proton donor/acceptor solvents. The molar extinction coefficient at the absorption maximum around 260 nm ( e max ) changed up to ∼10% with change of the solvent. The intensities of 257 nm-excited Raman bands varied dramatically (up to ∼1000%) from solvent to solvent. The e max of UV absorption and the intensities of six Raman bands of AcAdo in the nine solvents were plotted against the Kamlet–Taft solvent parameters α , β , and π *, which represent the hydrogen-bond donor acidity, acceptor basicity, and the polarity–polarizability of the solvent, respectively. Both e max and the Raman band intensities increased with α . Similar but weaker correlations were seen for β . π * had the least influence. These observations strongly suggest that hydrogen bonding is the main factor that affects the intensities of UV absorption and resonance Raman scattering. Multiple regression analysis has shown that the correlations with α and β are improved by taking linear combinations of Raman band intensities. We propose a new method to evaluate the environmental α and β values of the adenine ring from the relative intensities of three strong Raman bands at ∼1500, 1480, and 1330 cm −1 . UV resonance Raman intensities of adenine ring vibrations are useful in analyzing the strength of hydrogen bonding at the proton acceptor (N1, N3, and N7) and donor (C6–NH 2 ) sites.

Molecular dynamics analyses were performed to examine conformational changes in the C-domain of calmodulin and the N-domain of troponin C induced by binding of Ca(2+) ions. Analyses of conformational changes in calmodulin and troponin C indicated that the shortening of the distance between Ca(2+) ions and Ca(2+) binding sites of helices caused widening of the distance between Ca(2+) binding sites of helices on opposite sides, while the hydrophobic side chains in the center of helices hardly moved due to their steric hindrance. This conformational change acts as the clothespin mechanism.

Subband energy levels of AlGaAs double quantum well (QW) layer structure with a separate confinement scheme are determined by photoreflectance at room temperature. Also subband energy levels are compared with those determined by the self-excited electron Raman scattering of lasers fabricated from the same QW structure but with different waveguide thickness outside the QWs. Electron subbands, heavy hole subbands, light hole subbands, determined both measurements, are in good agreement.

We have investigated Franz–Keldysh oscillations (FKOs) from a base-emitter junction in an InGaP/GaAs heterojunction bipolar transistor structure using photoreflectance spectroscopy. The profiles of the FKOs originating from the InGaP emitter are compared with the line shapes calculated with the use of electro-optic functions. It is found that the line shape of the FKOs is remarkably affected by interference of probe light due to the multiple layer structure. Taking account of the interference effect, we have derived a novel analysis method for a convenient linear plot of the extremum positions of FKOs. The band-gap energy estimated with the present method well agrees with the band-gap energy obtained from the photoluminescence measurement of an InGaP/GaAs heterostructure for a reference.

We have studied photoreflectance spectra of GaAs/Al0.3Ga0.7As heterostructures from the viewpoint of the phase of Franz–Keldysh (FK) oscillations. The phase of the FK oscillations originating from the GaAs buffer layer shifts with the change of the Al0.3Ga0.7As-layer thickness, while the period does not vary. The FK-oscillation phase does not depend on the pump power, which suggests that the phase shift is not caused by a difference in the magnitude of modulation. We propose a calculation model for FK oscillations that includes the interference of probe light. Photoreflectance spectra calculated on the basis of this model are compared with the measured spectra. We conclude that mixing of the real and imaginary parts of a modulated dielectric function, which is caused by the probe-light interference, gives rise to the phase shift of the FK oscillations. We also derive a novel analysis method for a linear plot of the extremum positions of FK oscillations based on the above line-shape model. The present method remarkably reduces ambiguity in the estimation of band-gap energy that is considerable in a conventional analysis.

Background: Patients with non-invasive (Ta/T1) transitional cell carcinoma (TCC) of the urinary bladder are often observed without progression in the long-term follow-up period, although many of them experience recurrence of disease. It is difficult to accurately predict the disease outcome of each patient with Ta/T1 TCC using conventional prognostic criteria. In this study, we examined the usefulness of artificial neural networks (ANNs) to predict the long-term disease outcome of patients with TCC of the urinary bladder. Methods: A retrospective, prognostic study of 90 patients with Ta/T1 TCC of the urinary bladder, diagnosed by transurethral resection of the bladder tumor between April 1981 and March 1985, and then followed up for 15 years or longer, was carried out. Data were analyzed using the Bayesian network tool of SPSS Neural Connection 2.1. The input neural data consisted of tumor stage, grade, tumor number, age, gender, tumor architecture and estimates of mean nuclear volume. The data set was randomly divided into 68 training and 22 testing examples for the prediction of disease progression and tumor recurrence within 15 years. Results: During 15 years follow-up, tumor recurrence was noted in 42/90 (47%) Ta/T1 tumors. The ANN model could not predict tumor recurrence. Conversely, disease progression was noted in 17/90 (19%) Ta/T1 tumors, and, in the test set, 4/22 (18%) Ta/T1 tumors underwent disease progression. The sensitivity of the ANN model to predict progression was 100% (specificity 67%; positive predictive value 40%; negative predictive value 100%). Patients who were judged to have a favorable prognosis using ANN analysis did not progress within the 15-year follow-up period. Conclusion: The results of the ANN study indicate that long-term progression-free survival of patients with non-invasive TCC of the urinary bladder can be precisely predicted. A favorable prognosis using ANNs would be one of the exclusion criteria for immediate or future total cystectomy.

The matrix protein M1 of influenza A virus forms a shell beneath the viral envelope and sustains the virion architecture by interacting with other viral components. A structural change of M1 upon acidification of the virion interior in an early stage of virus infection is considered to be a key step to virus uncoating. We examined the structure of a 28-mer peptide (M1Lnk) representing a putative linker region between the N- and C-terminal domains of M1 by using circular dichroism, Raman, and absorption spectroscopy. M1Lnk assumes an alpha-helical structure in a mildly hydrophobic environment irrespective of pH, being consistent with the X-ray crystal structures of an N-terminal fragment of M1 at pH 7 and 4. In the presence of Zn(2+), on the other hand, M1Lnk takes a partially unfolded conformation at neutral pH with a tetrahedral coordination of two Cys residues and two His residues to a Zn(2+) ion in the central part of the peptide. Upon acidification, the peptide releases the Zn(2+) ion and refolds into the alpha-helix-rich structure with a midpoint of transition at pH 5.9. The pH-dependent conformational transition of M1Lnk strongly suggests that the interdomain linker region of M1 also undergoes a pH-dependent unfolding-refolding transition in the presence of Zn(2+). A small but significant portion of the M1 protein is bound to Zn(2+) in the virion, and the Zn(2+)-bound M1 molecule may play a special role in virus uncoating by changing the disposition of the N- and C-terminal domains upon acidification of the virion interior.

Protein structural changes during the photocycle of bacteriorhodopsin were examined by time-resolved ultraviolet resonance Raman (UVRR) spectroscopy. Most of the 244-nm UVRR difference signals of Trp were assigned to either Trp182 or Trp189 using the Trp182 --> Phe and Trp189 --> Phe mutants. The W17 mode of Trp182 shows a wavenumber downshift in the M(1) --> M(2) transition, indicating an increase in hydrogen bonding strength at the indole nitrogen. On the other hand, Trp189 shows Raman intensity increases of the W16 and W18 modes ascribable to an increased hydrophobic interaction. These observations suggest that the tilt of helix F, which ensures that reprotonation of the Schiff base is from the cytoplasmic side, occurs in the M(1) --> M(2) transition. In the M(2) --> N transition, the environment of Trp189 returns to the initial state, whereas the hydrophobic interaction of Trp182 decreases drastically. The decrease in hydrophobic interaction of Trp182 in the N state suggests an invasion of water molecules that promote the proton transfer from Asp96 to the Schiff base. Structural reorganization of the protein after the tilt of helix F may be important for efficient reprotonation of the Schiff base.

We have investigated coherent LO phonon–plasmon coupled (LOPC) modes in an (InAs) 1 /(GaAs) 30 strained-layer superlattice (SL) with a miniband structure. By generating carriers in the miniband, the GaAs-like LOPC modes are observed. In spectrally resolved pump–probe measurements, it is found that the intensity of the lower branch (L − ) of the LOPC mode is enhanced around the transition energies at the miniband critical points, the mini-Brillouin-zone center and edge. In addition, the decay time of the L − mode in the SL hardly depends on the detection energy. These properties of the LOPC mode will be discussed from the viewpoint of the effect of the miniband structure.

We have investigated dynamical properties of coherent folded longitudinal acoustic (FLA) phonons generated in (GaAs)10(AlAs)10 superlattices (SLs) with 20, 100 and 195 periods. In the time-domain signals of the SL with 20 periods, the coherent FLA phonon mode with the Raman-inactive B2 symmetry at the Brillouin zone centre, which is not observed in the SLs with more than 100 periods, is detected in addition to the Raman-active modes with the A1 symmetry at and near the zone centre. The appearance of the B2 mode is caused by the break of the mode symmetry due to the finiteness of the total number of periods. Moreover, it is found that the bandwidths of the coherent FLA phonon modes observed in the Fourier transform spectra depend on the finiteness of periodicity and the wavevector, which is discussed from the aspect of the relaxation of the wavevector conservation and the propagation of the phonon wavepacket through the SL region.

Isotope-edited Raman spectroscopy, a combination of site-selective isotopic labeling and Raman difference spectroscopy, is a useful method for studying the structure and interaction of individual nucleic acid residues in oligonucleotides. To obtain basic data for applying isotope-edited Raman spectroscopy to guanine residues, we studied the vibrational modes of UV resonance Raman bands of the C8-deuterated guanine ring by examining the wavenumber shifts upon seven isotopic substitutions (2-13C, 2-15N, 6-18O, 7-15N, 8-13C, 9-15N and 1′-13C). The hydrogen bond sensitivities of the Raman bands were also investigated by comparing the Raman spectra recorded in several solvents of different hydrogen bonding properties. Some of the Raman bands were found to be markers of hydrogen bonding at specific donor or acceptor sites on the guanine ring. The Raman bands, which shift on C8-deuteration, remain in the difference spectrum between the unlabeled and C8-deuterated guanine rings. Among them, a negative peak around 1525 cm−1 and a strong positive/negative peak pair around 1485/1465 cm−1 serve as markers of hydrogen bonding at N7 and C6O, respectively. Another weak positive/negative peak pair around 1025/1040 cm−1 is sensitive to hydrogen bonding at the proton donor sites (N1—H and N2—H2). The applicability of the hydrogen bond markers has been tested by using a 22-mer oligonucleotide duplex containing eight guanine residues and its analog in which a single guanine residue is C8-deuterated. The difference spectrum shows that the hydrogen bonding state of the guanine residue at the labeled position is consistent with the Watson–Crick base pair structure of DNA. Isotope-edited Raman spectroscopy is a useful tool for studying the hydrogen bonding state of selected guanine residues in oligonucleotides. Copyright © 2002 John Wiley & Sons, Ltd.

We have investigated the coherent plasmon photoexcited in the electron miniband of an InAs/GaAs strained superlattice (SL) using a reflection-type pump-probe technique. Under the condition that the center energy of the pump pulses is tuned to the fundamental transition energy of the SL, the coherent plasmon coupled with the longitudinal optical (LO) phonon of GaAs that is the barrier layer is observed. The time-domain signals of the coherent plasmon coupled with the GaAs-like LO phonon drastically change with varying the generation and detection energies. From the energy dependence of the time-domain signals, we discuss the relaxation process of the carriers photoexcited in the miniband of the SL.

Congo Red (CR) has long been used for staining amyloid fibrils and recently been found to inhibit amyloid formation. We examined the binding mode of CR to Alzheimer's amyloid β-peptide (Aβ) by UV Raman spectroscopy. The 244 nm-excited Raman spectrum of CR exhibits five bands in the 1620–1550 cm−1 region, where C C stretching vibrations of the naphthalene and biphenyl moieties are expected. Among the C C stretching bands, one at 1615 cm−1 becomes weaker and another at 1598 cm−1 gains intensity upon binding to Aβ, resulting in a reversal of the relative intensity of the two bands. Concomitant with the intensity reversal, a band at 1158 cm−1 assignable to the N–C stretch becomes stronger. These UV Raman spectral changes are in line with those observed when the fraction of the planar CR molecule is increased by crystallization. Furthermore, opposite spectral changes were observed when the central biphenyl group was methylated to force the two benzene rings in an orthogonal orientation. These observations suggest an increase in planarity of the biphenyl group in the CR–Aβ complex. A red shift of the visible absorption is consistent with an expansion of π-conjugation in the planar CR molecule. The torsional mobility of the biphenyl group permitting a planar conformation may be essential for the binding of CR to Aβ amyloid fibrils. Copyright © 2002 John Wiley & Sons, Ltd.

We investigated terahertz radiation from coherent GaAs-like longitudinal optical (LO) phonons in (11n)-oriented GaAs/In0.1Al0.9As strained multiple quantum wells for clarifying the screening effects of photogenerated carriers. We observed the intense quasi-monochromatic terahertz wave from the coherent GaAs-like LO phonon, which originates from the initial polarization enhanced by the strong piezoelectric field. The intensity of the coherent GaAs-like LO-phonon band exhibited a saturation behavior as the pump power was increased. We evaluated the saturation behavior in terms of excitation efficiency of the terahertz wave from the coherent GaAs-like LO phonon using the parameter of unit-power intensity. From the pump-power dependence of the unit-power intensity, we conclude that the screening effect of high density photogenerated carriers on the piezoelectric field causes saturation of the terahertz-wave intensity from the coherent GaAs-like LO phonon.

The authors investigated the scattering effect of photogenerated carriers on the decay of the coherent longitudinal optical (LO) phonons in an undoped GaAs/n-type GaAs epitaxial structure using a terahertz time-domain spectroscopic technique. The terahertz wave from the coherent LO phonon was observed together with those emitted both by the ultrafast photocurrent and by the coherent LO-phonon-plasmon coupled (LOPC) mode. The simultaneous observation of the coherent LO phonon and coherent LOPC mode originates from the fact that the photogenerated carrier density laterally distributes around the surface of the undoped GaAs layer owing the Gaussian profile of the pump beam. The authors found that the terahertz wave from the coherent LO phonon lives up to 5.0 ps, whereas those from the coherent LOPC mode and ultrafast photocurrent disappear within 1.0 ps. The decay time of the coherent LO phonon monotonically decreases with an increase in the pump power. This finding indicates that the dephasing of the terahe...

We conducted a retrospective review of 16 patients who were diagnosed with enterovesical fistula in our hospital between January 2000 and July 2013. The patient's median age was 74 years old and 4 were female. Most of the chief complaints were pneumaturia and fecaluria. There was a vesicosigmoidal fistula in 12 patients, an ileovesical fistula in 2, and a rectovesical fistula in 2. The main underlying cause was diverticulitis in 9 patients and a sigmoid colon carcinoma in 3. Diagnoses were made based on the findings of cystoscopy, barium enema, abdominal computed tomography and so on. Treatment varied in each case depending on the etiology and the patient's condition. The procedure was mostly open surgery, but laparoscopic sigmoidectomy was performed preserving the bladder in the two most recent cases.

The imidazole ring of histidine exists in two tautomeric forms in neutral-to-basic aqueous solution, and the tautomerism of the histidine residue sometimes plays a key role in catalytic reactions of enzymes. We have investigated the molecular vibrations of two tautomers of 4-methylimidazole (4-MeIm), a model compound for the histidine side chain, by Raman spectroscopy and ab initio calculations based on the density functional theory (DFT) approach. Examination of the temperature dependence of Raman intensity revealed nine pairs of bands characteristic of the N1-protonated and the N3-protonated tautomers of 4-MeIm at 1576/1596, 1452/1427, 1304/1344, 1265/1259, 1229/1234, 1165/1149, 1088/1104, 996/1014, and 942/934 cm-1. Five to six pairs of tautomerism-sensitive Raman bands were also identified for each of the C2-, N-, and C2,N-deuterated analogues of 4-MeIm. The observed Raman wavenumbers were used to determine nine scaling factors for the in-plane force constants derived from DFT calculations using the 6...

Raman spectroscopy has been combined with site-selective isotopic labeling techniques to obtain structural information on a selected nucleic acid residue in oligonucleotides. In the difference spectrum between the unlabeled and site-selectively labeled oligonucleotides, the Raman signals from the residue at the labeled position show up, while the signals from the residues at unlabeled positions are canceled out. To demonstrate the utility of this new method, we have prepared a self-complementary tetradecamer DNA, d(AGTGCTCGAGCACT)2, containing single C8-deuterated adenine at position 9 (A9) or 12 (A12). UV (257 nm) resonance Raman difference spectra between the unlabeled and labeled oligonucleotides in solution reveal slightly different microenvironments around A9 and A12 as expected for a double-stranded helical structure of the tetradecamer DNA. In the presence of an antitumor antibiotic, actinomycin D, which intercalates into the 5′-GC-3′ sequence of DNA, the Raman signals of A9 on the 5′-side of the intercalation site become significantly weaker, indicating an increased base stacking with adjacent guanine bases. In contrast, the Raman signals of A12 on the 3′-side are not affected by the binding of actinomycin D. This observation provides the first experimental evidence that the intercalation of actinomycin D induces an asymmetric structural alteration of DNA in solution.

We have investigated coherent longitudinal optical (LO) phonons in GaSb/AlSb superlattices. The coherent AlSb-like LO phonon in the barrier layer and the coherent GaSb-like LO phonon in the well la...

Aggregation of amyloid beta-peptide (Abeta), a key pathological event in Alzheimer's disease, has been shown in vitro to be profoundly promoted by Zn(II). This fact suggests that some factors in the normal brain protect Abeta from the Zn(II)-induced aggregation. We demonstrate for the first time that Cu(II) effectively inhibits the Abeta aggregation by competing with Zn(II) for histidine residues. The Raman spectrum of a metal-Abeta complex in the presence of both Zn(II) and Cu(II) shows that the cross-linking of Abeta through binding of Zn(II) to the N(tau) atom of histidine is prevented by chelation of Cu(II) by the N(pi) atom of histidine and nearby amide nitrogens. The inhibitory effect is strongest at a Cu/Abeta molar ratio of around 4. Above this ratio, Cu(II) itself promotes the Abeta aggregation by binding to the phenolate oxygen of Tyr10. These results emphasize the importance of regulation of Cu(II) levels to inhibit Abeta aggregation, and are consistent with an altered metal homeostasis in Alzheimer's disease.