Additional Spectral Features Research Articles

Computer-Aided Diagnosis for Preoperative Invasion Depth of Gastric Cancer with Dual-Energy Spectral CT Imaging

This study evaluates the accuracy of dual-energy spectral computed tomography (DEsCT) imaging with the aid of computer-aided diagnosis (CAD) system in assessing serosal invasion in patients with gastric cancer. Thirty patients with gastric cancer were enrolled in this study. Two types of features (information) were collected with the use of DEsCT imaging: conventional features including patient's clinical information (eg, age, gender) and descriptive characteristics on the CT images (eg, location of the lesion, wall thickness at the gastric cardia) and additional spectral CT features extracted from monochromatic images (eg, 60keV) and material-decomposition images (eg, iodine- and water-density images). The classification results of the CAD system were compared to pathologic findings. Important features can be found out using support vector machine classification method in combination with feature-selection technique thereby helping the radiologists diagnose better. Statistical analysis showed that for the collected cases, the feature "long axis" was significantly different between group A (serosa negative) and group B (serosa positive) (P < .05). By adding quantitative spectral features from several regions of interest (ROIs), the total classification accuracy was improved from 83.33% to 90.00%. Two feature ranking algorithms were used in the CAD scheme to derive the top-ranked features. The results demonstrated that low single-energy (approximately 60keV) CT values, tumor size (long axis and short axis), iodine (water) density, and Effective-Z values of ROIs were important for classification. These findings concurred with the experience of the radiologist. The CAD system designed using machine-learning algorithms may be used to improve the identification accuracy in the assessment of serosal invasion in patients of gastric cancer with DEsCT imaging and provide some indicators which may be useful in predicting prognosis.

Raman study of phonons inCaMn7O12: Effects of structural modulation and structural transition

Polarized Raman spectra of oriented $\mathrm{Ca}{\mathrm{Mn}}_{7}{\mathrm{O}}_{12}$ single crystals have been studied in a broad temperature range (5--500 K) covering the crystallographic, ferroelectric, and magnetic transitions. From the spectra obtained at room temperature (RT) 10 out of the total 12 Raman active $6{A}_{g}+6{E}_{g}$ modes of the trigonal $R\overline{3}$ phase have been identified and assigned to definite atomic motions in close comparison to results of lattice-dynamics modeling. With the decrease in temperature below 250 K some Raman bands split, and additional spectral features, not expected for the $R\overline{3}$ structure, arise well above the magnetic transitions near 90 and 50 K. Their appearance, however, correlates with the transformation due to incommensurate structural modulation revealed by recent x-ray and neutron-diffraction studies. As temperature increases above RT the intensity of the Raman lines strongly decreases, and entering the high-temperature $Im\overline{3}$ phase the spectrum transforms its shape to that expected for a structure with disordered Jahn-Teller distortions.

Origin of additional spectral features in modulated reflectance spectra of 2-dimensional semiconductor systems

High resolution photoreflectance (PR) spectroscopy study on a single GaAs/AlGaAs quantum well representing a two-dimensional (2D) system, shows additional distinct spectral features on the high energy side of the first confined heavy-hole and light-hole exciton transitions. The PR experiments involved a special dual detection technique which significantly improved the measurement sensitivity. Photoluminescence excitation spectroscopy data on the sample showed broadened step-like features around these energies. A detailed lineshape analysis, including first principles simulations, was performed to understand the origins of these additional PR spectral features. They are shown to arise primarily from inhomogeneously broadened first excited state transition of the excitons, rather than from a change in the joint density of states at the exciton continuum edge. The analysis suggests that such features are more likely in the case of 2D excitons as compared to 3D excitons in bulk material. Apart from its significance for post-growth characterization, identification of these additional PR features enables direct estimation of the exciton binding energy.

Finite temperature effects on the X-ray absorption spectra of lithium compounds: first-principles interpretation of X-ray Raman measurements.

We elucidate the role of room-temperature-induced instantaneous structural distortions in the Li K-edge X-ray absorption spectra (XAS) of crystalline LiF, Li2SO4, Li2O, Li3N, and Li2CO3 using high resolution X-ray Raman spectroscopy (XRS) measurements and first-principles density functional theory calculations within the eXcited electron and Core Hole approach. Based on thermodynamic sampling via ab initio molecular dynamics simulations, we find calculated XAS in much better agreement with experiment than those computed using the rigid crystal structure alone. We show that local instantaneous distortion of the atomic lattice perturbs the symmetry of the Li 1s core-excited-state electronic structure, broadening spectral line-shapes and, in some cases, producing additional spectral features. The excellent agreement with high-resolution XRS measurements validates the accuracy of our first-principles approach to simulating XAS, and provides both accurate benchmarks for model compounds and a predictive theoretical capability for identification and characterization of multi-component systems, such as lithium-ion batteries, under working conditions.

NEXAFS spectromicroscopy of suspended carbon nanohorns

We demonstrate that near-edge X-ray-absorption fine-structure spectroscopy combined with full-field transmission X-ray microscopy can be used to study the electronic structure of suspended carbon nanohorns. Based on reports of electronic structure calculations additional spectral features observed in the π region of the NEXAFS spectrum recorded on the carbon nanohorns were associated to the presence of the pentagonal rings and the folding of the graphene sheet.

Study of concentration-dependent quantum yield of Rhodamine 6G by gold nanoparticles using thermal-lens technique

Tailoring optical properties of the dye molecules using metal nanoparticles is a burgeoning area of research. In this work, we report our results on the studies of how the absorption and emission behavior of Rhodamine 6G dye is tailored using gold nanoparticles. Furthermore, the influence of dye concentration on these properties for a given concentration of nanoparticles in the dye-nanoparticle mixture is investigated. In addition, the difference between the concentration-dependent fluorescence quantum yield of the dye molecules is measured in the absence and presence of nanoparticles using the dual-beam thermal-lens technique. Our absorption spectral studies show additional spectral features due to nanoparticle aggregation on interaction with cationic Rhodamine 6G dye. Dye concentration-dependent steady-state fluorescence studies in the presence of nanoparticles indicate a blue shift in peak fluorescence emission wavelength. The quantum yield value measured using thermal-lens technique exhibit a non-monotonic behavior with dye concentration with substantial quenching for lower dye concentrations. The results are interpreted in terms of dye–nanoparticle interaction and the formation of dye shell around the nanoparticle.

Relations between X-ray timing features and spectral parameters of Galactic black hole X-ray binaries

We present a study of correlations between spectral and timing parameters for a sample of black hole X-ray binary candidates. Data are taken from GX 339-4, H 1743-322, and XTE J1650-500, as the Rossi X-ray Timing Explorer (RXTE) observed complete outbursts of these sources. In our study we investigate outbursts that happened before the end of 2009 to make use of the high-energy coverage of the HEXTE detector and select observations that show a certain type of quasi-periodic oscillations (type-C QPOs). The spectral parameters are derived using the empirical convolution model simpl to model the Comptonized component of the emission together with a disc blackbody for the emission of the accretion disc. Additional spectral features, namely a reflection component, a high-energy cut-off, and excess emission at 6.4 keV, are taken into account. Our investigations confirm the known positive correlation between photon index and centroid frequency of the QPOs and reveal an anticorrelation between the fraction of up-scattered photons and the QPO frequency. We show that both correlations behave as expected in the "sombrero" geometry. Furthermore, we find that during outburst decay the correlation between photon index and QPO frequency follow a general track, independent of individual outbursts.

Look, no hands! Spectral biomarkers from genetic association studies

Recent advances in our understanding of the genomics of the human metabolome have shed light on the pathways involved in metabolic and cardiovascular disease. Such studies crucially depend on the interpretation of complex molecular spectra. A recent study by Suhre and colleagues provides a way to identify potentially clinically relevant biomarkers without a priori information, such as reference spectra, thus aiding the discovery of additional spectral features and corresponding genomic loci associated with metabolism and disease.

Functional K-doping of eumelanin thin films: Density functional theory and soft x-ray spectroscopy experiments in the frame of the macrocyclic protomolecule model

We demonstrate the possibility to achieve the doping of eumelanin thin films through K(+) incorporation during the electrodeposition of the film. K-doping changes the optical properties of the eumelanin thin films, reducing the energy gap from 1.0 to 0.6 eV, with possible implications for the photophysical properties. We have identified the doping-related occupied and unoccupied electronic states and their spectral weight using resonant photoemission spectroscopy (ResPES) and x-ray absorption at the C and N K-edges (near edge x-ray absorption fine spectroscopy, NEXAFS). All data are consistently interpreted by ab initio calculations of the electronic structure within the frame of the macrocycle model developed for the eumelanin protomolecule. Our analysis puts in evidence the intercalation of K with one specific oligomer (a tetramer composed of one indolequinone and 3 hydroquinone monomers) in correspondence of the nitrogen macrocycle. The predicted variation of the tetramer spacing is also in agreement with the recent x-ray diffraction experiments. The charge donation from K to N and C atoms gives rise to new electronic states at the top of the valence band and in NEXAFS resonances of the unoccupied orbitals. The saturation of the tetramer macrocycles leaves an excess of K that bind to N and C atoms in alternative configurations, as witnessed by the occurrence of additional spectral features in the carbon-related ResPES measurements.

X-ray absorption spectroscopy by full-field X-ray microscopy of a thin graphite flake: Imaging and electronic structure via the carbon K-edge

We demonstrate that near-edge X-ray-absorption fine-structure spectra combined with full-field transmission X-ray microscopy can be used to study the electronic structure of graphite flakes consisting of a few graphene layers. The flake was produced by exfoliation using sodium cholate and then isolated by means of density-gradient ultracentrifugation. An image sequence around the carbon K-edge, analyzed by using reference spectra for the in-plane and out-of-plane regions of the sample, is used to map and spectrally characterize the flat and folded regions of the flake. Additional spectral features in both π and σ regions are observed, which may be related to the presence of topological defects. Doping by metal impurities that were present in the original exfoliated graphite is indicated by the presence of a pre-edge signal at 284.2 eV.

Revisiting the Yb electronic structure with low-energy photoemission spectroscopy

Low-energy photoemission spectroscopy in the photon energy range between 5.5 and 21 eV is used to investigate the valence electronic structure of Yb polycrystalline films. With the lowering of the photon energy below 11 eV, additional spectral features, nearly absent at higher photon energy, become predominant, in particular a peak located right at the Fermi level. With the help of an ab initio theoretical calculation, we interpret the peak as due to the joint influence of filled and empty densities of states, identifying a $p$-band contribution close to the Fermi level, whose intensity is strongly enhanced at certain photon energies corresponding to modulation of the empty $d$ band.

Surface enhanced Raman scattering from multiwalled carbon nanotubes at low temperatures

We report temperature dependent Raman spectra of multiwalled carbon nanotubes deposited as dilute dispersions on surface enhanced Raman scattering active substrate. At low temperature, i.e, below 30 K both the tangential and the disorder mode acquire additional spectral features which are otherwise absent in the room temperature spectra. Further, we observe that the surface enhancement effect is more for modes involving motion of atoms in the direction perpendicular to the substrate which is consistent with the surface selection rules. These experiments provide access to certain spectral features of multiwalled carbon nanotubes which are otherwise very difficult to see.

In Situ GIXAFS and HERFD-XAS Studies of a Pt-modified Rh(111) Electrode

The oxygen reduction reaction at Pt electrodes has a high overpotential which reduces the efficiency of fuel cells. The origin of the overpotential has been seen in the formation of stable Pt-O species at high potentials. Aiming at an unambiguous characterization of such species, we use in situ grazing incidence x-ray absorption spectroscopy at the Pt L3 edge to study the geometric and electronic structure of ultrathin Pt layers on M(111) substrates. We present Pt L3-edge grazing incidence x-ray absorption fine structure (GIXAFS) and high energy resolution fluorescence detection (HERFD) XAS measurements of Pt/Rh(111) in 0.01 M HClO4 solution. In the HERFD-XAS experiment, we used a multi-crystal analyzer to suppress the core hole lifetime broadening. The HERFD spectra reveal additional spectral features of the near-edge region which can be important for an accurate structure model of the Pt/electrolyte interface.

Signals from the epoch of cosmological recombination – Karl Schwarzschild Award Lecture 2008

AbstractThe physical ingredients to describe the epoch of cosmological recombination are amazingly simple and well‐understood. This fact allows us to take into account a very large variety of physical processes, still finding potentially measurable consequences for theenergy spectrumandtemperature anisotropiesof the Cosmic Microwave Background (CMB). In this contribution we provide a short historical overview in connection with the cosmological recombination epoch and its connection to the CMB. Also we highlight some of the detailed physics that were studied over the past few years in the context of the cosmological recombination ofhydrogenandhelium. The impact of these considerations is two‐fold:(i) The associated release of photons during this epoch leads to interesting andunique deviationsof the CosmicMicrowave Background (CMB) energy spectrumfrom a perfect blackbody, which, in particular at decimeter wavelength and the Wien part of the CMB spectrum, may become observable in the near future. Despite the fact that the abundance of helium is rather small, it still contributes a sizeable amount of photons to the full recombination spectrum, leading to additional distinct spectral features. Observing the spectral distortions from the epochs of hydrogen and helium recombination, in principle would provide an additional way to determine some of the key parameters of the Universe (e.g. the specific entropy, the CMB monopole temperature and the pre‐stellar abundance of helium). Also it permits us to confront our detailed understanding of the recombination process withdirect observational evidence. In this contribution we illustrate how the theoreticalspectral templateof the cosmological recombination spectrum may be utilized for this purpose. We also show that because hydrogen and helium recombine at very different epochs it is possible to address questions related to thethermal historyof our Universe. In particular the cosmological recombination radiation may allow us to distinguish between Comptony‐distortions that were created by energy releasebeforeorafterthe recombination of the Universe finished.(ii) With the advent of high precision CMB data, e.g. as will be available using the PLANCK Surveyor or CMBPOL, a very accurate theoretical understanding of theionization historyof the Universe becomes necessary for the interpretation of the CMB temperature and polarization anisotropies. Here we show that the uncertainty in the ionization history due to several processes, which until now were not taken in to account in the standard recombination code RECFAST, reaches the percent level. In particular He II → He I recombination occurs significantly faster because of the presence of a tiny fraction of neutral hydrogen atz∼ 2400. Also recently it was demonstrated that in the case of H I Lymanαphotons thetimedependenceof the emission process and theasymmetrybetween the emission and absorption profile cannot be ignored. However, it is indeed surprising howinertthe cosmological recombination history is even at percent‐level accuracy. Observing the cosmological recombination spectrum should in principle allow us to directly check this conclusion, which until now is purely theoretical. Also it may allow toreconstruct the ionization historyusing observational data (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Theoretical Simulation and Synchrotron Excitation Spectra of Lanthanide Ions in Hexafluoroelpasolite Lattices

Vacuum ultraviolet (VUV) excitation spectra at 10 K have been recorded for the lanthanide ions, Ln3+ ) Nd3+, Ho3+, Tm3+, and Yb3+, situated at octahedral site symmetry in hexafluoroelpasolite Cs2NaLnF6 lattices. The corresponding VUV/UV/visible/near-infrared emission spectra have also been recorded. The 4fN-15d energy levels and 4fN-4fN-15d spectral intensities have been calculated by judicious selection of parameters, without detailed fittings, when employing the M. F. Reid suite of programs. The simulations are in reasonable agreement with experimental data. Some additional spectral features for these systems have been assigned to charge transfer (CT) transitions, and CT emission is reported for the case of Tm3+. A comparison of the results with the spectra of LiYF4:Ln3+ has been included and the major difference lies in the greater crystalfield strengths for Ln3+ in the hexafluoroelpasolite lattices.

Resonant Raman study of phonons in high-quality colloidal CdTe nanoparticles

We report on a resonant Raman scattering study of colloidal CdTe nanoparticles (NPs). The perfect crystallinity and narrow size distribution of the NPs allowed at least three additional spectral features near the main longitudinal optical phonon peak to be resolved at 50 K. We assign these features to scattering by transverse (145 cm−1) and surface (159 cm−1) optical phonon modes as well as to a combined optical-acoustic phonon mode(s) (180–200 cm−1). Both the transverse and combined optical-acoustic phonon modes were not reported previously for CdTe NPs.

Pre-recombinational energy release and narrow features in the CMB spectrum

Energy release in the early Universe (z<~ 2x10^6) should lead to some broad spectral distortion of the cosmic microwave background (CMB) radiation field, which can be characterized as y-type distortion when the injection process started at redshifts z<~ 5x10^4. Here we demonstrate that if energy was released before the beginning of cosmological hydrogen recombination (z~1400), closed loops of bound-bound and free-bound transitions in HI and HeII lead to the appearance of (i) characteristic multiple narrow spectral features at dm and cm wavelengths, and (ii) a prominent sub-millimeter feature consisting of absorption and emission parts in the far Wien tail of CMB spectrum. The additional spectral features are generated in the pre-recombinational epoch of HI (z>~1800) and HeII (z>~7000), and therefore differ from those arising due to normal cosmological recombination in the undisturbed CMB blackbody radiation field. We present the results of numerical computations including 25 atomic shells for both HI and HeII, and discuss the contributions of several individual transitions in detail. As examples, we consider the case of instantaneous energy release (e.g. due to phase transitions) and exponential energy release because of long-lived decaying particles. Our computations show that due to possible pre-recombinational atomic transitions the variability of the CMB spectral distortion increases when comparing with the distortions arising in the normal recombination epoch. The existence of these narrow spectral features would open an unique way to separate y-distortions due to pre-recombinational ($1400<~ z <~5x10^4) energy release from those arising in the post-recombinational era at redshifts z<~800. (abridged)

Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications

Tandem mass spectra (MS/MS) produced using electron transfer dissociation (ETD) differ from those derived from collision-activated dissociation (CAD) in several important ways. Foremost, the predominant fragment ion series are different: c- and z(*)-type ions are favored in ETD spectra while b- and y-type ions comprise the bulk of the fragments in CAD spectra. Additionally, ETD spectra possess charge-reduced precursors and unique neutral losses. Most database search algorithms were designed to analyze CAD spectra, and have only recently been adapted to accommodate c- and z(*)-type ions; therefore, inclusion of these additional spectral features can hinder identification, leading to lower confidence scores and decreased sensitivity. Because of this, it is important to pre-process spectral data before submission to a database search to remove those features that cause complications. Here, we demonstrate the effects of removing these features on the number of unique peptide identifications at a 1% false discovery rate (FDR) using the open mass spectrometry search algorithm (OMSSA). When analyzing two biologic replicates of a yeast protein extract in three total analyses, the number of unique identifications with a approximately 1% FDR increased from 4611 to 5931 upon spectral pre-processing--an increase of approximately 28.6%. We outline the most effective pre-processing methods, and provide free software containing these algorithms.

Raman spectroscopy, 19F and 31P MAS-NMR of a series of fluorochloroapatites

We report the Raman spectra of a series of fluorochloroapatites Ca 5(PO 4) 3F 1− x Cl x , where x = 0.0, 0.1, 0.2, 0.4, 0.5, 0.6, 0.8, 0.9 and 1.0 (i.e. from pure fluorapatite to chlorapatite). The series did not appear to exhibit any immiscibility, however peak broadening and additional Raman and NMR spectral features on chlorine addition could be interpreted as reduction in symmetry and ordering in the ion channels. All Raman bands showed significant broadening with chlorine substitution, indicating disordering of the crystal lattice or ordering into fluorine and chlorine rich environments. There was also a general trend of the Raman bands to shift to lower wavenumber linearly with chlorine substitution with the ν 1 phosphate band decreasing from 966 cm −1 for x = 0.0 to 961 cm −1 for x = 1.0. The full width half maximum (FWHM) of this band increases linearly with chlorine addition from 5 cm −1 for x = 0.0 to 10 cm −1 for x = 1.0. The shift in a component in the ν 3 phosphate band with chlorine addition at around 1035 cm −1 agrees with data in the literature on chlorine containing geological apatites. An additional component was seen at around 586 cm −1 in the ν 4 phosphate region for chlorapatite and the area of this band decreased linearly to zero as fluorine replaced chlorine. This could be due to E g symmetry phonons splitting into A g and B g modes due to a symmetry change such as hexagonal to monoclinic with chlorine addition. 19F magic angle spinning nuclear magnetic resonance (MAS-NMR) spectra showed a shift to lower ppm values with chlorine addition and a broadening of resonances, consistent with the Raman data. The 31P spectra developed additional shoulders (at around 2 and 4 ppm) with chlorine addition with the main peak position (3.3 ppm for x = 0) decreasing for compositions moving away from x = 0.5 indicating maximum phosphorous nuclear shielding occurs at an approximate F:Cl ratio of 1:1. This discontinuity is a possible indication of a structural transition at x = 0.5 related to local short scale phosphate order ↔ disorder or a change in crystal symmetry.

Influence of Base-Pair Interaction on Vibrational Spectrum of a Poly-dG Molecule Bonded to Si Substrates

A theoretical investigation is presented that characterizes the interaction dynamics of a double deoxyguanonsine molecular system, where two guanine bases are coupled via a sugar-phosphate backbone that is bound to the surface of silicon. Molecular dynamical simulations show that the influence of the coupling between the guanine bases (i.e., as compared with individual deoxyguanonsine molecules) leads to a significant increase of the absorption intensity from microwave to infrared (IR) frequencies. Furthermore, these results show that the strong coupling between the guanine bases leads to a much larger number of distinguishable vibrational modes at frequency below the IR at ~ 1350 cm-1. These effects also produce double-peak features in the Far-IR absorption intensity, which represent a splitting of the individual peaks associated with a single deoxyguanonsine molecule. Guanine base coupling also leads to a general shifting of all the absorption peaks towards the terahertz frequency regime (i.e., ~10 THz and below), which is also accompanied by a reduction of the absorption intensity as one progresses to longer wavelengths. Most importantly, this interaction phenomenon creates additional spectral features, which may be useful in a long-wavelength optics-based technique for DNA sequencing.