Comparing Peak Intensities Research Articles

Multilevel atomic structural model for interstratified opal materials

The structure of opal has long fascinated scientists. It occurs in a number of structural states, ranging from amorphous to exhibiting features of stacking disorder. Opal-CT, where C and T signify cristobalite- and tridymite-like interstratification, represents an important link in the length scales between amorphous and crystalline states. However, details about local atomic (dis)order and arrangements extending to long-range stacking faults in opal polymorphs remain incompletely understood. Here, a multilevel modeling approach is reported that considers stacking states in correlation with the abundance of C and T segments as a high-level structural parameter (i.e. not each atom). Optimization accounting for inter-tetrahedral bond lengths and angles and the regularity of the silicate tetrahedra is included as lower levels of structural parameters. Together, a set of parameters with both coarse-grained and atomistic features for different levels of structural details is refined. Structural disorder at the ∼10–100 Å distance scale is evaluated using experimental pair distribution function and diffraction datasets, comparing peak intensities, widths and asymmetry. This work presents a complete multilevel structural description of natural opal-CT and explains many of the unusual features observed in X-ray powder diffraction patterns. This modeling approach can be adopted generally for analyzing layered materials and their assembly into 3D structures.

Multi-focus composite spiral zone plate to generate focused vortices with the comparable intensity based on genetic algorithm.

In this study, we introduce an optical element, named Multi-focus Composite Spiral Zone Plate (MFCSZP), to generate multi focused vortices with approximately equal intensity along the optical axis. The genetic algorithm (GA) is used to optimize the parameters of the MFCSZP, which avoids manual parameter adjustment and improves computational efficiency. We analyze the focusing properties of the constructed MFCSZP theoretically and experimentally. The results provide evidence for its capability to generate multiple focused vortices with comparable peak intensities verified through experiment. This work shows the powerful ability of intelligent algorithms in the optimization of complex optical elements. The proposed optical element showcases potential applications within research areas of optical trapping and laser machining.

Determination of the Thickness of Nanofilms Using X-Ray Photoelectron Spectroscopy

Determination of coating thicknesses whose dimensions lie in the nanometer range is an important analytical application of X-ray photoelectron spectroscopy (XPS). The coating thickness is determined as a result of comparing peak intensities measured using lines corresponding to the coating with those of characteristic substrate lines. It is shown that the error in determining thicknesses using a procedure that completely disregards processes of elastic electron scattering reaches 50%. At present, the influence of elastic scattering processes is taken into account by replacing the inelastic mean free path with the fitting parameter called the effective attenuation length. Physical phenomena occurring in the case of the inclusion of an elastic photoelectron scattering channel are analyzed in this paper. Two approaches to the description of XPS spectra are considered: the first one is implemented using invariant embedding methods, and the second one used the method of discrete ordinates with the matrix exponent. On the basis of the first method, the influence of multiple elastic-scattering events on the XPS energy spectra is studied. The second one shows a high effectiveness when calculating no loss peaks of photoelectrons emitted by multilayer samples.

An adapted isotope dilution 1H-13C heteronuclear single-quantum correlation (ID-HSQC) for rapid and accurate quantification of endogenous and exogenous plasma glucose.

A wide variety of methods, such as enzymatic methods, LC-MS, and LC-MS/MS, are currently available for the concentration determination of plasma glucose in studies of diabetes, obesity, exercise, etc. However, these methods rarely discriminate endogenous and exogenous glucose in plasma. A novel NMR strategy for discriminative quantification of the endogenous and exogenous glucose in plasma has been developed using an adapted isotope dilution 1H-13C heteronuclear single-quantum correlation (ID-HSQC) with uniformly 13C-labeled glucose as a tracer of exogenous glucose. This method takes advantage of the distinct 1H-13C chemical shifts of the hemiacetal group of the α-D-glucopyranose and makes use of the 13C-13C one-bond J-coupling (1JCC) in uniformly 13C-labeled glucose to differentiate the 1H-13C HSQC signal of labeled glucose from that of its natural counterpart when data are acquired in high-resolution mode. The molar ratio between the endogenous and exogenous plasma glucose can then be calculated from the peak intensities of the natural and labeled glucose. The accuracy and precision of the method were evaluated using a series of standard mixtures of natural and uniformly 13C-labeled glucose with varied but known concentrations. Application of this method is demonstrated for the quantification of endogenous and exogenous glucose in plasma derived from healthy and diabetic cynomolgus monkeys. The results nicely agree with our previous LC-MS/MS results. Considering the natural abundance of 13C isotope at the level of 1.1% in endogenous glucose, comparable peak intensities of quantitatively measurable signals derived from natural and labeled glucose imply that the ID-HSQC can tolerate a significantly high ratio of isotope dilution, with labeled/natural glucose at ~ 1%. We expect that the ID-HSQC method can serve as an alternative approach to the biomedical or clinical studies of glucose metabolism.

Quantitation of Human Metallothionein Isoforms: A Family of Small, Highly Conserved, Cysteine-rich Proteins

Human metallothioneins (MTs) are important regulators of metal homeostasis and protectors against oxidative damage. Their altered mRNA expression has been correlated with metal toxicity and a variety of cancers. Current immunodetection methods lack the specificity to distinguish all 12 human isoforms. Each, however, can be distinguished by the mass of its acetylated, cysteine-rich, hydrophilic N-terminal tryptic peptides. These properties were exploited to develop a bottom-up MALDI-TOF/TOF-MS-based method for their simultaneous quantitation. Key features included enrichment of N-terminal acetylated peptides by strong cation exchange chromatography, optimization of C18 reversed-phase chromatography, and control of methionine oxidation. Combinations of nine isoforms were identified in seven cell lines and two tissues. Relative quantitation was accomplished by comparing peak intensities of peptides generated from pooled cytosolic proteins alkylated with ¹⁴N- or ¹⁵N-iodoacetamide. Absolute quantitation was achieved using ¹⁵N-iodoacetamide-labeled synthetic peptides as internal standards. The method was applied to the cadmium induction of MTs in human kidney HK-2 epithelial cells expressing recombinant MT-3. Seven isoforms were detected with abundances spanning almost 2 orders of magnitude and inductions up to 12-fold. The protein-to-mRNA ratio for MT-1E was one-tenth that of other MTs, suggesting isoform-specific differences in protein expression efficiency. Differential expression of MT-1G1 and MT-1G2 suggested tissue- and cell-specific alternative splicing for the MT-1G isoform. Protein expression of MT isoforms was also evaluated in human breast epithelial cancer cell lines. Estrogen-receptor-positive cell lines expressed only MT-2 and MT-1X, whereas estrogen-receptor-negative cell lines additionally expressed MT-1E. The combined expression of MT isoforms was 38-fold greater in estrogen-receptor-negative cell lines than in estrogen-receptor-positive cells. These findings demonstrate that individual human MT isoforms can be accurately quantified in cells and tissues at the protein level, complementing and expanding mRNA measurement as a means for evaluating MTs as potential biomarkers for cancers or heavy metal toxicity.

Modeling the properties of plasmaspheric hiss: 1. Dependence on chorus wave emission

There is increasing evidence that plasmaspheric hiss is formed by the evolution of a portion of chorus waves that are excited in the plasmatrough and propagate into the plasmasphere. Comparison between the statistical spatial distributions of these two emissions in the morning sector during active times from THEMIS over ∼3 years shows that the two emissions have comparable peak intensities but are distinct in their spatial distributions. We present a modeling study of the hiss spectrum, based on ray tracing, by taking the observed chorus source region as an input in the magnetosphere, which contains cold and suprathermal electrons. Our modeling results show that we are able to reproduce the main features of typical hiss, including the frequency spectrum, wave normal angle and spatial distribution. However, the simulated hiss intensity is weaker (∼15 dB less) than the observed intensity, which suggests some modest internal amplification inside the plasmasphere. The responses of hiss to variations in the spatial distribution, wave normal angle distribution and frequency distribution of the source chorus are examined. We find that the majority of hiss formation is due to a small portion of chorus emission originating within ∼3 RE from the plasmapause, with wave normal directions pointing toward the Earth at an angle of 30°–60°, and over a frequency range of 0.1–0.3 fce. If the chorus power is made to increase closer to the plasmapause, the hiss intensity and the peak frequency also increases, which roughly mimics active geomagnetic conditions. Variations of the chorus source distribution do not significantly affect the wave normal angle distribution and frequency distribution of hiss, but does impact the absolute intensity of the resulting hiss.

Size and defect related broadening of photoluminescence spectra in ZnO:Si nanocomposite films

Nanocomposite films of zinc oxide and silicon were grown by thermal evaporation technique using varying ratios of ZnO:Si in the starting material. Structural analyses reveal the role of ZnO and amorphous silicon interface in contributing to the relatively less common blue photoluminescence emissions (at ∼410 and 470nm). These blue peaks are observed along with the emissions resulting from band edge transition (370nm) and those related to defects (520nm) of ZnO. Careful analysis shows that along with the grain size of ZnO, a suitable compositional ratio of ZnO to silicon is critical for the coexistence of all the four peaks. Proper selection of conditions can give comparable photoluminescence peak intensities leading to broad-band emission.

Combining capillary electrophoresis matrix-assisted laser desorption/ionization mass spectrometry and stable isotopic labeling techniques for comparative crustacean peptidomics

Herein we describe a sensitive and straightforward off-line capillary electrophoresis (CE) matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) interface in conjunction with stable isotopic labeling (SIL) technique for comparative neuropeptidomic analysis in crustacean model organisms. Two SIL schemes, including a binary H/D formaldehyde labeling technique and novel, laboratory-developed multiplexed dimethylated leucine-based isobaric tagging reagents, have been evaluated in these proof-of-concept experiments. We employ these isotopic labeling techniques in conjunction with CE-MALDI-MS for quantitative peptidomic analyses of the pericardial organs isolated from two crustacean species, the European green crab Carcinus maenas and the blue crab Callinectes sapidus. Isotopically labeled peptide pairs are found to co-migrate in CE fractions and quantitative changes in relative abundances of peptide pairs are obtained by comparing peak intensities of respective peptide pairs. Several neuropeptide families exhibit changes in response to salinity stress, suggesting potential physiological functions of these signaling peptides.

An atomic inner-shell laser pumped with an x-ray free-electron laser

Focusing an x-ray free electron laser (XFEL) pulse into a gas target, a plasma of transiently core-excited ions can be created within a few femtoseconds, building a pathway to an inner-shell keV atomic x-ray laser. Varying the XFEL parameters, a wide variety of pulse structures can be created with comparable peak-intensities to XFELs: isolated pulses of sub-femtosecond duration, trains of pulses with increased temporal coherence, and trains of femtosecond pulses of different wavelengths. We present self-consistent gain and amplification calculations, tailored to predict first experiments on lasing on neon pumped by the Linac Coherent Light Source at Stanford.

Coherent continuum generation above 100 eV driven by an ir parametric source in a two-color scheme

High-order harmonics were generated in a two-color scheme exploiting an infrared parametric source with self-stabilization of the carrier-envelope phase. A significant cutoff extension was observed with respect to single color, 800 nm driving pulses at comparable peak intensities. Exploiting the wavelength tuning of the parametric source in the $1.5\char21{}1.6\text{ }\ensuremath{\mu}\text{m}$ range, a continuous xuv spectrum extending from 36 to 70 eV was generated in krypton. A broader xuv continuum, extending beyond 100 eV, was observed in argon. These results represent a step forward in the extension of attosecond science toward the soft x-rays region and open new perspectives in the investigation of quantum effects in atoms and molecules.

Comparative LC‐MS: A landscape of peaks and valleys

Quantitative proteomics approaches using stable isotopes are well-known and used in many labs nowadays. More recently, high resolution quantitative approaches are reported that rely on LC-MS quantitation of peptide concentrations by comparing peak intensities between multiple runs obtained by continuous detection in MS mode. Characteristic of these comparative LC-MS procedures is that they do not rely on the use of stable isotopes; therefore the procedure is often referred to as label-free LC-MS. In order to compare at comprehensive scale peak intensity data in multiple LC-MS datasets, dedicated software is required for detection, matching and alignment of peaks. The high accuracy in quantitative determination of peptide abundance provides an impressive level of detail. This approach also requires an experimental set-up where quantitative aspects of protein extraction and reproducible separation conditions need to be well controlled. In this paper we will provide insight in the critical parameters that affect the quality of the results and list an overview of the most recent software packages that are available for this procedure.

XPS studies of amino acids adsorbed on titanium dioxide surfaces

Adsorption of amino acids from aqueous solutions on TiO2 surfaces as a function of pH is monitored quantitatively by X-ray photoelectron spectroscopy (XPS). Because of the amphoteric character of the TiO2 and the “zwitterionic” behaviour of the amino acids the pH of adsorption indicates what chemical groups are involved in the adsorption reaction. The results confirm the ligand exchange model: in acidic milieu the carboxylic group replaces a basic surface hydroxyl group on a Ti site and binds to this Ti. For homocysteine the resulting position of the adsorbed molecule can also be concluded by comparing peak intensities.

The vibronic structure of mixed-ligand osmium(iv) complexes

Mixed-ligand osmium(iv) complexes, OsCl5X2- and cis-OsCl4X2- 2, with X = Br or I, are optically investigated by recording the 10 K absorption spectra of the caesium and tetrabutylammonium salts in KBr pellets and the 10–20 K emission spectra of complexes doped in Cs2SnCl6, both in the energy region between 5000 and 17 000 cm-1. The measured peaks (origins and vibronics) are due to zero-phonon and vibronic transitions respectively within the (t2g)4 subshell configuration, which gives rise to a maximum of 15 energy levels at low symmetry. From the well-resolved absorption and emission spectra the d-level energies can be obtained for many of the split states that are expected in the region considered. For an assignment to symmetry types, selection rules for electric dipole transitions are applied, comparing peak intensities in the spectra. Ligand-field calculations using angular overlap parameters support these assignments, which must, however, be considered as partially tentative.

Effects of variations in rectangular pulse duty cycle and intensity on pulsating direct current electro-analgesia of cat tooth pulp

Action potentials in single pulp-driven units of the trigeminal ganglion were elicited by bipolar electrical stimulation of the maxillary canine tooth pulp in cats anaesthetized with a barbiturate. The effects of electro-analgesia currents ranging in peak values from 10 to 100 μA applied to the test tooth were investigated independently for three pulsating direct-current waveforms comprised of trains of monopolar anodal rectangular pulses of various duty cycles. The effects of constant direct-current analgesia were used as a standard for comparison. Logarithmically-spaced duty cycles (per cent on time) of 1.00, 3.16 and 10.0 per cent were investigated, using a fixed frequency of 1000 Hz. Intensity-dependent pulp threshold elevations reaching approximately 400–500 per cent were observed for both constant direct current and 10 per cent duty cycle pulsating direct current analgesia of 20–70μA. In contrast, pulsating direct current analgesia waveforms having duty cycles of 3.16 and 1.00 per cent were approximately 25 per cent effective and ineffective, respectively, when compared to continuous direct current analgesia. The maximum effect was attained with waveforms of 70 μA. Averaged pulp thresholds dropped to near normal values within a few minutes following the termination of effective electro-analgesia. The results indicate that pulsating direct-current analgesia composed of rectangular anodal pulses of 10 per cent duty cycle and 1000 Hz frequency produces effects indistinguishable from that of continuous direct current analgesia at comparable peak intensities.

Identification of amino sugars from bacterial lipopolysaccharides by gas chromatography electron impact and chemical ionization mass spectrometry.

Amino sugars isolated from lipopolysaccharides of Brucella suis, Brucella abortus and Neisseria gonorrhoeae colony types 1 and 4 were identified using gas chromatography electron impact and chemical ionization mass spectrometry. Lipopolysaccharides were obtained by aqueous ether or aqueous phenol extraction. Isolated lipopolysaccharides were hydrolyzed in 1% acetic acid followed by hydrolysis of the polysaccharide moiety in 2 NHCl for 6 h at 100 degrees C. Amino sugars were first isolated by elution from Dowex 50 H+ and then N-acetylated, followed by trimethylsilylation. Trimethylsilyl ethers of 2-acetamido-2-deoxysugars; N-acetylglucosamine, N-acetylmannosamine, N-acetylgalactosamine, and a 2-acetamido-2.6-dideoxysugar, N-acetylquinovosamine, were identified by their fragmentation patterns. In the electron impact mode, N-acetylglucosamine and N-acetyl-galactosamine were distinguished from one another by comparing peak intensities at m/e 233 and 305. However, N-acetylglucosamine and N-acetylmannosamine could not be differentiated by electron impact mass spectrometry. In the chemical ionization mode, N-acetylglucosamine and N-acetylmannosamine both with base peaks at m/e 494, could be distinguished from N-acetylgalactosamine and N-acetylquinovosamine by their base peaks at m/e 420 and 332, respectively. N-Acetylglucosamine and N-acetylmannosamine were differentiated from one another by comparing peak intensities at m/e 330, 404, 420, and 510 [MH]+. This is the first report of chemical ionization mass spectrometry applied to the identification of amino sugars in bacterial lipopolysaccharides and shows that some 2-amino-2-deoxysugars can be differentiated by both electron impact and chemical ionization mass spectrometry.