Structural descriptors and information extraction from X-ray emission spectra: aqueous sulfuric acid.

Machine learning can reveal new insights into X-ray spectroscopy of liquids when the local atomistic environment is presented to the model in a suitable way. Many unique structural descriptor families have been developed for this purpose. We benchmark the performance of six different descriptor families using a computational data set of 24 200 sulfur Kß X-ray emission spectra of aqueous sulfuric acid simulated at six different concentrations. We train a feed-forward neural network to predict the spectra from the corresponding descriptor vectors and find that the local many-body tensor representation, smooth overlap of atomic positions and atom-centered symmetry functions excel in this comparison. We found a similar hierarchy when applying the emulator-based component analysis to identify and separate the spectrally relevant structural characteristics from the irrelevant ones. In this case, the spectra were dominantly dependent on the concentration of the system, whereas adding the second most significant degree of freedom in the decomposition allowed for distinction of the protonation state of the acid molecule.

Isotope effects in dynamics of water isotopologues induced by core ionization at an x-ray free-electron laser.

Dynamical response of water exposed to x-rays is of utmost importance in a wealth of science areas. We exposed isolated water isotopologues to short x-ray pulses from a free-electron laser and detected momenta of all produced ions in coincidence. By combining experimental results and theoretical modeling, we identify significant structural dynamics with characteristic isotope effects in H2O2+, D2O2+, and HDO2+, such as asymmetric bond elongation and bond-angle opening, leading to two-body or three-body fragmentation on a timescale of a few femtoseconds. A method to disentangle the sequences of events taking place upon the consecutive absorption of two x-ray photons is described. The obtained deep look into structural properties and dynamics of dissociating water isotopologues provides essential insights into the underlying mechanisms.

Sensitivity of the Kß″ X-ray Emission Line to Coordination Changes in GeO2 and TiO2.

The hard X-ray Kß″ emission line shows sensitivity with respect to a wide range of cation-ligand coordination, which we investigate in the cases of GeO2 and TiO2 on the basis of ab initio spectral calculations on amorphous and crystalline structures. In compressed amorphous GeO2, the sampling of a large number of instantaneous coordination polyhedra from an ab initio molecular dynamics trajectory reveals that the functional relation between the Kß″ shift and coordination is close to linear between 4-fold and 7-fold coordination. A similar sensitivity of the Kß″ emission line exists in the coordination range between six and nine of crystalline high-pressure TiO2 polymorphs. Our results demonstrate the potential of the Kß″ emission line in research on the structure of amorphous oxide material.

Emulator-based decomposition for structural sensitivity of core-level spectra.

We explore the sensitivity of several core-level spectroscopic methods to the underlying atomistic structure by using the water molecule as our test system. We first define a metric that measures the magnitude of spectral change as a function of the structure, which allows for identifying structural regions with high spectral sensitivity. We then apply machine-learning-emulator-based decomposition of the structural parameter space for maximal explained spectral variance, first on overall spectral profile and then on chosen integrated regions of interest therein. The presented method recovers more spectral variance than partial least-squares fitting and the observed behaviour is well in line with the aforementioned metric for spectral sensitivity. The analysis method is able to independently identify spectroscopically dominant degrees of freedom, and to quantify their effect and significance.

A new benchmark of soft X-ray transition energies of Ne , CO 2 , and SF 6 : paving a pathway towards ppm accuracy.

Abstract: A key requirement for the correct interpretation of high-resolution X-ray spectra is that transition energies are known with high accuracy and precision. We investigate the K-shell features of Ne , CO 2 , and SF 6 gases, by measuring their photo ion-yield spectra at the BESSY II synchrotron facility simultaneously with the 1s-np fluorescence emission of He-like ions produced in the Polar-X EBIT. Accurate ab initio calculations of transitions in these ions provide the basis of the calibration. While the CO 2 result agrees well with previous measurements, the SF 6 spectrum appears shifted by ∼ 0.5 eV, about twice the uncertainty of the earlier results. Our result for Ne shows a large departure from earlier results, but may suffer from larger systematic effects than our other measurements. The molecular spectra agree well with our results of time-dependent density functional theory. We find that the statistical uncertainty allows calibrations in the desired range of 1-10 meV, however, systematic contributions still limit the uncertainty to ∼ 40-100 meV, mainly due to the temporal stability of the monochromator energy scale. Combining our absolute calibration technique with a relative energy calibration technique such as photoelectron energy spectroscopy will be necessary to realize its full potential of achieving uncertainties as low as 1-10 meV.

A novel genomic region on chromosome 11 associated with fearfulness in dogs.

The complex phenotypic and genetic nature of anxieties hampers progress in unravelling their molecular etiologies. Dogs present extensive natural variation in fear and anxiety behaviour and could advance the understanding of the molecular background of behaviour due to their unique breeding history and genetic architecture. As dogs live as part of human families under constant care and monitoring, information from their behaviour and experiences are easily available. Here we have studied the genetic background of fearfulness in the Great Dane breed. Dogs were scored and categorised into cases and controls based on the results of the validated owner-completed behavioural survey. A genome-wide association study in a cohort of 124 dogs with and without socialisation as a covariate revealed a genome-wide significant locus on chromosome 11. Whole exome sequencing and whole genome sequencing revealed extensive regions of opposite homozygosity in the same locus on chromosome 11 between the cases and controls with interesting neuronal candidate genes such as MAPK9/JNK2, a known hippocampal regulator of anxiety. Further characterisation of the identified locus will pave the way for molecular understanding of fear in dogs and may provide a natural animal model for human anxieties.

High-Precision Determination of Oxygen K_{α} Transition Energy Excludes Incongruent Motion of Interstellar Oxygen.

We demonstrate a widely applicable technique to absolutely calibrate the energy scale of x-ray spectra with experimentally well-known and accurately calculable transitions of highly charged ions, allowing us to measure the K-shell Rydberg spectrum of molecular O_{2} with 8 meV uncertainty. We reveal a systematic ∼450 meV shift from previous literature values, and settle an extraordinary discrepancy between astrophysical and laboratory measurements of neutral atomic oxygen, the latter being calibrated against the aforementioned O_{2} literature values. Because of the widespread use of such, now deprecated, references, our method impacts on many branches of x-ray absorption spectroscopy. Moreover, it potentially reduces absolute uncertainties there to below the meV level.

Ventricular arrhythmia and sudden cardiac death in young Leonbergers.

INTRODUCTION: To describe unexpected sudden cardiac death (SCD) in young Leonbergers (<3 years) and to review the circumstances before death and necropsy findings; to prospectively evaluate the presence of possible arrhythmias in young Leonbergers; and to examine pedigrees for determining potential modes of inheritance. ANIMALS: Postmortem evaluations included 21 Leonbergers. Clinical evaluation consisted of 46 apparently healthy Leonbergers with and without a close family history of SCD. MATERIALS AND METHODS: Necropsy reports were reviewed retrospectively. Prospective clinical evaluation included physical examination, 5-min electrocardiogram, 24-h Holter, echocardiography, and laboratory tests. Pedigree data were examined for mode of inheritance. RESULTS: Based on necropsy reports, SCD occurred at a median age of 12 months (range, 2.0-32.0 months) without any previous clinical signs and usually in rest. No evidence of structural cardiac disease was found; arrhythmia-related death was suspected. Clinical evaluation and 24-h Holter showed ventricular arrhythmia (VA) in 14 apparently healthy Leonbergers (median age, 18 months; range, 12-42 months). Severity of VA varied from infrequent couplets/triplets to frequent complexity (couplets, triplets, nonsustained ventricular tachycardias,VTs) characterized by polymorphology. During follow-up, two dogs with polymorphic VT died. Although breed specificity and high prevalence indicate a heritable disease, based on available pedigree data, the mode of inheritance could not be determined. CONCLUSIONS: Sudden cardiac death in young Leonbergers is associated with malignant VA characterized by complexity and polymorphic nature. Diagnosis is based on 24-h Holter monitoring. Pedigree analysis suggests that the arrhythmia is familial.

A novel KRT71 variant in curly-coated dogs.

Curly fur is a common phenotype in many dog breeds, known to result from a missense variant (c.451C>T) in exon 2 of the keratin 71 (KRT71) gene. During screening for this variant across various breeds, we found that Curly Coated Retrievers (CCRs) fixed with the trait did not carry the known variant. By analysis of whole-genome sequencing data of one CCR we identified a novel genetic cause for curly fur. We found a novel structural variant in exon 7 of the KRT71 gene (c.1266_1273delinsACA) that was predicted to result in a frameshift and stop loss, therefore significantly affecting the structure of the protein, if translated. The variant was also found at lower frequencies in five other breeds, including Lagotto Romagnolo, Bichon Frise, Spanish Water Dog, Chesapeake Bay Retriever and Irish Terrier. One curly-coated Lagotto carried neither of the two KRT71 variants. These results identify a second variant for curly coat in KRT71 and suggest the existence of additional alleles. This study enables the development of an additional KRT71 gene test for breeders to understand and manage coat types.

QED effects in 1s and 2s single and double ionization potentials of the noble gases.

We present calculations on the quantum electrodynamics (QED) effects in 1s and 2s single and double ionization potentials of noble gases from Ne to Rn as perturbations on relativistic four-component Dirac-Fock wavefunctions. The most dominant effect originates from the self-energy of the core-electron that yields corrections of similar order as the transverse interaction. For 1s ionization potentials, a match within few eV against the known experimental values is obtained, and our work reveals considerable QED effects in the photoelectron binding energies across the periodic table-most strikingly even for Ne. We perform power-law fits for the corrections as a function of Z and interpolate the QED correction of ∼-0.55 eV for S1s. Due to this, the K-edge electron spectra of the third row and below need QED for a match in the absolute energy when using state-of-the-art instrumentation.

A miniature closed-circle flow cell for high photon flux X-ray scattering experiments.

A closed-circle miniature flow cell for high X-ray photon flux experiments on radiation-sensitive liquid samples is presented. The compact cell is made from highly inert material and the flow is induced by a rotating magnetic stir bar, which acts as a centrifugal pump inside the cell. The cell is ideal for radiation-sensitive yet precious or hazardous liquid samples, such as concentrated acids or bases. As a demonstration of the cell's capabilities, X-ray Raman scattering spectroscopy data on the oxygen K-edge of liquid water under ambient conditions are presented.

Planning, performing and analyzing X-ray Raman scattering experiments.

A compilation of procedures for planning and performing X-ray Raman scattering (XRS) experiments and analyzing data obtained from them is presented. In particular, it is demonstrated how to predict the overall shape of the spectra, estimate detection limits for dilute samples, and how to normalize the recorded spectra to absolute units. In addition, methods for processing data from multiple-crystal XRS spectrometers with imaging capability are presented, including a super-resolution method that can be used for direct tomography using XRS spectra as the contrast. An open-source software package with these procedures implemented is also made available.

Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

Optical emission from a small scale model electric arc furnace in 250-600 nm region.

Optical emission spectroscopy has been for long proposed for monitoring and studying industrial steel making processes. Whereas the radiative decay of thermal excitations is always taking place in high temperatures needed in steel production, one of the most promising environment for such studies are electric arc furnaces, creating plasma in excited electronic states that relax with intense characteristic emission in the optical regime. Unfortunately, large industrial scale electric arc furnaces also present a challenging environment for optical emission studies and application of the method is not straightforward. To study the usability of optical emission spectroscopy in real electric arc furnaces, we have developed a laboratory scale DC electric arc furnace presented in this paper. With the setup, optical emission spectra of Fe, Cr, Cr2O3, Ni, SiO2, Al2O3, CaO, and MgO were recorded in the wavelength range 250-600 nm and the results were analyzed with the help of reference data. The work demonstrates that using characteristic optical emission, obtaining in situ chemical information from oscillating plasma of electric arc furnaces is indeed possible. In spite of complications, the method could possibly be applied to industrial scale steel making process in order to improve its efficiency.

Temperature dependence of CO2 and N2 core-electron excitation spectra at high pressure.

We report a study on the temperature dependence of the core-electron excitation spectra of CO2 and N2, performed using non-resonant inelastic X-ray scattering spectroscopy. The spectra were measured at two temperatures (300 K and 850 K) and at high pressure (40 bar). For CO2 a clear temperature dependence was observed at the C and O near-edge regions. The spectra of CO2 were simulated by density functional theory calculations, and the temperature was accounted for by sampling the initial state molecular geometries using the Metropolis algorithm. This model is able to account for the experimentally observed temperature dependence of the spectrum. The experiment fortifies the status of the non-resonant inelastic X-ray scattering spectroscopy as a valuable technique for physics and chemistry for in situ studies under extreme sample conditions. Especially in the case of gas phase the sample conditions of considerably elevated temperature and pressure are unfeasible for many other spectroscopic techniques.

Electron-ion coincidence study of photofragmentation of the CdCl(2) molecule.

In this work, the photofragmentation subsequent to valence and Cd4d photoionization of cadmium dichloride (CdCl(2)) were studied using He I and synchrotron excitation. The measurements were performed with a photoelectron-photoion coincidence (PEPICO) setup, and the connection between the singly ionized electronic states and cationic fragments was investigated. The valence-ionized states were found to lead to CdCl(2)(+), Cd(+) and CdCl(+). The Cd4d(- 1) states were found to lead only to Cl(+) ions. The observed charge transfer effect between Cd and Cl was concluded to take place due to internal conversion or fluorescence decay to dissociating valence states either directly or through consecutive fragmentation. The fragmentation energetics were investigated with molecular ab initio calculations, and the calculated energies were found to agree with the detected fragment appearances.

Relativistic contributions to single and double core electron ionization energies of noble gases.

We have performed relativistic calculations of single and double core 1s hole states of the noble gas atoms in order to explore the relativistic corrections and their additivity to the ionization potentials. Our study unravels the interplay of progression of relaxation, dominating in the single and double ionization potentials of the light elements, versus relativistic one-electron effects and quantum electrodynamic effects, which dominate toward the heavy end. The degree of direct relative additivity of the relativistic corrections for the single electron ionization potentials to the double electron ionization potentials is found to gradually improve toward the heavy elements. The Dirac-Coulomb Hamiltonian is found to predict a scaling ratio of ∼4 for the relaxation induced relativistic energies between double and single ionization. Z-scaling of the computed quantities were obtained by fitting to power law. The effects of nuclear size and form were also investigated and found to be small. The results indicate that accurate predictions of double core hole ionization potentials can now be made for elements across the full periodic table.

Core-valence double photoionization of the CS(2) molecule.

Double photoionization spectra of the CS(2) molecule have been recorded using the TOF-PEPECO technique in combination with synchrotron radiation at the photon energies hν=220, 230, 240, 243, and 362.7 eV. The spectra were recorded in the S 2p and C 1s inner-shell ionization regions and reflect dicationic states formed out of one inner-shell vacancy and one vacancy in the valence region. MCSCF calculations were performed to model the energies of the dicationic states. The spectra associated with a S 2p vacancy are well structured and have been interpreted in some detail by comparison to conventional S 2p and valence photoelectron spectra. The lowest inner-shell-valence dicationic state is observed at the vertical double ionization energy 188.45 eV and is associated with a (2p(3/2))(-1)(2π(g))(-1) double vacancy. The spectrum connected to the C 1s vacancy shows a distinct line at 310.8 eV, accompanied by additional broad features at higher double ionization energies. This line is associated with a (C 1s)(-1)(2π(g))(-1) double vacancy.

Water spin dynamics during apoptotic cell death in glioma gene therapy probed by T1rho and T2rho.

Longitudinal and transverse relaxations in the rotating frame, with characteristic time constants T1rho and T2rho, respectively, have potential to provide unique MRI contrast in vivo. On-resonance spin-lock T1rho with different spin-lock field strengths and adiabatic T2rho with different radiofrequency-modulation functions were measured in BT4C gliomas treated with Herpes Simplex Virus thymidine kinase (HVS-tk) gene therapy causing apoptotic cell death. These NMR tools were able to discriminate different treatment responses in tumor tissue from day 4 onward. An equilibrium two-site exchange model was used to calculate intrinsic parameters describing changes in water dynamics. Observed changes included increased correlation time of water associated with macromolecules and a decreased fractional population of this pool. These results are consistent with destructive intracellular processes associated with cell death and the increase of extracellular space during the treatment. Furthermore, association between longer exchange correlation time and decreased pH during apoptosis is discussed. In this study, we demonstrated that T1rho and T2rho MR imaging are useful tools to quantify early changes in water dynamics reflecting treatment response during gene therapy.

On correlation between single-trial ERP and GSR responses: a principal component regression approach.

In this study we investigate the correlation between single-trial evoked brain responses and galvanic skin responses (GSR). The correlation between the two signals is examined by using a modified principal component regression based approach. A potential application of the study is to utilize the GSR measurements in a form of a prior information in the estimation of the brain potentials when only small number of trials is available.