Ethical considerations for Forensic Genetic Frequency databases: First Report conception and development

The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received.

The Application of HEXS and HERFD XANES for Accurate Structural Characterisation of Actinide Nanomaterials: The Case of ThO2

The structural characterisation of actinide nanoparticles (NPs) is of primary importance and hard to achieve, especially for non-homogeneous samples with NPs less than 3 nm. By combining high-energy X-ray scattering (HEXS) and high-energy-resolution fluorescence-detected X-ray absorption near-edge structure (HERFD XANES) analysis, we have characterised for the first time both the short- and medium-range order of ThO2 NPs obtained by chemical precipitation. By using this methodology, a novel insight into the structures of NPs at different stages of their formation has been achieved. The pair distribution function revealed a high concentration of ThO2 small units similar to thorium hexamer clusters mixed with 1 nm ThO2 NPs in the initial steps of formation. Drying the precipitates at around 150 °C promoted the recrystallisation of the smallest units into more thermodynamically stable ThO2 NPs. HERFD XANES analysis at the thorium M4 edge, a direct probe for f states, showed variations that we have correlated with the breakdown of the local symmetry around the thorium atoms, which most likely concerns surface atoms. Together, HEXS and HERFD XANES are a powerful methodology for investigating actinide NPs and their formation mechanism.

The Application of HEXS and HERFD XANES for Accurate Structural Characterisation of Actinide Nanomaterials: The Case of ThO2

Invited for the cover of this issue is Lucia Amidani and co-workers from the The European Synchrotron, Helmholtz Zentrum Dresden-Rossendorf, Lomonosov Moscow State University, Kurchatov Institute, and the Université Grenoble Alpes. The image depicts the atomic structure of the sample being viewed through "atomic googles", which represent the X-ray techniques used in this work. Read the full text of the article at 10.1002/chem.202003360.

Resonant nanodiffraction x-ray imaging reveals role of magnetic domains in complex oxide spin caloritronics

Spin electronic devices based on crystalline oxide layers with nanoscale thicknesses involve complex structural and magnetic phenomena, including magnetic domains and the coupling of the magnetism to elastic and plastic crystallographic distortion. The magnetism of buried nanoscale layers has a substantial impact on spincaloritronic devices incorporating garnets and other oxides exhibiting the spin Seebeck effect (SSE). Synchrotron hard x-ray nanobeam diffraction techniques combine structural, elemental, and magnetic sensitivity and allow the magnetic domain configuration and structural distortion to be probed in buried layers simultaneously. Resonant scattering at the Gd L₂ edge of Gd₃Fe₅O₁₂ layers yields magnetic contrast with both linear and circular incident x-ray polarization. Domain patterns facet to form low-energy domain wall orientations but also are coupled to elastic features linked to epitaxial growth. Nanobeam magnetic diffraction images reveal diverse magnetic microstructure within emerging SSE materials and a strong coupling of the magnetism to crystallographic distortion.

Crystal Orbital Overlap Population and X-ray Absorption Spectroscopy

We present an extension of an ab initio numerical tool calculating X-ray absorption spectroscopies and crystal orbital overlap populations at the same time. Density functional theory is used to calculate the electronic structure in both occupied (valence to core X-ray emission spectroscopy) and nonoccupied states (i.e., X-ray absorption near the edge structure and X-ray magnetic circular dichroism) and to evaluate the orbital overlap typifying the covalency between neighboring atoms. We show how the different features in the experimental spectra can be correlated to the chemical bonds around the absorbing atoms in several examples including acrylonitrile molecules, rutile TiO₂, Li₂RuO₃ high-energy density cathode, ZnO, and anti-ferromagnetic V₂O₃.

Transparent and luminescent glasses of gold thiolate coordination polymers

Obtaining transparent glasses made of functional coordination polymers (CPs) represents a tremendous opportunity for optical applications. In this context, the first transparent and red-emissive glasses of gold thiolate CPs have been obtained by simply applying mechanical pressure to amorphous powders of CPs. The three gold-based CP glasses are composed of either thiophenolate [Au(SPh)] n , phenylmethanethiolate [Au(SMePh)] n or phenylethanethiolate [Au(SEtPh)] n . The presence of a longer alkyl chain between the thiolate and the phenyl ring led to the formation of glass with higher transparency. The glass transitions, measured by thermomechanical analysis (TMA), occurred at lower temperature for CPs with longer alkyl chains. In addition, all three gold thiolate glasses exhibit red emission at 93 K and one of them, [Au(SMePh)] n , remains luminescent even at room temperature. An in-depth structural study of the amorphous gold thiolates by XRD, PDF and EXAFS analysis showed that they are formed of disordered doubly interpenetrated helical chains. These d10 metal-based compounds represent the first examples of transparent and luminescent CP glasses.

Epitaxial growth and structure of cobalt ferrite thin films with large inversion parameter on Ag(001)

Cobalt ferrite ultrathin films with the inverse spinel structure are among the best candidates for spin filtering at room temperature. High-quality epitaxial CoFe₂O₄ films about 4 nm thick have been fabricated on Ag(001) following a three-step method: an ultrathin metallic CoFe₂ alloy was first grown in coherent epitaxy on the substrate and then treated twice with O₂, first at room temperature and then during annealing. The epitaxial orientation and the surface, interface and film structure were resolved using a combination of low-energy electron diffraction, scanning tunnelling microscopy, Auger electron spectroscopy and in situ grazing-incidence X-ray diffraction. A slight tetragonal distortion was observed, which should drive the easy magnetization axis in-plane due to the large magneto-elastic coupling of such a material. The so-called inversion parameter, i.e. the Co fraction occupying octahedral sites in the ferrite spinel structure, is a key element for its spin-dependent electronic gap. It was obtained through in situ resonant X-ray diffraction measurements collected at both the Co and Fe K edges. The data analysis was performed using FDMNES, an ab initio program already extensively used to simulate X-ray absorption spectroscopy, and shows that the Co ions are predominantly located on octahedral sites with an inversion parameter of 0.88 (5). Ex situ X-ray photoelectron spectroscopy gives an estimation in accordance with the values obtained through diffraction analysis.

Ca and S K-edge XANES of CaS calculated by different methods: influence of full potential, core hole and Eu doping

Ca and S K-edge spectra of CaS are calculated by the full-potential Green's function multiple-scattering method, by the FLAPW method and by the finite-difference method. All three techniques lead to similar spectra. Some differences remain close to the edge, both when comparing different calculations with each other and when comparing the calculations with earlier experimental data. Here it is found that using the full potential does not lead to significant improvement over the atomic spheres approximation and that the effect of the core hole can be limited to the photoabsorbing atom alone. Doping CaS with Eu will not affect the Ca and S K-edge XANES of CaS significantly but may give rise to a pre-edge structure not present for clean CaS.

The role of the 5f valence orbitals of early actinides in chemical bonding

One of the long standing debates in actinide chemistry is the level of localization and participation of the actinide 5f valence orbitals in covalent bonds across the actinide series. Here we illuminate the role of the 5f valence orbitals of uranium, neptunium and plutonium in chemical bonding using advanced spectroscopies: actinide M4,5 HR-XANES and 3d4f RIXS. Results reveal that the 5f orbitals are active in the chemical bonding for uranium and neptunium, shown by significant variations in the level of their localization evidenced in the spectra. In contrast, the 5f orbitals of plutonium appear localized and surprisingly insensitive to different bonding environments. We envisage that this report of using relative energy differences between the 5fδ/φ and 5fπ*/5fσ* orbitals as a qualitative measure of overlap-driven actinyl bond covalency will spark activity, and extend to numerous applications of RIXS and HR-XANES to gain new insights into the electronic structures of the actinide elements.

Determination of the cationic distribution in oxidic thin films by resonant X-ray diffraction: the magnetoelectric compound Ga2−xFexO3

The cationic distribution is decisive for both the magnetic and electric properties of complex oxides. While it can be easily determined in bulk materials using classical methods such as X-ray or neutron diffraction, difficulties arise for thin films owing to the relatively small amount of material to probe. It is shown here that a full determination of the cationic site distribution in thin films is possible through an optimized processing of resonant elastic X-ray scattering experiments. The method is illustrated using gallium ferrite Ga2−xFexO3samples which have been the focus of an increasing number of studies this past decade. They indeed represent an alternative to the, to date, only room-temperature magnetoelectric compound BiFeO3. The methodology can be applied to determine the element distribution over the various crystallographic sites in any crystallized system.

FDMX: extended X-ray absorption fine structure calculations using the finite difference method

A new theoretical approach and computational package, FDMX, for general calculations of X-ray absorption fine structure (XAFS) over an extended energy range within a full-potential model is presented. The final-state photoelectron wavefunction is calculated over an energy-dependent spatial mesh, allowing for a complete representation of all scattering paths. The electronic potentials and corresponding wavefunctions are subject to constraints based on physicality and self-consistency, allowing for accurate absorption cross sections in the near-edge region, while higher-energy results are enabled by the implementation of effective Debye-Waller damping and new implementations of second-order lifetime broadening. These include inelastic photoelectron scattering and, for the first time, plasmon excitation coupling. This is the first full-potential package available that can calculate accurate XAFS spectra across a complete energy range within a single framework and without fitted parameters. Example spectra are provided for elemental Sn, rutile TiO2 and the FeO6 octahedron.

Intramolecular Hg⋯π interactions of d-character with non-bridging atoms in mercury–aryl complexes

The late transition metal mercury, known for its propensity to not share 5d electrons, actually does so in short-range π-bonding and medium- to long-range π-interactions.

Optimized Finite Difference Method for the Full-Potential XANES Simulations: Application to Molecular Adsorption Geometries in MOFs and Metal-Ligand Intersystem Crossing Transients

Accurate modeling of the X-ray absorption near-edge spectra (XANES) is required to unravel the local structure of metal sites in complex systems and their structural changes upon chemical or light stimuli. Two relevant examples are reported here concerning the following: (i) the effect of molecular adsorption on 3d metals hosted inside metal-organic frameworks and (ii) light induced dynamics of spin crossover in metal-organic complexes. In both cases, the amount of structural models for simulation can reach a hundred, depending on the number of structural parameters. Thus, the choice of an accurate but computationally demanding finite difference method for the ab initio X-ray absorption simulations severely restricts the range of molecular systems that can be analyzed by personal computers. Employing the FDMNES code [Phys. Rev. B, 2001, 63, 125120] we show that this problem can be handled if a proper diagonalization scheme is applied. Due to the use of dedicated solvers for sparse matrices, the calculation time was reduced by more than 1 order of magnitude compared to the standard Gaussian method, while the amount of required RAM was halved. Ni K-edge XANES simulations performed by the accelerated version of the code allowed analyzing the coordination geometry of CO and NO on the Ni active sites in CPO-27-Ni MOF. The Ni-CO configuration was found to be linear, while Ni-NO was bent by almost 90°. Modeling of the Fe K-edge XANES of photoexcited aqueous [Fe(bpy)3](2+) with a 100 ps delay we identified the Fe-N distance elongation and bipyridine rotation upon transition from the initial low-spin to the final high-spin state. Subsequently, the X-ray absorption spectrum for the intermediate triplet state with expected 100 fs lifetime was theoretically predicted.

Core-shell-like Au sub-nanometer clusters in Er-implanted silica

The very early steps of Au metal cluster formation in Er-doped silica have been investigated by high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS). A combined analysis of the near-edge and extended part of the experimental spectra shows that Au cluster nucleation starts from a few Au and O atoms covalently interconnected, likely in the presence of embryonic Au-Au correlation. The first Au clusters, characterized by a well defined Au-Au coordination distance, form upon 400 °C inert annealing. The estimated upper limit of the Gibbs free energy for the associated heterogeneous nucleation is 0.06 eV per atom, suggesting that the Au nucleation is assisted by matrix defects, most likely non-bridging oxygen atoms. The experimental results indicate that the formed subnanometer Au clusters can be applied as effective core-shell systems in which the Au atoms of the 'core' develop a metallic character, whereas the Au atoms in the 'shell' can retain a partially covalent bond with O atoms of the silica matrix. High structural disorder at the Au site is found upon neutral annealing at a moderate temperature (600 °C), likely driven by the configurational disorder of the defective silica matrix. A suitable choice of the Au concentration and annealing temperature allows tailoring of the Au cluster size in the sub-nanometer range. The interaction of the Au cluster surface with the surrounding silica matrix is likely responsible for the infrared luminescence previously reported on the same systems.

Resonant X-ray scattering in low quartz to characterize the polarization light

The variation with energy of the diffracted peak intensities around the absorption edges has been known for very long time. It is only very recently that resonant elastic x-ray scattering (REXS) experiments were performed on enantiomers [1], showing the sensitivity of this technique to study tiny features in these materials. In right and left low quartz, azimuthal scans of the (001) reflection intensity show the angular anisotropy by presenting a 3 fold periodicity. These scans are shifted and their amplitude oscillations vary when changing from right to left the enantiomer or when changing the light helicity. Our purpose is to show that azimuthal scans recording the (001) reflection intensity in right and left low quartz can be completely explained by the proper taking into account of the polarization characteristics of the incoming electromagnetic wave. More importantly, we show that such experiments are an excellent way to fully determine the light properties, when this one is not perfectly known. From these scans, we get 3 equations giving their relative shift, the ratio between their amplitude oscillations and the polarization rate. Consequently, without need of simulations because these equations only depend on the symmetry and the geometry, we are able to get the three unknowns which are the Stokes parameter values. Such characterization does not depend on energy, or absorbing atom atomic number. This is thus feasible at other edges or with other compounds, such as GeO2, having the same symmetry. This opens the possibility of characterizing the light polarization on a wide energy range. This study is supported by ab initio simulations on REXS and linear dichroism to validate our demonstration and to eliminate the other possibilities such as higher contribution in term of transition channels (E1E2 or E2E2) or birefringence effects.

Monitoring morphology and hydrogen coverage of nanometric Pt/γ-Al2 O3 particles by in situ HERFD-XANES and quantum simulations

Platinum nanoclusters highly dispersed on γ-alumina are widely used as heterogeneous catalysts. To understand the chemical interplay between the Pt nanoparticles, the support, and the reductive atmosphere, we performed X-ray absorption near edge structure (XANES) in situ experiments recorded in high energy resolution fluorescence detection (HERFD) mode. Spectra are assigned by comparison with simulated XANES spectra on models obtained by molecular dynamics (DFT-MD). We propose platinum cluster morphologies and quantify the hydrogen coverages compatible with XANES spectra recorded at variable hydrogen pressures and temperatures. Using cutting-edge methodologies to assign XANES spectra, this work gives unequalled atomic insights into the characterization of supported nanoclusters.

Effects of dispersion and absorption in resonant Bragg diffraction of x-rays

Resonant diffraction of x-rays by crystals with anisotropic optical properties is investigated theoretically, to assess how the intensity of a Bragg spot is influenced by effects related to dispersion (birefringence) and absorption (dichroism). Starting from an exact but opaque expression, simple analytic results are found to expose how intensity depends on dispersion and absorption in the primary and secondary beams and, also, the azimuthal angle (rotation of the crystal about the Bragg wavevector). If not the full story for a given application, our results are more than adequate to explore consequences of dispersion and absorption in the intensity of a Bragg spot. Results are evaluated for antiferromagnetic copper oxide, and low quartz. For CuO, one of our results reproduces all salient features of a previously published simulation of the azimuthal-angle dependence of a magnetic Bragg peak. It is transparent in our analytic result that dispersion and absorption effects alone cannot reproduce published experimental data. Available data for the azimuthal-angle dependence of space-group forbidden reflections (0,0, l), with l ≠ 3n, of low quartz depart from symmetry imposed by the triad axis of rotation symmetry. The observed asymmetry can be induced by dispersion and absorption even though absorption coefficients are constant, independent of the azimuthal angle, in this class of reflections.

Surface science approach to the solid-liquid interface: surface-dependent precipitation of Ni(OH)2 on α-Al2O3 surfaces

Surface-dependent precipitation: The adsorption of Ni(II) complexes in aqueous solution on (0001) and (1102) α-Al(2)O(3) single-crystal surfaces has been studied (see the X-ray absorption spectra obtained for parallel and perpendicular polarization directions). The use of planar model systems emphasizes the crucial role of the Al(2)O(3) orientation for Ni dispersion with practical implications in catalyst preparation procedures.

Full potential x-ray absorption calculations using time dependent density functional theory

We report the implementation of a fully relativistic time dependent density functional theory (TDDFT) method for carrying out x-ray absorption spectroscopy calculations for extended systems. This is the first time that a TDDFT simulation of x-ray absorption in extended systems has featured a full potential ground state calculation. We prove that this unusual feature of the TDDFT implementation unequivocally yields improvement over the previous muffin-tin calculation methods.

Ground state of the quasi-1D compound BaVS3 resolved by resonant magnetic x-ray scattering

Resonant magnetic x-ray scattering near the vanadium L2,3-absorption edges has been used to investigate the low temperature magnetic structure of high quality BaVS3 single crystals. Below T(N)=31  K, the strong resonance revealed a triple-incommensurate magnetic ordering at the wave vector (0.226   0.226   ξ) in hexagonal notation, with ξ=0.033. The azimuthal-angle dependence of the scattering signal and time-dependent density functional theory simulations indicate an antiferromagnetic order within the ab plane with the spins polarized along a in the monoclinic structure.

Informed consent in the context of pharmacogenomic research: ethical considerations

Although the scientific research surrounding pharmacogenomics (PGx) has been relatively plentiful, the ethical research concerning this discipline has developed rather conservatively. Following investigation of the ethical, legal and social issues (ELSI) of PGx research, as well as consulting with key stakeholders, we identified six outstanding ethical issues raised by the informed consent process in PGx research: (1) scope of consent; (2) consent to 'add-on' studies; (3) protection of personal information; (4) commercialization; (5) data sharing; and (6) potential risks stemming from population-based research. In discussing these six areas as well as offering specific considerations, this article offers a solid base from which future practical guidelines for informed consent in PGx research can be constructed. As such, this effort works toward filling the ELSI gap and provides ethical support to the numerous PGx projects undertaken by researchers every year.

Antiferromagnetically spin polarized oxygen observed in magnetoelectric TbMn2O5

We report the direct measurement of antiferromagnetic spin polarization at the oxygen sites in the multiferroic TbMn2O5, through resonant soft x-ray magnetic scattering. This supports recent theoretical models suggesting that the oxygen spin polarization is key to the magnetoelectric coupling mechanism. The spin polarization is observed through a resonantly enhanced diffraction signal at the oxygen K edge at the commensurate antiferromagnetic wave vector. Using the fdmnes code we have accurately reproduced the experimental data. We have established that the resonance arises through the spin polarization on the oxygen sites hybridized with the square based pyramid Mn3+ ions. Furthermore we have discovered that the position of the Mn3+ ion directly influences the oxygen spin polarization.

Full polarization analysis of resonant superlattice and forbidden x-ray reflections in magnetite

Despite being one of the oldest known magnetic materials, and the classic mixed valence compound, thought to be charge ordered, the structure of magnetite below the Verwey transition is complex and the presence and role of charge order is still being debated. Here, we present resonant x-ray diffraction data at the iron K-edge on forbidden (0, 0, 2n+1)(C) and superlattice [Formula: see text] reflections. Full linear polarization analysis of the incident and scattered light was conducted in order to explore the origins of the reflections. Through simulation of the resonant spectra we have confirmed that a degree of charge ordering takes place, while the anisotropic tensor of susceptibility scattering is responsible for the superlattice reflections below the Verwey transition. We also report the surprising result of the conversion of a significant proportion of the scattered light from linear to nonlinear polarization.

Self-consistent aspects of x-ray absorption calculations

We implemented a self-consistent, real-space x-ray absorption calculation within the FDMNES code. We performed the self-consistency within several schemes and identified which one is the most appropriate. We show a method that allows a rigorous setting of the Fermi level and thus an estimation of the energy cutoff for the identification and elimination of the occupied states. We investigated what are the structures where one can afford performing the self-consistent calculation at a lesser cluster radius than the absorption one. We exemplify the effects of the self-consistency at the K-edge and for several reference cases, including the copper Cu and the rutile TiO(2). We verified the robustness of our procedure on the transitional 3d and 4d elements. Although amelioration can be noticed, the self-consistency performed at the K-edge does not bring a major improvement of the calculated spectra. Taking into consideration a non-self-consistent, non-spherical potential gives better results than a self-consistent muffin-tin approximation calculation.

Interplay of inequivalent atomic positions in resonant x-ray diffraction of Fe(3)BO(6)

'Forbidden' Bragg reflections of iron orthoborate Fe(3)BO(6) were studied theoretically and experimentally in the vicinity of the iron K edge. Their energy spectra are explained as resulting from the interference of x-rays scattered from two inequivalent crystallographic sites occupied by iron ions. This particular structure property gives rise to complex azimuthal dependences of the reflection intensities in the pre-edge region as they result from the interplay of site specific dipole-quadrupole and quadrupole-quadrupole resonant scattering. Also evidenced is an anisotropic character of the absorption spectrum. Self-absorption correction to the diffraction data, as well as possible contributions of thermal vibrations and magnetic order, are discussed. Particular care is given to extracting clean spectra from the data, and it is demonstrated that excellent results can be obtained even from measurements that appear corrupted by several effects such as poor crystal quality and multiple scattering.

Researchers' perceptions of the ethical implications of pharmacogenomics research with children

BACKGROUND

This paper presents the results of an exploratory qualitative study that assesses Canadian pediatric researchers' perceptions of a pre-selected group of ethical issues raised by pharmacogenomics research with children.

METHODS

As a pilot study, we conducted semi-structured telephone interviews with Canadian pediatric pharmacogenomic researchers. The interviews were guided by the following themes: (1) benefits and risks of inclusion, (2) the consent/assent process, and (3) the return of research results.

RESULTS

Issues about assent, consent, risks and benefits, as well as the communication of results were addressed by the respondents. Some issues, such as the unique vulnerability of children, the long term privacy concerns associated with biobanking, additional core elements that need to be discussed and included in the consent/assent forms, as well as the challenges of communicating research results in a pediatric research were not explicitly identified by the respondents.

CONCLUSION

Further consideration should be given to address the ethical challenges of including children in pharmacogenomics research. This exploratory study indicates that further guidance is needed if children are to be protected and yet benefit from such research.

Charge and orbital correlations at and above the Verwey phase transition in magnetite

The subtle interplay among electronic degrees of freedom (charge and orbital orderings), spin and lattice distortion that conspire at the Verwey transition in magnetite (Fe3O4) is still a matter of controversy. Here, we provide compelling evidence that these electronic orderings are manifested as a continuous phase transition at the temperature where a spin reorientation takes place at around 130 K, i.e., well above TV approximately 121 K. The Verwey transition seems to leave the orbital ordering unaffected whereas the charge ordering development appears to be quenched at this temperature and the temperature dependence below TV is controlled by the lattice distortions. Finally, we show that the orbital ordering does not reach true long range (disorder), and the correlation length along the c-direction is limited to 100 angstroms.