Artifact identification in X-ray diffraction data using machine learning methods.

In situ synchrotron high-energy X-ray powder diffraction (XRD) is highly utilized by researchers to analyze the crystallographic structures of materials in functional devices (e.g. battery materials) or in complex sample environments (e.g. diamond anvil cells or syntheses reactors). An atomic structure of a material can be identified by its diffraction pattern along with a detailed analysis of the Rietveld refinement which yields rich information on the structure and the material, such as crystallite size, microstrain and defects. For in situ experiments, a series of XRD images is usually collected on the same sample under different conditions (e.g. adiabatic conditions) yielding different states of matter, or is simply collected continuously as a function of time to track the change of a sample during a chemical or physical process. In situ experiments are usually performed with area detectors and collect images composed of diffraction patterns. For an ideal powder, the diffraction pattern should be a series of concentric Debye-Scherrer rings with evenly distributed intensities in each ring. For a realistic sample, one may observe different characteristics other than the typical ring pattern, such as textures or preferred orientations and single-crystal diffraction spots. Textures or preferred orientations usually have several parts of a ring that are more intense than the rest, whereas single-crystal diffraction spots are localized intense spots owing to diffraction of large crystals, typically >10 µm. In this work, an investigation of machine learning methods is presented for fast and reliable identification and separation of the single-crystal diffraction spots in XRD images. The exclusion of artifacts during an XRD image integration process allows a precise analysis of the powder diffraction rings of interest. When it is trained with small subsets of highly diverse datasets, the gradient boosting method can consistently produce high-accuracy results. The method dramatically decreases the amount of time spent identifying and separating single-crystal diffraction spots in comparison with the conventional method.

In situ X-ray area detector flat-field correction at an operating photon energy without flat illumination.

Flat-field calibration of X-ray area detectors is a challenge due to the inability to generate an X-ray flat-field at the selected photon energy the beamline operates at, which has a strong influence on the measurement behavior of the detector. A method is presented in which a simulated flat-field correction is calculated without flat-field measurements. Instead, a series of quick scattering measurements from an amorphous scatterer is used to calculate a flat-field response. The ability to rapidly obtain a flat-field response allows for recalibration of an X-ray detector as needed without significant expenditure of either time or effort. Area detectors on the beamlines used, such as the Pilatus 2M CdTe, PE XRD1621 and Varex XRD 4343CT, were found to have detector responses that drift slightly over timescales of several weeks or after exposure to high photon flux, suggesting the need to more frequently recalibrate with a new flat-field correction map.

In situ X-ray area detector flat-field correction at an operating photon energy without flat illumination. Corrigendum.

The name of an author in the article by Weng et al. (2023) [J. Synchrotron Rad. 30, 546-554] is corrected.

Guide RNA-binding complex from mitochondria of trypanosomatids.

In the mitochondria of trypanosomatids, the majority of mRNAs undergo massive uracil-insertion/deletion editing. Throughout the processes of pre-mRNA polyadenylation, guide RNA (gRNA) uridylylation and annealing to mRNA, and editing reactions, several multiprotein complexes must engage in transient interactions to produce a template for protein synthesis. Here, we report the identification of a protein complex essential for gRNA stability. The gRNA-binding complex (GRBC) interacts with gRNA processing, editing, and polyadenylation machineries and with the mitochondrial edited mRNA stability (MERS1) factor. RNAi knockdown of the core subunits, GRBC1 and GRBC2, led to the elimination of gRNAs, thus inhibiting mRNA editing. Inhibition of MERS1 expression selectively abrogated edited mRNAs. Homologous proteins unique to the order of Kinetoplastida, GRBC1 and GRBC2, form a stable 200 kDa particle that directly binds gRNAs. Systematic analysis of RNA-mediated and RNA-independent interactions involving the GRBC and MERS1 suggests a unified model for RNA processing in the kinetoplast mitochondria.

Circumventing thermodynamics to synthesize highly metastable perovskites: nano eggshells of SnHfO3.

Sn(ii)-based perovskite oxides, being the subject of longstanding theoretical interest for the past two decades, have been synthesized for the first time in the form of nano eggshell particle morphologies. All past reported synthetic attempts have been unsuccessful owing to their metastable nature, i.e., by their thermodynamic instability towards decomposition to their constituent oxides. A new approach was discovered that finally provides an effective solution to surmounting this intractable synthetic barrier and which can be the key to unlocking the door to many other predicted metastable oxides. A low-melting KSn2Cl5 salt was utilized to achieve a soft topotactic exchange of Sn(ii) cations into a Ba-containing perovskite, i.e., BaHfO3 with particle sizes of ∼350 nm, at a low reaction temperature of 200 °C. The resulting particles exhibit nanoshell-over-nanoshell morphologies, i.e., with SnHfO3 forming as ∼20 nm thick shells over the surfaces of the BaHfO3 eggshell particles. Formation of the metastable SnHfO3 is found to be thermodynamically driven by the co-production of the highly stable BaCl2 and KCl side products. Despite this, total energy calculations show that Sn(ii) distorts from the A-site asymmetrically and randomly and the interdiffusion has a negligible impact on the energy of the system (i.e., layered vs. solid solution). Additionally, nano eggshell particle morphologies of BaHfO3 were found to yield highly pure SnHfO3 for the first time, thus circumventing the intrinsic ion-diffusion limits occurring at this low reaction temperature. In summary, these results demonstrate that the metastability of many theoretically predicted Sn(ii)-perovskites can be overcome by leveraging the high cohesive energies of the reactants, the exothermic formation of a stable salt side product, and a shortened diffusion pathway for the Sn(ii) cations.

Novel TUTase associates with an editosome-like complex in mitochondria of Trypanosoma brucei.

Expression of mitochondrial genomes in Kinetoplastida protists requires massive uracil insertion/deletion mRNA editing. The cascade of editing reactions is accomplished by a multiprotein complex, the 20S editosome, and is directed by trans-acting guide RNAs. Two distinct RNA terminal uridylyl transferases (TUTases), RNA Editing TUTase 1 (RET1) and RNA Editing TUTase 2 (RET2), catalyze 3' uridylylation of guide RNAs and U-insertions into the mRNAs, respectively. RET1 is also involved in mitochondrial mRNA turnover and participates in numerous heterogeneous complexes; RET2 is an integral part of the 20S editosome, in which it forms a U-insertion subcomplex with zinc finger protein MP81 and RNA editing ligase REL2. Here we report the identification of a third mitochondrial TUTase from Trypanosoma brucei. The mitochondrial editosome-like complex associated TUTase (MEAT1) interacts with a 20S editosome-like particle, effectively substituting the U-insertion subcomplex. MEAT1 and RET2 are mutually exclusive in their respective complexes, which otherwise share several components. Similarly to RET2, MEAT1 is exclusively U-specific in vitro and is active on gapped double-stranded RNA resembling editing substrates. However, MEAT1 does not require a 5' phosphate group on the 3' mRNA cleavage fragment produced by editing endonucleases. The functional RNAi complementation experiments showed that MEAT1 is essential for viability of bloodstream and insect parasite forms. The growth inhibition phenotype in the latter can be rescued by coexpressing an RNAi-resistant gene with double-stranded RNA targeting the endogenous transcript. However, preliminary RNA analysis revealed no gross effects on RNA editing in MEAT1-depleted cells and indicated its possible role in regulating the mitochondrial RNA stability.

Coronary artery calcification across ethnic groups in Singapore.

INTRODUCTION: In Singapore, the age-standardised event rates of myocardial infarction (MI) are 2- and 3-fold higher for Malays and Indians respectively compared to the Chinese. The objectives of this study were to determine the prevalence and quantity of coronary artery calcification (CAC) and non-calcified plaques across these 3 ethnic groups. MATERIALS AND METHODS: This was a retrospective descriptive study. We identified 1041 patients (810 Chinese, 139 Malays, 92 Indians) without previous history of cardiovascular disease who underwent cardiac computed tomography for atypical chest pain evaluation. A cardiologist, who was blinded to the patients' clinical demographics, reviewed all scans. We retrospectively analysed all their case records. RESULTS: Overall, Malays were most likely to be active smokers (P = 0.02), Indians had the highest prevalence of diabetes mellitus (P = 0.01) and Chinese had the highest mean age (P <0.0001). The overall prevalence of patients with non-calcified plaques as the only manifestation of sub-clinical coronary artery disease was 2.1%. There was no significant difference in the prevalence of CAC, mean CAC score or prevalence of non-calcified plaques among the 3 ethnic groups. Active smoking, age and hypertension were independent predictors of CAC. Non-calcified plaques were positively associated with male gender, age, dyslipidaemia and diabetes mellitus. CONCLUSION: The higher MI rates in Malays and Indians in Singapore cannot be explained by any difference in CAC or non-calcified plaque. More research with prospective follow-up of larger patient populations is necessary to establish if ethnic-specific calibration of CAC measures is needed to adjust for differences among ethnic groups.