THORONDOR: a software for fast treatment and analysis of low-energy XAS data

MOF-Derived CeO2 and CeZrOx Solid Solutions: Exploring Ce Reduction through FTIR and NEXAFS Spectroscopy

The development of Ce-based materials is directly dependent on the catalyst surface defects, which is caused by the calcination steps required to increase structural stability. At the same time, the evaluation of cerium's redox properties under reaction conditions is of increasing relevant importance. The synthesis of Ce-UiO-66 and CeZr-UiO-66 and their subsequent calcination are presented here as a simple and inexpensive approach for achieving homogeneous and stable CeO₂ and CeZrO_x nanocrystals. The resulting materials constitute an ideal case study to thoroughly understand cerium redox properties. The Ce³⁺/Ce⁴⁺ redox properties are investigated by H₂-TPR experiments exploited by in situ FT-IR and Ce M₅-edge AP-NEXAFS spectroscopy. In the latter case, Ce³⁺ formation is quantified using the MCR-ALS protocol. FT-IR is then presented as a high potential/easily accessible technique for extracting valuable information about the cerium oxidation state under operating conditions. The dependence of the OH stretching vibration frequency on temperature and Ce reduction is described, providing a novel tool for qualitative monitoring of surface oxygen vacancy formation. Based on the reported results, the molecular absorption coefficient of the Ce³⁺ characteristic IR transition is tentatively evaluated, thus providing a basis for future Ce³⁺ quantification through FT-IR spectroscopy. Finally, the FT-IR limitations for Ce³⁺ quantification are discussed.

Gwaihir: Jupyter Notebook graphical user interface for Bragg coherent diffraction imaging

In a world where data are steadily made more available, Gwaihir is a tool that overcomes multiple issues by bridging remote access, cluster computing and a user-friendly interface, consequentially improving the link between synchrotrons and their users for Bragg coherent diffraction imaging.

Bragg coherent X-ray diffraction is a nondestructive method for probing material structure in three dimensions at the nanoscale, with unprecedented resolution in displacement and strain fields. This work presents Gwaihir, a user-friendly and open-source tool to process and analyze Bragg coherent X-ray diffraction data. It integrates the functionalities of the existing packages bcdi and PyNX in the same toolbox, creating a natural workflow and promoting data reproducibility. Its graphical interface, based on Jupyter Notebook widgets, combines an interactive approach for data analysis with a powerful environment designed to link large-scale facilities and scientists.

Identification of hub genes related to the progression of type 1 diabetes by computational analysis

BACKGROUND

Type 1 diabetes (T1D) is a serious threat to childhood life and has fairly complicated pathogenesis. Profound attempts have been made to enlighten the pathogenesis, but the molecular mechanisms of T1D are still not well known.

METHODS

To identify the candidate genes in the progression of T1D, expression profiling by high throughput sequencing dataset GSE123658 was downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and gene ontology (GO) and pathway enrichment analyses were performed. The protein-protein interaction network (PPI), modules, target gene - miRNA regulatory network and target gene - TF regulatory network analysis were constructed and analyzed using HIPPIE, miRNet, NetworkAnalyst and Cytoscape. Finally, validation of hub genes was conducted by using ROC (Receiver operating characteristic) curve and RT-PCR analysis. A molecular docking study was performed.

RESULTS

A total of 284 DEGs were identified, consisting of 142 up regulated genes and 142 down regulated genes. The gene ontology (GO) and pathways of the DEGs include cell-cell signaling, vesicle fusion, plasma membrane, signaling receptor activity, lipid binding, signaling by GPCR and innate immune system. Four hub genes were identified and biological process analysis revealed that these genes were mainly enriched in cell-cell signaling, cytokine signaling in immune system, signaling by GPCR and innate immune system. ROC curve and RT-PCR analysis showed that EGFR, GRIN2B, GJA1, CAP2, MIF, POLR2A, PRKACA, GABARAP, TLN1 and PXN might be involved in the advancement of T1D. Molecular docking studies showed high docking score.

CONCLUSIONS

DEGs and hub genes identified in the present investigation help us understand the molecular mechanisms underlying the advancement of T1D, and provide candidate targets for diagnosis and treatment of T1D.

Spectral Decomposition of X-ray Absorption Spectroscopy Datasets: Methods and Applications

X-ray absorption spectroscopy (XAS) today represents a widespread and powerful technique, able to monitor complex systems under in situ and operando conditions, while external variables, such us sampling time, sample temperature or even beam position over the analysed sample, are varied. X-ray absorption spectroscopy is an element-selective but bulk-averaging technique. Each measured XAS spectrum can be seen as an average signal arising from all the absorber-containing species/configurations present in the sample under study. The acquired XAS data are thus represented by a spectroscopic mixture composed of superimposed spectral profiles associated to well-defined components, characterised by concentration values evolving in the course of the experiment. The decomposition of an experimental XAS dataset in a set of pure spectral and concentration values is a typical example of an inverse problem and it goes, usually, under the name of multivariate curve resolution (MCR). In the present work, we present an overview on the major techniques developed to realize the MCR decomposition together with a selection of related results, with an emphasis on applications in catalysis. Therein, we will highlight the great potential of these methods which are imposing as an essential tool for quantitative analysis of large XAS datasets as well as the directions for further development in synergy with the continuous instrumental progresses at synchrotron sources.