Medium-Range Order Structure Controls Thermal Stability of Pores in Zeolitic Imidazolate Frameworks.

Metal-organic framework (MOF) glasses have multiple potential applications, as they combine advantages of traditional glasses with those of MOFs. The melt-quenching process used to form MOF glasses typically leads to a significant decrease in porosity, but the structural origin of this thermally induced pore collapse remains largely unknown. Here, we study the melting process of three zeolitic imidazolate frameworks (ZIFs), namely ZIF-4, ZIF-62, and ZIF-76, using ab initio molecular dynamics (MD) simulations. By analyzing the MD data using topological data analysis, we show that while the three ZIF systems exhibit similar short-range order structural changes upon heating, they exhibit significant differences in their medium-range order structure. Specifically, ZIF-76 retains more of its medium-range order structures in the liquid state compared to the other glass-forming ZIF systems, which allows it to remain more porous than ZIF-4 and ZIF-62. As such, our results may aid in understanding the structural features that govern the ability to maintain porosity in the melt-quenched glassy state.

Using the R Package Spatstat to Assess Inhibitory Effects of Microregional Hypoxia on the Infiltration of Cancers of the Head and Neck Region by Cytotoxic T Lymphocytes.

(1) Background: The immune system has physiological antitumor activity, which is partially mediated by cytotoxic T lymphocytes (CTL). Tumor hypoxia, which is highly prevalent in cancers of the head and neck region, has been hypothesized to inhibit the infiltration of tumors by CTL. In situ data validating this concept have so far been based solely upon the visual assessment of the distribution of CTL. Here, we have established a set of spatial statistical tools to address this problem mathematically and tested their performance. (2) Patients and Methods: We have analyzed regions of interest (ROI) of 22 specimens of cancers of the head and neck region after 4-plex immunofluorescence staining and whole-slide scanning. Single cell-based segmentation was carried out in QuPath. Specimens were analyzed with the endpoints clustering and interactions between CTL, normoxic, and hypoxic tumor areas, both visually and using spatial statistical tools implemented in the R package Spatstat. (3) Results: Visual assessment suggested clustering of CTL in all instances. The visual analysis also suggested an inhibitory effect between hypoxic tumor areas and CTL in a minority of the whole-slide scans (9 of 22, 41%). Conversely, the objective mathematical analysis in Spatstat demonstrated statistically significant inhibitory interactions between hypoxia and CTL accumulation in a substantially higher number of specimens (16 of 22, 73%). It showed a similar trend in all but one of the remaining samples. (4) Conclusion: Our findings provide non-obvious but statistically rigorous evidence of inhibition of CTL infiltration into hypoxic tumor subregions of cancers of the head and neck. Importantly, these shielded sites may be the origin of tumor recurrences. We provide the methodology for the transfer of our statistical approach to similar questions. We discuss why versions of the Kcross and pcf.cross functions may be the methods of choice among the repertoire of statistical tests in Spatstat for this type of analysis.

Revealing hidden medium-range order in amorphous materials using topological data analysis.

Despite the numerous technological applications of amorphous materials, such as glasses, the understanding of their medium-range order (MRO) structure-and particularly the origin of the first sharp diffraction peak (FSDP) in the structure factor-remains elusive. Here, we use persistent homology, an emergent type of topological data analysis, to understand MRO structure in sodium silicate glasses. To enable this analysis, we introduce a self-consistent categorization of rings with rigorous geometrical definitions of the structural entities. Furthermore, we enable quantitative comparison of the persistence diagrams by computing the cumulative sum of all points weighted by their lifetime. On the basis of these analysis methods, we show that the approach can be used to deconvolute the contributions of various MRO features to the FSDP. More generally, the developed methodology can be applied to analyze and categorize molecular dynamics data and understand MRO structure in any class of amorphous solids.