Research Progress of Caspase in Endometriosis.

Endometriosis, a common chronic gynecological disease, refers to the presence and proliferation of endometrial tissue in locations other than the uterine cavity. Approximately 6 to 10% of the population of women of childbearing age are known to have endometriosis; the most common clinical signs are pelvic pain and infertility. Although endometriosis is a benign disease, it exhibits some typical features of malignant tumors, such as proliferation, invasion, metastasis, and recurrence. Endometriosis is considered a chronic, inflammatory, and estrogen-dependent disease, and multiple factors contribute to its occurrence and development. In recent years, increasing attention has been given to the role of apoptosis in the pathogenesis of this disease. Some researchers believe that spontaneous apoptosis of the endometrium is critical in maintaining its normal structure and function, and abnormal apoptosis can promote the occurrence and development of endometriosis. Inflammation is another likely process in the pathogenesis of endometriosis. Inflammation mediates the adhesion, proliferation, differentiation, and invasion of ectopic lesions of endometriosis, primarily by regulating the function of immune cells and increasing the level of proinflammatory cytokines in body fluids. The ultimate initiators of apoptosis and inflammatory cell death (pyroptosis) are the caspase family proteases. In this article, we review the progress in recent years in caspase function as well as the possible role of these enzymes in the pathogenesis of endometriosis, indicating potential treatment strategies.

Fluorine spillover for ceria- vs silica-supported palladium nanoparticles: A MD study using machine learning potentials.

Supported metallic nanoparticles play a central role in catalysis. However, predictive modeling is particularly challenging due to the structural and dynamic complexity of the nanoparticle and its interface with the support, given that the sizes of interest are often well beyond those accessible via traditional ab initio methods. With recent advances in machine learning, it is now feasible to perform MD simulations with potentials retaining near-density-functional theory (DFT) accuracy, which can elucidate the growth and relaxation of supported metal nanoparticles, as well as reactions on those catalysts, at temperatures and time scales approaching those relevant to experiments. Furthermore, the surfaces of the support materials can also be modeled realistically through simulated annealing to include effects such as defects and amorphous structures. We study the adsorption of fluorine atoms on ceria and silica supported palladium nanoparticles using machine learning potential trained by DFT data using the DeePMD framework. We show defects on ceria and Pd/ceria interfaces are crucial for the initial adsorption of fluorine, while the interplay between Pd and ceria and the reverse oxygen migration from ceria to Pd control spillover of fluorine from Pd to ceria at later stages. In contrast, silica supports do not induce fluorine spillover from Pd particles.

Generic two-phase coexistence in a type-2 Schloegl model for autocatalysis on a square lattice: Analysis via heterogeneous master equations.

Schloegl's second model (also known as the quadratic contact process) on a square lattice involves spontaneous annihilation of particles at lattice sites at rate p, and their autocatalytic creation at unoccupied sites with n≥2 occupied neighbors at rate k_{n}. Kinetic Monte Carlo (KMC) simulation reveals that these models exhibit a nonequilibrium discontinuous phase transition with generic two-phase coexistence: the p value for equistability of coexisting populated and vacuum states, p_{eq}(S), depends on the orientation or slope, S, of a planar interface separating those phases. The vacuum state displaces the populated state for p>p_{eq}(S), and the opposite applies for p

Nucleation-mediated reshaping of facetted metallic nanocrystals: Breakdown of the classical free energy picture.

Shape stability is key to avoiding degradation of performance for metallic nanocrystals synthesized with facetted non-equilibrium shapes to optimize properties for catalysis, plasmonics, and so on. Reshaping of facetted nanocrystals is controlled by the surface diffusion-mediated nucleation and growth of new outer layers of atoms. Kinetic Monte Carlo (KMC) simulation of a realistic stochastic atomistic-level model is applied to precisely track the reshaping of Pd octahedra and nanocubes. Unexpectedly, separate constrained equilibrium Monte Carlo analysis of the free energy profile during reshaping reveals a fundamental failure of the classical nucleation theory (CNT) prediction for the reshaping barrier and rate. Why? Nucleation barriers can be relatively low for these processes, so the system is not locally equilibrated before crossing the barrier, as assumed in CNT. This claim is supported by an analysis of a first-passage problem for reshaping within a master equation framework for the model that reasonably captures the behavior in KMC simulations.

1H chemical shift anisotropy: a high sensitivity solid-state NMR dynamics probe for surface studies?

Dynamics play significant roles in chemistry and biochemistry-molecular motions impact both large- and small-scale chemical reactions in addition to biochemical processes. In many systems, including heterogeneous catalysts, the characterization of dynamics remains a challenge. The most common approaches involve the solid-state NMR measurement of anisotropic interactions, in particular 2H quadrupolar coupling and 1H-X dipolar coupling, which generally require isotope enrichment. Due to the high sensitivity of 1H NMR, 1H chemical shift anisotropy (CSA) is a particularly enticing, and underexplored, dynamics probe. We carried out 1H CSA and 1H-13C dipolar coupling measurements in a series of model supported complexes to understand how 1H CSA can be leveraged to gain dynamic information for heterogeneous catalysts. Mathematical descriptions are given for the dynamic averaging of the CSA tensor, and its dependence on orientation and asymmetry. The variability of the orientation of the tensor in the molecular frame, in addition to its magnitude and asymmetry, negatively impacts attempts to extract quantitative dynamic information. Nevertheless, 1H CSA measurements can reveal useful qualitative insights into the motions of a particularly dilute site, such as from a surface species.

Spatial arrangement of dynamic surface species from solid-state NMR and machine learning-accelerated MD simulations.

The surface arrangement of motional organic functionalities is explored by experimental dipolar coupling measurements and the prediction of motionally-averaged coupling constant from molecular dynamics simulations. The use of machine learning potentials was key to reaching the timescale required. The distance between dynamic surface species are important in cooperative heterogeneous catalysis.

Reaction processes at step edges on S-decorated Cu(111) and Ag(111) surfaces: MD analysis utilizing machine learning derived potentials.

A variety of complexation, reconstruction, and sulfide formation processes can occur at step edges on the {111} surfaces of coinage metals (M) in the presence of adsorbed S under ultra-high vacuum conditions. Given the cooperative many-atom nature of these reaction processes, Molecular Dynamics (MD) simulation of the associated dynamics is instructive. However, only quite restricted Density Functional Theory (DFT)-level ab initio MD is viable. Thus, for M = Ag and Cu, we instead utilize the DeePMD framework to develop machine-learning derived potentials, retaining near-DFT accuracy for the M-S systems, which should have broad applicability. These potentials are validated by comparison with DFT predictions for various key quantities related to the energetics of S on M(111) surfaces. The potentials are then utilized to perform extensive MD simulations elucidating the above diverse restructuring and reaction processes at step edges. Key observations from MD simulations include the formation of small metal-sulfur complexes, especially MS2; development of a local reconstruction at A-steps featuring an S-decorated {100} motif; and 3D sulfide formation. Additional analysis yields further information on the kinetics for metal-sulfur complex formation, where these complexes can strongly enhance surface mass transport, and on the propensity for sulfide formation.

Phase transitions in Schloegl's second model for autocatalysis on a Bethe lattice.

Schloegl's second model (also known as the quadratic contact process) on a lattice involves spontaneous particle annihilation at rate p and autocatalytic particle creation at empty sites with n≥2 occupied neighbors. The particle creation rate for exactly n occupied neighbors is selected here as n(n-1)/[z(z-1)] for lattice coordination number z. We analyze this model on a Bethe lattice. Precise behavior for stochastic models on regular periodic infinite lattices is usually surmised from kinetic Monte Carlo simulation on a finite lattice with periodic boundary conditions. However, the persistence of boundary effects for a Bethe lattice complicates this process, e.g., by inducing spatially heterogenous states. This motivates the exploration of various boundary conditions and unconventional simulation ensembles on the Bethe lattice to predict behavior for infinite size. We focus on z=3, and predict a discontinuous transition to the vacuum state on the infinite lattice when p exceeds a threshold value of around 0.053.

Enhanced Nanostructure Dynamics on Au(111) with Adsorbed Sulfur due to Au-S Complex Formation.

Chemisorbed species can enhance the fluxional dynamics of nanostructured metal surfaces which has implications for applications such as catalysis. Scanning tunneling microscopy studies at room temperature reveal that the presence of adsorbed sulfur (S) greatly enhances the decay rate of 2D Au islands in the vicinity of extended step edges on Au(111). This enhancement is already significant at S coverages, θS , of a few hundredths of a monolayer (ML), and is most pronounced for 0.1-0.3 ML where the decay rate is increased by a factor of around 30. For θS close to saturation at about 0.6 ML, sulfur induces pitting and reconstruction of the entire surface, and Au islands are stabilized. Enhanced coarsening at lower θS is attributed to the formation and diffusion across terraces of Au-S complexes, particularly AuS2 and Au4 S4 , with some lesser contribution from Au3 S4 . This picture is supported by density functional theory analysis of complex formation energies and diffusion barriers.

Structure of chalcogen overlayers on Au(111): Density functional theory and lattice-gas modeling.

Ordering of different chalcogens, S, Se, and Te, on Au(111) exhibit broad similarities but also some distinct features, which must reflect subtle differences in relative values of the long-range pair and many-body lateral interactions between adatoms. We develop lattice-gas (LG) models within a cluster expansion framework, which includes about 50 interaction parameters. These LG models are developed based on density functional theory (DFT) analysis of the energetics of key adlayer configurations in combination with the Monte Carlo (MC) simulation of the LG models to identify statistically relevant adlayer motifs, i.e., model development is based entirely on theoretical considerations. The MC simulation guides additional DFT analysis and iterative model refinement. Given their complexity, development of optimal models is also aided by strategies from supervised machine learning. The model for S successfully captures ordering motifs over a broader range of coverage than achieved by previous models, and models for Se and Te capture the features of ordering, which are distinct from those for S. More specifically, the modeling for all three chalcogens successfully explains the linear adatom rows (also subtle differences between them) observed at low coverages of ∼0.1 monolayer. The model for S also leads to a new possible explanation for the experimentally observed phase with a (5 × 5)-type low energy electron diffraction (LEED) pattern at 0.28 ML and to predictions for LEED patterns that would be observed with Se and Te at this coverage.

Extended families of critical and stationary droplets for nonequilibrium phase transitions in spatially discrete bistable systems.

Bistable nonequilibrium systems are realized in catalytic reaction-diffusion processes, biological transport and regulation, spatial epidemics, etc. Behavior in spatially continuous formulations, described at the mean-field level by reaction-diffusion type equations (RDEs), often mimics that of classic equilibrium van der Waals type systems. When accounting for noise, similarities include a discontinuous phase transition at some value, p_{eq}, of a control parameter, p, with metastability and hysteresis around p_{eq}. For each p, there is a unique critical droplet of the more stable phase embedded in the less stable or metastable phase which is stationary (neither shrinking nor growing), and with size diverging as p→p_{eq}. Spatially discrete analogs of these mean-field formulations, described by lattice differential equations (LDEs), are more appropriate for some applications, but have received less attention. It is recognized that LDEs can exhibit richer behavior than RDEs, specifically propagation failure for planar interphases separating distinct phases. We show that this feature, together with an orientation dependence of planar interface propagation also deriving from spatial discreteness, results in the occurrence of entire families of stationary droplets. The extent of these families increases approaching the transition and can be infinite if propagation failure is realized. In addition, there can exist a regime of generic two-phase coexistence where arbitrarily large droplets of either phase always shrink. Such rich behavior is qualitatively distinct from that for classic nucleation in equilibrium and spatially continuous nonequilibrium systems.

Identification of an AgS2 Complex on Ag(110).

Adsorbed sulfur has been investigated on the Ag(110) surface at two different coverages, 0.02 and 0.25 monolayers. At the lower coverage, only sulfur adatoms are present. At the higher coverage, there are additional bright features which we identify as linear, independent AgS2 complexes. This identification is based upon density functional theory (DFT) and its comparison with experimental observations including bias dependence and separation between complexes. DFT also predicts the absence of AgS2 complexes at low coverage, and the development of AgS2 complexes around a coverage of 0.25 monolayers of sulfur, as is experimentally observed. To our knowledge, this is the first example of an isolated linear sulfur-metal-sulfur complex.

Sulfur adsorption on coinage metal(100) surfaces: propensity for metal-sulfur complex formation relative to (111) surfaces.

Experimental data from low-temperature Scanning Tunneling Microscopy (LTSTM) studies on coinage metal surfaces with very low coverages of S is providing new insights into metal-S interactions. A previous LTSTM study for Cu(100), and a new analysis reported here for Ag(100), both indicate no metal-sulfur complex formation, but an Au4S5 complex was observed previously on Au(100). In marked contrast, various complexes have been proposed and/or observed on Ag(111) and Cu(111), but not on Au(111). Also, exposure to trace amounts of S appears to enhance mass transport far more dramatically on (111) than on (100) surfaces for Cu and Ag, a feature tied to the propensity for complex formation. Motivated by these observations, we present a comprehensive assessment at the level of DFT to assess the existence and stability of complexes on (100) surfaces, and compare results with previous analyses for (111) surfaces. Consistent with experiment, our DFT analysis finds no stable complexes on Ag(100) and Cu(100), but several exist for Au(100). In addition, we systematically relate stability for adsorbed and gas-phase species within the framework of Hess's law. We thereby provide key insight into the various energetic contributions to stability which in turn elucidates the difference in behavior between (100) and (111) surfaces.

Reshaping, Intermixing, and Coarsening for Metallic Nanocrystals: Nonequilibrium Statistical Mechanical and Coarse-Grained Modeling.

Self-assembly of supported 2D or 3D nanocrystals (NCs) by vacuum deposition and of 3D NCs by solution-phase synthesis (with possible subsequent transfer to a support) produces intrinsically nonequilibrium systems. Individual NCs can have far-from-equilibrium shapes and composition profiles. The free energy of NC ensembles is lowered by coarsening which can involve Ostwald ripening or Smoluchowski ripening (NC diffusion and coalescence). Preservation of individual NC structure and inhibition of coarsening are key, e.g., for avoiding catalyst degradation. This review focuses on postsynthesis evolution of metallic NCs. Atomistic-level modeling typically utilizes stochastic lattice-gas models to access appropriate time and length scales. However, predictive modeling requires incorporation of realistic rates for relaxation mechanisms, e.g., periphery diffusion and intermixing, in numerous local environments (rather than the use of generic prescriptions). Alternative coarse-grained modeling must also incorporate appropriate mechanisms and kinetics. At the level of individual NCs, we present analyses of reshaping, including sintering and pinch-off, and of compositional evolution in a vacuum environment. We also discuss modeling of coarsening including diffusion and decay of individual NCs and unconventional coarsening processes. We describe high-level modeling integrated with scanning tunneling microscopy (STM) studies for supported 2D epitaxial nanoclusters and developments in modeling for 3D NCs motivated by in situ transmission electron microscopy (TEM) studies.

Characteristics of sulfur atoms adsorbed on Ag(100), Ag(110), and Ag(111) as probed with scanning tunneling microscopy: experiment and theory.

In this paper, we report that S atoms on Ag(100) and Ag(110) exhibit a distinctive range of appearances in scanning tunneling microscopy (STM) images, depending on the sample bias voltage, VS. Progressing from negative to positive VS, the atomic shape can be described as a round protrusion surrounded by a dark halo (sombrero) in which the central protrusion shrinks, leaving only a round depression. This progression resembles that reported previously for S atoms on Cu(100). We test whether DFT can reproduce these shapes and the transition between them, using a modified version of the Lang-Tersoff-Hamann method to simulate STM images. The sombrero shape is easily reproduced, but the sombrero-depression transition appears only for relatively low tunneling current and correspondingly realistic tip-sample separation, dT, of 0.5-0.8 nm. Achieving these conditions in the calculations requires sufficiently large separation (vacuum) between slabs, together with high energy cutoff, to ensure appropriate exponential decay of electron density into vacuum. From DFT, we also predict that an analogous transition is not expected for S atoms on Ag(111) surfaces. The results are explained in terms of the through-surface conductance, which defines the background level in STM, and through-adsorbate conductance, which defines the apparent height at the point directly above the adsorbate. With increasing VS, for Ag(100) and Ag(110), we show that through-surface conductance increases much more rapidly than through-adsorbate conductance, so the apparent adsorbate height drops below background. In contrast, for Ag(111) the two contributions increase at more comparable rates, so the adsorbate level always remains above background and no transition is seen.

Discontinuous Phase Transitions in Nonlocal Schloegl Models for Autocatalysis: Loss and Reemergence of a Nonequilibrium Gibbs Phase Rule.

We consider Schloegl models (or contact processes) where particles on a square grid annihilate at a rate p and are created at a rate of k_{n}=n(n-1)/[N(N-1)] at empty sites with n particles in a neighborhood Ω_{N} of size N. Simulation reveals a discontinuous transition between populated and vacuum states, but equistable p=p_{eq} determined by the stationarity of planar interfaces between these states depends on the interface orientation and on Ω_{N}. The behavior for large Ω_{N} follows from continuum equations. These also depend on the interface orientation and on Ω_{N} shape, but a unique p_{eq}=0.211 376 320 4 emerges imposing a Gibbs phase rule.

Oxygen and sulfur adsorption on vicinal surfaces of copper and silver: Preferred adsorption sites.

We present an extensive density functional theory (DFT) study of adsorption site energetics for oxygen and sulfur adsorbed on two vicinal surfaces of Cu and Ag, with the goal of identifying the most stable adsorption site(s), identifying trends and common themes, and comparing with experimental work in the literature where possible. We also present benchmark calculations for adsorption on the flat (111) and (100) surfaces. The first vicinal surface is the (211), and results are similar for both metals. We find that the step-doubling reconstruction is favored with both adsorbates and is driven by the creation of a special stable fourfold hollow (4fh) site at the reconstructed step. Zig-zag chain structures consisting of X-M-X units (X = chalcogen, M = metal) at the step edge are considered, in which the special 4fh site is partially occupied. The zig-zag configuration is energetically competitive for oxygen but not sulfur. DFT results for oxygen agree with experiment in terms of the stability of the reconstruction, but contradict the original site assignment. The second vicinal surface is the (410), where again results are similar for both metals. For oxygen, DFT predicts that step sites are filled preferentially even at lowest coverage, followed by terrace sites, consistent with the experiment. For sulfur, in contrast, DFT predicts that terrace sites fill first. Oxygen forms O-M-O rows on the top edge of the step, where it occupies incomplete 4fh sites. This resolves an experimental ambiguity in the site assignment. For both the (211) and (410) surfaces, the interaction energy that stabilizes the X-M-X chain or row correlates with the linearity of the X-M-X unit, which may explain key differences between oxygen and sulfur.

Long-term results of CT-guided percutaneous radiofrequency ablation of inoperable patients with stage Ia non-small cell lung cancer: A retrospective cohort study.

BACKGROUND: This study was performed to retrospectively evaluate the 10-year overall survival (OS), progression-free survival (PFS), and local control rates of patients with inoperable stage Ia non-small cell lung cancer (NSCLC) who underwent computed tomography (CT)-guided radiofrequency ablation (RFA) in a single center. MATERIALS AND METHODS: Fifty patients with inoperable NSCLC underwent RFA between 2004 and 2016. Thoracic surgeons evaluated the patients and performed RFA under CT guidance. Follow-up CT and positron emission tomography/CT scans were obtained. Local control rates and recurrence patterns were analyzed. RESULTS: Seventy-three lesions in 50 patients (M:F = 22:28; median age: 73 years; range: 52-82 years) were treated with CT-guided RFA. The mean lesion size was 2.2 cm (range: 1-3 cm). No procedure-related deaths occurred. Low-grade fever was the most common post-ablation complication, with an incidence rate of 36%. The 1-, 2-, 3-, 5-, and 10-year OS rates of patients with Ia NSCLC were 96.0%, 86.5%, 67.1%, 36.3%, and 1%, respectively, and the 1-, 2-, 3-, and 5-year PFS rates were 94.0%, 77.5%, 43.5%, and 10.8%, respectively. The most common pattern of recurrence was local, and 15 patients with recurrence were treated with repeat RFA. Tumor size <2.0 cm was associated with a significantly improved 3-year survival rate of 78.9%. CONCLUSION: CT-guided RFA is feasible and well tolerated by inoperable patients with inoperable stage Ia NSCLC.

Sulfur Atoms Adsorbed on Cu(100) at Low Coverage: Characterization and Stability against Complexation.

Using scanning tunneling microscopy, we characterize the size and bias-dependent shape of sulfur atoms on Cu(100) at low coverage (below 0.1 monolayers) and low temperature (quenched from 300 to 5 K). Sulfur atoms populate the Cu(100) terraces more heavily than steps at low coverage, but as coverage approaches 0.1 monolayers, close-packed step edges become fully populated, with sulfur atoms occupying sites on top of the step. Density functional theory (DFT) corroborates the preferential population of terraces at low coverage as well as the step adsorption site. In experiment, small regions with p(2 × 2)-like atomic arrangements emerge on the terraces as sulfur coverage approaches 0.1 monolayer. Using DFT, a lattice gas model has been developed, and Monte Carlo simulations based on this model have been compared with the observed terrace configurations. A model containing eight pairwise interaction energies, all repulsive, gives qualitative agreement. Experiment shows that atomic adsorbed sulfur is the only species on Cu(100) up to a coverage of 0.09 monolayers. There are no Cu-S complexes. In contrast, prior work has shown that a Cu2S3 complex forms on Cu(111) under comparable conditions. On the basis of DFT, this difference can be attributed mainly to stronger adsorption of sulfur on Cu(100) as compared with Cu(111).

Communication: Diverse nanoscale cluster dynamics: Diffusion of 2D epitaxial clusters.

The dynamics of nanoscale clusters can be distinct from macroscale behavior described by continuum formalisms. For diffusion of 2D clusters of N atoms in homoepitaxial systems mediated by edge atom hopping, macroscale theory predicts simple monotonic size scaling of the diffusion coefficient, DN ∼ N-ß, with ß = 3/2. However, modeling for nanoclusters on metal(100) surfaces reveals that slow nucleation-mediated diffusion displaying weak size scaling ß < 1 occurs for "perfect" sizes Np = L2 and L(L+1) for integer L = 3,4,… (with unique square or near-square ground state shapes), and also for Np+3, Np+4,…. In contrast, fast facile nucleation-free diffusion displaying strong size scaling ß ≈ 2.5 occurs for sizes Np+1 and Np+2. DN versus N oscillates strongly between the slowest branch (for Np+3) and the fastest branch (for Np+1). All branches merge for N = O(102), but macroscale behavior is only achieved for much larger N = O(103). This analysis reveals the unprecedented diversity of behavior on the nanoscale.