Reconstruction of steps on the Cu(111) surface induced by sulfur.

A rich menagerie of structures is identified at 5 K following adsorption of low coverages (≤0.05 monolayers) of S on Cu(111) at room temperature. This paper emphasizes the reconstructions at the steps. The A-type close-packed step has 1 row of S atoms along its lower edge, where S atoms occupy alternating pseudo-fourfold-hollow (p4fh) sites. Additionally, there are 2 rows of S atoms of equal density on the upper edge, bridging a row of extra Cu atoms, together creating an extended chain. The B-type close-packed step exhibits an even more complex reconstruction, in which triangle-shaped groups of Cu atoms shift out of their original sites and form a base for S adsorption at (mostly) 4fh sites. We propose a mechanism by which these triangles could generate Cu-S complexes and short chains like those observed on the terraces.

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage.

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derived using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.

Self-assembly of metal nanostructures on binary alloy surfaces.

Deposition of metals on binary alloy surfaces offers new possibilities for guiding the formation of functional metal nanostructures. This idea is explored with scanning tunneling microscopy studies and atomistic-level analysis and modeling of nonequilibrium island formation. For Au/NiAl(110), complex monolayer structures are found and compared with the simple fcc(110) bilayer structure recently observed for Ag/NiAl(110). We also consider a more complex codeposition system, (Ni + Al)/NiAl(110), which offers the opportunity for fundamental studies of self-growth of alloys including deviations for equilibrium ordering. A general multisite lattice-gas model framework enables analysis of structure selection and morphological evolution in these systems.

Communication: Structure, formation, and equilibration of ensembles of Ag-S complexes on an Ag surface.

We have utilized conditions of very low temperature (4.7 K) and very low sulfur coverage to isolate and identify Ag-S complexes that exist on the Ag(111) surface. The experimental conditions are such that the complexes form at temperatures above the temperature of observation. These complexes can be regarded as polymeric chains of varying length, with an Ag4S pyramid at the core of each monomeric unit. Steps may catalyze the formation of the chains and this mechanism may be reflected in the chain length distribution.

Formation of a novel ordered Ni3Al surface structure by codeposition on NiAl(110).

The formation of a new type of ordered 2D Ni3Al overlayer by low-temperature codeposition on NiAl(110) is demonstrated by kinetic Monte Carlo simulation of a multisite atomistic lattice-gas model with a precise treatment of surface diffusion kinetics. Simultaneous codeposition with 3:1 Ni:Al yields poor ordering at 300 K but well-ordered structures by ~500 K. Sequential codeposition of Ni then Al yields unmixed core-ring nanostructures at 300 K but strong intermixing and ordering by ~500 K.

Temperature-dependent growth shapes of Ni nanoclusters on NiAl(110).

Scanning tunneling microscopy studies reveal that two-dimensional nanoscale Ni islands formed by deposition of Ni on NiAl(110) between 200-400 K exhibit far-from-equilibrium growth shapes which change systematically with temperature. Island structure reflects the two types of adsorption sites available for Ni adatoms, and island shapes are controlled by the details of adatom diffusion along island edges accounting for numerous local configurations. The temperature dependence of the island shapes is captured and elucidated by kinetic Monte Carlo simulation of a realistic atomistic-level multisite lattice-gas model incorporating precise diffusion barriers. These barriers are obtained by utilizing density functional theory to probe energetics not just at adsorption sites but also at transition states for diffusion. This success demonstrates a capability for predictive atomistic-level modeling of nanocluster formation and shape selection in systems that have a high level of energetic and kinetic complexity.

Group specific optimisation of fMRI processing steps for child and adult data.

Motion is a major issue in functional magnetic resonance imaging (fMRI) dataseries and causes artifacts or increased overall noise obscuring signals of interest. It is particularly important to be able to control for and correct these artifacts when dealing with child data. We analysed the data from 35 children (4-8 years old) and 13 adults (18-30 years old) during an emotional face paradigm. The children were split into low and high motion groups on the basis of having less or more than an estimated maximal movement of one voxel (3.75 mm) and one degree of rotation in any motion direction between any pair of scans in the run. Several different preprocessing steps were evaluated for their ability to correct for the excess motion using agnostic canonical variates analysis (aCVA) in the NPAIRS (Nonparametric, Prediction, Activation, Influence, Reproducibility, re-Sampling) framework. The adult dataset was reasonably stable whereas the motion-prone child datasets benefited greatly from motion parameter regression (MPR). Motion parameter regression had a strong beneficial impact on all datasets, a result that was largely unaffected by other preprocessing choices; however, motion correction on its own did not have as much impact. The low motion child group subjected to MPR had reproducibility values at par with those of the adult group, but needed almost twice as many subjects to achieve this result, indicating weaker responses in young children. The aCVA showed greater sensitivity to the task response pattern than the mixed effects general linear model (mGLM) in the expected face processing regions, although the mGLM showed more responses in some other areas. This work illustrates that preprocessing choices must be made in a group-specific fashion to optimise fMRI results.

Polymer length distributions for catalytic polymerization within mesoporous materials: non-Markovian behavior associated with partial extrusion.

We analyze a model for polymerization at catalytic sites distributed within parallel linear pores of a mesoporous material. Polymerization occurs primarily by reaction of monomers diffusing into the pores with the ends of polymers near the pore openings. Monomers and polymers undergo single-file diffusion within the pores. Model behavior, including the polymer length distribution, is determined by kinetic Monte Carlo simulation of a suitable atomistic-level lattice model. While the polymers remain within the pore, their length distribution during growth can be described qualitatively by a Markovian rate equation treatment. However, once they become partially extruded, the distribution is shown to exhibit non-Markovian scaling behavior. This feature is attributed to the long-tail in the "return-time distribution" for the protruding end of the partially extruded polymer to return to the pore, such return being necessary for further reaction and growth. The detailed form of the scaled length distribution is elucidated by application of continuous-time random walk theory.

Tidal Growth Increments in the Cockle Clinocardium nuttalli.

Sets of growth lines in the shell of Clinocardium nuttalli are extinguished every 13 or 14 increments only to be replaced by other sets, half an increment out of phase with the first. This can be explained only by assuming that the lines are deposited during periods of exposure at low tide. The average duration of an increment is 24 hours and 50 minutes.

DNA-dependent kinase (p350) as a candidate gene for the murine SCID defect.

Severe combined immunodeficient (SCID) mice are deficient in a recombination process utilized in both DNA double-strand break repair and in V(D)J recombination. The phenotype of these mice involves both cellular hypersensitivity to ionizing radiation and a lack of B and T cell immunity. The catalytic subunit of DNA-dependent protein kinase, p350, was identified as a strong candidate for the murine gene SCID. Both p350 and a gene complementing the SCID defect colocalize to human chromosome 8q11. Chromosomal fragments expressing p350 complement the SCID phenotype, and p350 protein levels are greatly reduced in cells derived from SCID mice compared to cells from wild-type mice.

Schloegl's second model for autocatalysis with particle diffusion: Lattice-gas realization exhibiting generic two-phase coexistence.

We analyze a discontinuous nonequilibrium phase transition between an active (or reactive) state and a poisoned (or extinguished) state occurring in a stochastic lattice-gas realization of Schloegl's second model for autocatalysis. This realization, also known as the quadratic contact process, involves spontaneous annihilation, autocatalytic creation, and diffusion of particles on a square lattice, where creation at empty sites requires a suitable nearby pair of particles. The poisoned state exists for all annihilation rates p>0 and is an absorbing particle-free "vacuum" state. The populated active steady state exists only for p below a critical value, p(e). If p(f) denotes the critical value below which a finite population can survive, then we show that p(f)

Accelerated coarsening of Ag adatom islands on Ag(111) due to trace amounts of S: mass-transport mediated by Ag-S complexes.

Scanning tunneling microscopy studies reveal that trace amounts of adsorbed S below a critical coverage on the order of 10 mML have little effect on the coarsening and decay of monolayer Ag adatom islands on Ag(111) at 300 K. In contrast, above this critical coverage, decay is greatly accelerated. This critical value appears to be determined by whether all S can be accommodated at step edges. Accelerated coarsening derives from the feature that the excess S (above that incorporated at steps) produces significant populations on the terraces of metal-sulfur complexes, which are stabilized by strong Ag-S bonding. These include AgS(2), Ag(2)S(2), Ag(2)S(3), and Ag(3)S(3). Such complexes are sufficiently populous and mobile that they can potentially lead to greatly enhanced metal mass transport across the surface. This picture is supported by density functional theory analysis of the relevant energetics, as well as by reaction-diffusion equation modeling to assess the mechanism and degree of enhanced coarsening.

Statistical mechanical modeling of catalytic polymerization within surface-functionalized mesoporous materials.

A discrete lattice model is developed to describe diffusion-mediated polymerization occurring within mesopores, where reaction is enhanced at catalytic sites distributed within the interior of the pores. Diffusive transport of monomers and polymers is one-dimensional, diffusion coefficients for the latter decreasing with polymer length. Kinetic Monte Carlo simulation is utilized to analyze model behavior focusing on a "clogging" regime, where the amount of polymer within the pores grows. We characterize the evolution of the overall and mean length of polymers, the mean number of polymers, as well as the polymer spatial and length distributions.

Formation of complex wedding-cake morphologies during homoepitaxial film growth of Ag on Ag(111): atomistic, step-dynamics, and continuum modeling.

An atomistic lattice-gas model is developed which successfully describes all key features of the complex mounded morphologies which develop during deposition of Ag films on Ag(111) surfaces. We focus on this homoepitaxial thin film growth process below 200 K. The unstable multilayer growth mode derives from the presence of a large Ehrlich-Schwoebel step-edge barrier, for which we characterize both the step-orientation dependence and the magnitude. Step-dynamics modeling is applied to further characterize and elucidate the evolution of the vertical profiles of these wedding-cake-like mounds. Suitable coarse-graining of these step-dynamics equations leads to instructive continuum formulations for mound evolution.

Time for a Time Window Extension: Insights from Late Presenters in the ESCAPE Trial.

BACKGROUND AND PURPOSE: The safety and efficacy of endovascular therapy for large-artery stroke in the extended time window is not yet well-established. We performed a subgroup analysis on subjects enrolled within an extended time window in the Endovascular Treatment for Small Core and Proximal Occlusion Ischemic Stroke (ESCAPE) trial. MATERIALS AND METHODS: Fifty-nine of 315 subjects (33 in the intervention group and 26 in the control group) were randomized in the ESCAPE trial between 5.5 and 12 hours after last seen healthy (likely to have groin puncture administered 6 hours after that). Treatment effect sizes for all relevant outcomes (90-day mRS shift, mRS 0-2, mRS 0-1, and 24-hour NIHSS scores and intracerebral hemorrhage) were reported using unadjusted and adjusted analyses. RESULTS: There was no evidence of treatment heterogeneity between subjects in the early and late windows. Treatment effect favoring intervention was seen across all clinical outcomes in the extended time window (absolute risk difference of 19.3% for mRS 0-2 at 90 days). There were more asymptomatic intracerebral hemorrhage events within the intervention arm (48.5% versus 11.5%, P = .004) but no difference in symptomatic intracerebral hemorrhage. CONCLUSIONS: Patients with an extended time window could potentially benefit from endovascular treatment. Ongoing randomized controlled trials using imaging to identify late presenters with favorable brain physiology will help cement the paradigm of using time windows to select the population for acute imaging and imaging to select individual patients for therapy.

Generic two-phase coexistence, relaxation kinetics, and interface propagation in the quadratic contact process: simulation studies.

The quadratic contact process is formulated as an adsorption-desorption model on a two-dimensional square lattice. It involves random adsorption at empty sites and correlated desorption requiring diagonally adjacent pairs of empty neighbors. We assess the model behavior utilizing kinetic Monte Carlo simulations. One finds generic two-phase coexistence between a low-coverage active steady state and a completely covered or "poisoned" absorbing steady state; i.e., both states are stable over a finite range of adsorption rates or "pressures." This behavior is in marked contrast to that for equilibrium phase separation. For spatially homogeneous systems, we provide a comprehensive characterization of the kinetics of relaxation to the steady states. We analyze rapid poisoning for higher pressures above an effective spinodal point terminating a metastable active state, nucleation-mediated poisoning in the metastable region, the dynamics of poisoned droplets within the two-phase coexistence region, and behavior reminiscent of bootstrap percolation dynamics for lower pressures. For spatially inhomogeneous systems, we analyze the propagation of planar interfaces between active and absorbing states, fully characterizing an orientation dependence which underlies the generic two-phase coexistence.

Tirapazamine is metabolized to its DNA-damaging radical by intranuclear enzymes.

Tirapazamine (TPZ), a new anticancer drug that is currently in Phase II and III clinical trials, has a unique mechanism of action. Its cytotoxicity is selective for hypoxic cells in solid tumors and results from DNA damage produced by a free radical, which is generated by enzymatic reduction of the parent molecule. However, there is no agreement as to which enzyme(s) are involved. Here, we have measured both DNA damage and TPZ metabolism in A549 human lung cancer cells and in isolated nuclei derived from the cells. We show that, although the nuclei metabolize TPZ at a rate that is only 20% of that of whole cells, they have levels of DNA damage that are similar to those of the cells. We also show that TPZ radicals that are formed outside nuclei do not contribute to intranuclear DNA damage. Thus, essentially all of the DNA damage from TPZ results from radicals generated within the nucleus, and the 80% of the drug metabolism that occurs in the cytoplasm is probably irrelevant for the activity of this drug in killing hypoxic cells.

Stable translocations detected by fluorescence in situ hybridization: a rapid surrogate end point to evaluate the efficacy of a potentiator of tumor response to radiotherapy.

Testing potential modifiers of the response of tumors to radiation therapy requires large, expensive, and time-consuming clinical trials. It would, therefore, be of value to have a rapid surrogate end point of tumor response that could be used to evaluate such modifiers. We here propose that radiation-induced stable chromosome translocations measured by fluorescence in situ hybridization (FISH) could fulfill this purpose. The assay requires that the ratio of nonlethal stable translocations to lethal dicentric aberrations be unity and not change with radiation dose and that radiation-induced stable translocations remain in the tumor cell population essentially indefinitely after irradiation. We have tested these assumptions with four human tumor cell lines in vitro at doses of 1-5 Gy and found them to be valid. We also modified the response to fractionated irradiation of a human tumor xenograft in three different ways and quantitated the tumor response using clonogenic cell survival and using the FISH stable translocation assay. Both assays gave similar values for the extent of radiation modification. These data suggest that this assay could allow clinical evaluation of potential radiation sensitizers with fewer patients and in shorter times than is the case with conventional clinical trials.

The hypersensitivity of the Chinese hamster ovary variant BL-10 to bleomycin killing is due to a lack of glutathione S-transferase-alpha activity.

As a means to understand the fundamental mechanisms of bleomycin cell killing, we previously isolated 19 bleomycin-sensitive mutants which represent at least six genetically distinct complementation groups (T.D. Stamato, B. Peters, P. Patil, N. Denko, R. Weinstein, and A. Giaccia. Cancer Res., 47: 1588-1592, 1987). One class of mutants represented by the cell line BL-10 displays only hypersensitivity to killing by bleomycin in both acute (16 h) and chronic treatments but no sensitivity to killing by other DNA-damaging agents. Complementation studies between this mutant and human fibroblasts suggested that the human gene which corrects the defect of BL-10 rested on human chromosome 6. It has been reported that the gene for human glutathione S-transferase (GST) alpha also resides on chromosome 6. Measurements of selenium-independent peroxidase (alpha-GST + glutathione peroxidase) activity in wild-type Chinese hamster ovary (CHO) cells, using cumene hydrogen peroxide as a substrate, gave a value of 112 nmol of glutathione oxidized/min/mg protein compared with 88.1 nmol of glutathione oxidized/min/mg protein for BL-10. Measurement of the selenium-dependent peroxidase activity, using H2O2 as a substrate, resulted in 65.9 nmol of reduced glutathione oxidized/min/mg protein in CHO and 81.5 nmol of reduced glutathione oxidized/min/mg protein for BL-10. In other words, BL-10 cells did not exhibit a difference in their ability to metabolize both substrates in contrast to CHO cells. This indicates that BL-10 possesses little alpha-GST activity. Transfection of BL-10 cells with a mammalian expression vector containing the alpha-GST gene increases the survival of BL-10 to bleomycin and does not increase the bleomycin resistance of two other bleomycin mutants which lie in different genetic complementation groups. These data strongly implicate a role for alpha-GST in the resistance of cells to bleomycin.

Loss of the intrinsic heat resistance of human cells and changes in Mr 70,000 heat shock protein expression in human x hamster hybrids.

Since mammalian cells vary widely in their intrinsic thermoresistance, we have investigated the genetic basis underlying this phenomenon in human and rodent cell lines. Typically, human cells are considerably more resistant to killing by heat than rodent cell lines. To determine whether the heat-resistant phenotype is dominant or recessive and to locate the chromosome(s) bearing determinants for heat resistance, we have prepared hybrids of heat-resistant human HT1080 cells and heat-sensitive Chinese hamster ovary (CHO) cells to test their response to heat. For both mass hybrid cultures and individual clones, the heat response of the hybrids was similar to that of the CHO parent. Analysis by in situ hybridization revealed the presence of five to 20 human chromosomes per cell in the mass hybrids and four to eight intact chromosomes plus some fragments in individual clones isolated from the hybrid cell population. A similar result was obtained using a different human cell line, AG1522. These data suggest that heat resistance is a recessive trait. Consistent with this conclusion are the results from a study of a fusion of HT1080 to a CHO mutant, BL-10, which was found to be hypersensitive to heat-induced killing. These hybrids had a normal CHO heat response and not the more heat-resistant phenotype of HT1080 cells. Two hybrid clones, H2 and H4, from the HT1080/BL-10 fusion were studied in more detail. Both clones possess similar amounts of Mr 70,000 heat shock protein (HSP70), despite the fact that H4 contains three human chromosomes (Nos. 6, 14, and 21) which carry HSP70 genes while H2 contains only one (chromosome 6). Both hybrid cell lines have the same response to heat. Although we found a wide range of sensitivities to heat, all cell lines contained a similar amount of constitutive HSP70, suggesting that HSP70 levels per se are not the critical determinant of intrinsic heat resistance.