ASU Scholarship Showcase

The number and variety of connectivity estimation methods is likely to continue to grow over the coming decade. Comparisons between methods are necessary to prune this growth to only the most accurate and robust methods. However, the nature of connectivity is elusive with different methods potentially attempting to identify different aspects of connectivity. Commonalities of connectivity definitions across methods upon which base direct comparisons can be difficult to derive. Here, we explicitly define “effective connectivity” using a common set of observation and state equations that are appropriate for three connectivity methods: dynamic causal modeling (DCM), multivariate autoregressive modeling (MAR), and switching linear dynamic systems for fMRI (sLDSf). In addition while deriving this set, we show how many other popular functional and effective connectivity methods are actually simplifications of these equations. We discuss implications of these connections for the practice of using one method to simulate data for another method. After mathematically connecting the three effective connectivity methods, simulated fMRI data with varying numbers of regions and task conditions is generated from the common equation. This simulated data explicitly contains the type of the connectivity that the three models were intended to identify. Each method is applied to the simulated data sets and the accuracy of parameter identification is analyzed. All methods perform above chance levels at identifying correct connectivity parameters. The sLDSf method was superior in parameter estimation accuracy to both DCM and MAR for all types of comparisons.

The compositional dependence of the lowest direct and indirect band gaps in Ge_1-ySn_y alloys has been determined from room-temperature photoluminescence measurements. This technique is particularly attractive for a comparison of the two transitions because distinct features in the spectra can be associated with the direct and indirect gaps. However, detailed modeling of these room temperature spectra is required to extract the band gap values with the high accuracy required to determine the Sn concentration y_c at which the alloy becomes a direct gap semiconductor. For the direct gap, this is accomplished using a microscopic model that allows the determination of direct gap energies with meV accuracy. For the indirect gap, it is shown that current theoretical models are inadequate to describe the emission properties of systems with close indirect and direct transitions. Accordingly, an ad hoc procedure is used to extract the indirect gap energies from the data. For y < 0.1 the resulting direct gap compositional dependence is given by ΔE₀ = −(3.57 ± 0.06)y (in eV). For the indirect gap, the corresponding expression is ΔE_ind = −(1.64 ± 0.10)y (in eV). If a quadratic function of composition is used to express the two transition energies over the entire compositional range 0 ≤ y ≤ 1, the quadratic (bowing) coefficients are found to be b₀ = 2.46 ± 0.06 eV (for E0) and b_ind = 1.03 ± 0.11 eV (for E_ind). These results imply a crossover concentration y_c = $0.073 [+0.007 over -0.006], much lower than early theoretical predictions based on the virtual crystal approximation, but in better agreement with predictions based on large atomic supercells.

Earth-abundant sustainable inorganic thin-film solar cells, independent of precious elements, pivot on a marginal material phase space targeting specific compounds. Advanced materials characterization efforts are necessary to expose the roles of microstructure, chemistry, and interfaces. Herein, the earth-abundant solar cell device, Cu₂ZnSnS_(4-x)Se_x, is reported, which shows a high abundance of secondary phases compared to similarly grown Cu₂ZnSnSe₄.

We present two-dimensional Mg(OH)₂ sheets and their vertical heterojunctions with CVD-MoS₂ for the first time as flexible 2D insulators with anomalous lattice vibration and chemical and physical properties. New hydrothermal crystal growth technique enabled isolation of environmentally stable monolayer Mg(OH)₂ sheets. Raman spectroscopy and vibrational calculations reveal that the lattice vibrations of Mg(OH)₂ have fundamentally different signature peaks and dimensionality effects compared to other 2D material systems known to date. Sub-wavelength electron energy-loss spectroscopy measurements and theoretical calculations show that Mg(OH)₂ is a 6 eV direct-gap insulator in 2D, and its optical band gap displays strong band renormalization effects from monolayer to bulk, marking the first experimental confirmation of confinement effects in 2D insulators. Interestingly, 2D-Mg(OH)₂ sheets possess rather strong surface polarization (charge) effects which is in contrast to electrically neutral h-BN materials. Using 2D-Mg(OH)₂ sheets together with CVD-MoS₂ in the vertical stacking shows that a strong change transfer occurs from n-doped CVD-MoS₂ sheets to Mg(OH)₂, naturally depleting the semiconductor, pushing towards intrinsic doping limit and enhancing overall optical performance of 2D semiconductors. Results not only establish unusual confinement effects in 2D-Mg(OH)₂, but also offer novel 2D-insulating material with unique physical, vibrational, and chemical properties for potential applications in flexible optoelectronics.

Transition metal trichalcogenides form a class of layered materials with strong in-plane anisotropy. For example, titanium trisulfide (TiS₃) whiskers are made out of weakly interacting TiS₃ layers, where each layer is made of weakly interacting quasi-one-dimensional chains extending along the b axis. Here we establish the unusual vibrational properties of TiS₃ both experimentally and theoretically. Unlike other two-dimensional systems, the Raman active peaks of TiS₃ have only out-of-plane vibrational modes, and interestingly some of these vibrations involve unique rigid-chain vibrations and S–S molecular oscillations. High-pressure Raman studies further reveal that the A_g^S-S S-S molecular mode has an unconventional negative pressure dependence, whereas other peaks stiffen as anticipated. Various vibrational modes are doubly degenerate at ambient pressure, but the degeneracy is lifted at high pressures. These results establish the unusual vibrational properties of TiS₃ with strong in-plane anisotropy, and may have relevance to understanding of vibrational properties in other anisotropic two-dimensional material systems.

In vitro models that mimic in vivo host-pathogen interactions are needed to evaluate candidate drugs that inhibit bacterial virulence traits. We established a new approach to study Pseudomonas aeruginosa biofilm susceptibility on biotic surfaces, using a three-dimensional (3-D) lung epithelial cell model. P. aeruginosa formed antibiotic resistant biofilms on 3-D cells without affecting cell viability. The biofilm-inhibitory activity of antibiotics and/or the anti-biofilm peptide DJK-5 were evaluated on 3-D cells compared to a plastic surface, in medium with and without fetal bovine serum (FBS). In both media, aminoglycosides were more efficacious in the 3-D cell model. In serum-free medium, most antibiotics (except polymyxins) showed enhanced efficacy when 3-D cells were present. In medium with FBS, colistin was less efficacious in the 3-D cell model. DJK-5 exerted potent inhibition of P. aeruginosa association with both substrates, only in serum-free medium. DJK-5 showed stronger inhibitory activity against P. aeruginosa associated with plastic compared to 3-D cells. The combined addition of tobramycin and DJK-5 exhibited more potent ability to inhibit P. aeruginosa association with both substrates. In conclusion, lung epithelial cells influence the efficacy of most antimicrobials against P. aeruginosa biofilm formation, which in turn depends on the presence or absence of FBS.

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

This study presents the first global transcriptional profiling and phenotypic characterization of the major human opportunistic fungal pathogen, Candida albicans, grown in spaceflight conditions. Microarray analysis revealed that C. albicans subjected to short-term spaceflight culture differentially regulated 452 genes compared to synchronous ground controls, which represented 8.3% of the analyzed ORFs. Spaceflight-cultured C. albicans–induced genes involved in cell aggregation (similar to flocculation), which was validated by microscopic and flow cytometry analysis. We also observed enhanced random budding of spaceflight-cultured cells as opposed to bipolar budding patterns for ground samples, in accordance with the gene expression data. Furthermore, genes involved in antifungal agent and stress resistance were differentially regulated in spaceflight, including induction of ABC transporters and members of the major facilitator family, downregulation of ergosterol-encoding genes, and upregulation of genes involved in oxidative stress resistance.

Finally, downregulation of genes involved in actin cytoskeleton was observed. Interestingly, the transcriptional regulator Cap1 and over 30% of the Cap1 regulon was differentially expressed in spaceflight-cultured C. albicans. A potential role for Cap1 in the spaceflight response of C. albicans is suggested, as this regulator is involved in random budding, cell aggregation, and oxidative stress resistance; all related to observed spaceflight-associated changes of C. albicans. While culture of C. albicans in microgravity potentiates a global change in gene expression that could induce a virulence-related phenotype, no increased virulence in a murine intraperitoneal (i.p.) infection model was observed under the conditions of this study. Collectively, our data represent an important basis for the assessment of the risk that commensal flora could play during human spaceflight missions. Furthermore, since the low fluid-shear environment of microgravity is relevant to physical forces encountered by pathogens during the infection process, insights gained from this study could identify novel infectious disease mechanisms, with downstream benefits for the general public.

Purpose: PET (positron emission tomography) imaging researches of functional metabolism using fluorodeoxyglucose ([superscript 18]F-FDG) of animal brain are important in neuroscience studies. FDG-PET imaging studies are often performed on groups of rats, so it is desirable to establish an objective voxel-based statistical methodology for group data analysis.

Material and Methods: This study establishes a statistical parametric mapping (SPM) toolbox (plug-ins) named spmratIHEP for voxel-wise analysis of FDG-PET images of rat brain, in which an FDG-PET template and an intracranial mask image of rat brain in Paxinos & Watson space were constructed, and the default settings were modified according to features of rat brain. Compared to previous studies, our constructed rat brain template comprises not only the cerebrum and cerebellum, but also the whole olfactory bulb which made the later cognitive studies much more exhaustive. And with an intracranial mask image in the template space, the brain tissues of individuals could be extracted automatically. Moreover, an atlas space is used for anatomically labeling the functional findings in the Paxinos & Watson space. In order to standardize the template image with the atlas accurately, a synthetic FDG-PET image with six main anatomy structures is constructed from the atlas, which performs as a target image in the co-registration.

Results: The spatial normalization procedure is evaluated, by which the individual rat brain images could be standardized into the Paxinos & Watson space successfully and the intracranial tissues could also be extracted accurately. The practical usability of this toolbox is evaluated using FDG-PET functional images from rats with left side middle cerebral artery occlusion (MCAO) in comparison to normal control rats. And the two-sample t-test statistical result is almost related to the left side MCA.

Conclusion: We established a toolbox of SPM8 named spmratIHEP for voxel-wise analysis of FDG-PET images of rat brain.

The probiotic effects of Lactobacillus reuteri have been speculated to partly depend on its capacity to produce the antimicrobial substance reuterin during the reduction of glycerol in the gut. In this study, the potential of this process to protect human intestinal epithelial cells against infection with Salmonella enterica serovar Typhimurium was investigated. We used a three-dimensional (3-D) organotypic model of human colonic epithelium that was previously validated and applied to study interactions between S. Typhimurium and the intestinal epithelium that lead to enteric salmonellosis. Using this model system, we show that L. reuteri protects the intestinal cells against the early stages of Salmonella infection and that this effect is significantly increased when L. reuteri is stimulated to produce reuterin from glycerol. More specifically, the reuterin-containing ferment of L. reuteri caused a reduction in Salmonella adherence and invasion (1 log unit), and intracellular survival (2 log units). In contrast, the L. reuteri ferment without reuterin stimulated growth of the intracellular Salmonella population with 1 log unit. The short-term exposure to reuterin or the reuterin-containing ferment had no observed negative impact on intestinal epithelial cell health. However, long-term exposure (24 h) induced a complete loss of cell-cell contact within the epithelial aggregates and compromised cell viability. Collectively, these results shed light on a potential role for reuterin in inhibiting Salmonella-induced intestinal infections and may support the combined application of glycerol and L. reuteri. While future in vitro and in vivo studies of reuterin on intestinal health should fine-tune our understanding of the mechanistic effects, in particular in the presence of a complex gut microbiota, this the first report of a reuterin effect on the enteric infection process in any mammalian cell type.