Query-driven visualization of time-varying adaptive mesh refinement data

The visualization and analysis of AMR-based simulations is integral to the process of obtaining new insight in scientific research. We present a new method for performing query-driven visualization and analysis on AMR data, with specific emphasis on time-varying AMR data. Our work introduces a new method that directly addresses the dynamic spatial and temporal properties of AMR grids that challenge many existing visualization techniques. Further, we present the first implementation of query-driven visualization on the GPU that uses a GPU-based indexing structure to both answer queries and efficiently utilize GPU memory. We apply our method to two different science domains to demonstrate its broad applicability.     

Semantic email: theory and applications

This paper investigates how the vision of the Semantic Web can be carried over to the realm of email. We introduce a general notion of semantic email, in which an email message consists of a structured query or update coupled with corresponding explanatory text. Semantic email opens the door to a wide range of automated, email-mediated applications with formally guaranteed properties. In particular, this paper introduces a broad class of semantic email processes. For example, consider the process of sending an email to a program committee, asking who will attend the PC dinner, automatically collecting the responses, and tallying them up. We define both logical and decision-theoretic models where an email process is modeled as a set of updates to a data set on which we specify goals via certain constraints or utilities. We then describe a set of inference problems that arise while trying to satisfy these goals and analyze their computational tractability. In particular, we show that for the logical model it is possible to automatically infer which email responses are acceptable w.r.t. a set of constraints in polynomial time, and for the decision-theoretic model it is possible to compute the optimal message-handling policy in polynomial time. In addition, we show how to automatically generate explanations for a process's actions, and identify cases where such explanations can be generated in polynomial time. Finally, we discuss our publicly available implementation of semantic email and outline research challenges in this realm.¹     

Reduction of defects and improvement in the performance of blue phosphor for thick‐dielectric electroluminescent displays using Color‐by‐Blue

Abstract— Defect‐free large‐area inorganic thick‐dielectric EL (TDEL) displays using Color by Blue (CBB) technology have been successfully developed. We have achieved the world's highest blue‐phosphor luminance of 900 cd/m² for a single‐pixel device by using CBB and by optimizing the e‐beam gun configuration and the flow rate of H₂S in the vacuum chamber. By analyzing the defects on panels with triple‐pattern phosphors and CBB panels, we also found that the number of defects on CBB panels can be drastically reduced compared with those on triple‐pattern panels. The defect‐free 17‐in. VGA CBB panels show better characteristics, a high peak luminance of 600 cd/m² and a high contrast ratio of 1000:1, compared with those of triple‐pattern panels.     

Glioblastoma Extracellular Vesicle-Specific Peptides Inhibit EV-Induced Neuronal Cytotoxicity

WHO Grade 4 IDH-wild type astrocytoma (GBM) is the deadliest brain tumor with a poor prognosis. Meningioma (MMA) is a more common “benign” central nervous system tumor but with significant recurrence rates. There is an urgent need for brain tumor biomarkers for early diagnosis and effective treatment options. Extracellular vesicles (EVs) are tiny membrane-enclosed vesicles that play essential functions in cell-to-cell communications among tumor cells. We aimed to identify epitopes of brain tumor EVs by phage peptide libraries. EVs from GBM plasma, MMA plasma, or brain tumor cell lines were used to screen phage-displayed random peptide libraries to identify high-affinity peptides. We purified EVs from three GBM plasma pools (23 patients), one MMA pool (10 patients), and four brain tumor cell lines. We identified a total of 21 high-affinity phage peptides (12 unique) specific to brain tumor EVs. The peptides shared high sequence homologies among those selected by the same EVs. Dose–response ELISA demonstrated that phage peptides were specific to brain tumor EVs compared to controls. Peptide affinity purification identified unique brain tumor EV subpopulations. Significantly, GBM EV peptides inhibit brain tumor EV-induced complement-dependent cytotoxicity (necrosis) in neurons. We conclude that phage display technology could identify specific peptides to isolate and characterize tumor EVs.     

The Variety of Variables in Computer-Aided Real-Time Programming

The refinement calculus is a well-established theory for translating specifications to program code. Recent research has extended the calculus to handle real-time requirements and we have developed an interactive support tool based on these extensions. Via a case study, this paper shows how the tool helps the programmer by supporting the many forms of variables used in the theory. These include simple state variables as in the untimed calculus, timed-trace variables that model the evolution of properties over time, and auxiliary variables that exist to support formal reasoning only.     

An EBIC equation for solar cells

When an electron beam of a scanning electron microscope (SEM) impinges on an N-P junction, the generation of electron-hole pairs by impact ionization causes a characteristic short circuit current I_SC to flow. The I_SC, i.e. EBIC (electron beam induced current) depends strongly on the configuration used to investigate the cell's response. In this paper we consider the case where the plane of the junction is perpendicular to the surface. An EBIC equation amenable to numerical computations is derived as a function of cell thickness, source depth, surface recombination velocity, diffusion length, and distance of the junction to the beam-cell interaction point for a cell with an ohmic contact at its back surface. It is shown that the EBIC equation presented here is more general and easier to use than those previously reported. The effects of source depth, ohmic contact, and diffusion length on the normalized EBIC characteristic are discussed.     

Decoupled Roles for the Atypical,Bifurcated Binding Pocket of the ybfF Hydrolase

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate‐binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc‐ybfF) by using a 21‐member library of fluorogenic ester substrates. We assigned the roles of the two substrate‐binding clefts in controlling the substrate selectivity and folded stability of Vc‐ybfF by comprehensive substitution analysis. The overall substrate preference of Vc‐ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc‐ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc‐ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc‐ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.     

Structure–property relationships in BaTiO3–BiFeO3–BiYbO3 ceramics

Ba_1?xBi_xTi_1?xYb_x/2Fe_x/2O₃ ceramics were fabricated by the solid state reaction method. X-ray diffraction analyses show 0 ≤ x ≤ 0.04 ceramics to have an average crystal structure described by the non-centrosymmetric tetragonal P4 mm space group, whereas x ≥ 0.08 ceramics are consistent with a centrosymmetric cubic perovskite (space group Pm-3 m). Coexistence of both tetragonal and cubic symmetries is observed for x = 0.06. Raman spectroscopy analysis corroborate a change in average structure with increasing x, but also show the local crystal symmetry for x ≥ 0.08 ceramics to deviate from the idealized cubic perovskite structure. Dielectric data show a ferroelectric-to-relaxor crossover, which occurs in conjunction with the change in both the average and local crystal symmetry as indicated by X-ray and Raman data. For x ≥ 0.08, ceramics exhibit relaxor behavior, which is also accompanied by a shift of the permittivity maxima towards higher temperatures with increasing x.