Optical sensors for the detection of trace chloroform.

Optical thin film sensors have been developed to detect chloroform in aqueous and nonaqueous solutions. These sensors utilize a modified Fujiwara reaction, one of the only known methods for detecting halogenated hydrocarbons in the visible spectrum. The modified Fujiwara reagents, 2,2'-dipyridyl and tetra-n-butyl ammonium hydroxide (n-Bu4NOH or TBAH), are encapsulated in an ethyl cellulose (EC) or sol-gel film. Upon exposure of the EC sensor film to HCCl3 in petroleum ether, a colored product is produced within the film, which is analyzed spectroscopically, yielding a detection limit of 0.830 ppm (parts per million v/v or µL/L hereinafter) and a quantification limit of 2.77 ppm. When the chloroform concentration in pentane is ≥5 ppm, the color change of the EC sensor is visible to the naked eye. In aqueous chloroform solution, reaction in the sol-gel sensor film turns the sensor from colorless to dark yellow/brown, also visible to the naked eye, with a detection limit of 500 ppm. This is well below the solubility of chloroform in water (ca. 5,800 ppm). To our knowledge, these are the first optical quality thin film sensors using Fujiwara reactions for halogenated hydrocarbon detection.

Energy Harvesting by Mesoporous Reduced Graphene Oxide Enhanced the Mediator-Free Glucose-Powered Enzymatic Biofuel Cell for Biomedical Applications.

Harnessing electrochemical energy in an engineered electrical circuit from biochemical substrates in the human body using biofuel cells is gaining increasing research attention in the current decade due to the wide range of biomedical possibilities it creates for electronic devices. In this report, we describe and characterize the construction of just such an enzymatic biofuel cell (EBFC). It is simple, mediator-free, and glucose-powered, employing only biocompatible materials. A novel feature is the two-dimensional mesoporous thermally reduced graphene oxide (rGO) host electrode. An additionally novelty is that we explored the potential of using biocompatible, low-cost filter paper (FP) instead of carbon paper, a conductive polymer, or gold as support for the host electrode. Using glucose (C6H12O6) and molecular oxygen (O2) as the power-generating fuel, the cell consists of a pair of bioelectrodes incorporating immobilized enzymes, the bioanode modified by rGO-glucose oxidase (GOx/rGO), and the biocathode modified by rGO-laccase (Lac/rGO). Scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDX), transmission electron microscopy, and Raman spectroscopy techniques have been employed to investigate the surface morphology, defects, and chemical structure of rGO, GOx/rGO, and Lac/rGO. N2 sorption, SEM/EDX, and powder X-ray diffraction revealed a high Brunauer-Emmett-Teller surface area (179 m2 g-1) mesoporous rGO structure with the high C/O ratio of 80:1 as well. Results from the Fourier transform infrared spectroscopy, UV-visible spectroscopy, and electrochemical impedance spectroscopy studies indicated that GOx remained in its native biochemical functional form upon being embedded onto the rGO matrix. Cyclic voltammetry studies showed that the presence of mesoporous rGO greatly enhanced the direct electrochemistry and electrocatalytic properties of the GOx/rGO and Lac/rGO nanocomposites. The electron transfer rate constant between GOx and rGO was estimated to be 2.14 s-1. The fabricated EBFC (GOx/rGO/FP-Lac/rGO/FP) using a single GOx/rGO/FP bioanode and a single Lac/rGO/FP biocathode provides a maximum power density (Pmax) of 4.0 nW cm-2 with an open-circuit voltage (VOC) of 0.04 V and remains stable for more than 15 days with a power output of ∼9.0 nW cm-2 at a pH of 7.4 under ambient conditions.

Fast GPU-Based Generation of Large Graph Networks From Degree Distributions.

Synthetically generated, large graph networks serve as useful proxies to real-world networks for many graph-based applications. The ability to generate such networks helps overcome several limitations of real-world networks regarding their number, availability, and access. Here, we present the design, implementation, and performance study of a novel network generator that can produce very large graph networks conforming to any desired degree distribution. The generator is designed and implemented for efficient execution on modern graphics processing units (GPUs). Given an array of desired vertex degrees and number of vertices for each desired degree, our algorithm generates the edges of a random graph that satisfies the input degree distribution. Multiple runtime variants are implemented and tested: 1) a uniform static work assignment using a fixed thread launch scheme, 2) a load-balanced static work assignment also with fixed thread launch but with cost-aware task-to-thread mapping, and 3) a dynamic scheme with multiple GPU kernels asynchronously launched from the CPU. The generation is tested on a range of popular networks such as Twitter and Facebook, representing different scales and skews in degree distributions. Results show that, using our algorithm on a single modern GPU (NVIDIA Volta V100), it is possible to generate large-scale graph networks at rates exceeding 50 billion edges per second for a 69 billion-edge network. GPU profiling confirms high utilization and low branching divergence of our implementation from small to large network sizes. For networks with scattered distributions, we provide a coarsening method that further increases the GPU-based generation speed by up to a factor of 4 on tested input networks with over 45 billion edges.

Mesoscopic Modeling and Rapid Simulation of Incremental Changes in Epidemic Scenarios on GPUs: Fast What-If Analyses of Localized and Dynamic Effects.

In simulation-based studies and analyses of epidemics, a major challenge lies in resolving the conflict between fidelity of models and the speed of their simulation. Another related challenge arises in dealing with the large number of what-if scenarios that need to be explored. Here, we describe new computational methods that together provide an approach to dealing with both challenges. A mesoscopic modeling approach is described that strikes a middle ground between macroscopic models based on coupled differential equations and microscopic models built on fine-grained behaviors at the individual entity level. The mesoscopic approach offers the ability to incorporate complex compositions of multiple layers of dynamics even while retaining the potential for aggregate behaviors at varying levels. It also is an excellent match to the accelerator-based architectures of modern computing platforms in which graphical processing units (GPUs) can be exploited for fast simulation via the parallel execution mode of single instruction multiple thread (SIMT). The challenge of simulating a large number of scenarios is addressed via a method of sharing model state and computation across a tree of what-if scenarios that are localized, incremental changes to a large base simulation. A combination of the mesoscopic modeling approach and the incremental what-if scenario tree evaluation has been implemented in the software on modern GPUs. Synthetic simulation scenarios are presented to demonstrate the computational characteristics of our approach. Results from the experiments with large population data, including USA, UK, and India, illustrate the modeling methodology and computational performance on thousands of synthetically generated what-if scenarios. Execution of our implementation scaled to 8192 GPUs of supercomputing platforms demonstrates the ability to rapidly evaluate what-if scenarios several orders of magnitude faster than the conventional methods.

Phosphine Oxide Containing Poly(pyridinium salt)s as Fire Retardant Materials.

Six new rugged, high-temperature tolerant phosphine oxide-containing poly(4,4'-(p-phenylene)-bis(2,6-diphenylpyridinium)) polymers P-1, P-2, P-3, P-4, P-5, and P-6 are synthesized, characterized, and evaluated. Synthesis results in high yield and purity, as confirmed by elemental, proton (1H), and carbon 13 (13C) nuclear magnetic resonance (NMR) spectra analyses. High glass transition temperatures (Tg > 230 °C) and high char yields (>50% at 700 °C) are determined by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA), respectively. These new ionic polymers exhibit excellent processability, thin-film forming, high-temperature resistance, fire-resistance and retardation, coating, adhesion, mechanical and tensile strength, and n-type (electron transport) properties. The incorporation of phosphine oxide and bis(phenylpyridinium) moieties in the polymer backbones leads to high glass transition temperatures and excellent fire retardant properties, as determined by microcalorimetry measurements. The use of organic counterions allows these ionic polymers to be easily processable from several common organic solvents. A large variety of these polymers can be synthesized by utilizing structural variants of the bispyrylium salt, phosphine oxide containing diamine, and the counterion in a combinatorial fashion. These results make them very attractive for a number of applications, including as coating and structural component materials for automobiles, aircrafts, power and propulsion systems, firefighter garments, printed circuit boards, cabinets and housings for electronic and electrical components, construction materials, mattresses, carpets, upholstery and furniture, and paper-thin coatings for protecting important paper documents.

Electrolyte-gated transistors based on conducting polymer nanowire junction arrays.

In this study, we describe the electrolyte gating and doping effects of transistors based on conducting polymer nanowire electrode junction arrays in buffered aqueous media. Conducting polymer nanowires including polyaniline, polypyrrole, and poly(ethylenedioxythiophene) were investigated. In the presence of a positive gate bias, the device exhibits a large on/off current ratio of 978 for polyaniline nanowire-based transistors; these values vary according to the acidity of the gate medium. We attribute these efficient electrolyte gating and doping effects to the electrochemically fabricated nanostructures of conducting polymer nanowires. This study demonstrates that two-terminal devices can be easily converted into three-terminal transistors by simply immersing the device into an electrolyte solution along with a gate electrode. Here, the field-induced modulation can be applied for signal amplification to enhance the device performance.

Measurement of Heme Synthesis Levels in Mammalian Cells.

Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in various molecular and cellular processes such as gene transcription, translation, cell differentiation and cell proliferation. The biosynthesis levels of heme vary across different tissues and cell types and is altered in diseased conditions such as anemia, neuropathy and cancer. This technique uses [4-(14)C] 5-aminolevulinic acid ([(14)C] 5-ALA), one of the early precursors in the heme biosynthesis pathway to measure the levels of heme synthesis in mammalian cells. This assay involves incubation of cells with [(14)C] 5-ALA followed by extraction of heme and measurement of the radioactivity incorporated into heme. This procedure is accurate and quick. This method measures the relative levels of heme biosynthesis rather than the total heme content. To demonstrate the use of this technique the levels of heme biosynthesis were measured in several mammalian cell lines.

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection.

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close "neighborhood" of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa.

Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection.

T helper (Th) cells play a major role in the immune response and pathology at the gastric mucosa during Helicobacter pylori infection. There is a limited mechanistic understanding regarding the contributions of CD4+ T cell subsets to gastritis development during H. pylori colonization. We used two computational approaches: ordinary differential equation (ODE)-based and agent-based modeling (ABM) to study the mechanisms underlying cellular immune responses to H. pylori and how CD4+ T cell subsets influenced initiation, progression and outcome of disease. To calibrate the model, in vivo experimentation was performed by infecting C57BL/6 mice intragastrically with H. pylori and assaying immune cell subsets in the stomach and gastric lymph nodes (GLN) on days 0, 7, 14, 30 and 60 post-infection. Our computational model reproduced the dynamics of effector and regulatory pathways in the gastric lamina propria (LP) in silico. Simulation results show the induction of a Th17 response and a dominant Th1 response, together with a regulatory response characterized by high levels of mucosal Treg) cells. We also investigated the potential role of peroxisome proliferator-activated receptor γ (PPARγ) activation on the modulation of host responses to H. pylori by using loss-of-function approaches. Specifically, in silico results showed a predominance of Th1 and Th17 cells in the stomach of the cell-specific PPARγ knockout system when compared to the wild-type simulation. Spatio-temporal, object-oriented ABM approaches suggested similar dynamics in induction of host responses showing analogous T cell distributions to ODE modeling and facilitated tracking lesion formation. In addition, sensitivity analysis predicted a crucial contribution of Th1 and Th17 effector responses as mediators of histopathological changes in the gastric mucosa during chronic stages of infection, which were experimentally validated in mice. These integrated immunoinformatics approaches characterized the induction of mucosal effector and regulatory pathways controlled by PPARγ during H. pylori infection affecting disease outcomes.

ENteric Immunity SImulator: a tool for in silico study of gastroenteric infections.

Clinical symptoms of microbial infection of the gastrointestinal (GI) tract are often exacerbated by inflammation induced pathology. Identifying novel avenues for treating and preventing such pathologies is necessary and complicated by the complexity of interacting immune pathways in the gut, where effector and inflammatory immune cells are regulated by anti-inflammatory or regulatory cells. Here we present new advances in the development of the ENteric Immunity SImulator (ENISI), a simulator of GI immune mechanisms in response to resident commensal bacteria as well as invading pathogens and the effect on the development of intestinal lesions. ENISI is a tool for identifying potential treatment strategies that reduce inflammation-induced damage and, at the same time, ensure pathogen removal by allowing one to test plausibility of in vitro observed behavior as explanations for observations in vivo, propose behaviors not yet tested in vitro that could explain these tissue-level observations, and conduct low-cost, preliminary experiments of proposed interventions/treatments. An example of such application is shown in which we simulate dysentery resulting from Brachyispira hyodysenteriae infection and identify aspects of the host immune pathways that lead to continued inflammation-induced tissue damage even after pathogen elimination.

Generation of long-lived radical ions through enhanced photoinduced electron transfer processes between [60]fullerene and phenothiazine derivatives.

Photoinduced electron transfer processes between fullerenes (C60) and four phenothiazine derivatives (PTZs) in the absence and presence of hexylviologen dication (HV2+) have been studied by the transient absorption method in the visible and near-IR regions. Electron-transfer takes place from PTZs to the triplet states of fullerenes (3C60*) giving the radical anion of fullerenes (C60.-) and the radical cations of PTZs (PTZ.+). The rate constants and efficiencies of electron transfer are quite high, because of the high electron-donor abilities of PTZs as elucidated by their low oxidation potentials. On addition of HV2+ to the C60 and PTZ systems, the electron-mediating process occurs from C60.- to HV2+, yielding the viologen radical cation (HV.+). In the presence of a sacrificial donor, HV.+ persisted for a long time.

Individually addressable crystalline conducting polymer nanowires in a microelectrode sensor array.

An efficient, site-specific and scalable approach has been developed to produce high-quality and individually addressable conducting polymer nanowire electrode junctions (CPNEJs) in a parallel-oriented array. Polypyrrole and PEDOT conducting polymer nanowires (CPNWs) with uniform diameters (ca. 60-150 nm) were introduced into the desired electrode junctions in a precise manner by performing a three-step constant-current electrochemical process at a low current density and a low concentration of monomers. A low scan rate, cyclic voltammetric method was also employed and gave similar results. These CPNEJ arrays function as a miniaturized sensor for the parallel and real-time detection of gas and organic vapour. The electrochemical approaches utilized allow the conducting polymer chains to self-organize in the CPNWs to form novel polycrystalline structures, observed by high resolution TEM. The weak diffraction rings at 4.88 Å and 4.60 Å were observed for PEDOT and polypyrrole CPNWs, respectively.

New n-type organic semiconductors: synthesis, single crystal structures, cyclic voltammetry, photophysics, electron transport, and electroluminescence of a series of diphenylanthrazolines.

The synthesis, properties, and electroluminescent device applications of a series of five new diphenylanthrazoline molecules 1a-1e are reported. Compounds 1b, 1c, and 1d crystallized in the monoclinic system with the space groups P2(1)/c, C2/c, and P2(1)/c, respectively, revealing highly planar molecules. Diphenylanthrazolines 1a-1e have a formal reduction potential in the range -1.39 to -1.58 V (versus SCE) and estimated electron affinities (LUMO levels) of 2.90-3.10 eV. Compounds 1a-1e emit blue light with fluorescence quantum yields of 58-76% in dilute solution, whereas they emit yellow-green light as thin films. The diphenylanthrazoline molecules as the emissive layers in light-emitting diodes gave yellow light with a maximum brightness of 133 cd/m(2) and an external quantum efficiency of up to 0.07% in ambient air. Bilayer light-emitting diodes using compounds 1a-1e as the electron-transport layer and poly(2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene) as the emissive layer had a maximum external efficiency of 3.1% and 2.0 lm/W and a brightness of up to 965 cd/m(2) in ambient air. These results represent enhancements of up to 50 times in external quantum efficiency and 17 times in brightness when using 1a-1e as the electron-transport materials in polymer light-emitting diodes. These results demonstrate that the new diphenylanthrazolines are promising n-type semiconductors for organic electronics.