Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

Improving Transient Performance of Adaptive Control Architectures using Frequency-Limited System Error Dynamics

We develop an adaptive control architecture to achieve stabilization and command following of uncertain dynamical systems with improved transient performance. Our framework consists of a new reference system and an adaptive controller. The proposed reference system captures a desired closed-loop dynamical system behavior modified by a mismatch term representing the high-frequency content between the uncertain dynamical system and this reference system, i.e., the system error. In particular, this mismatch term allows to limit the frequency content of the system error dynamics, which is used to drive the adaptive controller. It is shown that this key feature of our framework yields fast adaptation with- out incurring high-frequency oscillations in the transient performance. We further show the effects of design parameters on the system performance, analyze closeness of the uncertain dynamical system to the unmodified (ideal) reference system, discuss robustness of the proposed approach with respect to time-varying uncertainties and disturbances, and make connections to gradient minimization and classical control theory.Comment: 27 pages, 7 figure

Fluctuations and the Effective Moduli of an Isotropic, Random Aggregate of Identical, Frictionless Spheres

We consider a random aggregate of identical frictionless elastic spheres that has first been subjected to an isotropic compression and then sheared. We assume that the average strain provides a good description of how stress is built up in the initial isotropic compression. However, when calculating the increment in the displacement between a typical pair of contaction particles due to the shearing, we employ force equilibrium for the particles of the pair, assuming that the average strain provides a good approximation for their interactions with their neighbors. The incorporation of these additional degrees of freedom in the displacement of a typical pair relaxes the system, leading to a decrease in the effective moduli of the aggregate. The introduction of simple models for the statistics of the ordinary and conditional averages contributes an additional decrease in moduli. The resulting value of the shear modulus is in far better agreement with that measured in numerical simulations

Design and fabrication of high quality-factor 1-d photonic crystal/photonic wire extended microcavities

We have successfully demonstrated experimentally the fabrication and measurement of high quality-factor one-dimensional photonic crystal/photonic wire extended cavities based on silicon-on-insulator. The cavities that we have investigated ranged from 3 to 8 m in length. A quality-factor of nearly 74 000 was measured at a cavity length of 5 m through the use of tapering both within and outside the cavity, showing good agreement with the finite-difference time-domain simulation approach use

Analysis of resonant responses of split ring resonators using conformal mapping techniques

We report a novel method for modeling the resonant frequency response of infra-red light, in the range of 2 to 10 microns, reflected from metallic spilt ring resonators (SRRs) fabricated on a silicon substrate. The calculated positions of the TM and TE peaks are determined from the plasma frequency associated with the filling fraction of the metal array and the equivalent LC circuit defined by the SRR elements. The capacitance of the equivalent circuit is calculated using conformal mapping techniques to determine the co-planar capacitance associated with both the individual and the neighbouring elements. The inductance of the equivalent circuit is based on the self-inductance of the individual elements and the mutual inductance of the neighboring elements. The results obtained from the method are in good agreement with experimental results and simulation results obtained from a commercial FDTD simulation software package. The method allows the frequency response of a SRR to be readily calculated without complex computational methods and enables new designs to be optimised for a particular frequency response by tuning the LC circuit

Optical properties of split ring resonator metamaterial structures on semiconductor substrates

Metamaterials based on single-layer metallic Split Ring Resonators (SRR) and Wires have been demonstrated to have a resonant response in the near infra-red wavelength range. The use of semiconductor substrates gives the potential for control of the resonant properties of split-ring resonator (SRR) structures by means of active changes in the carrier concentration obtained using either electrical injection or photo-excitation. We examine the influence of extended wires that are either parallel or perpendicular to the gap of the SRRs and report on an equivalent circuit model that provides an accurate method of determining the polarisation dependent resonant response for incident light perpendicular to the surface. Good agreement is obtained for the substantial shift observed in the position of the resonances when the planar metalisation is changed from gold to aluminium

AFM imaging and plasmonic detection of organic thin-films deposited on nanoantenna arrays

In this study, atomic force microscopy (AFM) imaging has been used to reveal the preferential deposition of organic thin-films on patterned nanoantenna array surfaces - identifying the localised formation of both monolayer and multilayer films of octadecanethiol (ODT) molecules, depending on the concentration of the solutions used. Reliable identification of this selective deposition process has been demonstrated for the first time, to our knowledge. Organic thin-films, in particular films of ODT molecules, were deposited on plasmonic resonator surfaces through a chemi-sorption process - using different solution concentrations and immersion times. The nanoantennas based on gold asymmetric-split ring resonator (A-SRR) geometries were fabricated on zinc selenide (ZnSe) substrates using electron-beam lithography and the lift-off technique. Use of the plasmonic resonant-coupling technique has enabled the detection of ODT molecules deposited from a dilute, micromolar (1 M) solution concentration - with attomole sensitivity of deposited material per A-SRR – a value that is three orders of magnitude lower in concentration than previously reported. Additionally, on resonance, the amplitude of the molecular vibrational resonance peaks is typically an order of magnitude larger than that for the non-resonant coupling. Fourier-transform infrared (FTIR) spectroscopy shows molecule specific spectral responses – with magnitudes corresponding to the different film thicknesses deposited on the resonator surfaces. The experimental results are supported by numerical simulation

Deposition of Organic Molecules on Gold Nanoantennas for Sensing

The deposition of organic molecules on gold nanoantennas is reported through chemisorption for sensing in the midinfrared (mid-IR) spectral range. The specific nanostructures are gold asymmetric-split ring resonators (A-SRRs) based on circular-geometry with two different ‘arc’ lengths. The plasmonic resonant coupling technique was used to match the vibrational responses of the targeted molecules for their enhanced detection. Gold nanostructures are functionalised through chemisorption of octadecanethiol (ODT) in ethanol solution. The molecular vibrational responses were measured using a microscope coupled Fourier Transform Infrared (FTIR) spectroscopy. The experimental findings are closely supported using FDTD simulation. The modified nanoantennas surfaces are capable of supporting wide range of organic-sensing applications

Intergenerational Communication Strategies for Generation X Supervisors

Millennials, who by 2024 will make up approximately 34% of the U.S. workforce, will play a critical role in organizational strategies and productivity, as will the supervisors who manage them. The purpose of this multiple case study was to explore the intergenerational communication strategies that Generation X supervisors used to motivate and engage high performing millennials in the workplace. The framework for this study was Mannheim\u27s generation theory and the 2-factor theory of motivation by Herzberg, Mausner, and Snyderman. Data were collected from parks and recreation employees in the southeastern region of the United States, including 4 Generation X supervisors who completed semistructured interviews and 2 millennial cohort focus groups. Data were transcribed, coded, and validated through member checking and methodological triangulation. The 4 themes identified were culture and socialization, relationship building and intergenerational connectedness, employee growth and development, and rewards and recognition. The findings of this research may benefit millennials, frontline supervisors, parks and recreation agencies, and leaders in other organizations by providing an understanding of generational needs. The data presented in this study may support positive social change by showing that supervisors and millennial employees can build high quality relationships within their organizations, enabling those organizations to support the communities they serve