3,956 research outputs found

    ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

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    The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

    Private Pensions: ERISA Permits Offsets of Private Pension Benefits by Amounts Received in Worker\u27s Compensation Awards, Preempting State Laws Prohibiting Such Offsets

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    Alessi v. Raybestos-Manhattan, Inc., 101 S. Ct. 1895 (1981). In response to a growing national concern over the loss of private pension benefits by employees, Congress enacted the Employee Retirement Income Security Act of 1974 (ERISA). Congress\u27 primary concern was correcting the inadequate vesting and funding requirements which frequently resulted in defeating retirees\u27 post employment expectations. Through ERISA Congress sought to improve the equitable character and soundness of such plans by providing (1) nonforfeitable vested rights, (2) minimum funding requirements, and (3) termination insurance to protect retirees from insolvent employers. An additional goal of Congress was to encourage expansion of private pension plans. Congress was aware of the need to. minimize the cost of maintaining a plan in order to achieve this additional goal. Thus, ERISA is an attempt to eliminate the inequities which plagued the private pension system prior to its enactment, while simultaneously avoiding undue expense to employers. In order to fulfill these objectives without intrusive state interference, Congress included in the Act a general preemption provision. Due to the complexity of the Act and the existence of competing interests, i.e., assuring adequate funding to insure benefits upon retirement versus minimizing the cost to employer to encourage expansion, various disputes have arisen over whether certain reductions in pension benefits constitute. a forfeiture of vested rights in violation of section 1053 of ERISA. The United States Supreme Court resolved such a dispute in Alessi v. Raybestos-Manhattan, Inc. The Alessi Court was confronted with the issue whether a collectively bargained pension plan allowing offsets of pension benefits by the amount of workers’ compensation awards constitutes such a forfeiture; and if not, whether the Act preempts a state worker\u27s compensation law which expressly prohibits such offsets. To determine the permissibility of the offsets it was necessary for the Court to concern itself with the competing interest involved in such a dispute. To permit such an offset may appear inconsistent with Congress\u27 desire to assure a nonforfeiture of retiree\u27s vested rights to his pension benefits, but would be consistent with Congress\u27 desire to reduce the cost to the employer, and thus encourage expansion of the private pension system. Allowing this offset would enable the employer to reduce his cost of maintaining the plan by calculating these payments into it

    Plywood adhesive development.

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    This thesis is primarily a study of two-step plywood adhesives made with varying amounts of phenol, 1, 3, 5 xylenol, resorcin, and formaldehyde. Each resin was evaluated by using it as the adhesive in making plywood. The plywood was then tested for shear strength and wood failure after a four hour boil. Procedures are given for making and testing various straight phenolic resins and resins modified with 1, 3, 5 xylenol or resorcin, or comibinations of both of these accelerating resins. The straight phenolic resins gave boil-proof bonds, but the curing cycle was too long. Those phenolics modified with 1, 3, 5 xylenol gave relatively short cures, but large quantities of this modifier were necessary. Modification of phenolic resins with resorcin gave very rapid cures, but the pot life of these resins was too short. The best compromise was obtained with a combination of 1, 3, 5 xylenol and resorcin as modifying agents for the phenolic. Some of these three-component resin adhesives had sufficient pot life and produced boil-proof bonds during short curing cycles

    Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

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    BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

    Primary Group Contact and Elderly Morale: An Exchange/Power Analysis

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    Using a sample of 757 middle-aged and older residents of the Atlanta metropolitan region, the relationship between primary group contact and morale was investigated. Controlling on sex and dependency, it was found that interaction with children had a negative impact on the morale of dependent, older males. This finding was explained in terms of the power-dependence relationships that exist within the family. It was argued that visits with children and grandchildren are perceived by the dependent older male as a drama in which the ascending generations legitimate their claims to leadership through a gradual process of situation redefinition. One manifest result of having to cede control to his middle-aged offspring is lower morale

    The Q(weak) Experiment: First Direct Measurement of the Weak Charge of the Proton

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    The recently completed Qweak experiment at Jefferson Laboratory made the first direct determination of the proton\u27s weak charge, Q(W)(p), via a measurement of the parity-violating asymmetry in elastic electron-proton scattering at low four-momentum transfer. The Standard Model (SM) makes a precise prediction of Q(W)(p)(SM) = 0.0710 +/- 0.0007. A deviation from this prediction could be an indicator of new physics. A longitudinally polarized electron beam was scattered off a liquid hydrogen target and detected in eight azimuthally symmetric fused silica detectors. The small asymmetry, A(ep) = 279 +/- 35 (stat) +/- 31 (syst) ppb, was measured by observing the difference in rates seen in the detectors when the helicity of the electron beam was rapidly reversed. The measured asymmetry is the most precise and smallest asymmetry ever measured in an ep scattering experiment. Combining this asymmetry with previous parity violating electron scattering (PVES) data, we obtained a value of Q(W)(p)(PVES) = 0.064 +/- 0.012, which agrees well with the SM value. The results of the experiment\u27s commissioning run, which constitutes about 4% of the total data set, are reported here. Analysis of the remainder of the data set is ongoing and will significantly reduce the statistical and systematic uncertainties; several aspects of this analysis will be highlighted

    Optical properties and plasmon resonances of titanium nitride nanostructures

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    We examine the optical properties of nanostructures comprised of titanium nitride, TiN, an electrically conducting intermetallic-like compound. This material can be deposited in the form of durable films by physical vapor deposition. Use of nanosphere templating techniques extends the range of nanostructures that can be produced to include the versatile semi-shell motif. The dielectric properties of TiN1 - x depend upon stoichiometry and are favorable for plasmon resonance phenomena in the mid-visible to near-infrared range of the spectrum and for x≈0. We analyze the optical phenomena operating in such structures using a combination of experiment and simulation and show that semi-shells of TiN exhibit a tunable localized plasmon resonance with light. The material is, however, unsuitable for applications in which a long-distance surface plasmon polariton is desired. © 2010 IOP Publishing Ltd
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