Size-selective concentration and label-free characterization of protein aggregates using a Raman active nanofluidic device

Trace detection and physicochemical characterization of protein aggregates have a large impact in understanding and diagnosing many diseases, such as ageing-related neurodegeneration and systemic amyloidosis, for which the formation of protein aggregates is one of the pathological hallmarks. Here we demonstrate an innovative label-free method for detecting and characterizing small amounts of early stage protein aggregates using a Raman active nanofluidic device. Sub-micrometre channels formed by a novel elastomeric collapse technique enable the separation and concentration of matured protein aggregates from small protein molecules. The Raman enhancement by gold nanoparticle clusters fixed below a micro/nanofluidic junction allows characterization of intrinsic properties of protein aggregates at concentration levels (～fM) much lower than can be done with traditional analytical tools. With our device we show for the first time the concentration dependence of protein aggregation over these low concentration ranges. We expect that our method could facilitate definitive diagnosis and possible therapeutics of diseases at early stages.     

Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR

Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (>10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815A>G, SMN1). Results of a pilot study with SMA patients are presented.     

Empirically supporting school STEM culture—The creation and validation of the STEM Culture Assessment Tool (STEM‐CAT)

School STEM Culture—an aspect of culture within a school community—is defined as the beliefs, values, practices, and resources in STEM fields as perceived by students, parents, teachers, and administrators and counselors within a school. This study validates the STEM Culture Assessment Tool (STEM‐CAT), an instrument intended to advance the use of the School STEM Culture construct within the research community. Internal consistency was determined through the use of Cronbach's alpha and factor analyses, and the instrument was found to be a reliable measure of School STEM Culture. The instrument can be used in future research to quantify School STEM Culture to determine if interventions change the culture of a school to further STEM education.     

On the possible production and detection of coherent low-energy neutrino beams

Seminal experiments are discussed to prove or disprove the possibility of producing and detecting collimated coherent beams of low-energy neutrinos with the assistance of lasers. Expressions are given for the relative probability that a laser-beam-aligned co- or counter-propagating neutrino-antineutrino pair is emitted instead of a laser photon, during stimulated de-excitations of lasable excited states inside a lasing medium. For a neodymium laser this probability is approximately 10^?7. To detect coherent beams of epithermal neutrinos and antineutrinos emitted from a pulsed high-power laser, it is anticipated that resonant non-absorptive stimulated de-excitations of lasing levels by neutrinos can be exploited to register their fly-through in a second near-threshold laser.     

On lattices with M:obius function ±1, 0

We provide simple arguments of a geometric nature to explain why the Möbius functions of certain lattices take only the values –1, 0, 1.Supported in part by NSF Grant MCS83-01867 and by a Sloan Research Fellowship.     

A General Deterministic Treatment of Derivatives in Particle Methods

A unified approach to approximating spatial derivatives in particle methods using integral operators is presented. The approach is an extension of particle strength exchange, originally developed for treating the Laplacian in advection–diffusion problems. Kernels of high order of accuracy are constructed that can be used to approximate derivatives of any degree. A new treatment for computing derivatives near the edge of particle coverage is introduced, using “one-sided” integrals that only look for information where it is available. The use of these integral approximations in wave propagation applications is considered and their error is analyzed in this context using Fourier methods. Finally, simple tests are performed to demonstrate the characteristics of the treatment, including an assessment of the effects of particle dispersion, and their results are discussed.     

Synchrotron fourier transform infrared microspectroscopy: A new tool to monitor the fate of organic contaminants in plants

FTIR microspectroscopy, with synchrotron radiation as a source, was used for the first time to study changes in plant structure induced by organic contaminants. Sunflower (Helianthus annuus L.) plants were grown hydroponically in the presence of benzotriazole. Changes in the plant structure due to uptake, incorporation, and/or transformation of benzotriazole were observed. False color intensity maps of benzotriazole treated secondary root sections showed changes in plant structure, as well as the presence of aromatic CH peaks due to incorporation of benzotriazole within the plant. The presence of the characteristic benzotriazole CH out-of-plane bending mode suggests that the contaminant aromatic ring remains intact upon the uptake by the plant. Simultaneously, the changes in the lignin structure suggest that the plant suffered damage by the uptake of the benzotriazole. Spectral variations between the untreated and benzotriazole treated sunflowers were uncovered using principal components analysis (PCA). PCA also revealed clustering according to the different benzotriazole treatments.     

The empirical behavior of sampling methods for stochastic programming

We investigate the quality of solutions obtained from sample-average approximations to two-stage stochastic linear programs with recourse. We use a recently developed software tool executing on a computational grid to solve many large instances of these problems, allowing us to obtain high-quality solutions and to verify optimality and near-optimality of the computed solutions in various ways. Research supported by the Mathematical, Information, and Computational Sciences Division subprogram of the Office of Advanced Scientific Computing Research, U.S. Department of Energy, under Contract W-31-109-Eng-38, and by the National Science Foundation under Grant 9726385. Research supported by the Mathematical, Information, and Computational Sciences Division subprogram of the Office of Advanced Scientific Computing Research, U.S. Department of Energy, under Contract W-31-109-Eng-38, and by the National Science Foundation under Grant DMS-0073770. Research supported by the Mathematical, Information, and Computational Sciences Division subprogram of the Office of Advanced Scientific Computing Research, U.S. Department of Energy, under Contract W-31-109-Eng-38, and by the National Science Foundation under Grants 9726385 and 0082065.