Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping

Mass spectrometry proteomics typically relies upon analyzing outcomes of single analyses; however, comparing raw data across multiple experiments should enhance both peptide/protein identification and quantitation. In the absence of convincing tandem MS identifications, comparing peptide quantities between experiments (or fractions) requires the chromatographic alignment of MS signals. An extension of dynamic time warping (DTW), termed ordered bijective interpolated warping (OBI-Warp), is presented and used to align a variety of electrospray ionization liquid chromatography mass spectrometry (ESI-LC-MS) proteomics data sets. An algorithm to produce a bijective (one-to-one) function from DTW output is coupled with piecewise cubic hermite interpolation to produce a smooth warping function. Data sets were chosen to represent a broad selection of ESI-LC-MS alignment cases. High confidence, overlapping tandem mass spectra are used as standards to optimize and compare alignment parameters. We determine that Pearson's correlation coefficient as a measure of spectra similarity outperforms covariance, dot product, and Euclidean distance in its ability to produce correct alignments with optimal and suboptimal alignment parameters. We demonstrate the importance of penalizing gaps for best alignments. Using optimized parameters, we show that OBI-Warp produces alignments consistent with time standards across these data sets. The source and executables are released under MIT style license at http://obi-warp.sourceforge.net/.     

Millimeter-wave antireflection coating for cryogenic silicon lenses

We have developed and tested an antireflection (AR) coating method for silicon lenses used at cryogenic temperatures and millimeter wavelengths. Our particular application is a measurement of the cosmic microwave background. The coating consists of machined pieces of Cirlex glued to the silicon. The measured reflection from an AR-coated flat piece is less than 1.5% at the design wavelength. The coating has been applied to flats and lenses and has survived multiple thermal cycles from 300 to 4 K. We present the manufacturing method, the material properties, the tests performed, and estimates of the loss that can be achieved in practical lenses.     

Chemical loading into surface water along a hydrological, biogeochemical, and land use gradient: a holistic watershed approach

Identifying the sources and impacts of organic and inorganic contaminants at the watershed scale is a complex challenge because of the multitude of processes occurring in time and space. Investigation of geochemical transformations requires a systematic evaluation of hydrologic, landscape, and anthropogenic factors. The 1160 km2 Boulder Creek Watershed in the Colorado Front Range encompasses a gradient of geology, ecotypes, climate, and urbanization. Streamflow originates primarily as snowmelt and shows substantial annual variation. Water samples were collected along a 70-km transect during spring-runoff and base-flow conditions, and analyzed for major elements, trace elements, bulk organics, organic wastewater contaminants (OWCs), and pesticides. Major-element and trace-element concentrations were low in the headwaters, increased through the urban corridor, and had a step increase downstream from the first major wastewater treatment plant (WWTP). Boron, gadolinium, and lithium were useful inorganic tracers of anthropogenic inputs. Effluent from the WWTP accounted for as much as 75% of the flow in Boulder Creek and was the largest chemical input. Under both hydrological conditions, OWCs and pesticides were detected in Boulder Creek downstream from the WWTP outfall as well as in the headwater region, and loads of anthropogenic-derived contaminants increased as basin population density increased. This report documents a suite of potential endocrine-disrupting chemicals in a reach of stream with native fish populations showing indication of endocrine disruption.     

Reduced inorganic sulfur speciation in drain sediments from acid sulfate soil landscapes

We examined processes regulating reduced inorganic sulfur (RIS) speciation in drain sediments from coastal acid sulfate soil (ASS) landscapes. Pore water sulfide was undetectable or present at low levels (0.6-18.8 microM), consistent with FeS(s) precipitation in the presence of high concentrations of Fe2+ (generally >2 mM). Acid-volatile sulfide (AVS), with concentrations up to 1019 micromol g(-1), comprised a major proportion of RIS. The AVS to pyrite-S ratios were up to 2.6 in sediment profiles containing abundant reactive Fe (up to approximately 4000 micromol g(-1)). Such high AVS:pyrite-S ratios are indicative of inefficient conversion of FeS(s) to pyrite. This may be due to low pore water sulfide levels causing slow rates of pyrite formation via the polysulfide and H2S oxidation pathways. Overall, RIS speciation in ASS-associated drain sediments is unique and is largely regulated by abundant reactive Fe.     

Calculation and uses of mean sediment quality guideline quotients: a critical review

Fine-grained sediments contaminated with complex mixtures of organic and inorganic chemical contaminants can be toxic in laboratory tests and/or cause adverse impacts to resident benthic communities. Effects-based, sediment quality guidelines (SQGs) have been developed over the past 20 years to aid in the interpretation of the relationships between chemical contamination and measures of adverse biological effects. Mean sediment quality guideline quotients (mSQGQ) can be calculated by dividing the concentrations of chemicals in sediments by their respective SQGs and calculating the mean of the quotients for the individual chemicals. The resulting index provides a method of accounting for both the presence and the concentrations of multiple chemicals in sediments relative to their effects-based guidelines. Analyses of considerable amounts of data demonstrated that both the incidence and magnitude of toxicity in laboratory tests and the incidence of impairment to benthic communities increases incrementally with increasing mSQGQs. Such concentration/response relationships provide a basis for estimating toxicological risks to sediment-dwelling organisms associated with exposure to contaminated sediments with a known degree of accuracy. This sediment quality assessment tool has been used in numerous surveys and studies since 1994. Nevertheless, mean SQGQs have some important limitations and underlying assumptions that should be understood by sediment quality assessors. This paper provides an overview of the derivation methods and some of the principal advantages, assumptions, and limitations in the use of this sediment assessmenttool. Ideally, mean SQGQs should be included with other measures including results of toxicity tests and benthic community surveys to provide a weight of evidence when assessing the relative quality of contaminated sediments.     

Viewing angle enhancement for two- and three-dimensional holographic displays with random superresolution phase masks

Holographic displays employing binary phase modulation have been demonstrated to be attractive on the grounds of efficiency and miniaturization, and they offer a plausible approach to two-dimensional (2D) and three-dimensional (3D) image projection and display. A novel algorithm--one-step phase retrieval--and corresponding hardware architecture have recently been proposed, providing the performance required for real-time holographic display. However, since viewing angle varies inversely with pixel size, very small display pixels are required to achieve a wide field of view. This is particularly problematic for 3D displays, as the requirement for a large display with small pixels has hitherto necessitated an unachievably large electrical bandwidth. We present a novel approach, utilizing fixed random pixelated quaternary phase masks of greater resolution than the displayed hologram, to dramatically increase the viewing angle for 2D and 3D holographic displays without incurring a bandwidth penalty or significantly degrading image quality. Furthermore, an algorithm is presented to generate holograms accounting for the presence of such a phase mask, so that only one mask is required.     

Noninvasive Raman spectroscopy of human tissue in vivo

We report the first transcutaneous Raman spectrum of human bone in vivo obtained at skin-safe laser illumination levels. The spectrum of thumb distal phalanx was obtained using spatially offset Raman spectroscopy (SORS), which provides chemically specific information on deep layers of human tissue, well beyond the reach of existing comparative approaches. The spectroscopy is based on collecting Raman spectra away from the point of laser illumination using concentric rings of optical fibers. As a generic analytical tool this approach paves the way for a range of uses including disease diagnosis, noninvasive probing of pharmaceutical products, biofilms, catalysts, paints, and in dermatological applications.     

Direct writing of metal nanoparticle films inside sealed microfluidic channels

Herein we demonstrate the ability to pattern Ag nanoparticle films of arbitrary geometry inside sealed PDMS/TiO2/glass microfluidic devices. The technique can be employed with aqueous solutions at room temperature under mild conditions. A 6 nm TiO2 film is first deposited onto a planar Pyrex or silica substrate, which is subsequently bonded to a PDMS mold. UV light is then exposed through the device to reduce Ag+ from an aqueous solution to create a monolayer-thick film of Ag nanoparticles. We demonstrate that this on-chip deposition method can be exploited in a parallel fashion to synthesize nanoparticles of varying size by independently controlling the solution conditions in each microchannel in which the film is formed. The film morphology was checked by atomic force microscopy, and the results showed that the size of the nanoparticles was sensitive to solution pH. Additionally, we illustrate the ability to biofunctionalize these films with ligands for protein capture. The results indicated that this could be done with good discrimination between addressed locations and background. The technique appears to be quite general, and films of Pd, Cu, and Au could also be patterned.