In situ measurement of dissolved inorganic carbon speciation in natural waters, pH, pC02, TA, & TC02, Honolulu, Hawaii, February 16-18, 2005: workshop proceedings

The Alliance for Coastal Technology (ACT) convened a workshop on the in situ measurement of dissolved inorganic carbon species in natural waters in Honolulu, Hawaii, on February 16, 17, and 18, 2005. The workshop was designed to summarize existing technologies for measuring the abundance and speciation of dissolved inorganic carbon and to make strategic recommendations for future development and application of these technologies to coastal research and management. The workshop was not focused on any specific technology, however, most of the attention of the workshop was on in situ pC02 sensors given their recent development and use on moorings for the measurement of global carbon fluxes. In addition, the problems and limitations arising from the long-term deployment of systems designed for the measurement of pH, total dissolved inorganic carbon (DIC), and total alkalinity (TA) were discussed. Participants included researchers involved in carbon biogeochemistry, industry representatives, and coastal resource managers. The primary questions asked during the workshop were: I. What are the major impediments to transform presently used shipboard pC02 measurement systems for use on cost-eficient moorings? 2. What are the major technical hurdles for the in situ measurement of TA and DIC? 3. What specific information do we need to coordinate efforts for proof of concept' testing of existing and new technologies, inter-calibration of those technologies, better software development, and more precise knowledge quantzjjing the geochemistry of dissolved inoeanic carbon species in order to develop an observing system for dissolved inorganic carbon? Based on the discussion resulting from these three questions, the following statements were made: Statement No. 1 Cost-effective, self-contained technologies for making long-term, accurate measurements of the partial pressure of C02 gas in water already exist and at present are ready for deployment on moorings in coastal observing systems. Statement No. 2 Cost-effective, self-contained systems for the measurement of pH, TA, and DIC are still needed to both fully define the carbonate chemistry of coastal waters and the fluxes of carbon between major biogeochemical compartments (e.g., air-sea, shelf-slope, water column-sediment, etc.). (pdf contains 23 pages)

Annual westward propagating anomalies near 26 degrees N and eddy generation south of the Canary Islands: remote sensing (altimeter/SeaWIFS) and in situ measurement

Seasonal changes in altimeter data are derived for the North Atlantic Ocean. Altimeter data are then used to examine annually propagating structure along 26 degree N. By averaging the altimeter data into monthly values or by Fourier analysis, a positive anomaly can be followed from 17 degree W to similar to 50 degree W along similar to 26 degree N. The methods give a westward travel speed of 1 degree of longitude a month and a half-life of one year for the average decaying structure. At similar to 50 degree W 26 degree N, the average structure is about 2.8 years old with an elevation signal of similar to 1 cm, having gravelled similar to 3300 km westward. The mean positive anomaly results from the formation of anticyclonic eddies which are generally formed annually south of the Canary Islands by late summer and which then travel westward near 26 degree N. Individual eddy structure along 26 degree N is examined and related to in situ measurements and anomalies in the annual seasonal concentration cycle of SeaWiFS chlorophyll-a.

Ocean structure and climate (Eastern North Atlantic): in situ measurement and remote sensing

Structure and climate of the east North Atlantic are appraised within a framework of in situ measurement and altimeter remote sensing from 0 degree - 60 degree N. Long zonal expendable bathythermograph /conductivity-temperature-depth probe sections show repeating internal structure in the North Atlantic Ocean. Drogued buoys and subsurface floats give westward speeds for eddies and wavelike structure. Records from longterm current meter deployments give the periodicity of the repeating structure. Eddy and wave characteristics of period, size or wavelength, westward propagation speed, and mean currents are derived at 20 degree N, 26 degree N, 32.5 degree N, 36 degree N and 48 degree N from in situ measurements in the Atlantic Ocean. It is shown that ocean wave and eddy-like features measured in situ correlate with altimeter structure. Interior ocean wave crests or cold dome-like temperature structures are cyclonic and have negative surface altimeter anomalies; mesoscale internal wave troughs or warm structures are anticyclonic and have positive surface height anomalies. Along the Eastern Boundary, flows and temperature climate are examined in terms of sla and North Atlantic Oscillation (NAO) Index. Longterm changes in ocean climate and circulation are derived from sla data. It is shown that longterm changes from 1992 to 2002 in the North Atlantic Current and the Subtropical Gyre transport determined from sla data correlate with winter NAO Index such that maximum flow conditions occurred in 1995 and 2000. Minimum circulation conditions occurred between 1996-1998. Years of extreme negative winter NAO Index result in enhanced poleward flow along the Eastern Boundary and anomalous winter warming along the West European Continental Slope as was measured in 1990, 1996, 1998 and 2001.

In situ measurement of UHF wearable antenna radiation efficiency using a reverberation chamber

The radiation efficiency and resonance frequency of five compact antennas worn by nine individual test subjects was measured at 2.45 GHz in a reverberation chamber. The results show that, despite significant differences in body mass, wearable antenna radiation efficiency had a standard deviation less than 0.6 dB and the resonance frequency shift was less than 1% between test subjects. Variability in the radiation efficiency and resonance frequency shift between antennas was largely dependant on body tissue coupling which is related to both antenna geometry and radiation characteristics. The reverberation chamber measurements were validated using a synthetic tissue phantom and compared with results obtained in a spherical near field chamber and finite-difference time-domain (FDTD) simulation.

In-situ measurement and characterization of cloud particles using digital in-line holography

Satellite measurement validations, climate models, atmospheric radiative transfer models and cloud models, all depend on accurate measurements of cloud particle size distributions, number densities, spatial distributions, and other parameters relevant to cloud microphysical processes. And many airborne instruments designed to measure size distributions and concentrations of cloud particles have large uncertainties in measuring number densities and size distributions of small ice crystals. HOLODEC (Holographic Detector for Clouds) is a new instrument that does not have many of these uncertainties and makes possible measurements that other probes have never made. The advantages of HOLODEC are inherent to the holographic method. In this dissertation, I describe HOLODEC, its in-situ measurements of cloud particles, and the results of its test flights. I present a hologram reconstruction algorithm that has a sample spacing that does not vary with reconstruction distance. This reconstruction algorithm accurately reconstructs the field to all distances inside a typical holographic measurement volume as proven by comparison with analytical solutions to the Huygens-Fresnel diffraction integral. It is fast to compute, and has diffraction limited resolution. Further, described herein is an algorithm that can find the position along the optical axis of small particles as well as large complex-shaped particles. I explain an implementation of these algorithms that is an efficient, robust, automated program that allows us to process holograms on a computer cluster in a reasonable time. I show size distributions and number densities of cloud particles, and show that they are within the uncertainty of independent measurements made with another measurement method. The feasibility of another cloud particle instrument that has advantages over new standard instruments is proven. These advantages include a unique ability to detect shattered particles using three-dimensional positions, and a sample volume size that does not vary with particle size or airspeed. It also is able to yield two-dimensional particle profiles using the same measurements.

Development of an In Situ Measurement Device for Obtaining Material Thermal Properties

This thesis presents a methodology for measuring thermal properties in situ, with a special focus on obtaining properties of layered stack-ups commonly used in armored vehicle components. The technique involves attaching a thermal source to the surface of a component, measuring the heat flux transferred between the source and the component, and measuring the surface temperature response. The material properties of the component can subsequently be determined from measurement of the transient heat flux and temperature response at the surface alone. Experiments involving multilayered specimens show that the surface temperature response to a sinusoidal heat flux forcing function is also sinusoidal. A frequency domain analysis shows that sinusoidal thermal excitation produces a gain and phase shift behavior typical of linear systems. Additionally, this analysis shows that the material properties of sub-surface layers affect the frequency response function at the surface of a particular stack-up. The methodology involves coupling a thermal simulation tool with an optimization algorithm to determine the material properties from temperature and heat flux measurement data. Use of a sinusoidal forcing function not only provides a mechanism to perform the frequency domain analysis described above, but sinusoids also have the practical benefit of reducing the need for instrumentation of the backside of the component. Heat losses can be minimized by alternately injecting and extracting heat on the front surface, as long as sufficiently high frequencies are used.

In-situ measurement and the reconstruction in 3D of femtosecond inscription induced complex permittivity modification in glass

We demonstrate a new approach to in-situ measurement of femtosecond laser pulse induced changes in glass enabling the reconstruction in 3D of the induced complex permittivity modification. The technique can be used to provide single shot and time resolved quantitative measurements with a micron scale spatial resolution.

Measurement of atmospheric formaldehyde using a drop collector and in-situ colorimetry

A sensitive and affordable approach is described for the in-situ measurement of ambient formaldehyde. Air is sampled around a 100 microliter aqueous drop containing 3-methyl-2-benzothiazoline hydrazone. After a desired period of sampling (typ. 5 min) and a waiting period of 10 min for the reaction to be completed, a second reagent (FeCl3) is added to the drop by means of a conjoined conduit. A blue product is formed and is read after an additional 10 min of reaction by a fiber-optic/light emitting diode based photodetector. A fresh drop is then formed and the process begins anew. As demonstrated here, the limit of detection is similar to 6.25 mu g m(-3) HCHO but can be significantly improved by using longer sampling times and a sampling rate higher than 100 mi min(-1) used in most of this work. This is the first example of a chromogenic drop sensor that utilizes sequential reagent addition.

Towards in situ Single Cell Systems Biology

Systems-level studies of biological systems rely on observations taken at a resolution lower than the essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled measurements of the transcriptomes in single cells excised from their environment, but it remains a daunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In this thesis I develop methods for the routine, quantitative in situ measurement of gene expression using fluorescence microscopy.

The number of molecular species that can be measured simultaneously by fluorescence microscopy is limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally limited to the simultaneous measurement of only five labeled biomolecules at a time. The two methods described in this thesis, super-resolution barcoding and temporal barcoding, represent strategies for overcoming this limitation to monitor expression of many genes in a single cell. Super-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial labeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual mRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically increases the optical space in a cell, allowing a large numbers of barcodes to be visualized simultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium stress response. The second method, sequential barcoding, reads out a temporal barcode through multiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of sequential barcoding increases exponentially with the number of rounds of hybridization, allowing over a hundred genes to be profiled in only a few rounds of hybridization.

The utility of sequential barcoding was further demonstrated by adapting this method to study gene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of auto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An amplified single molecule detection technology, smHCR (single molecule hairpin chain reaction), was developed to allow for the quantification of mRNA in tissue. This technology is demonstrated in combination with light sheet microscopy and background reducing tissue clearing technology, enabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact mammalian tissue.

The methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed transcriptional observations in any tissue of interest. These technologies will serve as a general platform for future transcriptomic studies of complex tissues.