This PDF file contains the front matter associated with SPIE Proceedings Volume 7312, including the Title Page, Copyright information, Table of Contents, and the Conference Committee listing.

This project uses function-based detection via a fundamental understanding of the genetic markers of AR to distinguish harmful organisms from innocuous ones. This approach circumvents complex analyses to unravel the taxonomic details of 1399 pathogen species, enormously simplifying detection requirements. Laval Hospital's fast permeabilization strategy enables AR revelation in <1hr. Packaging the AR protocols in liquid-processing cartridges and coupling these to our in-house miniature fiber optic flow cell (FOFC) provides first responders with timely information on-site. INO's FOFC platform consists of a specialty optical fiber through which a hole is transversally bored by laser micromachining. The analyte solution is injected into the hole of the fiber and the particles are detected and counted. The advantage with respect to classic free space FC is that alignment occurs in the fabrication process only and complex excitation and collection optics are replaced by optical fibers. Moreover, we use a sheathless configuration which has the advantage of increase the portability of the system, to reduce excess biohazard material and the need for weekly maintenance. In this paper we present the principle of our FOFC along with a, demonstration of the basic capability of the platform for detection of bacillus cereus spores using permeabilized staining.

Nanoplasmonic resonance spectroscopy enhances sensitivity and throughput of conventional SPR detection technique while still suffers with modest molecular specificity. Here we demonstrated a new sensing technique --- nano plasmonic resonance energy transfer (PRET) spectroscopy to detect complex biomolecular activities including conformational change, electron transfer and protein interactions with ultrahigh sensitivity and specificity. Compared to FRET sensing technology, PRET has much stronger optical signal to noise ratio and minimal photobleaching problems. Nano PRET spectroscopic molecular imaging technique can be used in multiplexed label-free cancer biomarker detections and environmental sensing applications.

We describe the development of small molecule-sensitive plasmonics-active fiber-optic nanoprobes suitable for intracellular bioanalysis in single living human cells using surface-enhanced Raman scattering (SERS) detection. The practical utility of SERS-based fiber-optic nanoprobes is illustrated by measurements of intracellular pH in HMEC- 15/hTERT immortalized "normal" human mammary epithelial cells and PC-3 human prostate cancer cells. The results indicate that fiber-optic nanoprobe insertion and interrogation provide a sensitive and selective means to monitor biologically-relevant small molecules at the single cell level.

In this paper the performance of a magnetoelastic biosensor detection system for the simultaneous identification of B. anthracis spores and S. typhimurium was investigated. This system was also designed for selective in-situ detection of B. anthracis spores in the presence a mixed microbial population. The system was composed of a reference sensor (devoid of phage), an E2 phage sensor (coated with phage specific to S. typhimurium) and a JRB7 phage sensor (coated with phage specific to B. anthracis spores). When cells/spores are bound to the specific phage-based ME biosensor surface, only the resonance frequency of the specific sensor changed. The instantaneous response of the multiple sensor system was studied by exposing the system to B. anthracis spores and S. typhimurium suspensions sequentially. A detection limit of 1.6×10³ cfu/mL and 1.1×10³ cfu/m was observed for JRB7 phage sensor and E2 phage sensor, respectively. Additionally, the performance of the system was also evaluated by exposure to a flowing mixture of B. anthracis spores (5×10¹-5×10⁸ cfu/ml) in the presence of B. cereus spores (5×10⁷ cfu/ml). Only the JRB7 phage biosensor responded to the B. anthracis spores. Moreover, there was no appreciable frequency change due to non-specific binding when other microorganisms (spores) were in the mixture. A detection limit of 3×10² cfu/mL was observed for JRB7 phage sensor. The results show that the multi-sensor detection system offers good performance, including good sensitivity, selectivity and rapid detection.

The past decade has seen increased development and subsequent adoption of rapid molecular techniques involving DNA analysis for detection of pathogenic microorganisms, also termed microbial forensics. The continued accumulation of microbial sequence information in genomic databases now better positions the field of high-throughput DNA analysis to proceed in a more manageable fashion. The potential to build off of these databases exists as technology continues to develop, which will enable more rapid, cost effective analyses. This wealth of genetic information, along with new technologies, has the potential to better address some of the current problems and solve the key issues involved in DNA analysis of pathogenic microorganisms. To this end, a high density fiber optic microarray has been employed, housing numerous DNA sequences simultaneously for detection of various pathogenic microorganisms, including Bacillus anthracis, among others. Each organism is analyzed with multiple sequences and can be sub-typed against other closely related organisms. For public health labs, real-time PCR methods have been developed as an initial preliminary screen, but culture and growth are still considered the gold standard. Technologies employing higher throughput than these standard methods are better suited to capitalize on the limitless potential garnered from the sequence information. Microarray analyses are one such format positioned to exploit this potential, and our array platform is reusable, allowing repetitive tests on a single array, providing an increase in throughput and decrease in cost, along with a certainty of detection, down to the individual strain level.

A Severinghaus-type CO₂ sensor was prepared for in-situ downhole CO₂ monitoring during geological carbon sequestration. The sensor consists of: a porous support material; gas-permeable membranes coated onto the inner and outer surface of the support material; a metal-oxide electrode and a reference electrode; and an internal electrolyte composed of equal amounts of bicarbonate source and a halide salt. The sensor was tested by measuring the output potential between the metal-oxide electrode and the reference electrode. The prepared CO₂ sensor demonstrated an excellent linear interrelation between the sensor response potential and the logarithm of the CO₂ concentration at high pressure. A microcontroller-based data acquisition system was designed for downhole CO₂ sensor data logging, which could convert the sensor's analog signal to a digital signal without discharging the sensor during data collection.

This paper reports the development of surface modified ZSM-5 zeolite thin-film coated long-period fiber grating (LPFG) sensors for in situ detection of ammonia (NH3). The sensor was fabricated by growing MFI-type zeolite thin film (i.e. ZSM-5 with Si/Al ratio of 15) on the optical fiber grating by in situ hydrothermal crystallization. The sensor measures ammonia concentration by monitoring the molecular adsorption-induced shift of LPFG resonant wavelength (λ_R) in near infrared (IR) region. Upon loading the analyte (NH3) molecules, the refractive index of the zeolite film changes in the close vicinity of the fiber index where the LPFG has a large response to achieve high sensitivity. High sensitivity of this sensor also comes from the ability of the nanoporous zeolite to effectively concentrate the target molecules by selective adsorption. The sensor was capable of sensitive detection of ammonia at lower ppm level. The zeolite's internal surface was modified by ion exchange with NH₄+ followed by thermal treatments to enhance the surface acidity. The acidic ZSM-5 (i.e. H-ZSM-5) film exhibited higher sensitivity and improved selectivity for NH₃.

This paper reports the development of a sensor based on surface-enhanced Raman scattering (SERS) for analyses in seawater. Polycyclic aromatic hydrocarbons (PAHs) are targeted by these sensors and their detection in situ summons up chemical synthesis and optical development. Firstly, a relevant synthesis of SERS active substrates based on gold nanostructures is presented. Different kinds of substrates have been synthesized under variable experimental conditions to modify some parameters such as i) gold shape, size and distribution and such as ii) chemical functionalization: (i) gold nanoparticles were prepared either by chemical reduction of HAuCl₄ or by physical deposition. (ii) Substrates were functionalized by hydrophobic films to allow nonpolar molecules pre-concentration. Low concentration from ppb to ppm of PAHs were detected with a Raman microscope designed for lab experiments. Sensors exhibit strong enhancement of Raman scattering from molecules adsorbed on the films. Spectra were recorded for two PAHs (naphthalene and pyrene) in artificial sea-water with limits of detection of 10ppb for both with a short integration time (10s) and a low incident laser power (~0.1mW). Active substrate surface morphology was characterized with scanning electron microscopy (SEM) measurements. Secondly, an home-made in situ Raman spectrometer was developed and has been connected to a micro-fluidic system. This system was designed to host SERS-active sensors in order to ensure measurements with a flow cell. This original configuration of in situ Raman spectroscopy was then achieved. Such a device is now ready to use to confirm the PAH detection at ppb levels during the offshore experiments thanks to SERS sensors.

The Digital Array Gas Radiometer (DAGR) concept is based on traditional and reliable Gas Filter Correlation Radiometry (GFCR) for remote trace gas detection and monitoring. GFCR sensors have been successful in many infrared remote sensing applications. Historically however, solar backscatter measurements have not been as successful because instrument designs have been susceptible to natural variations in surface albedo, which induce clutter and degrade the sensitivity. DAGR overcomes this limitation with several key innovations. First, a pupil imaging system scrambles the received light, removing nearly all spatial clutter and permitting a small calibration source to be easily inserted. Then, by using focal plane arrays rather than single detectors to collect the light, dramatic advances in dynamic range can be achieved. Finally, when used with the calibration source, data processing approaches can further mitigate detector non-uniformity effects. DAGR sensors can be made as small as digital cameras and are well suited for downlooking detection of gases in the boundary layer, where solar backscatter measurements are needed to overcome the lack of thermal contrast in the IR. Easily integrated into a satellite platform, a space-based DAGR would provide near-global sensing of climatically important species such as such as CO, CH₄, and N₂O. Aircraft and UAV measurements with a DAGR could be used to monitor agricultural and industrial emissions. Ground-based or portable DAGRs could augment early warning systems for chemical weapons or toxic materials. Finally, planetary science applications include detection and mapping of biomarkers such as CH₄ in the Martian atmosphere.

A novel compact wavelength stabilized diode laser system at 671 nm on a micro-optical bench as a light source for shifted excitation Raman difference spectroscopy (SERDS) is presented. Two broad-area gain media in separate laser cavities are used with two reflection Bragg-gratings with slightly different center wavelengths. A constant wavenumber difference of 13 cm^-1 ± 1.3 cm^-1 together with a spectral width below 100 pm is obtained up to output powers of 250 mW. The suitability of this light source for SERDS is demonstrated using Raman spectra of ethanol with increasing concentrations of cresyl violet as fluorescent contaminant.

A hand-held Raman sensor head was developed for the in-situ characterization of meat quality. As light source, a microsystem based external cavity diode laser module (ECDL) emitting at 671 nm was integrated in the sensor head and attached to a miniaturized optical bench which contains lens optics for excitation and signal collection as well as a Raman filter stage for Rayleigh rejection. The signal is transported with an optical fiber to the detection unit which was in the initial phase a laboratory spectrometer with CCD detector. All elements of the ECDL are aligned on a micro optical bench with 13 x 4 mm² footprint. The wavelength stability is provided by a reflection Bragg grating and the laser has an optical power of up to 200 mW. However, for the Raman measurements of meat only 35 mW are needed to obtain Raman spectra within 1 - 5 seconds. Short measuring times are essential for the hand-held device. The laser and the sensor head are characterized in terms of stability and performance for in-situ Raman investigations. The function is demonstrated in a series of measurements with raw and packaged pork meat as samples. The suitability of the Raman sensor head for the quality control of meat and other products will be discussed.

We created novel SERS substrates by metalizing (Ag or Au) Si nanograss fabricated by a Bosch process on single crystalline silicon. We demonstrated that the fabricated SERS substrates are highly sensitive. The sensitivity of the substrates depends on the target molecules, the excitation laser wavelengths and the metal coating on the silicon nanograss. With the optimal excitation condition at 633 nm, an enhancement factor of 6 × 10⁷ can be achieved for trans- 1,2-bis(4-pyridyl)-ethylene (BPE) molecules on the gold coated silicon nanograss substrate.

The detection of flame retardants is critical for the recycling of polymers. To investigate the possibility of reliable purefraction sorting, a sample set containing a wide range of relevant polymers and polymer blends containing various practically relevant flame-retardant additives was produced and investigated. NIR point spectra were acquired with an FTIR laboratory spectrometer and hyper-spectral NIR images were obtained using a spectrograph-based hyper-spectral imaging system. The laboratory spectrometer measurements were used to assign spectral features to the corresponding chemical compounds and derive a chemometric model that can be used to detect flame-retardant additives. The hyperspectral NIR images were used to adapt the chemometric model to the spectral features present in the hyper-spectral image data for the real-time detection.

The light scattering and absorption properties of gold nanoparticles (GNPs) can be utilised for the detection of DNA. Binding of molecules to the GNP influences the local refractive index. The increase in refractive index can be measured as proportional red-shift of the GNPs extinction maximum; therefore GNPs are suitable for use as nanoparticle chemical sensors. Utilizing this method it is possible to detect DNA in naturally occurring quantities. In bulk measurements we have shown a red-shift of 7 nm of the absorption maximum (λ_max) upon binding of thiolated ssDNA. Subsequently, we were able to follow the interaction between two sets of GNPs functionalised with complementary strands. Randomly immobilised GNPs were visualised with an inverted darkfield microscope. The use of a colour camera enables us to analyse the colour change of each individual particle in the field of view. A change of λ_max of 1 nm can be detected by the colour camera, which corresponds to ~100 20mer ssDNA molecules. For the detection of a single DNA binding events we are developing an assay for DNA detection, utilizing a second set of GNPs. The interaction of two GNPs within a range of 2.5 times the radius of each other results in a shift of ~7 nm in λ_max for the presence of one DNA strand. This increased shift makes the method not only more accurate but also easier to detect.

Remote sensing of enemy installations or their movements by trace gas detection is a critical but challenging military objective. Open path measurements over ranges of a few meters to many kilometers with sensitivity in the parts per million or billion regime are crucial in anticipating the presence of a threat. Previous approaches to detect ground level chemical plumes, explosive constituents, or combustion have relied on low-resolution, short range Fourier transform infrared spectrometer (FTIR), or low-sensitivity near-infrared differential optical absorption spectroscopy (DOAS). As mid-infrared quantum cascade laser (QCL) sources have improved in cost and performance, systems based on QCL's that can be tailored to monitor multiple chemical species in real time are becoming a viable alternative. We present the design of a portable, high-resolution, multi-kilometer open path trace gas sensor based on QCL technology. Using a tunable (1045-1047cm-1) QCL, a modeled atmosphere and link-budget analysis with commercial component specifications, we show that with this approach, accuracy in parts per billion ozone or ammonia can be obtained in seconds at path lengths up to 10 km. We have assembled an open-path QCL sensor based on this theoretical approach at City College of New York, and we present preliminary results demonstrating the potential of QCLs in open-path sensing applications.

The present security environment has created a need for robust, sensitive, portable gas-phase chemical sensors. The ready availability of high performance quantum cascade lasers, which can operate at ambient temperatures with only thermoelectric cooling, has made the possibility of such sensors quite realistic. A compact, sensitive, cost-effective photo-acoustic sensor capable of sub-part-per-million sensitivity is described. The sensor can be entirely selfcontained in a small volume weighing only a few pounds. The quantum cascade laser is enclosed in a sealed package incorporating a collimating lens and thermoelectric cooler. The package sits on an external thermoelectric cooler. Both the laser and thermoelectric coolers are driven by a self-contained power supply and controller specifically designed for the purpose. The photo-acoustic gas cell contains input and output ports and anti-reflection coated optical windows. Details of the sensor's configuration and performance will be described as it relates to explosive detection using thermal fragmentation.

Trace detection of toxic industrial compounds has been investigated with the help of a laser ion mobility spectrometer (LIMS). The LIMS was equipped with a tuneable UV laser source for enabling two-photon ionization of the analyte gases and an ion drift tube for the measurement of the ion mobility. Different aromatic and aliphatic hydrocarbons as well as amines were investigated. We find that the first class of molecules can be well ionized due to the delocalization of their valence electron shells and the second due to the presence of non-bonding electrons in lone-pair orbitals. Selectivity of detection is attained on the basis of molecule-specific photo-ionization and drift time spectra. Ion currents were found to scale linearly with the substance concentration over several orders of magnitude down to the detection limits in the ppt range. As besides toxic industrial compounds, similar electron configurations also occur in illicit drugs, toxins and pharmaceutical substances, LIMS can be applied in a variety of fields ranging from environmental analysis, air pollution monitoring, drug detection and chemical process monitoring.

A better understanding of the relationship between malaria epidemics, satellite data and the climatic anomalies could help mitigate the world-wide increase in incidence of the mosquitotransmitted diseases. This paper analyzes correlation between malaria cases and vegetation health (VH) Indices (Vegetation Condition Index (VCI) and Temperature Condition Index (TCI)) computed for each week over a period of 14 years (1992-2005). Following the results of correlation analysis the principal components regression (PCR) method was performed on weather components (TCI, VCI) of satellite data and climate variability during each of the two annual malaria seasons to construct a model to predict malaria as a function of the VH. A statistically significant relation was found between malaria cases and TCI during the month of June-July and September-October. Furthermore the simulated results found from PCR model were compared with observed malaria statistics showing that the error of the estimates of malaria is 5%.

Optical Autocovariance Wind Lidar (OAWL) is a new direct-detection interferometric Doppler lidar approach that inherently enables simultaneous acquisition of multiple-wavelength High Spectral Resolution Lidar calibrated aerosol profiles (OA-HSRL). Unlike other coherent and direct detection Doppler systems, the receiver is self referencing; no specific optical frequency lock is required between the receiver and transmitter. This property facilitates frequency-agile modalities such as DIAL. Because UV laser wavelengths are accommodated, a single transmitter can simultaneously support winds, Raman, fluorescence, DIAL, and HSRL receiver channels, each sampling identical spatial and temporal volumes. LOS species flux measurements are acquired without the usual spatial and temporal sampling errors (or cost, volume, mass, power, and logistical issues) incurred by separate lidar systems, or lidars in combination with other remote or in-situ sensors. A proof of concept (POC) OAWL system has been built and demonstrated at Ball, and OAHSRL POC is in progress. A robust multi-wavelength, field-widened OAWL/OA-HSRL system is under development with planned airborne demonstration from a WB-57 in late 2010. Detailed radiometric and dynamic models have been developed to predict performance in both airborne and space borne scenarios. OA theory, development, demonstration status, advantages, limitations, space and airborne performance, and combined measurement synergies are discussed.

We have recently implemented a dual-band optical imaging scheme for offshore stand-off oil spill monitoring using visible and long-wave-infrared (LWIR) cameras. Based on differences in intrinsic optical properties, the visible cameral provides daytime images and monitoring capability as if observed by human personnel. The LWIR camera provides both day and night monitoring capabilities based on additional thermal and emissivity contrasts. We have demonstrated the feasibility of such a scheme at various testing sites and under various ambient conditions. We have developed an analytical model to explain observed oil/water contrast. We also discuss limitations in the dual-band scheme using detection boundary analysis and experimental examples. We believe this scheme can provide robust and cost-effective offshore stand-off oil spill monitoring.

The financial losses and destruction of crops due to insect infestation in the United States are estimated by the USDA to exceed 20 billion dollars annually. Much of these losses could be avoided by having a sensor that could effectively identify the early stages of insect infestation. However, traditional detection methods are time consuming, require trained personnel, and are not sufficient for early detection. Several previous research studies showed that emitting organic volatile compounds is a defensive mechanism activated by some plant species after being attacked by herbivores and parasites. Corn, cotton, pine, Brussels sprouts when attacked by Beet army worm, spider mites, bark beetles and caterpillars respectively, emits different blends of plant volatiles including γ-terpinene, α-pinene, p-cymene, farnesene, limonene and cis-hexenyl acetate, with a concentration of about 50 ppm. Therefore, monitoring for these volatile compounds may enable on-site early detection of insect infestations. In this study, a chemical resistor sensor to detect plant volatiles was designed and fabricated. The sensor platform consists of micro electronically fabricated interdigitated electrodes. On to this platform, a poly3-hexylthiophene (P3HT) thin film was deposited, using a spin coater at 8000 rpm for 30 seconds. The sensor was tested and found to be sensitive to a variety of plant volatiles, including γ-terpinene, α-pinene, p-cymene, farnesene, limonene and cis-hexenyl acetate at room temperature. These vapors interacted with the P3HT film causing an increase in the resistance of the sensor by more than one order of magnitude

Self-absorption is used in laser induced breakdown spectroscopy to obtain quantitative analytical information. In this approach two plasmas are generated with a laser pulse that is split into two beams separated by a few millimeters and incident on the target material. One of the beams generates plasma that acts as the light source analogous to that used in standard atomic absorption spectroscopy, while the other generates plasma that is used as the analyte. The lines emitted from the light source plasma are absorbed while passing through the analyte plasma. This technique was applied to Cu- Zn samples with different Cu/Zn concentrations. The results show that the strongly self absorbed Cu 324 nm and 327 nm lines can be effectively used to probe the Cu concentration, while the Cu 330 nm line does not show strong selfabsorption.

A compact remote Raman spectroscopy system was developed at NASA Langley Research center and was previously demonstrated for its ability to identify chemical composition of various rocks and minerals. In this study, the Raman sensor was utilized to perform time-resolved Raman studies of various samples such as minerals and rocks, Azalea leaves, and a few fossil samples. The Raman sensor utilizes a pulsed 532 nm Nd:YAG laser as excitation source, a 4-inch telescope to collect the Raman-scattered signal from a sample several meters away, a spectrograph equipped with a holographic grating, and a gated intensified CCD (ICCD) camera system. Time resolved Raman measurements were carried out by varying the gate delay with fixed short gate width of the ICCD camera, allowing measurement of both Raman signals and fluorescence signals. Rocks and mineral samples were characterized, including marble, which contains CaCO₃. Analysis of the results reveals the short (~10^-13 s) lifetime of the Raman process and shows that the Raman spectra of some mineral samples contain fluorescence emission due to organic impurities. Also analyzed were a green (pristine) and a yellow (decayed) sample of Gardenia leaves. It was observed that the fluorescence signals from the green and yellow leaf samples showed stronger signals compared to the Raman lines. It was also observed that the fluorescence of the green leaf was more intense and had a shorter lifetime than that of the yellow leaf. For the fossil samples, Raman shifted lines could not be observed due to the presence of very strong short-lived fluorescence.