Engineering Commons^™

Improved Sensitivity To Fluorescence For Cancer Detection In Wide-Field Image-Guided Neurosurgery, Michael Jermyn, Yoann Gosselin, Pablo A. Valdes, Mira Sibai, Kolbein Kolste

Dartmouth Scholarship

In glioma surgery, Protoporphyrin IX (PpIX) fluorescence may identify residual tumor that could be resected while minimizing damage to normal brain. We demonstrate that improved sensitivity for wide-field spectroscopic fluorescence imaging is achieved with minimal disruption to the neurosurgical workflow using an electron-multiplying charge-coupled device (EMCCD) relative to a state-of-the-art CMOS system. In phantom experiments the EMCCD system can detect at least two orders-of-magnitude lower PpIX. Ex vivo tissue imaging on a rat glioma model demonstrates improved fluorescence contrast compared with neurosurgical fluorescence microscope technology, and the fluorescence detection is confirmed with measurements from a clinically-validated spectroscopic probe. Greater PpIX …

Calibration And Optimization Of 3d Digital Breast Tomosynthesis Guided Near Infrared Spectral Tomography, Kelly E. Michaelsen, Venkataramanan Krishnaswamy, Linxi Shi, Srinivasan Vedantham, Steven Poplack, Andrew Karellas, Brian Pogue, Keith Paulsen

Dartmouth Scholarship

Calibration of a three-dimensional multimodal digital breast tomosynthesis (DBT) x-ray and non-fiber based near infrared spectral tomography (NIRST) system is challenging but essential for clinical studies. Phantom imaging results yielded linear contrast recovery of total hemoglobin (HbT) concentration for cylindrical inclusions of 15 mm, 10 mm and 7 mm with a 3.5% decrease in the HbT estimate for each 1 cm increase in inclusion depth. A clinical exam of a patient's breast containing both benign and malignant lesions was successfully imaged, with greater HbT was found in the malignancy relative to the benign abnormality and fibroglandular regions (11 μM vs. …

Physiological Roles Of Pyruvate Ferredoxin Oxidoreductase And Pyruvate Formate-Lyase In Thermoanaerobacterium Saccharolyticum Jw/Sl-Ys485, Jilai Zhou, Daniel G. Olson, Anthony A. Lanahan, Liang Tian, Sean Jean-Loup Murphy, Jonathan Lo, Lee R. Lynd

Dartmouth Scholarship

Background:

Thermoanaerobacter saccharolyticum is a thermophilic microorganism that has been engineered to produce ethanol at high titer (30–70 g/L) and greater than 90 % theoretical yield. However, few genes involved in pyruvate to ethanol production pathway have been unambiguously identified. In T. saccharolyticum, the products of six putative pfor gene clusters and one pfl gene may be responsible for the conversion of pyruvate to acetyl-CoA. To gain insights into the physiological roles of PFOR and PFL, we studied the effect of deletions of several genes thought to encode these activities.

Results:

It was found that pyruvate ferredoxin oxidoreductase enzyme …

Spectroscopic Separation Of Čerenkov Radiation In High-Resolution Radiation Fiber Dosimeters, Arash Darafsheh, Rongxiao Zhang, Stephen Chad Kanick, Brian W. Pogue, Jarod C. Finlay

Dartmouth Scholarship

We have investigated Čerenkov radiation generated in phosphor-based optical fiber dosimeters irradiated with clinical electron beams. We fabricated two high-spatial resolution fiber-optic probes, with 200 and 400  μm core diameters, composed of terbium-based phosphor tips. A generalizable spectroscopic method was used to separate Čerenkov radiation from the transmitted signal by the fiber based on the assumption that the recorded signal is a linear superposition of two basis spectra: characteristic luminescence of the phosphor medium and Čerenkov radiation. We performed Monte Carlo simulations of the Čerenkov radiation generated in the fiber and found a strong dependence of the recorded Čerenkov …

Review Of Fluorescence Guided Surgery Visualization And Overlay Techniques, Jonathan T. Elliott, Alisha V. Dsouza, Scott C. Davis, Jonathan D. Olson, Keith Paulsen, David Roberts, Brian Pogue

Dartmouth Scholarship

In fluorescence guided surgery, data visualization represents a critical step between signal capture and display needed for clinical decisions informed by that signal. The diversity of methods for displaying surgical images are reviewed, and a particular focus is placed on electronically detected and visualized signals, as required for near-infrared or low concentration tracers. Factors driving the choices such as human perception, the need for rapid decision making in a surgical environment, and biases induced by display choices are outlined. Five practical suggestions are outlined for optimal display orientation, color map, transparency/alpha function, dynamic range compression, and color perception check.

Direct Regularization From Co-Registered Anatomical Images For Mri-Guided Near-Infrared Spectral Tomographic Image Reconstruction, Limin Zhang, Yan Zhao, Shudong Jiang, Brian W. Pogue, Keith Paulsen

Dartmouth Scholarship

Combining anatomical information from high resolution imaging modalities to guide near-infrared spectral tomography (NIRST) is an efficient strategy for improving the quality of the reconstructed spectral images. A new approach for incorporating image information directly into the inversion matrix regularization was examined using Direct Regularization from Images (DRI), which encodes the gray-scale data into the NIRST image reconstruction problem. This process has the benefit of eliminating user intervention such as image segmentation of distinct regions. Specifically, the Dynamic Contrast Enhanced Magnetic Resonance (DCE-MR) image intensity value differences within the anatomical image were used to implement an exponentially-weighted regularization function between …

Logarithmic Intensity Compression In Fluorescence Guided Surgery Applications, Alisha V. Dsouza, Huiyun Lin, Jason Gunn, Brian W. Pogue

Dartmouth Scholarship

The use of fluorescence video imaging to guide surgery is rapidly expanding, and improvements in camera readout dynamic range have not matched display capabilities. Logarithmic intensity compression is a fast, single-step mapping technique that can map the useable dynamic range of high-bit fluorescence images onto the typical 8-bit display and potentially be a variable dynamic contrast enhancement tool. We demonstrate a ∼4.6  times improvement in image quality quantified by image entropy and a dynamic range reduction by a factor of ∼380 by the use of log-compression tools in processing in vivo fluorescence images.

Review Of Biomedical Čerenkov Luminescence Imaging Applications, Kaveh Tanha, Ali Mahmoud Pashazadeh, Brian W. Pogue

Dartmouth Scholarship

Čerenkov radiation is a fascinating optical signal, which has been exploited for unique diagnostic biological sensing and imaging, with significantly expanded use just in the last half decade. Čerenkov Luminescence Imaging (CLI) has desirable capabilities for niche applications, using specially designed measurement systems that report on radiation distributions, radiotracer and nanoparticle concentrations, and are directly applied to procedures such as medicine assessment, endoscopy, surgery, quality assurance and dosimetry. When compared to the other imaging tools such as PET and SPECT, CLI can have the key advantage of lower cost, higher throughput and lower imaging time. CLI can also provide imaging …

The Role Of Damage And Recrystallization In The Elastic Properties Of Columnar Ice, Scott A. Snyder, Erland M. Schulson, Carl E. Renshaw

Dartmouth Scholarship

Effects of damage on elastic properties were studied in columnar-grained specimens of freshwater and saline ice, subjected, at −10°C, to varying levels of inelastic strain. The ice was compressed uniaxially at constant strain rates up to 0.20 strain, which caused localized recrystallization and imparted damage in the form of non-propagating cracks. Damage was quantified in terms of dimensionless crack density, which, along with recrystallized area fraction, was determined from thin sections. The change in porosity due to stress-induced cracks served as another indicator of damage. Elastic properties were derived using P-wave and S-wave ultrasonic transmission velocities measured in across-column directions …

Deletion Of Nfnab In Thermoanaerobacterium Saccharolyticum And Its Effect On Metabolism, Jonathan Lo, Tianyong Zheng, Daniel G. Olson, Natalie Ruppertsberger, Shital Tripathi, Adam Guss, Lee Lynd

Dartmouth Scholarship

NfnAB catalyzes the reversible transfer of electrons from reduced ferredoxin and NADH to 2 NADP⁺. The NfnAB complex has been hypothesized to be the main enzyme for ferredoxin oxidization in strains of Thermoanaerobacterium saccharolyticum engineered for increased ethanol production. NfnAB complex activity was detectable in crude cell extracts of T. saccharolyticum. Activity was also detected using activity staining of native PAGE gels. The nfnAB gene was deleted in different strains of T. saccharolyticum to determine its effect on end product formation. In wild-type T. saccharolyticum, deletion of nfnAB resulted in a 46% increase in H₂ formation but …

Cofactor Specificity Of The Bifunctional Alcohol And Aldehyde Dehydrogenase (Adhe) In Wild-Type And Mutant Clostridium Thermocellum And Thermoanaerobacterium Saccharolyticum, Tianyong Zheng, Daniel G. Olson, Liang Tian, Yannick J. Bomble, Michael Himmel, Jonathan Lo, Shuen Hon, A. Joe Shaw, Johannes P. Van Dijken, Lee Lynd

Dartmouth Scholarship

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic bacteria that have been engineered to produce ethanol from the cellulose and hemicellulose fractions of biomass, respectively. Although engineered strains of T. saccharolyticum produce ethanol with a yield of 90% of the theoretical maximum, engineered strains of C. thermocellum produce ethanol at lower yields (∼50% of the theoretical maximum). In the course of engineering these strains, a number of mutations have been discovered in their adhE genes, which encode both alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes. To understand the effects of these mutations, the adhE genes from six strains of C. …

Optimization Of Image Reconstruction For Magnetic Resonance Imaging–Guided Near-Infrared Diffuse Optical Spectroscopy In Breast, Yan Zhao, Michael A. Mastanduno, Shudong Jiang, Fadi Ei-Ghussein, Jiang Gui, Brian W. Pogue, Keith D. Paulsen

Dartmouth Scholarship

An optimized approach to nonlinear iterative reconstruction of magnetic resonance imaging (MRI)–guided near-infrared spectral tomography (NIRST) images was developed using an L-curve-based algorithm for the choice of regularization parameter. This approach was applied to clinical exam data to maximize the reconstructed values differentiating malignant and benign lesions. MRI/NIRST data from 25 patients with abnormal breast readings (BI-RADS category 4-5) were analyzed using this optimal regularization methodology, and the results showed enhanced p values and area under the curve (AUC) for the task of differentiating malignant from benign lesions. Of the four absorption parameters and two scatter parameters, the most significant …

Molecular Dyes Used For Surgical Specimen Margin Orientation Allow For Intraoperative Optical Assessment During Breast Conserving Surgery, David M. Mcclatchy, Venkataramanan Krishnaswamy, Stephen C. Kanick, Jonathan T. Elliott, Wendy A. Wells, Richard J. Barth Jr., Keith D. Paulsen, Brian W. Pogue

Dartmouth Scholarship

A variety of optical techniques utilizing near-infrared (NIR) light are being proposed for intraoperative breast tumor margin assessment. However, immediately following a lumpectomy excision, the margins are inked, which preserves the orientation of the specimen but prevents optical interrogation of the tissue margins. Here, a workflow is proposed that allows for both NIR optical assessment following full specimen marking using molecular dyes which have negligible absorption and scattering in the NIR. The effect of standard surgical inks in contrast to molecular dyes for an NIR signal is shown. Further, the proposed workflow is demonstrated with full specimen intraoperative imaging on …

Microscale Magnetic Field Modulation For Enhanced Capture And Distribution Of Rare Circulating Tumor Cells, Peng Chen, Yu-Yen Huang, Kazunori Hoshino, John X.J Zhang

Dartmouth Scholarship

Immunomagnetic assay combines the powers of the magnetic separation and biomarker recognition and has been an effective tool to perform rare Circulating Tumor Cells detection. Key factors associated with immunomagnetic assay include the capture rate, which indicates the sensitivity of the system, and distributions of target cells after capture, which impact the cell integrity and other biological properties that are critical to downstream analyses. Here we present a theoretical framework and technical approach to implement a microscale magnetic immunoassay through modulating local magnetic field towards enhanced capture and distribution of rare cancer cells. Through the design of a two-dimensional micromagnet …

Macroscopic-Imaging Technique For Subsurface Quantification Of Near-Infrared Markers During Surgery, Michael Jermyn, Kolbein Kolste, Julien Pichette, Guillaume Sheehy, Leticia Angulo-Rodriguez, Keith D. Paulsen, David W. Roberts, Brian C. Wilson, Kevin Petrecca, Frederic Leblond

Dartmouth Scholarship

Obtaining accurate quantitative information on the concentration and distribution of fluorescent markers lying at a depth below the surface of optically turbid media, such as tissue, is a significant challenge. Here, we introduce a fluorescence reconstruction technique based on a diffusion light transport model that can be used during surgery, including guiding resection of brain tumors, for depth-resolved quantitative imaging of near-infrared fluorescent markers. Hyperspectral fluorescence images are used to compute a topographic map of the fluorophore distribution, which yields structural and optical constraints for a three-dimensional subsequent hyperspectral diffuse fluorescence reconstruction algorithm. Using the model fluorophore Alexa Fluor 647 …

Elimination Of Hydrogenase Active Site Assembly Blocks H2 Production And Increases Ethanol Yield In Clostridium Thermocellum, Ranjita Biswas, Tianyong Zheng, Daniel G. Olson, Lee R. Lynd, Adam M. Guss

Dartmouth Scholarship

Background: The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H₂ , and amino acids that compete with ethanol production for carbon and electrons. Elimination of H₂ production could redirect carbon flux towards ethanol production by making more electrons available for acetyl coenzyme A reduction to ethanol. Results: H₂ production in C. thermocellum is encoded by four hydrogenases. Rather than delete each individually, we targeted hydrogenase maturase gene hydG, involved in converting the …

Next-Generation Raman Tomography Instrument For Non-Invasive In Vivo Bone Imaging, Jennifer-Lynn H. Demers, Francis W. L. Esmonde-White, Karen A. Esmonde-White, Michael D. Morris, Brian Pogue

Dartmouth Scholarship

Combining diffuse optical tomography methods with Raman spectroscopy of tissue provides the ability for in vivo measurements of chemical and molecular characteristics, which have the potential for being useful in diagnostic imaging. In this study a system for Raman tomography was developed and tested. A third generation microCT coupled system was developed to combine 10 detection fibers and 5 excitation fibers with laser line filtering and a Cytop reference signal. Phantom measurements of hydroxyapatite concentrations from 50 to 300 mg/ml had a linear response. Fiber placement and experiment design was optimized using cadaver animals with live animal measurements acquired to …

The Bifunctional Alcohol And Aldehyde Dehydrogenase Gene, Adhe, Is Necessary For Ethanol Production In Clostridium Thermocellum And Thermoanaerobacterium Saccharolyticum, Jonathan Lo, Tianyong Zheng, Shuen Hon, Daniel G. Olson, Lee Lynd

Dartmouth Scholarship

Thermoanaerobacterium saccharolyticum and Clostridium thermocellum are anaerobic thermophilic bacteria being investigated for their ability to produce biofuels from plant biomass. The bifunctional alcohol and aldehyde dehydrogenase gene, adhE, is present in these bacteria and has been known to be important for ethanol formation in other anaerobic alcohol producers. This study explores the inactivation of the adhE gene in C. thermocellum and T. saccharolyticum. Deletion of adhE reduced ethanol production by >95% in both T. saccharolyticum and C. thermocellum, confirming that adhE is necessary for ethanol formation in both organisms. In both adhE deletion strains, fermentation products shifted from ethanol …

Macroscopic Optical Imaging Technique For Wide-Field Estimation Of Fluorescence Depth In Optically Turbid Media For Application In Brain Tumor Surgical Guidance, Kolbein K. Kolste, Stephen C. Kanick, Pablo A. Valdés, Michael Jermyn, Brian C. Wilson, David W. Roberts, Keith D. Paulsen, Frederic Leblond

Dartmouth Scholarship

A diffuse imaging method is presented that enables wide-field estimation of the depth of fluorescent molecular markers in turbid media by quantifying the deformation of the detected fluorescence spectra due to the wavelength-dependent light attenuation by overlying tissue. This is achieved by measuring the ratio of the fluorescence at two wavelengths in combination with normalization techniques based on diffuse reflectance measurements to evaluate tissue attenuation variations for different depths. It is demonstrated that fluorescence topography can be achieved up to a 5 mm depth using a near-infrared dye with millimeter depth accuracy in turbid media having optical properties representative of …

Does Material Choice Drive Sustainability Of 3d Printing?, Jeremy Faludi, Zhongyin Hu, Shahd Alrashed, Christopher Braunholz, Suneesh Kaul, Leulekal Kassaye

Dartmouth Scholarship

Environmental impacts of six 3D printers using various materials were compared to determine if material choice drove sustainability, or if other factors such as machine type, machine size, or machine utilization dominate. Cradle-to-grave life-cycle assessments were performed, comparing a commercial-scale FDM machine printing in ABS plastic, a desktop FDM machine printing in ABS, a desktop FDM machine printing in PET and PLA plastics, a polyjet machine printing in its proprietary polymer, an SLA machine printing in its polymer, and an inkjet machine hacked to print in salt and dextrose. All scenarios were scored using ReCiPe Endpoint H methodology to combine …

Quantitative Spatial Frequency Fluorescence Imaging In The Sub-Diffusive Domain For Image-Guided Glioma Resection, Mira Sibai, Israel Veilleux, Jonathan T. Elliott, Frederic Leblond, Brian Wilson

Dartmouth Scholarship

Intraoperative 5- aminolevulinic acid induced-Protoporphyrin IX (PpIX) fluorescence guidance enables maximum safe resection of glioblastomas by providing surgeons with real-time tumor optical contrast. However, visual assessment of PpIX fluorescence is subjective and limited by the distorting effects of light attenuation and tissue autofluorescence. We have previously shown that non-invasive point measurements of absolute PpIX concentration identifies residual tumor that is otherwise non-detectable. Here, we extend this approach to wide-field quantitative fluorescence imaging by implementing spatial frequency domain imaging to recover tissue optical properties across the field-of-view in phantoms and ex vivo tissue.