Master of Science

thesisThe purpose of this work was to design and construct a radio-frequency coil optimized for imaging the Optic Nerve (ON) on a Siemens 3T magnetic resonance imaging (MRI) scanner. The specific goals were to optimize signal sensitivity from the orbit to the optic chiasm and improve SNR over designs currently in use. The constructed coil features two fiberglass formers that can slide over each other to accommodate any arbitrary head size, while maintaining close coupling near the eyes and around the head in general. This design eliminates the air void regions that occur between the coil elements and the forehead when smaller heads are imaged in one-piece, nonadjustable coil formers. The 28 coil elements were placed using a soccer-ball pattern layout to maximize head coverage. rSNR profiles from phantom imaging studies show that the ON coil provides approximately 55% greater rSNR at the region of the optic chiasm and approximately 400% near the orbits compared to the 12-channel commercial coil. The improved rSNR in the optic nerve region allows performance of high resolution DTI, which provides a qualitative measurement for evaluating optic neuritis. Images from volunteer and patient studies with the ON coil reveal plaques that correspond well with the patient disease history of chronic bilateral optic neuritis. Correspondence of image findings with patient disease histories demonstrates that optic neuritis can be visualized and detected in patients using 3T MRI with advanced imaging coils, providing improved patient care

Regulation of Coronary Blood Flow

The heart is uniquely responsible for providing its own blood supply through the coronary circulation. Regulation of coronary blood flow is quite complex and, after over 100 years of dedicated research, is understood to be dictated through multiple mechanisms that include extravascular compressive forces (tissue pressure), coronary perfusion pressure, myogenic, local metabolic, endothelial as well as neural and hormonal influences. While each of these determinants can have profound influence over myocardial perfusion, largely through effects on end-effector ion channels, these mechanisms collectively modulate coronary vascular resistance and act to ensure that the myocardial requirements for oxygen and substrates are adequately provided by the coronary circulation. The purpose of this series of Comprehensive Physiology is to highlight current knowledge regarding the physiologic regulation of coronary blood flow, with emphasis on functional anatomy and the interplay between the physical and biological determinants of myocardial oxygen delivery. © 2017 American Physiological Society. Compr Physiol 7:321-382, 2017

Behavioral responses of terrestrial mammals to COVID-19 lockdowns

DATA AND MATERIALS AVAILABILITY : The full dataset used in the final analyses (33) and associated code (34) are available at Dryad. A subset of the spatial coordinate datasets is available at Zenodo (35). Certain datasets of spatial coordinates will be available only through requests made to the authors due to conservation and Indigenous sovereignty concerns (see table S1 for more information on data use restrictions and contact information for data requests). These sensitive data will be made available upon request to qualified researchers for research purposes, provided that the data use will not threaten the study populations, such as by distribution or publication of the coordinates or detailed maps. Some datasets, such as those overseen by government agencies, have additional legal restrictions on data sharing, and researchers may need to formally apply for data access. Collaborations with data holders are generally encouraged, and in cases where data are held by Indigenous groups or institutions from regions that are under-represented in the global science community, collaboration may be required to ensure inclusion.COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals’ 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.The Radboud Excellence Initiative, the German Federal Ministry of Education and Research, the National Science Foundation, Serbian Ministry of Education, Science and Technological Development, Dutch Research Council NWO program “Advanced Instrumentation for Wildlife Protection”, Fondation Segré, RZSS, IPE, Greensboro Science Center, Houston Zoo, Jacksonville Zoo and Gardens, Nashville Zoo, Naples Zoo, Reid Park Zoo, Miller Park, WWF, ZCOG, Zoo Miami, Zoo Miami Foundation, Beauval Nature, Greenville Zoo, Riverbanks zoo and garden, SAC Zoo, La Passarelle Conservation, Parc Animalier d’Auvergne, Disney Conservation Fund, Fresno Chaffee zoo, Play for nature, North Florida Wildlife Center, Abilene Zoo, a Liber Ero Fellowship, the Fish and Wildlife Compensation Program, Habitat Conservation Trust Foundation, Teck Coal, and the Grand Teton Association. The collection of Norwegian moose data was funded by the Norwegian Environment Agency, the German Ministry of Education and Research via the SPACES II project ORYCS, the Wyoming Game and Fish Department, Wyoming Game and Fish Commission, Bureau of Land Management, Muley Fanatic Foundation (including Southwest, Kemmerer, Upper Green, and Blue Ridge Chapters), Boone and Crockett Club, Wyoming Wildlife and Natural Resources Trust, Knobloch Family Foundation, Wyoming Animal Damage Management Board, Wyoming Governor’s Big Game License Coalition, Bowhunters of Wyoming, Wyoming Outfitters and Guides Association, Pope and Young Club, US Forest Service, US Fish and Wildlife Service, the Rocky Mountain Elk Foundation, Wyoming Wild Sheep Foundation, Wild Sheep Foundation, Wyoming Wildlife/Livestock Disease Research Partnership, the US National Science Foundation [IOS-1656642 and IOS-1656527, the Spanish Ministry of Economy, Industry and Competitiveness, and by a GRUPIN research grant from the Regional Government of Asturias, Sigrid Rausing Trust, Batubay Özkan, Barbara Watkins, NSERC Discovery Grant, the Federal Aid in Wildlife Restoration act under Pittman-Robertson project, the State University of New York, College of Environmental Science and Forestry, the Ministry of Education, Youth and Sport of the Czech Republic, the Ministry of Agriculture of the Czech Republic, Rufford Foundation, an American Society of Mammalogists African Graduate Student Research Fund, the German Science Foundation, the Israeli Science Foundation, the BSF-NSF, the Ministry of Agriculture, Forestry and Food and Slovenian Research Agency (CRP V1-1626), the Aage V. Jensen Naturfond (project: Kronvildt - viden, værdier og værktøjer), the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy, National Centre for Research and Development in Poland, the Slovenian Research Agency, the David Shepherd Wildlife Foundation, Disney Conservation Fund, Whitley Fund for Nature, Acton Family Giving, Zoo Basel, Columbus, Bioparc de Doué-la-Fontaine, Zoo Dresden, Zoo Idaho, Kolmården Zoo, Korkeasaari Zoo, La Passarelle, Zoo New England, Tierpark Berlin, Tulsa Zoo, the Ministry of Environment and Tourism, Government of Mongolia, the Mongolian Academy of Sciences, the Federal Aid in Wildlife Restoration act and the Illinois Department of Natural Resources, the National Science Foundation, Parks Canada, Natural Sciences and Engineering Research Council, Alberta Environment and Parks, Rocky Mountain Elk Foundation, Safari Club International and Alberta Conservation Association, the Consejo Nacional de Ciencias y Tecnología (CONACYT) of Paraguay, the Norwegian Environment Agency and the Swedish Environmental Protection Agency, EU funded Interreg SI-HR 410 Carnivora Dinarica project, Paklenica and Plitvice Lakes National Parks, UK Wolf Conservation Trust, EURONATUR and Bernd Thies Foundation, the Messerli Foundation in Switzerland and WWF Germany, the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions, NASA Ecological Forecasting Program, the Ecotone Telemetry company, the French National Research Agency, LANDTHIRST, grant REPOS awarded by the i-Site MUSE thanks to the “Investissements d’avenir” program, the ANR Mov-It project, the USDA Hatch Act Formula Funding, the Fondation Segre and North American and European Zoos listed at http://www.giantanteater.org/, the Utah Division of Wildlife Resources, the Yellowstone Forever and the National Park Service, Missouri Department of Conservation, Federal Aid in Wildlife Restoration Grant, and State University of New York, various donors to the Botswana Predator Conservation Program, data from collared caribou in the Northwest Territories were made available through funds from the Department of Environment and Natural Resources, Government of the Northwest Territories. The European Research Council Horizon2020, the British Ecological Society, the Paul Jones Family Trust, and the Lord Kelvin Adam Smith fund, the Tanzania Wildlife Research Institute and Tanzania National Parks. The Eastern Shoshone and Northern Arapahoe Fish and Game Department and the Wyoming State Veterinary Laboratory, the Alaska Department of Fish and Game, Kodiak Brown Bear Trust, Rocky Mountain Elk Foundation, Koniag Native Corporation, Old Harbor Native Corporation, Afognak Native Corporation, Ouzinkie Native Corporation, Natives of Kodiak Native Corporation and the State University of New York, College of Environmental Science and Forestry, and the Slovenia Hunters Association and Slovenia Forest Service. F.C. was partly supported by the Resident Visiting Researcher Fellowship, IMéRA/Aix-Marseille Université, Marseille. This work was partially funded by the Center of Advanced Systems Understanding (CASUS), which is financed by Germany’s Federal Ministry of Education and Research (BMBF) and by the Saxon Ministry for Science, Culture and Tourism (SMWK) with tax funds on the basis of the budget approved by the Saxon State Parliament. This article is a contribution of the COVID-19 Bio-Logging Initiative, which is funded in part by the Gordon and Betty Moore Foundation (GBMF9881) and the National Geographic Society.https://www.science.org/journal/sciencehj2023Mammal Research InstituteZoology and Entomolog

Open Source Skin Cooling System for Focused Ultrasound Applications

The adverse event of skin burns and the restrictions caused by multi-hour treatment times continue to limit the clinical efficacy and cost effectiveness of MRgFUS thermal therapies. This proposal directly addresses these unmet needs with two primary aims. Aim 1 includes design and fabrication of a prototype cooling device, testing of clinically identified design specifications, and initial experimental validation ex vivo tissue experiments. This conformable skin-cooling device will reduce the potential for skin burns in desmoid tumor and other MRgFUS treatments. Aim 2 will assess the skin cooling device on a pre-clinical MRgFUS system with rabbit and pig studies and will integrate the device with the clinical ExAblate 2100 system. The ultimate goal of the device design is to be MRgFUS system independent. This may require a modular design that allows for both clinical and veterinarian applications. The completion of this proposal will deliver the engineering schematic, parts list and use manual of the completed device, validation data and install a single device at the Focused Ultrasound Center of Excellence at Stanford University.Presented here are the open-source parts list and assembly files to reproduce the skin cooling device, along with the device user manual. An open-access publication on the design methods and preclinical results will be published soon.</p

Open Source Skin Cooling System for Focused Ultrasound Applications

The adverse event of skin burns and the restrictions caused by multi-hour treatment times continue to limit the clinical efficacy and cost effectiveness of MRgFUS thermal therapies. This proposal directly addresses these unmet needs with two primary aims. Aim 1 includes design and fabrication of a prototype cooling device, testing of clinically identified design specifications, and initial experimental validation ex vivo tissue experiments. This conformable skin-cooling device will reduce the potential for skin burns in desmoid tumor and other MRgFUS treatments. Aim 2 will assess the skin cooling device on a pre-clinical MRgFUS system with rabbit and pig studies and will integrate the device with the clinical ExAblate 2100 system. The ultimate goal of the device design is to be MRgFUS system independent. This may require a modular design that allows for both clinical and veterinarian applications. The completion of this proposal will deliver the engineering schematic, parts list and use manual of the completed device, validation data and install a single device at the Focused Ultrasound Center of Excellence at Stanford University. Presented here are the open-source parts list and assembly files to reproduce the skin cooling device, along with the device user manual. An open-access publication on the design methods and preclinical results will be published soon

MRI-compatible electromagnetic servomotor for image-guided medical robotics

AbstractThe soft-tissue imaging capabilities of magnetic resonance imaging (MRI) combined with high precision robotics has the potential to improve the precision and safety of a wide range of image-guided medical procedures. However, functional MRI-compatible robotics have not yet been realized in part because conventional electromagnetic servomotors can become dangerous projectiles near the strong magnetic field of an MRI scanner. Here we report an electromagnetic servomotor constructed from non-magnetic components, where high-torque and controlled rotary actuation is produced via interaction between electrical current in the servomotor armature and the magnetic field generated by the superconducting magnet of the MRI scanner itself. Using this servomotor design, we then build and test an MRI-compatible robot which can achieve the linear forces required to insert a large-diameter biopsy instrument in tissue during simultaneous MRI. Our electromagnetic servomotor can be safely operated (while imaging) in the patient area of a 3 Tesla clinical MRI scanner.</jats:p

Design and evaluation of an open-source block face imaging system for 2D histology to magnetic resonance image registration

This study introduces a comprehensive hardware-software framework designed to enhance the quality of block face image capture—an essential intermediary step for registering 2D histology images to ex vivo magnetic resonance (MR) images. A customized camera mounting and lighting system is employed to maintain consistent relative positioning and lighting conditions. Departing from traditional transparent paraffin, dyed paraffin is utilized to enhance contrast for subsequent automatic segmentation. Our software facilitates fully automated data collection and organization, complemented by a real-time Quality Assurance (QA) section to assess the captured image's quality during the sectioning process. The setup is evaluated and validated using rabbit muscle and rat brain which underwent MR-guided focused ultrasound ablations. The customized hardware system establishes a robust image capturing environment. The software with a real-time QA section, enables operators to promptly rectify low-quality captures, thereby preventing data loss. The execution of our proposed framework produces robust registration results for H&E images to ex vivo MR images. • The presented hardware-software framework ensures the uniformity and resilience of the block face image capture process, contributing to a more reliable and efficient registration of 2D histology images to ex vivo MR images