Development of an Online Course in Research for Undergraduate Students

This Work in Progress paper will cover the development of an online course in research practices for undergraduate students. Active participation in research is an important part of experiential learning, which can help to prepare students for careers in a variety of settings including industrial R&D departments, academia, and government research labs. Undergraduate students’ research experiences may be limited in their value, however, by the learning curve students face as they begin to conduct research. The quality of their training may also be limited, with some receiving excellent training and orientation from a strong research lab or faculty mentor, and others receiving little guidance. In order to better prepare undergraduate students for research, faculty members in different departments at a midwestern STEM-focused University received an internal grant to develop a class in research for undergraduates. This class, which is designed to be offered online either for cohorts or for individual students as an independent study, contains information and resources on a diverse range of issues such as motivation for research, research ethics, planning a research project, conducting literature searches, experimental procedures, keeping lab documentation for various types of projects, data analysis, technical writing, intellectual property, and issues relevant to scoping out one’s own research project. This paper will give the background for the course development, evaluation of the required content and decisions on structure and format, and describe the various modules in the course. It will also describe the future plans for deployment, evaluation, and continuous improvement of the course, and suggest ways in which it could benefit a wide range of undergraduate students in different disciplines

A method for measuring the Neel relaxation time in a frozen ferrofluid

We report a novel method of determining the average Neel relaxation time and its temperature dependence by calculating derivatives of the measured time dependence of temperature for a frozen ferrofluid exposed to an alternating magnetic field. The ferrofluid, composed of dextran-coated Fe3O4 nanoparticles (diameter 13.7 nm +/- 4.7 nm), was synthesized via wet chemical precipitation and characterized by x-ray diffraction and transmission electron microscopy. An alternating magnetic field of constant amplitude (H0 = 20 kA/m) driven at frequencies of 171 kHz, 232 kHz and 343 kHz was used to determine the temperature dependent magnetic energy absorption rate in the temperature range from 160 K to 210 K. We found that the specific absorption rate of the ferrofluid decreased monotonically with temperature over this range at the given frequencies. From these measured data, we determined the temperature dependence of the Neel relaxation time and estimate a room-temperature magnetocrystalline anisotropy constant of 40 kJ/m3, in agreement with previously published results

Characterization of Lesion Formation and Bubble Activities during High Intensity Focused Ultrasound Ablation using Temperature-Derived Parameters

Successful high-intensity focused ultrasound (HIFU) thermal tissue ablation relies on accurate information of the tissue temperature and tissue status. Often temperature measurements are used to predict and monitor the ablation process. In this study, we conducted HIFU ablation experiments with ex vivo porcine myocardium tissue specimens to identify changes in temperature associated with tissue coagulation and bubble/cavity formation. Using infrared (IR) thermography and synchronized bright-field imaging with HIFU applied near the tissue surface, parameters derived from the spatiotemporal evolution of temperature were correlated with HIFU-induced lesion formation and overheating, of which the latter typically results in cavity generation and/or tissue dehydration. Emissivity of porcine myocardium was first measured to be 0.857 ± 0.006 (n = 3). HIFU outcomes were classified into non-ablative, normal lesion, and overheated lesion. A marked increase in the rate of temperature change during HIFU application was observed with lesion formation. A criterion using the maximum normalized second time derivative of temperature change provided 99.1% accuracy for lesion identification with a 0.05 s−1 threshold. Asymmetric temperature distribution on the tissue surface was observed to correlate with overheating and/or bubble generation. A criterion using the maximum displacement of the spatial location of the peak temperature provided 90.9% accuracy to identify overheated lesion with a 0.16 mm threshold. Spatiotemporal evolution of temperature obtained using IR imaging allowed determination of the critical cumulative equivalent minutes at 43 °C (CEM43) for lesion formation to be 170 min. Similar temperature characteristics indicative of lesion formation and overheating were identified for subsurface HIFU ablation. These results suggest that parameters derived from temperature changes during HIFU application are associated with irreversible changes in tissue and may provide useful information for monitoring HIFU treatment

Intracellular Delivery and Calcium Transients Generated in Sonoporation Facilitated by Microbubbles

Published in PubMed Central on 25 February 2011Ultrasound application in the presence of microbubbles is a promising strategy for intracellular delivery drug and gene, but it may also trigger other cellular responses. This study investigates the relationship between the change of cell membrane permeability generated by ultrasound-driven microbubbles and the changes in intracellular calcium concentration ([Ca2+]i). Cultured rat cardiomyoblast (H9c2) cells were exposed to a single ultrasound pulse (1 MHz, 10–15 cycles, 0.27 MPa) in the presence of a Definity™ microbubble. Intracellular transport via sonoporation was assessed in real time using propidium iodide (PI), while [Ca2+]i and dye loss from the cells were measured with preloaded fura-2. The ultrasound exposure generated fragmentation or shrinking of the microbubble. Only cells adjacent to the ultrasound-driven microbubble exhibited propidium iodide (PI) uptake with simultaneous [Ca2+]i increase and fura-2 dye loss. The amount of PI uptake was correlated with the amount of fura-2 dye loss. Cells with delayed [Ca2+]i transients from the time of ultrasound application had no uptake of PI. These results indicate the formation of nonspecific pores in the cell membrane by ultrasound-stimulated microbubbles and the generation of calcium waves in surrounding cells without pores.National Institutes of Health grant R01CA116592Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/84358/1/nihms-154938.pd

Design of a Scanning Acoustic and Photoacoustic Microscopy System Using Open-Source Hardware and Software Components

We have designed and started construction of an instrument that will be able to operate as both a scanning acoustic microscope and photoacoustic microscope. To keep costs down, we are using open-source hardware and software components wherever possible. The system is designed to scan specimens that are approximately 2 cm × 2 cm in lateral dimensions with lateral steps of 1 micron or less. When operating as a scanning acoustic microscope, the specimen will be water-coupled to a high-frequency ultrasound transducer operating in pulse-echo mode. When operating as a photoacoustic microscope, short light pulses infrared laser diode located under the specimen will generate ultrasound pulses thermoelastically, which will then be received by a confocal high-frequency transducer. In both cases, the specimen will be raster-scanned under the transducer by a moving stage. The mechanical scanning system was designed and built using a spring-loaded microscope stage, micrometers, stepper motors, a shield board used for 3D printers, an Arduino Mega microcontroller, and a Raspberry Pi 4 microcomputer. A graphical user interface has been written in Python using Tkinter to send the motion control commands to the stage. Future work will include incorporation of the laser and transducer control systems

A Method for Measuring the Néel Relaxation Time in a Frozen Ferrofluid

We report a novel method of determining the average Néel relaxation time and its temperature dependence by calculating derivatives of the measured time dependence of temperature for a frozen ferrofluid exposed to an alternating magnetic field. The ferrofluid, composed of dextran-coated Fe3O4 nanoparticles (diameter 13.7 nm ± 4.7 nm), was synthesized via wet chemical precipitation and characterized by x-ray diffraction and transmission electron microscopy. An alternating magnetic field of constant amplitude (H0=20H0=20 kA/m) driven at frequencies of 171 kHz, 232 kHz, and 343 kHz was used to determine the temperature dependent magnetic energy absorption rate in the temperature range from 160 K to 210 K. We found that the specific absorption rate of the ferrofluid decreased monotonically with temperature over this range at the given frequencies. From these measured data, we determined the temperature dependence of the Néel relaxation time and estimate a room-temperature magnetocrystalline anisotropy constant of 40 kJ/m3, in agreement with previously published results

Tomographic Reconstruction of Tissue Properties and Temperature Increase for High-Intensity Focused Ultrasound Applications

The acoustic and thermal properties as well as the temperature change within a tissue volume during high-intensity focused ultrasound ablation are critically important for treatment planning and monitoring. Described in this article is a tomographic reconstruction method used to determine the tissue properties and increase in temperature in a 3-D volume. On the basis of the iterative finite-element solution to the bioheat equation coupled with Tikhonov regularization techniques, our reconstruction algorithm solves the inverse problem of bioheat transfer and uses the time-dependent temperature measured on a tissue surface to obtain the acoustic absorption coefficient, thermal diffusivity and temperature increase within the subsurface volume. Numerical simulations were performed to validate the reconstruction algorithm. The method was initially conducted in ex vivo experiments in which time-dependent temperature on a tissue surface was measured using high-resolution, non-invasive infrared thermography

Spatiotemporal Effects of Sonoporation Measured by Real-Time Calcium Imaging

Published in PubMed Central on 01 March 2010To investigate the effects of sonoporation, spatiotemporal evolution of ultrasound-induced changes in intracellular calcium ion concentration ([Ca2+]i) was determined using real time fura-2AM fluorescence imaging. Monolayers of Chinese hamster ovary (CHO) cells were exposed to 1-MHz ultrasound tone burst (0.2 s, 0.45 MPa) in the presence of Optison™ microbubbles. At extracellular [Ca2+]o of 0.9 mM, ultrasound application generated both non-oscillating and oscillating (periods 12–30 s) transients (changes of [Ca2+]i in time) with durations of 100–180 s. Immediate [Ca2+]i transients after ultrasound application were induced by ultrasound-mediated microbubble–cell interactions. In some cases, the immediately-affected cells did not return to pre-ultrasound equilibrium [Ca2+]i levels, thereby indicating irreversible membrane damage. Spatial evolution of [Ca2+]i in different cells formed a calcium wave and was observed to propagate outward from the immediately-affected cells at 7–20 μm/s over a distance greater than 200 μm, causing delayed transients in cells to occur sometimes 60 s or more after ultrasound application. In calcium-free solution, ultrasound-affected cells did not recover, consistent with the requirement of extracellular Ca2+ for cell membrane recovery subsequent to sonoporation. In summary, ultrasound application in the presence of Optison™ microbubbles can generate transient [Ca2+]i changes and oscillations at a focal site and in surrounding cells via calcium waves that last longer than the ultrasound duration and spread beyond the focal site. These results demonstrate the complexity of downstream effects of sonoporation beyond the initial pore formation and subsequent diffusion-related transport through the cellular membraneNational Institutes of Health R01CA116592Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/84355/1/nihms99796.pd