Stephen Ramsey
Stephen Ramsey

In August, Stephen Ramsey, assistant professor of computer science in the College of Engineering, along with his collaborators, received an additional $351,443 in funding to develop a biomedical data translator, bringing the total funds this year to $788,443.

The award is part of a program by the National Institutes of Health (NIH) to  build a tool that brings together medical data from various sources to better understand health and disease and, ultimately, to diagnose and treat patients more quickly.

Ten teams across the country are working on the biomedical data translator, in what started out as a competition, but is now a collaborative effort.

The unusual program required the teams to first solve a series of puzzles before they could view the RFA (request for application). The funding is not a grant, but instead called an “other transaction” award. The National Center for Advancing Translational Sciences (NCATS), the branch of NIH that is running the program, continually assesses the progress of the teams and doles out funding for short periods of time based on the progress of the teams.

“It’s a very flexible model which enables us to be nimble,” Ramsey said. “They can make adjustments to the deliverables to focus resources on things that are working, and not dedicate resources to approaches that aren’t working.”

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Photo of Mark Clements
Mark Clements, senior development and QA manager for CASS, teaches during the workshop.

Employees in the Center for Applied Systems and Software (CASS) in the College of Engineering are teaching a workshop for high school teachers to learn how to create mobile apps for Apple devices. The three-day workshop is being held August 13 – 15, 2018 by Professional and Continuing Education (PACE) at Oregon State University.

The course is intended for any interested teacher, even if they have no programming experience. By the end of the workshop the participants will create their own app that can run on an Apple device using the programming language called Swift. They will also have the tools, including lesson plans, to teach programming in their class. Another benefit is that they will continue to have online support with CASS when they are implementing the program in their class.

“By teaching this workshop, we are enabling teachers to use this really awesome curriculum from Apple in their high schools. And then hopefully that will help interest more young people in computer science,” said Carrie Hertel, director of the Software Development Group for CASS.

Hertel is excited to expand CASS’s outreach to high school teachers and hopes to hold more workshops in the future, as well as provide a modified workshop for professionals.

Zander Work at NW Cyber Camp
Zander Work (right) helps a student at the NW Cyber Camp held at Oregon State University.

A week-long camp to introduce high-school students to cybersecurity was held on the Oregon State University campus last week. Although it was the first time the camp was held in Corvallis, it is the third year the camp has been operating.

The location was not happenstance. NW Cyber Camp co-founder, Zander Work, just completed his freshman year at Oregon State where he made connections with faculty and graduate students in cyber security who helped teach the courses. Instructors also included alumni and other industry representatives from NuScale Power, McAfee, Splunk, NetSPI, Cylance, and PKI Solutions.

“The students were awesome,” Work said. “Everyone was very engaged with the speakers and they asked a lot of good questions.”

The goal of the camp is to get more students interested in the field of cybersecurity which has over 300,000 unfilled job openings, according to Cyber Seek.

“The camp has definitely shown me a lot more opportunities for what I can do in the future with cybersecurity,” said Grace, one of the camp participants. “There are a lot of different fields you can go into like data science, machine learning, ethical hacking, or security work. That’s been really cool to learn about.”

Jayde, another camp participant, already has plans to join the Air Force and focus on cybersecurity.

“I really liked the hands-on activities and learning about real examples of hacking,” Jayde said.

Both students mentioned it was harder than they were expecting, but in a good way.

“The guest speakers have been fantastic. Everyone is knowledgeable and teach at a rigorous enough level that people don’t get bored,” Grace said.

The 20 students at the Oregon State camp came from Corvallis, Albany, Philomath and Lebanon. The camp overall hosted 110 students this summer including sites in Portland, Gresham, Wilsonville, and Bend.

Rakesh Bobba, assistant professor of electrical and computer engineering and the faculty organizer for the event said, “It was really fun. We would definitely like to host it at Oregon State again, and hopefully expand it to reach more students.”

Students working at NW Cyber Camp
Students working at NW Cyber Camp held at Oregon State University.
Photo of Spencer Liverman and Thinh Nguyen.
Spencer Liverman (left) and Thinh Nguyen (right) are co-principal investigators with Arun Natarajan on a Navy contract.

E-Lambda LLC, an Oregon State University spin-off, was just awarded a Navy Small Business Innovation Research contract for $225,000 to develop a high-speed, secure, wireless communication system for underwater platforms.

Alan Wang, associate professor of electrical and computer science in the College of Engineering, co-founded E-Lambda LLC with his graduate student, Jyotindra Shakya, to commercialize research from the Engineering Photonic Research Laboratory.

The Navy contract is the first project for E-Lambda. The principal investigator for this Navy SBIR project is Spencer Liverman, a Ph.D. student in in Dr. Wang’s group. Thinh Nguyen, professor of electrical and computer engineering, and Arun Natarajan, associate professor of electrical and computer engineering serve as co-principal investigators.

For the network they will be developing free space optical technologies, using lasers to transmit high-speed data. Potential commercial applications include an alternative to Wi-Fi, smart-home technology, and secure communication infrastructure for governmental agencies such as FBI and CIA.

photo Christopher Mendez and Alannah Oleson
Christopher Mendez and Alannah Oleson received NSF Graduate Research Fellowships this year.

Two students of computer science in the College of Engineering at Oregon State University received National Science Foundation (NSF) Graduate Research Fellowships that will provide three years of research funding while they attend graduate school. This prestigious award recognizes and supports outstanding early career graduate students in science, technology, engineering and mathematics disciplines.

Christopher Mendez, a graduate student, and Alannah Oleson, an undergraduate, received the awards for research in the field of human-computer interaction (HCI). There were a total of eight students across the U.S. to receive the award for HCI research.

This prestigious award recognizes and supports outstanding early career graduate students in science, technology, engineering and mathematics (STEM) disciplines. A total of 2,000 fellowships are awarded per year across all STEM fields.

Both Mendez and Oleson are advised by Distinguished Professor Margaret Burnett who co-founded the area of end-user software engineering, which aims to improve software for computer users who are not trained in programming. Her current research investigates gender-neutral software, uncovering gender inclusiveness issues in software from spreadsheets to programming environments.

Mendez and Oleson are extending Burnett’s research into different areas: Mendez is investigating how technology can empower people of low socioeconomic status; and Oleson is researching how best to teach inclusive software design methods and principles to university-level computer science students.

Mendez is continuing his research with Burnett at Oregon State, and Oleson will be starting graduate school next fall at the University of Washington.

photo of Oregon State team
Oregon State took first place at the regional DOE Cyber Defense Competition 2018. Pictured are (left to right) Zach Rogers, Khuong Luu, Hadi Rahal-Arabi, Yeongjin Jang, Devon Streit (DOE), Zander Work, Cody Holliday, and Aidan Grimshaw

A team of six computer science students at Oregon State University competed for the first time and won the regional Department of Energy Cyber Defense Competition held at Pacific Northwest Laboratory in Richland, Washington.

The competition simulates a real-world situation in which the teams defend a corporate network infrastructure from professional hackers. Each team built a mock infrastructure including a web server, a file server, a database server, email, and other network operations. During the competition, a group of users utilized the services while the hackers launched attacks. The defending teams had to monitor and respond to the cyberattacks throughout the day and were scored on how well they defended their infrastructure and how well they documented what they had done.

The Oregon State team placed first among six teams from the western U.S. at the regional competition, and placed fourth nationally among 29 teams.

“The competition was a lot of work, but it was also a lot of fun,” said Zander Work, a freshman in computer science who led the team. “The team put in many long nights leading up to the competition to finish hardening our defenses, and it paid off.”

Zander and the other five students who competed — Aidan Grimshaw, Cody Holliday, Khuong Luu, Hadi Rahal-Arabi and Zach Rogers — are all members of the OSU Security Club.

“Although it was a very first time the students participated in such a competition, they did a great job,” said Yeongjin Jang, assistant professor of computer science in the College of Engineering who advised the team. “I was very happy to see the students working hard for an entire month of preparation, not hesitating to tackle difficult tasks, and working well as a team at the competition venue.”

Kenneth Squire did not know what to expect when attending his first academic conference — SPIE Photonics West 2018, a conference about light-based science and technology. So, he was pretty surprised to take home two awards.

“It’s really exciting to get that recognition and to know that I am capable of doing research and presenting my findings at that level,” said Squire, a graduate student in electrical and computer engineering in the College of Engineering at Oregon State University.

Squire’s research advances techniques to detect antigens such as biotoxins that can infect food or biomarkers for disease. His research is under the direction of Alan Wang, associate professor of electrical and computer engineering who heads the Engineering Photonics Research Laboratory in the School of Electrical Engineering and Computer Science.

The paper for which Squire received the Prizmatix Young Investigator Award was “Ultra-sensitive fluorescent imaging-biosensing using biological photonic crystals.”

In this research, Squire, along with Dr. Xianming Kong and other collaborators, were able to enhance the optical signals for florescence imaging using diatoms, which are single-celled algae.

“The hope is that this can be used for cellphone based biosensors,” Squire said. Sensitivity is the challenge for developing sensors that can be used outside of pristine laboratory conditions.

“Using these diatoms, we were able to enhance the sensitivity. So, even though your equipment isn’t quite as good, and even though you don’t have the perfect conditions, you can still get detection levels that are practical,” Squire said.

They have applied for a patent on the technology and are currently working on an application to detect a biomarker for cardiovascular disease.

Squire’s second award at the conference was runner up for Best Student Presentation for his paper entitled, “Facile detection of toxic ingredients in seafood using biologically enabled photonic crystal materials.“

This research utilized the fossilized remains of diatoms, called diatomaceous earth, which is sometimes used for filters. The device that Squire, Kong and collaborators developed was able to separate the target from other material in the sample, and enhance the optical signals for better detection of biotoxins that can infect food.

The study demonstrated successful detection of Sudan I, an illegal carcinogenic dye, in various chili products, and histamine, a naturally occurring toxin, in seafood that was intentionally contaminated and in decomposing tuna.

The device, called a thin layer chromatography plate, separates the target molecule from the rest of the sample matrix and enhances the performance of the detection.  The detection method that was employed uses scattered light from a laser which creates a unique fingerprint for different molecules (surface-enhanced Raman scattering).

“The Photonics West conference was a great opportunity to present our work.  Leading up to the conference, many of our group members were instrumental in the preparation and polishing of the presentations that led to these awards and I am very grateful to them for their help and support,” Squire said.

Abstracts

Ultra-sensitive fluorescent imaging-biosensing using biological photonic crystals

Kenneth Squire, Xianming Kong, Paul LeDuff, Gregory Rorrer, Alan X. Wang

Optical biosensing is a growing area of research known for its low limits of detection.  Among optical sensing techniques, fluorescence detection is among the most established and prevalent.  Fluorescence imaging is an optical biosensing modality that exploits the sensitivity of fluorescence in an easy-to-use process. Fluorescence imaging allows a user to place a sample on a sensor and use an imager, such as a camera, to collect the results.  The image can then be processed to determine the presence of the analyte.  Fluorescence imaging is appealing because it can be performed with as little as a light source, a camera and a data processor thus being ideal for nontrained personnel without any expensive equipment.  Fluorescence imaging sensors generally employ an immunoassay procedure to selectively trap analytes such as antigens or antibodies.  When the analyte is present, the sensor fluoresces thus transducing the chemical reaction into an optical signal capable of imaging.  Enhancement of this fluorescence leads to an enhancement in the detection capabilities of the sensor.  Diatoms are unicellular algae with a biosilica shell called a frustule.  The frustule is porous with periodic nanopores making them biological photonic crystals.  Additionally, the porous nature of the frustule allows for large surface area capable of multiple analyte binding sites.  In this paper, we fabricate a diatom based ultra-sensitive fluorescence imaging biosensor capable of detecting the antibody mouse immunoglobulin down to a concentration of 1 nM.  The measured signal has an enhancement of 6× when compared to sensors fabricated without diatoms.

 

Facile detection of toxic ingredients in seafood using biologically enabled photonic crystal materials

Xianming Kong, Kenneth Squire, and Alan X. Wang

Surface-enhanced Raman scattering (SERS) spectroscopy has attracted considerable attention recently as a powerful detection platform in biosensing because of the wealth of inherent information ascertained about the chemical and molecular composition of a sample. However, real-world samples are often composed of many components, which renders the detection of constitutes of mixed samples very challenging for SERS sensing. Accordingly, separation techniques are needed before SERS measurements. Thin layer chromatography (TLC) is a simple, fast and cost-effective technique for analyte separation and can a play pivotal role for on-site sensing. However, combining TLC with SERS is only successful to detect a limited number of analytes that have large Raman scattering cross sections. As a kind of biogenic amine, histamine (2-(4-imidazolyl)-ethylamine) has a relationship with many health problems resulting from seafood consumption occurring worldwide. Diatomaceous earth consists of fossilized remains of diatoms, a type of hard-shelled algae. As a kind of natural photonic biosilica from geological deposits, it has a variety of unique properties including highly porous structure, excellent adsorption capacity, and low cost. In addition, the two dimensional periodic pores on diatomite earth with hierarchical nanoscale photonic crystal features can enhance the localized optical field. Herein, we fabricate TLC plates from diatomite as the stationary phase combining with SERS to separate and detect histamine from seafood samples. We have proved that the diatomite on the TLC plate not only functions as stationary phase, but also provides additional Raman enhancement, in which the detection limit of 2 ppm was achieved for pyrene in mixture.

Alannah Oleson

Alannah Oleson was selected as a finalist for the Computing Research Association’s (CRA) Outstanding Undergraduate Researcher Award. The award recognizes undergraduates who have made significant contributions to research.

For the past three years Oleson has been working with Margaret Burnett, Distinguished Professor of computer science in the College of Engineering, who studies human computer interaction. Oleson has worked on two different areas of research with Burnett: end-user programming and gender-inclusive software.

Oleson’s involvement has been extensive, including helping to plan and program the studies, debug procedures, collect and analyze data, and write up the results. She is co-author on six research papers and is one of the primary co-authors of a document describing the foundations of GenderMag, which is a software inspection process for programmers to uncover gender inclusiveness issues in software.

In the nomination letter for the CRA award Burnett wrote of Oleson: “In my 25 years as a faculty member, she is one of the very best undergraduate students I have seen.”

Last year, Oleson was one of 10 women to win the Adobe Research Women-in-Technology Scholarship.

Conference photo
ACM OOPSLA’17 conference. From left to right: Michael Bond, Danny Dig, Davood Mazinian, Jonathan Aldrich, Gail Murphy, Sam Tobin- Hochstadt.

Danny Dig with his students and collaborators won four prestigious research paper awards at international conferences this year. Dig, an associate professor of computer science in the College of Engineering at Oregon State University, researches software engineering. His focus is on interactive program transformations that improve programmer productivity and software quality.

conference photo
ICSME ’17 conference. From left to right: Nick Nelson and Thomas Zimmermann.

Distinguished Paper Award (awarded by ACM SIGSOFT at FSE ’17)

Trade-Offs in Continuous Integration: Assurance, Security, and Flexibility
Authors: Michael Hilton, Nicholas Nelson, Timothy Tunnell, Darko Marinov, and Danny Dig

Distinguished Paper Award (awarded by IEEE TCSE at ICSME’17)

Software Practitioner Perspectives on Merge Conflicts and Resolutions
Authors: Shane McKee, Nicholas Nelson, Anita Sarma, and Danny Dig

Distinguished Artifact Award (awarded by ACM SIGPLAN at OOPSLA’17)

Understanding the Use of Lambda Expressions in Java
Authors: Davood Mazinanian, Ameya Ketkar, Nikolaos Tsantalis, and Danny Dig

Best Paper Award (awarded by IBM at HICSS’17)

Are Web Applications Ready for Parallelism?
Authors: Cosmin Radoi, Stephan Herhut, Jaswanth Sreeram, and Danny Dig

Mike Rosulek
Mike Rosulek, assistant professor of computer science

Mike Rosulek, assistant professor of computer science in the College of Engineering at Oregon State University, received a Visa Faculty Research Award to advance methods of customer privacy and fraud detection.

“We’ve known for several decades that cryptography can protect not just data at rest, but also data in use, at least in principle. Finally, in the last several years these cryptographic ideas have been improved to become truly practical,” Rosulek said.

Rosulek and his colleague at Visa, Payman Mohassel, will be working to improve a tool from cryptology called private set intersection, which allows two parties to find items in common on two separate lists without revealing any other information from the lists.

Their research will help make complicated queries faster to process. For example, a company may want to know how many customers they have in common with another company without revealing who those customers are.

The funds will support one graduate student for a year who will be helping to develop new prototypes that would make advanced cryptography practical for companies.

“This award demonstrates that industry leaders see the potential of advanced cryptography to protect data during use and solve real-world privacy challenges,” Rosulek said.