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.

Gabor Temes, professor of electrical and computer engineering in the College of Engineering at Oregon State University, will recieve the 2017 University Research Award from the Semiconductor Industry Association (SIA). The award recognizes his excellence in research for contributions in interface electronics, including analog-to-digital and digital-to-analog converters, switched-capacitor filters and amplifiers, and sensor interfaces.

Temes has a 60-year career that has spanned industry and academia. His research in the area of analog integrated circuits – the interface between the “real” analog world and digital signal processors – has improved the quality of sound and data communications.

He holds 14 patents and has more than 500 publications, including several books. His long career has earned him many accolades including the IEEE Kirchhoff Award and election to the National Academy of Engineering.

He will  receive the award in conjunction with the SIA Annual Award Dinner on Nov. 14, 2017 in San Jose, Calif.

Alannah Oleson
Alannah Oleson’s award led to a summer internship with Adobe in San Jose.

Alannah Oleson, undergraduate student in computer science at Oregon State University, was one of a handful of students from all over the world to win the Adobe Research Women-in-Technology Scholarship. The scholarship acknowledges women who are improving technology and have demonstrated outreach for their community.

Oleson is helping to improve technology in the area of human-computer interaction (HCI) with Margaret Burnett, distinguished professor of computer science. Oleson is working on the GenderMag project which helps programmers to design gender inclusive software.

Her outreach to the community included mentoring two high school students through Saturday Academy, which is a program designed to help students from under-represented communities gain experience in STEM fields. She taught them how to program and what it is like to work on a research project. A couple of years after the summer-long program, Oleson saw one of her students at Oregon State going through engineering orientation. Oleson felt proud to see him choose to major in computer science after participating in the Saturday Academy program.

“To see him go from whatever he had overcome to being a computer scientist and feeling like I played a part in that was really cool,” Oleson said.

Scholarship winners are awarded $10,000 and a one-year creative cloud subscription; are assigned an Adobe research mentor; and are given an opportunity to interview for an Adobe internship. Oleson succeeded in receiving an Adobe internship and worked in San Jose, CA for 10 weeks on a research team this summer.

“All I had known was living in Roseburg, so the experience of being in the middle of the tech world was fantastic. It made me feel more confident in my career,” she said.

After the internship, Adobe decided to sponsor Oleson’s senior capstone project. In the future, Oleson hopes to pursue a Ph.D. in human-computer interaction and eventually work in industry research.

Story by Raiza de Vera

2017 Rohde & Schwarz Engineering Competition team photo.
Braxton Cuneo, Erich Kramer, Andy Tolvstad, Karen Harper, and Aaron Schraner (left to right) advanced to the world final of the 2017 Rohde & Schwarz Engineering Competition.

Five students in the School of Electrical Engineering and Computer Science will be heading to Germany this summer to compete in the 2017 Rohde & Schwarz Engineering Competition. Their performance in the U.S. preliminary round earned them a spot at the world league competition.

Aaron Schraner, an electrical and computer engineering student, was motivated to compete since he participated last year on a team from the Oregon Institute of Technology that won the 2016 regional competition. Based on his experience there, he recruited Karen Harper for additional electrical engineering knowledge. All the other team members are in computer science:  Braxton Cuneo, Erich Kramer, and Andy Tolvstad.

Their task was to make improvements to software for a digital-signal processing application that could ultimately make video streaming better. Specifically, they were asked to speed up the processing of the software-based DVB-T2-Coder, based on the open source GNU Radio project, while maintaining accuracy.

“Signal processing is traditionally very, very computationally intensive, so any optimizations you can get out of something like that are going to be very beneficial to your workflow,” Andrew Tolvstad said.

“There was one loop we optimized that was run about 1.2 million times,” Karen Harper agreed.

“Just by changing a data type that was 32-bits wide to one that was 64-bits wide, we took another 5 to 10 percent off the total amount of time it took to run the program,” Aaron Schraner said.

During the competition, students made improvements to the code that was then automatically compiled and tested for performance once they submitted it via Git. Rohde & Schwarz continuously published a leader board of the top performing teams so the teams could watch their ranking move up or down.

The team members are excited to have an all-expenses paid trip to Germany, and are squeezing the trip into very busy lives of classes and internships. They also have a chance to win $3,000 for the top prize, $1,500 for second place, and $750 for third place.

But the money was not the only objective.

“It’s been a lot of fun,” Tolvstad said. “Just the thrill of trying to take something and make it the best it can possibly be by just rearranging its parts.”

This final will be held in Munich, Germany at the Rohde & Schwarz headquarters. Rohde & Schwarz is a privately held company with over 10,000 employees worldwide, including a design center in Beaverton.

Margaret BurnettProfessor Margaret Burnett has been on a roll lately, to put it mildly. Her most recent award is the 2017 Undergraduate Research Faculty Mentoring Award announced this month by the Education Committee of the Computing Research Association. This follows a string of awards from national organizations including the CHI Academy, the National Center for Women and Technology, ACM SIGSOFT, and IEEE Symposium on Visual Languages and Human-Centric Computing. She was also named 2016 Distinguished Professor recipient by Oregon State University, the highest academic honor the university can bestow on a faculty member.

The following quote comes from the the Education Committee of the Computing Research Association award announcement:

Margaret Burnett, Ph.D., is a distinguished professor in the School of Electrical and Computer Engineering at Oregon State University (OSU), a member of the ACM CHI Academy, and an ACM Distinguished Scientist. Burnett has contributed pioneering research on how ordinary users interact with software and optimizing that interaction. This resulted, in part, in the development of a new subarea, which is at the intersection of human-computer interaction and software engineering, called end-user software engineering.

 

Throughout her academic career, Burnett has continuously worked with undergraduate researchers and even accommodated high school students in her lab. She has mentored 39 undergraduate students in research; 21 were from underrepresented groups in computing, 32 co-authored published research papers, and 25 went on to graduate studies. A selection of the honors of her highly accomplished mentees includes three Google Scholarships, three NSF Graduate Fellowships, and two National Physical Sciences Consortium Graduate Fellowships. In her nomination, several mentees attested to her personal influence on and involvement in their lives and careers.

 

Impressively, Burnett influenced the culture of faculty undergraduate research mentoring in her school, increasing it to 50% participation. She has also led efforts to better support a diverse undergraduate population through trips to the Grace Hopper Celebration of Women in Computing, the adoption of a diversity plan, and new experimental scholarships for incoming freshmen women in computing. She has received awards from NCWIT, Microsoft, and OSU for her mentoring and research.