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• 1. [Image] Ventilation Control System

  	This paper describes a ventilation control system designed using off-the-shelf components. The system has outputs for two fans, inputs for two wind meters, a power switch, a touchscreen monitor, and three ...
  	Citation × Citation Citation Abstract Copy Title: Ventilation Control System Author: Strauss, Tyler Year: 2014 This paper describes a ventilation control system designed using off-the-shelf components. The system has outputs for two fans, inputs for two wind meters, a power switch, a touchscreen monitor, and three warning indicators. The system measures air flow within ± 1 f/m using the WeatherFlow wind meters. The microprocessor used to control the system offers manual or automated control. The automated system maintains air flow within ± 24 f/m and can re-establish air flow within 160 seconds of partial air flow blockage Title: Ventilation Control System Author: Strauss, Tyler Year: 2014 This paper describes a ventilation control system designed using off-the-shelf components. The system has outputs for two fans, inputs for two wind meters, a power switch, a touchscreen monitor, and three warning indicators. The system measures air flow within ± 1 f/m using the WeatherFlow wind meters. The microprocessor used to control the system offers manual or automated control. The automated system maintains air flow within ± 24 f/m and can re-establish air flow within 160 seconds of partial air flow blockage Close

• 2. [Image] John Ousterhout and Gretchen Hunter

  	John Ousterhout and daughter Gretchen Hunter stand in front of a row of Sauvignon Blanc.
  	Citation × Citation Citation Abstract Copy Title: John Ousterhout and Gretchen Hunter Author: Ousterhout Wine & Vineyard (Or.), Maureen Battistella Year: 2014 John Ousterhout and daughter Gretchen Hunter stand in front of a row of Sauvignon Blanc. Title: John Ousterhout and Gretchen Hunter Author: Ousterhout Wine & Vineyard (Or.), Maureen Battistella Year: 2014 John Ousterhout and daughter Gretchen Hunter stand in front of a row of Sauvignon Blanc. Close

• 3. [Image] Old Vines, Inverted Lyre

  	Old vines at Ousterhout Vineyard showing John's Inverted Lyre trellis system, and the horizontal positioning made possible by their wide rows.
  	Citation × Citation Citation Abstract Copy Title: Old Vines, Inverted Lyre Author: Ousterhout Wine & Vineyard (Or.), Maureen Battistella Year: 2014 Old vines at Ousterhout Vineyard showing John's Inverted Lyre trellis system, and the horizontal positioning made possible by their wide rows. Title: Old Vines, Inverted Lyre Author: Ousterhout Wine & Vineyard (Or.), Maureen Battistella Year: 2014 Old vines at Ousterhout Vineyard showing John's Inverted Lyre trellis system, and the horizontal positioning made possible by their wide rows. Close

• 4. [Article] Focus on a STEM, Based in Place, Watershed Curriculum: A confluence of stormwater, humans, knowledge, attitudes, and skills

  This case study investigated the potential of a place-based watershed curriculum, using STEM principles, to increase watershed literacy and knowledge of human impacts on stormwater in the environment. ...

  Citation × Citation Citation Abstract Copy Title: Focus on a STEM, Based in Place, Watershed Curriculum: A confluence of stormwater, humans, knowledge, attitudes, and skills Author: Schall, Lecia Molineux Year: 2015 This case study investigated the potential of a place-based watershed curriculum, using STEM principles, to increase watershed literacy and knowledge of human impacts on stormwater in the environment. A secondary goal was to examine whether the place-based connection and increased exposure to issues within their local watershed impacted the students' environmental attitudes and sense of place. Over 500 sixth graders participated in this localized curriculum, where they learned the science behind watershed issues on their own school campuses. They focused on ways humans can monitor and mitigate their impacts on stormwater, through engineering investigations. The mixed-method research study investigated the effectiveness of the OLWEDU curriculum, to address these key questions: 1) To what degree did the OLWEDU increase the students' combined watershed literacy? 2) To what extent did the OLWEDU affect their environmental attitudes? 3) How did using a STEM oriented and place-based curriculum make the learning more relevant? In order to provide a solid triangulation of data, this study used a quasi-experimental design format with multiple measures: a) A Pre-Posttest (PPT), was given to all of the students to gather quantitative changes in knowledge of watershed concepts, stormwater issues related to human impacts on the environment, and engineering techniques; b) A constructed-knowledge questionnaire (CKQ) was used with forty four of the participants, to gather additional quantitative data on the students' local watershed knowledge; c) an environmental attitudes survey (EAS) was included in this sub-sample group; d) interviews were conducted with ten of the students to examine their opinions on the STEM aspects of the curriculum in addition to the place-based connections between the unit and their community. The statistically significant results showed increases in overall watershed literacy, knowledge of human impacts on stormwater, engineering principles, and environmental attitudes. These findings will be used to improve the current curriculum, and have broader implications concerning the benefits of using a formalized middle-school 21st century standards-based curriculum to teach watershed literacy and promote pro-environmental attitudes by using a combination of Science, Technology, Engineering, and Math in a local, place-based context. Title: Focus on a STEM, Based in Place, Watershed Curriculum: A confluence of stormwater, humans, knowledge, attitudes, and skills Author: Schall, Lecia Molineux Year: 2015 This case study investigated the potential of a place-based watershed curriculum, using STEM principles, to increase watershed literacy and knowledge of human impacts on stormwater in the environment. A secondary goal was to examine whether the place-based connection and increased exposure to issues within their local watershed impacted the students' environmental attitudes and sense of place. Over 500 sixth graders participated in this localized curriculum, where they learned the science behind watershed issues on their own school campuses. They focused on ways humans can monitor and mitigate their impacts on stormwater, through engineering investigations. The mixed-method research study investigated the effectiveness of the OLWEDU curriculum, to address these key questions: 1) To what degree did the OLWEDU increase the students' combined watershed literacy? 2) To what extent did the OLWEDU affect their environmental attitudes? 3) How did using a STEM oriented and place-based curriculum make the learning more relevant? In order to provide a solid triangulation of data, this study used a quasi-experimental design format with multiple measures: a) A Pre-Posttest (PPT), was given to all of the students to gather quantitative changes in knowledge of watershed concepts, stormwater issues related to human impacts on the environment, and engineering techniques; b) A constructed-knowledge questionnaire (CKQ) was used with forty four of the participants, to gather additional quantitative data on the students' local watershed knowledge; c) an environmental attitudes survey (EAS) was included in this sub-sample group; d) interviews were conducted with ten of the students to examine their opinions on the STEM aspects of the curriculum in addition to the place-based connections between the unit and their community. The statistically significant results showed increases in overall watershed literacy, knowledge of human impacts on stormwater, engineering principles, and environmental attitudes. These findings will be used to improve the current curriculum, and have broader implications concerning the benefits of using a formalized middle-school 21st century standards-based curriculum to teach watershed literacy and promote pro-environmental attitudes by using a combination of Science, Technology, Engineering, and Math in a local, place-based context. Close

• 5. [Article] Behavioral Observation and Paternal Investment of Eastern Kingbirds at Malheur National Wildlife Refuge

  We have been studying the population of Eastern Kingbirds breeding in riparian habitats in Malheur National Wildlife Refuge (eastern Oregon) since 2002. These efforts have created an ideal research environment ...

  Citation × Citation Citation Abstract Copy Title: Behavioral Observation and Paternal Investment of Eastern Kingbirds at Malheur National Wildlife Refuge Author: Chutter, Christopher Michael Year: 2014 We have been studying the population of Eastern Kingbirds breeding in riparian habitats in Malheur National Wildlife Refuge (eastern Oregon) since 2002. These efforts have created an ideal research environment wherein most adults in the population have been color banded and DNA sampled and, as part of other research projects, nearly all broods since 2003 have been paternity tested. I decided to use behavioral video recordings of parental nest behavior undertaken between 2003 and 2010 for two unrelated projects. First, I tested the effectiveness of video sampling nesting behavior (see below and chapter 2). Second, I tested whether male kingbirds were able to affect their level of paternal investment in accordance with their level or realized paternity (see below and chapter 3). Chapter 2 was split into three distinct questions: 1) are parental nesting behaviors repeatable, 2) is a one hour sample sufficient to capture variability in these behaviors, and 3) is the first hour of recording sufficient to capture variability in these behaviors. I found overwhelming evidence that the behaviors I measured were repeatable. This is truly important, for if repeatability was disproven, it would call into question the use of sampling throughout the field of animal behavior. I similarly found strong evidence that a one hour sample was sufficient to capture variability in parental behaviors. From this I was able to suggest that further sampling effort would be better spent increasing sample size rather than observation length. Testing whether the first hour of recording was sufficient to capture variability in parental behavior found more muddled results. While there generally was correlation between behavioral values in the first hour and those over a longer observation period, most behaviors were found to have significantly lower values in the first hour. I tested whether this was the result of a lingering observer effect or a natural effect of time of day and concluded that an observer effect was the more likely explanation. In chapter 3, I ran one of the more in depth and complicated tests for a relationship between paternal investment and realized paternity that I was able to find in the literature. I used the standard male feeding rate as a measure of male investment as well as a far more nuanced measure derived from the first Eigenvector of an analysis of six different paternal behaviors. These were both tested using Akaike's Information Criterion against a number of variables likely to affect parental behavior, including realized paternity. Ultimately, I found no evidence that kingbirds were able to affect paternal investment in response to lost paternity, and conclude that they likely had no means to assess realized paternity within the nest of their social mate. However, from the other parameters tested I was able to find that males increased their investment as brood size increased and as the female spent more time attending, but not feeding, the nestlings. Also, male investment decreased as territory density increased and flight feather length increased. Theory surrounding the variability of extrapair paternity in birds can be used to account for these results. In a denser population males are predicted to reduce paternal effort for one of two reasons: increased likelihood of paternity loss in his own nest and an increased investment in pursuing extrapair copulations of his own. Longer flight feathers are a sign of age and quality in kingbirds, so males with this trait are expected to spend more time pursuing extrapair copulations as they are more likely to be successful in this endeavor. Title: Behavioral Observation and Paternal Investment of Eastern Kingbirds at Malheur National Wildlife Refuge Author: Chutter, Christopher Michael Year: 2014 We have been studying the population of Eastern Kingbirds breeding in riparian habitats in Malheur National Wildlife Refuge (eastern Oregon) since 2002. These efforts have created an ideal research environment wherein most adults in the population have been color banded and DNA sampled and, as part of other research projects, nearly all broods since 2003 have been paternity tested. I decided to use behavioral video recordings of parental nest behavior undertaken between 2003 and 2010 for two unrelated projects. First, I tested the effectiveness of video sampling nesting behavior (see below and chapter 2). Second, I tested whether male kingbirds were able to affect their level of paternal investment in accordance with their level or realized paternity (see below and chapter 3). Chapter 2 was split into three distinct questions: 1) are parental nesting behaviors repeatable, 2) is a one hour sample sufficient to capture variability in these behaviors, and 3) is the first hour of recording sufficient to capture variability in these behaviors. I found overwhelming evidence that the behaviors I measured were repeatable. This is truly important, for if repeatability was disproven, it would call into question the use of sampling throughout the field of animal behavior. I similarly found strong evidence that a one hour sample was sufficient to capture variability in parental behaviors. From this I was able to suggest that further sampling effort would be better spent increasing sample size rather than observation length. Testing whether the first hour of recording was sufficient to capture variability in parental behavior found more muddled results. While there generally was correlation between behavioral values in the first hour and those over a longer observation period, most behaviors were found to have significantly lower values in the first hour. I tested whether this was the result of a lingering observer effect or a natural effect of time of day and concluded that an observer effect was the more likely explanation. In chapter 3, I ran one of the more in depth and complicated tests for a relationship between paternal investment and realized paternity that I was able to find in the literature. I used the standard male feeding rate as a measure of male investment as well as a far more nuanced measure derived from the first Eigenvector of an analysis of six different paternal behaviors. These were both tested using Akaike's Information Criterion against a number of variables likely to affect parental behavior, including realized paternity. Ultimately, I found no evidence that kingbirds were able to affect paternal investment in response to lost paternity, and conclude that they likely had no means to assess realized paternity within the nest of their social mate. However, from the other parameters tested I was able to find that males increased their investment as brood size increased and as the female spent more time attending, but not feeding, the nestlings. Also, male investment decreased as territory density increased and flight feather length increased. Theory surrounding the variability of extrapair paternity in birds can be used to account for these results. In a denser population males are predicted to reduce paternal effort for one of two reasons: increased likelihood of paternity loss in his own nest and an increased investment in pursuing extrapair copulations of his own. Longer flight feathers are a sign of age and quality in kingbirds, so males with this trait are expected to spend more time pursuing extrapair copulations as they are more likely to be successful in this endeavor. Close

• 6. [Article] Novel Methods for Learning and Adaptation in Chemical Reaction Networks

  State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be re-programmed or trained once fabricated. The implementation of adaptive biochemical ...

  Citation × Citation Citation Abstract Copy Title: Novel Methods for Learning and Adaptation in Chemical Reaction Networks Author: Banda, Peter Year: 2015 State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be re-programmed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. Currently, biochemistry lacks a systems vision on how the user-level programming interface and abstraction with a subsequent translation to chemistry should look like. By developing adaptation in chemistry, we could replace multiple hard-wired systems with a single programmable template that can be (re)trained to match a desired input-output profile benefiting smart drug delivery, pattern recognition, and chemical computing. I aimed to address these challenges by proposing several approaches to learning and adaptation in Chemical Reaction Networks (CRNs), a type of simulated chemistry, where species are unstructured, i.e., they are identified by symbols rather than molecular structure, and their dynamics or concentration evolution are driven by reactions and reaction rates that follow mass-action and Michaelis-Menten kinetics. Several CRN and experimental DNA-based models of neural networks exist. However, these models successfully implement only the forward-pass, i.e., the input-weight integration part of a perceptron model. Learning is delegated to a non-chemical system that computes the weights before converting them to molecular concentrations. Autonomous learning, i.e., learning implemented fully inside chemistry has been absent from both theoretical and experimental research. The research in this thesis offers the first constructive evidence that learning in CRNs is, in fact, possible. I have introduced the original concept of a chemical binary perceptron that can learn all 14 linearly-separable logic functions and is robust to the perturbation of rate constants. That shows learning is universal and substrate-free. To simplify the model I later proposed and applied the "asymmetric" chemical arithmetic providing a compact solution for representing negative numbers in chemistry. To tackle more difficult tasks and to serve more complicated biochemical applications, I introduced several key modular building blocks, each addressing certain aspects of chemical information processing and learning. These parts organically combined into gradually more complex systems. First, instead of simple static Boolean functions, I tackled analog time-series learning and signal processing by modeling an analog chemical perceptron. To store past input concentrations as a sliding window I implemented a chemical delay line, which feeds the values to the underlying chemical perceptron. That allows the system to learn, e.g., the linear moving-average and to some degree predict a highly nonlinear NARMA benchmark series. Another important contribution to the area of chemical learning, which I have helped to shape, is the composability of perceptrons into larger multi-compartment networks. Each compartment hosts a single chemical perceptron and compartments communicate with each other through a channel-mediated exchange of molecular species. Besides the feedforward pass, I implemented the chemical error backpropagation analogous to that of feedforward neural networks. Also, after applying mass-action kinetics for the catalytic reactions, I succeeded to systematically analyze the ODEs of my models and derive the closed exact and approximative formulas for both the input-weight integration and the weight update with a learning rate annealing. I proved mathematically that the formulas of certain chemical perceptrons equal the formal linear and sigmoid neurons, essentially bridging neural networks and adaptive CRNs. For all my models the basic methodology was to first design species and reactions, and then set the rate constants either "empirically" by hand, automatically by a standard genetic algorithm (GA), or analytically if possible. I performed all simulations in my COEL framework, which is the first cloud-based chemistry modeling tool, accessible at http://coel-sim.org. I minimized the amount of required molecular species and reactions to make wet chemical implementation possible. I applied an automatized mapping technique, Soloveichik's CRN-to-DNA-strand-displacement transformation, to the chemical linear perceptron and the manual signalling delay line and obtained their full DNA-strand specified implementations. As an alternative DNA-based substrate, I mapped these two models also to deoxyribozyme-mediated cleavage reactions reducing the size of the displacement variant to a third. Both DNA-based incarnations could directly serve as blue-prints for wet biochemicals. Besides an actual synthesis of my models and conducting an experiment in a biochemical laboratory, the most promising future work is to employ so-called reservoir computing (RC), which is a novel machine learning method based on recurrent neural networks. The RC approach is relevant because for time-series prediction it is clearly superior to classical recurrent networks. It can also be implemented in various ways, such as electrical circuits, physical systems, such as a colony of Escherichia Coli, and water. RC's loose structural assumptions therefore suggest that it could be expressed in a chemical form as well. This could further enhance the expressivity and capabilities of chemically-embedded learning. My chemical learning systems may have applications in the area of medical diagnosis and smart medication, e.g., concentration signal processing and monitoring, and the detection of harmful species, such as chemicals produced by cancer cells in a host (cancer miRNAs) or the detection of a severe event, defined as a linear or nonlinear temporal concentration pattern. My approach could replace hard-coded solutions and would allow to specify, train, and reuse chemical systems without redesigning them. With time-series integration, biochemical computers could keep a record of changing biological systems and act as diagnostic aids and tools in preventative and highly personalized medicine. Title: Novel Methods for Learning and Adaptation in Chemical Reaction Networks Author: Banda, Peter Year: 2015 State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be re-programmed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. Currently, biochemistry lacks a systems vision on how the user-level programming interface and abstraction with a subsequent translation to chemistry should look like. By developing adaptation in chemistry, we could replace multiple hard-wired systems with a single programmable template that can be (re)trained to match a desired input-output profile benefiting smart drug delivery, pattern recognition, and chemical computing. I aimed to address these challenges by proposing several approaches to learning and adaptation in Chemical Reaction Networks (CRNs), a type of simulated chemistry, where species are unstructured, i.e., they are identified by symbols rather than molecular structure, and their dynamics or concentration evolution are driven by reactions and reaction rates that follow mass-action and Michaelis-Menten kinetics. Several CRN and experimental DNA-based models of neural networks exist. However, these models successfully implement only the forward-pass, i.e., the input-weight integration part of a perceptron model. Learning is delegated to a non-chemical system that computes the weights before converting them to molecular concentrations. Autonomous learning, i.e., learning implemented fully inside chemistry has been absent from both theoretical and experimental research. The research in this thesis offers the first constructive evidence that learning in CRNs is, in fact, possible. I have introduced the original concept of a chemical binary perceptron that can learn all 14 linearly-separable logic functions and is robust to the perturbation of rate constants. That shows learning is universal and substrate-free. To simplify the model I later proposed and applied the "asymmetric" chemical arithmetic providing a compact solution for representing negative numbers in chemistry. To tackle more difficult tasks and to serve more complicated biochemical applications, I introduced several key modular building blocks, each addressing certain aspects of chemical information processing and learning. These parts organically combined into gradually more complex systems. First, instead of simple static Boolean functions, I tackled analog time-series learning and signal processing by modeling an analog chemical perceptron. To store past input concentrations as a sliding window I implemented a chemical delay line, which feeds the values to the underlying chemical perceptron. That allows the system to learn, e.g., the linear moving-average and to some degree predict a highly nonlinear NARMA benchmark series. Another important contribution to the area of chemical learning, which I have helped to shape, is the composability of perceptrons into larger multi-compartment networks. Each compartment hosts a single chemical perceptron and compartments communicate with each other through a channel-mediated exchange of molecular species. Besides the feedforward pass, I implemented the chemical error backpropagation analogous to that of feedforward neural networks. Also, after applying mass-action kinetics for the catalytic reactions, I succeeded to systematically analyze the ODEs of my models and derive the closed exact and approximative formulas for both the input-weight integration and the weight update with a learning rate annealing. I proved mathematically that the formulas of certain chemical perceptrons equal the formal linear and sigmoid neurons, essentially bridging neural networks and adaptive CRNs. For all my models the basic methodology was to first design species and reactions, and then set the rate constants either "empirically" by hand, automatically by a standard genetic algorithm (GA), or analytically if possible. I performed all simulations in my COEL framework, which is the first cloud-based chemistry modeling tool, accessible at http://coel-sim.org. I minimized the amount of required molecular species and reactions to make wet chemical implementation possible. I applied an automatized mapping technique, Soloveichik's CRN-to-DNA-strand-displacement transformation, to the chemical linear perceptron and the manual signalling delay line and obtained their full DNA-strand specified implementations. As an alternative DNA-based substrate, I mapped these two models also to deoxyribozyme-mediated cleavage reactions reducing the size of the displacement variant to a third. Both DNA-based incarnations could directly serve as blue-prints for wet biochemicals. Besides an actual synthesis of my models and conducting an experiment in a biochemical laboratory, the most promising future work is to employ so-called reservoir computing (RC), which is a novel machine learning method based on recurrent neural networks. The RC approach is relevant because for time-series prediction it is clearly superior to classical recurrent networks. It can also be implemented in various ways, such as electrical circuits, physical systems, such as a colony of Escherichia Coli, and water. RC's loose structural assumptions therefore suggest that it could be expressed in a chemical form as well. This could further enhance the expressivity and capabilities of chemically-embedded learning. My chemical learning systems may have applications in the area of medical diagnosis and smart medication, e.g., concentration signal processing and monitoring, and the detection of harmful species, such as chemicals produced by cancer cells in a host (cancer miRNAs) or the detection of a severe event, defined as a linear or nonlinear temporal concentration pattern. My approach could replace hard-coded solutions and would allow to specify, train, and reuse chemical systems without redesigning them. With time-series integration, biochemical computers could keep a record of changing biological systems and act as diagnostic aids and tools in preventative and highly personalized medicine. Close

• 7. [Article] Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications

  Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are ...

  Citation × Citation Citation Abstract Copy Title: Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications Author: Lopez-Johnston, Siena Marie Year: 2014 Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are threatened severely by a lack of passage at mainstem dams, lamprey specific passage structures have been designed and constructed to address the problem. The Cascades Island Lamprey Passage Structure (LPS) at Bonneville Dam is the longest and steepest structure of its type, following the addition of an exit pipe which allows lampreys to travel from the tailrace of the dam to the forebay. The intent of this study was to assess lamprey use of the structure and whether the structure hinders lamprey migration to subsequent dams. The study was carried out during the 2013 migration season. The study used three different treatment groups of lampreys released on five dates spanning the migration season (n=75 lamprey). Two of these groups (n=50), with different tagging methods, were released directly into the LPS to assess passage success, travel time, and tagging effect. The third group (n=25) was released into the forebay to test whether the structure impedes migration upstream. Fish were monitored via receiver arrays on the LPS and at dams on the river system. Overall passage efficiency was 74% (37 of 50 used the CI LPS successfully). Mean travel time to navigate the structure was 12 h. Fish size had no significant effect on travel time in the LPS. Water temperature had a significant effect on travel time in the LPS. There was no statistically significant effect of tagging on passage efficiency or travel time. The groups that used the LPS performed slightly better migrating upstream to the next dam than the group that bypassed the structure, but the difference was not significant. The groups that used the LPS traveled to more subsequent dams upstream than did the group that bypassed the LPS. It can be concluded that lamprey passed the structure successfully. Temperature (proxy for seasonality) had an effect on travel time in the LPS; however fish size and tagging had no effect. The LPS does not affect the ability of migrating lampreys to continue migration to subsequent dams. Such findings have important implications for management of lamprey in the region. Title: Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications Author: Lopez-Johnston, Siena Marie Year: 2014 Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are threatened severely by a lack of passage at mainstem dams, lamprey specific passage structures have been designed and constructed to address the problem. The Cascades Island Lamprey Passage Structure (LPS) at Bonneville Dam is the longest and steepest structure of its type, following the addition of an exit pipe which allows lampreys to travel from the tailrace of the dam to the forebay. The intent of this study was to assess lamprey use of the structure and whether the structure hinders lamprey migration to subsequent dams. The study was carried out during the 2013 migration season. The study used three different treatment groups of lampreys released on five dates spanning the migration season (n=75 lamprey). Two of these groups (n=50), with different tagging methods, were released directly into the LPS to assess passage success, travel time, and tagging effect. The third group (n=25) was released into the forebay to test whether the structure impedes migration upstream. Fish were monitored via receiver arrays on the LPS and at dams on the river system. Overall passage efficiency was 74% (37 of 50 used the CI LPS successfully). Mean travel time to navigate the structure was 12 h. Fish size had no significant effect on travel time in the LPS. Water temperature had a significant effect on travel time in the LPS. There was no statistically significant effect of tagging on passage efficiency or travel time. The groups that used the LPS performed slightly better migrating upstream to the next dam than the group that bypassed the structure, but the difference was not significant. The groups that used the LPS traveled to more subsequent dams upstream than did the group that bypassed the LPS. It can be concluded that lamprey passed the structure successfully. Temperature (proxy for seasonality) had an effect on travel time in the LPS; however fish size and tagging had no effect. The LPS does not affect the ability of migrating lampreys to continue migration to subsequent dams. Such findings have important implications for management of lamprey in the region. Close

• 8. [Article] Last Mile Asset Monitoring: Low Cost Rapid Deployment Asset Monitoring

  Installation and utilization of residential distribution transformers has not changed substantially over a long period of time. Utilities typically size their transformers based on a formula that takes ...

  Citation × Citation Citation Abstract Copy Title: Last Mile Asset Monitoring: Low Cost Rapid Deployment Asset Monitoring Author: Zumr, Zdenek Year: 2014 Installation and utilization of residential distribution transformers has not changed substantially over a long period of time. Utilities typically size their transformers based on a formula that takes into account broadly what types and how many dwellings will be connected. Most new residential dwellings feature 200 Amp service per household with an anticipated energy demand of under 20,000 kWh per year. Average electrical energy consumption varies from state to state but averages to 11,280 kWh per year. Energy demand is expected to fall into a typical residential load curve that shows increased demand early in the morning, then decreasing during the day and another peak early to late evening. Distribution transformers are sized at the limit of the combined evening peak with the assumption that the transformer has enough thermal mass to absorb short overloads that may occur when concurrent loading situations among multiple dwellings arise. The assumption that concurrent loading is of short duration and the transformer can cool off during the night time has been validated over the years and has become standard practice. This has worked well when dwelling loads follow an averaging scheme and low level of coincidence. With the arrival of electric vehicles (EV's) this assumption has to be reevaluated. The acquisition of an electric vehicle in a household can drive up energy demand by over 4000 kWh per year. Potentially problematic is the increased capacity of battery packs and the resulting proliferation of Level 2 chargers. The additional load of a single Level 2 charger concurring with the combined evening peak load will push even conservatively sized distribution transformers over their nameplate rating for a substantial amount of time. Additionally, unlike common household appliances of similar power requirements such as ovens or water heaters, a Level 2 battery charger will run at peak power consumption for several hours, and the current drawn by the EVs has very high levels of harmonic distortion. The excessive loading and harmonic profile can potentially result in damaging heat build-up resulting in asset degradation. In this thesis I present a device and method that monitors pole mounted distribution transformers for overheating, collect and wirelessly upload data and initiate commands to chargers to change output levels from Level 2 to Level 1 or shut down EV charging altogether until the transformer returns into safe operational range. Title: Last Mile Asset Monitoring: Low Cost Rapid Deployment Asset Monitoring Author: Zumr, Zdenek Year: 2014 Installation and utilization of residential distribution transformers has not changed substantially over a long period of time. Utilities typically size their transformers based on a formula that takes into account broadly what types and how many dwellings will be connected. Most new residential dwellings feature 200 Amp service per household with an anticipated energy demand of under 20,000 kWh per year. Average electrical energy consumption varies from state to state but averages to 11,280 kWh per year. Energy demand is expected to fall into a typical residential load curve that shows increased demand early in the morning, then decreasing during the day and another peak early to late evening. Distribution transformers are sized at the limit of the combined evening peak with the assumption that the transformer has enough thermal mass to absorb short overloads that may occur when concurrent loading situations among multiple dwellings arise. The assumption that concurrent loading is of short duration and the transformer can cool off during the night time has been validated over the years and has become standard practice. This has worked well when dwelling loads follow an averaging scheme and low level of coincidence. With the arrival of electric vehicles (EV's) this assumption has to be reevaluated. The acquisition of an electric vehicle in a household can drive up energy demand by over 4000 kWh per year. Potentially problematic is the increased capacity of battery packs and the resulting proliferation of Level 2 chargers. The additional load of a single Level 2 charger concurring with the combined evening peak load will push even conservatively sized distribution transformers over their nameplate rating for a substantial amount of time. Additionally, unlike common household appliances of similar power requirements such as ovens or water heaters, a Level 2 battery charger will run at peak power consumption for several hours, and the current drawn by the EVs has very high levels of harmonic distortion. The excessive loading and harmonic profile can potentially result in damaging heat build-up resulting in asset degradation. In this thesis I present a device and method that monitors pole mounted distribution transformers for overheating, collect and wirelessly upload data and initiate commands to chargers to change output levels from Level 2 to Level 1 or shut down EV charging altogether until the transformer returns into safe operational range. Close

• 9. [Article] Device, Method, and Algorithm to Assess Changes in Cardiac Output via Intracardiac Impedance Monitoring

  Cardiac output, the volume of blood pumped by the heart over time, is a powerful clinical metric used by physicians to assess overall cardiac health and patient well-being. However, current cardiac output ...

  Citation × Citation Citation Abstract Copy Title: Device, Method, and Algorithm to Assess Changes in Cardiac Output via Intracardiac Impedance Monitoring Author: Schau, Geoffrey Fredrick Year: 2015 Cardiac output, the volume of blood pumped by the heart over time, is a powerful clinical metric used by physicians to assess overall cardiac health and patient well-being. However, current cardiac output estimation methods are typically invasive, time-consuming, expensive, or some combination of all three. Patients that receive artificial cardiac pacemaker devices are particularly susceptible to cardiac dysfunction and often require long-term cardiac monitoring support. This thesis proposes a novel cardiac output monitoring solution which leverages an implantable intracardiac medical device. The principles of traditional impedance cardiography, an established cardiac output monitoring technique in practice for over fifty years, have been adapted to incorporate a leadless artificial cardiac pacemaker, an implantable medical device contained entirely within the heart. This novel method, colloquially referred to as Z-Cardio, monitors time-varying intracardiac impedance modulation to assess changes in cardiac output. In this study, technologies both old and new are synthesized to produce a novel and effective method of monitoring a critical metric of cardiac health. Title: Device, Method, and Algorithm to Assess Changes in Cardiac Output via Intracardiac Impedance Monitoring Author: Schau, Geoffrey Fredrick Year: 2015 Cardiac output, the volume of blood pumped by the heart over time, is a powerful clinical metric used by physicians to assess overall cardiac health and patient well-being. However, current cardiac output estimation methods are typically invasive, time-consuming, expensive, or some combination of all three. Patients that receive artificial cardiac pacemaker devices are particularly susceptible to cardiac dysfunction and often require long-term cardiac monitoring support. This thesis proposes a novel cardiac output monitoring solution which leverages an implantable intracardiac medical device. The principles of traditional impedance cardiography, an established cardiac output monitoring technique in practice for over fifty years, have been adapted to incorporate a leadless artificial cardiac pacemaker, an implantable medical device contained entirely within the heart. This novel method, colloquially referred to as Z-Cardio, monitors time-varying intracardiac impedance modulation to assess changes in cardiac output. In this study, technologies both old and new are synthesized to produce a novel and effective method of monitoring a critical metric of cardiac health. Close

• 10. [Article] Hardware/Software Interface Assurance with Conformance Checking

  Hardware/Software (HW/SW) interfaces are pervasive in modern computer systems. Most of HW/SW interfaces are implemented by devices and their device drivers. Unfortunately, HW/SW interfaces are unreliable ...

  Citation × Citation Citation Abstract Copy Title: Hardware/Software Interface Assurance with Conformance Checking Author: Lei, Li Year: 2015 Hardware/Software (HW/SW) interfaces are pervasive in modern computer systems. Most of HW/SW interfaces are implemented by devices and their device drivers. Unfortunately, HW/SW interfaces are unreliable and insecure due to their intrinsic complexity and error-prone nature. Moreover, assuring HW/SW interface reliability and security is challenging. First, at the post-silicon validation stage, HW/SW integration validation is largely an ad-hoc and time-consuming process. Second, at the system deployment stage, transient hardware failures and malicious attacks make HW/SW interfaces vulnerable even after intensive testing and validation. In this dissertation, we present a comprehensive solution for HW/SW interface assurance over the system life cycle. This solution is composited of two major parts. First, our solution provides a systematic HW/SW co-validation framework which validates hardware and software together; Second, based on the co-validation framework, we design two schemes for assuring HW/SW interfaces over the system life cycle: (1) post-silicon HW/SW co-validation at the post-silicon validation stage; (2) HW/SW co-monitoring at the system deployment stage. Our HW/SW co-validation framework employs a key technique, conformance checking which checks the interface conformance between the device and its reference model. Furthermore, property checking is carried out to verify system properties over the interactions between the reference model and the driver. Based on the conformance between the reference model and the device, properties hold on the reference model/driver interface also hold on the device/driver interface. Conformance checking discovers inconsistencies between the device and its reference model thereby validating device interface implementations of both sides. Property checking detects both device and driver violations of HW/SW interface protocols. By detecting device and driver errors, our co-validation approach provides a systematic and ecient way to validate HW/SW interfaces. We developed two software tools which implement the two assurance schemes: DCC (Device Conformance Checker), a co-validation framework for post-silicon HW/SW integration validation; and CoMon (HW/SW Co-monitoring), a runtime verication framework for detecting bugs and malicious attacks across HW/SW interfaces. The two software tools lead to discovery of 42 bugs from four industry hardware devices, the device drivers, and their reference models. The results have demonstrated the signicance of our approach in HW/SW interface assurance of industry applications. Title: Hardware/Software Interface Assurance with Conformance Checking Author: Lei, Li Year: 2015 Hardware/Software (HW/SW) interfaces are pervasive in modern computer systems. Most of HW/SW interfaces are implemented by devices and their device drivers. Unfortunately, HW/SW interfaces are unreliable and insecure due to their intrinsic complexity and error-prone nature. Moreover, assuring HW/SW interface reliability and security is challenging. First, at the post-silicon validation stage, HW/SW integration validation is largely an ad-hoc and time-consuming process. Second, at the system deployment stage, transient hardware failures and malicious attacks make HW/SW interfaces vulnerable even after intensive testing and validation. In this dissertation, we present a comprehensive solution for HW/SW interface assurance over the system life cycle. This solution is composited of two major parts. First, our solution provides a systematic HW/SW co-validation framework which validates hardware and software together; Second, based on the co-validation framework, we design two schemes for assuring HW/SW interfaces over the system life cycle: (1) post-silicon HW/SW co-validation at the post-silicon validation stage; (2) HW/SW co-monitoring at the system deployment stage. Our HW/SW co-validation framework employs a key technique, conformance checking which checks the interface conformance between the device and its reference model. Furthermore, property checking is carried out to verify system properties over the interactions between the reference model and the driver. Based on the conformance between the reference model and the device, properties hold on the reference model/driver interface also hold on the device/driver interface. Conformance checking discovers inconsistencies between the device and its reference model thereby validating device interface implementations of both sides. Property checking detects both device and driver violations of HW/SW interface protocols. By detecting device and driver errors, our co-validation approach provides a systematic and ecient way to validate HW/SW interfaces. We developed two software tools which implement the two assurance schemes: DCC (Device Conformance Checker), a co-validation framework for post-silicon HW/SW integration validation; and CoMon (HW/SW Co-monitoring), a runtime verication framework for detecting bugs and malicious attacks across HW/SW interfaces. The two software tools lead to discovery of 42 bugs from four industry hardware devices, the device drivers, and their reference models. The results have demonstrated the signicance of our approach in HW/SW interface assurance of industry applications. Close