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Addressing Challenges in the U.S. West Coast Groundfish Bottom Trawl Fishery: An Evaluation of Trawl Gear Modifications
No full textThe U.S. West Coast groundfish bottom trawl fishery is a multispecies fishery that uses conventional bottom contact doors, sweeps, and trawl nets along the continental shelf break and upper slope to harvest groundfishes. These techniques are highly effective, as the fishery harvests nearly 30,000 mt of fishes earning over US$26 million annually in ex-vessel revenue, making this industry a staple along the West Coast. Although this fishery has experienced times of stock depletion, implementation of a catch share program, improved scientific understanding, and other management measures have greatly improved the economic and biological productivity of the fishery and rebuilt overfished stocks. Sablefish (Anoplopoma fimbria) is the most economically valuable stock in the fishery, but recent strong recruitment years have caused large catches of smaller-sized sablefish, limiting fishery participants’ economic yield. This compounds issues of underutilization for other species when constraining sablefish quota is used on undesirable-sized fish. Additionally, the characteristics of conventional bottom-tending trawl gear used to harvest these fishes can impact benthic habitats, cause unobserved mortalities of benthic organisms, and require high energy consumption for harvesting fishes. Trawl modifications that increase the gear size selectivity or reduce seafloor contact have been developed collectively between fishery researchers and the fishing industry around the globe, which may be beneficial for the West Coast groundfish bottom trawl fishery. Through this thesis, I evaluated a size-selective sorting grid to exclude smaller-sized sablefish from trawl catches, and the efficacy of a semi-pelagic trawl to harvest demersal groundfishes and reduce trawl-seafloor interactions within this fishery. Statistical analysis of retention probabilities, exploitation pattern indicators, and catch comparisons were used to quantify the catch efficiency performance of each modification. Measurements of the width of trawl tracks in the sediment created by the trawl groundgear using Dual-Frequency Identification SONar imagery were also used to quantify changes in trawl-seafloor interactions between conventional and semi-pelagic trawls.
I found that using a sorting grid system within a selective flatfish trawl can improve the size composition of sablefish catches by providing an escapement opportunity for smaller-sized fish, however, further improvements to the grid design are necessary. The size of the sorting grid openings is important for selectivity, where larger grid size openings resulted in higher escapement probability of smaller-sized fishes but a loss of target size fishes, and smaller openings had no significant selectivity effect beyond that of the mesh codend currently used in the fishery. I show that sorting grid systems have the potential to enhance catches when fishers are primarily targeting sablefish. Still, design improvements or combinations with other selectivity devices may have better results in this mixed species fishery. In evaluating the semi-pelagic trawl, I found no change in catch efficiencies of target groundfishes when compared to a conventional trawl. The midwater door aspect of the semi-pelagic trawl design resulted in increased door spread and fishing area, and likely resulted in the improved catch rates of species such as sablefish. The elevation of the midwater doors and sweeps from the seafloor can provide clearance for low-profile benthic organisms to pass beneath without disturbance. This demonstrates that semi-pelagic trawl gear can effectively harvest demersal groundfishes in the fishery while substantially reducing trawl-seafloor interactions.
The application of sorting grid systems and semi-pelagic trawling in the groundfish bottom trawl fishery can potentially improve sustainable fishing practices within the West Coast groundfish bottom trawl fishery by reducing seafloor contact and enhancing catches of valuable groundfish species. Ecosystem-based approaches increasingly influence fishery management and industry objectives and priorities within the fishery. By continuing to promote the development, improvement, and implementation of new fishing technology, fisheries will have more tools to face new challenges arising in a dynamic industry
Pruning the Third Dimension: Using 2D Images for Perception and Control in Outdoor Environments
No full textDespite high demand for robots to perform labor-intensive agricultural tasks such as fruit picking, few robotic systems have demonstrated robust performance in outdoor environments. This is because dynamic, semi-structured outdoor environments present several challenges that indoor robots do not face, including variable lighting and weather conditions, uneven terrain, imprecise localization, and, in agricultural settings, the need to model complex biological systems that change appearance across seasons. To this end, much of the existing research on outdoor robots has focused on using 3D sensors such as laser-based scanners, stereo vision camera systems, and time-of-flight depth sensors to model the environment. These sensors typically return 3D data in the form of a point cloud, i.e. an arbitrarily ordered set of 3D points in space, which can then be processed into a format that can be used to guide the robot towards a desired target. However, using point clouds comes with a number of disadvantages due to the cost/complexity of the hardware, the computation time required to create and process point clouds, and the difficulties of capturing thin structures such as tree branches, trellis wires, etc.. On the other hand, developments in deep neural networks over the past decade have led to models that can quickly and robustly process 2D images to detect regions of interest.
In this work, we present methodologies for using continuous 2D RGB image streams from an eye-in-hand robot configuration to perform outdoor tasks where depth matters. We apply our work to the task of dormant pruning in orchards, an important activity in which workers selectively cut off branches to optimize fruiting growth for the next season. Our first contribution is an algorithm for extracting tree topology from a point cloud. The difficulty of solving this problem motivates our subsequent contributions that use only 2D data. The second contribution presents the use of optical flow as a proxy for depth that enables us to train a deep neural network for branch segmentation. Our third contribution is the development of a hybrid reinforcement learning-based controller that uses visual and force feedback to perform accurate cuts on branches. We validated the controller in a field trial at a real cherry tree orchard. Finally, we present a framework for 3D branch modeling using only an RGB camera feed and demonstrate that we can extract highly accurate local 3D models of the tree and identify prunable branches in real-time. Our work demonstrates the potential for robots in agricultural environments to perform robustly with minimal hardware overhead, aiding in the long term goal of lowering the barrier of entry for deploying robots in agricultural environments
Plant-Parasitic Nematode Genera Associated with Date Palm in Central Iraq
No full textA survey of plant-parasitic nematode genera associated with roots of mature date palm trees was conducted in central Iraq to study their occurrence, population density, and geographical distribution. This study in Baghdad, Babil, Diyala, Karbela, Najaf, and Wasit governorates was conducted from 2019 to 2023, during the months from October to April. A total of 150 soil and root samples were gathered from 46 fields, and plant-parasitic nematodes were extracted and morphologically identified to genus level. Eleven genera of plant-parasitic nematodes were detected in the declining order of frequency: Tylenchorhynchus spp. (20%) in Baghdad, Babil, Diyala, Karbala, and Najaf; Meloidogyne spp. (17.3%) in Baghdad, Babil, Diyala, Najaf, and Wasit; Paratylenchus spp. (16%) in Diyala and Najaf; Helicotylenchus spp. (12%) in Baghdad, Diyala, Najaf, and Wasit; Tylenchus spp. (12%) in Baghdad, Babil, Diyala, Najaf, and Wasit; Aphelenchoides spp. (6.7%) in Babil, Diyala, Karbala, and Wasit; Pratylenchus spp. (4%) in Baghdad, Diyala, Najaf, and Wasit; Ditylenchus spp. (3.3%) in Babil and Najaf; Hoplolaimus spp. (1.3%) in Diyala; and Heterodera spp. and Scutellonema spp. (0.7% each) in Diyala. Population density was low in Baghdad. High population density was recorded for Meloidogyne spp. (37,625 J2/1,000 cm3 of soil) and the lowest population density occurred with Paratylenchus spp. (20 nematodes/1,000 cm3 of soil) in Diyala (Al-Jadidah). This appears to be the first report of occurrences of plant-parasitic nematodes of date palm in central Iraq
Optimization and Performance Evaluation of Calcium-Based Chemical Stabilizers for Rapid Soil Stabilization: Engineering Properties, Mineralogical Transformations, and Thermodynamic Modeling
No full textThis research is aimed at addressing the need for rapid soil stabilization methods, particularly in rapid construction related problems or seismically vulnerable regions such as Oregon, where infrastructure faces potential damage from high-magnitude earthquakes. The focus is on the engineering and mineralogical investigation of four selected rapid stabilizers to identify the most effective chemical admixture to improve the engineering performance for shallow surface soils within one hour after deployment. Additionally, this research aims to develop a mineralogical testing methodology for assessing the formation of strength enhancing phases at earlier curing times.
The first goal of this research is to compare the strength and durability performance of native soil treated with rapid stabilizers, emphasizing the one-hour curing strength and compare to the untreated material utilizing unconfined compressive strength testing. Additionally, the consideration of durability for each rapid stabilizer was also investigated to ensure the effects of wet and dry season dependency did not reduce the engineering performance significantly. The second goal was to verify the rapid soil stabilization is working by using mineralogical tests like X-ray diffraction, thermogravimetric analysis, and scanning electron microscopy. Additionally, computational modeling of the kinetics of the soil-stabilizer reactions was carried out to predict the likelihood of the formation of strength-enhancing products. A novel testing procedure to extract pore solution from rapidly stabilized soil samples, coupled with inductively coupled plasma optical emission spectroscopy, was developed to collect the necessary inputs for the thermodynamic model.
Overall, this research contributes to the advancement of rapid soil stabilization methods, offering insights into effective dosages needed to obtain adequate engineering performance within one hour after curing. Furthermore, proposing a novel mineralogical methodology and modeling procedure to better understand the early curing time strength for rapid soil stabilization applications
Knowledge-building in a dynamic representation : student orientation to an electrostatic task in a graphing applet
No full textIn this thesis, I investigated how upper-division physics students engaged with a dynamic graphing applet in the context of a junior-level electrostatics task I drew on think-aloud inter- views with students exploring a GeoGebra applet that visualizes electric potential. Through qualitative analysis, I examined how students manipulate parameters, interpret visual repre- sentations, and reason about the applet’s behavior. Using the framework of epistemic games, I identified and characterized two distinct reasoning strategies: the Predict-style Parameter Analysis and Explain-style Parameter Analysis epistemic games. The predict-style strategy involves formulating hypotheses, manipulating parameters, and confirming or refuting out- comes, while the explain-style strategy involves observation and reasoning post-manipulation. These results contribute to understanding how interactive tools can foster representational fluency and support learning in physics education. Implications for instructional design and future research were discussed.KEYWORDS: resource theory, epistemic games, geogebra, simulations, physic
Yaquina Head Seabird Colony Monitoring : 2014 Season Summary
No full textYaquina Head Outstanding Natural Area (YHONA) is home to some of Oregons’s largest and most publically visible seabird colonies, including over 60,000 Common Murres (Uria aalge). The seabird colonies surrounding Yaquina Head present a unique opportunity for research and monitoring given their close proximity to viewing platforms and intensive oceanographic studies of surrounding waters. Additionally, this has been one of the most rapidly growing and productive murre colonies on the Oregon coast. In the past 4 years however, reproductive success has been greatly reduced and colony size has fluctuated markedly. Summer 2014 was the 8th consecutive year of collaboration between Oregon State University, U.S. Fish and Wildlife Service, and the Bureau of Land Management. Combined with similar studies conducted by Julia Parrish (University of Washington) at YHONA from 1998 to 2002, we are now developing a much needed time series investigation for the Oregon Coast (currently at 13 years). Unfortunately, no reproduction and diet data (other than stable isotope samples) were collected at YHONA from 2003-2006, a timeframe containing highly anomalous ocean conditions. 2014 was a mixed year in regards to environmental conditions. Following the La Niña influenced 2011, neutral ENSO conditions persisted in 2012 and 2013. Early models suggested that weak El Niño conditions were likely to develop during the spring or summer of 2014, but conditions in the NE tropical Pacific remained below the El Niño threshold throughout the summer and into the early fall. The conditions in 2014 started with a slightly later than average spring transition but average upwelling winds during May through July, somewhat similar to the conditions during 2012. Observations of bottom water offshore from the Yaquina Head colonies continued to be nearly 1.5°C colder than average through March, 2014. Therefore, these continue to be interesting years to capture seabird responses to environmental variability on the central Oregon coast
Taking action before the heat : a review of current humanitarian policy and protection around dangerous heat exposure in East African refugee contexts
No full textOut of all extreme weather events, heat waves cause the greatest rates of mortality, which are often thought to be underestimated and could be up to thirty times greater than current approximations (IPCC, 2023; USAID, 2024). The East and Horn of Africa Great Lakes (EHAGL) region is expected to experience some of the greatest magnification in extreme heat globally (IFRC et al., 2022). As one of the largest refugee hosting regions in the world, providing asylum to 4.8 million refugees in 2023, this raises concerns regarding the protection of refugee health (Kovats & Hajat, 2007; UNHCR, 2017; IFRC et al., 2022; IFRC, 2023; UNHCR, 2024-a; UNHCR, 2024-c). This report summarizes the state of practice in developing, enabling, and introducing measures to decrease dangerous heat risk in EHAGL refugee contexts. A manual literature review of policies and frameworks guided by selected keywords related to extreme heat and refugee health was conducted on six of the most prominent international humanitarian organizations active in refugee contexts and all eleven EHAGL countries. Three of the six international humanitarian organizations (the IFRC, USAID, and MSF) and nine of the eleven countries (all except Djibouti and Rwanda) acknowledge threats to public health raised by extreme heat. Despite this concern, no leading humanitarian organizations or countries have any dangerous heat risk policies or frameworks that guide on-the-ground action. Climate-related policies and frameworks most commonly focused on agriculture and forestry concerns, such as environmental protection and sustainable development. Attainable, actionable policy and guidelines informed by research on extreme heat and empowering those on the ground to take action need to be more solidly established in order to protect the health of refugees
Measurement of Phospholipid Lateral Diffusion at High Pressure by In Situ Magic-angle Spinning NMR Spectroscopy
No full textThe development of experimental methodologies that enable investigations of biochemistry at high pressure promises to yield significant advances in our understanding of life on Earth and its origins. Here, we introduce a method for studying lipid membranes at thermodynamic conditions relevant for life at deep sea hydrothermal vents. Using in situ high pressure magic-angle spinning solid state nuclear magnetic resonance spectroscopy (NMR), we measure changes in the fluidity of model microbial membranes at pressures up to 28 MPa. We find that the fluid-phase lateral diffusion of phospholipids at high pressure is significantly affected by the stoichiometric ratio of lipids in the membrane. Our results were facilitated by an accessible pressurization strategy that we have developed to enable routine preparation of solid state NMR rotors to pressures of 30 MPa or greater
ASLC-X.doc
No full textThe purpose of this book is to
provide you with a bit more information about the organisms maintained at the ASLC so that you
may deepen your understanding and appreciation of them.
However, as a prelude to the more species-specific information contained in this document, there
are three short chapters that explain more basic topics such as what criteria constitute living
organisms, the basis for classification of living organisms, and the characteristics of a marine
ecosystem. Reading these chapters should help to place the more species-oriented information
(which can get quite detailed) into the broader frameworks of general and marine biology.
Chapters IV through XVIII are descriptions of various phyla (e.g., Mollusks, Echinoderms, and
Chordates) and/or species within those phyla that are maintained at the ASLC.
In addition, a glossary, defining many of the less familiar, more biologically-oriented terms
appears at the end of this handbook. When seen for the first time in the regular text of this
handbook, such terms are presented in boldface type (the word domain, just immediately above,
is an example.
Identification of Myosin XI Receptors in Arabidopsis Defines a Distinct Class of Transport Vesicles
Full text linkTo characterize the mechanism through which myosin XI-K attaches to its principal endomembrane cargo, a yeast two-hybrid library of Arabidopsis thaliana cDNAs was screened using the myosin cargo binding domain as bait. This screen identified two previously uncharacterized transmembrane proteins (hereinafter myosin binding proteins or MyoB1/2) that share a myosin binding, conserved domain of unknown function 593 (DUF593). Additional screens revealed that MyoB1/2 also bind myosin XI-1, whereas myosin XI-I interacts with the distantly related MyoB7. The in vivo interactions of MyoB1/2 with myosin XI-K were confirmed by immunoprecipitation and colocalization analyses. In epidermal cells, the yellow fluorescent protein-tagged MyoB1/2 localize to vesicles that traffic in a myosin XI-dependent manner. Similar to myosin XI-K, MyoB1/2 accumulate in the tip-growing domain of elongating root hairs. Gene knockout analysis demonstrated that functional cooperation between myosin XI-K and MyoB proteins is required for proper plant development. Unexpectedly, the MyoB1-containing vesicles did not correspond to brefeldin A-sensitive Golgi and post-Golgi or prevacuolar compartments and did not colocalize with known exocytic or endosomal compartments. Phylogenomic analysis suggests that DUF593 emerged in primitive land plants and founded a multigene family that is conserved in all flowering plants. Collectively, these findings indicate that MyoB are membrane-anchored myosin receptors that define a distinct, plant-specific transport vesicle compartment.Keywords: Protein body formation, Endoplasmic reticulum motility, Membrane, Brefeldin-A, trafficking, Golgi stacks, Rppt hair, F actin organization, Terminal domain, Plant CellsKeywords: Protein body formation, Endoplasmic reticulum motility, Membrane, Brefeldin-A, trafficking, Golgi stacks, Rppt hair, F actin organization, Terminal domain, Plant Cell