The Biodiversity Impact Mitigation (BIM) hierarchy provides an overarching conservation framework for bycatch reduction, and more broadly for biodiversity conservation. This framework includes four steps, which are implemented sequentially to: (i) avoid and (ii) minimize impacts; (iii) rehabilitate/restore impacted biodiversity; and (iv), compensate such impacts, usually elsewhere. The first three steps...
This presentation explores the interaction of the fishery sector and the emerging push for marine biodiversity conservation. These are viewed as two ‘streams’ of governance – flowing through global bodies (notably the United Nations), through nations (with interacting environmental and fisheries agencies), and through thousands of coastal communities worldwide (which...
Payments for Ecosystem Services (PES) is a relatively new tool for fisheries and aquaculture. Being part of the broader incentive- or market-based incentives, PES is a positive and voluntary incentive mechanism that compensates actors for increasing or maintaining the provision of ecosystem services. Our investigation considers potential and actual PES...
Marine protected areas (MPAs) have become a widely used tool for marine conservation and fisheries management. In coastal areas, it has become clear that the success of MPAs, and the achievement of sustainable fishery production, requires a combination of effective management and conservation frameworks, maintenance of decent fisheries livelihoods, and...
We present student perceptions of a new first-year engineering programming class that was designed by informed research practices. While the College of Engineering at Oregon State University saw a lot of major switching in the first year, there were not many students switching into computer science (CS). This could have...
When characterizing the processes that shape ecosystems, ecologists increasingly use the unique perspective
offered by repeat observations of remotely sensed imagery. However, the concept of change embodied in much of
the traditional remote-sensing literature was primarily limited to capturing large or extreme changes occurring
in natural systems, omitting many more...
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change to
Landsat-based remote sensing
Robert E Kennedy1*, Serge Andréfouët2, Warren B Cohen3, Cristina
The ecologically and socio-economically important marine ecosystems of Europe are facing severe threats from a variety of human impacts. To mitigate and potentially reverse some of these impacts, the European Union (EU) has mandated the implementation of the Marine Strategy Framework Directive (MSFD) in order to achieve Good Environmental Status...
Outcrops of old strata at the shelf edge resulting from erosive gravity‐driven flows
have been globally described on continental margins. The reexposure of old strata allows
for the reintroduction of aged organic carbon (OC), sequestered in marine sediments for
thousands of years, into the modern carbon cycle. This pool of...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Bigeye tunas are bycatch to skipjack tunas when tuna purse seine vessels set their nets on floating aggregator devices (FADs). Current approaches to managing bigeye in both the Eastern Pacific Ocean (EPO) and the Western and Central Pacific Ocean (WCPO) entail permanently closed areas, such as the “correlito” in the...
The use and management of fish supplies, fish stocks and those who work in fishing and related businesses needs to be governed by good policies and actions, based as far as possible on good research-based advice and other expert information. Fisheries policy makers and managers work in a milieu that...
The World Summit on Sustainable Development (Johannesburg, 2002)
encouraged the application of the ecosystem approach by 2010.
We propose a framework that deals jointly with i) ecosystem dynamics,
ii) conflicting issues of production and preservation and
iii) robustness with respect to dynamics uncertainties.
More specifically, we define robust viability kernels...
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:1–48, 1995.
IIFET 2012 Tanzania Proceedings
Philippe M. Cury, Christian Mullon, Serge M. Garcia
The ability to create reproducible cryptographically secure keys from temporal environments (e.g., images) has the potential to be a contributor to effective cryptographic mechanisms. Due to the noisy nature of these environments, achieving this goal in a user friendly fashion is a very challenging task, especially since there exists a...
This paper discusses the use of resource assessment surveys as the basis for effective fisheries management drawing on the resource assessment survey of the Arabian Sea coast of Oman. This survey, completed in 2009, has been undertaken in the context of the primary aim of the Oman Ministry of Fisheries...
Society has agreed on the goal of sustainable fisheries but achieving the goal is often submerged by more
immediate national and international demands causing fisheries to slip down the political agenda or diverting attention to other fisheries issues, e.g., profitability under high fuel prices. Among the problems
challenging marine capture...
Following a history of tensions surrounding concubinage in medieval and early modern Spain, the Church sought greater control of religious life, particularly over the sacrament of marriage, via the Holy Office of the Inquisition. The Church exercised its strengthened restrictions and prosecuted these relationships with more frequency, as did civil...
Himalaya blackberry (Rubus armeniacus) is a widespread, exotic, invasive plant now common over much of western Oregon and Washington. An observational experiment revealed that disturbance to a monoculture of Himalaya blackberry allows the soil seed bank to be expressed and return the inhabited area to an earlier successional stage. This...
The discovery of new antibiotics reached its peak during the golden era of antibiotics in the mid 20th century and continued to thrive until the 1980s. However, after more than 50 years of fruitful exploration and exploitation of microbial natural products the discovery rate of new antibiotics has dropped drastically...
ICES – the International Council for the Exploration of the Sea – was founded more than a century ago out of
concern for overfishing. However, today’s global marine ecosystems are for the most part in a degraded state, many
alarmingly so. Why is the science used so little to make...
This paper examines four community forest enterprises (CFEs) in Oaxaca, Mexico, where CFEs have been held up as a positive example of community forestry that simultaneously addresses both conservation and development goals. CFEs are community-owned businesses that manage their forests to provide income and other benefits and may be considered...
Transportation systems are facing safety and operational challenges with a cost of billions of dollars annually in lost production time and wasted fuel. Infrastructure expansion, previously held as a panacea to most transportation challenges has lost its appeal due to financial, land-use and environmental constraints. Interest is surging in intelligent...
This thesis discusses both theoretical and practical considerations inherent in conducting community-based research within a case study of sea turtle conservation in Baja California, Mexico. A brief background, including the general ecology, status and distribution of sea turtles of the Baja peninsula is presented, with an overview of the current...
Data variations are prevalent in real-world applications. For example, software vendors have to handle numerous variations in the business requirements, conventions, and environmental settings of a software product. In database-backed software, the database of each version may have a different schema and content. As another example, data scientists often need...
Soft robots are designed to utilize their compliance and contortionistic abilities to both interact safely with their environment and move through it in ways a rigid robot cannot. To more completely achieve this, the robot should be made of as many soft components as possible. Here we present a completely...
In recent years, many studies have focused on the molecular and biochemical mechanisms regulating the development of wine grapes. The course of grape berry development is directed by genetic design and is mediated by phytohormones, which regulate grape berry growth and development by orchestrating a complex network of interacting genes,...
Natural products from both terrestrial and marine sources represent a significant source of novel drug leads, and have previously been developed into clinically-approved agents for the treatment of various human diseases. This work represents the biological characterization of the mechanistic basis for activity of several natural product structures in models...
The dissertation focuses on the engineering of light-matter interaction using plasmonic nanoparticles and metamaterials to achieve enhanced luminescence and based on which to improve the performance of biosensing and light-emitting technologies. We designed and fabricated a spectrum of nanostructures to exhibit particular dispersion relations capable of controlling the spontaneous emission...
Real-world datasets are dirty and contain many errors. Examples of these issues are violations of integrity constraints, duplicates, and inconsistencies in representing data values and entities. Applying machine learning on dirty databases may lead to inaccurate results. Users have to spend a lot of time and effort repairing data errors...
The yeast Brettanomyces bruxellensis is the most important wines spoilage yeast encountered during winemaking as it can survive in wine for long periods, requires minimal nutrients for growth, and can be difficult to control. Brettanomyces produces two major spoilage products, the volatile phenols 4-ethylphenol (Band-Aid, medicinal smell) and 4-ethylguaiacol (smoke,...
Mental health among student athletes has gotten much more attention in the world of sport today. However, there has been a lack of research focusing on how the socioeconomic backgrounds of Division 1 student athletes can play a role in their mental health and their desire to seek out help...
Ph.D. candidate Qi Wei's thesis consists of two projects: Chemotherapy Project: a study based on the research paper "Predicting chemotherapy response of various cancer types using a variational auto-encoder approach" submitted to the bioRxiv preprint archive and accepted by the BMC bioinformatics; and Wound Monitor Project: implementing and assessing analytics...
In a software development cycle, programs go through many iterations. Identifying and
understanding program changes is a tedious but necessary task for programmers, especially when
software is developed in a collaborative environment. Existing tools used by the programmers
either lack in finding the structural differences, or report the differences as...
Many database users are not familiar with formal query languages, the concept of schema, or the exact content of their database. Thus, it is challenging for these users to formulate their information needs over semi-structured and structured databases. To address this problem, researchers have proposed usable query interfaces over which...
What makes invasive species successful, and how do they affect native populations and communities? I addressed these key questions in the context of the invasion of Atlantic coral reefs by Pacific red lionfish (Pterois volitans). To assess the role of parasites in contributing to the success of this invasion, I...
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D’Cotta, and
Serge Morand. Paul Sikkel, you tie-dyed man, you deserve overwhelming thanks. I
have
To facilitate the evaluation and design of structures subjected to fluid loading, a study of fluid-structure interaction (FSI) using the particle finite element method (PFEM) is presented to approximate the responses and sensitivities of structures which interact with fluid. A wide range of structural types are permissible by making no...
The advancement of artificial intelligence (AI) has led to transformative developments across multiple sectors, fostering innovation and redefining our interactions with technology. As AI matures and becomes integrated into society, it offers numerous opportunities to address global challenges and revolutionize a wide array of human endeavors. These advances are driven...
The economic analysis of land use decisions provides insight into incentive structures faced by landowners and the impacts of landowner decisions on others. Qualifying and quantifying these incentives and impacts offers insight into the relevant characteristics of decision-making. In turn, this allows the researcher to model and predict land use...
Recognizing human actions in videos is a long-standing problem in computer vision with a wide range of applications including video surveillance, content retrieval, and sports analysis. This thesis focuses on addressing efficiency and robustness of video classification in unconstrained real-world settings. The thesis work can be broadly divided into four...
Bipedal locomotion is a complex phenomenon to understand and control, making it difficult for legged robots to achieve the speed, agility, efficiency, and robustness of their animal counterparts. This thesis argues for the use of numerical optimization to investigate and implement bipedal control as it applies to biology, dynamical models,...
The isoprenoid pathway is one of the major biosynthetic pathways of secondary metabolites. Isoprenoids with a C₂₀ skeleton are known as diterpenoids and are derived from the common precursor, geranylgeranyl diphosphate (GGPP). This dissertation describes approaches to discover the diterpene synthase enzymes which provide the backbone structures for pleuromutilin and...
Animals aggregate and interact in nonuniform and nonrandom patterns, which lead to group level characteristics that have important evolutionary and ecological consequences. Network analysis provides a useful conceptual framework for linking animal interactions at all scales from dyads to communities, to populations and ecosystems. Despite exciting theoretical and applied advances...
Software systems are becoming an essential part of the lives of both individuals and organizations, and as a consequence, these systems are getting bigger and more complex. Because of this, the tasks of maintaining the quality in these complex software systems are becoming increasingly difficult. Furthermore, these systems are subject...
The objective of this dissertation is to enhance the monitoring of forest ecosystems through the utilization of remotely sensed data to address the exigencies posed by the Anthropocene. On a global scale, rising temperatures and fluctuating precipitation patterns have strained forests and produced shifts in natural disturbance regimes. Additionally, the...
Mathematical modeling plays a pivotal role in understanding the mechanism of radiation-induced cellular effects, and also in quantifying the radiation risk to the cell. However, there are still compelling challenges facing the conventional modeling in radiobiology, such as lacking a generalized theory structure of quantifying target effect and non-target effect...
Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, held July 11-15, 2016 at Aberdeen Exhibition and Conference Center (AECC), Aberdeen, Scotland, UK.
Developers frequently change the type of a program element and update all its references for performance, security, concurrency, library migration, or better maintainability. Despite type changes being a common program transformation, it is the least automated and the least studied. Manually performing type changes is tedious since the programmers have...
The development of a transient electric birefringence (TEB) apparatus for macroparticle characterization is herein discussed. The experimental difficulties encountered were related largely to poor data resolution. Misalignment and strain birefringence in optical components further complicated results. Improved data digitization methods were developed, and precise mathematical models were derived in order...
Learning novel concepts from relational databases is an important problem with applications in several disciplines, such as data management, natural language processing, and bioinformatics. For a learning algorithm to be effective, the input data should be clean and in some desired representation. However, real-world data is usually heterogeneous – the...