The Ag Summit is a social as well as educational event, bringing farmers together for dining, dancing, and community building. The education of young people is a crucial opportunity for scaling agroecologial practices. On Lopez Island, farm to school programming is run through the Lopez Island Farm Education program. It began as a collaboration between LCLT, the Lopez Island School District, Lopez Island Education Foundation, the Family Resource Center, S & S Center for Sustainable Agriculture, the SJI Conservation District, WSU SJC Extension and the HellerFamily. The program uses an “integrated systems approach” to delivering hands-on education in nutrition, ecology, sustainability, and land stewardship . In practice, this consists of educating students in a garden classroom elective for elementary and middle school, hosting a high school farm elective course where students visit local farms, and preparing and preserving food from the school farm in the cafeteria, where local scratch-cooked meals are served year round. Part of the growing national movement around improving the quality of school meals through locally sourced produce, the LIFE program takes advantage of the exceptional quality of both locally produced foods and farm-based educational opportunities on the island.Midnight’s Farm, a 100-acre property located near the center of Lopez Island, heralds the diversity of its operations from the initial entry point down a gravel driveway. A signpost indicates the direction of the compost operations, yoga studio, farm stand selling beef, pork and vegetables, rolling hydro tables and wood-fired bakery . In the words of the farm owners, “we farm to steward this wonderfully beautiful piece of earth and for the tangible, hands-dirty love of connecting people to the soil and storing a little bit of carbon there, too.”

The land was purchased with savings from a previous career as an Alaskan salmon fishing captain, and the past 20 years have seen a progressive investment in land restoration and diversified agriculture operations. From the establishment of hundreds of trees at the property border to rotational grazing plans for cows on pasture and marshland, to fruit trees and ¼ acre home garden with greenhouse, to a blueberry patch being prepared for planting in 2019, biodiversity continues to grow. Revenue streams are accordingly diverse, with the compost and woodchips bringing in the most revenue annually, followed by Field House vacation rentals, beef and pork products, and vegetable sales. The Field House, available for short term farm stays, hosts visitors year round and is booked throughout busy summer tourism season, capitalizing on the growing market for agritourism opportunities. The farm has typically provided housing for another couple in a barn apartment, in exchange for regular workdays or some combination of paid labor and housing work-trade. Sustainable Agriculture Interns coordinated by LCLT help out during summer months, and the farm is a popular destination for “WWOOFers” as well . Other Lopez Island youth work on the farm several days a week during the summer. At maximum capacity, the farm hosted nine farm employees during the summer 2019 season. Farming practices are the product of decades of experience, and soil fertility is the product of countless yards of compost and mulch application. In the vegetable garden, dozens of crops feed the farm families and neighbors each year. From spring seeding to bed preparation and transplanting, to weeding, irrigation, harvesting, cover cropping and winter greens cultivation in the greenhouse, every activity has its seasonal rhythm. Several planting strips are gradually converting to no-till farming, with compost, mulch, and broad-forking substituting for the mechanical mixing of the soil.

Tilling is associated with carbon release and disturbance of the soil biota, so reducing or eliminating tillage is an effort several farmers are working towards, in balance with weed management. Irrigation ponds, dug on most farm properties, fill up with rain in the winter, and provide water to crops through the dry summer months. Pasture area is grazed rotationally and managed for optimal plant biomass communities. The cows contribute to the regeneration of pasture soils, providing aeration from their hooves, growth stimulation from grass consumption, and fertilizer from their manure. David and Faith, the owners of Midnight’s Farm, are passionate about researching and implementing agricultural solutions to climate change on their farm. Their bookshelves are filled with books such as Grass, Soil, Hope; Dirt to Soil; and Growing a Revolution: Bringing our Soil Back to Life, and their social calendar is filled with attending climate talks and hosting climate researchers from University of Washington , WSU, and other institutions. Most recently they are engaged in a carbon footprint analysis of their compost operation, land use, and cattle herd, in order to understand highest impact opportunities for emissions reduction and carbon removal. The results show that currently the farm is contributing to the sequestration of approximately 250 mtCO2e, via forest cover, marshland, managed pastures, compost production and application, which together more than offset emissions from farm machinery, diesel use, and cattle as shown in Figure 9. David and Faith advocate for a “big tent” approach to food systems transition where many different people and groups can see themselves in a process of growing food with a lighter climate impact, and better human health impact. Their vision rests on a premise of developing strong interpersonal relationships, infusing the work with joy, humor, social connection, and opportunities for personal growth. An onsite yoga studio offers space for interns and farming friends to stretch and reinvigorate bodies feeling the effects of hard physical work.

David and Faith continue to articulate better and brighter ideas for the future, such as finding long-term land partners and helping launch a climate farm school on the island, pushing forward the vision of a truly regenerative agroecosystem on Lopez.Orderly rows of greens and vegetables lend a sense of efficiency and purpose to the fields of Lopez Harvest. Successional plantings of diverse lettuce varieties march westward across the field, with the largest plants cut for weekly harvests while each neighboring row showcases one fewer week in the field. 500 lettuce plants go in the ground on Wednesdays, and plants are harvested on Tuesdays and Fridays for twice a week deliveries. The humming schedule of running a successful greens production farm serving the two island grocery stores as well as 5-6 island restaurants and food businesses creates a strong weekly rhythm for farm owner and farm workers. Dig, transplant, bed down, repeat. Six inch spacing, four rows per planting bed. Finish the row, water it in, keep moving. Lopez Harvest sells lettuce mix, a specialty blend of “Island Greens,” chard, microgreens, arugula, herbs, and various seasonal vegetables and specialty crops to most of the for-profit food retail and business operations on the island. Christine, the farm owner, sends out a “pick list” to all customers a week in advance, takes orders by a certain day, and harvests and delivers all orders herself. This is her answer to the question “what does it take to be a successful small-scale farmer on a small island?” She sells her surplus produce directly to retail and restaurant, finding this to be more profitable than selling at the seasonal weekly Farmer’s Market or direct to consumers. She raises additional vegetables for personal consumption, reducing her own need to purchase store-bought foods, and facilitates a meat-share program where costs and benefits from raising meat chickens are shared among participating households. These non-monetary and cooperative forms of exchange are important to the economic viability of her operations. Christine now receives additional revenue from her participation in a beginning farmer mentoring program, where she earns up to $1,000 annually for mentoring younger farmers in their first year of operation . Her farm is on shared land purchased by three couples, and was acquired with family support, a common method for overcoming high barriers to entry for farmland access . While some rows of her field are planted to commercial crops, others are in rye-vetch cover crop mix gaining fertility for next year, vertical horticulture or mustards to deter wireworms. The cover crop is mowed down and incorporated into the beds, with some beds serving as experiments for no-till practices where she has also tried occultation techniques to germinate and kill weeds prior to transplanting. This is difficult to enact on her land due to heavy clay soils that need some disturbance to be made ready for tender transplants and is a work in progress. Commercial crops are rotated onto previously cover cropped beds, a dance between production of plants and soil. In Christine’s mind, “good farming is good for the climate;” she adopts practices when they prove beneficial for her land, crops, soil, and business model, and it just so happens that many of these practices are anointed in academic research as climate mitigating strategies.

Christine exemplifies a successful independent, woman-owned business model. She receives seasonal labor support through the LCLT intern program and through informal work trade agreements with friends and neighbors. Christine is a vocal contributor at the monthly farmer coffees, sharing what she’s learned about effective weed control strategies , and a gifted farmer educator. She collaborates with WSU San Extension on a research project to reduce wire worm pest pressure in lettuce crops and is also a collaborator on the Western SARE biochar cocompost grant, participating in the field trial and soil/crop data collection processes. Christine recognizes the attractiveness of entering into farming cooperatively or with farm partners but struggles with the difficult proposition of supporting multiple households with limited farm revenue streams and land use restrictions. When it comes to sharing land in her current situation, she would love to be able to build and provide more farm worker housing, but is restricted from doing so by county zoning policies that prevent more than two houses from being built on a parcel designated as “farmland7.” The county zoning codes are ripe for reform, but notoriously difficult to get right in terms of regulatory verbiage that protects farmland from becoming housing developments yet allows for ample and affordable farmworker housing. Currently grappling with her own problems of farmland succession, scaling back, and transitioning her land, Christine hopes that the land can continue to be farmed, while still allowing her and her partner to extract their equity and support their own retirement. On the way to working out these details, Christine continues to get up early each morning of the summer, turn on the irrigation system and harvest high-quality vegetables, sharing her beautiful food production space and boundless stores of knowledge with those seeking it in her community.Meike Meissner and Mike McMahon moved to Lopez Island with their three children in spring 2018, after signing on to a 15-year long term affordable lease of Stonecrest Farm through LCLT. Meike and Mike got their farming start in California, where they both worked at the Occidental Arts and Ecology Center. They grew their experience in the American West, participating in a rangeland internship in Montana and establishing an award-winning contract grazing operation in Colorado. Thinking holistically and with climate change in mind, Meike and Mike practice a combination of farming and conservation work. They are both trained in managed grazing through Holistic Management International, an offshoot of the Savory Institute, and believe in the value of animals as regenerative elements for degraded rangeland. Upon moving to Lopez, they have faced inevitable start-up obstacles in establishing pasture-raised heritage pigs, rotationally grazed beef cattle, chickens, and kitchen processing facility. The pasture areas have been so degraded from repeated haying that there is little nutritious forage available for their cattle operation, which they would like to be 100% grass-fed and finished, with no supplemental hay fed to their animals. Before this is possible, they must regenerate the available forage and bring back high-nutrient plant biomass on their land, through a creative, locally tailored approach to grassland ecosystem restoration. In the meantime, they are leasing other land for rotational grazing of their beef cows. Adding to the quandary is decades of selective cattle breeding in the United States to maximize high-protein feed-to-meat conversion as quickly as possible. Venturing into the field of epigenetics, Meike laments the fact that there are few cattle breeds in the U.S. particularly well suited to convert poor forage to high quality meat, which would represent another opportunity for minimizing external inputs in the form of supplemental animal feed.

The research presented in the following chapters offers a partial answer to these questions, developing a food systems and climate change curriculum as an example of more creatively integrating environmental challenges into already-successful educational avenues such as school gardens and food-based education. Partnerships with farms, school gardens, food systems researchers, and climate change educators help foster this curriculum into existence and shape it as a work in progress. Food and climate literacy come together in a food production focused series of activities that guide students towards taking informed action to mitigate climate change through food production and consumption choices. Teaching students how to grow food has an inherent tie to promoting food security and food sovereignty; going one step further, there is an embedded hypothesis underlying this curriculum development that, through participating in where food comes from , students can better understand other aspects of the food system such as the consumption choices and importance of composting rather than throwing away food waste, making the production element an important leverage point for food systems education. Furthermore, food production spaces offer hopeful examples of removing carbon from the atmosphere, acting out the carbon cycle on a local scale. In the words of one school garden teacher, “the garden system is a perfect metaphor for the complexity of the climate system,” and thus a promising venue for engaging students in CCE.The research studies compiled in this dissertation employ participatory, collaborative, and interdisciplinary research designs.

Mixed-method approaches to inquiry combine to yield results, drawing from participant observation, semi-structured interviews, key stakeholder surveys, GIS analysis, grow trays 4×4 and literature review methodologies. The studies draw heavily from interdisciplinary epistemologies that value multiple ways of knowing and seek to incorporate multiple voices, especially those that have been historically marginalized, into the research design, implementation, analysis, and communication of results. The relevant spheres of influence for this grassroots and bottom-up approach to knowledge creation are ultimately decision-makers in climate policy making and those negotiating food systems power structures. The research methods are grounded in the study of social science, drawing from texts such as Constructing Social Research: The Unity and Diversity of Method , What is a Case? Exploring the Foundations of Social Inquiry and Making Sense of Qualitative Data: Complementary Research Strategies . Michael Burawoy and Pierre Bourdieu inspire the practice of interpreting case studies, embedding them in an appropriate theoretical framework, and understanding interview subjects . As Walton illustrates in his essay “Making the Theoretical Case,” a case can change as you dive into it, and finding the appropriate theoretical frame is the work of the researcher; he cautions against the danger of coming in with a set theoretical frame in mind and trying to force the incoming data into that frame . Chapter 2 in particular exemplifies a case that started as a case of one thing and became a case of something else as the layers of research methodology, like layers of an onion, peeled back initial assumptions and observations until it struck at the core. Incorporating Elinor Ostrom’s call for better integration of the social and ecological sciences in governing sustainable social-ecological systems , interdisciplinary research questions in the chapters that follow incorporate natural and social scientists, as well as practical agricultural science. Doing participatory research requires a mix of experience and immersion in the literature to guide those who seek to do social justice oriented, empowering work with non-academic research partners.

The scholarship of Jill Harrison , Jules Pretty , Nicole Klenk , and Alastair Iles is instrumental for guiding researchers towards effective practices that co-produce rather than extract knowledge. These researchers share a focus on climate and food systems research that is especially relevant for this dissertation.The chapters that follow investigate food systems research questions in the contexts of the San Juan Islands in Washington State, and the East Bay region of the San Francisco Bay Area. While all chapters engage with food systems holistically, each chapter enters into the food systems research question from a different element of the system. The second chapter focuses on the production side, introducing a case study of small-scale sustainable farming at the community scale on Lopez Island. The third chapter presents a food access and distribution research project taking place in the East Bay, investigating pathways through which urban produced foods do make it into the hands of food insecure consumers. The fourth chapter uses the lens of education to present an evaluation of a food and climate change curriculum, illustrating how climate change education and food systems research can work together to achieve common goals . The conclusion synthesizes key findings from all three chapters, pointing out what bigger picture food system questions are answered as well as questions requiring further investigation in the arena of relocalizing climate-friendly food systems. Key strands of literature running throughout the paper include the literature on agroecology and emerging research on its application to the urban context- urban agroecology . Chapter 2 engages with the agroecological paradigm for food systems reform in a rural context, and Chapter 3 turns over new questions in the urban East Bay context. The chapter draws on scholarship from a recent RUAF magazine titled “Urban Agroecology,” that proposes UAE “not as a goal, yet an entry point into, and part of, much wider discussions of desirable presents and futures… [it is] a stepping stone to collectively think and act upon food system knowledge production, access to healthy and culturally appropriate food, decent living conditions for food producers and the cultivation of living soils and biodiversity, all at once” . Agroecology and UAE have important implications for how food systems education should be conducted , which are implicit in the pedagogical foundations underpinning the food and climate curriculum in Chapter 4. The chapters, with their diverse research questions and publication outlets, push back against a food system that destroys human and environmental health alike, and seek out climate friendly alternatives through collaborative, participatory research projects. The research presented in chapters 2, 3, and 4 make the case for diverse values and benefits associated with relocalizing sustainable and equitable food systems centered around small diversified farms, in places where this type of food system transformation is sought. Rather than arguing for the complete overthrow of the current industrial food system, the primary contribution of these cases is to argue that shifts to current practices are both necessary and possible yet must be supported by appropriate and enabling governance structures. There are social, ecological, and educational benefits to adopting agroecological food system practices, but it is difficult to enact these practices holistically and systemically across food system elements in the current U.S. political economy. The cases offer lessons or “pilots” that are relevant to the operations of large-scale farms and industrial processes as well as small scale, agroecological operations: through adding plant diversity and minimizing soil disturbance, for example, numerous benefits can be achieved for farmers , for local ecology, and for global climate change.

Therefore, findings implicate the policy and planning domain in terms of action needed to sustain and scale positive food system reform impacts, on a variety of levels and with attention to social justice implications. The findings also make important contributions to methods of climate change communication and education: effective CCE will manifest differently in different contexts and must allow for each audience to express the environmental concerns that are most pressing, immediate, and relevant in that context. Through considering food systems and climate systems holistically, opportunities for public health benefits, local environmental improvements, and educational growth can be realized.Lopez Island is situated 4 miles off the Washington State mainland in the Salish Sea, where it is Figure 3- Lopez Island Farmland a lighthouse for an alternative, agroecological model of food production at the community scale. Approximately 18,000 acres of agricultural land in the San Juan Islands chain form a network of non-GMO, non-chemical based agricultural land. The 5,000 acres of Lopez Island farms stand in direct contrast to conventional farming: they are largely small scale, human powered, diversified, educational, knowledge-intensive, horticulture products reliant on natural fertilizers and integrated pest management strategies, and localized in terms of who they serve2 . The Lopez Community Land Trust lists 27 farms on their annually published “farm products guide,” on this island of 2,500 year-round inhabitants. Lopez farmers seek to optimize many outcomes besides yield and several actively cultivate seed diversity through seed saving and local exchange. Seeds are selected for drought resilience, flavor, nutrient content, ability to withstand disease and pest pressure, and general endurance and adaptability to local conditions. The resident community is invested in local farms, through school food procurement, local markets, and regular volunteer presence. The summer tourism industry can attribute some fraction of its success to the local food system, as a recent tourism survey indicated “natural/rural scenery” as the top reason and “local food” in the top half of 15 listed reasons tourists come to the San Juan Islands . However, the tourism industry simultaneously poses a challenge to the local agriculture community, as the real estate and land markets are increasingly displacing farmers due to development pressures and desires for second homes on the islands. As an island community, Lopez has unique considerations around food procurement. Importing food from the mainland is expensive and risky in the face of natural disasters, as ferry service to the islands is easily disrupted and unreliable in the face of adverse weather conditions. Ferry service costs $47 roundtrip from Anacortes to Lopez per vehicle and driver in the summer season. There is an added incentive on Lopez to adopt self sufficient and soil regenerating farming practices at the community scale due to its geographic isolation in combination with rocky, relatively poor soil quality. This “island incentive” is important to factor in when considering the widespread adoption of sustainable agriculture on Lopez; as the San Juan County Agricultural Strategic Action Plan reports, “islanders naturally place a high value on food security and may benefit from their isolation to preserve genetic diversity, for example, by establishing an organic seed industry” . As food supply chains in today’s globalized food system are increasingly threatened by natural and climate-exacerbated disasters, all communities will soon have increased incentives to invest in sustainable food production as a form of resilience, food security, and climate adaptation. In the realm of food self-sufficiency, innovative production systems, and climate resilience, there is much to learn from island nations and communities that are on the front lines of adapting food systems to and mitigating climate change. Lopez is striving to create a robust, resilient, socially just local food system, a distinct and more complex goal than merely investing in and promoting local food production. Individual farmers starting to adopt and successfully deploy regenerative practices is not the same as creating a sustainable and resilient local food system. A local food system, as outlined in the previous chapter, includes not just production, but transportation, distribution, marketing, retail, preparation, consumption, waste recycling, and education across system elements. A food system that is socially just, compensating farmers fairly for their labor while balancing affordability for the consumer across income groups, requires a change in food system economic transactions from the status quo. A food system that is environmentally sustainable and mitigates climate change, storing more carbon in the soil than it releases and minimizing emissions throughout the system elements, requires transformation of the dominant industrial food system. Lopez farmers are striving to increase and quantify their soil carbon reservoir, with less progress to date on reconfiguring the economic status quo. What can this island farming community tell us about creating and scaling alternatives to the chemical-industrial farming industry? What are the key challenges, tensions, and opportunities on Lopez for building a local food system that is socially just and environmentally sustainable? What are the next steps for Lopez, and other counties or regions, in moving towards goals and vision statements for re-localized food systems? These questions, when answered, become relevant not just to farmers and researchers, but importantly, to policymakers, economists, and businesses that must implement new policies and economic structures effectively in partnership with farmer- and community-generated vision statements.

The survey asked respondents to indicate from whom they get information about best practices for food safety and for conservation. We summarize the responses in figure 3. It should be noted that these questions were asked at the end of the survey, and the response rate is lower most likely due to survey fatigue. It is possible that respondents might not have answered these questions because they felt uncomfortable with the topic, but no concerns were raised on these questions during either phase of piloting. Respondents reported receiving information on food safety and conservation primarily from other growers , government agencies , Cooperative Extension advisors and trade associations . For information exclusively about food safety, however, more respondents rely on their buyers , third-party auditors/inspectors and trade associations than on government agencies or Cooperative Extension advisors . Furthermore, respondents with large farms were significantly more likely than respondents with small farms to rely on third-party auditors/inspectors and their buyers exclusively for food safety information . For information about conservation, conversely, Cooperative Extension and government stand out, with 57% and 55% of all respondents seeking some form of conservation information from them, respectively . There was no statistically significant difference between large and small farms for information only about conservation . The survey also asked growers to rank the factors of importance in resolving their buyers’ food safety concerns. Respondents with large farms were much more likely to rank certification more important and to rank the length of the relationship with their buyer and buyer site visits less important than were growers with small farms .

Respondents were also asked how they prefer to get information and what topics are of most use to them. On a scale of 1 to 6 useful, indoor grow rack respondents ranked in-person workshops and written guidance available either online or in paper format significantly more highly than online webinars/trainings or videos . Using a bootstrap method with case resampling to estimate 95% confidence intervals for the rankings, no significant differences were observed across crop type or farm size . Most respondents wanted information on regulatory requirements , detailed best practice guidance , what technologies and tools are available , implementation costs , and evidence of the effectiveness of tools and practices for managing food safety hazards . Around half of respondents felt that information about how to co-manage food safety and agricultural conservation , how to prepare for a food safety audit , and guidance/tools for developing good agricultural practices would be useful. Only 39% felt that information about available consulting services would be of use. No significant differences were observed across crop type or farm size.The results of our survey suggest that on farm practices for food safety that target wildlife and potentially impact natural communities and ecosystem services via vegetation and habitat removal are still used in produce agriculture in California. Past surveys of on-farm practices used by leafy greens growers in the Central Coast found that the most common practices were buffers around cropped fields and poison bait , followed by wildlife trapping and wildlife exclusion fencing . Respondents to our survey reported similar if not higher rates of use for these same practices, suggesting that practices have remained constant within the leafy greens sector over the past 6 years and that, possibly due to expanding food safety regulations, food safety pressures and practices now reach into other sectors of the produce industry, as well.

As discussed above, many of these legacy practices have not been shown to reduce food safety risk, and growing evidence points to their impacts on ecosystem services and other public goods and benefits . Nevertheless, we found that many growers still use these and similar practices, suggesting that the on-farm practices which growers perceive to be required of them do not yet reflect available scientific information. The impact of requiring on-farm practices for food safety depends upon how and by whom rules are written and enforced, and the scale of the farm. Future field-based research should address whether this difference is due to the greater resources available to large farms or to different levels of risk and oversight associated with different market channels and supply chains. Our survey suggests that food safety and conservation are practiced and interpreted differently by growers of different size and crop type. Farms in our sample with annual sales over $500,000, for example, were more likely than farms with annual sales under $500,000 to report practicing some form of animal intrusion prevention, such as fencing or trapping. However, even among farms of similar size growing similar crops, we found a wide range of variation. Rather than converging as scientific evidence and experience grow, on-farm practices for food safety are highly heterogeneous across produce agriculture in California, suggesting that either requirements, or grower interpretations of those requirements, are inconsistent. Inconsistency in real or perceived food safety pressures raises several concerns. Our results show that many growers rely on each other for both food safety and conservation information, but perceptions of practices for food safety and knowledge of regulations varied greatly among growers. Mixed messages from their peers could lead to uncertainty over legal requirements and the potential consequences of noncompliance. In the face of uncertainty, growers may take what seems to be a conservative approach by adopting wildlife deterrence and vegetated habitat removal practices that have not been scientifically shown to reduce risk.

While open-ended or flexible regulation may aim to give farmers more freedom, inconsistencies in food safety pressures can also make it more difficult to provide guidance on strategies to comanage food safety and sustainability goals. In addition, the majority of our survey respondents reported that auditors are inconsistent in their assessments. A high degree of inconsistency may make food safety requirements appear arbitrary to growers, especially if evidence is not provided along with the justification for decisions or recommendations. A significant proportion of our respondents also did not believe that food safety certification has made their products safer, despite the high importance of certification in securing access to larger buyers. Lastly, the higher the degree of inconsistency in interpreting and responding to food safety pressures, the higher the degree of difficulty for regulators — and the consuming public — to know whether the produce industry has effectively made food safer.Taken together, our findings highlight that discrepancies remain among California produce growers with respect to their access to current, relevant food safety science and other information; their perceptions of what environmental factors pose food safety risks; and how decisions are made about which practices best suit their farming context. At the very least, there is a need for greater support for outreach programs on food safety for buyers, auditors and trade associations as well as growers, particularly further guidance as to which suite of food safety practices are most effective and compatible with protection of natural resources and ecosystem services in a variety of farm settings. However, the desire for consistency must be balanced against the need for flexibility. Farms are complex and variable environments, and interpretation of food safety risks and appropriate preventive actions depends upon the particular context of a given operation. As discussed above, the FDA Produce Safety Rule acknowledges this need by providing a degree of flexibility to growing operations, but it is necessary to evaluate the extent to which that flexibility will lead to on-farm practices that actually improve safety while minimizing environmental and economic costs. Our results suggest that in some cases pressures from third-party auditors and produce buyers may lead to inconsistency in the interpretation and implementation of food safety regulations and guidance, but our survey was conducted prior to the finalization of the Produce Safety Rule. In light of this significant regulatory development since the survey was administered, additional survey and interview based research is needed to determine the extent to which growers adopt practices based on their own goals or perceived pressures from their buyers, infoor farming equipment third-party certifiers/auditors or government regulators. Future research should investigate who has the power to decide what practices are best for food safety, and whether and in what ways the distribution of decision-making authority affects the balance between consistency and flexibility. Greater alignment and collaboration between environmental and food safety science is needed to establish a more comprehensive catalogue of practices that can help growers mitigate pathogen risks while also protecting the environment and ecosystem services. A call for consistent rules and enforcement must allow a responsive flexibility in implementing food safety guidelines.

A balance is necessary. While we cannot say what that balance should be, it is apparent from our survey that any discussion of balance can only improve with better understanding of extant food safety pressures and the ways in which they are perceived and put into practice by growers. More transparent information on what practices growers adopt in the name of food safety, and why growers adopt those practices, is urgently needed. It would improve consistency and help promote food safety efficiently and without unnecessary impacts on the environment. That would benefit both farmers and consumers.One of the most common causes of fatal and nonfatal farm injuries among youth in agricultural settings is farm machinery. ATVs are commonly used in agricultural operations to apply fertilizer and chemicals, inspect livestock and crops, supervise workers, transport personnel and material, mow grass, round up livestock, and carry and tow implements. ATVs are reported as the primary source of vehicle injury for youth on farms, causing 63% of vehicle-related injuries. Despite efforts to prevent childhood injuries through engineering controls, administrative controls, application of PPE, and training, the number of ATV-related injuries among farm youth has increased 150% in recent years. And more broadly, beyond agriculture, there are over 24,000 estimated ATV-related injuries annually among youth younger than 16 years-ofage. Youth perform a wide range of tasks on farms, including operating farm machinery like tractors and ATVs. Due to physical limitations in strength and anthropometric dimensions, some work tasks could be riskier for youth than adults, thus increasing their likelihood of being injured or even killed. Several studies have shown a strong relationship between the injuries of youth and their ages, anthropometric characteristics, and developmental abilities. For example, the results of previous studies showed that youth younger than 16 are not capable of safely operating tractors or ATVs. Different recommendations exist regarding the minimum age, required physical and mental capabilities, and safety requirements for ATV operation. Those recommendations are inconsistent and may be affected by variances in state law. Also, to our knowledge, none of the reviewed recommendations are evidence-based due to a lack of quantitative and systematic information about the extent of the physical and mental mismatches between requirements for operating ATVs and youth’s capabilities. The lack of clear and consistent information may mislead young ATV riders and their parents, thus increasing the risk of injury to young operators. This study aimed to review the available ATV standards, recommendations, guidelines, regulations, and studies related to age limitations, physical and mental capabilities, safety requirements, and injuries and fatalities of youth riding ATVs on the farm. The main goal of this study is to identify the research voids and propose changes to improve current ATV guidelines. Results of this study will contribute to the scientific basis for developing regulatory and advisory guidelines for youth operating ATVs on farms. We conducted a systematic review30 of the literature and identified relevant articles, guidelines, standards, state laws, and recommendations on age limitations, physical and mental capabilities, safety requirements, and injuries and fatalities of children riding ATVs on farms. The literature review procedures included: conducting a literature search, selection of relevant sources using inclusion and exclusion criteria, extracting information from each source, and consolidation of the results. These two search engines include different types of sources, such as conference proceedings, books, reports, guidelines, and standards. Also, Google Scholar can search the full text of articles rather than just the citation, abstract, and tagging information in the PubMed and Web of Science search. Five separate searches were performed to incorporate age limitations, physical and mental capabilities, safety requirements, and injuries and fatalities of youth riding ATVs on farms.The next step was the selection of relevant sources using inclusion and exclusion criteria.

Individuals were sampled at random from the compartments affected by the event. For example, for an external transfer event of n smolt from farm 1 to farm 2, n smolt were randomly selected from all smolts in farm 1 and placed into the same compartments in farm 2. Fish that entered the model were assumed to be susceptible in their respective age category. Imported fish were assumed to be susceptible, noting the aim of the study to explore spread in Ireland without considering international importation of PMCV. On average, 2,176,111 eggs were imported per year during the study period, according to information from the Irish Marine Institute . Fish remained in the same infection state whilst changing age category, from egg-juvenile to smolt or smolt to growth-repro, or moving between farms. Figure 1 presents the conceptual SIE compartment model for PMCV spread in farmed Atlantic salmon, including indirect transmission via the environment and fish movements between holdings.There is an EU legal requirement for aquaculture production businesses to be registered, and to keep records of all movements of aquaculture animals and products, both into and out of the farm . In Ireland, the storage of these movement data is undertaken by the MI. This database contains several variables, including the date of fish movement, origin and destination sites with geographic coordinates, life stage, species and quantity of fish moved. The present study was based on all fish movement reports to the Fish Health Unit of the MI covering the period from 1 January 2009 to 23 October 2017. This included 648 reports, with information about the identifier of the origin farm, grow racks with lights idetifier of the destination farm, the number of fish and age group and the date of the movement. Each record was linked to the geographical coordinates of the farms provided by the aquaculture production business records, to allow for incorporation of local spread during the modeling phase of this study.

A farm was considered “active” if any fish were present on the farm, according to movement records. Enter events, i.e., hatchings or imports , were imputed as needed to ensure that farm-level fish numbers were sufficient to allow fish shipments between farms as recorded in the fish movement database . The date of the imputed hatching events was calculated based on the average residence time of fish prior to shipment in the farm. In total, 90 enter events were imputed, including approximately a third of these during the first year of the simulation . This represented on average 10 imputed enter events per year. Most of this imputed enter events corresponded to eggs or juvenile fish , but some fish were entered as smolts , growth , or broodstock fish . Internal transfer events, i.e., moving from eggjuvenile to smolt or from smolt to growth-repro, were imputed when the relevant time during the simulation had been reached. When moving from egg-juvenile to smolt, fish were aged a week prior to shipping to seawater farms, and for aging from smolt to growth-repro, smolts were allowed to remain on the farm for 180 days. Exit events, i.e., mortality, slaughter, or euthanasia, were generated either the day prior to the last shipment of a fish cohort, when it was evident, based on the records, that the fish destination of the whole cohort was another farm , or after a fixed amount of time if it was clear from the records that the farm was the final destination of the fish . The duration of this period was 300 days in freshwater farms and 600 days for seawater farms. Broodstock fish in freshwater farms were assumed to live until 1 week prior to an egg shipment. A total of 55 unique farms were used for the simulation, with the following event types: enter, including reported imports , internal transfer , external transfer , and exit .

A time-series was created to explore seasonality in the input data, focusing on the number of events, the number of farms with at least one fish and the number of fish per age category. A further time-series was produced to investigate the proportion of farms connected to at least one other farm, for each month of the year. A smoother was added to each of these time-series, using local polynomial regression fitting in order to describe the temporal trend .In addition, we evaluated the effectiveness of an improved bio-security in specific farms. For the purposes of the simulations, our definition of bio-security refers to measures that prevent infected fish from entering a farm, akin to a bio-security strategy that is 100% effective in preventing infected fish from entering or leaving a farm. As described above, this was done by moving all fish shipped to the susceptible compartment at the time of shipment. Six strategies were tested. In the first strategy, all farms were targeted for an increase in bio-security. This would be a very costly approach, but a good ideal for comparison. In the remaining strategies, we targeted the 8 most central farms in terms of a specific farm centrality measure, which were indegree, out degree, incloseness, outcloseness, and betweenness,using the same methodology described previously by Yatabe et al. . The sample size was chosen arbitrarily, representing ∼25% of farms in Ireland at that time. Briefly, indegree describes the number of different farms from which a farm receives fish, out degree describes the number of different farms to which a particular farm sends fish, incloseness is an estimate of how close all other farms reach to a respective farm, outcloseness is an estimate of how close a respective farm reaches to other farms, and betweenness is a measure of the degree to which a particular farm falls on the shortest path between all pairs of farms in the network .

For estimating these centrality measures, at the beginning of every year the movement records from the preceding 2 years were used for estimation. For example, on 1 January 2011 centrality measures of all farms were estimated based on fish movement data from 1 January 2009 to 31 December 2010, farms were ranked and the top 8 for each centrality measure were selected for an increased bio-security. There were two exceptions to this 2-year window for estimation of centrality measures: the year 2010, where only the data from 2009 was used to estimate centrality measures, and 2009, where no data from previous years were available. Therefore, during this latter year no control measures were applied. The former six strategies were evaluated using two approaches for preventing the spread of a newly introduced agent into the country: firstly, by applying the control measures 1 month after the agent was first detected , from now on the ‘reactive’ approach, and secondly by applying the control measures as a standard practice from before the first detection of the agent , from now on the “proactive” approach.Based on the data available for 2009, a rapid increase was observed that year in the number of active farms and fish . However, this is an artifact as many farms had not yet been involved in fish movement and thereby appeared inactive . As a consequence, our results are reported from the start of 2010. The number of active farms declined slightly during the period 2010–2017 with relatively stable numbers during the 2010-2014 period, and a decrease during the 2015–2017 period . The total farmed Atlantic salmon population in Ireland had an increasing trend from 2010, with a peak of more than 32 million fish in early 2015, to later decrease until the end of the simulation, although not dropping to previous levels, rolling benches for growing where it reached ∼13 million fish. This increase was related to a large increase in the number of juveniles during 2014 and 2015. The number of fish within each age category varied seasonally, with juvenile fish showing peaks during winter and dips during autumn , the former associated with spawning and the latter with the transition of juvenile fish to smolts prior to stocking in seawater farms in autumn and spring. For the smolts, the converse was true, with peaks during autumn and spring. This age group decreases roughly every 180 days, as this is the amount of time after which they were aged into the growth-repro age group. This in turn determines the peaks of this latter age group. The reduction in the numbers of fish in the growth-repro age group were mainly in spring-summer and autumn-winter, being a mixture of elimination of fish stocked in a farm as smolts after 600 days and elimination of fish stocked at older ages after spending the mean residence time in the farm . Based on reported fish movement data, the externally scheduled events showed a moderate increase during the study period, except for the enter events, and exhibited seasonal variation.

External transfers increased from autumn through to spring, decreasing during summer, showing the seasonality in the smolt stocking in autumn and spring, and the spawning season in winter, where fish and eggs are moved from broodstock sites to hatcheries. The enter events peaked from autumn to winter, this being associated with the entry of fertilized eggs by local broodstock fish and tended to drop during spring and summer. Overall, the enter events showed a moderate decrease during the study period. Internal transfers had a seasonal pattern in line with the external transfers, as it was often the case that fish will be aged before movement to other farm, specifically fish in the egg-juvenile age group were aged to smolt when moving from a freshwater to a seawater farm, and smolts were aged to growth-repro age group when moving smolt from a seawater to a seawater farm. Exit events also followed external transfers closely. This is because these events were scheduled to occur the day prior to a fish shipment, if the number of fish to be shipped was less than the number of fish initially stocked with the cohort . The proportion of farms connected with at least one other farm within a month through live fish movements also showed a cyclical pattern, with peaks in February through to April, June through to August, and October through to December .Following introduction of infection in mid and late 2009, i.e., the index cases, a between-farm prevalence of 50% was reached on early 2011 , and 90% of the fish farms were infected by early 2013 . By 5 years after the simulated introduction in late 2014, 100% of the farms were infected, oscillating around this value until the end of the simulation. The farms holding growth fish and broodstock and smolts had a faster modeled epidemic curve, the first group reaching a between-farm prevalence of 50% by early 2011 and 100% by mid 2012, stabilizing around that value in late 2013. For the farms holding smolts, a between-farm prevalence of 50% was reached in late 2010, and 100% between-farm prevalence was reached for the first time in late 2011, dropping to 50–75% during most of 2012, to finally oscillate around 100% from mid 2013 onward. The modeled epidemic curve for farms holding eggs and juvenile fish was slower, reaching a between-farm prevalence of 50% by late 2012, and a between farm prevalence around 90% since early 2013, oscillating around this value until the end of 2016, where it stabilized at 100% until the end of the simulation . Fish prevalence follows a similar dynamic, with total and juvenile fish prevalence lagging behind fish prevalence in the growth-broodstock and smolt age groups, but with the former two age groups never reaching a level of 100%. This is due to the constant input of newly hatched fish, which the model assumes are introduced into the susceptible compartment. This can be seen as a drop in the egg-juvenile and total fish prevalence around winter, when the fertilized eggs and juvenile fish are entered into the fish population. A similar cyclical trend can be seen with fish prevalence in smolt, which declines in autumn and spring as juvenile fish are transitioning into this stage prior to the stocking in seawater farms.

Implicit surface reconstruction methods have been shown to address these issues well, including hole-filling, reconstructing surfaces from noisy samples, reconstructing sharp corners and edges, and reconstructing surfaces without normal vectors in the point cloud. Basis functions are commonly used to define the space of implicit functions for implicit surface reconstruction. Basis functions are constructed from a discrete set of points scattered throughout the domain, whose distribution and locations play an important role to defining the implicit function. Examples of these points include control points for B-splines, centers for radial basis functions, and shifts for wavelets. Implicit surface reconstruction methods distribute these points in various ways. Heuristics include point density, error-controlled, and curvature-based subdivisions. Octrees are notable because the error of the surface reconstruction decays with the sampling width between control points, which decreases exponentially with respect to the octree depth. Additionally, the neighborhoods of control points from octrees can be solved for and evaluated in parallel using graphics processing units , which allows for on-demand surface reconstruction as demonstrated in [43]. Another approach for distributing the points that control the implicit function is to locate them directly on the points in the point cloud. In the formulation by Carr et al., a chosen subset of points in the point cloud and points projected in the direction of the normal vectors are used to place the radial basis function centers, rolling grow tables resulting in fewer centers than octrees that are still distributed near the surface. The explicit formulation by Hicken and Kaur uses all points in the point cloud to define the implicit function and shows favorable decay in surface reconstruction error as the number of points in the point cloud NΓ increases.

This structure has been used in combination with RBFs for hole-filling in [37] and anisotropic basis functions for representing sharp corners in [40]. Another approach is to construct a uniform grid of points to control the implicit function. Unlike the aforementioned approaches, the distribution of points is decoupled from the resolution of the point cloud. As a result, deformations to the geometric shape can be represented without loss in accuracy near the surface as shown by Zhao et al.. This makes it a popular structure in partial differential equation based reconstruction methods that evolve the surface during reconstruction, such as in [47, 48]. In general, more points representing the implicit function are required to achieve the same level of accuracy to other approaches. As a result, implicit functions defined by a uniform grid are more computationally expensive to solve for in both time and memory usage than the aforementioned approaches, as experienced by Sibley and Taubin, but can be reduced by a GPU-based multigrid approach as implemented by Jakobsen et al..The signed distance function presents an ideal candidate for implicit surface reconstruction and geometric non-interference constraints. It is known that the zero level set of the SDF is a smooth representation of the points in a point cloud, and its gradient field is a smooth representation of the normal vector field from the normal vectors in a point cloud. As a result, many formulations to approximate the SDF have been researched for implicit surface reconstruction. We note that there exists other methodologies, such as wavelet and a Fast Fourier Transform based method, that fit a smooth indicator function instead, but are less applicable for non-interfernce constraints where a measurement of distance is desired. We identify four categories that approximate the SDF in some way: explicit formulations, interpolation formulations with RBFs, PDE-based formulations, and energy minimization formulations.Explicit formulations use the data defined in the point cloud to define linear approximations to the SDF.

These formulations then apply smoothing to these linear approximations in order to define the level set function. Risco et al. present the simplest approach which uses the nearest edge and normal vector to define the function explicitly. The resultant constraint function is piecewise continuous but non-differentiable at points where the nearest edge switches. Belyaev et al. derive a special smoothing method for defining signed Lp-distance functions, which is a continuous and smooth transition between piecewise functions. Hicken and Kaur use modified constraint aggregation methods to define the function in a smooth and differentiable way. Upon the investigation of Hicken and Kaur, the signed Lp-distance functions give poor approximations of the surface. Additionally, Hicken and Kaur’s formulation is shown to increase in accuracy as the data in the point cloud, number of points NΓ, increases. We identify Hicken and Kaur’s explicit formulation as a good candidate for enforcing non-interference constraints,as it is continuous and differentiable with good accuracy.Another method to construct the level set function is to solve an interpolation problem given an oriented point cloud P. Because the data points of P always lie on the zero contour, nonzero interpolation points for the implicit function can be defined on the interior and exterior, as originally done by Turk and O’Brien. Radial basis functions are then formulated to interpolate the data. To avoid overfitting, thinplate splines can be used to formulate the smoothest interpolator for the data, as noted in [37, 45]. Solving for the weights of a RBF involves solving a linear system, which is often dense and very computationally expensive due to their global support. Turk and O’Brien solve up to 3,000 RBF centers, and improvements by Carr et al. allow up to 594,000 RBF centers to be constructed in reasonable time . The vector field is then integrated and fit, usually by a least squares fitting, to make the zero level set fit the point cloud. We classify the methods that solve for the vector field as a solution to a partial differential equations as PDE-based methods. Poisson’s method uses variational techniques to Poisson’s equation to construct a vector field. Improvements to this method add penalization weights to better fit the zero contour to the point cloud in [54].

Tasdizen et al. prioritize minimal curvature and minimal error in the vector field by solving a set of coupled second order PDEs to derive their level set function. Zhao et al. use the level set method, originally introduced by Osher and Sethian, for surface reconstruction, with the advantage of modeling deformable shapes. In the aformentionedPDE-based methods, the setup for the implicit function reduces to solving a PDE by time-stepping or a sparse linear system in the case of Poisson’s equation. In the analysis done by Calakli and Taubin, they found that Poisson’s method often over-smooths some surfaces. We also note that solutions to PDEs are more difficult to implement than other methods in practice.Another methodology is to solve an optimization problem that minimizes some energy function with respect to the values of the basis function directly. The smooth signed distance surface reconstruction method minimizes an energy function with three terms. Minimizing these three terms maximizes smoothness and minimizes the approximation error of the zero level set and the gradient field to the data in P, all in a least squares sense. Alternative forms, such as in [18, 44], propose a different energy term to this formulation, which does a direct least squares fit to the approximate signed distance function. We perform a more thorough discussion of the four energy terms in Chapter 3, as our method also poses an energy minimization problem. The energy minimization problem posed by these papers is a well-posed unconstrained quadratic programming problem. The solution to these unconstrained QP problems reduces to the solution of a linear system. Making use of hierarchical structures, such as octrees, and compactly supported basis functions, the linear system is sparse and recursively solved at increasing depths of the structure. These advantages allow for fast solutions on the order of minutes as reported by [19, 44]. It should be noted that the time and space consumed by hierarchical approaches grows exponentially with the depth of the octree, so many implementations limit the depth up to 11. The resultant number of control points in Tang and Feng are on the order of 106 .We note that interpolation formulations with RBFs, growing rack PDE-based formulations, and energy minimization formulations are different approaches to the same problem of approximating the SDF. The primary differences lie within the derivation and implementation of such methods. The energy minimization formulation by Calakli and Taubin performs a least squares fit to the data in the point cloud. Thin-plate spline RBFs are an exact solution to the same energy minimization formulation to interpolate the data and maximize smoothness, as derived by [56]. The two-step energy minimization formulation by Sibley and Taubin follows the same approach as PDE-based methods, where a vector field is solved for and then a least squares fit is done to fit the surface. We recommend the interested reader to Calakli and Taubin who discuss the similarities and differences between SSD and Poisson surface reconstruction methods.We summarize the context for all the methods in Table 2.1, highlighting the main differences in their formulation, basis function representation, and distribution of points controlling the function. We note our method is an energy minimization formulation, which uses the same energy terms as Calakli and Taubin, but with a different basis function and different distribution of control points. This section, in part, is currently being prepared for submission for publication of the material. The authors of this work are Ryan C. Dunn, Anugrah Jo Joshy, Jui-Te Lin, C´edric Girerd, Tania K. Morimoto, and John T. Hwang. The thesis author was the primary investigator and author of this material.Wind farm optimization problems contain an objective to be minimized with respect to design variables.

The objective function is important to the optimization problem because its minimum defines the optimal design of the wind farm. When an objective function is narrow in scope, the optimal result often compromises other aspects of the design. We tabulate the different objective functions in Table 2.2. Historically, many wind farm optimizations have focused on the annual energy production of a wind farm, which is considered to be too narrow of a scope. When optimizing AEP, solutions may be difficult to manufacture, economically impractical, and over-reliant on the model’s assumptions making it impractical in the real-world. The levelized cost of energy objective function is larger in scope and emphasizes efficient and economically feasible solutions, and is often considered a better objective than AEP. Recent work has converted an existing hub height optimization using AEP to improve the economic viability and competitiveness using LCoE as the objective function. Other optimizations such as cable length, noise, and mass are considered more narrow in scope. In some cases, multiple objective functions are considered in an optimization. For further conversation on the selection of an appropriate objective function, we direct the reader to [57].The design variables of the wind farm optimization are also important to defining the problem. In terms of decreasing the wake interactions of wind turbines, three main methods emerge that define the design variables of each problem. The first method uses the turbine positions as design variables and is called the wind farm layout optimization problem . The WFLOP has a highly multi-modal design space that is especially challenging for gradient-based optimization. The second method uses the turbine’s tower, blade, and rotor-nacelle assembly as design variables and is the turbine design optimization problem. The third method uses the turbine’s control to affect its wakes and is the turbine control optimization problem. We refer the reader to two reviews on wind turbine controls strategies. A summary of the design variables considered in previous gradient-based optimization studies is in Table 2.3. Note that some recent studies consider two optimization problems at once: simultaneous layout and control optimization and simultaneous layout and turbine design optimization. In these studies, the optimal results were improved compare to solving the optimization problems individually.An important problem in the wind farm layout optimization problem is the representation of the wind farm boundary. The wind farm boundary defines the feasible regions of a wind farm, and can be limited due to the geographic features of the land or sea. In optimization, these zones must be enforced as constraints to ensure turbines are placed in a feasible zone. For gradient-free optimization, the representation of these boundaries are simple. Wind farm boundaries may be enforced by a binary function or by discretizing the domain and excluding the points outside of the feasible space. However, a gradient-based boundary constraint function must be continuous and differentiable.

They all but disappeared during the Dark Ages of Medieval Europe and were rediscovered in France in the 1700s. Sir William Gage introduced the gages to England in the 1720s and subsequently both lost the varietal labels and named them after himself. The trees are weak to moderate in vigor and extremely narrow and upright. At their tree-ripe perfection in late July and August, the gages feature a green, yellow, or golden skin and a sugary sweet taste with slight tangy undertones that is arguably the most intensely rich-tasting fruit on the planet. True green gage plums are hard to find but worth the search.This species originated in China 2,000 years ago, was introduced to Japan in the 1600s, and subsequently brought to the U.S. by horticulturists John Kelsey and Luther Burbank.Burbank used this stock to breed the Satsuma, the Santa Rosa plum, and countless other varieties that founded the California plum industry. The fruit is large and heart-shaped to conical. The skin color can range from golden yellow, orange-red, or blood red to purple and black. Flesh color usually reflects a variation on the skin color. The taste is slightly acid over sweet. They are best eaten fresh. The flesh is juicy and unlike European plums they are not freestone, two notable exceptions being Satsuma and its improvement, Mariposa. These two varieties also feature less acidity and thus can be dried, a la prune plums. Japanese plums bloom abundantly early in the season , and thus fruit earlier than European plums . They generally produce heavy crops; if even 1–2% of the blooms set fruit, thinning is required. They tolerate milder winters, that is to say they bloom and set fruit with less chill hours than European plums. The trees tend to be vigorous, rambunctious growers, often exceeding 10 feet a year on standard rootstocks. They are very upright growers with the exception of the Satsuma and Mariposa varieties, trimming cannabis which again exhibit a prune plum-like growth habit. Their pollination needs are similar to European plums.Domestica plums should be pruned hard to stimulate continued vegetative growth throughout their life. As with peaches, when a plum branch goes flat it weakens and produces smaller and smaller fruit.

Prune to an inward or upward facing bud to redirect flat growth upward. Japanese plums should rarely be stimulated via heading cuts once established. Heading causes multiple narrow-angled , excessively vigorous regrowth. Pruning at maturation devolves to the occasional thinning cut and the renewal of the brushy lateral fruit bearing growth. Japanese flower buds have a cluster of 3–5 blossoms that live for 3–5 years. In any given pruning session 20% of these laterals should be stubbed back to 1–3 buds and regrown. They will fruit in the second year after renewal. Thinning for Japanese and European plums should be one to a cluster every 4–6 inches. Oversetting results in a nutrient sink that inhibits bloom and fruiting the next year . As with peaches they can and probably should be rescaffolded periodically .The current way we produce and consume food threatens both human health and environmental sustainability. In 2019, the EAT-Lancet Commission launched the planetary health diet, a global reference diet with focus on healthy diet produced in a sustainable way. The main objective of this diet is to increase the consumption of plant-based foods including vegetables, fruits, legumes, whole grains, and nuts while reducing the consumption of animal-sourced foods such as red and processed meat and dairy products. Another rapidly expanding area of research is understanding the complex relationships between diet, gut microbiome, and human health. Human gut microbiota refers to a complex community of trillions of different micro-organismsresiding in the human gut. Diet is considered one of the most important factors influencing composition and function of the gut microbiome, and thus, determining its metabolic outputs that may play a role in human health and disease. Consequently, many diet-associated conditions have been associated with the gut microbiome including obesity and several chronic diseases such as type 2 diabetes and cardiovascular diseases. Thus, it is important to examine the specific roles of different food groups on the gut microbiome.

The associations of plant-based foods, red and processed meat and dairy consumption with gut microbiome have not been extensively examined. Controlled small-scale human trials conducted mainly on individuals with obesity have demonstrated shifts in microbiome diversity or composition and adverse changes in microbial metabolites on diets high in animal-based foods and low in carbohydrates during 5-days to 8-weeks. Larger-scale observational studies on healthy French adults and on Chinese middle-aged and elderly have reported inconsistent results on the associations between individual plant-based foods, red meat or dairy with gut microbiome. These studies, however, lacked data on actual consumption of the foods due to the utilized dietary assessment method and on some foods in the core of this current study such as dairy subgroups . These apply also to our previous study, consisting partly of the same study population, where we also used frequency-based FPQ to examine diet quality-microbiome links . Furthermore, another Chinese study on middle-aged and elderly individuals utilized a more detailed dietary assessment method but focused on associations of vegetables or fruits with gut microbiome. To address these limitations, we used dietary recalls which capture wider range of foods and provide detailed dietary data on the quantitative consumption of these foods allowing for a more comprehensive assessment of the associations of plant-based foods, red meat, or dairy with gut microbiome. Furthermore, in contrast to our previous study where we examined genus-level microbiome associations we now examined species-level associations. The specific aims of the current study were to examine whether the consumption of plant-based foods , red and processed meat or dairy is related to individual gut microbiome diversity , inter-individual differences in gut microbiome composition , and differences in relative abundances of bacterial species in Finnish adults. We also examined how the functional properties of the microbiome relate to these food groups.We used data from the National FINDIET 2002 Study, a sub-study of the National FINRISK 2002 Study. The FINRISK Studies have been conducted by the Finnish Institute for Health and Welfare every five years from 1972 until 2012 to monitor risk factors for non-communicable diseases in Finnish adults. FINRISK 2002 comprised of a self-administered health questionnaire and a health examination, involving a random sample from six large geographical areas in Finland drawn from the national population information system . Stool shallow shotgun sequencing was successfully performed for a total of 7231 participants of which additional 20 participants were excluded due low read counts . One third of the FINRISK participants belonged to the FINDIET 2002 subsample where dietary habits of the participants were assessed by a 48-hour dietary recall. Of those invited, 2045 completed the recall and 2007 of the recalls were accepted. After excluding pregnant women and those who had a registered purchase of antibacterial medications for systemic use code: J01) within six months prior to the baseline examination , the final data included 1273 participants with available stool samples and dietary recalls.Food consumption was assessed with a 48-hour dietary recall. Dietary recalls were conducted during the health examination by trained nutritionists who interviewed participants and recorded all foods and beverages consumed. Portion sizes were estimated using commonly used food packaging, gardening rack household measures and a validated portion size picture booklet. The mean daily energy intake and consumption of food groups were assessed using the in-house calculation software Finessi and the Finnish national food composition database maintained by the THL.

Food consumption was calculated at the ingredient level by decomposing mixed dishes into individual ingredients using standard recipes. The main food groups and their subgroups used in the study are presented in Table 1. As we were unable to analyze nuts and seeds separately due to their very low consumption, we included them within the vegetables subgroup and for the same reason we also kept legumes within the vegetables. Similarly due its low consumption, we included ice cream within the other dairy products subgroup. The food variables were categorized based on the study specific consumption quartiles for principal coordinates analysis and distance-based redundancy analysis .All who participated in the health examination of FINRISK 2002 were asked to donate a stool sample. Those willing were given a stool sampling kit and instructions during the health examination to promptly gather the sample at home at their earliest convenience. Participants collected the samples into 50 ml Falcon tubes without a stabilizing solution and then sent them overnight under Finnish winter conditions to the study personnel preferably on Monday, Tuesday, Wednesday, or Thursday, to ensure optimal preservation of the sample. The samples were immediately stored at −20 °C and were kept unthawed until sequencing in 2017. The samples were sequenced based on whole-genome, untargeted shallow shotgun sequencing at the University of California San Diego. Normalizing of the samples to 5-ng inputs were done using an Echo 550 acoustic liquid handling robot and the samples were sequenced using Illumina Hi-Seq 4000 for paired-end 150-bp reads. The average read count was approximately 900,000 reads per sample. A more detailed description of protocols for DNA extraction and library preparation can be found elsewhere. Quality trimming of the sequences and removal of sequencing adapters was performed using Atropos. After removing human DNA reads by mapping them against the reference genome assembly GRCh38 using Bowtie2, the raw sequences were taxonomically annotated using SHallow shOtGUN profiler v1.0.5 by comparing them against complete archaeal, bacterial, and viral genomes in NCBI Reference Sequence Database v82 , U.S. National Library of Medicine, Bethesda, MD, USA; May 8, 2017). The classified microbial data were used in a compositional form, meaning their relative abundances were calculated by scaling their raw counts to the total sum of reads. For taxa analyses, the data were filtered to bacterial taxa and down to a core microbiome including any bacterial species with a minimum abundance of 0.01% and a prevalence of at least 1% across all samples, similar to Salosensaari et al..Trained nurses at the study site measured weight and height using standardized international protocols with participants wearing light clothing and no shoes . Height was measured to the nearest 0.1 cm using a wall attached stadiometer and weight to the nearest 0.1 kg using a beam balance scale. BMI was calculated as kg/ m². Participants’ age was calculated based on the birth date and study date, and sex was self-reported. The self-administered questionnaire included questions on participant´s smoking history and current smoking habits. For the analysis two groups were formed: current smokers and nonsmokers who had not smoked in the last 6 months. Information on medicines which could potentially affect the microbiome in addition to the excluded systemic antimicrobial medicines was acquired from the prescription medicine purchase register maintained by the Social Insurance Institution of Finland. Participants were linked to the register through the unique personal identifier assigned to each Finnish citizen. In contrast to assessing the use of systemic antimicrobial medication, an individual was flagged as using these other drugs if he/she had at least 3 separate purchase events including a purchase within 4 months prior to baseline investigation.The analyses were conducted jointly for men and women because the results in general were similar by sex. Characteristics of the study participants are reported as means with their standard deviations for continuous variables and as percentages for categorical variables. Alpha-diversity refers to intra-individual diversity of the microbiome and it was measured using the Shannon index. The associations between alpha-diversity and the main food groups and their subgroups were assessed using linear regression analysis. Beta-diversity refers to inter-individual diversity of the gut microbiome and thus acts as a measure of compositional difference. It was measured using the Bray-Curtis dissimilarity score. Permutational multivariate analysis of variance was used to assess the amount of compositional variation in microbiomes between individuals were explained by main food groups and their subgroups. Principal coordinates analysis was used to assess and visualize clustering of microbiomes in the highest and the lowest consumption quartile of each main food group. PCoA was paired with the function “factorfit” from the vegan package to test whether the averages of the PCoA ordination scores of the highest and the lowest consumption quartiles of the main food groups differ significantly .

The asymmetry of information detected in this study might result in deterrence for some producers to participate in the program if they perceive that producers that do not share PRRS status have competitive advantages over those that do share information. This study used data from a 24-month period to evaluate a disease that has been present in the US for more than 30 years. The decreasing PRRS trend shown here is consistent with a similar trend reported at a national level, however, clearly, our discussion must consider that any short-term trend can be affected by some random shock and may not reflect the true long-term trend of the disease. For example, the decrease of PRRS incidence may be explained, at least inpart, by the emergence of PED in 2013, which had a major impact on the US swine industry. Because producers and veterinarians became more worried about certain practices that might facilitate PED spread, increased bio-security might also have helped PRRS control. Another interesting finding was the negative correlation between the probability of sharing PRRS status and occurrence of disease . This result may be explained, at least in part, by the expectation that negatives premises may have been more willing to share PRRS status than positive premises, because of the differential in the perceived economic consequences of sharing that infected and non-infected premises have. However, an alternative explanation for this finding is that producers may have recognized the value of increasing their level of PRRS-related information collected from neighbors and trading-partners that may have helped them to select their suppliers of inputs. Some have suggested that information obtained via the production chain can achieve desirable outputs more efficiently than by using laboratory analyses to detect system failure, arguing, for example, that efforts to reduce information asymmetries and ensure product quality has led to vertical integration and extended production contracts in animal food systems. Vertical integration allows perfect information throughout the production chains, drying weed which may be more efficient than laboratory tests to identify disease prevalence, which then must be translated into control efforts.

Similarly, certain attributes of the voluntary cooperation in RCPs, in terms of accessibility to data and information among producers located in a specific area, may resemble those observed in vertical systems, which may be useful and complementary to regular surveillance and strategy selection to control PRRS. Results in this study also reveal that the higher the density of medium and large premises at the county level, the higher the probability of occurrence of PRRS for farms in those counties. This result suggests that disease spread is positively related to the density of production premises and/or the number of swine. Consequently, one may hypothesize that given that larger premises have higher odds of being infected, they could act as sources of infection for secondary cases, given the larger susceptible population and associated management factors. The final model included premises nested into counties, which indicates certain heterogeneity among counties in terms of the relative importance of the variables assessed here. Indeed, and despite the declining incidence of PRRS over the study time, spatial, temporal and spatial-temporal aggregations were detected through the study period . Additionally, results from this study are consistent with a combination of direct and indirect mechanisms of spread, as suggested by the persistence of spatial aggregation in some areas, but with extensions into others regions that may result as a consequence of between premises movements. In conclusion, this study has established a systematic approach to quantify the effect of RCPs on PRRS control. There is evidence that RCP-N212 has attracted a growing proportion of producers to share disease status information, suggesting a rising awareness that sharing information can lead to more effective disease control. By evaluating the effect of participation on the occurrence of PRRS, the value of sharing information among producers may be demonstrated, in turn justifying the existence of RCPs. These results provide useful indicators regarding the evolution of the RCP-N212, and, ultimately, support for disease control in Minnesota. Furthermore, the methods presented here may be applied to measure progress in other RCPs.farming offers a sustainable solution to scarcity of fresh produce.

The concept of indoor farming has been explored for millennia. The concept of shielding plants from vacillating weather conditions by growing plants inside a greenhouse was first implemented by agrarian communities in 30 CE. As time and technology progressed, full control over ventilation, air flow, growth medium, and light exposure became feasible. One of the first fully-fledged controlled environment research facilities began operation at North Carolina State University in 1968. Recent developments in the semiconductor industry have made it cost effective for light-emitting diodes , which can provide the specific wavelengths of light for photosynthesis, to supplant broadspectrum sunlight. This has given rise to “plant factories”and indoor farming “pods” : warehouses and shipping containers outfitted with LEDs, hydroponics, cameras and advanced sensors which are nominally more efficient than traditional farms and greenhouses.Shade is not a concern for indoor farms as, with optimal optical design, all plants can receive the requisite light for photosynthesis. As such, many indoor farms will organize hydroponically grown plants in either 1) vertically-stacked shelves or 2) adjacent panels hanging from the ceiling. This dense packing of plants facilitates more growth on less land. To put this into perspective, a 30-story vertical indoor farm with a 5-acre base could produce a crop yield equivalent to 2400 acres of a traditional farm.Different plants require different wavelengths of light for optimal photosynthesis and optimal growth of features such as stem length and leaf thickness. LEDs are perfectly suited to supply plants with the specific, optimal combination of colors of light they need, because LEDs emit a narrow band of wavelengths depending on the bandgap of their constituent semiconductor material. Thus, indoor pod farms with “walls” of LED light strips reduce energy waste by maximizing the amount of power absorbed by the plants and minimizing the power lost to excess heat. Beams of light supplied by LEDs can be collimated by addition of optical lenses, further reducing energy lost to non-plant targets and reducing the distance between the plants and LEDs. Additionally, exponential development in the semiconductor industry over the past three decades has made LEDs smaller, faster-actuating, more efficient, and more durable than traditional incandescent light sources, rendering LEDs economically viable for indoor farming applications.Hydroponics is a method of growing plants in a nutrient rich solution without the need for soil. Depending on the type of crop, this method can be executed via drip irrigation, aeroponics, nutrient film technique, ebb and flow, aquaponics, or deep-water culture. Although physically very different in the method of delivery, most of these techniques share the same fundamentals: a nutrient solution is pumped to the plants via a specialized delivery system and then circulated back to a reservoir where the nutrients are replenished. We refer the reader to for a comprehensive description of these techniques. Hydroponic methods use, on average, 10% of the water utilized in traditional farming as nutrients are delivered directly to the plant roots, minimizing water lost to evaporation. This mode of growing plants can be easily automated and, vertical growing systems combined with the fact that the lack of soil protects against pests, these systems make it easier to cater to the unique physiological needs of the plants while eliminating the need for pesticides and other chemicals. These systems, however, have high start-up costs and thus present a dire need for high operational efficiency to recoup these costs.The practice of vertical indoor farming in shipping container “pods,” enabled by LED light sources and hydroponic nutrient sources, is still nascent and little work has been done to quickly and efficiently model and optimize such systems. A digital-twin of an indoor pod farm can be safely and cheaply manipulated without jeopardizing the system or the plants’ well-being, making it an exceedingly quick, inexpensive, and useful approach for identifying optimal operational parameters.

The indoor farming pod is a complex system with a multitude of physical phenomena including air flow, light propagation, and energy transfer. Several digital-twin frameworks have been developed to capture the physics of light propagation in greenhouse, agrophotovoltaic, and food decontamination applications using ray tracing techniques and to capture and optimize the physics of energy flow and air flow. Ray tracing techniques decompose light into rays whose interactions with surfaces are quickly geometrically traced, facilitating fast computation of a large number of interactions between rays and surfaces and optimization of the surface shape for maximum absorption/reflection. Digital-twins have been scarcely employed in optimizing agricultural systems, and they are even more rarely implemented in indoor farming pods. Two such implementations were carried out by Randolph et al. and Sambor et al. to optimize the energy consumption of an off grid indoor farming pod to determine optimal operation time for each component of the system. These implementations, however, do not allow for manipulation of the orientation and/or shape of the system’s components for maximum operational efficiency. In [29], computational fluid dynamics methods were utilized to model the air flow inside an indoor farming pod, but such methods have a prohibitively high computational cost, especially when running various configurations and performing optimization. Thus, an easily manipulated, computationally inexpensive model that accurately captures the system’s physics is desired.Indoor farming is a promising mode of next-generation agriculture offering numerous benefits such as year-round crop cultivation, reduced transportation costs, and enablement of urban farms. However, these systems still face challenges related to energy consumption, and there has been limited quantitative analysis of their overall efficiency. To fill this gap and promote innovative design, we introduce a cost-effective digital-twin to analyze the optical properties of an indoor farming pod using a ray-tracing model. We utilize a genomic optimization scheme to identify the most optimal LED geometric configurations and emission characteristics toward maximizing energy absorbed by the constituent plants. The proposed digital-twin and optimization framework serves as a foundational framework that takes a physics-driven approach to optimize energy flow and paves the way for more sustainable indoor farming practices. To adapt the framework to other indoor farming configurations, we can adjust design objectives via cost function design and incorporate constraints via parameter search bounds. The framework could also be extended to include models for water usage or crop-specific reactions to different chemical/pesticides, thereby enhancing the accuracy of the digital-twin. Extending the framework to include wavelength-specific power flow could further improve predictions of energy efficiency and crop yield by providing each plant with its ideal lighting conditions. Such refined models can serve as a valuable tools for testing and estimating how a particular design would perform in the real world, enabling farmers to make informed decisions and effectively optimize their own indoor farming setups.The growth of the dairy industry has been accompanied by an increased volume of waste emissions that mainly consist of fecal and farm matrices. Manure contains a large number of undigested organic nutrients such as sugars, amino acids, nucleic acids, and vitamins. It is thus a valuable source of organic matter, nitrogen, phosphorus, potassium, and some micronutrients. Animal manure has therefore been used on farms as one of the most important and valuable sources of nutrients to improve soil fertility and increase agricultural crop production. Some farms recycle the solids in manure to use as bedding material, which can have advantages for farmers in terms of availability, convenience, and cost effectiveness. Researches have demonstrated that the use of organic manure, whether it is used alone or in combination with inorganic fertilizers, can have positive effects on crop yield and can improve the soil quality. In China, manure has been used in many agricultural regions of the country for centuries. The application of manure to agricultural land is an environmentally friendly method of waste disposal. However, in addition to organic matter, manure also contains many harmful gases, heavy metals, parasite eggs, antibiotic resistance genes, and a variety of intestinal microflora and opportunistic pathogens, as well as antimicrobial resistant bacteria. Pathogenic and antimicrobial-resistant microorganisms contained in the manure can lead to the contamination of edible agricultural products. Thus,if these manures are used as fertilizer without treatment or are not treated properly, dangerous microorganisms could be transferred from animals to humans, bringing about a threat to the environment and to human health. In addition, bacterial contamination of dairy farm environments can cause disease or spoilage of milk and its secondary products.

Free range environment in poultry farms, natural diet, and strict bio-security measures might cause the lower prevalence of Salmonella in organic poultry farms. However, the present study’s absence of Salmonella in farm environments might be caused by study design, as including some variables might play a crucial role and may result in different outcomes. Additionally good farm management, bio-security measures and external factors such as proximity to other farms might be potential confounders of not recovering Salmonella in the present study.Generic E. coli were prevalent in 50 out of 70 collected samples, being detected across all sample types except LH cage and egg swab samples. The population of generic E. coli and aerobic bacteria counts are shown in Table 2.1. Both E. coli and aerobic bacteria counts were lower in outwear and boots swabs compared to LH and FH fecal samples . However, both E. coli and aerobic bacteria counts for the FH door swab were not significantly different compared to outwear and boots swab counts . Generic E. coli counts were higher in the fecal samples collected from LH and FH compared to FH door swab samples . Similarly, aerobic bacteria counts were higher in fecal samples from both LH and FH followed by FH door swab samples and LH cage swab while egg swab samples had the lowest counts . Previous studies on E. coli prevalence from poultry farm environmental samples and worker’s samples varied . As mentioned before, the diverse prevalence of recovery of E. coli from farm environments depends on factors such as geographical location, heavy duty propagation trays scale of farms, antimicrobial usage and cleaning and sanitation practices on farms . Counts of E. coli in fecal samples in the present study were similar to the findings of previous studies .

Prior studies reported contaminations of egg surfaces with E. coli . In the present study, LH was cleaned frequently , which might be the reason for the lower bacterial load in LH and possibly caused not discovering E. coli in cage and egg swabs. Isolates from the FH door swab were resistant to 14 drugs, FH fecal sample isolates were resistant to 8 drugs, LH fecal sample isolates were resistant to 5 drugs, outwear swab isolates were resistantto 4 drugs, and of boots swab isolates were resistant to 2 drugs . The E. coli isolates from all types of samples were susceptible to amikacin, piperacillin / tazobactam constant 4, ticarcillin / clavulanic acid constant 2, ceftazidime, gatifloxacin, aztreonam, ciprofloxacin, imipenem, and piperacillin. The highest phenotypic resistance was observed for ampicillin , followed by nitrofurantoin and cefoxitin . A full antibiogram pattern of the antimicrobial susceptibility testing is presented in Table 2. Isolates of E. coli from FH door swabs and worker’s outwear swabs were resistant to the same drugs, such as ampicillin, nitrofurantoin, cefuroxime and trimethoprim/sulfamethoxazole . Isolates from all the environmental sample types and one isolate of boot swab samples were resistant to cefoxitin. All the environmental and worker’s sample types were resistant to ampicillin. Generic E. coli isolates from the FH door swab had a higher prevalence of resistance to at least one drug compared to isolates from the boot swabs . However, there was no difference in the occurence of resistance to at least one drug between the isolates from FH feces , LH feces and outwear swabs. Thirty five percent of all the tested generic E. coli isolates were resistant to at least one drug, nine percent to two drugs, and six percent of isolates were resistant to three or more antimicrobial drugs. Most prevalent non multi-drug resistant pattern was AMP-NIT . Four isolates from FH door swab samples were MDR, one isolate from LH fecal samples, and one outwear sample was MDR .

The present study observed the highest resistance in E. coli isolates for ampicillin and nitrofurantoin . However, these levels of resistance rates are not considered high resistance rate since, in the medical community the, resistance rates 20-30% above are considered as the highest level of resistance in bacteria that raise concern for public health. These antimicrobials are essential for veterinary and human medicine . The resistance prevalence to ampicillin was lower compared to other related previous studies. In most of these studies, the high resistance of ampicillin in E. coli was due to increased use of this prescription drug for treatment and ampicillin is a commonly prescribed antimicrobial to treat a wide range of infections worldwide . Besides, factors such as the horizontal transfer of resistance genes from other bacteria species to E.coli and the production of enzymes degrade or modify ampicillin might be possible reasons for the increased resistance to ampicillin in E. coli . Resistance rates of E. coli for nitrofurantoin in the present study were consistent with findings of previous occupational expose related studies in poultry farming . Nitrofurantoin is not widely used as ampicillin, only to treat urinary tract infections. Therefore, the low prevalence of antimicrobial resistance in E. coli in the present study and previous studies is an expected outcome. Our results showed a high prevalence of AMR in E. coli isolates from FH door swabs and fecal samples, suggesting that the FH environment might be a potential ARB or ARG reservoir and routes of exposure. Moreover, isolates from LH fecal samples and FH samples shared similar antimicrobial resistance patterns with worker’s outwear and boots sample isolates. Previous studies on occupational exposure of poultry farm workers to AMR concluded that ARB could be transmitted from the farm environments to workers . These previous studies compared antimicrobial resistance patterns in E. coli from environmental samples to worker’s urine or stool samples and found that resistance patterns were similar. Additionally, some studies found ARB or resistance genes in farm dust or hand-wash water on farms .

A study conducted in Tunisia reported that antimicrobial-resistant Campylobacter was found in 3% of chicken farm workers boot samples, but researchers did not recover the bacteria from worker’s outwear . To our best knowledge, the present study is the first study characterizing antimicrobial resistance patterns of E. coli in a poultry facility environment and comparing these patterns with farm worker’s outwear and footwear. The present study shows the importance of using personal protective equipment in reducing the spread of ARB or ARG from farm environments to workers. Additionally, the high prevalence of antimicrobial-resistant E. coli in door handles could suggest a potential risk of AMR transmission to farm workers. Because workers might touch their face or mouth after touching the door handles, we noticed that workers did not wear gloves, which might expose them to ARB. Therefore, wearing gloves and frequently sanitizing door handles is an important measure to minimize the risk of transmission of ARB or ARG, as bio-security measures have been proven to play a crucial role in minimize the transmission of pathogens in farms . Different sample matrices yield different prevalence outcomes. For example, fecal samples might have higher bacteria prevalence compared to surface swab samples, affecting overall prevalence significantly in a study. Additionally, in the present study, birds and workers did not receive antibiotics before and during the sample collection period, and consequently, overall resistance prevalence was low , and our results support the findings of Tang et al. where authors systematically reviewed 181 studies and found out that restriction of antimicrobials in food-producing animals are associated with reduced ARB in these animals. However, previous research has shown that ARB can still be present and transmitted in facilities with no antimicrobial drug use ; and our study found that the poultry facility might be a reservoir of AMR in which workers may be exposed to ARB. The present study cannot imitate intensive poultry production, vertical cannabis where antibiotics are usually used to prevent, control the disease, and treat birds. However, antibiotic usage in food animals in Western countries, including the U.S., has changed over the years. Implementing the Veterinary Feed Directive in the U.S. restricted certain antibiotics, and medically necessary antibiotics are allowed only with veterinary oversight and prescription. Additionally, there might be differences in population density and management practices between small-scale and intensive large-scale poultry production. In the U.S., a surveillance program, NARMS, was established in 1996 to monitor antimicrobial resistance in hospitals, retail meats, and food animals . However, currently, there is a lack of systematic surveillance of AMR in farmworkers. Additionally, there is a lack of awareness or education among the public and policymakers about the risks of AMR affecting farmworkers in livestock production . Moreover, a large body of previous and current AMR studies and regulatory efforts mainly focused on food safety from farm to retail and have considered pathogens as a food safety issue .

The above mentioned facts might explain the scarcity of research or data related to occupational exposure of animal farmworkers in the U.S. Therefore, more research is needed to identify possible ARB routes from the farm environment to workers in order to raise awareness of farmworkers and producers to avoid the risk of occupational exposure to AMR.The development of antibiotics in the 20th century was a groundbreaking advancement in medicine and one of the most significant advances in modern science . However, after a few decades, this great achievement has been compromised by the emergence and spread of antimicrobial resistance . AMR is the ability of microorganisms to protect themselves from the effects of antimicrobial agents via different mechanisms such as enzymatic inactivation, alteration of target sites, efflux pumps, reduced intake, horizontal gene transfer and formation of biofilms . Nowadays, AMR is a major global threat to public health . For example, AMR causes 2.6 million infections and 44,000 deaths each year in the U.S., while costing around 20 billion USD in healthcare and 35 billion USD in lost productivity annually . Overuse and misuse of antimicrobials in humand medine and food animal production have been considered as major contributors to the emergence of AMR around the globe. Moreover, the World Health Organization acknowledged the usage of antibiotics in food animal production as one of the leading causes of the development and spread of AMR . Many studies have shown the assosiation between the usage of antibiotics in food animal production and the emergence of Antimicrobial-resistant bacteria . ARB with their genetic determinants can be transmitted from food animal production to humans via various pathways such as direct contact with animals, environmental and air routes, cross-contamination, water and the food chain, and global trade . Among these transmission pathways, food chain is considered as critical. Previous studies documented that among animal food products, meat is a major reservoir of ARB and AMR in enteric bacteria such as Campylobacter, Eschericchia coli and Salmonella is a serious threat . Non-typhoidal Salmonella is a common and widespread pathogen that causes foodborne infections and outbreaks in the U.S. and around the world . AMR in Salmonella, especially multidrug resistance has become a serious health concern. For example, Salmonella resistance to critically important drugs such as extended spectrum cephalosporins, fluoroquinolones, and carbapenems limits treatment options and heightens the risk of morbidity and mortality among the patients to an estimated 40% . California is a highly populous and demographically diverse state in the U.S. with almost 40 million people which constitutes a major consumer market for retail meat products. Hence, research on the prevalence, distribution and AMR patterns of major foodborne pathogens such as Salmonella is integral to ensuring food safety and public health. The perpetual nature of bacterial populations to evolve over time highlights the importance of continuous monitoring of the trends of pathogens circulating in the food supply chain. Previously, we have characterized AMR of Salmonella from retail meat collected in California in 2018 . The aim of the current study was to characterize the AMR profiles of Salmonella isolated from retail meats in California using samples collected by NARMS routine surveillance in 2019. The specific objectives of the study were to assess the prevalence and phenotypic and genotypic AMR in various Salmonella serovars, to identify the resistance patterns of Salmonella, and to assess the correlation between Salmonella AMR phenotypes and genotypes.Fresh retail meat samples were collected twice a month from January to December 2019 as a part of the NARMS Retail Meat Surveillance. A total of 849 samples were purchased from randomly selected grocery stores in Northern and Southern California.

These systems consist of perforated drain lines that are buried approximately 6 feet deep and between 250 and 400 feet apart. The water flows into and through the network of tubes to a collection sump where it is pumped to the surface. The amount of water that leaves the root zone is the same amount as enters the drain system; this water travels through pathways of variable length depending on the location where the water enters the saturated zone and the position of the drain line . As a result, water that originates far from the drain line has a considerably longer distance to travel than water that enters the system from directly over the drain. Jury developed a simple mathematical model to calculate chemical concentrations in the drain, which takes into account these variable travel times. This model was used recently to calculate the transition time for drainage water to reach steady state in the western San Joaquin Valley. Steady state is the point at which the concentration of salts in the water in the drain line remains the same over time. For large drain spacings typical of those found in this region, such as 400 feet, the model predicted many decades of transition time before steady state could be reached. Prior to this time, the drainage water concentrations are influenced strongly by pre-existing salinity in the saturated zone. A flushing process occurs over time, rolling benches hydroponics which explains why selenium continues to occur in drainage water even though essentially no selenium has been added in irrigation water applied to the soil surface. All irrigation waters contain some dissolved salts, which become more concentrated as water is removed by the crop via transpiration.

The ratio of drainage volume to irrigation volume is called the leaching fraction, which is approximately equal to the ratio of the irrigation water’s salinity to the drainage water’s salinity in steady state. In the western San Joaquin Valley the concentration of irrigation water is low enough that for typical leaching fractions, the salinity of water leaving the root zone is less than that of the resident groundwater being displaced. In general, more salts are removed in the drainage water than are being applied with irrigation water. As a result, some of the salts stored in groundwater originating from geologic times are mined through the drainage process. One option for disposing of drainage water is to reuse it on salt-tolerant crops. For this type of operation, however, the water percolating below the root zone would be very high in salinity because of the initial high salinity of the applied water and the concentrating effects of water removal by the plant. In this case, the concentration leaving the root zone would be higher than the resident groundwater, so that salts would be stored in groundwater. The combination of irrigating salt sensitive crops with good-quality irrigation water and then irrigating salt-tolerant crops with the resulting drainage water creates a cyclic process in which salts are first extracted from groundwater and subsequently recharged to it. However, since there is a continual input of salts to the valley through imported irrigation water, salts gradually accumulate in the system and eventually must be disposed of in some manner. We simulated the long-term consequences of a farm system that included irrigating salt-sensitive crops with good-quality water , followed by irrigating salt tolerant crops with a blend of drainage and good waters, and eventually using an evaporation pond for ultimate disposal of the salts.

The imposed conditions, typical of normal farm operations, included planting only economic crops and restricting yield reductions to less than 10%.Water leaving the root zone at a location a short distance from the drain reaches the place of removal in a relatively short time, whereas it may take considerably longer for water originating at greater horizontal distances from the drainage line to arrive . As a result, at any given time following the start of an irrigation operation on a field overlying saline groundwater, the drain will contain a mixture of water originating from the irrigation and resident groundwater. Using the Jury method, it is possible to calculate the fraction of water in each category removed by the drain as a function of time. The percentage of water collected in the drainage system that comes from the root zone can be expressed as a function of a term where T = 2Qt/ θS, and Q is deep percolation in acre feet/acre/year, S is drain spacing in feet, θ is the saturated water content of the soil, and t is the time in years . This relationship depends upon the ratio of drain spacing and depth to an impermeable/restricting layer. Note that it can take a number of years before the water collected in the drain line originates entirely from the root zone. The time increases with the drain-line spacing and/or depth to the impermeable layer. Because the Corcoran clay layer — the restricting layer — is very deep compared to the region’s typical drain spacing, our computations were done for the curve where S/D = 1. The Jury et al. model makes a number of simplifying assumptions, including neglecting groundwater movement. However, the effect of moving groundwater, if any, would be to decrease the amount of drainage water in the drain compared to resident storage, delaying the time needed to reach steady state indefinitely. Neglecting its effect is therefore conservative.

Other influences such as the spatial variability of soil properties are site specific; but, if random they would not affect travel paths appreciably. The salinity of drainage waters in the valley typically creates an EC approximately equal to 10 dS/m. We assumed that the drainage water initially collected from the salt-sensitive crop would be at this concentration. Since irrigation water salinity of 10 dS/m is very high for irrigating cotton, our simulation assumed that drainage water and good water would be combined to an average of 5 dS/m. For this analysis, we relied on Letey and Dinar for the relationships between cotton lint yield and the amount of water applied at various irrigation water salinities. Furthermore, the uniformity of irrigation affects the relationship between yield and the amount of applied water . We assumed a Christiansen’s uniformity coefficient equal to 70, which is typical for a furrow irrigation system. We also assumed that the cotton irrigation would produce a lint yield equal to 92% of maximum potential yield. These conditions specified that a total of 3.2 feet of water would be applied, resulting in 1.2 feet of deep percolation . We assumed two irrigation management cases for the salt-sensitive crop area. One produced 8.8 inches per year of drainage water, and the second imposed a high level of irrigation management that resulted in 4.4 inches per year of drainage water. The EC of the water collected in the drainage system was computed each year using the travel time information in figures 1 and 2. The EC of the drainage water from the salt-sensitive crop area would decrease with time because the salinity of the water leaving the root zone wouldbe less than the resident groundwater’s salinity. The EC of the water collected in the drainage system would dictate how much good-quality water should be used to achieve an average of 5 dS/m irrigation water for cotton. Rainfall that did not evaporate during the winter would provide a fraction of the “good quality” water. As the EC of the drainage water decreased, the required amount of good water decreased. The EC of the drainage water from cotton was calculated yearly. In this case it increased with time, and relatively more good water was required to achieve the average 5 dS/m water. The analyses were done for various numbers of reuse cycles on cotton before the drainage water was disposed of in an evaporation pond.We calculated the percentage of the farm that could be retained in salt sensitive crops — such as tomatoes — for up to 100 years, when the drainage volume from the salt-sensitive area is 8.8 inches per year at various numbers of times that it is recycled through cotton . Increasing the number of cycles decreases the fraction of the farm that can be retained in salt-sensitive crops. However, cannabid indoor grow system cycling the drainage water through cotton also decreases the percentage of the farm that must be devoted to evaporation ponds .

We assumed that evaporation from the ponds was 4 feet per year. Imposing good irrigation management that reduces drainage volume to 4.4 inches per year increases the percentage of the farm that can be planted in salt-sensitive crops . When compared with drainage of 8.8 inches per year , decreasing the drainage volume from the salt-sensitive crop area also reduces the percentage of the farm that must be devoted to evaporation ponds . As expected, increasing the number of reuse cycles increases the percentage of the farm that must be devoted to cotton, at 8.8 inches per year of drainage water from the salt-sensitive crop area . If the drainage water from the salt-sensitive crops is reduced, the percentage of the farm devoted to cotton could also be reduced. Cotton is a common crop in the western San Joaquin Valley and is usually irrigated with good-quality water. In our scenarios, drainage water was partially used to irrigate the cotton. Therefore, we computed the difference in the amount of good water thatwould be used for cotton with and without blending in drainage water. The difference between these two numbers is considered the amount of fresh water saved by using the drainage water. On a 1,235-acre farm, the increase in acre-feet of fresh water saved by increasing the number of cycles is partially attributed to the fact that more land was also farmed to cotton . There are two benefits to recycling drainage water through cotton: the percentage of the farm required for evaporation ponds decreases and fresh water is saved. The monetary value of the water saved depends upon whether the returns are simply associated with applying less fresh water or whether the fresh water can be marketed and sold to the urban sector, where its value is greater. If this is possible, cycling drainage water through cotton could produce significant revenue to offset some of the costs associated with total farm operations.The results of this simulation indicate that a system which irrigates salt sensitive crops with good-quality irrigation water and reuses the drainage water to partially supply water for a salt-tolerant crop, with eventual disposal into an evaporation pond, can be physically sustained for centuries in the western San Joaquin Valley. Management to reduce drainage volumes from the salt-sensitive crop area has a high payoff, in that it allows a greater percentage of the farm to be maintained in salt-sensitive crops and a lower proportion to be devoted to evaporation ponds. Although cotton was selected for this analysis, any salt-tolerant crop could be substituted. It is possible to utilize solar evaporator ponds, in which the drainage water is discharged at rates equal to or less than the evaporation rate. We know of no other option for disposing salts on farmland while maintaining high crop productivity on the major part of the farm. Because of selenium in drainage water, evaporation ponds must also be managed to mitigate wildlife hazards. This may require netting the ponds and/or a combination of management and compensation habitat. The costs associated with the mitigation procedures depend on the extent to which they are required. Therefore, although this system is physically sustainable for centuries, its economic sustainability must still be evaluated. In areas where the selenium concentration in drainage water is particularly high, the selenium concentration in the evaporation pond could exceed the level established for classifying water as a toxic waste, greatly increasing costs and perhaps making the system economically unfeasible. The criteria used to classify selenium-tainted water as toxic waste play a critical role in future opportunities to maintain agricultural production in a sustainable manner without out-of-valley disposal of drainage waters. The current soluble threshold limit concentration for classifying selenium as toxic waste is 1.0 mg/L. This STLC was derived by multiplying the California drinking water standard for selenium by an environmental accumulation factor of 100. The California drinking water standard was 10 mg/L in the early 1980s when the hazardous waste limits were adopted.