Posts Tagged: science

Extreme weather accelerates nitrate pollution in groundwater

Extreme weather spurred by climate change, including droughts and heavy rains, may increase the risk of nitrates from fertilizers ending up in groundwater, according to a recent study from researchers at the University of California, Davis. The study found heavy rains after a drought caused nitrates to seep 33 feet under farm fields in as little as 10 days. The study was published in Water Resources Research.

“The conventional wisdom was that it could take several weeks to years for nitrates to move from the crop root zones to reach groundwater,” said corresponding author Isaya Kisekka, a professor in the Departments of Land, Air and Water Resources and Biological and Agricultural Engineering. “We found these extreme events, such as California's atmospheric rivers, are going to move nitrate more quickly.”

In this study, different methods were used to measure how much nitrate, a component of nitrogen fertilizer, was seeping down through the soil in a tomato and cucumber crop near Esparto, California. Scientists conducted their research from 2021 until 2023 when California was experiencing periods of drought followed by atmospheric rivers. They measured nitrate during both the growing seasons and the rainy seasons.

Drought can leave more nitrogen in soil

Previous studies have shown about 40% of nitrogen fertilizer used for vegetables isn't absorbed by the plants but remains in the soil. During droughts, crops don't use nitrogen efficiently, leading to excess nitrogen in the soil. This study found that if a drought is then followed by heavy rainfall, that sudden burst of water causes nitrate to seep in groundwater more quickly. The nitrate concentration in the shallow groundwater exceeded the U.S. Environmental Protection Agency maximum contaminant level of 10 milligrams per liter for drinking water.

“In California, we often say we swing between droughts and floods,” said Kisekka. “These extreme events that come with climate change are going to make the risk of these chemicals ending up in our drinking water much more severe.”

Groundwater is the primary source of drinking water for most of California's Central Valley. In some regions, such as the Tulare Lake Basin, nearly one-third of drinking and irrigation wells exceed the EPA's safe nitrate level. High nitrate levels in drinking water can increase health risks, especially for young children. It may also increase the risk of colorectal cancer.

Need for real-time soil nitrate monitoring

Central Valley farmers are required to report to the Regional Water Board how much nitrogen they applied to their field and how much was removed as part of the crop's yield. The study compared different ways of monitoring when nitrate from fertilizers seep into groundwater. Kisekka said the results highlight the need for affordable, real-time soil nitrate monitoring tools to help farmers manage fertilizer use efficiently.

By using conservation practices that limit leftover nitrates in the crop's root zone after harvest, farmers can help reduce nitrate contamination in groundwater.  

This study's data will also help improve a model called SWAT, which is used to track nitrate seepage into groundwater across California's Central Valley. This effort is part of the Central Valley Water Board's program to regulate irrigated farmlands.

Other UC Davis authors include Iael Raij Hoffman, Thomas Harter and Helen Dahlke.

The study was supported by the USDA Natural Resource Conservation Service through its Conservation Effects Assessment Project. The national project is designed to assess the effectiveness of conservation practices across different watersheds. The study also had support from the USDA National Institute of Food and Agriculture.

Reminder: Science-to-Practice Grant Program 2024-25 request for proposals

UC Agriculture and Natural Resources is accepting proposals to the Science-to-Practice (S2P) Grant Program through Monday, Sept. 30, 2024. Full proposals must be submitted as a single PDF by 11:59 p.m. on Sept. 30, 2024. Proposals are to be emailed to Brent Hales, Associate Vice President, at bdhales@ucanr.edu and to Kathryn Stein at kathryn.stein@ucop.edu. Please see original message below for full details.

UC Agriculture and Natural Resources (UCANR) invites proposals to the Science-to-Practice (S2P) Grant Program for new projects that integrate research and extension. The S2P program provides funding to support the formation and development of teams proposing to explore innovative methods, structures and projects that foster the translation of research into programs and outputs for dissemination and implementation.

Interdisciplinary teams of eligible participants can apply for grants up to $10,000 for one year, renewable as funding permits for up to three years. In addition, UC ANR's Research and Extension Center System will match funding levels awarded, up to $10,000 per year, to offset the cost of any research and extension conducted at one of its nine Research and Extension Centers.

The S2P program's purpose is to foster integrated research and extension teams to address pressing, complex challenges requiring multiple perspectives and modes of knowledge. The S2P supports applied research-based activities that prioritize the development of collaborative networks in the UC ANR system across research and extension faculty, specialists and/or advisors as well as engaging partners beyond, such as practitioners, decisionmakers and thought leaders in the field.

Eligibility

The team must be composed of a research leader and an extension leader, both of whom will serve as the principal investigators co-leading the project. Team leadership must meet the following criteria:

1. Research PI must be a faulty member (tenured, tenure-track or non-tenure-track) with a research appointment in one of the Agricultural Experiment Station (AES) designated campuses and have an active Hatch or USDA multistate project.

2. Extension PI must be a Cooperative Extension specialist or advisor.

Additional participants are encouraged and may be from UC ANR, from other UC-affiliated campuses or from outside the university. All funds must be used to directly support UC ANR activities and personnel. Funds cannot be used to support graduate students, employees or other persons not employed by or not enrolled in a UC ANR program.

Proposal Requirements

The full proposal will be submitted online as a PDF. The required components are outlined below with page limits and guidelines.

Proposal information:

A. Project Participants

1. Designate only the research and extension principal investigators who will co-lead the project. Refer to the eligibility requirements stated above.

     i. Applicant may be either research or extension lead; include the other project lead in the “Co-Applicant” field.

     ii. Include the two project leads and all other team participants in the Team Roles section.

B. Summary (300 words maximum)

1. Summarize the integrated project, including the primary stakeholders or clientele standing to benefit by the project, a brief statement of the goal(s) and the integrative strategy.

C. Total Research and Extension Budgets

Unified PDF must contain all the following components:

D. Title and Project Narrative (90 points)

Three pages maximum for new proposals does not include team roles, budget and justification or references.

1. Research Component (20 points)
• What is the research problem, defined in the context of a field of research or discipline?
• What are the gaps in data or knowledge that make this project significant?
• What is this project's potential to impact knowledge advancement in a particular research field/discipline/area?
• Identify research-specific activities required to advance the integrative strategy outlined below, including defined research-related deliverables (e.g., publications, grant applications, etc.) and expected outcomes and impacts.
2. Extension Component (20 points)
• What are the learning objectives that will deliver the science-based knowledge generated through the research component?
• What is the significant public benefit of this project?
• Who will benefit from or be affected by this project?
• Identify education-specific activities required to advance the integrative strategy outlined below, including defined extension-related deliverables and expected outcomes and impacts.
3. Integrative Strategy (40 points)
• What is the strategy that combines the generation, translation, and transfer of technology and/or knowledge into practical applications or practices?
• How do the research and extension components complement one another?
• Why does this project require an integrated approach and interdisciplinary team to create societal value through research-based education relevant to identified stakeholders' needs?
• How will the identified stakeholders be engaged in the research and extension activities?
4. Project Timeline (10 points)
• Outline significant benchmarks along this project's timeline that can illustrate the team's vision and trajectory during and beyond this proposal's timeframe. The benchmarks should align with the objectives described above in the research, extension and integrative strategies.
• Identify all approvals required to complete the project (e.g., IRB, IACUC, etc.) and the timeline for obtaining them.
• This may be presented as a diagram or table.

E. Team Member Roles (10 total points)

1. Briefly describe the roles and expertise of the research and extension PIs.
2. Include a coordination plan for integrating team members across UC ANR functions and units and university and external partners.
3. List all team members with their affiliations. Describe the role and responsibilities of each member, including how the expertise of each will contribute to the research, extension or integrated activities. A balanced team representing both research and extension is important.

F. Budget and Justification

1. Provide a two-column budget, dividing research and extension expenses.
2. Successful projects will be awarded up to $10,000, with the funding period beginning on Jan. 1, 2025.

          i. All budgets should be constructed so that up to $5,000 in expenses support research activities and up to $5,000 support extension activities.

          ii. If the project's research and/or extension will be conducted at a Research and Extension Center, a budget should be developed in collaboration with the specific REC Director to ensure funding levels requested are aligned with the Center's recharge rates and do not exceed $10,000 for the funding period.

          iii. Please note that submissions to this internal competition do not require the budget to be created through the UC ANR Office of Contracts & Grants (OGC).

1. Include a detailed budget justification, providing a brief description and explanation of need for costs associated with project activities.
2. Funds used to pay part-time wage-payroll must be for activities outside of any job description currently paid for by UC ANR, or it must support work on a new activity.

          i. Part-time wage-payroll must be paid through the UC ANR system (funds cannot be transferred to county systems).

    5. All other project costs typically allowed by federal extramural sponsors are allowed in this program.

    6. Funds cannot be used for the following:

            i. Faculty salaries (including supplemental) or standing appointment salaries

           ii. Travel to professional meetings

           iii. Out-of-country travel

           iv. Equipment purchases exceeding $5,000

           v. Support of non-UC ANR personnel

     7. Funds to support personnel outside the UC ANR must be obtained from other units and require a letter of commitment from the non-UC ANR unit, submitted with the proposal as a supplemental document.

     8. Budgets are constructed for a maximum of one year and must be expended by Dec. 31, 2025. No carryover is allowed.

     9. Funded projects can be competitively renewed up to two times, for three years of support; unexpended funds in one year will not carry over. Extensions for unexpended funds are not allowed for any projects.

Evaluation Criteria

Proposals will be evaluated and scored on the following criteria:

• Presents a clear plan for building or supporting an interdisciplinary team
• Demonstrates the potential for effective strategies to integrate research and extension activities
• Proposes activities that help to initiate, advance and strengthen teams and projects to obtain extramural support
• Defines both research and extension deliverables and provides clear benchmarks for achieving expected outcomes and impacts
• Incorporates audiences traditionally not targeted
• Projects that demonstrate considerable opportunities to achieve the UC ANR mission and our commitment to diversity, equity and inclusion are especially encouraged
• Identifies outcomes that are easily measurable and scalable
• Contributes to the knowledge base through distribution of results that benefit other efforts.

Submission and Review Process

Full proposals must be submitted as a single PDF by 11:59 p.m. on Sept. 30, 2024. Proposals are to be emailed to Brent Hales, Associate Vice President, at bdhales@ucanr.edu and to Kathryn Stein at kathryn.stein@ucop.edu.

Proposals will be evaluated by a panel of reviewers established by the Associate Vice President. Applicants will be notified of decisions by mid-November 2024.

Please direct any questions regarding your proposal to Brent Hales at bdhales@ucanr.edu.

Reporting Guidelines:

The period of performance for S2P grants will begin Jan. 1, 2025, and terminate Dec. 31, 2025. Projects may be renewed for up to three years of support. Proposals for renewal can

Be submitted in the next cycle for the S2P grants. An interim report for all awarded proposals will be due on July 15, 2025. Final reports will be due Jan. 15, 2026.

Takeaways from Posit::Conf 2024

R and Python together at last, the AI takeover, and Quarto ups its game.

Posit::Conf, Posit's annual conference, was held last week in Seattle, WA. While the name might be unfamiliar, many of you might recognize Posit's previous iteration, RStudio. Posit has produced many products R users know and love, including RStudio, Shiny and the Tidyverse. After a whirlwind three days, here are some takeaways from the conference!

A New All-in-One IDE

Togetherness was a key theme, with Posit rolling out the beta version of Positron, an IDE that combines elements of RStudio, VS Code, and introduces its own unique features. While switching IDEs is generally not at the top of any coder's to-do list, Positron is multilingual, enabling users to code in R, Python, and Julia within a single project. It also introduces new ways to interact with your data, such as readily available summary statistics, the ability to filter or sort data by multiple fields while retaining the active query in the window at all times, and the option to resize graphs and figures in the plots pane through a simple user interface. Positron also leverages many new and existing VS Code extensions, offering a wealth of customization and additional capabilities. Rstudio is by no means leaving the picture– Positron is still in beta, and Rstudio will continue to be supported for a good, long time. However, if you (like me) crave a unified interface for your R and Python coding, Positron may be worth trying out.

Helping R Users Learn Python

For Py-curious R coders, a session on “Python Rgonomics” suggested some packages to make the transition easier for those of us spoiled by the tidyverse.

• Polars for exceptionally fast data wrangling and dplyr-like syntax

• Plotnine and seaborn for ggplot-like syntax when making graphs and figures

• Great tables for producing functional, readable tables (also available in R as the gt package).

• Pyenv for environment management.

• Pins (for R and Python!) publishes objects to “boards” that allows users (or multiple users) to access them across projects. Boards can include shared/networked folders, like DropBox or Google Drive.

 

AI for All

Melissa Van Bussel provided practical tips for using generative AI. She highlighted some new capabilities of ChatGPT 4o, including the ability to transcribe handwritten notes and tables, preserving colors and formatting. GPT can even convert these into HTML or Quarto formats.

She shared insights on prompt engineering (i.e., how you ask questions to AI engines), noting, “Writing effective prompts goes hand in hand with your existing expertise.” Achieving correct and effective output requires providing specific prompts and making corrections when errors occur. She recommended structuring prompts in a way that mirrors coding practices. For example, to generate a graph, start by specifying the data, then define how to map each axis and assign colors. Next, specify the graph or chart type and indicate any grouping by other variables. Finish with aesthetic (eg palette, theme, title, legend) preferences.

While presenters were enthusiastic about the possibilities of generative AI, a recurring theme was the necessity for users to provide clear direction and verify the results. One presenter compared AI to hiring a new human assistant—AI can assist with tasks effectively when given proper guidance but will make mistakes and requires careful supervision. Generative AI performs best when used to quickly accomplish tasks that users already have the knowledge and skills to handle themselves.

One of the most prevalent use cases for generative AI was in combination with Shiny. Joe Cheng's presentation demonstrated integrating AI into Shiny apps, specifically into Shiny dashboards. Users could request modifications to the data displayed on the dashboard using plain language, which the AI translated into SQL queries to adjust the output based on the request. This is particularly noteworthy as the AI accessed only the schema, not the actual data, to apply the filters.

Winston Chang developed an AI assistant to help people build Shiny apps and did a live demonstration. Although still experimental, Shiny for R is widely used, and the assistant showed promising outputs.

Quarto Expands its Horizons

Quarto is a relatively new version of R Markdown (a publishing tool) that allows users to knit together code into documents, dashboards, web pages, PDFs, and even eBooks. An added advantage of Quarto is its multilingual capability– it, like Positron, supports both R and Python. Some new capabilities were highlighted at the conference:

• Dashboards: Easily build dashboards using the Quarto extension in RStudio or Positron. Each visualization (graphs, maps, tables, and even just text boxes) can be arranged like tiles or cards. Dashboards can also include sidebars and toolbars, and can support interactivity, including cards that use  jupyter widgets, leaflet, and shiny.

• PDFs: Quarto now uses typst instead of LaTeX, enabling users to create customized PDF outputs with a more intuitive language.

• HTML (Websites): Quarto (like R Markdown) can produce HTML outputs. However, now it also supports more flexible HTML code chunks, and allows for HTML/CSS/JavaScript integration.

• Quarto live: A quarto extension that allows users to embed code blocks and exercises for R and Python into Quarto documents. This has lots of teaching applications, and can be used to generate exercises similar to those you find in DataCamp and other online coding courses.

• Closeread: A scrollytelling extension for quarto that enables interactive storytelling similar to that seen in fancy New York Times articles or Esri Storymaps. The gallery has some example outputs, while the guide can walk you through the process of creating your own scrollytelling page.

Finally, one of my favorite quality-of-life take homes was simply that it is possible to include emoji in your R or Python code, either using unicode or simply pasting them in. While the demonstrated use case was to make specific messages stand out in your log or printed statements, sometimes a picture can convey what 1000 characters cannot and help you enjoy coding just a little bit more.

If you love (or begrudgingly engage in) data science, I encourage you to check it out next year– virtual registration for educators and academics in 2024 was free, and hopefully will be next year too!

 

Science-to-Practice Grant Program 2024-25 request for proposals

UC Agriculture and Natural Resources (UC ANR) invites proposals to the Science-to-Practice (S2P) Grant Program for new projects that integrate research and extension. The S2P program provides funding to support the formation and development of teams proposing to explore innovative methods, structures, and projects that foster the translation of research into programs and outputs for dissemination and implementation.

Interdisciplinary teams of eligible participants can apply for grants up to $10,000 for one year, renewable as funding permits for up to three years. In addition, UC ANR's Research and Extension Center System will match funding levels awarded, up to $10, 000 per year, to offset the cost of any research and extension conducted at one of its nine Research and Extension Centers.

The S2P program's purpose is to foster integrated research and extension teams to address pressing, complex challenges requiring multiple perspectives and modes of knowledge. The S2P supports applied research-based activities that prioritize the development of collaborative networks in the UC ANR system across research and extension faculty, specialists and/or advisors as well as engaging partners beyond, such as practitioners, decisionmakers and thought leaders in the field.

Eligibility

The team must be composed of a research leader and an extension leader, both of whom will serve as the principal investigators co-leading the project. Team leadership must meet the following criteria:

1.    Research PI must be a faulty member (tenured, tenure-track, or non-tenure-track)with a research appointment in one of the Agricultural Experiment Station (AES) designated campuses and have an active Hatch or USDA multistate project.

2.    Extension PI must be a Cooperative Extension specialist or advisor.

Additional participants are encouraged and may be from UC ANR, from other UC-affiliated campuses or from outside the university. All funds must be used to directly support UC ANR activities and personnel. Funds cannot be used to support graduate students, employees or other persons not employed by or not enrolled in a UC ANR program.

Proposal Requirements

The full proposal will be submitted online as a PDF. The required components are outlined below with page limits and guidelines.

Proposal information:

A.    Project Participants

1. Designate only the research and extension principal investigators who will co-lead the project. Refer to the eligibility requirements stated above.

           i. Applicant may be either research or extension lead; include the other project lead in the “Co-Applicant” field.

           ii. Include the two project leads and all other team participants in the Team Roles section.

B.    Summary (300 words maximum)

1. Summarize the integrated project, including the primary stakeholders or clientele standing to benefit by the project, a brief statement of the goal(s) and the integrative strategy.

C.    Total Research and Extension Budgets

Unified PDF must contain all the following components:

D.    Title and Project Narrative (90 points)

Three pages maximum for new proposals does not include team roles, budget and justification or references.

1. Research Component (20 points)
• What is the research problem, defined in the context of a field of research or discipline?
• What are the gaps in data or knowledge that make this project significant?
• What is this project's potential to impact knowledge advancement in a particular research field/discipline/area?
• Identify research-specific activities required to advance the integrative strategy outlined below, including defined research-related deliverables (e.g., publications, grant applications, etc.) and expected outcomes and impacts.
2. Extension Component (20 points)
• What are the learning objectives that will deliver the science-based knowledge generated through the research component?
• What is the significant public benefit of this project?
• Who will benefit from or be affected by this project?
• Identify education-specific activities required to advance the integrative strategy outlined below, including defined extension-related deliverables and expected outcomes and impacts.
3. Integrative Strategy (40 points)
• What is the strategy that combines the generation, translation, and transfer of technology and/or knowledge into practical applications or practices?
• How do the research and extension components complement one another?
• Why does this project require an integrated approach and interdisciplinary team to create societal value through research-based education relevant to identified stakeholders' needs?
• How will the identified stakeholders be engaged in the research and extension activities?
4. Project Timeline (10 points)
• Outline significant benchmarks along this project's timeline that can illustrate the team's vision and trajectory during and beyond this proposal's timeframe. The benchmarks should align with the objectives described above in the research, extension and integrative strategies.
• Identify all approvals required to complete the project (e.g., IRB, IACUC, etc.) and the timeline for obtaining them.
• This may be presented as a diagram or table.

E.     Team Member Roles (10 total points)

1. Briefly describe the roles and expertise of the research and extension PIs.
2. Include a coordination plan for integrating team members across UC ANR functions and units and university and external partners.
3. List all team members with their affiliations. Describe the role and responsibilities of each member, including how the expertise of each will contribute to the research, extension or integrated activities. A balanced team representing both research and extension is important.

F.     Budget and Justification

1. Provide a two-column budget, dividing research and extension expenses.
2. Successful projects will be awarded up to $10,000, with the funding period beginning on January 1, 2025.

          i. All budgets should be constructed so that up to $5,000 in expenses support research activities and up to $5,000 support extension activities.

          ii. If the project's research and/or extension will be conducted at a Research and Extension Center, a budget should be developed in collaboration with the specific REC Director to ensure funding levels requested are aligned with the Center's recharge rates and do not exceed $10,000 for the funding period.

          iii. Please note that submissions to this internal competition do not require the budget to be created through the UC ANR Office of Contracts & Grants (OGC).

     3. Include a detailed budget justification, providing a brief description and explanation of need for costs associated with project activities.

     4. Funds used to pay part-time wage-payroll must be for activities outside of any job description currently paid for by UC ANR, or it must support work on a new activity.

          i. Part-time wage-payroll must be paid through the UC ANR system (funds cannot be transferred to county systems).

     5. All other project costs typically allowed by federal extramural sponsors are allowed in this program.

     6. Funds cannot be used for the following:

          i. Faculty salaries (including supplemental) or standing appointment salaries

          ii. Travel to professional meetings

          iii. Out-of-country travel

          iv. Equipment purchases exceeding $5,000

          v. Support of non-UC ANR personnel

     7. Funds to support personnel outside the UC ANR must be obtained from other units and require a letter of commitment from the non-UC ANR unit, submitted with the proposal as a supplemental document.

     8. Budgets are constructed for a maximum of one year and must be expended by Dec. 31, 2025. No carryover is allowed.

     9. Funded projects can be competitively renewed up to two times, for three years of support; unexpended funds in one year will not carry over. Extensions for unexpended funds are not allowed for any projects.

Evaluation Criteria

Proposals will be evaluated and scored on the following criteria:

• Presents a clear plan for building or supporting an interdisciplinary team
• Demonstrates the potential for effective strategies to integrate research and extension activities
• Proposes activities that help to initiate, advance and strengthen teams and projects to obtain extramural support
• Defines both research and extension deliverables and provides clear benchmarks for achieving expected outcomes and impacts
• Incorporates audiences traditionally not targeted
• Projects that demonstrate considerable opportunities to achieve the UC ANR mission and our commitment to diversity, equity and inclusion are especially encouraged
• Identifies outcomes that are easily measurable and scalable
• Contributes to the knowledge base through distribution of results that benefit other efforts.

Submission and Review Process

Full proposals must be submitted as a single PDF by 11:59 p.m. on Sept. 30, 2024. Proposals are to be emailed to Brent Hales, Associate Vice President, at bdhales@ucanr.edu and to Kathryn Stein at kathryn.stein@ucop.edu.

Proposals will be evaluated by a panel of reviewers established by the Associate Vice President. Applicants will be notified of decisions by mid-November 2024.

Please direct any questions regarding your proposal to Brent Hales at bdhales@ucanr.edu.

Reporting Guidelines:

The period of performance for S2P grants will begin Jan. 1, 2025, and terminate Dec. 31, 2025. Projects may be renewed for up to three years of support. Proposals for renewal can

Be submitted in the next cycle for the S2P grants. An interim report for all awarded proposals will be due on July 15, 2025. Final reports will be due Jan. 15, 2026.

Lawn-pocalypse! Surviving Drought

Ah, summer! The season of sunburns, pool parties, and… lawn droughts. If your once lush, green carpet now looks like a crunchy brown doormat, you're not alone. Let's dive into why your yard is staging a dramatic death scene and what you can do to...

Bermuda grass and weeds overtaking drought stressed turf grass.

A patch of former lawn, mostly dead, with a few green weeds and Bermudagrass

Read more