California State University, Monterey Bay
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ShinyCore: An R/Shiny program for establishing core collection based on single nucleotide polymorphism data
Get PDFBackground: Managing and investigating all available genetic resources are challenging. As an alternative, breeders and researchers use core collection—a representative subset of the entire collection. A good core is characterized by high genetic diversity and low repetitiveness. Among the several available software, GenoCore uses a coverage criterion that does not require computationally expensive distance-based metrics.
Results: ShinyCore is a new method to select a core collection through two phases. The first phase uses the coverage criterion to quickly attain a fixed coverage, and the second phase uses a newly devised score (referred to as the rarity score) to further enhance diversity. It can attain a fixed coverage faster than a currently available algorithm devised for the coverage criterion, so it will benefit users who have big data. ShinyCore attains the minimum coverage specified by a user faster than GenoCore, and it then seeks to add entries with the rarest allele for each marker. Therefore, measures of genetic diversity and distance can be improved.
Conclusion: Although GenoCore is a fast algorithm, its implementation is difficult for those unfamiliar with R, ShinyCore can be easily implemented in Shiny with RStudio and an interactive web applet is available for those who are not familiar with programming languages
Adriana Camarena Makes a Supply Run to the Wildfires in Healdsburg and Petaluma During Covid-19
Get PDFhttps://digitalcommons.csumb.edu/auntiesewing_teaching/1000/thumbnail.jp
Benefits of Creating an Inclusive Collections of Literature Books for K-8 Students at the School Libraries
Get PDFReading is an essential skill for students of all ages. The ability to read and comprehend what the text is saying helps with the ability to learn topics at a deeper level. This senior capstone project examines the benefits of having diverse and inclusive literature available in K-8 school libraries. Through the use of a literature review, interviews with 2 librarians, 1 teacher and 1 principal, the findings revealed that all the subject participants gave similar answers in that diverse and inclusive literature are extremely beneficial to students. It instills empathy and understanding in students, which brings a sense of belonging and personal growth. It is recommended that a variety of books should be available and easily accessible to young readers at the elementary and middle school levels
Improving Species Distribution Models of Continental Shelf Fishes off California
Get PDFSpecies distribution models (SDMs) relate species occurrences, or abundances, with oceanographic or bathymetric data to predict species distributions. SDMs are used to forecast the effects of climate change on species distributions, evaluate existing protected areas and identify locations for future protected areas, estimate the effects of invasive species on a community, and determine how community assemblages change spatially or temporally. Articles describing marine SDMs are becoming increasingly common in the scientific literature; however, their efficacy for predicting the distribution and relative abundance of continental shelf fishes off California is not universally accepted. SDM performance can be affected by the inclusion of seascape variables, different spatial resolutions, the number of years of data, and the choice of statistical model. I examined how SDM performances changed with inclusion of these other factors. I combined multibeam bathymetry maps with remotely operated vehicle surveys to obtain remotely-sensed habitat data and the abundances and presence/absence of four continental shelf fishes: Blue Rockfish (Sebastes mystinus), Gopher Rockfish (Sebastes carnatus), Lingcod (Ophiodon elongatus), and Vermilion Rockfish (Sebastes miniatus). Using this information, I examined the strength of species-habitat associations and the spatial extent to which different SDM models were able to accurately predict presence/absence. Species-habitat associations for each species were determined from generalized linear models (GLMs) at three widely-spaced locations: a Northern California location (Bodega Bay or the Farallon Islands), a Central location (Point Sur or Point Buchon), and a Southern location (Harris Point). Model performance was evaluated using information about the overall accuracy, area under the curve (AUC), and Cohen’s Kappa statistics. Seascape characteristics (habitat patch area, perimeter:area ratio, and distance to habitat edge) at Point Sur were used in GLMs to determine if those variables increased model performance. Remotely-sensed habitat variables were created at three different resolutions (2, 5, and 10 m) at Bodega Bay and used in GLMs to evaluate the effect of spatial resolution on model performance. The effect of the number of years of data on model performance was evaluated at Harris Point, with GLMs and independent years of data. Additionally, at Harris Point, the choice of statistical model on model performance was evaluated with GLMs, generalized additive models, random forest, and boosted regression tree models. A coastwide model that optimized model performance was generated and tested against an independent site, Point Lobos. Lastly, an optimized model was created at Point Sur and tested against the independent sites of Point Lobos and Big Creek.
Each species exhibited differences in habitat associations among the three regions. For example, Blue Rockfish distributions were positively associated with eastness at the Farallon Islands and Harris Point but negatively associated with eastness at Point Sur. Additionally, Gopher Rockfish distributions were positively associated with broad-scale BPI at each of the three locations, but exhibited differences in associations with other metrics, such as vector ruggedness measure and eastness. The inclusion of seascape models and the different spatial resolutions either decreased or did not affect model performance. In general, model performance increased with more years of data, but was dependent on the number of observations in a test year. Furthermore, model performance increased with machine learning methods such as random forest or boosted regression tree models. However, the coastwide models that were tested at Point Lobos exhibited poor performance metrics when predicting presence/absence, except for Lingcod. Additionally, models created at Point Sur and tested at Point Lobos or Big Creek were only successful for Lingcod at Point Lobos and Gopher Rockfish at Big Creek. These results suggest that SDMs for continental shelf fishes can be improved through different methods, but their efficacy in predicting presence/absence in unsurveyed areas of the coast remains poor
Valuable Resources for Spanish-Speakers & Non-Residents of Monterey County in Addiction Recovery
Get PDFSun Street Centers in King City is a non-profit organization that offers a residential treatment program for men and women experiencing addiction. Their mission is to prevent alcohol and drug addiction by providing resources to individuals and families despite their income level. The main issue was that Spanish-speaking clients and clients that are non-residents of Monterey County were in need of resources to guide them during their recovery process. The idea for this project is to provide resources to all residential clients in both English and Spanish and also offer them to clients who are non-residents of Monterey County. The resource binder will provide resources at a glance for all clients that come into Sun Street Centers despite their residential status and will be offered in two languages. The resource binder was an opportunity to gather a great amount of valuable information in one binder and give residents the opportunity to use it during the program, after completion of the program, or in case of a relapse. My hope is to spread awareness that addiction is not by choice, addiction is the inability to cope with life
Oral Health Program Assessment
Get PDFThe Local Oral Health Program is a chronic disease prevention program focusing on providing educational workshops to parents who have children enrolled in schools with rates of 80% or higher of free or reduced lunch. Studies and surveys have revealed that low-income children have more cavities than those children in moderate and high-income families and they are not being addressed. The purpose of this project is to assess the effectiveness of the Oral Health Program which provides parents with educational workshops regarding dental services, government assistance, oral hygiene, and nutritional information. Post-surveys were distributed and collected after each workshop by the program intern and then evaluated collectively. Over 60% of the participants reported that they learned a lot regarding oral health and hygiene. Participants also stated that they would like these workshops to be reoccurring. Recommendations for the program include the development of an online resource guide that includes access to online informational resources about topics discussed in the workshops
Unstable Housing for Former Foster Youth in Santa Cruz County
Get PDFA lot of former foster youth are currently homeless. Homeless youth face the financial burdens of having to afford the cost of application fees. Rental application fees range from 50. The Community Action Board of Santa Cruz County (CAB) is a non-profit organization made up of six separate anti-poverty initiatives that concentrate on addressing the needs of people with limited resources. The Transitional Age Youth Housing Navigation (TAY NAV) is a program that works with former foster youth. The purpose of my project was to help raise funds in order to help pay for rental applications. The project was a fundraiser in the form of a bake sale. People were able to make monetary donations. We anticipate for the fundraiser to be an annual event to be able to help former foster youth with rental application fees. The event was implemented on April 1st, 2023, and raised a total of $625. It is encouraged that TAY NAV continues to promote the annual bake sale on social media and in local newspapers
The Effects of Gender on Students’ Learning
Get PDFThere are many struggles students face when pursuing an education. These barriers often leave students weary and disheartened, dreading the seven hours a day they are forced to spend at an institution that does not value their needs or identity. This paper will focus on how gender affects students’ learning in schools. In particular, it will discuss the sexualization of feminine-presenting students, the assumption of violence in masculine-presenting students, and the failure to provide safe and inclusive environments for gender-nonconforming students. All of this will be examined through the lens of gender’s effect on relationships within the education system, as well as the impact of shifting student mindsets. Many school systems have failed to create a space where students feel valued, safe, and understood. The first step to promoting learning is to ensure that gender norms and expectations do not affect student progress. The effects of a gendered binary system are detrimental to the growth of students, no matter the individual’s gender expression. The gender binary—and the societal norms that fall within it—serve to shame, stereotype, and constrain students. To create change and truly foster a positive learning environment, an effort must be made on an institutional and cultural level
Life Skills to Help Reduce Juvenile Recidivism
No full textYouth Alliance is a nonprofit organization based in Hollister, California. Within this organization there is a program for at-promise youth who are currently in the juvenile justice system, Guidance and Navigation to Achieve Success or GANAS. California has a 74.2% recidivism rate for minors. By developing a 5 week group curriculum for the youth enrolled in the GANAS program the project intended to provide at-promise youth with life skills to help reduce recidivism within the community. Findings from this project were established by a post survey; the survey revealed that youth were positively impacted by the topics covered in the group, 100% shared that they now feel confident in setting priorities for themselves. It is recommended that this program continues to teach the youth about life skills