Now showing items 1-20 of 10611

    • Skewed Distribution Models: Data Analysis, Identification, and Applications in Biomolecular Systems and R-loop Biology of Cancer

      Grageda, Andre (2023-09)
      Modeling and computational analysis can be used to crystallize, integrate, and extract knowledge from large datasets generated by biology, medicine, and next-generation sequencing. The use of probability models, multifactor hypothesis testing, and computational analyses is crucial to studies in systems biology. These studies provide insights into understanding large and diverse molecular biology data sets. It is no longer enough to study individual molecules, their properties, and their interactions with other molecules in cells and organisms. In addition to generating numerous case studies with unique data, such studies provide a limited understanding of the underlying complexity and dynamics of the leading mechanisms determining the states and behaviors of a whole biological system. Sequencing and multi-omics experiments generate big data needed to model processes, organization and behavior of biological systems in a more comprehensive, less biased manner. Analysis of such enormously heterogeneous and complex information requires mathematical models and computational algorithms. It is the motivation and challenge of current systems biology and medicine. Applied to cancer systems biology, we will consider basic probabilistic aspects of big data. We study skewed frequency distributions commonly observed in diverse omics experiments. We focus on modeling and developing computational algorithms to quantify big data's statistical characteristics, aiming for accurate and unbiased characterization of the systems variation. In several applications, we focus on the identification of the skewed distributions for quantification and differentiation of the of R-loop formation patterns in non-cancer, pre-malignant states and cancer genomes. Current studies involving R-loops rely on the S9.6 antibody which generates noisy signals. We show that using R-loop forming sequences for filtering specific S9.6 signals selects biologically meaningful signals. R-loops have been shown to play a role in tumorigenesis. Using our R-loop forming sequence enrichment method, we investigate the roles of R-loops in tumorigenesis across different detection modalities primarily in breast cancer.
    • Self-Affirmation’s Effect on Personal Development

      Reyes, Gabriella (SUNY Oneonta Academic Research (SOAR): A Journal of Undergraduate Social Science, 2022)
      Every day individuals are faced with threats, ranging in severity, that challenge one’s self-adequacy. While stress and self-protective defensives are aroused, the practice of self affirmation allows an individual to assess the asperity of the situation and find confidence in one’s abilities by confirming their self-adequacy. Self-affirmation is beneficial while confronting psychological threats in the disciplines of education, health, and personal well-being. However, the individuals most significantly benefitting from this practice belong to the most threatened domains—minorities, the chronically ill, and the low esteemed. While self-affirmation is said to broaden the perspective of individuals with high self-esteem or self-worth, further research is necessary to determine if self-affirmation practices generally apply to society, not just the struggling subgroups.
    • Sexual minority women and depressive symptoms throughout adulthood.

      Pyra, Maria; Weber, Kathleen M; Wilson, Tracey E; Cohen, Jennifer; Murchison, Lynn; Goparaju, Lakshmi; Golub, Elizabeth T; Cohen, Mardge H (2014-10-16)
      We examined the associations between depressive symptoms and sexual identity and behavior among women with or at risk for HIV.
    • Clinic-wide intervention lowers financial risk and improves revenue to HIV clinics through fewer missed primary care visits.

      Gardner, Lytt I; Marks, Gary; Wilson, Tracey E; Giordano, Thomas P; Sullivan, Meg; Raper, James L; Rodriguez, Allan E; Keruly, Jeanne; Malitz, Faye (2015-04-01)
      : We calculated the financial impact in 6 HIV clinics of a low-effort retention in care intervention involving brief motivational messages from providers, patient brochures, and posters. We used a linear regression model to calculate absolute changes in kept primary care visits from the preintervention year (2008-2009) to the intervention year (2009-2010). Revenue from patients' insurance was also assessed by clinic. Kept visits improved significantly in the intervention year versus the preintervention year (P < 0.0001). We found a net-positive effect on clinic revenue of +$24,000/year for an average-size clinic (7400 scheduled visits/year). We encourage HIV clinic administrators to consider implementing this low-effort intervention.
    • Estimating the cost of increasing retention in care for HIV-infected patients: results of the CDC/HRSA retention in care trial.

      Shrestha, Ram K; Gardner, Lytt; Marks, Gary; Craw, Jason; Malitz, Faye; Giordano, Thomas P; Sullivan, Meg; Keruly, Jeanne; Rodriguez, Allan; Wilson, Tracey E; et al. (2015-03-01)
      Background: Retaining HIV patients in medical care promotes access to antiretroviral therapy, viral load suppression, and reduced HIV transmission to partners. We estimate the programmatic costs of a US multisite randomized controlled trial of an intervention to retain HIV patients in care.
    • Changes in knowledge of cervical cancer following introduction of human papillomavirus vaccine among women at high risk for cervical cancer.

      Massad, L Stewart; Evans, Charlesnika T; Weber, Kathleen M; D'Souza, Gypsyamber; Hessol, Nancy A; Wright, Rodney L; Colie, Christine; Strickler, Howard D; Wilson, Tracey E (2015-04-01)
      Purpose: To describe changes in knowledge of cervical cancer prevention, human papillomavirus (HPV), and HPV vaccination among women at high risk for cervical cancer in the first five years after introduction of HPV vaccination.
    • Longitudinal Trends in Sexual Behaviors with Advancing Age and Menopause Among Women With and Without HIV-1 Infection.

      Taylor, Tonya N; Weedon, Jeremy; Golub, Elizabeth T; Karpiak, Stephen E; Gandhi, Monica; Cohen, Mardge H; Levine, Alexandra M; Minkoff, Howard L; Adedimeji, Adebola A; Goparaju, Lakshmi; et al. (2015-05)
      We assessed changes in self-reported sexual activity (SA) over 13 years among HIV-infected and uninfected women. The impact of aging and menopause on SA and unprotected anal or vaginal intercourse (UAVI) was examined among women in the Women's Interagency HIV Study (WIHS), stratifying by HIV status and detectable viral load among HIV-infected women. Generalized mixed linear models were fitted for each outcome, adjusted for relevant covariates. HIV-uninfected women evidenced higher levels of SA and UAVI than HIV-infected. The odds of SA declined by 62-64 % per decade of age. The odds of SA in a 6-month interval for women aged 40-57 declined by 18-22 % post-menopause (controlling for age). Among HIV+/detectable women only, the odds of any UAVI decreased by 17 % per decade of age; the odds of UAVI were unchanged pre-menopause, and then decreased by 28 % post-menopause. Elucidating the factors accounting for ongoing unprotected sex among older women should inform interventions.
    • The Contribution of Missed Clinic Visits to Disparities in HIV Viral Load Outcomes.

      Zinski, Anne; Westfall, Andrew O; Gardner, Lytt I; Giordano, Thomas P; Wilson, Tracey E; Drainoni, Mari-Lynn; Keruly, Jeanne C; Rodriguez, Allan E; Malitz, Faye; Batey, D Scott; et al. (2015-08-13)
      Objectives: We explored the contribution of missed primary HIV care visits ("no-show") to observed disparities in virological failure (VF) among Black persons and persons with injection drug use (IDU) history.
    • Physician morality and perinatal decisions.

      Minkoff, Howard; Zafra, Katherine; Amrita, Sabharwal; Wilson, Tracey E; Homel, Peter (2016-08-31)
      Objective: Given the same set of "facts" (e.g. fetal prognosis) different physicians may not give the same advice to patients. Studies have shown that people differ in how they prioritize moral domains, but how those domains influence counseling and management has not been assessed among obstetricians. Our objective was to see if, given the same set of facts, obstetricians' counseling would vary depending on their prioritization of moral domains.
    • "The Pleasure Is Better as I've Gotten Older": Sexual Health, Sexuality, and Sexual Risk Behaviors Among Older Women Living With HIV.

      Taylor, Tonya N; Munoz-Plaza, Corrine E; Goparaju, Lakshmi; Martinez, Omar; Holman, Susan; Minkoff, Howard L; Karpiak, Stephen E; Gandhi, Monica; Cohen, Mardge H; Golub, Elizabeth T; et al. (2016-05-24)
      There is limited research examining the sexual health and well-being of older women living with HIV (OWLH). Most studies focus on sexual dysfunction, leaving aside the richer context of sexuality and sexual health, including the effect of age-related psychosocial and interpersonal changes on sexual health behaviors. Guided by the integrative biopsychosocial model and the sexual health model, this study explored the importance of sex and sexuality among OWLH to identify their sexual health and HIV prevention needs for program planning. A purposive sample (n = 50) of OWLH was selected from a parent study (n = 2052). We conducted 8 focus groups and 41 in-depth interviews with 50 African American and Latina OWLH aged 50-69 years old in three U.S. cities. The triangulation approach was used to synthesize the data. Six salient themes emerged: sexual pleasure changes due to age, sexual freedom as women age, the role of relationships in sexual pleasure, changes in sexual ability and sexual health needs, sexual risk behaviors, and ageist assumptions about older women's sexuality. We found that sexual pleasure and the need for intimacy continue to be important for OWLH, but that changing sexual abilities and sexual health needs, such as the reduction of sexual desire, as well as increased painful intercourse due to menopause-associated vaginal drying, were persistent barriers to sexual fulfillment and satisfaction. Particular interpersonal dynamics, including low perceptions of the risk of HIV transmission as related to gender, viral suppression, and habitual condomless sex with long-term partners without HIV transmission have resulted in abandoning safer sex practices with serodiscordant partners. These findings suggest that HIV prevention for OWLH should focus on how sexual function and satisfaction intersect with sexual risk. HIV prevention for OWLH should promote ways to maintain satisfying and safe sex lives among aging women.
    • Mechanisms for the Negative Effects of Internalized HIV-Related Stigma on Antiretroviral Therapy Adherence in Women: The Mediating Roles of Social Isolation and Depression.

      Turan, Bulent; Smith, Whitney; Cohen, Mardge H; Wilson, Tracey E; Adimora, Adaora A; Merenstein, Daniel; Adedimeji, Adebola; Wentz, Eryka L; Foster, Antonina G; Metsch, Lisa; et al. (2016-06-01)
      Background: Internalization of HIV-related stigma may inhibit a person's ability to manage HIV disease through adherence to treatment regimens. Studies, mainly with white men, have suggested an association between internalized stigma and suboptimal adherence to antiretroviral therapy (ART). However, there is a scarcity of research with women of different racial/ethnic backgrounds and on mediating mechanisms in the association between internalized stigma and ART adherence.
    • Physical and Sexual Violence Predictors: 20 Years of the Women's Interagency HIV Study Cohort.

      Decker, Michele R; Benning, Lorie; Weber, Kathleen M; Sherman, Susan G; Adedimeji, Adebola; Wilson, Tracey E; Cohen, Jennifer; Plankey, Michael W; Cohen, Mardge H; Golub, Elizabeth T (2016-08-29)
      Introduction: Gender-based violence (GBV) threatens women's health and safety. Few prospective studies examine physical and sexual violence predictors. Baseline/index GBV history and polyvictimization (intimate partner violence, non-partner sexual assault, and childhood sexual abuse) were characterized. Predictors of physical and sexual violence were evaluated over follow-up.
    • Trends in Nonlipid Cardiovascular Disease Risk Factor Management in the Women's Interagency HIV Study and Association with Adherence to Antiretroviral Therapy.

      Hanna, David B; Jung, Molly; Xue, Xiaonan; Anastos, Kathryn; Cocohoba, Jennifer M; Cohen, Mardge H; Golub, Elizabeth T; Hessol, Nancy A; Levine, Alexandra M; Wilson, Tracey E; et al.
      Cardiovascular disease (CVD) is increasingly common among women with HIV, but literature on nonlipid CVD risk factor management is lacking. We examined semiannual trends from 2006 to 2014 in hypertension treatment and control (blood pressure <140/90 mmHg), diabetes treatment and control (fasting glucose <130 mg/dL), and smoking quit rates in the Women's Interagency HIV Study. Unadjusted and adjusted Poisson regression models tested time trends and differences between HIV+ and HIV- women. Among antiretroviral therapy (ART) users, we examined the association of ART adherence and virologic suppression with each outcome. We evaluated 1636 HIV+ and 683 HIV- women, with a hypertension prevalence of 40% and 38%, respectively; diabetes prevalence of 21% and 22%; and smoking prevalence of 37% and 48%. Hypertension treatment was higher among HIV+ than HIV- women (77% vs. 67%, p < 0.001) and increased over time with no difference in trend by HIV status. Hypertension control was greater among HIV+ women (56% vs. 43%, p < 0.001) and increased over time among HIV+ but not HIV- women. Diabetes treatment was similar among HIV+ and HIV- women (48% vs. 49%) and increased over time in both groups. Diabetes control was greater among HIV+ women (73% vs. 64%, p = 0.03) and did not change over time. The percent of recent smokers who reported no longer smoking was similar between HIV+ and HIV- women (10% vs. 9%), with no differences over time. Virologic suppression was significantly associated with increased hypertension treatment and greater control. HIV+ women have better control of hypertension and diabetes than HIV- women, but many are still not at target levels.
    • All About SUNY Oneonta Open Access Repository

      Peña, Alondra (2023)
      The SUNY Open Access Repository (SOAR) is an online digital repository that makes scholarly works of SUNY campuses widely available. This is an available resource for both faculty and students that should be more used and known about throughout our community. I have worked with our campus’ head of scholarly communications, in the backend of the SOAR website uploading these documents and making the website more readily accessible to our community. After working closely with SOAR while also attending SUNY Oneonta, I have realized how little students know about it along with how rarely faculty members and professors advertise SOAR as a resource for not only getting reliable information but also promoting their scholarly works. My goal for this research is to spread awareness of the benefits of SOAR and Open Access as a whole, along with what qualifications your work must meet in order to be eligible for submission into the repository. Furthermore, I wish to share my knowledge of open access scholarly works and the pros and cons that come with them.
    • Analyzing Water Levels and Harmful Algal Blooms in Moreau Lake

      Rose, Asia (2023)
      Analyzing Water Levels and Harmful Algal Blooms in Moreau Lake Moreau Lake is a 122-acre (49- hectare) lake located in the Town of Moreau, Saratoga County, New York in NYSDEC Region 5. The lake is located within Moreau Lake State Park, offering an assortment of recreational activities for tourists and residents. In recent years, stakeholders have become concerned with the changes in water level along with the reoccurring algal blooms, though it has been deemed a mild risk at this time. The goal of this project is to collect profile data, assess the stakeholder’s concerns, and compile previous data to create a comprehensive management plan of the state of Moreau Lake. This will be the first management plan ever created for a lake located within the NYSDEC park system, bringing new light to the need for management plans of this kind.
    • Putting Your Data to Work! Using Long-Term Volunteer Data to Establish Water Quality Trends

      Shea, Derek (2023)
      Craine Lake is a 26-acre lake located in Madison County, New York. The Craine Lake Association has been a consistent participant in the Citizen Statewide Lake Assessment Program (CSLAP) and is entering its 35thyear of participation. This long-term dataset allows us to analyze trends and investigate how water quality parameters may relate to stakeholder concerns such as harmful algal blooms, sedimentation, and nuisance levels of aquatic plants. The lake has a long history of summertime blue-green algae and was used as one of the first lakes in the NYSDEC harmful algal bloom reporting program. The eventual management plan for the lake aims to utilize the long-term dataset along with our own lake profiling and mapping to inform future management strategies.
    • Analysis of Northwestern Montana Lakes Based on Transparency and Temperature

      Minissale, Kari (2023)
      Lakes in virtually unmodified regions such as national parks are indicators of shifts in the climate and other ecological agitations caused by humans, often responding with physical, chemical, and biological changes. To better understand responses of lakes to regional and large-scale climatological changes, lakes near Glacier National Park have been regularly monitored through the Northwest Montana Lakes Network since 1992. Citizen science volunteers measured Secchi disk depths, temperature, and total phosphorus in over 40 lakes in Montana, USA, to assess water quality and monitor long-term trends in lakes between June and August from 1992 through 2021. We modeled trends in Secchi depth, temperature, and total phosphorus concentrations to determine support for hypotheses regarding long-term, seasonal, and regional variability. Secchi depth varied by month differently among lakes, generally decreasing from June through August, and there was a slight decrease in Secchi depth by year across all lakes. Peak temperatures were reached during July across all years and lakes on average, and long-term temperature changes varied among lakes. Total phosphorus concentrations varied between lakes but did not display any variability across years. The results suggest that while trends in lake water quality parameters over time can be detected, these changes may be lake-specific, and some parameters may not change over time at all. Measurements of total nitrogen and chlorophyll a collected alongside total phosphorus will be used to formulate a comprehensive analysis of trophic shifts concurrent with climate change.