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.

We examined the associations between depressive symptoms and sexual identity and behavior among women with or at risk for HIV.

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.

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.

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.

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.

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.

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.

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.