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Browsing by Subject "Interaction"

Now showing 1 - 4 of 4
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    The Association Between Citrus Consumption and Skin Cancer: An Analysis of Risk and Nutrient-Gene Interaction
    (2020-12) Marley, Andrew Raymond; Han, Jiali; Sibg, Yiqing; Li, Xin; Li, Ming; Champion, Victoria L.
    Purpose. In the US, melanoma and non-melanoma skin cancer (NMSC) rates have increased substantially in recent decades. While many skin cancer risk factors have been established, the impact of dietary citrus, which is naturally abundant in photocarcinogenic psoralens, remains enigmatic. The purpose of this research was to investigate associations between citrus consumption and risks of melanoma and NMSC, and to conduct a genome-wide study to identify genetic variants that may modify this association. Methods. Participants from the UK Biobank were leveraged for these analyses. Citrus consumption was collected via five rounds of 24-hour recall questionnaires, with complete citrus data available for n=210,126 participants. Ascertainment of melanoma and NMSC cases were identified by international classification of disease codes via linkage with national registries. Logistic regression was used to estimate odds ratios and 95% confidence intervals for the associations between citrus consumption and skin cancer outcomes. Individual citrus products were assessed for independent associations with skin cancer risk, and established skin cancer risk factors were tested for interaction. Joint 2-degree-of-freedom (df) and 1-df tests were used to assess interaction between total citrus consumption and genetic variants. Results. After controlling for covariates, high total citrus consumption was significantly associated with increased melanoma risk, an association primarily driven by orange and orange juice consumption. Skin color was found to be a significant effect modifier for the association between total citrus consumption and melanoma risk, but only before adjusting for multiple comparisons. No significant associations were observed for high total citrus consumption or consumption of any individual citrus products and NMSC risk. Significant associations for half a serving of citrus consumption and NMSC risk were likely due to chance or confounding. Index SNPs on chromosomes 3, 9, and 16 were significant according to the joint 2-df test, and 7 SNPs on chromosome 16 displayed evidence of a citrus-gene interaction. Conclusion. My analyses provide evidence in support of high citrus consumption significantly increasing risk of melanoma, but not NMSC. I also identified SNPs on AFG3L1P that may modify this association. Future research should further explore these associations, particularly for NMSC and to confirm my genetic findings.
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    Creating a Conversation
    (2016) Jacob, Andrew; Hull, Greg
    Living with a hearing disability, as well as being shy, has always been a challenge for me and has affected my ability to communicate with others. With a difficulty in initiating conversation, I would instead stand back and observe how people around me acted and communicated with each other in hopes of learning how to converse like them. From this understanding, I began to devise ways that would allow initiating a conversation with my sculptures rather than becoming the conversation starter directly through voice. When I began my BFA studies in Fine Arts, I continued to look for ways to initiate conversations with those around me, attempting to bring others my way by sparking their interests in my artwork, rather than approaching them with words.
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    Designing cost-efficient randomized trials by using flexible recruitment strategies
    (Springer Nature, 2012-07-24) Yu, Menggang; Wu, Jingwei; Burns, Debra S.; Carpenter, Janet S.; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health
    Background: Sample size planning for clinical trials is usually based on detecting a target effect size of an intervention or treatment. Explicit incorporation of costs into such planning is considered in this article in the situation where effects of an intervention or treatment may depend on (interact with) baseline severity of the targeted symptom or disease. Because much larger sample sizes are usually required to establish such an interaction effect, investigators frequently conduct studies to establish a marginal effect of the intervention for individuals with a certain level of baseline severity. Methods: We conduct a rigorous investigation on how to determine optimum baseline symptom or disease severity inclusion criteria so that the most cost-efficient design can be used. By using a regression model with an interaction term of treatment by symptom severity, power functions were derived for various levels of baseline symptom severity. Computer algorithms and mathematical optimization were used to determine the most cost-efficient research designs assuming either single- or dual-stage screening procedures. Results: In the scenarios we considered, impressive cost savings can be achieved by informed selection of baseline symptom severity via the inclusion criteria. Further cost-savings can be achieved if a two stage screening procedure is used and there are some known, relatively inexpensively collected, pre-screening information. The amount of total cost savings are shown to depend on the ratio of the screening and intervention costs. In our investigation, we assumed that: 1) the cost of approaching available subjects for screening is constant, and 2) all variables are normally distributed. There is a need to carry out further investigations with more relaxed assumptions (e.g., skewed data distribution). Conclusions: As cost becomes a more and more prominent issue in modern clinical trials, cost-saving strategies will become more and more important. Strategies, such as the ones we propose here, can help to minimize costs while maximizing knowledge generation.
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    Lantern: an integrative repository of functional annotations for lncRNAs in the human genome
    (BMC, 2021-05-26) Daulatabad, Swapna Vidhur; Srivastava, Rajneesh; Janga, Sarath Chandra; BioHealth Informatics, School of Informatics and Computing
    Background: With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. Results: We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Lantern's annotations were benchmarked against lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. Conclusions: Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
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