Browsing by Subject "phenotype"

Now showing 1 - 6 of 6
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    CMAX3: A Robust Statistical Test for Genetic Association Accounting for Covariates
    (MDPI, 2021) Chen, Zhongxue; Zang, Yong; Biostatistics, School of Public Health
    The additive genetic model as implemented in logistic regression has been widely used in genome-wide association studies (GWASs) for binary outcomes. Unfortunately, for many complex diseases, the underlying genetic models are generally unknown and a mis-specification of the genetic model can result in a substantial loss of power. To address this issue, the MAX3 test (the maximum of three separate test statistics) has been proposed as a robust test that performs plausibly regardless of the underlying genetic model. However, the original implementation of MAX3 utilizes the trend test so it cannot adjust for any covariates such as age and gender. This drawback has significantly limited the application of the MAX3 in GWASs, as covariates account for a considerable amount of variability in these disorders. In this paper, we extended the MAX3 and proposed the CMAX3 (covariate-adjusted MAX3) based on logistic regression. The proposed test yielded a similar robust efficiency as the original MAX3 while easily adjusting for any covariate based on the likelihood framework. The asymptotic formula to calculate the p-value of the proposed test was also developed in this paper. The simulation results showed that the proposed test performed desirably under both the null and alternative hypotheses. For the purpose of illustration, we applied the proposed test to re-analyze a case-control GWAS dataset from the Collaborative Studies on Genetics of Alcoholism (COGA). The R code to implement the proposed test is also introduced in this paper and is available for free download
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    Dysmenorrhea Symptom-Based Phenotypes: A Replication and Extension Study
    (2020-09-16) Chen, Chen X.; Carpenter, Janet S.; Ofner, Susan; LaPradd, Michelle; Fortenberry, J. Dennis; School of Nursing
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    Global Deletion of Sost Increases Intervertebral Disc Hydration But May Trigger Chondrogenesis
    (2020-05) Kroon, Tori; Holguin, Nilsson; Wallace, Joseph; Wagner, Diane
    Intervertebral discs (IVD) degenerate earlier than many other musculoskeletal tissues and will continue to degenerate with aging. IVD degeneration affects up to 80 percent of the adult population and is a major contributing factor to low back pain. Anti-sclerostin antibody is an FDA-approved treatment for osteoporosis in postmenopausal women at high-risk for fracture and, as a systemic stimulant of the Wnt/LRP5/β-Catenin signaling pathway, may impact the IVD. Stabilization of β-Catenin in the IVD increases Wnt signaling and is anabolic to the extracellular matrix (ECM), while deletion of β-catenin or LRP5 decreases Wnt signaling and is catabolic to the ECM. Here, we hypothesized that a reduction of Sost would stimulate ECM anabolism. Lumbar and caudal (tail) IVD and vertebrae of Sost KO and WT (wildtype) mice (n=8 each) were harvested at 16 weeks of age and tested by MRI, histology, immunohistochemistry, Western Blot, qPCR, and microCT. Compared to WT, Sost KO reduced sclerostin protein and Sost gene expression. Next, Sost KO increased the hydration of the IVD and the proteoglycan stain in the nucleus pulposus and decreased the expression of genes associated with IVD degeneration, e.g., heat shock proteins. However, deletion of Sost was compensated by less unphosphorylated (active) β-Catenin protein in the cell nucleus, upregulation of Wnt signaling inhibitors Dkk1 and sFRP4, and catabolic ECM gene expression. Consequently, notochordal and early chondrocyte-like cells (CLCs) were replaced by mature CLCs. Overall, Sost deletion increased hydration and proteoglycan protein content, but activated a compensatory suppression of Wnt signaling that may trigger chondrogenesis and may potentially be iatrogenic to the IVD in the long-term.
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    Molecular targets of alcohol action: translational research for pharmacotherapy development and screening.
    (Elsevier, 2011) Gorini, Giorgio; Bell, Richard L.; Mayfield, R. Dayne; Department of Psychology, School of Science
    Alcohol abuse and dependence are multifaceted disorders with neurobiological, psychological, and environmental components. Research on other complex neuropsychiatric diseases suggests that genetically influenced intermediate characteristics affect the risk for heavy alcohol consumption and its consequences. Diverse therapeutic interventions can be developed through identification of reliable biomarkers for this disorder and new pharmacological targets for its treatment. Advances in the fields of genomics and proteomics offer a number of possible targets for the development of new therapeutic approaches. This brain-focused review highlights studies identifying neurobiological systems associated with these targets and possible pharmacotherapies, summarizing evidence from clinically relevant animal and human studies, as well as sketching improvements and challenges facing the fields of proteomics and genomics. Concluding thoughts on using results from these profiling technologies for medication development are also presented.
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    Susceptibility Provision Enhances Effective De-escalation (SPEED): utilizing rapid phenotypic susceptibility testing in Gram-negative bloodstream infections and its potential clinical impact
    (Oxford Academic, 2019-01-01) Schneider, Jack G.; Wood, James B.; Schmitt, Bryan H.; Emery, Christopher L.; Davis, Thomas E.; Smith, Nathan W.; Blevins, Sarah; Hiles, Jon; Desai, Armisha; Wrin, Justin; Bocian, Brittany; Manaloor, John J.; Medicine, School of Medicine
    Abstract Objectives We evaluated the performance and time to result for pathogen identification (ID) and antimicrobial susceptibility testing (AST) of the Accelerate Pheno™ system (AXDX) compared with standard of care (SOC) methods. We also assessed the hypothetical improvement in antibiotic utilization if AXDX had been implemented. Methods Clinical samples from patients with monomicrobial Gram-negative bacteraemia were tested and compared between AXDX and the SOC methods of the VERIGENE® and Bruker MALDI Biotyper® systems for ID and the VITEK® 2 system for AST. Additionally, charts were reviewed to calculate theoretical times to antibiotic de-escalation, escalation and active and optimal therapy Results ID mean time was 21 h for MALDI-TOF MS, 4.4 h for VERIGENE® and 3.7 h for AXDX. AST mean time was 35 h for VITEK® 2 and 9.0 h for AXDX. For ID, positive percentage agreement was 95.9% and negative percentage agreement was 99.9%. For AST, essential agreement was 94.5% and categorical agreement was 93.5%. If AXDX results had been available to inform patient care, 25% of patients could have been put on active therapy sooner, while 78% of patients who had therapy optimized during hospitalization could have had therapy optimized sooner. Additionally, AXDX could have reduced time to de-escalation (16 versus 31 h) and escalation (19 versus 31 h) compared with SOC. Conclusions By providing fast and reliable ID and AST results, AXDX has the potential to improve antimicrobial utilization and enhance antimicrobial stewardship.
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    Therapy-Induced Senescence: Opportunities to Improve Anticancer Therapy
    (Oxford, 2021-10) Prasanna, Pataje G.; Citrin, Deborah E.; Hildesheim, Jeffrey; Ahmed, Mansoor M.; Venkatachalam, Sundar; Riscuta, Gabriela; Xi, Dan; Zheng, Guangrong; van Deursen, Jan; Goronzy, Jorg; Kron, Stephen J.; Anscher, Mitchell S.; Sharpless, Norman E.; Campisi, Judith; Brown, Stephen L.; Niedernhofer, Laura J.; O’Loghlen, Ana; Georgakilas, Alexandros G.; Paris, Francois; Gius, David; Gewirtz, David A.; Schmitt, Clemens A.; Abazeed, Mohamed E.; Kirkland, James L.; Richmond, Ann; Romesser, Paul B.; Lowe, Scott W.; Gil, Jesus; Mendonca, Marc S.; Burma, Sandeep; Zhou, Daohong; Coleman, C. Norman; Radiation Oncology, School of Medicine
    Cellular senescence is an essential tumor suppressive mechanism that prevents the propagation of oncogenically activated, genetically unstable, and/or damaged cells. Induction of tumor cell senescence is also one of the underlying mechanisms by which cancer therapies exert antitumor activity. However, an increasing body of evidence from preclinical studies demonstrates that radiation and chemotherapy cause accumulation of senescent cells (SnCs) both in tumor and normal tissue. SnCs in tumors can, paradoxically, promote tumor relapse, metastasis, and resistance to therapy, in part, through expression of the senescence-associated secretory phenotype. In addition, SnCs in normal tissue can contribute to certain radiation- and chemotherapy-induced side effects. Because of its multiple roles, cellular senescence could serve as an important target in the fight against cancer. This commentary provides a summary of the discussion at the National Cancer Institute Workshop on Radiation, Senescence, and Cancer (August 10-11, 2020, National Cancer Institute, Bethesda, MD) regarding the current status of senescence research, heterogeneity of therapy-induced senescence, current status of senotherapeutics and molecular biomarkers, a concept of “one-two punch” cancer therapy (consisting of therapeutics to induce tumor cell senescence followed by selective clearance of SnCs), and its integration with personalized adaptive tumor therapy. It also identifies key knowledge gaps and outlines future directions in this emerging field to improve treatment outcomes for cancer patients.