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  • 1
    Online Resource
    Online Resource
    BMI-CNV: a Bayesian framework for multiple genotyping platforms detection of copy number variants
    Oxford University Press (OUP) ; 2022
    In:  Genetics Vol. 222, No. 4 ( 2022-11-30)
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 222, No. 4 ( 2022-11-30)
    Abstract: Whole-exome sequencing (WES) enables the detection of copy number variants (CNVs) with high resolution in protein-coding regions. However, variants in the intergenic or intragenic regions are excluded from studies. Fortunately, many of these samples have been previously sequenced by other genotyping platforms which are sparse but cover a wide range of genomic regions, such as SNP array. Moreover, conventional single sample-based methods suffer from a high false discovery rate due to prominent data noise. Therefore, methods for integrating multiple genotyping platforms and multiple samples are highly demanded for improved copy number variant detection. We developed BMI-CNV, a Bayesian Multisample and Integrative CNV (BMI-CNV) profiling method with data sequenced by both whole-exome sequencing and microarray. For the multisample integration, we identify the shared copy number variants regions across samples using a Bayesian probit stick-breaking process model coupled with a Gaussian Mixture model estimation. With extensive simulations, BMI-copy number variant outperformed existing methods with improved accuracy. In the matched data from the 1000 Genomes Project and HapMap project data, BMI-CNV also accurately detected common variants and significantly enlarged the detection spectrum of whole-exome sequencing. Further application to the data from The Research of International Cancer of Lung consortium (TRICL) identified lung cancer risk variant candidates in 17q11.2, 1p36.12, 8q23.1, and 5q22.2 regions.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1093/genetics/iyac147
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
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    SSG: 12
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  • 2
    Online Resource
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    Targeting NF-κB RelA/p65 phosphorylation overcomes RITA resistance
    Elsevier BV ; 2016
    In:  Cancer Letters Vol. 383, No. 2 ( 2016-12), p. 261-271
    Details
    In: Cancer Letters, Elsevier BV, Vol. 383, No. 2 ( 2016-12), p. 261-271
    Type of Medium: Online Resource
    ISSN: 0304-3835
    URL: Article
    DOI: 10.1016/j.canlet.2016.10.006
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
    detail.hit.zdb_id: 195674-7
    detail.hit.zdb_id: 2004212-7
    SSG: 12
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  • 3
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    Mitochondrial Ca2+ uniporter is critical for store-operated Ca2+ entry-dependent breast cancer cell migration
    Elsevier BV ; 2015
    In:  Biochemical and Biophysical Research Communications Vol. 458, No. 1 ( 2015-02), p. 186-193
    Details
    In: Biochemical and Biophysical Research Communications, Elsevier BV, Vol. 458, No. 1 ( 2015-02), p. 186-193
    Type of Medium: Online Resource
    ISSN: 0006-291X
    URL: Article
    DOI: 10.1016/j.bbrc.2015.01.092
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2015
    detail.hit.zdb_id: 1461396-7
    SSG: 12
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  • 4
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    Enterococci Contamination on Edisto Island, South Carolina: Frequency, Sources of Contamination, and Prospects on How to Improve Water Quality
    Clemson University ; 2021
    In:  Journal of South Carolina Water Resources ( 2021), p. 68-82
    Details
    In: Journal of South Carolina Water Resources, Clemson University, ( 2021), p. 68-82
    Abstract: Beach monitoring samples were collected from 18 (14 currently in use) locations on Edisto Island, South Carolina, from 2000 to 2016 to assess patterns of water quality violations (contraventions) indicated by the presence of multiple Enterococcus species, including Enterococcus faecalis and Enterococcus faecium, bacteria used to assess the health of surface waters for contact recreation. Statistical analyses were conducted comparing Enterococci levels and different environmental variables including location, tidal stages, wind direction, and time. Specific focus was placed on temporal and spatial patterns for dates when the bacteria levels exceeded 104 Most Probable Numbers (MPN) per 100 milliliters (ml), which is the Enterococcus single sample maximum (SSM) water quality standard in South Carolina. Results indicated that 2.2% of the samples exceeded the Enterococcus SSM standard and that the majority of these SSM contraventions occurred in September, during periods without significant rainfall but when primarily easterly winds occurred, at or near the time of flooding associated with King Tides (flood tides higher than 7.5 ft). Statistical analysis indicated that wind direction and tidal stage (at or around high tide—¾ flood to ¼ ebb) appeared to have more of an impact on bacterial levels than rainfall, per se. Microbial source tracking using quantitative polymerase chain reaction (qPCR) analysis was conducted and used to identify potential bacterial pollution sources causing Enterococci levels to exceed the SSM. Results indicated that birds and domestic dogs, rather than humans, were the major sources of bacterial pollution. These findings suggested that flooding during King Tides inundated a larger area of the beach-face surface containing bird and dog waste, which resulted in elevated levels of Enterococcus SSM contraventions, primarily on the southern end of the island. These findings are particularly relevant due to the increasing sea-level rise associated with climate change. Changes in population growth on Edisto Island were also analyzed and indicated that permanent population has been increasing at a relatively low rate, while high rates of tourism growth have been observed and may play a factor in observed increases in Enterococcus SSM contraventions. Comparisons of contact recreational water quality with other South Carolina (SC) beaches indicated that Edisto Island (2.2% of Enterococcus SSM contraventions) was third only behind the Grand Strand (10.9%) and Sullivan’s Island (3.9%), both of which have much higher population densities (777–1,300 people/sq. mile) compared to Edisto Island (36 people/sq. mile). These low population densities at Edisto Island and microbial source tracking results further indicate that most pollution sources were from birds and dogs and indicate the important role of coastal flooding associated with climate change. Coastal flooding is continuing to significantly increase as 24.4% of all King Tide flooding events in Charleston, South Carolina, over the past 67 years have occurred from 2019 to 2020. Better management of microbial pollution sources from dogs and birds is essential to prevent further degradation and loss of ecosystem services.
    Type of Medium: Online Resource
    ISSN: 2334-4962
    URL: Article
    DOI: 10.34068/JSCWR/08.01.08
    Language: Unknown
    Publisher: Clemson University
    Publication Date: 2021
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  • 5
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    Online Resource
    Reply to Polverino: Cigarette Smoking and COVID-19: A Complex Interaction
    American Thoracic Society ; 2020
    In:  American Journal of Respiratory and Critical Care Medicine Vol. 202, No. 3 ( 2020-08-01), p. 472-474
    Details
    In: American Journal of Respiratory and Critical Care Medicine, American Thoracic Society, Vol. 202, No. 3 ( 2020-08-01), p. 472-474
    Type of Medium: Online Resource
    ISSN: 1073-449X , 1535-4970
    URL: Article
    DOI: 10.1164/rccm.202005-1807LE
    RVK:
    XA 21200
    Language: English
    Publisher: American Thoracic Society
    Publication Date: 2020
    detail.hit.zdb_id: 1468352-0
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  • 6
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    Abstract P204: Association Of Plasma Proteome With Inflammatory Markers Crp And Glyca And Their Responses To Exercise Training
    Ovid Technologies (Wolters Kluwer Health) ; 2022
    In:  Circulation Vol. 145, No. Suppl_1 ( 2022-03)
    Details
    In: Circulation, Ovid Technologies (Wolters Kluwer Health), Vol. 145, No. Suppl_1 ( 2022-03)
    Abstract: Introduction: C-reactive protein (CRP) and GlycA are established biomarkers of inflammation. Regular exercise tends to decrease CRP and GlycA levels. However, the molecules underlying CRP and GlycA and their responses to exercise training are less known. Hypothesis: We hypothesized that distinct protein signatures exist for both baseline levels and exercise responsiveness of CRP and GlycA, however with some overlap of proteins across signatures. Methods: Measures were performed before and after 20 weeks of exercise training in 652 Black and White adults from the HERITAGE Family Study. 4,979 circulating proteins were measured using SomaScan. High-sensitivity CRP was measured using automated assays. GlycA was quantified by NMR spectroscopy (LabCorp). Linear mixed models were used to test: 1) Association of baseline proteins with baseline hsCRP and GlycA and 2) Association of change in protein with changes in hsCRP and GlycA. Models were adjusted for age, sex, race, BMI, with family membership as a random variable, with change models also adjusting for baseline trait value. Significance was determined as FDR 〈 0.05. Results: Baseline levels (r=0.51, p 〈 0.0001) and change (r=0.31, p 〈 0.0001) of hsCRP and GlycA were moderately correlated. hsCRP did not change with training, while GlycA trended towards decreasing (Table 1). Across time points, 388 and 1746 unique proteins were associated with hsCRP and GlycA, respectively, with substantial overlap across traits and time points (Table 1). The CRP protein was the top association in 3 of 4 models (range: 1.4x10 -40 〈 p 〈 1.2x10 -08 ), with serum amyloid A-2 and A-1 (SAA2, SAA) among the top 6 hits for 3 of 4 models (Table 1). Conclusions: More unique proteins were associated with GlycA levels at both timepoints, with most hsCRP proteins overlapping with GlycA proteins. Overall, a substantial number of proteins are associated with CRP and GlycA levels regardless of when they are measured, which has potential implications for using proteins as signatures of these inflammatory biomarkers.
    Type of Medium: Online Resource
    ISSN: 0009-7322 , 1524-4539
    URL: Article
    DOI: 10.1161/circ.145.suppl_1.P204
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2022
    detail.hit.zdb_id: 1466401-X
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  • 7
    Online Resource
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    Abstract P206: Proteomic And Metabolomic Signatures Of Plasma Triglyceride-related Trait Responses To Regular Exercise
    Ovid Technologies (Wolters Kluwer Health) ; 2022
    In:  Circulation Vol. 145, No. Suppl_1 ( 2022-03)
    Details
    In: Circulation, Ovid Technologies (Wolters Kluwer Health), Vol. 145, No. Suppl_1 ( 2022-03)
    Abstract: Introduction: Elevated plasma triglycerides (TG) are associated with risk of cardiovascular disease and are modifiable through lifestyle interventions such as regular exercise. However, TG responses to regular exercise are characterized by significant inter-individual differences. Hypothesis: We hypothesized that baseline levels of circulating proteins and metabolites are associated with TG response to exercise and can predict exercise-induced changes in plasma TG traits. Methods: We measured circulating proteins (n=4979 proteins) and metabolites (n=300) in 650 Black and White adults of the HERITAGE Family Study who completed 20 weeks of exercise training and had complete data on TG traits. We investigated two TG-related traits that significantly improved with training: fasting TG and large TG-rich lipoprotein particle concentration (LTRLP). The association between baseline analyte values and exercise-induced changes in TG traits were examined using linear mixed models adjusted for age, sex, race, BMI, baseline trait value, and the random effect of family membership. Significance was determined as FDR 〈 0.05. Molecular signatures of TG trait responses were generated via elastic net regression tuned using leave-one-out cross validation. Results: Regular exercise significantly reduced plasma TG (-1.03±1.3 mmol/L, p=0.01) and LTRLP (-0.24±2.2 nmol/L, p= 0.007), with their training-induced changes moderately correlated (r=0.4, p 〈 0.0001). We identified largely distinct panels of baseline analytes associated with changes in TG and LTRLP ( Table 1 ). Similarly, elastic net regression yielded distinct models of 99 analytes for TG and 315 analytes for LTRLP responses to exercise with accuracy of RMSE=1.28 mmol/L for TG and 2.16 nmol/L for the LTRLP model. Conclusions: We identified panels of proteins and metabolites associated with exercise-induced changes in TG traits and demonstrate, within our data, circulating analytes hold promise for predicting the exercise responsiveness of plasma TG-related traits.
    Type of Medium: Online Resource
    ISSN: 0009-7322 , 1524-4539
    URL: Article
    DOI: 10.1161/circ.145.suppl_1.P206
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2022
    detail.hit.zdb_id: 1466401-X
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  • 8
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    Abstract 15316: Associations Between Plasma Proteins With Body Composition Traits and Their Responses to Exercise Training
    Ovid Technologies (Wolters Kluwer Health) ; 2022
    In:  Circulation Vol. 146, No. Suppl_1 ( 2022-11-08)
    Details
    In: Circulation, Ovid Technologies (Wolters Kluwer Health), Vol. 146, No. Suppl_1 ( 2022-11-08)
    Abstract: Introduction: Although exercise training is known to alter body composition, the molecular biomarkers and mechanisms related to these changes have not been fully elucidated. The purpose of this study was to examine the associations between plasma proteins and body composition traits before and after exercise training. Methods: Measurements were taken before and after 20 weeks of standardized, endurance training in self-identified Black and White adults of the HERITAGE Family Study (n=647). Plasma proteins were measured using an affinity-based platform (n=4979 aptamers). 11 body composition traits were measured using underwater weighing, CT scans, and anthropometry: BMI, body surface area, fat mass, fat free mass, %fat, waist circumference, waist-to-hip ratio, body weight, and abdominal visceral, subcutaneous, and total fat. Linear mixed models were used to test the association between plasma proteins and each trait at baseline and in response to training with full covariate adjustment ( Table 1 ). Significance was set to FDR 〈 0.05. Results: On average, subjects were [mean and (SD)] 35 (14) years old, 33% Black, 54% female, and had BMI 26.2 (5.2) kg/m 2 . The number of significant associations between proteins and traits at baseline and in response to exercise training ranged from 645-1714 and 0-42, respectively ( Table 1 ). While leptin was among the top associated proteins at both time points for almost all traits, our analysis revealed many novel associations between changes in proteins with changes in body composition. Changes in DLK-1 significantly associated with changes in 9 of 11 traits but was not associated with baseline measures. Conclusions: Numerous plasma proteins were associated with body composition traits at baseline, with fewer associated with trait responses to training. Notably, we identified a subset of proteins uniquely associated with exercise-induced changes in body composition traits.
    Type of Medium: Online Resource
    ISSN: 0009-7322 , 1524-4539
    URL: Article
    DOI: 10.1161/circ.146.suppl_1.15316
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2022
    detail.hit.zdb_id: 1466401-X
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  • 9
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    Discovery of potent anticancer agent HJC0416, an orally bioavailable small molecule inhibitor of signal transducer and activator of transcription 3 (STAT3)
    Elsevier BV ; 2014
    In:  European Journal of Medicinal Chemistry Vol. 82 ( 2014-07), p. 195-203
    Details
    In: European Journal of Medicinal Chemistry, Elsevier BV, Vol. 82 ( 2014-07), p. 195-203
    Type of Medium: Online Resource
    ISSN: 0223-5234
    URL: Article
    DOI: 10.1016/j.ejmech.2014.05.049
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2014
    detail.hit.zdb_id: 2005170-0
    SSG: 15,3
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  • 10
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    Data_Sheet_1.docx
    Frontiers Media SA ; 2023
    In:  Frontiers in Microbiology Vol. 13 ( 2023-1-10)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 13 ( 2023-1-10)
    Abstract: Marine bacteria often exist in biofilms as communities attached to surfaces, like plastic. Growing concerns exist regarding marine plastics acting as potential vectors of pathogenic Vibrio , especially in a changing climate. It has been generalized that Vibrio vulnificus and Vibrio parahaemolyticus often attach to plastic surfaces. Different strains of these Vibrios exist having different growth and biofilm-forming properties. This study evaluated how temperature and strain variability affect V. parahaemolyticus and V. vulnificus biofilm formation and characteristics on glass (GL), low-density polyethylene (LDPE), polypropylene (PP), and polystyrene (PS). All strains of both species attached to GL and all plastics at 25, 30, and 35°C. As a species, V. vulnificus produced more biofilm on PS ( p  ≤ 0.05) compared to GL, and biofilm biomass was enhanced at 25°C compared to 30° ( p  ≤ 0.01) and 35°C ( p  ≤ 0.01). However, all individual strains’ biofilm biomass and cell densities varied greatly at all temperatures tested. Comparisons of biofilm-forming strains for each species revealed a positive correlation ( r  = 0.58) between their dry biomass weight and OD 570 values from crystal violet staining, and total dry biofilm biomass for both species was greater ( p  ≤ 0.01) on plastics compared to GL. It was also found that extracellular polymeric substance (EPS) chemical characteristics were similar on all plastics of both species, with extracellular proteins mainly contributing to the composition of EPS. All strains were hydrophobic at 25, 30, and 35°C, further illustrating both species’ affinity for potential attachment to plastics. Taken together, this study suggests that different strains of V. parahaemolyticus and V. vulnificus can rapidly form biofilms with high cell densities on different plastic types in vitro . However, the biofilm process is highly variable and is species-, strain-specific, and dependent on plastic type, especially under different temperatures.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2022.1099502
    DOI: 10.3389/fmicb.2022.1099502.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2587354-4
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