PLoS Articles
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UNC-authored articles published by the Public Library of Science (PLoS)
Works (2113)
2111. Oxygen Microbubbles Improve Radiotherapy Tumor Control in a Rat Fibrosarcoma Model – A Preliminary Study
- Title Tesim:
- Oxygen Microbubbles Improve Radiotherapy Tumor Control in a Rat Fibrosarcoma Model – A Preliminary Study
- Creator:
- Papadopoulou, Virginie, Chang, Sha, Kasoji, Sandeep K., Rivera, Judith N., Dayton, Paul A., Fix, Samantha M., Velds, Hunter, and Borden, Mark A.
- Date Created:
- January 3, 2019
- Date of publication:
- April 9, 2018
- Abstract Tesim:
- Cancer affects 39.6% of Americans at some point during their lifetime. Solid tumor microenvironments are characterized by a disorganized, leaky vasculature that promotes regions of low oxygenation (hypoxia). Tumor hypoxia is a key predictor of poor treatment outcome for all radiotherapy (RT), chemotherapy and surgery procedures, and is a hallmark of metastatic potential. In particular, the radiation therapy dose needed to achieve the same tumor control probability in hypoxic tissue as in normoxic tissue can be up to 3 times higher. Even very small tumors (<2–3 mm3) comprise 10–30% of hypoxic regions in the form of chronic and/or transient hypoxia fluctuating over the course of seconds to days. We investigate the potential of recently developed lipid-stabilized oxygen microbubbles (OMBs) to improve the therapeutic ratio of RT. OMBs, but not nitrogen microbubbles (NMBs), are shown to significantly increase dissolved oxygen content when added to water in vitro and increase tumor oxygen levels in vivo in a rat fibrosarcoma model. Tumor control is significantly improved with OMB but not NMB intra-tumoral injections immediately prior to RT treatment and effect size is shown to depend on initial tumor volume on RT treatment day, as expected.
- Resource type:
- Article
- Affiliation Label Tesim:
- UNC/NCSU Joint Department of Biomedical Engineering, Joint Department of Biomedical Engineering, Department of Radiation Oncology, and Eshelman School of Pharmacy
- Deposit Record:
- de07c033-63de-42cd-ac27-251d03fbb124
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/ht8n-wp22
- Edition:
- Publisher
- Identifier:
- https://doi.org/10.1371/journal.pone.0195667
- Journal Issue:
- 4
- Journal Title:
- PLoS ONE
- Journal Volume:
- 13
- Keyword:
- hypoxia, oxygen, cancer treatment, anesthesia, radiation therapy, fibrosarcoma, and ultrasound imaging
- Language Label:
- English
- Note:
- Eshelman Institute for Innovation, UNC-CH; Carolina Center of Cancer Nanotechnology Excellence, UNC-CH; Office of Naval Research
- ORCID:
- Other Affiliation:
- and University of Colorado
- Person:
- Papadopoulou, Virginie, Chang, Sha, Kasoji, Sandeep K., Rivera, Judith N., Dayton, Paul A., Fix, Samantha M., Velds, Hunter, and Borden, Mark A.
- Rights Statement Label:
- In Copyright
- Source:
- pz50gz302
2112. Data Supplement to "Clinical Evidence Supports a Protective Role for CXCL5 in Coronary Artery Disease"
- Title Tesim:
- Data Supplement to "Clinical Evidence Supports a Protective Role for CXCL5 in Coronary Artery Disease"
- Creator:
- Schisler, Jonathan
- Date Created:
- June 14, 2017
- Date of publication:
- 2017
- Abstract Tesim:
- This dataset consists of an excel file containing two data tables. Table S4: Correlation of microarray-derived gene expression levels to either circulating CXCL5 or CAD severity. The Agilent probe ID (Probeset ID) and gene information are provided as well as the correlation coefficient (rs), the absolute value of rs (|rs|), and the p value for both CXCL5 and CAD variables for 143 total study participants Table S9: cis-eQTL analysis on PMBMCs of SAMARA2 subjects. The top 10,000 cis-eQTLs are provided. The dbSNP identifier (dbSNP RS ID) is provided indicated for each SNP as well as the gene, the beta coefficient, t-stat, p, and false discovery rate (FDR) from the eQTL analysis. The Affymetrix SNP Array 6.0 probe identifier (Affy6 SNP), position, and strand identifier relative to dbSNP is indicated. The Agilent probe ID (Probeset ID) used for gene expression values and the indication of CXCL5 or CAD correlation with gene expression are included in addition to the location information of the cRNA probe.
- Resource type:
- Dataset
- Affiliation Label Tesim:
- UNC McAllister Heart Institute
- Deposit Record:
- 1c9b6994-b4ee-4411-b951-bf62e207fb37
- Type:
- http://purl.org/dc/dcmitype/Software
- DOI:
- https://doi.org/10.17615/C66P42
- Keyword:
- microarray, eQTL, coronary artery disease, and cytokine
- Kind of Data:
- Numeric
- Language Label:
- English
- License Label:
- CC0 1.0 Universal
- Methodology:
- Gene chip analyses. RNA labeling, hybridization, and data extraction were performed in our laboratory. RNA was co-hybridized to Agilent G4112F Whole Human Genome 4x44K oligonucleotide arrays in the presence of Cyanine-3 labeled Universal Human Reference RNA (UHRR, Stratagene, LaJolla, CA) for array normalization, as described (Charles et al., 2008). Slides were hybridized and washed, then scanned on an Axon 4000b microarray scanner; data were processed using Agilent software. Probes were filtered by only including probes flagged as “detected” in at least 85% of all SAMARA phase 2 samples, resulting in 18,411 probes available for analysis. In addition, samples were filtered by only including RNA samples with at least 90% of the 18,411 probes flagged as “detected”. Missing data were imputed using the k-nearest neighbor algorithm (k=10). Datasets were deposited in the Gene Expression Omnibus of the National Center for Biotechnology Information (GEO Series accession number GSE90074) containing the 143 samples used in the biomarker analyses. The processing date (batch effect) and gender were controlled for using an analysis of variance (ANOVA) linear model using Partek Genomics Suite (v6.6, Partek Incorporated). Probes were updated using the annotations updated by Agilent on June 12, 2015. We used BioMart ID conversion for all significant probes that contained missing associated gene name annotations. Spearman rank correlation was utilized to generate a list of genes that correlated with the CAD score (0-4) or plasma levels of CXCL5 with a predefined cutoff of | rs | ≥0.25 using Partek Genomics Suite (v6.6) as described (Sinnaeve et al., 2009). SAMARA phase 1 microarray data was downloaded from GEO (accession number GSE12959), previously described (Schisler et al., 2009). DNA labeling, hybridization, and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL). The Genome-Wide Human SNP Array 6.0 (Affymetrix®) was used for hybridizations. Of the 143 subjects with gene expression and biomarker analyses, 126 were analyzed via SNP array. Subsequently, 20 of the 126 arrays had “no call” rates > 20% and were dropped from further analysis, leaving 106 samples with 909,624 probes. Datasets were deposited in the Gene Expression Omnibus of the National Center for Biotechnology Information (GEO Series accession number GSE90073) containing 106 of the 143 samples used in the biomarker and RNA analyses. SNP probes were filtered to include only those with minor allele frequencies > 0.05 and Hardy-Weinberg equilibrium > 0.01 leaving 398,997 available for analysis. Principal components analysis was used to classify subjects as either Americans with African or European ancestry and missing genotypes were imputed using MaCH (v1.0.6) (Li et al., 2010) with estimated mismatch rates in the Markov model of 0.1256 and 0.00481 in each group, respectively. Expression quantitative trait loci analysis. Identification of local elements associated with expression (eQTLs) was performed with Matrix eQTL (v2.1.0) (Shabalin, 2012) in the software package R (v3.2.1). We used the linear additive model to identify cis-acting eQTLs (distance between SNP and expression probe < 1e6 base pairs) accounting for ancestry covariance and population structure. This resulted in testing 4,600,673 SNP-gene pairs in the 106 subjects with both DNA and RNA analyses. The DNA and RNA datasets are collated as a SuperSeries in the Gene Expression Omnibus of the National Center for Biotechnology Information (GEO Series accession number GSE90076). 1. Charles PC, Alder BD, Hilliard EG, Schisler JC, Lineberger RE, Parker JS, Mapara S, Wu SS, Portbury A, Patterson C, Stouffer GA: Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males. BMC Med Genomics 2008, 1:38. 2. Sinnaeve PR, Donahue MP, Grass P, Seo D, Vonderscher J, Chibout S-D, Kraus WE, Sketch M, Nelson C, Ginsburg GS, Goldschmidt-Clermont PJ, Granger CB: Gene expression patterns in peripheral blood correlate with the extent of coronary artery disease. PloS One 2009, 4:e7037. 3. Schisler JC, Charles PC, Parker JS, Hilliard EG, Mapara S, Meredith D, Lineberger RE, Wu SS, Alder BD, Stouffer GA, Patterson C: Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry. PloS One 2009, 4:e8183. 4. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR: MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes. Genet Epidemiol 2010, 34:816–834. 5. Shabalin AA: Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 2012, 28:1353–1358.
- ORCID:
- http://orcid.org/0000-0001-7382-2783
- Other Affiliation:
- Person:
- Schisler, Jonathan
- Source:
- 4b29b7747
2113. Chapel Hill Town Center Alternative Transportation Level of Service
- Title Tesim:
- Chapel Hill Town Center Alternative Transportation Level of Service
- Creator:
- Day, Matthew
- Date Created:
- December 10, 2010
- Date of publication:
- April 14, 2004
- Abstract Tesim:
- There are two main objectives addressed in this paper. The first objective is to show how various level of service models that have been developed for pedestrian, bicycle, and transit facilities compare with each other. The second is to use these level of service models to determine the level of service provided for alternative transportation modes in the Chapel Hill Town Center and use the results to show locations in need of facility or service improvements. Level of service (LOS) is a concept used to illustrate the service being provided by a given transportation facility. The service can be graded on a letter grade scale from A to F (A being best and F being worst). Many different methods and approaches to level of service have been discussed in scholarly literature. Traditionally, level of service has been measured as a function of the volume of users on a facility and the capacity of the facility -- this concept is usually applied to highways, but capacity-based methods of measuring level of service have been developed for many modes of transportation, including the pedestrian, bicycle, and transit modes. This capacity-based approach to level of service has come under criticism lately for not adequately measuring the quality of service being provided and for focusing on mobility instead of accessibility. New level of service measures have been developed that incorporate physical characteristics of destinations and the environment into pedestrian and bicycle level of service and incorporate transit service quality measures into transit level of service. Several of these models are examined in this paper, and applied to a portion of Downtown Chapel Hill in order to find similarities and differences between the models, potential flaws in their application, and to begin looking for ways to integrate the models. There are five models used in this analysis. For pedestrian facilities, the Pedestrian Level Of Service (PLOS) model and Fruin method are used to determine level of service. The PLOS method was developed by Sprinkle Consulting and uses a regression model based on certain sidewalk, roadway, and environmental characteristics to determine level of service. The Fruin method comes from the Highway Capacity Manual and is based on a volume-to-capacity ratio for a sidewalk facility. The Bicycle Level Of Service (BLOS) model and Bicycle Compatibility Index (BCI) model are used to measure bicycle level of service. The BLOS model was developed by Sprinkle (as a companion to the PLOS model discussed above); it uses a regression formula based on roadway and environmental characteristics to determine level of service. The BCI method was developed by the Federal Highway Administration as a tool to determine the compatibility of motor vehicle and bicycle traffic on a given roadway -- in doing so, the BCI also provides a measure of the quality of bicycle service along a given road segment (or level of service). Transit Level Of Service (TLOS), a model developed by the Florida Department of Transportation to measure transit level of service based on service frequency and hours of transit service, is used to measure transit level of service. The models discussed above are applied to a study area in the Town Center area of Chapel Hill, North Carolina. In general, the models produced a varied picture of the quality of transportation services in this study area. The results of the Fruin method showed level of service "A" throughout the study area, while the PLOS model found some areas with adequate pedestrian facilities and others with failing level of service grades. The BLOS and BCI results showed many of the same deficient facilities in terms of bicycle accommodation, but also contained important differences. The BCI results appeared to be biased against narrow lowvolume roads, so a new grading scale was developed to offset this effect. The TLOS analysis was done looking at service frequency in isolation and looking at service frequency and hours of service together. The results of these analyses were similar to each other, and highlighted the same problem areas. In general, except for the Fruin method, which produced very skewed results, the various models produced results that seemed reasonable in isolation and in comparison with each other. Many road segments in the Town Center study area are found to be deficient in the results of these models. Many different mitigation strategies may be appropriately applied to improve these segments. Some of the recommended mitigation measures include the provision of new sidewalks and bicycle lanes, the addition of transit service, the retiming of transit service, and the addition or removal of on-street parking. The mitigation strategies presented in this paper are not prioritized, but it is recommended that level of service raw scores could be used to determine which improvements receive priority in implementation. The mitigation strategies presented are also only given as a suggested guideline -- any actual improvements would need to be determined by the appropriate town agencies and officials. In general, the analysis found the following areas to be most deficient in terms of current service: Pedestrian: local side streets; areas near the UNC campus; Rosemary Street; and Hillsborough Street Bicycle: areas near the UNC campus (especially Columbia Street); portions of Franklin, Cameron, and Rosemary Streets; and local side streets (especially narrow streets with on-street parking) Transit: the Rosemary Street and Cameron Avenue corridors and West Franklin Street (especially westbound)
- Resource type:
- Masters Paper
- Location:
- Chapel Hill, North Carolina, United States
- Access Right:
- Open access
- Affiliation Label Tesim:
- Department of City and Regional Planning
- Degree:
- Master of City and Regional Planning
- Degree Granting Institution:
- University of North Carolina at Chapel Hill
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/y46k-4j21
- Extent:
- 93 p.
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Rodriguez, Daniel and Day, Matthew
- Rights Statement Label:
- In Copyright
Collection Details
- Total items
-
2113
- Size
-
unknown
- Date created
-
February 2, 2022