Frontiers
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UNC-authored articles published by Frontiers
Works (762)
521. Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs
- Title Tesim:
- Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs
- Creator:
- Zhong, W., Dong, L., Darville, T., Li, Q., Mohlke, K.L., Zheng, X., Li, Y., Spracklen, C.N., Poston, T.B., and Wu, D.
- Date of publication:
- 2020
- Abstract Tesim:
- Construction of regulatory networks using cross-sectional expression profiling of genes is desired, but challenging. The Directed Acyclic Graph (DAG) provides a general framework to infer causal effects from observational data. However, most existing DAG methods assume that all nodes follow the same type of distribution, which prohibit a joint modeling of continuous gene expression and categorical variables. We present a new mixed DAG (mDAG) algorithm to infer the regulatory pathway from mixed observational data containing both continuous variables (e.g. expression of genes) and categorical variables (e.g. categorical phenotypes or single nucleotide polymorphisms). Our method can identify upstream causal factors and downstream effectors closely linked to a variable and generate hypotheses for causal direction of regulatory pathways. We propose a new permutation method to test the conditional independence of variables of mixed types, which is the key for mDAG. We also utilize an L1 regularization in mDAG to ensure it can recover a large sparse DAG with limited sample size. We demonstrate through extensive simulations that mDAG outperforms two well-known methods in recovering the true underlying DAG. We apply mDAG to a cross-sectional immunological study of Chlamydia trachomatis infection and successfully infer the regularity network of cytokines. We also apply mDAG to a large cohort study, generating sensible mechanistic hypotheses underlying plasma adiponectin level. The R package mDAG is publicly available from CRAN at https://CRAN.R-project.org/package=mDAG.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Biostatistics, Department of Pediatrics, and Department of Genetics
- DOI:
- https://doi.org/10.17615/awe1-qk20
- Edition:
- Publisher
- Identifier:
- https://dx.doi.org/10.3389/fgene.2020.00008
- ISSN:
- 1664-8021
- Journal Title:
- Frontiers in Genetics
- Journal Volume:
- 11
- Keyword:
- mixed observational data, continuous and categorical variables, regulatory network, directed acyclic graphs, and causal regulatory pathways
- Language Label:
- English
- License Label:
- Attribution 3.0 United States
- Person:
- Zhong, W., Dong, L., Darville, T., Li, Q., Mohlke, K.L., Zheng, X., Li, Y., Spracklen, C.N., Poston, T.B., and Wu, D.
- Publisher:
- Frontiers Media S.A.
- Rights Statement Label:
- In Copyright
- Source:
- yun_li_15
522. Using MapMyFitness to place physical activity into neighborhood context
- Title Tesim:
- Using MapMyFitness to place physical activity into neighborhood context
- Creator:
- Laden, F., Evenson, K.R., Conley, K.D., Robinson, J.R.M., Hirsch, J.A., Eastman, K.M., and James, P.
- Date of publication:
- 2014
- Abstract Tesim:
- It is difficult to obtain detailed information on the context of physical activity at large geographic scales, such as the entire United States, as well as over long periods of time, such as over years. MapMyFitness is a suite of interactive tools for individuals to track theirworkouts online or using global positioning system in their phones or other wireless trackers. This method article discusses the use of physical activity data tracked using MapMyFitness to examine patterns over space and time. An overview of MapMyFitness, including data tracked, user information, and geographic scope, is explored. We illustrate the utility of MapMyFitness data using tracked physical activity by users in Winston-Salem, NC, USA between 2006 and 2013. Types of physical activities tracked are described, as well as the percent of activities occurring in parks. Strengths of MapMyFitness data include objective data collection, low participant burden, extensive geographic scale, and longitudinal series. Limitations include generalizability, behavioral change as the result of technology use, and potential ethical considerations. MapMyFitness is a powerful tool to investigate patterns of physical activity across large geographic and temporal scales.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/frdh-nt72
- Edition:
- Publisher
- Identifier:
- https://dx.doi.org/10.3389/fpubh.2014.00019
- ISSN:
- 2296-2565
- Journal Issue:
- MAR
- Journal Title:
- Frontiers in Public Health
- Journal Volume:
- 2
- Keyword:
- MapMyRun, Big data, GPS, Recreation, MapMyFitness, Ysical activity, Parks, and Quantified self
- Language Label:
- English
- License Label:
- Attribution 3.0 United States
- Other Affiliation:
- Harvard School of Public Health, Stanford University, University of Michigan School of Public Health, and MapMyFitness, Inc.
- Person:
- Laden, F., Evenson, K.R., Conley, K.D., Robinson, J.R.M., Hirsch, J.A., Eastman, K.M., and James, P.
- Publisher:
- Frontiers Media S. A
- Rights Statement Label:
- In Copyright
- Source:
- kelly_evenson_101
523. The Role of the Physical and Social Environment in Observed and Self-Reported Park Use in Low-Income Neighborhoods in New York City
- Title Tesim:
- The Role of the Physical and Social Environment in Observed and Self-Reported Park Use in Low-Income Neighborhoods in New York City
- Creator:
- Dorn, J.M., Evenson, K.R., Thorpe, L.E., Huang, T.T.K., Ferris, E., Wyka, K., Low, S., Kodali, H., and Otero Peña, J.E.
- Date of publication:
- 2021
- Abstract Tesim:
- Physical and social environments of parks and neighborhoods influence park use, but the extent of their relative influence remains unclear. This cross-sectional study examined the relationship between the physical and social environment of parks and both observed and self-reported park use in low-income neighborhoods in New York City. We conducted community- (n = 54 parks) and individual-level (n = 904 residents) analyses. At the community level, observed park use was measured using a validated park audit tool and regressed on the number of facilities and programmed activities in parks, violent crime, stop-and-frisk incidents, and traffic accidents. At the individual level, self-reported park use was regressed on perceived park quality, crime, traffic-related walkability, park use by others, and social cohesion and trust. Data were collected in 2016–2018 and analyzed in 2019–2020. At the community level, observed park use was negatively associated with stop-and-frisk (β = −0.04; SE = 0.02; p < 0.05) and positively associated with the number of park facilities (β = 1.46; SE = 0.57; p < 0.05) and events (β = 0.16; SE = 0.16; p < 0.01). At the individual level, self-reported park use was positively associated with the social cohesion and trust scale (β = 0.02; SE = 0.01; p < 0.05). These results indicate that physical and social attributes of parks, but not perceptions of parks, were significantly associated with park use. The social environment of neighborhoods at both community and individual levels was significantly related to park use. Policies for increasing park use should focus on improving the social environment of parks and surrounding communities, not only parks' physical attributes. These findings can inform urban planning and public health interventions aimed at improving the well-being of residents in low-income communities.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Epidemiology
- DOI:
- https://doi.org/10.17615/h946-8z70
- Edition:
- Publisher
- Identifier:
- https://dx.doi.org/10.3389/fpubh.2021.656988 and PMID 33959584
- ISSN:
- 2296-2565
- Journal Title:
- Frontiers in Public Health
- Journal Volume:
- 9
- Keyword:
- stop and frisk, social environment, community health, park use, built environment, low-income neighborhoods, physical environment, and physical activity and redesigned community spaces study
- Language Label:
- English
- License Label:
- Attribution 3.0 United States
- Other Affiliation:
- City University of New York School of Medicine, New York University, and City University of New York
- Person:
- Dorn, J.M., Evenson, K.R., Thorpe, L.E., Huang, T.T.K., Ferris, E., Wyka, K., Low, S., Kodali, H., and Otero Peña, J.E.
- Publisher:
- Frontiers Media S.A.
- Rights Statement Label:
- In Copyright
- Source:
- kelly_evenson_5
524. Approaches to advance scientific understanding of macrosystems ecology
- Title Tesim:
- Approaches to advance scientific understanding of macrosystems ecology
- Creator:
- Toomey, Michael, Bond-Lamberty, Ben, Ball, Becky, Xiao, Jingfeng, Buckley, Lauren, Cheruvelil, Kendra, Knapp, Alan, Voordeckers, James, Filstrup, Christopher, Kellner, James, Vargas, Rodrigo, Levy, Ofir, Wagner, Tyler, Keitt, Tim, Tcheng, David, Williams, John, Lottig, Noah, Zhou, Jizhong, Richardson, Andrew, Punyasena, Surangi, and Finley, Andrew
- Date of publication:
- 2014
- Abstract Tesim:
- The emergence of macrosystems ecology (MSE), which focuses on regional- to continental-scale ecological pat- terns and processes, builds upon a history of long-term and broad-scale studies in ecology. Scientists face the difficulty of integrating the many elements that make up macrosystems, which consist of hierarchical processes at interacting spatial and temporal scales. Researchers must also identify the most relevant scales and variables to be considered, the required data resources, and the appropriate study design to provide the proper inferences. The large volumes of multi-thematic data often associated with macrosystem studies typically require valida- tion, standardization, and assimilation. Finally, analytical approaches need to describe how cross-scale and hierarchical dynamics and interactions relate to macroscale phenomena. Here, we elaborate on some key methodological challenges of MSE research and discuss existing and novel approaches to meet them.
- Resource type:
- Article
- Affiliation Label Tesim:
- University of North Carolina at Chapel Hill
- DOI:
- https://doi.org/10.17615/e90d-4p83
- Edition:
- Publisher
- Identifier:
- https://dx.doi.org/10.1890/130019 and Onescience ID: 4de456802867ae12215db17f7fc703380749909d
- ISSN:
- 1540-9309 and 1540-9295
- Journal Issue:
- 1
- Journal Title:
- Frontiers in Ecology and the Environment
- Journal Volume:
- 12
- Keyword:
- ecology, experimental design, analytical methods, and researchers
- Other Affiliation:
- Harvard University, Pacific Northwest National Lab, Arizona State University, University of New Hampshire, Michigan State University, Colorado State University, University of Oklahoma, Iowa State University, Brown University, University of Delaware, Pennsylvania State University, University of Texas at Austin, University of Illinois at Urbana-Champaign, University of Wisconsin-Madison, and University of Wisconsin Center for Limnology
- Page End:
- 23
- Page Start:
- 15
- Person:
- Toomey, Michael, Bond-Lamberty, Ben, Ball, Becky, Xiao, Jingfeng, Buckley, Lauren, Cheruvelil, Kendra, Knapp, Alan, Voordeckers, James, Filstrup, Christopher, Kellner, James, Vargas, Rodrigo, Levy, Ofir, Wagner, Tyler, Keitt, Tim, Tcheng, David, Williams, John, Lottig, Noah, Zhou, Jizhong, Richardson, Andrew, Punyasena, Surangi, and Finley, Andrew
- Rights Statement Label:
- In Copyright
- Source:
- 1Science_batch3_stragglers_part8_2
525. The rich get richer: patterns of plant invasions in the United States
- Title Tesim:
- The rich get richer: patterns of plant invasions in the United States
- Creator:
- Kartesz, John T., Barnett, David T., and Stohlgren, Thomas J.
- Date of publication:
- 2003
- Abstract Tesim:
- Observations from islands, small-scale experiments, and mathematical models have generally supported the paradigm that habitats of low plant diversity are more vulnerable to plant invasions than areas of high plant diversity. We summarize two independent data sets to show exactly the opposite pattern at multiple spatial scales. More significant, and alarming, is that hotspots of native plant diversity have been far more heavily invaded than areas of low plant diversity in most parts of the United States when considered at larger spatial scales. Our findings suggest that we cannot expect such hotspots to repel invasions, and that the threat of invasion is significant and predictably greatest in these areas.
- Resource type:
- Article
- Affiliation Label Tesim:
- University of North Carolina at Chapel Hill
- DOI:
- https://doi.org/10.17615/rr2h-cx96
- Edition:
- Publisher
- Identifier:
- https://dx.doi.org/10.1890/1540-9295(2003)001[0011:TRGRPO]2.0.CO;2 and Onescience ID: 83988f53baa1d1d80cb885f514d56dfd66efde97
- ISSN:
- 1540-9309 and 1540-9295
- Journal Issue:
- 1
- Journal Title:
- Frontiers in Ecology and the Environment
- Journal Volume:
- 1
- ORCID:
- Other Affiliation:
- , Colorado State University, and Fort Collins Science Center
- Page End:
- 14
- Page Start:
- 11
- Person:
- Kartesz, John T., Barnett, David T., and Stohlgren, Thomas J.
- Rights Statement Label:
- In Copyright
- Source:
- 1Science_batch3_stragglers_part8_1
526. Albuminuria, Hypertension, and Reduced Kidney Volumes in Adolescents Born Extremely Premature
- Title Tesim:
- Albuminuria, Hypertension, and Reduced Kidney Volumes in Adolescents Born Extremely Premature
- Creator:
- Hu, Y., O'Shea, T.M., Hogan, S.L., Askenazi, D., Bjornstad, E., Chang, E., Sanderson, K.R., and Fry, R.C.
- Date of publication:
- 2020
- Abstract Tesim:
- Background: Premature birth is associated with decreased nephron number and an increased risk for chronic kidney disease (CKD). To inform the development of guidelines for kidney follow up of children born prematurely, we undertook a study of individuals born extremely preterm, with the aim of characterizing the prevalence and predictors of microalbuminuria, elevated blood pressure, and/or abnormal kidney volume in adolescence. Methods: Study participants (n = 42) were born before 28 weeks of gestation and were enrolled at birth in the Extremely Low Gestational Age Newborns (ELGAN) study. When participants were 15 years old, we obtained 2 manual blood pressures, a spot urine microalbumin measurement, and sonographic measurements of kidney length and volume. Results: Of the 42 participants, 60% were male, 52% were Caucasian (18% Hispanic), and 43% were African-American. Their median age was 15 (IQR 15, 15.3) years. In 33.3% of the cohort, blood pressure was elevated (>120/80 mmHg). Microalbuminuria (>30 mg/g) was present in 11.9% of the cohort, and kidney volume below the 10th percentile of normative data was present in 14%. Twenty-one (50%) of the sample had at least one kidney abnormality (microalbuminuria, elevated blood pressures, and/or kidney hypoplasia); these individuals were more likely to have experienced neonatal hypotension [55% vs. 17% among those with no kidney abnormality, p = 0.02]. Conclusions: Half of adolescents in this subset of ELGAN cohort have at least one risk factor of kidney disease (reduced kidney volume, microalbuminuria, and/or elevated blood pressures) at 15 years of age. This study suggests the importance of monitoring kidney outcomes in children after extremely preterm birth, especially those with a history of neonatal hypotension.
- Resource type:
- Article
- Affiliation Label Tesim:
- Department of Medicine, Department of Pediatrics, and Department of Environmental Sciences and Engineering
- DOI:
- https://doi.org/10.17615/35mq-bd68
- Edition:
- Publisher
- Identifier:
- https://dx.doi.org/10.3389/fped.2020.00230
- ISSN:
- 2296-2360
- Journal Title:
- Frontiers in Pediatrics
- Journal Volume:
- 8
- Keyword:
- proteinuria, kidney volume reduction, kidney ultrasound, preterm birth, pediatric, hypertension, extremely preterm birth, and chronic kidney disease
- Language Label:
- English
- License Label:
- Attribution 3.0 United States
- ORCID:
- Other Affiliation:
- and University of Alabama at Birmingham
- Person:
- Hu, Y., O'Shea, T.M., Hogan, S.L., Askenazi, D., Bjornstad, E., Chang, E., Sanderson, K.R., and Fry, R.C.
- Publisher:
- Frontiers Media S.A.
- Rights Statement Label:
- In Copyright
- Source:
- keia_sanderson_5
527. AKTivation of PI3K/AKT/mTOR signaling pathway by KSHV
- Title Tesim:
- AKTivation of PI3K/AKT/mTOR signaling pathway by KSHV
- Creator:
- Bhatt, Aadra P. and Damania, Blossom
- Date of publication:
- 2013
- Abstract Tesim:
- As an obligate intracellular parasite, Kaposi sarcoma-associated herpesvirus (KSHV) relies on the host cell machinery to meet its needs for survival, viral replication, production, and dissemination of progeny virions. KSHV is a gammaherpesvirus that is associated with three different malignancies: Kaposi sarcoma (KS), and two B cell lymphoproliferative disorders, primary effusion lymphoma (PEL) and multicentric Castleman’s disease. KSHV viral proteins modulate the cellular phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway, which is a ubiquitous pathway that also controls B lymphocyte proliferation and development. We review the mechanisms by which KSHV manipulates the PI3K/AKT/mTOR pathway, with a specific focus on B cells.
- Resource type:
- Article
- Affiliation Label Tesim:
- University of North Carolina at Chapel Hill
- Deposit Record:
- http://windsor.libint.unc.edu:8181/fcrepo/rest/prod/30/d3/57/ba/30d357ba-bb6d-45eb-984e-a5ac88b0b56e
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/pr6w-a446
- Identifier:
- PMCID: PMC3539662, Onescience id: 064761442b787a837e5412fe25aaa702a95c23f8, Publisher DOI: https://doi.org/10.3389/fimmu.2012.00401, and PMID: 23316192
- ISSN:
- 1664-3224
- Journal Issue:
- jan
- Journal Title:
- Frontiers in Immunology
- Journal Volume:
- 3
- Keyword:
- mTOR, B cells, PI3K, KSHV, and Akt
- Language Label:
- English
- ORCID:
- Person:
- Bhatt, Aadra P. and Damania, Blossom
- Rights Statement Label:
- In Copyright
528. Guiding concepts for park and wilderness stewardship in an era of global environmental change
- Title Tesim:
- Guiding concepts for park and wilderness stewardship in an era of global environmental change
- Creator:
- Landres, Peter B., Cole, David N., Graber, David M., Aplet, Gregory H., Millar, Constance I., Yung, Laurie, Randall, John M., Stephenson, Nathan L., Woodley, Stephen, Zavaleta, Erika S., Tonnessen, Kathy A., Parsons, David J., Hobbs, Richard J., Higgs, Eric S., White, Peter S., and Chapin III, F. Stuart
- Date of publication:
- 2010
- Abstract Tesim:
- The major challenge to stewardship of protected areas is to decide where, when, and how to intervene in physical and biological processes, to conserve what we value in these places. To make such decisions, planners and managers must articulate more clearly the purposes of parks, what is valued, and what needs to be sustained. A key aim for conservation today is the maintenance and restoration of biodiversity, but a broader range of values are also likely to be considered important, including ecological integrity, resilience, historical fidelity (ie the ecosystem appears and functions much as it did in the past), and autonomy of nature. Until recently, the concept of "naturalness" was the guiding principle when making conservation-related decisions in park and wilderness ecosystems. However, this concept is multifaceted and often means different things to different people, including notions of historical fidelity and autonomy from human influence. Achieving the goal of nature conservation intended for such areas requires a clear articulation of management objectives, which must be geared to the realities of the rapid environmental changes currently underway. We advocate a pluralistic approach that incorporates a suite of guiding principles, including historical fidelity, autonomy of nature, ecological integrity, and resilience, as well as managing with humility. The relative importance of these guiding principles will vary, depending on management goals and ecological conditions.
- Resource type:
- Article
- Affiliation Label Tesim:
- University of North Carolina at Chapel Hill
- Deposit Record:
- http://windsor.libint.unc.edu:8181/fcrepo/rest/prod/30/d3/57/ba/30d357ba-bb6d-45eb-984e-a5ac88b0b56e
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/wa53-km23
- Identifier:
- Onescience id: 21ba8591d60cd609a1badcabbec0920b54460a88 and Publisher DOI: https://doi.org/10.1890/090089
- ISSN:
- 1540-9309 and 1540-9295
- Journal Issue:
- 9
- Journal Title:
- Frontiers in Ecology and the Environment
- Journal Volume:
- 8
- Keyword:
- conservation areas, global change, humans, parks, managers, decision making, wilderness, biodiversity, and ecosystems
- Language Label:
- English
- ORCID:
- Other Affiliation:
- USDA ARS Rocky Mountain Research Station, Sequoia and Kings Canyon National Parks, Wilderness Society, Washington DC, USDA Forest Service Pacific Southwest Research Station, University of Montana, University of California, Davis, United States Geological Survey Western Region, Ecosystem Science, University of California, Santa Cruz, The University of Western Australia, University of Victoria, and University of Alaska Fairbanks
- Page End:
- 490
- Page Start:
- 483
- Person:
- Landres, Peter B., Cole, David N., Graber, David M., Aplet, Gregory H., Millar, Constance I., Yung, Laurie, Randall, John M., Stephenson, Nathan L., Woodley, Stephen, Zavaleta, Erika S., Tonnessen, Kathy A., Parsons, David J., Hobbs, Richard J., Higgs, Eric S., White, Peter S., and Chapin III, F. Stuart
- Rights Statement Label:
- In Copyright
529. Cascading effects of predator richness
- Title Tesim:
- Cascading effects of predator richness
- Creator:
- Cardinale, Bradley J. and Bruno, John F.
- Date of publication:
- 2008
- Abstract Tesim:
- Biologists have long known that predators play a key role in structuring ecological communities, but recent research suggests that predator richness - the number of genotypes, species, and functional groups that comprise predator assemblages - can also have cascading effects on communities and ecosystem properties. Changes in predator richness, including the decreases resulting from extinctions and the increases resulting from exotic invasions, can alter the composition, diversity, and population dynamics of lower trophic levels. However, the magnitude and direction of these effects are highly variable and depend on environmental context and natural history, and so are difficult to predict. This is because species at higher trophic levels exhibit many indirect, non-additive, and behavioral interactions. The next steps in predator biodiversity research will be to increase experimental realism and to incorporate current knowledge about the functional role of predator richness into ecosystem management.
- Resource type:
- Article
- Affiliation Label Tesim:
- University of North Carolina at Chapel Hill
- Deposit Record:
- http://windsor.libint.unc.edu:8181/fcrepo/rest/prod/30/d3/57/ba/30d357ba-bb6d-45eb-984e-a5ac88b0b56e
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/zqca-9v87
- Identifier:
- Publisher DOI: https://doi.org/10.1890/070136 and Onescience id: 2d732d7fac7b5357f88070d0e8e21be942c6cefc
- ISSN:
- 1540-9295 and 1540-9309
- Journal Issue:
- 10
- Journal Title:
- Frontiers in Ecology and the Environment
- Journal Volume:
- 6
- Keyword:
- predators, population dynamics, biodiversity, natural history, biologists, ecosystems, ecosystem management, and genotype
- Language Label:
- English
- ORCID:
- Other Affiliation:
- University of California, Santa Barbara
- Page End:
- 546
- Page Start:
- 539
- Person:
- Cardinale, Bradley J. and Bruno, John F.
- Rights Statement Label:
- In Copyright
530. Incorporating positive interactions in aquatic restoration and conservation
- Title Tesim:
- Incorporating positive interactions in aquatic restoration and conservation
- Creator:
- Silliman, Brian R., Bruno, John P., Olden, Julian D., Bertness, Mark D., and Halpern, Benjamin S.
- Date of publication:
- 2007
- Resource type:
- Article
- Deposit Record:
- http://windsor.libint.unc.edu:8181/fcrepo/rest/prod/30/d3/57/ba/30d357ba-bb6d-45eb-984e-a5ac88b0b56e
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/hn9j-sw49
- Identifier:
- Publisher DOI: https://doi.org/10.1890/1540-9295(2007)5[153:IPIIAR]2.0.CO;2 and Onescience id: 763c37ab83bb190c0546549c731df4a8cfe9d61c
- ISSN:
- 1540-9295 and 1540-9309
- Journal Issue:
- 3
- Journal Title:
- Frontiers in Ecology and the Environment
- Journal Volume:
- 5
- Language Label:
- English
- Page End:
- 160
- Page Start:
- 153
- Person:
- Silliman, Brian R., Bruno, John P., Olden, Julian D., Bertness, Mark D., and Halpern, Benjamin S.
- Rights Statement Label:
- In Copyright
Collection Details
- Total items
-
762
- Size
-
unknown
- Date created
-
May 26, 2022