632 research outputs found
Efficient preservation of young terrestrial organic carbon in sandy turbidity-current deposits
No full text© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hage, S., Galy, V. V., Cartigny, M. J. B., Acikalin, S., Clare, M. A., Grocke, D. R., Hilton, R. G., Hunt, J. E., Lintern, D. G., McGhee, C. A., Parsons, D. R., Stacey, C. D., Sumner, E. J., & Talling, P. J. Efficient preservation of young terrestrial organic carbon in sandy turbidity-current deposits. Geology, 48(9), (2020): 882-887, doi:10.1130/G47320.1.Burial of terrestrial biospheric particulate organic carbon in marine sediments removes CO2 from the atmosphere, regulating climate over geologic time scales. Rivers deliver terrestrial organic carbon to the sea, while turbidity currents transport river sediment further offshore. Previous studies have suggested that most organic carbon resides in muddy marine sediment. However, turbidity currents can carry a significant component of coarser sediment, which is commonly assumed to be organic carbon poor. Here, using data from a Canadian fjord, we show that young woody debris can be rapidly buried in sandy layers of turbidity current deposits (turbidites). These layers have organic carbon contents 10× higher than the overlying mud layer, and overall, woody debris makes up >70% of the organic carbon preserved in the deposits. Burial of woody debris in sands overlain by mud caps reduces their exposure to oxygen, increasing organic carbon burial efficiency. Sandy turbidity current channels are common in fjords and the deep sea; hence we suggest that previous global organic carbon burial budgets may have been underestimated.We thank C. Johnson, M. Lardie, A. Gagnon, A. McNichol, and the NOSAMS (National Ocean Sciences Accelerator Mass Spectrometry) team (Woods Hole Oceanographic Institution [WHOI], Massachusetts, USA) for their help with ramped oxidation system and isotopes. We thank the captain and crew of CCGS Vector. Support was provided by UK Natural Environment Research Council (NERC) grants NE/M007138/1 (to Cartigny) and NE/L013142/1 (to Talling), NE/P005780/1 and NE/P009190/1 (to Clare); a Royal Society Research Fellowship (to Cartigny); an International Association of Sedimentologists Postgraduate Grant and National Oceanography Centre Southampton–WHOI exchange program funds (to Hage); an independent study award from WHOI (to Galy); the Climate Linked Atlantic Sector Science (CLASS) program (NERC grant NE/R015953/1); and the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant 725955, to Parsons). We thank François Baudin, Xingqian Cui, editor James Schmitt, and three anonymous reviewers
Neurophysiological Correlates of Sensory-Based Subtypes in Autism
No full textAbstract
Date Presented 3/30/2017
Substantial heterogeneity within the population of children with autism suggests possible sensory subtypes that may help to explain behavioral differences. This study considers objective neurophysiological measurements in response to sensory exposure as a means to better characterize such subtypes.
Primary Author and Speaker: Kelle DeBoth
Contributing Authors: Stacey Reynolds, Shelly J. Lane, Henry Carretta, Alison E. Lane, Roseann C. Schaaf</jats:p
A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.
No full textWe conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis
An R package implementation of multifactor dimensionality reduction
No full textAbstract Background A breadth of high-dimensional data is now available with unprecedented numbers of genetic markers and data-mining approaches to variable selection are increasingly being utilized to uncover associations, including potential gene-gene and gene-environment interactions. One of the most commonly used data-mining methods for case-control data is Multifactor Dimensionality Reduction (MDR), which has displayed success in both simulations and real data applications. Additional software applications in alternative programming languages can improve the availability and usefulness of the method for a broader range of users. Results We introduce a package for the R statistical language to implement the Multifactor Dimensionality Reduction (MDR) method for nonparametric variable selection of interactions. This package is designed to provide an alternative implementation for R users, with great flexibility and utility for both data analysis and research. The 'MDR' package is freely available online at http://www.r-project.org/. We also provide data examples to illustrate the use and functionality of the package. Conclusions MDR is a frequently-used data-mining method to identify potential gene-gene interactions, and alternative implementations will further increase this usage. We introduce a flexible software package for R users.</p
Abstract 3368: <i>Omics</i> data integration analysis in high grade serous ovarian cancer: results from three studies
No full textAbstract
High grade serous ovarian cancer (HGSOC) is a complex disease in which initiation and progression have been associated with gene mutation, DNA methylation changes, genetic variation, and epigenetic processes. Variation in several susceptibility regions and cancer-typical global methylation patterns have been observed in HGSOC; however, this knowledge has not been compelling in understanding HGSOC intiation or progression. As ingetration of genomic, epigenomic, and transcriptomic data has increased mechanistic understanding in other cancers, we hypothesized that tumor methylation alone or in combination with germline genetic variation influences tumor gene expression in HGSOC. We examined three nested models using an Elastnic Net (ENET) penalized regression method while adjusting for somatic copy number (CNV): a) germline genotype and tumor DNA methylation (full model), b) genotype only, and c) DNA methylation only. We included 339 cases from The Cancer Genome Atlas (TCGA), 54 cases from Mayo Clinic, and 78 cases from the Australian Ovarian Cancer Study (AOCS). Genotyping and copy number calls on germline DNA, expression, methylation and copy number on somatic samples were collected and analyzed on different platforms separately at each study site. We excluded genes with low overall expression and thus analyzed a total of 11,922 genes available in three datasets ( Ensembl IDs, 500kb window up- and downstream). In general, combining genomic data in HGSOC did not reveal a role for germline genetic variation in altering gene expression. However, in methylation only models 79 genes were associated with differential expression in the TCGA cases (permutation multiple testing adjusted p-val &lt;0.05), in the Mayo cases (unadjusted p-val &lt;0.05) and AOCS cases (unadjusted p-val &lt;0.05). A known tummor suppressor (FBXW7) was associated with differential expression in the three datasets at p-val &lt;0.01. This work demonstrates the feasibility, utility, and statistical power of ENET gene-level analyses incoporating maximal genomic information.
Citation Format: Yanina Natanzon, Madalene Earp, Julie M. Cunningham, Kimberly R. Kalli, Stacey J. Winham, Sebastian M. Armasu, Melissa C. Larson, Chen Wang, David D. Bowtell, Dale W. Garsed, Ellen Goode. Omics data integration analysis in high grade serous ovarian cancer: results from three studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3368. doi:10.1158/1538-7445.AM2017-3368</jats:p
"The ""lived-in"" moment: the aesthetic potential of nonfiction literature in a third grade classroom"
No full text"Despite the fact that ""emphasis on nonfiction literature in the development of literacy understandings, content knowledge, and literacy abilities is not new"" (Möller, 2013, p. 59) at the university level, having been advocated by literacy scholars across all decades since the 1970s, research has documented across two decades that elementary students have received and continue to receive only minimal exposure to nonfiction texts in classrooms and schools (Duke, 2000; Jeong, Gaffney, & Choi, 2002; Ness, 2011; Pappas, 1991). Given the requirements in the Common Core State Standards (CCSS), which call for 50 percent of classroom reading to be nonfiction by fourth grade, there is a need to investigate how students respond to different formats of nonfiction literature.
The dissertation investigates the selection and use of nonfiction literature in a third grade class as well as students' responses to different formats of nonfiction. This project explores the nonfiction literature selections of the teacher, the responses of the students, and the link between the two. In a four-month qualitative study of a third-grade teacher and five focal students I highlight the complex web that links the teacher's instruction with the evocation of an aesthetic response by the students. The main research questions that guided this study are: How and why do teachers select nonfiction literature for classroom use? In what ways are teachers including nonfiction literature in their classroom instruction? What do students notice and discuss about different formats of nonfiction literature? How do specific types/formats of nonfiction literature invite students to take and develop personally meaningful stances (aesthetic, efferent, mixed or shifting stances) when reading?
Data sources for this study come from the perspective of a third-grade teacher through interviews and classroom literacy observations. In addition, this study presents the ""lived-through"" response of five focal students as I observed their response to reading nonfiction literature and engagement in literature discussion groups. Analysis of the data unravels a complex web of classroom practice, social reading context, and personal preference that shaped the responses that students evoked when reading nonfiction literature. In sum, this study demonstrates the potential for third grade students to evoke an aesthetic response when reading different formats of nonfiction literature."Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2018-08-01The student, Stacey Korson, accepted the attached license on 2016-05-13 at 14:07.The student, Stacey Korson, submitted this Dissertation for approval on 2016-05-13 at 14:14.This Dissertation was approved for publication on 2016-05-16 at 15:03.DSpace SAF Submission Ingestion Package generated from Vireo submission #9611 on 2016-11-10 at 12:18:57Made available in DSpace on 2016-11-10T18:27:18Z (GMT). No. of bitstreams: 3
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Previous issue date: 2016-05-16Embargo set by: Seth Robbins for item 95307
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The Effect of Retrospective Sampling on Estimates of Prediction Error for Multifactor Dimensionality Reduction
No full textSoftware for detecting gene-gene interactions using Multifactor Dimensionality Reduction: Introducing the R package MDR
No full textGene–environment interactions in genome‐wide association studies: current approaches and new directions
No full textAbstract 2420: Integrative analyses of gene expression, DNA methylation, genotype and copy number alterations characterize X-chromosome inactivation in ovarian cancer
No full textAbstract
Introduction: In females, X-chromosome inactivation (XCI) epigenetically silences transcription of one copy of the X chromosome. Which chromosome is silenced is randomly selected, and is tissue- and cell-specific. While some genes are known to escape XCI under normal conditions, aberrant XCI patterns are thought to occur in female-specific cancers, although the role of XCI in ovarian tumorigenesis and progression is largely unknown. The process of XCI is complex, and integration of gene expression, DNA methylation, and copy number data can inform the XCI status of individual genes and chromosome-wide XCI patterns for individual patients.
Methods: We evaluated gene- and chromosome-level patterns of XCI by integrating RNA sequence, copy number alteration, genotype, and DNA methylation data to study XCI escape patterns in tumor samples from 99 ovarian cancer patients. We measured allele-specific expression (ASE) for 397 X-linked genes to identify the active alleles for each tumor. Combining ASE data with knowledge of copy number status, we used a Bayesian beta-binomial mixture model to estimate which genes escaped XCI for each patient, and validated our findings using DNA methylation data. To assess global XCI patterns, we performed cluster analyses on the ASE and methylation data, after adjusting for loss of heterozygosity. We examined the relationship between the clusters and clinical factors, including overall survival and time to recurrence.
Results: DNA promoter methylation demonstrated inverse regional correlations with ASE. Cluster analyses using ASE and methylation data demonstrated evidence of two tumor clusters, representing normal XCI and global XCI dysregulation. The dysregulated XCI cluster (N=52) was associated with lower X-inactive specific transcript expression as expected (p&lt;0.01). Patients with XCI dysregulated tumors were higher grade, stage, serous histology and were sub-optimally debulked (p&lt;0.05). These patients also had shorter overall survival time (HR=1.87, p=0.02) and time to recurrence (HR=2.34, p&lt;0.01), although associations were attenuated after covariate adjustment. In 45 tumor samples with sufficient data, we observed escape patterns largely consistent with previous reports of multiple tissue types. When comparing tumor to normal ovarian tissue, eight genes (CXorf23, CXorf36, BRWD3, ELF4, SLITRK4, GABRE, CLCN4, SH3BGRL) showed putative escape in the tumor and two genes (RBBP7, OFD1) showed discrepant tumor inactivation.
Conclusions: We identified discrepant gene-level XCI tumor classifications compared to normal tissue and identified a group of patients with chromosome-wide XCI dysregulation associated with worse clinical prognosis. This provides evidence of the role of XCI in ovarian cancer and highlights the need to integrate multiple genomic data types to study XCI.
Citation Format: Stacey J. Winham, Nicholas B. Larson, Sebastian M. Armasu, Zachary C. Fogarty, Melissa C. Larson, Kimberly R. Kalli, Kate Lawrenson, Simon Gayther, Brooke L. Fridley, Ellen L. Goode. Integrative analyses of gene expression, DNA methylation, genotype and copy number alterations characterize X-chromosome inactivation in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2420. doi:10.1158/1538-7445.AM2017-2420</jats:p
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