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2. A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear.

Author

Schrauwen, Isabelle, Hasin-Brumshtein, Yehudit, Corneveaux, Jason, Ohmen, Jeffrey, White, Cory, Allen, April, Lusis, Aldons, Van Camp, Guy, Huentelman, Matthew, and Friedman, Rick

Subjects
Balance, Cochlea, Hearing, RNA-Seq, Transcriptome, Vestibule, Animals, Computational Biology, Databases, Genetic, Deafness, Ear, Inner, Gene Expression Profiling, Genetic Predisposition to Disease, Hearing, Humans, Mice, Oligonucleotide Array Sequence Analysis, Phenotype, RNA, Messenger, RNA, Untranslated, Sequence Analysis, RNA, Transcriptome
Abstract

The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.

Published
2016

3. Understanding the Role of Coaching in Implementing and Sustaining Interventions in Child Welfare: A Review of the Literature

Author

Allen, April, Hafer, Nancy, and Brooks, Susan

Subjects
Organizational effectiveness -- Measurement -- Evaluation, Child welfare -- Research, Mentors -- Influence, Organizational learning -- Methods -- Evaluation, Family and marriage, Sociology and social work
Abstract

This article outlines how coaching has been used to support professionals in child welfare settings, providing a comprehensive overview of empirical evidence of the effect of coaching related to individual attitudes and skills and organizational outcomes. Using best practices for evaluating research developed for systematic reviews, an in-depth synthesis of how coaching is situated within the broader literature of implementation science identifies opportunities for considering coaching beyond the narrow focus on sustaining evidence-based interventions., Child welfare organizations are tasked with improving outcomes while juggling a host of sometimes conflicting concerns: child and family needs, worker competencies, organizational structures, policy environments, and funding mechanisms, to [...]

Published
2019

4. Integrating Research, Quality Improvement, and Medical Education for Better Handoffs and Safer Care: Disseminating, Adapting, and Implementing the I-PASS Program

Author

Landrigan, Christopher P., Spector, Nancy D., Starmer, Amy J., Sectish, Theodore C., Srivastava, Rajendu, West, Daniel C., Menon, Aravind Ajakumar, Ali, Arshia, Allair, Brenda K., Allen, April D., Almaddah, Nureddin, Alminde, Claire, Alvarado-Little, Wilma, Anson, Elizabeth, Ashland, Michele, Atsatt, Marisa, Aylor, Megan, Baird, Jennifer D., Bale, James F., Jr, Balmer, Dorene, Barber, Aisha, Barton, Kevin, Bates, Kimberly, Beck, Carolyn, Berchelmann, Kathleen, Bhan, Renuka, Bismilla, Zia, Blankenburg, Rebecca L., Boa-Hocbo, Aileen, Bordin-Wosk, Talya, Brooks, Michelle, Calaman, Sharon, Campe, Julie, Campos, Maria Lucia, Chandler, Debra, Cheung, Yvonne, Choudhary, Amanda, Christensen, Eileen, Clark, Katherine, Coffey, Maitreya, Coghlan-McDonald, Sally, Cohen, Ellen, Cole, F. Sessions, Corless, Elizabeth, Cray, Sharon, Da Silva, Roxi, Dahale, Devesh, Dalal, Anuj K., Destino, Lauren A., Doroshow, Jonathan, Dreyer, Benard, duPont, Katharine, Eagle, Steven, Edgar-Zarate, Courtney, Etzenhouser, Angie, Everhart, Jennifer L., Feraco, Angela M., Ferrer, Alexandra, Galardy, Paul, Garcia, Briana M., Gaspar-Oishi, Maria, Goldstein, Jenna, Good, Brian P., Graham, Dionne A, Growdon, Amanda S., Gubler, LeAnn, Guiot, Amy, Hanlon, Charin, Hanna-Attisha, Mona, Harris, Roben, Haskell, Helen, Hecht, Melvyn, Hehn, Rebecca S, Held, Justin, Hepps, Jennifer H., Hillier, Debra, Hiraoka, Mark, Howell, Eric, Hrach, Christine, Hughes, Helen, Huskins, Charles, Kaatz, Scott, Kanala, Vishnu, Kantrowitz, Michael, Kaplan, Peter, Kashiwagi, Deanne, Kaul, Rajat, Keohane, Carol A., Kern, Jeremy, Khan, Alisa, Khan, Nazia Naz S., Kitch, Barry, Kocolas, Irene, Kothari, Lara, Kruvand, Elizabeth, Kuzma, Nicholas, Lacy, Mary, Lane, Michele, Langrish, Kate, Ledford, Christy J.W., LeRoux, Laura, Lewis, Kheyandra, Lipsitz, Stuart, Litterer, Katherine P., Lopreiato, Joseph O., Lyons, Aimee, Mack, Avram, Mallouk, Meghan, Maloney, Christopher G., Mangan, Amanda, Mann, Keith, Markle, Peggy, Marrese, Christine, Marseille, David, Maynard, Greg, Mehta, Bijal, Mendoza, Fernando, Mercer, Alexandra N., Micalizzi, Dale, Mims, Lisa, Mittal, Vineeta, Mueller, Stephanie, Ngo, Thuy L., Nolan, Ann, Nyenpan, Christopher, Obermeyer, Maria, O'Donnell, Katherine, O'Toole, Jennifer K., Ottolini, Mary, Owolabi, Mobola, Patel, Aarti, Patel, Rajesh, Patel, Shilpa J., Perron, Catherine, Pickler, Rita, Popa, Alina, Reppert, Patrick, Riss, Robert, Roesch, Justin, Rogers, Jayne E., Rosenbluth, Glenn, Rothschild, Jeffrey M., Sanders, Lee, Sauder, Kimberly, Schnipper, Jeff, Schnock, Kumiko O, Scholtz, Amy, Seltz, Barry, Serra, Theresa, Serwint, Janet, Shah, Samir, Sharma, Meesha, Sheppard, Kathleen, Simpkin, Arabella, Sloan, Karin A, Solan, Lauren G., Southgate, Michael W, Spackman, Jaime Blank, Stevens, Scott M., Stevenson, Adam, Stevenson, Windy, Subramony, Anupama, Surkis, William, Thangarasu, Sudhagar, Thompson, E. Douglas, Toole, Cheryl, Trueman, Laura, Trujillo, Tanner, Tse, Lisa, Turmelle, Michael P., Vaniawala, Vishwas, Wagner, Tamara, Warnick, Cindy, Webster, John, Webster, Mary, Weinerman, Adina, Welch, Chelsea, White, Andrew J., Wien, Matthew F., Winn, Ariel S., Wintch, Stephanie, Yin, H. Shonna, Yoon, Catherine S., Yu, Clifton E., Zampino, Dominick, and Zigmont, Katherine R.

Published
2017
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6. A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly

Author

Ho, April J., Stein, Jason L., Hua, Xue, Lee, Suh, Hibar, Derrek P., Leow, Alex D., Dinov, Ivo D., Toga, Arthur W., Saykin, Andrew J., Shen, Li, Foroud, Tatiana, Pankratz, Nathan, Huentelman, Matthew J., Craig, David W., Gerber, Jill D., Allen, April N., Corneveaux, Jason J., Stephan, Dietrich A., DeCarli, Charles S., DeChairo, Bryan M., Potkin, Steven G., Jack,, Clifford R., Weiner, Michael W., Raji, Cyrus A., Lopez, Oscar L., Becker, James T., Carmichael, Owen T., Thompson, Paul M., and Raichle, Marcus E.

Published
2010

7. Circulating microRNAs as Stable Blood-Based Markers for Cancer Detection

Author

Mitchell, Patrick S., Parkin, Rachael K., Kroh, Evan M., Fritz, Brian R., Wyman, Stacia K., Pogosova-Agadjanyan, Era L., Peterson, Amelia, Noteboom, Jennifer, O'Briant, Kathy C., Allen, April, Lin, Daniel W., Urban, Nicole, Drescher, Charles W., Knudsen, Beatrice S., Stirewalt, Derek L., Gentleman, Robert, Vessella, Robert L., Nelson, Peter S., Martin, Daniel B., and Tewari, Muneesh

Published
2008
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8. Association between GAB2 haplotype and higher glucose metabolism in Alzheimer's disease-affected brain regions in cognitively normal APOEε4 carriers

Author

Liang, Winnie S., Chen, Kewei, Lee, Wendy, Sidhar, Kunal, Corneveaux, Jason J., Allen, April N., Myers, Amanda, Villa, Stephen, Meechoovet, Bessie, Pruzin, Jeremy, Bandy, Daniel, Fleisher, Adam S., Langbaum, Jessica B.S., Huentelman, Matthew J., Jensen, Kendall, Dunckley, Travis, Caselli, Richard J., Kaib, Susan, and Reiman, Eric M.

Published
2011
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10. Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease

Author

Stein, Jason L., Hua, Xue, Morra, Jonathan H., Lee, Suh, Hibar, Derrek P., Ho, April J., Leow, Alex D., Toga, Arthur W., Sul, Jae Hoon, Kang, Hyun Min, Eskin, Eleazar, Saykin, Andrew J., Shen, Li, Foroud, Tatiana, Pankratz, Nathan, Huentelman, Matthew J., Craig, David W., Gerber, Jill D., Allen, April N., Corneveaux, Jason J., Stephan, Dietrich A., Webster, Jennifer, DeChairo, Bryan M., Potkin, Steven G., Jack, Clifford R., Jr., Weiner, Michael W., and Thompson, Paul M.

Published
2010
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11. Extracellular circular RNA profiles in plasma and urine of healthy, male college athletes

Author

Hutchins, Elizabeth, primary, Reiman, Rebecca, additional, Winarta, Joseph, additional, Beecroft, Taylor, additional, Richholt, Ryan, additional, De Both, Matt, additional, Shahbander, Khalouk, additional, Carlson, Elizabeth, additional, Janss, Alex, additional, Siniard, Ashley, additional, Balak, Chris, additional, Bruhns, Ryan, additional, Whitsett, Timothy G., additional, McCoy, Roger, additional, Anastasi, Matthew, additional, Allen, April, additional, Churas, Brian, additional, Huentelman, Matthew, additional, and Van Keuren-Jensen, Kendall, additional

Published
2021
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14. Changes in Medical Errors after Implementation of a Handoff Program

Author

Starmer, Amy J., Spector, Nancy D., Srivastava, Rajendu, West, Daniel C., Rosenbluth, Glenn, Allen, April D., Noble, Elizabeth L., Tse, Lisa L., Dalal, Anuj K., Keohane, Carol A., Lipsitz, Stuart R., Rothschild, Jeffrey M., Wien, Matthew F., Yoon, Catherine S., Zigmont, Katherine R., Wilson, Karen M., O’Toole, Jennifer K., Solan, Lauren G., Aylor, Megan, Bismilla, Zia, Coffey, Maitreya, Mahant, Sanjay, Blankenburg, Rebecca L., Destino, Lauren A., Everhart, Jennifer L., Patel, Shilpa J., Bale, James F., Jr., Spackman, Jaime B., Stevenson, Adam T., Calaman, Sharon, Cole, Sessions F., Balmer, Dorene F., Hepps, Jennifer H., Lopreiato, Joseph O., Yu, Clifton E., Sectish, Theodore C., and Landrigan, Christopher P.

Published
2014
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17. Voxelwise genome-wide association study (vGWAS)

Author

Stein, Jason L., Hua, Xue, Lee, Suh, Ho, April J., Leow, Alex D., Toga, Arthur W., Saykin, Andrew J., Shen, Li, Foroud, Tatiana, Pankratz, Nathan, Huentelman, Matthew J., Craig, David W., Gerber, Jill D., Allen, April N., Corneveaux, Jason J., DeChairo, Bryan M., Potkin, Steven G., Weiner, Michael W., and M. Thompson, Paul

Published
2010
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18. Association of CR1, CLU and PICALM with Alzheimerʼs disease in a cohort of clinically characterized and neuropathologically verified individuals

Author

Corneveaux, Jason J., Myers, Amanda J., Allen, April N., Pruzin, Jeremy J., Ramirez, Manuel, Engel, Anzhelika, Nalls, Michael A., Chen, Kewei, Lee, Wendy, Chewning, Kendria, Villa, Stephen E., Meechoovet, Hunsar B., Gerber, Jill D., Frost, Danielle, Benson, Hollie L., OʼReilly, Sean, Chibnik, Lori B., Shulman, Joshua M., Singleton, Andrew B., Craig, David W., Van Keuren-Jensen, Kendall R., Dunckley, Travis, Bennett, David A., De Jager, Philip L., Heward, Christopher, Hardy, John, Reiman, Eric M., and Huentelman, Matthew J.

Published
2010
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20. Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

Author

Eckalbar Walter L, Hutchins Elizabeth D, Markov Glenn J, Allen April N, Corneveaux Jason J, Lindblad-Toh Kerstin, Di Palma Federica, Alföldi Jessica, Huentelman Matthew J, and Kusumi Kenro

Subjects
Annotation, Lizard, Anolis carolinensis, Transcriptome, Genome, RNA-Seq, Gene, Vertebrate, Embryo, Tissue-specific, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies. Results Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5’ and 3’ UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage. Conclusions Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.

Published
2013
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21. Genome-wide association between DNA methylation and alternative splicing in an invertebrate

Author

Flores Kevin, Wolschin Florian, Corneveaux Jason J, Allen April N, Huentelman Matthew J, and Amdam Gro V

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data. Results We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher’s exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation. Conclusions This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively influencing exon inclusion during transcription. The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.

Published
2012
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22. Integrating Research, Quality Improvement, and Medical Education for Better Handoffs and Safer Care: Disseminating, Adapting, and Implementing the I-PASS Program

Author

Starmer, Amy J., primary, Spector, Nancy D., additional, West, Daniel C., additional, Srivastava, Rajendu, additional, Sectish, Theodore C., additional, Landrigan, Christopher P., additional, Starmer, Amy J., additional, Menon, Aravind Ajakumar, additional, Ali, Arshia, additional, Allair, Brenda K., additional, Allen, April D., additional, Almaddah, Nureddin, additional, Alminde, Claire, additional, Alvarado-Little, Wilma, additional, Anson, Elizabeth, additional, Ashland, Michele, additional, Atsatt, Marisa, additional, Aylor, Megan, additional, Baird, Jennifer D., additional, Bale, James F., additional, Balmer, Dorene, additional, Barber, Aisha, additional, Barton, Kevin, additional, Bates, Kimberly, additional, Beck, Carolyn, additional, Berchelmann, Kathleen, additional, Bhan, Renuka, additional, Bismilla, Zia, additional, Blankenburg, Rebecca L., additional, Boa-Hocbo, Aileen, additional, Bordin-Wosk, Talya, additional, Brooks, Michelle, additional, Calaman, Sharon, additional, Campe, Julie, additional, Campos, Maria Lucia, additional, Chandler, Debra, additional, Cheung, Yvonne, additional, Choudhary, Amanda, additional, Christensen, Eileen, additional, Clark, Katherine, additional, Coffey, Maitreya, additional, Coghlan-McDonald, Sally, additional, Cohen, Ellen, additional, Cole, F. Sessions, additional, Corless, Elizabeth, additional, Cray, Sharon, additional, Da Silva, Roxi, additional, Dahale, Devesh, additional, Dalal, Anuj K., additional, Destino, Lauren A., additional, Doroshow, Jonathan, additional, Dreyer, Benard, additional, duPont, Katharine, additional, Eagle, Steven, additional, Edgar-Zarate, Courtney, additional, Etzenhouser, Angie, additional, Everhart, Jennifer L., additional, Feraco, Angela M., additional, Ferrer, Alexandra, additional, Galardy, Paul, additional, Garcia, Briana M., additional, Gaspar-Oishi, Maria, additional, Goldstein, Jenna, additional, Good, Brian P., additional, Graham, Dionne A, additional, Growdon, Amanda S., additional, Gubler, LeAnn, additional, Guiot, Amy, additional, Hanlon, Charin, additional, Hanna-Attisha, Mona, additional, Harris, Roben, additional, Haskell, Helen, additional, Hecht, Melvyn, additional, Hehn, Rebecca S, additional, Held, Justin, additional, Hepps, Jennifer H., additional, Hillier, Debra, additional, Hiraoka, Mark, additional, Howell, Eric, additional, Hrach, Christine, additional, Hughes, Helen, additional, Huskins, Charles, additional, Kaatz, Scott, additional, Kanala, Vishnu, additional, Kantrowitz, Michael, additional, Kaplan, Peter, additional, Kashiwagi, Deanne, additional, Kaul, Rajat, additional, Keohane, Carol A., additional, Kern, Jeremy, additional, Khan, Alisa, additional, Khan, Nazia Naz S., additional, Kitch, Barry, additional, Kocolas, Irene, additional, Kothari, Lara, additional, Kruvand, Elizabeth, additional, Kuzma, Nicholas, additional, Lacy, Mary, additional, Lane, Michele, additional, Langrish, Kate, additional, Ledford, Christy J.W., additional, LeRoux, Laura, additional, Lewis, Kheyandra, additional, Lipsitz, Stuart, additional, Litterer, Katherine P., additional, Lopreiato, Joseph O., additional, Lyons, Aimee, additional, Mack, Avram, additional, Mallouk, Meghan, additional, Maloney, Christopher G., additional, Mangan, Amanda, additional, Mann, Keith, additional, Markle, Peggy, additional, Marrese, Christine, additional, Marseille, David, additional, Maynard, Greg, additional, Mehta, Bijal, additional, Mendoza, Fernando, additional, Mercer, Alexandra N., additional, Micalizzi, Dale, additional, Mims, Lisa, additional, Mittal, Vineeta, additional, Mueller, Stephanie, additional, Ngo, Thuy L., additional, Nolan, Ann, additional, Nyenpan, Christopher, additional, Obermeyer, Maria, additional, O'Donnell, Katherine, additional, O'Toole, Jennifer K., additional, Ottolini, Mary, additional, Owolabi, Mobola, additional, Patel, Aarti, additional, Patel, Rajesh, additional, Patel, Shilpa J., additional, Perron, Catherine, additional, Pickler, Rita, additional, Popa, Alina, additional, Reppert, Patrick, additional, Riss, Robert, additional, Roesch, Justin, additional, Rogers, Jayne E., additional, Rosenbluth, Glenn, additional, Rothschild, Jeffrey M., additional, Sanders, Lee, additional, Sauder, Kimberly, additional, Schnipper, Jeff, additional, Schnock, Kumiko O, additional, Scholtz, Amy, additional, Seltz, Barry, additional, Serra, Theresa, additional, Serwint, Janet, additional, Shah, Samir, additional, Sharma, Meesha, additional, Sheppard, Kathleen, additional, Simpkin, Arabella, additional, Sloan, Karin A, additional, Solan, Lauren G., additional, Southgate, Michael W, additional, Spackman, Jaime Blank, additional, Stevens, Scott M., additional, Stevenson, Adam, additional, Stevenson, Windy, additional, Subramony, Anupama, additional, Surkis, William, additional, Thangarasu, Sudhagar, additional, Thompson, E. Douglas, additional, Toole, Cheryl, additional, Trueman, Laura, additional, Trujillo, Tanner, additional, Tse, Lisa, additional, Turmelle, Michael P., additional, Vaniawala, Vishwas, additional, Wagner, Tamara, additional, Warnick, Cindy, additional, Webster, John, additional, Webster, Mary, additional, Weinerman, Adina, additional, Welch, Chelsea, additional, White, Andrew J., additional, Wien, Matthew F., additional, Winn, Ariel S., additional, Wintch, Stephanie, additional, Yin, H. Shonna, additional, Yoon, Catherine S., additional, Yu, Clifton E., additional, Zampino, Dominick, additional, and Zigmont, Katherine R., additional

Published
2017
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23. Resident Experiences With Implementation of the I-PASS Handoff Bundle

Author

Coffey, Maitreya, primary, Thomson, Kelly, additional, Li, Shelly-Anne, additional, Bismilla, Zia, additional, Starmer, Amy J., additional, O'Toole, Jennifer K., additional, Blankenburg, Rebecca L., additional, Rosenbluth, Glenn, additional, Cole, F. Sessions, additional, Yu, Clifton E., additional, Hepps, Jennifer H., additional, Sectish, Theodore C., additional, Spector, Nancy D., additional, Srivastava, Rajendu, additional, Allen, April D., additional, Mahant, Sanjay, additional, and Landrigan, Christopher P., additional

Published
2017
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24. Mechanisms of CO2/H+Sensitivity of Astrocytes

Author

Turovsky, Egor, primary, Theparambil, Shefeeq M., additional, Kasymov, Vitaliy, additional, Deitmer, Joachim W., additional, del Arroyo, Ana Gutierrez, additional, Ackland, Gareth L., additional, Corneveaux, Jason J., additional, Allen, April N., additional, Huentelman, Matthew J., additional, Kasparov, Sergey, additional, Marina, Nephtali, additional, and Gourine, Alexander V., additional

Published
2016
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29. Transcriptomic Analysis of Tail Regeneration in the Lizard Anolis carolinensis Reveals Activation of Conserved Vertebrate Developmental and Repair Mechanisms

Author

Hutchins, Elizabeth D., primary, Markov, Glenn J., additional, Eckalbar, Walter L., additional, George, Rajani M., additional, King, Jesse M., additional, Tokuyama, Minami A., additional, Geiger, Lauren A., additional, Emmert, Nataliya, additional, Ammar, Michael J., additional, Allen, April N., additional, Siniard, Ashley L., additional, Corneveaux, Jason J., additional, Fisher, Rebecca E., additional, Wade, Juli, additional, DeNardo, Dale F., additional, Rawls, J. Alan, additional, Huentelman, Matthew J., additional, Wilson-Rawls, Jeanne, additional, and Kusumi, Kenro, additional

Published
2014
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30. Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

Author

Eckalbar, Walter L., Hutchins, Elizabeth D., Markov, Glenn J., Allen, April N., Corneveaux, Jason J., Lindblad-Toh, Kerstin, Di Palma, Federica, Alfoeldi, Jessica, Huentelman, Matthew J., Kusumi, Kenro, Eckalbar, Walter L., Hutchins, Elizabeth D., Markov, Glenn J., Allen, April N., Corneveaux, Jason J., Lindblad-Toh, Kerstin, Di Palma, Federica, Alfoeldi, Jessica, Huentelman, Matthew J., and Kusumi, Kenro

Abstract

Background: The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies. Results: Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5' and 3' UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage. Conclusions: Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.

Published
2013
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31. Complex Spatial Skills: The Link Between Visualization and Creativity

Author

Allen, April Diane, Near Environments, McLain-Kark, Joan H., Whitney, Bradley A., Wiedegreen, Eric A., and Bowker, Jeanette E.

Subjects
spatial skills, visualization, creativity
Abstract

The purpose of this study was to determine if there is a correlation between spatial skills and creativity in interior design students. Participants were subjects who took a visualization assessment and created the 33 projects used in the study, and 11 judges, professional design experts who rated the projects. The sample of subjects was comprised of interior design students at a FIDER-accredited institution in southwest Virginia. The judges included interior design educators and interior design graduate students having previous practice experience. Subjects completed a pencil-and-paper Visualization Assessment consisting of 36 questions using two-dimensional and three-dimensional drawings (Isham, 1997). A percentage score for spatial skills was calculated for each subject based on the number of correct answers. Design projects created by the students were assessed by subjective ratings on three Dimensions of Judgment taken from the Consensual Technique for Creativity Assessment (Barnard, 1992; Amabile, 1982). The three dimensions used in this study included Appropriateness, Creativity, and Novelty. Ratings were collected in two judging sessions at a local site. Interjudge reliabilities exceeded the established criterion level (.70 or greater) on all three dimensions, with coefficients ranging from .729 to .866. Interjudge reliability for the Creativity dimension was .866, indicating a high level of agreement among judges on creativity. Intercorrelations among the dimensions indicated a high degree of association between the variables with Appropriateness and Novelty both significantly correlated with the Creativity dimension. Pearson product-moment correlation was used to determine if there was a significant correlation between visualization and creativity in interior design students. No significant correlation was found. Master of Science

Published
2000

32. The Social Importance of a Small-town Theater: A Case Study of the Pulaski Theatre, Pulaski, Virginia

Author

Allen, April Diane, Environmental Design and Planning, Green, William R., Fine, Elizabeth C., Beamish, Julia O., Casto, Marilyn D., and McLain-Kark, Joan H.

Subjects
Pulaski, Theater, Small-town, Social importance, Sense of Place
Abstract

The purpose of this study was to discover the various meanings that the Pulaski Theatre held for the residents of Pulaski and the theatre's social importance to the town. The following research objectives directed this study: 1) to document the theatre's history from the time it was built in 1911 until the present day, 2) to uncover memories or feelings associated with the theatre, and 3) to determine if design features of the theatre building influenced those feelings/memories. In documenting the history of the theatre, design features of the original 1911 building were examined as well as changes over time. To determine if design features of the building influenced the feelings/memories that were associated with the structure it was important first to discover which architectural and design features people remembered, if any, and then to determine if these design features reflected a meaningful association, i.e. sense of place to participants. Also of interest was whether this association or sense of place would be similar or different for all. Participants were fifteen males and females aged 43 to 82 who had attended the theatre over time. All participants grew up in Pulaski and six had lived there their entire lives. Both African Americans and Caucasians participated. Subjects were asked to draw a picture of the theatre that expressed their experience of the space. After the drawing, they were asked to discuss the picture and its meaning to them. Clare Cooper Marcus and others used this environmental autobiography technique as a method to bring a person's experiences of a place to a conscious level. Tape-recorded interviews were conducted and transcribed by the researcher to discover memories of the theatre and the meaning of the theatre to the participants. Data were analyzed by coding to look for emerging themes or categories that relate to the research question. Of interest was whether or not the Pulaski Theatre represented a sense of place to residents and if that sense of place varied for different participants. Document research was conducted through old newspapers and artifacts in the Raymond Ratcliffe Museum (the historic museum in Pulaski), documents from scrapbooks, architectural plans, and the files of the Town of Pulaski. Themes that were identified from the research were (1) the structure was an integral part of the community, (2) the theatre was a reflection of the community's social norms and roles, such as segregation, and (3) the theatre interior contributed to the social atmosphere of the space. The theatre building, while transformed over time, retained a presence in the town and memories associated with it across time were significant in creating a sense of place in the community. The theatre was remembered as a setting that brought excitement and stimulation to children and adults for many years. Participants felt "at home" in the theatre, having favored sections of the theatre where they routinely sat. School children attending the weekly matinees in the summer and African Americans sitting in their special section of the balcony developed a special identity with that particular space within the theatre. Even after segregation, many African Americans continued to sit in the balcony where they had sat for many years and felt at home. The unique characteristics of these spaces were dependent on the people that frequented them rather than the architecture of the building. The sense of place was one of personal relationships and emotional attachments rather than of bricks and mortar. Memories of the theatre were stories of groups or individuals and their interactions in the space. The building represented these individuals and what they brought to this place and time. The Pulaski Theatre played a great role in interactions with friends and neighbors and was significant in reflecting a sense of place in this community. Ph. D.

Published
1999

34. Mechanisms of CO2/H+ Sensitivity of Astrocytes.

Author

Turovsky, Egor, Theparambil, Shefeeq M., Kasymov, Vitaliy, Deitmer, Joachim W., del Arroyo, Ana Gutierrez, Ackland, Gareth L., Corneveaux, Jason J., Allen, April N., Huentelman, Matthew J., Kasparov, Sergey, Marina, Nephtali, and Gourine, Alexander V.

Subjects
REGULATION of respiration, ASTROCYTES, BRAIN stem, CELL culture, NEURAL circuitry, INTRACELLULAR calcium, CELLULAR signal transduction, LABORATORY rats
Abstract

Ventral regions of the medulla oblongata of the brainstem are populated by astrocytes sensitive to physiological changes in PCO2/[H+]. These astrocytes respond to decreases in pH with elevations in intracellular Ca2+ and facilitated exocytosis of ATP-containing vesicles. Released ATP propagates Ca2+ excitation among neighboring astrocytes and activates neurons of the brainstem respiratory network triggering adaptive increases in breathing. The mechanisms linking increases in extracellular and/or intracellular PCO2/[H+] with Ca2+ responses in chemosensitive astrocytes remain unknown. Fluorescent imaging of changes in [Na+]i and/or [Ca2+]i in individual astrocytes was performed in organotypic brainstem slice cultures and acute brainstem slices of adult rats. It was found that astroglial [Ca2+]i responses triggered by decreases in pH are preceded by Na+ entry, markedly reduced by inhibition of Na+/HCO3− cotransport (NBC) or Na+/Ca2+ exchange (NCX), and abolished in Na+-free medium or by combined NBC/NCX blockade. Acidification-induced [Ca2+]i responses were also dramatically reduced in brainstem astrocytes of mice deficient in the electrogenic Na+/HCO3− cotransporter NBCe1. Sensitivity of astrocytes to changes in pH was not affected by inhibition of Na+/H+ exchange or blockade of phospholipase C. These results suggest that in pH-sensitive astrocytes, acidification activates NBCe1, which brings Na+ inside the cell. Raising [Na+]i activates NCX to operate in a reverse mode, leading to Ca2+ entry followed by activation of downstream signaling pathways. Coupled NBC and NCX activities are, therefore, suggested to be responsible for functional CO2/H+ sensitivity of astrocytes that contribute to homeostatic regulation of brain parenchymal pH and control of breathing. [ABSTRACT FROM AUTHOR]

Published
2016
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36. Somitogenesis in the anole lizard and alligator reveals evolutionary convergence and divergence in the amniote segmentation clock

Author

Eckalbar, Walter L., primary, Lasku, Eris, additional, Infante, Carlos R., additional, Elsey, Ruth M., additional, Markov, Glenn J., additional, Allen, April N., additional, Corneveaux, Jason J., additional, Losos, Jonathan B., additional, DeNardo, Dale F., additional, Huentelman, Matthew J., additional, Wilson-Rawls, Jeanne, additional, Rawls, Alan, additional, and Kusumi, Kenro, additional

Published
2012
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38. Corrigendum to “Association between GAB2 haplotype and higher glucose metabolism in Alzheimer's disease-affected brain regions in cognitively normal APOEε4 carriers” [NeuroImage 54/3 (2011) 1896–1902]

Author

Liang, Winnie S., primary, Chen, Kewei, additional, Lee, Wendy, additional, Sidhar, Kunal, additional, Corneveaux, Jason J., additional, Allen, April N., additional, Myers, Amanda, additional, Villa, Stephen, additional, Meechoovet, Bessie, additional, Pruzin, Jeremy, additional, Bandy, Daniel, additional, Fleisher, Adam S., additional, Langbaum, Jessica B.S., additional, Huentelman, Matthew J., additional, Jensen, Kendall, additional, Dunckley, Travis, additional, Caselli, Richard J., additional, Kaib, Susan, additional, and Reiman, Eric M., additional

Published
2011
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39. O3‐01‐04: A candidate causal variant in the CR1 locus

Author

Keenan, Brendan, primary, Shulman, Joshua, additional, Chibnik, Lori, additional, Corneveaux, Jason, additional, Allen, April, additional, Myers, Amanda, additional, Hardy, John, additional, Huentelman, Matthew, additional, Reiman, Eric, additional, Evans, Denis, additional, Bennett, David, additional, and De Jager, Philip, additional

Published
2011
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43. Activation of the MEK–S6 Pathway in High-grade Ovarian Cancers

Author

Ventura, Aviva P., primary, Radhakrishnan, Sabarinath, additional, Green, Ann, additional, Rajaram, Sunitha K., additional, Allen, April N., additional, O'Briant, Kathy, additional, Schummer, Michèl, additional, Karlan, Beth, additional, Urban, Nicole, additional, Tewari, Muneesh, additional, Drescher, Charles, additional, and Knudsen, Beatrice S., additional

Published
2010
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45. S4‐03‐02: Genome‐Wide Association Study for Alzheimer's Disease Risk in a Large Cohort Of Clinically Characterized And Neuropathologically Verified Subjects

Author

Huentelman, Matthew, primary, Corneveaux, Jason, additional, Myers, Amanda, additional, Allen, April, additional, Pruzin, Jeremy, additional, Nalls, Michael, additional, Chibnik, Lori, additional, Singleton, Andrew, additional, Craig, David, additional, Van Keuren-Jensen, Kendall, additional, Dunckley, Travis, additional, Bennett, David, additional, DeJager, Philip, additional, Hardy, John, additional, and Reiman, Eric, additional

Published
2010
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49. Low-impact housing: River Rouge, Michigan.

Author

Mingzhao Wang, Hyde, Rory Quentin, Burley, Jon Bryan, Allen, April, and Machemer, Trisha

Subjects
LANDSCAPE architecture, ENVIRONMENTAL psychology, WATER quality, LANDSCAPE assessment, URBAN planning
Abstract

Low-impact development (LID) is of great interest to planners, designers, governmental authorities, scientists, and concerning citizens. However, assessing the effectiveness of proposed spatial treatments for housing, commercial, industrial, and transportation projects remains an evolving and continuing process. In this study, researchers examined a post-industrial environmental setting near the mouth of the River Rouge River in the greater Detroit metropolitan area to develop the site for housing employing landscape-based composition approaches. The investigation assessed landscape treatments to measure general environmental quality and storm-water runoff quality. The results indicated that a landscape-based housing development had significantly better visual/environmental quality (p ≤ 0.0001) and that a bioretention water treatment area combined with a constructed wetland was able to improve water quality, removing approximately 96.3% of phosphorus. [ABSTRACT FROM AUTHOR]

Published
2015
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