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Prospective Doctoral Statement For The University Of Southern California's School Of Cinematic Arts Media Arts + Practice Program, Gabriel Leiner 2016 University of Southern California

Prospective Doctoral Statement For The University Of Southern California's School Of Cinematic Arts Media Arts + Practice Program, Gabriel Leiner

Gabriel Leiner

After visiting L.A. again and seeing the beautiful fountains on the University of Southern California's campus I am filled with all kinds of ideas about the future and brimming with energy. To all those at the University of Southern California's Cinematic Arts Department, thanks for reading my ideas over the past couple years and helping me to evolve and become a better person and a better writer. Starting a position as a doctoral student in the Media Arts + Practice Program in 2016 is an exciting opportunity. I've got a really positive outlook about Kiss The Water.


Histological And Molecular Analysis Of A Progressive Diffuse Intrinsic Pontine Glioma And Synchronous Metastatic Lesions: A Case Report., Javad Nazarian, Gary E Mason, Cheng Ying Ho, Eshini Panditharatna, Madhuri Kambhampati, Louis Gilbert Vezina, Roger J. Packer, Eugene I Hwang 2016 George Washington University

Histological And Molecular Analysis Of A Progressive Diffuse Intrinsic Pontine Glioma And Synchronous Metastatic Lesions: A Case Report., Javad Nazarian, Gary E Mason, Cheng Ying Ho, Eshini Panditharatna, Madhuri Kambhampati, Louis Gilbert Vezina, Roger J. Packer, Eugene I Hwang

Integrative Systems Biology Faculty Publications

There is no curative treatment for patients with diffuse intrinsic pontine glioma (DIPG). However, with the recent availability of biopsy and autopsy tissue, new data regarding the biologic behavior of this tumor have emerged, allowing greater molecular characterization and leading to investigations which may result in improved therapeutic options. Treatment strategies must address both primary disease sites as well as any metastatic deposits, which may be variably sensitive to a particular approach.In this case report, we present a patient with DIPG treated with irradiation and serial investigational agents. The clinical, pathological and molecular phenotypes of both the progressive primary ...


Ocean Acidification And Predator-Prey Relations: Correlating Disruption Of Predator Avoidance With Chemosensory Deficits, Alexandra FW Sidun 2016 Chapman University

Ocean Acidification And Predator-Prey Relations: Correlating Disruption Of Predator Avoidance With Chemosensory Deficits, Alexandra Fw Sidun

Student Research Day Abstracts and Posters

One of the most destructive effects of global climate change is the increased carbon sequestering and consequential acidification of our world’s oceans. The impacts of ocean acidification on marine organisms are still relatively unknown, especially effects on behavioral ecology. Avoiding predation has emerged from recent behavioral ecology literature as a critical feature in the life history of a wide array of animal species; experiments on marine fishes suggest acidic water compromises their predator-avoidance abilities. Recent assays in our lab suggest predator-induced behavior is reduced by weakly acidic water. These experiments do not address the potential factor of generalized malaise ...


Interspecific Divergence In Foliar Nutrient Dynamics And Stem Growth In A Temperate Forest In Response To Chronic Nitrogen Inputs, Jeffrey D. May, Sarah Beth Burdette, Frank S. Gilliam, Mary Beth Adams 2016 Marshall University

Interspecific Divergence In Foliar Nutrient Dynamics And Stem Growth In A Temperate Forest In Response To Chronic Nitrogen Inputs, Jeffrey D. May, Sarah Beth Burdette, Frank S. Gilliam, Mary Beth Adams

Jeffrey May

We studied the effects of excessive nitrogen (N) fertilization on foliar nutrient dynamics and stem growth in three important tree species in a mixed-deciduous forest. Stem diameter growth, foliar N concentrations, nitrogen–phosphorus (N/P) ratios, and nutrient resorption were determined for Acer rubrum L. (ACRU), Liriodendron tulipifera L. (LITU), and Prunus serotina Ehrh. (PRSE) on two 30-year-old watersheds at the Fernow Experimental Forest, West Virginia, USA: WS3, fertilized annually with 35 kg ammonium sulfate·ha-1 since 1989, and WS7, an untreated control watershed. In an earlier (1992) study, foliar N concentrations of all three species averaged 11% higher ...


Interspecific Divergence In Foliar Nutrient Dynamics And Stem Growth In A Temperate Forest In Response To Chronic Nitrogen Inputs, Jeffrey D. May, Sarah Beth Burdette, Frank S. Gilliam, Mary Beth Adams 2016 Marshall University

Interspecific Divergence In Foliar Nutrient Dynamics And Stem Growth In A Temperate Forest In Response To Chronic Nitrogen Inputs, Jeffrey D. May, Sarah Beth Burdette, Frank S. Gilliam, Mary Beth Adams

Frank S. Gilliam

We studied the effects of excessive nitrogen (N) fertilization on foliar nutrient dynamics and stem growth in three important tree species in a mixed-deciduous forest. Stem diameter growth, foliar N concentrations, nitrogen–phosphorus (N/P) ratios, and nutrient resorption were determined for Acer rubrum L. (ACRU), Liriodendron tulipifera L. (LITU), and Prunus serotina Ehrh. (PRSE) on two 30-year-old watersheds at the Fernow Experimental Forest, West Virginia, USA: WS3, fertilized annually with 35 kg ammonium sulfate·ha-1 since 1989, and WS7, an untreated control watershed. In an earlier (1992) study, foliar N concentrations of all three species averaged 11% higher ...


Long-Term Nitrogen Addition Decreases Carbon Leaching In A Nitrogen-Rich Forest Ecosystem, X. Lu, Frank S. Gilliam, G. Yu, H. Chen, J. Mo 2016 Marshall University

Long-Term Nitrogen Addition Decreases Carbon Leaching In A Nitrogen-Rich Forest Ecosystem, X. Lu, Frank S. Gilliam, G. Yu, H. Chen, J. Mo

Frank S. Gilliam

Dissolved organic carbon (DOC) plays a critical role in the carbon (C) cycle of forest soils, and has been recently connected with global increases in nitrogen (N) deposition. Most studies on effects of elevated N deposition on DOC have been carried out in N-limited temperate regions, with far fewer data available from N-rich ecosystems, especially in the context of chronically elevated N deposition. Furthermore, mechanisms for excess N-induced changes of DOC dynamics have been suggested to be different between the two kinds of ecosystems, because of the different ecosystem N status. The purpose of this study was to experimentally examine ...


Interactive Effects Of Nitrogen And Phosphorus On Soil Microbial Communities In A Tropical Forest, Lei Liu, Tao Zhang, Frank S. Gilliam, Per Gundersen, Wei Zhang, Hao Chen, Jiangming Mo 2016 Marshall University

Interactive Effects Of Nitrogen And Phosphorus On Soil Microbial Communities In A Tropical Forest, Lei Liu, Tao Zhang, Frank S. Gilliam, Per Gundersen, Wei Zhang, Hao Chen, Jiangming Mo

Frank S. Gilliam

Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of ...


Changes In Soil Carbon Sequestration In Pinus Massoniana Forests Along An Urban-To-Rural Gradient Of Southern China, H. Chen, W. Zhang, Frank S. Gilliam, L. Liu, J. Huang, T. Zhang, W. Wang, J. Mo 2016 Marshall University

Changes In Soil Carbon Sequestration In Pinus Massoniana Forests Along An Urban-To-Rural Gradient Of Southern China, H. Chen, W. Zhang, Frank S. Gilliam, L. Liu, J. Huang, T. Zhang, W. Wang, J. Mo

Frank S. Gilliam

Urbanization is accelerating globally, causing a variety of environmental changes such as increases in air temperature, precipitation, atmospheric CO2, and nitrogen (N) deposition. However, the effects of these changes on forest soil carbon (C) sequestration remain largely unclear. Here, we used urban-to-rural environmental gradients in Guangdong Province, southern China, to address the potential effects of these environmental changes on soil C sequestration in Pinus massoniana forests. In contrast to our expectations and earlier observations, soil C content in urban sites was significantly lower than that in suburban and rural sites. Lower soil C pools in urban sites were correlated ...


Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li 2016 Marshall University

Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li

Frank S. Gilliam

Improved management of soil carbon (C) and nitrogen (N) storage in agro-ecosystems represents an important strategy for ensuring food security and sustainable agricultural development in China. Accurate estimates of the distribution of soil C and N stores and their relationship to crop yield are crucial to developing appropriate cropland management policies. The current study examined the spatial variation of soil organic C (SOC), total soil N (TSN), and associated variables in the surface layer (0–40 cm) of soils from intensive agricultural systems in 19 counties within Henan Province, China, and compared these patterns with crop yield. Mean soil C ...


A Continental Analysis Of Ecosystem Vulnerability To Atmospheric Nitrogen Deposition, Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop, Donald M. Waller 2016 Marshall University

A Continental Analysis Of Ecosystem Vulnerability To Atmospheric Nitrogen Deposition, Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop, Donald M. Waller

Frank S. Gilliam

Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessedtheeffectofNdepositiononherbaceousrichnessfor15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg N·ha−1·y−1, we found a unimodal ...


Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li 2016 Marshall University

Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li

Frank S. Gilliam

Improved management of soil carbon (C) and nitrogen (N) storage in agro-ecosystems represents an important strategy for ensuring food security and sustainable agricultural development in China. Accurate estimates of the distribution of soil C and N stores and their relationship to crop yield are crucial to developing appropriate cropland management policies. The current study examined the spatial variation of soil organic C (SOC), total soil N (TSN), and associated variables in the surface layer (0–40 cm) of soils from intensive agricultural systems in 19 counties within Henan Province, China, and compared these patterns with crop yield. Mean soil C ...


Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens 2016 College of William and Mary

Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens

College of William & Mary Undergraduate Honors Theses

One way to study disease is to model specific biological reactions or processes involved in the generation of the disease in terms of a system of differential equations. The equations, called kinetic rate laws, are often non-linear and high order, making them difficult to solve. By approximating equations in complex biological networks as linear first order reactions, we can solve large sets of equations using computational software, such as MATLAB, to determine general trends in the change of molecular concentrations over time. These trends can tell us details about the disease and direct us toward areas worthy of further investigation ...


New Clues To A Mass Extinction: Colby Geologist Robert Gastaldo And Student Researchers Unearth Evidence That Contradicts Prevailing Models About Ancient Die-Offs, Stephen Collins 2016 Colby College

New Clues To A Mass Extinction: Colby Geologist Robert Gastaldo And Student Researchers Unearth Evidence That Contradicts Prevailing Models About Ancient Die-Offs, Stephen Collins

Colby Magazine

Colby geologists are rewriting deep time history, altering the script of how scientists understand the mother of all mass extinctions—the End-Permian event that occurred approximately 252 million years ago. Or to suggest that they don’t, in fact, understand it.


Density, Abundance, And Habitat Associations Of The Inland Swamp Sparrow (Melospiza Georgiana Georgiana) In Iowa, Tyler Harms, Stephen Dinsmore 2016 Iowa State University

Density, Abundance, And Habitat Associations Of The Inland Swamp Sparrow (Melospiza Georgiana Georgiana) In Iowa, Tyler Harms, Stephen Dinsmore

Tyler Harms

Wetlands continue to decline throughout North America and the Prairie Pothole Region, thus emphasizing the importance of understanding population trends and habitat associations of wetland species to ensure effective conservation and habitat management of those species. We estimated density and abundance and evaluated habitat associations of the Inland Swamp Sparrow (Melospiza georgiana georgiana) in Iowa. We conducted standardized distance sampling surveys for Swamp Sparrows and measured habitat characteristics at 307 wetlands in two regions of Iowa in 2009 and 2010. We used Program Distance to model detection probability and estimate region-specific breeding densities of Swamp Sparrows at Iowa wetlands. We ...


A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke 2016 University of Nebraska-Lincoln

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and ...


A Continental Analysis Of Ecosystem Vulnerability To Atmospheric Nitrogen Deposition, Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop, Donald M. Waller 2016 Marshall University

A Continental Analysis Of Ecosystem Vulnerability To Atmospheric Nitrogen Deposition, Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop, Donald M. Waller

Biological Sciences Faculty Research

Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg ...


A Modular Assembly Platform For Rapid Generation Of Dna Constructs, Elliot Akama-Garren, Nik Joshi, Tuomas Tammela, Gregory P. Chang, Bethany L. Wagner, Da-Yae Lee, William M. Rideout Iii, Thales Papagiannakopoulos, Wen Xue, Tyler Jacks 2016 Massachusetts Institute of Technology

A Modular Assembly Platform For Rapid Generation Of Dna Constructs, Elliot Akama-Garren, Nik Joshi, Tuomas Tammela, Gregory P. Chang, Bethany L. Wagner, Da-Yae Lee, William M. Rideout Iii, Thales Papagiannakopoulos, Wen Xue, Tyler Jacks

Open Access Articles

Traditional cloning methods have limitations on the number of DNA fragments that can be simultaneously manipulated, which dramatically slows the pace of molecular assembly. Here we describe GMAP, a Gibson assembly-based modular assembly platform consisting of a collection of promoters and genes, which allows for one-step production of DNA constructs. GMAP facilitates rapid assembly of expression and viral constructs using modular genetic components, as well as increasingly complicated genetic tools using contextually relevant genomic elements. Our data demonstrate the applicability of GMAP toward the validation of synthetic promoters, identification of potent RNAi constructs, establishment of inducible lentiviral systems, tumor initiation ...


Extremely Long-Range Chromatin Loops Link Topological Domains To Facilitate A Diverse Antibody Repertoire, Lindsey Montefiori, Robert Wuerffel, Damian Roqueiro, Bryan R. Lajoie, Changying Guo, Tatiana Gerasimova, Supriyo De, William Wood, Kevin G. Becker, Job Dekker, Jie Liang, Ranjan Sen, Amy L. Kenter 2016 National Institute on Aging

Extremely Long-Range Chromatin Loops Link Topological Domains To Facilitate A Diverse Antibody Repertoire, Lindsey Montefiori, Robert Wuerffel, Damian Roqueiro, Bryan R. Lajoie, Changying Guo, Tatiana Gerasimova, Supriyo De, William Wood, Kevin G. Becker, Job Dekker, Jie Liang, Ranjan Sen, Amy L. Kenter

Program in Systems Biology Publications and Presentations

Early B cell development is characterized by large-scale Igh locus contraction prior to V(D)J recombination to facilitate a highly diverse Ig repertoire. However, an understanding of the molecular architecture that mediates locus contraction remains unclear. We have combined high-resolution chromosome conformation capture (3C) techniques with 3D DNA FISH to identify three conserved topological subdomains. Each of these topological folds encompasses a major VH gene family that become juxtaposed in pro-B cells via megabase-scale chromatin looping. The transcription factor Pax5 organizes the subdomain that spans the VHJ558 gene family. In its absence, the J558 VH genes fail to associate ...


Evolutionary Analysis Across Mammals Reveals Distinct Classes Of Long Non-Coding Rnas, Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman, Jacob H. Hanna, Aviv Regev, Manuel Garber 2016 Broad Institute of MIT and Harvard

Evolutionary Analysis Across Mammals Reveals Distinct Classes Of Long Non-Coding Rnas, Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman, Jacob H. Hanna, Aviv Regev, Manuel Garber

Program in Bioinformatics and Integrative Biology Publications and Presentations

BACKGROUND: Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation.

RESULTS: We present slncky, a lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to ...


The Paradox Of Muscle Hypertrophy In Muscular Dystrophy., Joe Kornegay, Martin Childers, Daniel Bogan, Janet Bogan, Peter Nghiem, JiaHui Wang, Zheng Fan, James Howard, Scott Schatzberg, Jennifer Dow, Robert Grange, Martin Styner, Eric Hoffman, Kathryn Wagner 2016 University of North Carolina at Chapel Hill

The Paradox Of Muscle Hypertrophy In Muscular Dystrophy., Joe Kornegay, Martin Childers, Daniel Bogan, Janet Bogan, Peter Nghiem, Jiahui Wang, Zheng Fan, James Howard, Scott Schatzberg, Jennifer Dow, Robert Grange, Martin Styner, Eric Hoffman, Kathryn Wagner

Dow Scott

No abstract provided.


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