256 Works

Audio recordings of Atelpus varius calls from Panama

Justin Kitzes, Samuel Lapp, Corinne Richards-Zawacki, Jamie Voyles, Keely Michelle Rodriguez & Tianhao Wu
Anurans (frogs and toads) are among the most globally threatened taxonomic groups. Successful conservation of anurans will rely on improved data on the status and changes in local populations, particularly for rare and threatened species. Automated sensors, such as acoustic recorders, have the potential to provide such data by massively increasing the spatial and temporal scale of population sampling efforts. We used AudioMoth autonomous recorders to survey for the critically endangered Harlequin toad (Atelopus varius)...

Data from: Discovery of metabolic biomarkers for Duchenne Muscular Dystrophy within a natural history study

Simina M. Boca, Maki Nishida, Michael Harris, Shruti Rao, Amrita K. Cheema, Kirandeep Gill, Haeri Seol, Lauren P. Morgenroth, Erik Henricson, Craig McDonald, Jean K. Mah, Paula R. Clemens, Eric P. Hoffman, Yetrib Hathout & Subha Madhavan
Serum metabolite profiling in Duchenne muscular dystrophy (DMD) may enable discovery of valuable molecular markers for disease progression and treatment response. Serum samples from 51 DMD patients from a natural history study and 22 age-matched healthy volunteers were profiled using liquid chromatography coupled to mass spectrometry (LC-MS) for discovery of novel circulating serum metabolites associated with DMD. Fourteen metabolites were found significantly altered (1% false discovery rate) in their levels between DMD patients and healthy...

Data from: Fat, fibre and cancer risk in African Americans and rural Africans

Stephen J. D. O’Keefe, Jia V. Li, Leo Lahti, Junhai Ou, Franck Carbonero, Mohammed Khaled, Joram M. Posma, James Kinross, Elaine Wahl, Elizabeth Ruder, Kishore Vipperla, Vasudevan Naidoo, Lungile Mtshali, Sebastian Tims, Philippe G. B. Puylaert, James DeLany, Alyssa Krasinskas, Ann C. Benefiel, Hatem O. Kaseb, Keith Newton, Jeremy K. Nicholson, Willem M. De Vos, H. Rex Gaskins & Erwin G. Zoetendal
Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in...

Data from: Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed mating

Alice A Winn, Elizabeth Elle, Susan Kalisz, Pierre-Olivier Cheptou, Christopher G Eckert, Carol Goodwillie, Mark O. Johnston, David A Moeller, Richard H Ree, Risa D Sargent & Mario Vallejo-Marín
Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Greater average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary...

Data from: Extremely long-distance seed dispersal by an overfished Amazonian frugivore

Jill T. Anderson, Tim Nuttle, Joe S. Saldaña Rojas, Thomas H. Pendergast & Alexander S. Flecker
Throughout Amazonia, overfishing has decimated populations of fruit-eating fishes, especially the largebodied characid, Colossoma macropomum. During lengthy annual floods, frugivorous fishes enter vast Amazonian floodplains, consume massive quantities of fallen fruits and egest viable seeds. Many tree and liana species are clearly specialized for icthyochory, and seed dispersal by fish may be crucial for the maintenance of Amazonian wetland forests. Unlike frugivorous mammals and birds, little is known about seed dispersal effectiveness of fishes. Extensive...

Data from: Glucocorticoid-environment relationships align with responses to environmental change in two co-occurring congeners

Talisin T. Hammond, Rupert Palme & Eileen A. Lacey
As more species undergo range shifts in response to climate change, it is increasingly important to understand the factors that determine an organism’s realized niche. Physiological limits imposed by abiotic factors constrain the distributions of many species. Because glucocorticoids are essential to the maintenance of physiological homeostasis, identifying glucocorticoid-environment relationships may generate critical insights into both limits on species distributions and potential responses to environmental change. We explored relationships between variability in baseline glucocorticoids and...

Data from: The evolution of floral sonication, a pollen foraging behavior used by bees (Anthophila)

Sophie Cardinal, Stephen L. Buchmann & Avery Leigh Russell
Over 22,000 species of biotically pollinated flowering plants, including some major agricultural crops, depend primarily on bees capable of floral sonication for pollination services. The ability to sonicate (“buzz”) flowers is widespread in bees but not ubiquitous. Despite the prevalence of this pollinator behavior and its importance to natural and agricultural systems, the evolutionary history of floral sonication in bees has not been previously studied. Here, we reconstruct the evolutionary history of floral sonication in...

Data from: Adaptation, chance, and history in experimental evolutionary reversals to unicellularity

María Rebolleda-Gómez & Michael Travisano
Evolution is often deemed irreversible. The evolution of complex traits that require many mutations makes their reversal unlikely. Even in simpler traits, reversals might become less likely as neutral or beneficial mutations, with deleterious effects in the ancestral context, become fixed in the novel background. This is especially true in changes that involve large re-organizations of the organism and its interactions with the environment. The evolution of multicellularity involves the reorganization of previously autonomous cells...

Data from: Sensory limitations and the maintenance of color polymorphisms: viewing the ‘alba’ female polymorphism through the visual system of male Colias butterflies

Lisa B. Limeri & Nathan I. Morehouse
Although color polymorphisms are a widespread and conspicuous component of extant biodiversity, the selective pressures that act to maintain multiple morphs within populations remain poorly understood in most cases. In particular, the role that visual system limitations may play in maintaining multiple color morphs is not well explored. We used a female-limited color polymorphism common to the butterfly genus Colias, called the ‘alba’ polymorphism, to investigate the hypotheses that mate-searching males may struggle to discriminate...

Data from: The Achilles' heel hypothesis: misinformed keystone individuals impair collective learning and reduce group success

Jonathan Pruitt, Colin Wright, Carl Keiser, Alexander DeMarco, Matt Grobis, Noa Pinter-Wollman, Matthew M. Grobis, Alex E. DeMarco, Carl N. Keiser, Jonathan N. Pruitt & Colin M. Wright
Many animal societies rely on highly influential keystone individuals for proper functioning. When information quality is important for group success, such keystone individuals have the potential to diminish group performance if they possess inaccurate information. Here we test whether information quality (accurate or inaccurate) influences collective outcomes when keystone individuals are the first to acquire it. We trained keystone or generic individuals to attack or avoid novel stimuli and implanted these seed individuals within groups...

Data from: Differential requirements for the RAD51 paralogs in genome repair and maintenance in human cells

Edwige B. Garcin, Stéphanie Gon, Meghan R. Sullivan, Gregory J. Brunette, Anne De Cian, Jean-Paul Concordet, Carine Giovannangeli, Wilhelm G. Dirks, Sonja Eberth, Kara A. Bernstein, Rohit Prakash, Maria Jasin & Mauro Modesti
Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A...

Data from: Carotenoids and amphibians: effects on life history and susceptibility to the infectious pathogen, Batrachochytrium dendrobatidis

Rickey D. Cothran, Stephanie S. Gervasi, Cindy Murray, Beverly J. French, Paul W. Bradley, Jenny Urbina, Andrew R. Blaustein & Rick A. Relyea
Carotenoids are considered beneficial nutrients because they provide increased immune capacity. Although carotenoid research has been conducted in many vertebrates, little research has been done in amphibians, a group that is experiencing global population declines from numerous causes, including disease. We raised two amphibian species through metamorphosis on three carotenoid diets to quantify the effects on life-history traits and post-metamorphic susceptibility to a fungal pathogen (Batrachochytrium dendrobatidis; Bd). Increased carotenoids had no effect on survival...

Ericoid mycorrhizal shrubs alter the relationship between tree mycorrhizal dominance and soil carbon and nitrogen

Elisabeth Ward, Marlyse Duguid, Sara Kuebbing, James Lendemer, & Mark Bradford
1. Plant-fungal associations strongly influence forest carbon and nitrogen cycling. The prevailing framework for understanding these relationships is through the relative abundance of arbuscular (AM) versus ectomycorrhizal (EcM) trees. Ericoid mycorrhizal (ErM) shrubs are also common in forests and interactions between co-occurring ErM shrubs and AM and EcM trees could shift soil biogeochemical responses. Here we test hypotheses that the effects of ErM shrubs on soil carbon and nitrogen either extend or are redundant with...

Worn region size of shoe outsole impacts human slips: Testing a mechanistic model

Kurt Beschorner, Vani H. Sundaram, Sarah L. Hemler, Arnab Chanda, Joel M. Haight & Mark S. Redfern
Shoe outsole tread wear has been shown to increase slip risk by reducing the tread’s ability to channel fluid away from the shoe-floor interface. This study establishes a connection between geometric features of the worn region size and slipping. A mechanistic pathway that describes the relationship between the worn region size and slip risk is assessed. Specifically, it is hypothesized that an increased worn region size leads to an increase in under-shoe fluid pressure, which...

Highly Scalable and Efficient Deep Learning Accelerator Enabled by 3D Photonic Integration

Nathan Youngblood
The positive societal impacts of artificial intelligence (AI) through the field of deep learning have been thrilling to witness, but these advances come with an increasingly unsustainable appetite for computing resources. Thus, the generality and accuracy of deep learning—which fundamentally scale with the amount of training data and available computation—is also its Achilles’ heel. Novel approaches to computation are therefore needed to address the slowing growth in compute performance and efficiency of electronic hardware in...

Black on the Edge: Amplifying Pittsburgh HBCU Narratives

Khirsten Scott
Historically Black Colleges and Universities (HBCUs) were created as a corrective to the legacy of slavery’s having outlawed the formal education of Black people. Although the U.S.’s 107 HBCUs now account for merely 3 percent of US colleges and universities, public discourse surrounding them often hinges on questions about their efficacy and relevance in addressing structural racism. My developing book to satisfy tenure requirements, Black on the Edge: Rhetorics of HBCU Survival, poses the question:...

Data Mining Approach to Understand Tensor Properties in Turbulent Cascade

Lei Fang
Traditionally, turbulence study starts from unproven but plausible hypotheses (e.g. Kolmogorov's similarity hypotheses) and then proceeding in a systematic fashion to reach theory (e.g. K41). The results are then tested against the experimental data for correctness and completeness. While this hypothetical-deductive-like-method received many successes in history, it has its detrimental limitation: starting from a plausible hypothesis precludes any other possibilities. Since the turbulent data is the final test for turbulent theories, why not start by...

Making Skeletons of Shapes Dance

Paul Gartside
Topology is the study of shape. During this project a bridge will be built between the continuous, infinite world of shapes and the combinatorial, finite domain of graphs (networks). To each shape will be associated a sequence of `1-skeletons' which are graphs. By employing recent developments in graph theory these skeletons will be put to work (`made to dance') both as a theoretical tool in topology, but also as a practical tool to understand shapes...

Quarry 2 Floor Tile

Ruikang Ding, Abhijeet Gujrati, Matthew M. Pendolino, Kurt E. Beschorner & Tevis D. B. Jacobs
These are surface profiles of quarry 2 rough flooring. The quarry 1 (0T01881P, Daltile, Dallas, TX, USA) and quarry 2 (01 010 SM 1, Summitville, OH, USA) were commercial tiles, where the full composition was a trade secret, but they were known to include 15-25 wt% quartz, and quarry 2 also included abrasive grits on the surface, presumably to improve slip resistance. There are 30 profiles generated from image analysis and measured by SEM. 10...

Polished Ultrananocrystalline Diamond

Abhijeet Gujrati, Subarna R. Khanal, Lars Pastewka & Tevis D. B. Jacobs
Polished UNCD surface topography measured using TEM, AFM, and Stylus Profilometry

Supporting Data: Effect of various pore fluids on the strength of granite

guanyi lu, Wu Zhao, Jiangnan Zhang & Andrew Bunger

Transnational Dialogues in Afro-Latin American and Afro-Latinx Studies

Michele Reid, Shawn Michelle Alfonso Wells, Reid Andrews, Jerome Branche, Gina Ann Garcia, Martha Mantilla & Luis Van Fossen Bravo

The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

Corlett Wood, Shaniya Markalanda, Connor McFadden & Steven Cassidy
Evidence is accumulating that the soil microbiome—the community of microorganisms living in soils—has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural...

Improving Educational Opportunities for Black Youth in Pittsburgh: A Justice-Centered Intervention

Esohe Osai, Shanyce Campbell, Loius Maraj, Khirsten Scott, Jalyn Evans-Williams, Omid Fotuhi & Josefina Bañales
College going and completion is shown to provide substantial tangible (e.g., lifetime wages) and intangible (e.g., critical consciousness) benefits. Yet, Black youth often are excluded from opportunities to access college. For instance, in Pittsburgh, only 16% of Black students earn a college degree while 42% of White students earn a college degree. In response to higher education barriers, Justice Scholars Institute (JSI) was created for Black youth in Pittsburgh. JSI provides college-credit courses and various...

Understanding the Role of the Brain in Race/Ethnicity Based Stressors and Behavioral Challenges Among Youth of Color

Jamie Hanson, Jaime Booth & Seong Jae Hwang

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  • University of Pittsburgh
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  • Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
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  • Cluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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  • Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany
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