91 Works

Data from: Wind turbine blade shear web disbond detection using rotor blade operational sensing and data analysis

Noah J. Myrent, Douglas E. Adams, D. Todd Griffith & N. Myrent
A wind turbine blade's structural dynamic response is simulated and analysed with the goal of characterizing the presence and severity of a shear web disbond. Computer models of a 5 MW offshore utility-scale wind turbine were created to develop effective algorithms for detecting such damage. Through data analysis and with the use of blade measurements, a shear web disbond was quantified according to its length. An aerodynamic sensitivity study was conducted to ensure robustness of...

Data from: Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via a comparative genome scan of Neochlamisus bebbianae leaf beetles

Scott P. Egan, Patrik Nosil & Daniel J. Funk
This study uses a comparative genome scan to evaluate the contributions of host plant related divergent selection to genetic differentiation and ecological speciation in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. For each of 15 pairwise population comparisons, we identified "outlier loci" whose strong differentiation putatively reflects divergent selection. Of 447 AFLP loci, 15% were outliers across multiple population comparisons, and low linkage disequilibrium indicated that these outliers derived from multiple regions of...

Data from: Genetics of plasminogen activator inhibitor-1 (PAI-1) in a Ghanaian population

Marquitta J. White, Nuri M. Kodaman, Reed H. Harder, Folkert W. Asselbergs, Douglas E. Vaughan, Nancy J. Brown, Jason H. Moore & Scott M. Williams
Plasminogen activator inhibitor 1 (PAI-1), a major modulator of the fibrinolytic system, is an important factor in cardiovascular disease (CVD) susceptibility and severity. PAI-1 is highly heritable, but the few genes associated with it explain only a small portion of its variation. Studies of PAI-1 typically employ linear regression to estimate the effects of genetic variants on PAI-1 levels, but PAI-1 is not normally distributed, even after transformation. Therefore, alternative statistical methods may provide greater...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa

Rafal S. Sobota, Catherine M. Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P. Igo, Albert Magohe, LaShaunda L. Malone, Keith Chervenak, Noemi B. Hall, Mecky Matee, Harriet Mayanja-Kizza, Moses Joloba, Jason H. Moore, William K. Scott, Timothy Lahey, W. Henry Boom, C. Fordham Von Reyn, Scott M. Williams & Giorgio Sirugo
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts...

Data from: Water vascular system architecture in an Ordovician ophiuroid

Elizabeth G. Clark, Bhart-Anjan S. Bhullar, Simon A. F. Darroch & Derek E. G. Briggs
Understanding the water vascular system (WVS) in early fossil echinoderms is critical to elucidating the evolution of this system in extant forms. Here we present the first report of the internal morphology of the water vascular system of a stem ophiuroid. The radial canals are internal to the arm, but protected dorsally by a plate separate to the ambulacrals. The canals zig-zag with no evidence of constrictions, corresponding to sphincters, which control pairs of tube...

Data from: Ediacaran distributions in space and time: testing assemblage concepts of earliest macroscopic body fossils

Thomas H. Boag, Simon A. F. Darroch & Marc Laflamme
The mid-late Ediacaran Period (~579–541 Ma) is characterized by globally distributed marine soft-bodied organisms of unclear phylogenetic affinities colloquially called the “Ediacara biota.” Despite an absence of systematic agreement, previous workers have tested for underlying factors that may control the occurrence of Ediacaran macrofossils in space and time. Three taxonomically distinct “assemblages,” termed the Avalon, White Sea, and Nama, were identified and informally incorporated into Ediacaran biostratigraphy. After ~15 years of new fossil discoveries and...

Multimodal Molecular Imaging of Human Kidney Tissue From a 58 Year Old Black or African American Male Donor

Jeffrey Spraggins, Elizabeth Neumann, Nathan Patterson, David Anderson, Kavya Sharman, Lukasz Migas, Jamie Allen, Maya Brewer, Jennifer Harvey, Haichun Yang, Raymond Harris, Agnes Fogo, Mark deCaestecker, Danielle Gutierrez, Richard Caprioli & Raf Van de Plas
Multimodal molecular imaging data collected from the Left Kidney of a 58 year old Black or African American Male donor by the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University. BIOMIC is a Tissue Mapping Center that is part of the NIH funded Human Biomolecular Atlas Program (HuBMAP). Datasets generated by BIOMIC combine MALDI imaging mass spectrometry with various microscopy modalities including autofluorescence and stained microscopy. Support was provided by the NIH Common Fund and...

Multimodal Molecular Imaging of Human Kidney Tissue From a 48 Year Old White Male Donor

Jeffrey Spraggins, Elizabeth Neumann, Nathan Patterson, David Anderson, Kavya Sharman, Lukasz Migas, Jamie Allen, Maya Brewer, Jennifer Harvey, Haichun Yang, Raymond Harris, Agnes Fogo, Mark deCaestecker, Danielle Gutierrez, Richard Caprioli & Raf Van de Plas
Multimodal molecular imaging data collected from the Right Kidney of a 48 year old White Male donor by the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University. BIOMIC is a Tissue Mapping Center that is part of the NIH funded Human Biomolecular Atlas Program (HuBMAP). Datasets generated by BIOMIC combine MALDI imaging mass spectrometry with various microscopy modalities including autofluorescence and stained microscopy. Support was provided by the NIH Common Fund and National Institute of...

Multimodal Molecular Imaging of Human Kidney Tissue From a 53 Year Old Black or African American Male Donor

Jeffrey Spraggins, Elizabeth Neumann, Nathan Patterson, David Anderson, Kavya Sharman, Lukasz Migas, Jamie Allen, Maya Brewer, Jennifer Harvey, Haichun Yang, Raymond Harris, Agnes Fogo, Mark deCaestecker, Danielle Gutierrez, Richard Caprioli & Raf Van de Plas
Multimodal molecular imaging data collected from the Left Kidney of a 53 year old Black or African American Male donor by the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University. BIOMIC is a Tissue Mapping Center that is part of the NIH funded Human Biomolecular Atlas Program (HuBMAP). Datasets generated by BIOMIC combine MALDI imaging mass spectrometry with various microscopy modalities including autofluorescence and stained microscopy. Support was provided by the NIH Common Fund and...

Extinction of North American Cuvieronius (Mammalia, Proboscidea, Gomphotheriidae) driven by dietary resource competition with sympatric mammoths and mastodons

Gregory Smith & Larisa DeSantis
The gomphotheres were a diverse and widespread group of proboscideans occupying Eurasia, North America, and South America throughout the Neogene. Their decline was temporally and spatially heterogeneous and the gomphotheres ultimately became extinct during the late Pleistocene; however, the genus Cuvieronius is rarely represented in late Pleistocene assemblages in North America. Two alternative hypotheses have been invoked to explain this phenomenon: (1) competitive exclusion by sympatric mammoths and mastodons, or (2) ecologic displacement due to...

Epidermal Growth Factor signaling promotes sleep through a combined series and parallel neural circuit

Jan Konietzka, Maximilian Fritz, Silvan Spiri, Rebecca McWhirter, Andreas Leha, Sierra Palumbos, Wagner Steuer Costa, Alexandra Oranth, Alexander Gottschalk, , Alex Hajnal & Henrik Bringmann
Sleep requires sleep-active neurons that depolarize to inhibit wake circuits. Sleep-active neurons are under the control of homeostatic mechanisms that determine sleep need. However, little is known about the molecular and circuit mechanisms that translate sleep need into the depolarization of sleep-active neurons. During many stages and conditions in C. elegans, sleep requires a sleep-active neuron called RIS. Here, we defined the transcriptome of RIS to discover that genes of the Epidermal Growth Factor Receptor...

Microbiome reduction and endosymbiont gain from a switch in sea urchin life-history

Tyler Carrier, Brittany Leigh, Dione Deaker, Hannah Devens, Gregory Wray, Seth Bordenstein, Maria Byrne & Adam Reitzel
Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life-history transition from planktotrophy (feeding) to lecithotrophy (non-feeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds...

Data from: Postmating isolation and genetically variable host use in ecologically divergent host forms of Neochlamisus bebbianae leaf beetles

Scott P Egan, Eric M Janson, Christopher G Brown & Daniel J Funk
Ecological speciation studies have more thoroughly addressed premating than postmating reproductive isolation. This study examines multiple postmating barriers between host forms of Neochlamisus bebbianae leaf beetles that specialize on Acer versus Salix trees. We demonstrate cryptic isolation and reduced hybrid fitness via controlled matings of these host forms. These findings reveal host-associated postmating isolation, although a non-ecological, ‘intrinsic’ basis for these patterns cannot be ruled out. Host preference and performance results among cross types further...

Data from: The application of an oxygen isotope aridity index to terrestrial paleoenvironmental reconstructions in Pleistocene North America

Lindsey T. Yann, Larisa R. G. DeSantis, Ryan J. Haupt, Jennifer L. Romer, Sarah E. Corapi & David J. Ettenson
Geochemical tools, including the analysis of stable isotopes from fossil mammals, are often used to infer regional climatic and environmental differences. We have further developed an oxygen isotope aridity index and used oxygen (δ18O) isotope values and carbon (δ13C) isotope values to assess regional climatic differences between the southeastern and southwestern United States during the Pleistocene. Using data collected from previously published studies, we assigned taxa to evaporation-sensitivity categories by quantifying the frequency and magnitude...

Data from: Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions

James E. Cassat, Jessica L. Moore, Kevin J. Wilson, Zachary Stark, Boone M. Prentice, Raf Van De Plas, William J. Perry, Yaofang Zhang, John Virostko, Daniel C. Colvin, Kristie L. Rose, Audra M. Judd, Michelle L. Reyzer, Jeffrey M. Spraggins, Caroline M. Grunenwald, John C. Gore, Richard M. Caprioli & Eric P. Skaar
All diseases are characterized by distinct changes in tissue molecular distribution. Molecular analysis of intact tissues traditionally requires pre-existing knowledge of, and reagents for, the targets of interest. Conversely, label-free discovery of disease-associated tissue analytes requires destructive processing for downstream identification platforms. Tissue-based analyses therefore sacrifice discovery to gain spatial distribution of known targets, or sacrifice tissue architecture for discovery of unknown targets. To overcome these obstacles, we developed a multi-modality imaging platform for discovery-based...

Data from: The origin and genetic differentiation of the socially parasitic aphid Tamalia inquilinus

Don G. Miller, Sarah P. Lawson, David C. Rinker, Heather Estby & Patrick Abbot
Social and brood parasitisms are nonconsumptive forms of parasitism involving the exploitation of the colonies or nests of a host. Such parasites are often related to their hosts and may evolve in various ecological contexts, causing evolutionary constraints and opportunities for both parasites and their hosts. In extreme cases, patterns of diversification between social parasites and their hosts can be coupled, such that diversity of one is correlated with or even shapes the diversity of...

Data from: Inference of facultative mobility in the enigmatic Ediacaran organism Parvancorina

Simon A.F. Darroch, Imran A. Rahman, Brandt Gibson, Rachel A. Racicot, Marc Laflamme & Simon A. F. Darroch
Establishing how Ediacaran organisms moved and fed is critical to deciphering their ecological and evolutionary significance, but has long been confounded by their non-analogue body plans. Here, we use computational fluid dynamics to quantitatively analyze water flow around the Ediacaran taxon Parvancorina, thereby testing between competing models for feeding mode and mobility. The results show that flow was not distributed evenly across the organism, but was directed towards localized areas; this allows us to reject...

Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell & Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and...

Data from: Three-dimensional simulation for fast forward flight of a calliope hummingbird

Jialei Song, Bret W. Tobalske, Donald R. Powers, Tyson L. Hedrick & Haoxiang Luo
We present a computational study of flapping-wing aerodynamics of a calliope hummingbird (Selasphorus calliope) during fast forward flight. Three-dimensional wing kinematics were incorporated into the model by extracting time-dependent wing position from high-speed videos of the bird flying in a wind tunnel at 8.3 m s−1. The advance ratio, i.e. the ratio between flight speed and average wingtip speed, is around one. An immersed-boundary method was used to simulate flow around the wings and bird...

Ancient life and moving fluids

Brandt M. Gibson, David J. Furbish, Imran A. Rahman, Mark W. Schmeeckle, Marc Laflamme & Simon A.F. Darroch
Over 3.7 billion years of Earth history, life has evolved complex adaptations to help navigate and interact with the fluid environment. Consequently, fluid dynamics has become a powerful tool for studying ancient fossils, providing insights into the paleobiology and -ecology of extinct organisms from across the tree of life. In recent years, this approach has been extended to the Ediacara biota, an enigmatic assemblage of Neoproterozoic soft-bodied organisms that represent the first major radiation of...

Data from: Laminar microcircuitry of visual cortex producing attention-associated electric fields

Jacob Westerberg, Michelle Schall, Alexander Maier, Geoffrey Woodman & Jeffrey Schall
Cognitive operations are widely studied by measuring electric fields through EEG and ECoG. However, despite their widespread use, the component neural circuitry giving rise to these signals remains unknown. Specifically, the functional architecture of cortical columns which results in attention-associated electric fields has not been explored. Here we detail the laminar cortical circuitry underlying an attention-associated electric field often measured over posterior regions of the brain in humans and monkeys. First, we identified visual cortical...

Exploration of Vaccination Attitudes Among Parents and Caregivers in a Rural Appalachian Health Clinic

Radwa Omar, Karen Hande & Natasha McClure
At a rural Appalachian health clinic in Kentucky, 20% of patients under 18 years were not up to date with the CDC-recommended immunization schedule. Reasons parents or caregivers chose to delay or refuse their child’s immunizations were explored using the Caregiver Vaccination Attitude Scale. High levels of trust in the healthcare provider and self-reported vaccine knowledge highlight opportunities for rural healthcare providers to apply evidence-based communication strategies to address vaccine hesitancy and promote the safety...

Multimodal Molecular Imaging of Human Kidney Tissue From a 31 Year Old White Male Donor

Jeffrey Spraggins, Elizabeth Neumann, Nathan Patterson, David Anderson, Kavya Sharman, Lukasz Migas, Jamie Allen, Maya Brewer, Jennifer Harvey, Haichun Yang, Raymond Harris, Agnes Fogo, Mark deCaestecker, Danielle Gutierrez, Richard Caprioli & Raf Van de Plas
Multimodal molecular imaging data collected from the Right Kidney of a 31 year old White Male donor by the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University. BIOMIC is a Tissue Mapping Center that is part of the NIH funded Human Biomolecular Atlas Program (HuBMAP). Datasets generated by BIOMIC combine MALDI imaging mass spectrometry with various microscopy modalities including autofluorescence and stained microscopy. Support was provided by the NIH Common Fund and National Institute of...

Multimodal Molecular Imaging of Human Kidney Tissue From a 61 Year Old White Female Donor

Jeffrey Spraggins, Nathan Patterson, David Anderson, Kavya Sharman, Lukasz Migas, Jamie Allen, Maya Brewer, Jennifer Harvey, Haichun Yang, Raymond Harris, Agnes Fogo, Mark deCaestecker, Danielle Gutierrez, Richard Caprioli & Raf Van de Plas
Mulltimodal molecular imaging data collected from the Left Kidney of a 61 year old White Female donor by the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University. BIOMIC is a Tissue Mapping Center that is part of the NIH funded Human Biomolecular Atlas Program (HuBMAP). Datasets generated by BIOMIC combine MALDI imaging mass spectrometry with various microscopy modalities including autofluorescence and stained microscopy. Support was provided by the NIH Common Fund and National Institute of...

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