28 Works

Implementation of a learning healthcare system for Sickle Cell disease: List of smart data elements contained in the Epic Smartform and their SmartData types

Robin Miller, Erin Coyne, Erin Crowgey, Dan Eckrich, Jeffrey Myers, Raymond Villanueva, Jean Wadman, Sidnie Jacobs-Allen, Renee Gresh, Samuel Volchenboum & E Anders Kolb
Objective: Using Sickle Cell Disease (SCD) as a model, the objective of this study was to create a comprehensive learning healthcare system to support disease management and research. A multidisciplinary team developed a SCD clinical data dictionary to standardize bedside data entry and inform a scalable environment capable of converting complex electronic healthcare records (EHR) into knowledge accessible in real-time. Materials and Methods: Clinicians expert in SCD care developed a data dictionary to describe important...

Lit - A Collection of Literature Extracted Small Molecules to Speed Identification of COVID-19 Therapeutics

Yadu Babuji, Ben Blaiszik, Kyle Chard, Ryan Chard, Ian Foster, India Gordon, Zhi Hong, Kasia Karbarz, Zhuozhao Li, Linda Novak, Susan Sarvey, Marcus Schwarting, Julie Smagacz, Logan Ward & Monica Orozco White

Origin of complexity in hemoglobin evolution

Arvind Pillai
Most proteins associate into multimeric complexes with specific architectures, which often have functional properties like cooperative ligand binding, allosteric regulation, or the capacity to perform mechanical work. We have no detailed knowledge of how any multimer and its functions arose during historical evolution. Here we use ancestral protein reconstruction and biophysical assays to dissect the evolutionary origins of vertebrate hemoglobin (Hb), a heterotetramer of paralogous α and β subunits, which mediates oxygen transport and exchange...

Divergence, gene flow and the origin of leapfrog geographic distributions: the history of color pattern variation in Phyllobates poison-dart frogs

Roberto Márquez, Tyler Linderoth, Daniel Mejía-Vargas, Rasmus Nielsen, Adolfo Amézquita & Marcus Kronforst
The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not...

Data from: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

Andrew Skol, Segun Jung, Ana Marija Sokovic, Siquan Chen, Sarah Fazal, Olukayode Sosina, Poulami Borkar, Amy Lin, Maria Sverdlov, Dingcai Cao, Anand Swaroop, Ionut Bebu, Barbara Stranger & Michael Grassi
We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association to diabetic retinopathy in a genome-wide association study meta-analysis. Expression Quantitative Trait Loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose...

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Christian Kammerer, Michol Deutsch, Jacqueline Lungmus & Kenneth Angielczyk
Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical...

Pectoral fin kinematics and motor patterns are shaped by fin ray mechanosensation during steady swimming in Scarus quoyi

Brett R. Aiello, Aaron M. Olsen, Chris E. Mathis, Mark W. Westneat & Melina E. Hale
For many species of fish, rhythmic movement of the pectoral fins, or forelimbs, drives locomotion. In terrestrial vertebrates, normal limb- based rhythmic gaits require ongoing modulation with limb mechanosensors. Given the complexity of the fluid environment and dexterity of fish swimming through it, we hypothesize that mechanosensory modulation is also critical to normal fin-based swimming. Here, we examined the role of sensory feedback from the pectoral fin rays and membrane on the neuromuscular control and...

Phylogenetic and ecological correlates of pollen morphological diversity in a neotropical rainforest

Luke Mander, Caroline Parins-Fukuchi, Christopher W. Dick, Surangi W. Punyasena & Carlos Jaramillo.
Morphology varies enormously across clades, and the morphology of a trait may reflect ecological function or the retention of ancestral features. We examine the tension between ecological and phylogenetic correlates of morphological diversity through a case study of pollen grains produced by angiosperms in Barro Colorado Island, Panama (BCI). Using a molecular phylogeny of 730 taxa we demonstrate a statistically significant association between morphological and genetic distance for these plants. However, the relationship is non-linear,...

Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks

Linda Frey, Michael I. Coates, Kristen Tietjen, Martin Rücklin & Christian Klug
We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp. from the Famennian (Late Devonian) of the Maïder region in Morocco. This chondrichthyan is exceptionally well preserved and displays not only mineralized soft tissues but also undeformed cartilages of the head, gills, and shoulder girdle. A reconstruction of the head using 3D-prints revealed a previously unknown kind of jaw articulation. Here, we make the original cropped image stack and PLY-files of the single cartilaginous elements...

Raw images of targeted gearshifting in actin-based active nematic liquid crystals

Steven Redford, Rui Zhang, Paul Ruijgrok, Nitin Kumar, Ali Mozaffari, Sasha Zemsky, Aaron Dinner, Vincenzo Vitelli, Zev Bryant, Margaret Gardel & Juan De Pablo
Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to...

Transient intracellular acidification regulates the core transcriptional heat shock response

Catherine Triandafillou, Christopher Katanski, Aaron R. Dinner & D. Allan Drummond
Heat shock induces a conserved transcriptional program regulated by heat shock factor 1 (Hsf1) in eukaryotic cells. Activation of this heat-shock response is triggered by heat-induced misfolding of newly synthesized polypeptides, and so has been thought to depend on ongoing protein synthesis. Here, using the budding yeast Saccharomyces cerevisiae, we report the discovery that Hsf1 can be robustly activated when protein synthesis is inhibited, so long as cells undergo cytosolic acidification. Heat shock has long...

Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades

David Cerny, Daniel Madzia & Graham Slater
Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM,...

Neural population dynamics in motor cortex are different for reach and grasp

Aneesha Suresh, James Goodman, Elizaveta Okorokova, Matthew Kaufman, Nicholas Hatsopoulos & Sliman Bensmaia
Low-dimensional linear dynamics are observed in neuronal population activity in primary motor cortex (M1) when monkeys make reaching movements. This population-level behavior is consistent with a role for M1 as an autonomous pattern generator that drives muscles to give rise to movement. In the present study, we examine whether similar dynamics are also observed during grasping movements, which involve fundamentally different patterns of kinematics and muscle activations. Using a variety of analytical approaches, we show...

Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

Mark Bitter, Lydia Kapsenberg, Katherine Silliman, Jean-Pierre Gattuso & Catherine Pfister
Phenotypic plasticity is expected to facilitate the persistence of natural populations as global change progresses. The attributes of fluctuating environments that favor the evolution of plasticity have received extensive theoretical investigation, yet empirical validation of these findings is still in its infancy. Here, we combine high-resolution environmental data with a laboratory-based experiment to explore the influence of habitat pH fluctuation dynamics on the plasticity of gene expression in two populations of the Mediterranean mussel, Mytilus...

Temporal pole responds to subtle changes in local thyroid hormone signaling

Antonio Bianco, Marcelino Cicera, McAninch Elizabeth, Gustavo Fernandes, Barbara Bocco & Miriam Ribeiro
To study thyroid hormone (TH) signaling in the human brain, we analyzed published microarray data sets of the temporal pole (Brodmann area 38) of 19 deceased donors. An index of TH signaling built on the expression of 19 well known TH-responsive genes in mouse brains (T3S+) varied from 0.92 to 1.1. After Factor analysis, T3S+ correlated independently with the expression of TH transporters (MCT8, LAT2), TH receptor (TR) beta and TR coregulators (CARM1, MED1, KAT2B,...

Whole feeding apparatus 3D landmarks

Marion Segall, Daniel Rhoda, P. David Polly & Christopher Raxworthy
The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 µCT scanned skulls and high-density geometric morphometric methods to address the origin and patterns of...

The dynamics and stoichiometry of dissolved organic carbon release by kelp: Carbon fixation, DOC release and nutrient uptake data

Brooke Weigel & Catherine Pfister
Canopy-forming kelps are foundational species in coastal ecosystems, fixing tremendous amounts of carbon, yet we know little about the ecological and physiological determinants of dissolved organic carbon (DOC) release by kelps. We examined DOC release by the bull kelp, Nereocystis luetkeana, in relation to carbon fixation, nutrient uptake, tissue nitrogen content, and light availability. DOC release was approximately 3.5 times greater during the day than at night. During the day, N. luetkeana blades released an...

Topological structure and dynamics of three-dimensional active nematics

Guillaume Duclos, Thomas Powers, Aparna Baskaran, Zvonimir Dogic, Vincenzo Vitelli, Federico Toschi, Raymond Adkins, Debarghya Banerjee, Matthew Peterson, Minu Varghese, Itamar Kolvin, Robert Pelcovits, Sebastian Streichan, Daniel Beller, Arvind Baskaran, Michael Hagan, Matthew S. E. Peterson, Robert A. Pelcovits, Thomas R. Powers, Michael F. Hagan & Sebastian J. Streichan
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination...

Spine and dine: A key defensive trait promotes ecological success in spiny ants

Benjamin Blanchard, Akihiro Nakamura, Min Cao, Stephanie Chen & Corrie Moreau
A key focus of ecologists is explaining the origin and maintenance of morphological diversity and its association with ecological success. We investigate potential benefits and costs of a common and varied morphological trait, cuticular spines, for foraging behavior, interspecific competition, and predator-prey interactions in naturally co-occurring spiny ants (Hymenoptera: Formicidae: Polyrhachis) in an experimental setting. We expect that a defensive trait like spines might be associated with more conspicuous foraging, a greater number of workers...

Comment on “Ancient origins of allosteric activation in a Ser-Thr kinase”

Jaeda Patton, Yeonwoo Park, Georg Hochberg & Joseph Thornton
Hadzipasic et al. used ancestral sequence reconstruction to identify historical sequence substitutions that putatively caused Aurora kinases to evolve allosteric regulation. We show that their results arise from an implausible phylogeny and sparse sequence sampling. Addressing either problem reverses their inferences: allostery and the amino acids that confer it were not gained during the diversification of eukaryotes but were lost in a subgroup of Fungi.

Data from: Sensing the structural characteristics of surfaces: Texture encoding by a bottom-dwelling fish

Adam Hardy & Melina Hale
The texture of contacted surfaces influences our perception of the physical environment and modulates behavior. Texture perception and its neural encoding mechanisms have traditionally been studied in the primate hand, yet animals of all types live in richly textured environments and regularly interact with textured surfaces. Here we explore texture sensation in a different type of vertebrate limb by investigating touch and potential texture encoding mechanisms in the pectoral fins of fishes, the forelimb homologs....

Data from: Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an Afromontane sunbird (Cinnyris reichenowi)

Jacob C. Cooper, J. Dylan Maddox, Kellie McKague & John M. Bates
Africa’s montane ecosystems are noteworthy not only for their isolation, but for their morphologically similar bird populations that inhabit geographically disparate localities. Many species possess range disjunctions in excess of 2,000 km and appear to represent populations that have been isolated since at least the last Ice Age, including the Northern Double-collared Sunbird (Cinnyris reichenowi). Recent work on other Afromontane birds has demonstrated substantial phylogeographic structure can exist in phenotypically similar populations, with cryptic species...

Data for \"Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics\"

Zhaoyi Shen, Kyle Pressel, Zhihong Tan & Tapio Schneider
This dataset provides time-averaged GCM and LES data required to produce results in the paper "Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics". It also includes an example script that can be used to generate Figure 8.

Life history predicts flight muscle phenotype and function in birds

Shane DuBay, Yongjie Wu, Graham Scott, Yanhua Qu, Qiao Liu, Joel Smith, Chao Xin, Andrew Hart Reeve, Chen Juncheng, Dylan Meyer, Jing Wang, Jacob Johnson, Zachary Cheviron, Fumin Lei & John Bates
1. Functional traits are the essential phenotypes that underlie an organism’s life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals’ ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. 2. We asked how age- and sex-dependent demands on...

Reconstructing Ecological Niche Evolution via Ancestral State Reconstruction with Uncertainty Incorporated

Hannah Owens, Vivian Ribiero, Erin Saupe, Marlon E. Cobos, Peter Hosner, Jacob Cooper, Abdallah Samy, Vijay Barve, Narayani Barve, Carlos Muñoz & A. Townsend Peterson
Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods can infer the history of ecological niche evolution inaccurately because (1) species’ niches are often poorly characterized; and (2) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species’ environmental tolerances. Here we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty...

Registration Year

  • 2020
    28

Resource Types

  • Dataset
    28

Affiliations

  • University of Chicago
    28
  • Field Museum of Natural History
    3
  • University of Kansas
    2
  • Stanford University
    2
  • University of Copenhagen
    2
  • California Institute of Technology
    2
  • Northwestern University
    1
  • California Polytechnic State University
    1
  • Universidade Presbiteriana Mackenzie
    1
  • University of Montana
    1