14 Works

Data from: Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis

Shawn H. Pfeil, Kevin Y. Chen, Yale E. Goldman, Shane A. Fiorenza, Ryan M. Jamiolkowski & Alyssa M. Tate
In single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling...

Hepatic estrogen sulfotransferase distantly sensitizes mice to hemorrhagic shock-induced acute lung injury

Yang Xie, Anne Barbosa, Meishu Xu, Patrick Oberly, Songrong Ren, Robbert Gibbs, Samuel Poloyac, Wenchao Song, Jie Fan & Wen Xie
Hemorrhagic shock (HS) is a potential life-threatening condition that may lead to injury to multiple organs, including the lung. The estrogen sulfotransferase (EST, or SULT1E1) is a conjugating enzyme that sulfonates and deactivates estrogens. In this report, we showed that the expression of Est was markedly induced in the liver, but not in the lung of female mice subject to hemorrhagic shock and resuscitation (HS/R). Genetic ablation or pharmacological inhibition of Est effectively protected female...

Data from: Comparing radiomic classifiers and classifier ensembles for detection of peripheral zone prostate tumors on T2-weighted MRI: a multi-site study

Satish E. Viswanath, Prathyush V. Chirra, Michael C. Yim, Neil M. Rofsky, Andrei S. Purysko, Mark A. Rosen, Nicolas B. Bloch & Anant Madabhushi
Background: For most computer-aided diagnosis (CAD) problems involving prostate cancer detection via medical imaging data, the choice of classifier has been largely ad hoc, or been motivated by classifier comparison studies that have involved larger synthetic datasets. More significantly, it is currently unknown how classifier choices and trends generalize across multiple institutions, due to heterogeneous acquisition and intensity characteristics (especially when considering MR imaging data). In this work, we empirically evaluate and compare a number...

Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

Jessica J. Hayward, Michelle E. White, Michael Boyle, Laura M Shannon, Margret L. Casal, Marta G. Castelhano, Sharon A. Center, Vicki N. Meyers-Wallen, Kenneth W. Simpson, Nathan B. Sutter, Rory J. Todhunter & Adam R. Boyko
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference...

Data from: A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila

Esra Durmaz, Subhash Rajpurohit, Nicolas Betancourt, Daniel K. Fabian, Martin Kapun, Paul Schmidt & Thomas Flatt
A fundamental aim of adaptation genomics is to identify polymorphisms that underpin variation in fitness traits. In D. melanogaster latitudinal life-history clines exist on multiple continents and make an excellent system for dissecting the genetics of adaptation. We have previously identified numerous clinal SNPs in insulin/insulin-like growth factor signaling (IIS), a pathway known from mutant studies to affect life history. However, the effects of natural variants in this pathway remain poorly understood. Here we investigate...

Data from: Stability of spontaneous, correlated activity in mouse auditory cortex

Richard Betzel, Katherine Wood, Maria Geffen & Danielle Bassett
Neural systems can be modeled as complex networks in which neural elements are represented as nodes linked to one another through structural or functional connections. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system's topological organization and to better understand its function. Here, we used two-photon calcium imaging to record spontaneous activity from the same set of cells in mouse auditory cortex over the course...

Data from: Quantifying shape and ecology in avian pedal claws: the relationship between the bony core and keratinous sheath

Brandon Hedrick, Samantha Cordero, Lindsay Zanno, Christopher Noto & Peter Dodson
Terrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are often not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, yet have generated conflicting results, spanning from clear ecological groupings based on claw shape to...

Data from: 7 Tesla MRI of the ex vivo human brain at 100 micron resolution

Brian L. Edlow, Azma Mareyam, Andreas Horn, Jonathan R. Polimeni, Thomas Witzel, M. Dylan Tisdall, Jean Augustinack, Jason P. Stockmann, Bram R. Diamond, Allison Stevens, Lee S. Tirrell, Rebecca D. Folkerth, Lawrence L. Wald, Bruce Fischl & Andre Van Der Kouwe
We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of...

Data from: Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies

Mashaal Sohail, Robert M. Maier, Andrea Ganna, Alex Bloemendal, Alicia R. Martin, Michael C. Turchin, Charleston W. K. Chang, Joel Hirschhorn, Mark J. Daly, Nick Patterson, Benjamin Neale, Iain Mathieson, David Reich & Shamil R. Sunyaev
Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size...

Data from: Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback

Seth M. Rudman, Jared M. Goos, Joseph B. Burant, Kevin V. Brix, Taylor C. Gibbons, Colin J. Brauner & Punidan D. Jeyasingh
Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here we quantified the suite of elements in individuals (i.e., ionome) and the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony...

Association of EGLN1 gene with high aerobic capacity of Peruvian Quechua at high altitude

Abigail W. Bigham, Tom D. Brutsaert, Melisa Kiyamu, Gianpietro Elias Revollendo, Jenna L. Isherwood, Frank S. Lee, Maria Rivera-Ch., Fabiola Leon-Velarde & Sudipta Ghosh
Highland native Andeans have resided at altitude for millennia. They display high aerobic capacity (VO2max) at altitude and this may be a reflection of genetic adaptation to chronic hypoxia. Previous genome-wide (GW) scans for natural selection have nominated EGLN1 as a candidate gene. The encoded protein, EGLN1/PHD2, is an O2 sensor that controls levels of the Hypoxia Inducible Factor-a (HIF-a), which regulates the cellular response to hypoxia. From GWAS and ANCOVA performed on a total...

Data from: Thalamocortical synapses in the cat visual system in vivo are weak and unreliable

Madineh Sedigh-Sarvestani, Larry A. Palmer & Diego Contreras
The thalamocortical synapse of the visual system has been central to our understanding of sensory computations in the cortex. Although we have a fair understanding of the functional properties of the pre and post-synaptic populations, little is known about their synaptic properties, particularly in vivo. We used simultaneous recordings in LGN and V1 in cat in vivo to characterize the dynamic properties of thalamocortical synaptic transmission in monosynaptically connected LGN-V1 neurons. We found that thalamocortical...

Data from: An exploratory association analysis of the insulin gene region with diabetes mellitus in two dog breeds

Rebecka Hess, Paula Henthorn, Marcella Devoto, Fan Wang & Rui Feng
Samoyeds and Australian Terriers are the 2 dog breeds at highest risk (>10-fold) for diabetes mellitus in the United States. It is unknown if the insulin (INS) gene is involved in the pathophysiology of diabetes in Samoyeds and Australian Terriers. It was hypothesized that the INS gene region provides a common genetic causality for diabetes in Samoyeds and Australian Terriers. We conducted a 2-stage genetic association study involving both breeds. In the discovery stage (Stage...

Data from: Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation

Diana J. Rennison, Seth M. Rudman & Dolph Schluter
The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature....

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of Pennsylvania
  • University of British Columbia
  • Charité
  • Massachusetts General Hospital
  • West Chester University
  • University of Michigan–Ann Arbor
  • University of California, San Diego
  • University of Minnesota
  • New York University
  • University of Lausanne