89 Works

Common power laws for cities and spatial fractal structures

Tomoya Mori, Tony Smith & Wen-Tai Hsu
SI Datasets S1 for "Common power laws for cities and spatial fractal structures" i) cities.zip : This file includes six CSV files. For each country, there is a corresponding file containing the population sizes and location information of cities. In each file, there are four columns: city ID (UA), population size (POP), longitude (LON) and latitude (LAT) of the the most densely inhabited location in the city according to the geodetic reference system, WGS1984. ii)...

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: 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....

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...

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: 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: 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: 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: Seasonal variation in life history traits in two Drosophila species

Emily L. Behrman, Samuel S. Watson, Katherine R. O'Brien, Shane M. Heschel, Paul S. Schmidt, K. R. O'Brien, E. L. Behrman, P. S. Schmidt & S. S. Watson
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and D. simulans were sampled at four timepoints from June...

Data from: Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana

Yuan Chen, Anastasia P. Litvintseva, Aubrey E. Frazzitta, Miriam R. Haverkamp, Liuyang Wang, Charles Fang, Charles Muthoga, Thomas G. Mitchell & John R. Perfect
Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and...

Data from: Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

Timothy Linksvayer, Alexander Mikheyev, Timothy A Linksvayer & Alexander S Mikheyev
MySQL database for gene expression analysisMySQL database for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium_2014-12-08.sql.gzData tables from MySQL database for gene expression analysisseparated data tables from MySQL database as zipped .csv files for the transcriptional, network connectedness, molecular evolution, and GO term analysismonomorium tables.zipdata summary by genesummary of data listed by M. pharaonis gene in comma deliminated (.csv) format. Header line with variables: gene is the M. pharaonis gene name; SINV homolog...

Data from: Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

Shadi Shokralla, Joel F. Gibson, Hamid Nikbakht, Daniel H. Janzen, Winnie Hallwachs & Mehrdad Hajibabaei
DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need...

Data from: Identifying the morphologic basis for radiomic features in distinguishing different Gleason grades of prostate cancer on MRI: preliminary findings

Gregory Penzias, Asha Singanamalli, Robin Elliott, Jay Gollamudi, Natalie Shih, Michael Feldman, Phillip D. Stricker, Warick Delprado, Sarita Tiwari, Maret Böhm, Anne-Maree Haynes, Lee Ponsky, Pingfu Fu, Pallavi Tiwari, Satish Viswanath & Anant Madabhushi
Translation of radiomics into the clinic may require a more comprehensive understanding of the underlying morphologic tissue characteristics they reflect. In the context of prostate cancer (PCa), some studies have correlated gross histological measurements of gland lumen, epithelium, and nuclei with disease appearance on MRI. Quantitative histomorphometry (QH), like radiomics for radiologic images, is the computer based extraction of features for describing tumor morphology on digitized tissue images. In this work, we attempt to establish...

Data from: An inversion supergene in Drosophila underpins latitudinal clines in survival traits

Esra Durmaz, Clare Benson, Martin Kapun, Paul Schmidt & Thomas Flatt
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation, and survival upon cold shock). We generated homokaryon...

Data from: Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: isolating independent associations with diet/energy balance and body weight

Isaac J. Perron, Brendan T. Keenan, Karthikeyani Chellappa, Nicholas F. Lahens, Nicole Y. Yohn, Keith R. Shockley, Allan I. Pack, Sigrid C. Veasey & Nicole L. Yohn
Background and Aims: Associated with numerous metabolic and behavioral abnormalities, obesity is classified by metrics reliant on body weight (such as body mass index). However, overnutrition is the common cause of obesity, and may independently contribute to these obesity-related abnormalities. Here, we use dietary challenges to parse apart the relative influence of diet and/or energy balance from body weight on various metabolic and behavioral outcomes. Materials and Methods: Seventy male mice (mus musculus) were subjected...

Data from: The Victoria West: earliest prepared core technology in the Acheulean at Canteen Kopje and implications for the cognitive evolution of early hominids

Hao Li, Kathleen Kuman, Matt G. Lotter, George M. Leader & Ryan J. Gibbon
Prepared core technology illustrates in-depth planning and the presence of a mental template during the core reduction process. This technology is, therefore, a significant indicator in studying the evolution of abstract thought and the cognitive abilities of hominids. Here, we report on Victoria West cores excavated from the Canteen Kopje site in central South Africa, with a preliminary age estimate of approximately 1 Ma (million years ago) for these cores. Technological analysis shows that the...

Data from: Pharmacological inactivation does not support a unique causal role for intraparietal sulcus in the discrimination of visual number

Nicholas K. DeWind, Jiyun Peng, Andrew Luo, Elizabeth M. Brannon & Michael L. Platt
The “number sense” describes the intuitive ability to quantify without counting. Single neuron recordings in non-human primates and functional imaging in humans suggest the intraparietal sulcus is an important neuroanatomical locus of numerical estimation. Other lines of inquiry implicate the IPS in numerous other functions, including attention and decision making. Here we provide a direct test of whether IPS has functional specificity for numerosity judgments. We used muscimol to reversibly and independently inactivate the ventral...

Data from: Adaptive dynamics of cuticular hydrocarbons in Drosophila

Subhash Rajpurohit, Robert Hanus, Vladimir Vrkoslav, Emily L. Behrman, Alan O. Bergland, Dmitri Petrov, Josef Cvacka & Paul S. Schmidt
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions, and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern U.S., as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore,...

Data from: Strategic use of affiliative vocalizations by wild female baboons

Joan B. Silk, Robert M. Seyfarth & Dorothy L. Cheney
Although vocal production in non-human primates is highly constrained, individuals appear to have some control over whether to call or remain silent. We investigated how contextual factors affect the production of grunts given by wild female chacma baboons, Papio ursinus, during social interactions. Females grunted as they approached other adult females 28% of the time. Supporting previous research, females were much more likely to grunt to mothers with young infants than to females without infants....

Data from: Stimulation-based control of dynamic brain networks

Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott T. Grafton, Jean M. Vettel & Danielle S. Bassett
The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbations. To study the system wide impact of regional stimulation, we employ a data-driven computational model of nonlinear brain dynamics to systematically explore the effects of targeted stimulation. Validating predictions from...

Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST

Adrien Rieux & Camilo E. Khatchikian
Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions....

Data from: Parallel effects of the inversion In(3R)Payne on body size across the North American and Australian clines in Drosophila melanogaster

Martin Kapun, Chloe Schmidt, Esra Durmaz, Paul S. Schmidt, Thomas Flatt, P. S. Schmidt, M. Kapun, C. Schmidt, E. Durmaz & T. Flatt
Chromosomal inversions are thought to play a major role in climatic adaptation. In D. melanogaster, the cosmopolitan inversion In(3R)Payne exhibits latitudinal clines on multiple continents. Since many fitness traits show similar clines, it is tempting to hypothesize that In(3R)P underlies observed clinal patterns for some of these traits. In support of this idea, previous work in Australian populations has demonstrated that In(3R)P affects body size but not development time or cold resistance. However, similar data...

Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Alan O. Bergland, Ray Tobler, Josefa Gonzalez, Paul Schmidt, Dimitri A. Petrov & Dmitri Petrov
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America...

Data from: ASSET: analysis of sequences of synchronous events in massively parallel spike trains

Emiliano Torre, Carlos Canova, Michael Denker, Goerge Gerstein, Moritz Helias, Sonja Grün & George Gerstein
With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies, the chance to identify sub-networks involved in coordinated processing increases. Sequences of synchronous spike events (SSEs) constitute one type of such coordinated spiking that propagates activity in a temporally precise manner. The synfire chain was proposed as one potential model for such network processing. Previous work introduced a method for visualization of SSEs in massively parallel spike trains,...

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