54 Works

Data from: High fidelity detection of crop biomass QTL from low-cost imaging in the field

Darshi Banan, Rachel E. Paul, Max J. Feldman, Mark W. Holmes, Hannah Schlake, Ivan Baxter, Hui Jiang & Andrew D.B. Leakey
Field-based, rapid, and non-destructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype-to-phenotype relationships in next-generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field-grown grass crop. Plant area index (PAI) estimated from below-canopy hemispherical images, as well as a suite of thirteen traits assessed by manual...

Data from: How large spatially-explicit optimal reserve design models can we solve now? an exploration of current models’ computational efficiency

Yicheng Wang, Hayri Önal & Qiaoling Fang
Spatially-explicit optimal reserve design models select best sites from a set of candidate sites to assemble nature reserves to protect species (or habitats) and these reserves display certain spatial attributes which are desirable for species. These models are formulated with linear 0-1 programming and solved using standard optimization software, but they were run on different platforms, resulting in discrepant or even conflicting messages with regard to their computational efficiency. A fair and accurate comparison of...

Data from: Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

Jessica R. Brandt, Peter J. Van Coeverden De Groot, Kelsey E. Witt, Paige K. Engelbrektsson, Kristofer M. Hegen, Ripan S. Malhi, Oliver A. Ryder, Alfred L. Roca & Kristofer M Helgen
The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D....

MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide

Vetle I. Torvik
MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide. Prepared by Vetle Torvik 2018-04-05 The dataset comes as a single tab-delimited Latin-1 encoded file (only the City column uses non-ASCII characters), and should be about 3.5GB uncompressed. • How was the dataset created? The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in the first week of October, 2016. Check here for information...

Data from: Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles

Rachel L. Moran, Muchu Zhou, Julian M. Catchen & Rebecca C. Fuller
Behavioral isolation is thought to arise early in speciation due to differential sexual and/or natural selection favoring different preferences and traits in different lineages. Alternatively, behavioral isolation can arise due to reinforcement favoring traits and preferences that prevent maladaptive hybridization. In darters, female preference for male coloration has been hypothesized to drive speciation, because behavioral isolation evolves before F1 inviability. However, as with many long-lived organisms, the fitness of second generation hybrids has not been...

Data from: The role of parasite dispersal in shaping a host-parasite system at multiple evolutionary scales

Andrew Sweet & Kevin Johnson
Parasite dispersal can shape host-parasite interactions at both deep and shallow timescales. One approach to understanding the effects of dispersal is to study parasite lineages that differ in dispersal capability but are from the same group of hosts. We compared phylogenetic and population genetic patterns of wing and body lice from ground-doves. Wing lice are more capable of dispersal than body lice. We sequenced full genomes of individual lice for multiple representatives of several wing...

Data from: Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

Brandon L. Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwarq, , Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, , Muhammad G. Kibriya, Lin S. Chen & Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as methylation QTLs (cis-meQTLs), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing...

Data from: Linking host traits, interactions with competitors, and disease: mechanistic foundations for disease dilution

Alexander T. Strauss, Anna M. Bowling, Meghan A. Duffy, Carla E. Cáceres & Spencer R. Hall
1.The size of disease epidemics remains difficult to predict, especially when parasites interact with multiple species. Traits of focal hosts like susceptibility could directly predict epidemic size, while other traits including competitive ability might shape it indirectly in communities with a ‘dilution effect’. 2.In a dilution effect, diluter taxa can reduce disease by regulating (lowering) the density of focal hosts (i.e., through competition), or by reducing encounters between focal hosts and parasites. However, these dilution...

Data from: Nutrient-specific compensation for seasonal cold stress in a free-ranging temperate colobine monkey

Songtao Guo, Rong Hou, Paul A. Garber, David Raubenheimer, Nicoletta Righini, Weihong Ji, Ollie Jay, Shujun He, Fan Wu, Fangfang Li, Baoguo Li, Song-Tao Guo, Shu-Jun He, Fang-Fang Li, Bao-Guo Li & Wei-Hong Ji
1. Homeostatic responses of animals to environmentally-induced changes in nutrient requirements provide a powerful basis for predictive ecological models, and yet such responses are virtually unstudied in the wild. 2. We tested for macronutrient-specific compensatory feeding responses by free-ranging golden snub-nosed monkeys (Rhinopithecus roxellana) inhabiting high altitude temperate forests where they experience a substantial difference in ambient temperature in cold winters vs. warmer springs. The monkeys had free access to natural foods throughout the year,...

Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt

Srinidhi Balasubramanian, Sotiria Koloutsou-Vakakis & Mark Rood
This dataset contains scripts and data developed as a part of the research manuscript titled “Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt”. This includes (1) Spatial and temporal factors for ammonia emissions from agricultural fertilizer usage developed using the hybrid ISS-DNDC method for the Midwest U.S., (2) CAMx job scripts and outputs of predictions of ambient ammonia and total and speciated PM2.5, (3)...

Gulf survival weather data

Michael Ward
Weather data used in the survival (mark-recapture) analysis of Swainson's Thrushes crossing the Gulf of Mexico

Data from: Undocumented beetle diversity in the Southeastern United States: a case study of the minute clubbed beetles (Coleoptera: Monotomidae)

Thomas C. McElrath & Joseph V. McHugh
Studies of the saproxylic and predatory beetle family Monotomidae (Coleoptera: Cucujoidea) in the southeastern USA increased the known diversity for the family in the state of Georgia by one genus and nine species. Online records of Monotomidae from Georgia increased from 0 to 885. This work highlights the lack of basic diversity information about small beetles that inhabit wood, leaf litter, and other decaying plant matter in this region.

Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates

Benjamin Mattes, Yonglong Dang, Gediminas Greicius, Lilian Tamara Kaufmann, Benedikt Prunsche, Jakob Rosenbauer, Johannes Stegmaier, Ralf Mikut, Suat Özbek, Gerd Ulrich Nienhaus, Alexander Schug, David M. Virshup & Steffen Scholpp
Signaling filopodia, termed cytonemes, are dynamic actin-based membrane structures that regulate the exchange of signaling molecules and their receptors within tissues. However, how cytoneme formation is regulated remains unclear. Here, we show that Wnt/PCP autocrine signaling controls the emergence of cytonemes, and that cytonemes subsequently control paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP signaling leads to induction of cytonemes, which mediate transport...

Constraining a Historical Black Carbon Emission Inventory of U.S. for 1960 to 2000 data

Tianye Sun, Liang Liu, Mark Flanner, Thomas Kirchstetter, Jiao Chaoyi, Chelsea Preble, Wayne Chang & Tami Bond

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Hungry for the queen: honeybee nutritional environment affects worker pheromone response in a life stage‐dependent manner

Alexander Walton, Adam G. Dolezal, Marit A. Bakken & Amy L. Toth
1.Animal nutritional state can profoundly affect behavior, including an individual's tendency to cooperate with others. We investigated how nutritional restriction at different life stages affects cooperative behavior in a highly social species, Apis mellifera honey bees. 2.We found that nutritional restriction affects a worker's queen pheromone response, a behavioral indicator of investment in group vs. individual reproduction. Nutritional restriction at the larval stage led to reduced ovary size and increased queen pheromone response, whereas nutritional...

Data from: Bio-inspired imager improves sensitivity in near-infrared fluorescence image-guided surgery

Missael Garcia, Christopher Edmiston, Timothy York, Radoslav Marinov, Suman Mondal, Nan Zhu, Gail P. Sudlow, Walter J. Akers, Julie Margenthaler, Samuel Achilefu, Rongguang Liang, Mohamed A. Zayed, Marta Y. Pepino & Viktor Gruev
Image-guided surgery can enhance cancer treatment by decreasing, and ideally eliminating, positive tumor margins and iatrogenic damage to healthy tissue. Current state-of-the-art near-infrared fluorescence imaging systems are bulky and costly, lack sensitivity under surgical illumination, and lack co-registration accuracy between multimodal images. As a result, an overwhelming majority of physicians still rely on their unaided eyes and palpation as the primary sensing modalities for distinguishing cancerous from healthy tissue. Here we introduce an innovative design,...

Genni + Ethnea for the Author-ity 2009 dataset

Vetle Torvik
Prepared by Vetle Torvik 2018-04-15 The dataset comes as a single tab-delimited ASCII encoded file, and should be about 717MB uncompressed. • How was the dataset created? First and last names of authors in the Author-ity 2009 dataset was processed through several tools to predict ethnicities and gender, including Ethnea+Genni as described in: Torvik VI, Agarwal S. Ethnea -- an instance-based ethnicity classifier based on geocoded author names in a large-scale bibliographic database. International Symposium...

Data from: Comparing the sampling performance of sound recorders versus point counts in bird surveys: a meta-analysis

Kevin Darras, Péter Batáry, Brett Furnas, Antonio Celis-Murillo, Steven L. Van Wilgenburg, Yeni Ariyati Mulyani & Teja Tscharntke
1) Autonomous sound recording is a promising survey method for birds and other vocalising terrestrial wildlife. However, while there are clear advantages of sound recording methods over classical point counts conducted by humans, it has been difficult to quantitatively assess how they compare in their sampling performance. Quantitative comparisons of bird species richness between acoustic recorders and human point counts have previously been hampered by the differing and often unknown detection ranges among sampling methods....

Castilleja coccinea fruit set and seed set data from Illinois Beach State Park

Eun Sun Kim, David N. Zaya, Jeremie B. Fant & Mary V. Ashley
These data include information on a field experiment on Castilleja coccinea (L.) Spreng., scarlet Indian paintbrush (Orobanchaceae). There is intraspecific variation in scarlet Indian paintbrush in the color of the bracts surrounding the flowers. Two bract color morphs were included in this study, the scarlet and yellow morphs. The experiment was conducted at Illinois Beach State Park in 2012. The aim of the work was to compare the color morphs with regard to 1) self-compatibility,...

Data from: Phoretic dispersal influences parasite population genetic structure

Emily DiBlasi, Kevin P. Johnson, Sydney A. Stringham, Angela N. Hansen, Andrew B. Beach, Dale H. Clayton & Sarah E. Bush
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift, and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be done in the proper comparative context. Here we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of...

Data from: Parasite rearing and infection temperatures jointly influence disease transmission and shape seasonality of epidemics

Marta S. Shocket, Daniela Vergara, Andrew J. Sickbert, Jason M. Walsman, Alexander T. Strauss, Jessica L. Hite, Meghan A. Duffy, Carla E. Cáceres & Spencer R. Hall
Seasonal epidemics erupt commonly in nature and are driven by numerous mechanisms. Here, we suggest a new mechanism that could determine the size and timing of seasonal epidemics: rearing environment changes the performance of parasites. This mechanism arises when the environmental conditions in which a parasite is produced impact its performance—independently from the current environment. To illustrate the potential for ‘rearing effects’, we show how temperature influences infection risk (transmission rate) in a Daphnia-fungus disease...

Tetris artificial spin ice kinetics

Yuyang Lao & Peter Schiffer
This is the experimental data of tetris artificial spin ice. The islands are made of Permalloy materials with size of 170 nm by 470 nm by 2.5 nm. The systems are measured at a temperature where the islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the dataset can be found in the file Note.txt and Tetris_data_list.xlsx Note: 2 files name bl11_teris600_033 and bl11_tetris600_2_135 are not...

Lewis, Quinn; Bruce, Rhoads (2018): Data from: LSPIV Measurements of Two-dimensional Flow Structure in Streams using Small Unmanned Aerial Systems: Parts 1 and 2

Quinn Lewis & Rhoads Bruce
These data are for two companion papers on use of LSPIV obtained from UAS (i.e. drones) to measure flow structure in streams. The LSPIV1 folder contains spreadsheet data used in each case referred to in Table 1 in the manuscript. In the spreadsheets, there is a cell that denotes which figure was constructed with which data. The LSPIV2 folder contains spreadsheets with data used for the constructed figures, and are labeled by figure.

A Crawl of the Mobile Web Measuring Sensor Accesses

Anupam Das, Gunes Acar, Nikita Borisov & Amogh Pradeep
This dataset is the result of three crawls of the web performed in May 2018. The data contains raw crawl data and instrumentation captured by OpenWPM-Mobile, as well as analysis that identifies which scripts access mobile sensors, which ones perform some of browser fingerprinting, as well as clustering of scripts based on their intended use. The dataset is described in the included README.md file; more details about the methodology can be found in our ACM...

Registration Year

  • 2018

Resource Types

  • Dataset
  • Text


  • University of Illinois at Urbana Champaign
  • University of Illinois
  • North West Agriculture and Forestry University
  • Zhejiang University
  • Sir Run Run Shaw Hospital
  • Huazhong University of Science and Technology
  • First Affiliated Hospital of Guangzhou Medical University
  • Fudan University
  • Chongqing Medical University
  • University of Warwick