30 Works

Dataset associated with \"Volcanic ash ice nucleation activity is variably reduced by aging in water and sulfuric acid: the effects of leaching, dissolution, and precipitation\"

William Fahy, Elena Maters, Rona Giese-Miranda, Michael P. Adams, Leif G. Jahn, Ryan Sullivan & Benjamin Murray
Volcanic ash nucleates ice when immersed in supercooled water, giving it the potential to influence weather and climate from local to global scales. However, the ice nucleation activity (INA) of ash can be modified by interaction with various chemical species during atmospheric transport. In the experimental study associated with this dataset, we show that the INA of two mineralogically distinct ash samples from Fuego and Astroni volcanoes is variably reduced when immersed in water or...

Data from: The distribution of income is worse than you think: including pollution impacts into measures of income inequality

Nicholas Z. Muller, Peter Hans Matthews & Virginia Wiltshire-Gordon
This paper calculates the distribution of an adjusted measure of income that deducts damages due to exposure to air pollution from reported market income in the United States from 2011 to 2014. The Gini coefficient for this measure of adjusted income is 0.682 in 2011, as compared to 0.482 for market income. By 2014, we estimate that the Gini for adjusted income fell to 0.646, while the market income Gini did not appreciably change. The...

Data from: Selection, periodicity and potential function for highly iterative Palindrome-1 (HIP1) in cyanobacterial genomes

Minli Xu, Jeffrey G. Lawrence & Dannie Durand
Highly Iterated Palindrome 1 (HIP1, GCGATCGC) is hyper-abundant in most cyanobacterial genomes. In some cyanobacteria, average HIP1 abundance exceeds one motif per gene. Such high abundance suggests a significant role in cyanobacterial biology. However, 20 years of study have not revealed whether HIP1 has a function, much less what that function might be. We show that HIP1 is 15-300 fold over-represented in genomes analysed. More importantly, HIP1 sites are conserved both within and between open...

Data from: Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels

Thomas J. Hinton, Quentin Jallerat, Rachelle N. Palchesko, Joon Hyung Park, Martin S. Grodzicki, Hao-Jan Shue, Mohamed H. Ramadan, Andrew R. Hudson & Adam W. Feinberg
We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and...

Ambiguity in medical concept normalization: An analysis of types and coverage in electronic health record datasets

Denis Newman-Griffis, Guy Divita, Bart Desmet, Ayah Zirikly, Carolyn Rosé & Eric Fosler-Lussier
Objective: Normalizing mentions of medical concepts to standardized vocabularies is a fundamental component of clinical text analysis. Ambiguity—words or phrases that may refer to different concepts—has been extensively researched as part of information extraction from biomedical literature, but less is known about the types and frequency of ambiguity in clinical text. This study characterizes the distribution and distinct types of ambiguity exhibited by benchmark clinical concept normalization datasets, in order to identify directions for advancing...

Data for: Pendulum-based measurements reveal impact dynamics at the scale of a trap-jaw ant

Justin Jorge, Sarah Bergbreiter & Sheila Patek
Small organisms can produce powerful, sub-millisecond impacts by moving tiny structures at high accelerations. We developed and validated a pendulum device to measure the impact energetics of microgram-sized trap-jaw ant mandibles accelerated against targets at 105 m s-2. Trap-jaw ants (Odontomachus brunneus; 19 individuals; 212 strikes) were suspended on one pendulum and struck swappable targets that were either attached to an opposing pendulum or fixed in place. Mean post-impact kinetic energy (energy from strike converted...

An annotated set of audio recordings of Eastern North American birds containing frequency, time, and species information

Lauren M. Chronister, Tessa A. Rhinehart, Aidan Place & Justin Kitzes
Acoustic recordings of soundscapes are an important category of audio data which can be useful for answering a variety of questions, and an entire discipline within ecology, dubbed “soundscape ecology,” has risen to study them. Bird sound is often the focus of studies of soundscapes due to the ubiquitousness of birds in most terrestrial environments and their high vocal activity. Autonomous acoustic recorders have increased the quantity and availability of recordings of natural soundscapes while...

Dissociable use-dependent processes for volitional goal-directed reaching

Jonathan Tsay, Hyosub Kim, Arohi Saxena, Darius Parvin, Timothy Verstynen & Richard Ivry
Repetition of a specific movement biases subsequent actions towards the practiced movement, a phenomenon known as use-dependent learning (UDL). Recent experiments that impose strict constraints on planning time have revealed two sources of use-dependent biases, one arising from dynamic changes occurring during motor planning and another reflecting a stable shift in motor execution. Here, we used a distributional analysis to examine the contribution of these biases in reaching. To create the conditions for UDL, the...

Data from: Activation recovery interval imaging of premature ventricular contraction

Ting Yang, Long Yu, Qi Jin, Liqun Wu & Bin He
Dispersion of ventricular repolarization due to abnormal activation contributes to the susceptibility to cardiac arrhythmias. However, the global pattern of repolarization is difficult to assess clinically. Activation recovery interval (ARI) has been used to understand the properties of ventricular repolarization. In this study, we developed an ARI imaging technique to noninvasively reconstruct three-dimensional (3D) ARI maps in 10 premature ventricular contraction (PVC) patients and evaluated the results with the endocardial ARI maps recorded by a...

Data from: Does hugging provide stress-buffering social support? A study of susceptibility to upper respiratory infection and illness

Sheldon Cohen, Denise Janicki-Deverts, Ronald B. Turner & William J. Doyle
Perceived social support has been hypothesized to protect against the pathogenic effects of stress. How such protection might be conferred, however, is not well understood. Using a sample of 404 healthy adults, we examined the roles of perceived social support and received hugs in buffering against interpersonal stress-induced susceptibility to infectious disease. Perceived support was assessed by questionnaire, and daily interpersonal conflict and receipt of hugs were assessed by telephone interviews on 14 consecutive evenings....

ANI-FDA Drugs Archive

Olexandr Isayev
The dataset files contain low-energy conformers and tautomers of 6,433 FDA approved & investigational drugs. A collection consists of 32,036 tautomeric structures and ~3M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). [DOI: 10.26434/chemrxiv.11819268.v1 ] For each conformer we list total energy, relative energy, and dipole-consistent partial atomic charges....

Data from: Visual environment, attention allocation, and learning in young children: when too much of a good thing may be bad

Anna V. Fisher, Karrie E. Godwin & Howard Seltman
A large body of evidence supports the importance of focused attention for encoding and task performance. Yet young children with immature regulation of focused attention are often placed in elementary-school classrooms containing many displays that are not relevant to ongoing instruction. We investigated whether such displays can affect children’s ability to maintain focused attention during instruction and to learn the lesson content. We placed kindergarten children in a laboratory classroom for six introductory science lessons,...

Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

Pengcheng Zhou, Shanna L. Resendez, Jose Rodriguez-Romaguera, Jessica C. Jimenez, Shay Q. Neufeld, Andrea Giovannucci, Johannes Friedrich, Eftychios A Pnevmatikakis, Garret D. Stuber, Rene Hen, Mazen A. Kheirbek, Bernardo L. Sabatini, Robert E. Kass & Liam Paninski
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We...

Data from: Muscle-tendon mechanics explain unexpected effects of exoskeleton assistance on metabolic rate during walking

Rachel W. Jackson, Christopher L. Dembia, Scott L. Delp & Steve H. Collins
The goal of this study was to gain insight into how ankle exoskeletons affect the behavior of the plantarflexor muscles during walking. Using data from previous experiments, we performed electromyography-driven simulations of musculoskeletal dynamics to explore how changes in exoskeleton assistance affected plantarflexor muscle–tendon mechanics, particularly for the soleus. We used a model of muscle energy consumption to estimate individual muscle metabolic rate. As average exoskeleton torque was increased, while no net exoskeleton work was...

Causal links between parietal alpha activity and spatial auditory attention

Yuqi Deng, Robert MG Reinhart, Inyong Choi & Barbara G Shinn-Cunningham
Both visual and auditory spatial selective attention result in lateralized alpha (8-14 Hz) oscillatory power in parietal cortex: alpha increases in the hemisphere ipsilateral to attentional focus. Brain stimulation studies suggest a causal relationship between parietal alpha and suppression of the representation of contralateral visual space. However, there is no evidence that parietal alpha controls auditory spatial attention. Here, we performed high definition transcranial alternating current stimulation (HD-tACS) on human subjects performing an auditory task...

Data from: The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning

Eghbal A. Hosseini, Katrina P. Nguyen & Wilsaan M. Joiner
Motor adaptation paradigms provide a quantitative method to study short-term modification of motor commands. Despite the growing understanding of the role motion states (e.g., velocity) play in this form of motor learning, there is little information on the relative stability of memories based on these movement characteristics, especially in comparison to the initial adaptation. Here, we trained subjects to make reaching movements perturbed by force patterns dependent upon either limb position or velocity. Following training,...

ANI-CAS Antiviral Archive

Olexandr Isayev
The dataset files contain low-energy conformers and tautomers for 20,306 from the CAS Antiviral database. Original ~50K molecules were filtered for duplicates and drug-likeness. A collection consists of 67,167 tautomeric structures and ~6.6M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. [DOI: 10.26434/chemrxiv.11819268.v1 ] The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). For each conformer we list...

CRAWDAD dataset cmu/spring2021 (v. 2021-10-08)

Dimitrios-Georgios Akestoridis & Patrick Tague
This Carnegie Mellon University dataset contains Zigbee packets that were captured during energy depletion attack experiments. More specifically, the contributors used Zigator to deploy two stand-alone WIDS sensors and capture Zigbee packets, while HiveGuard was used to archive the pcap files that were generated by the WIDS sensors. Each WIDS sensor corresponded to a Raspberry Pi 3 Model B+ that was equipped with an ATUSB in monitor mode. Four experiments were conducted to test four...

Data from: Simultaneously uncovering the patterns of the brain regions involved in different story reading subprocesses

Leila Wehbe, Brian Murphy, Partha Talukdar, Alona Fyshe, Aaditya Ramdas & Tom Mitchell
Story understanding involves many perceptual and cognitive subprocesses, from perceiving individual words, to parsing sentences, to understanding the relationships among the story characters. We present an integrated computational model of reading that incorporates these and additional subprocesses, simultaneously discovering their fMRI signatures. Our model predicts the fMRI activity associated with reading arbitrary text passages, well enough to distinguish which of two story segments is being read with 74% accuracy. This approach is the first to...

Data from: Women’s preference for masculine traits is disrupted by images of male-on-female aggression

Yaoran Li, Drew H. Bailey, Benjamin Winegard, David A. Puts, Lisa L. M. Welling & David C. Geary
Women’s preferences for men’s masculinized faces and voices were assessed after women (n = 331) were primed with images of male-on-male aggression, male-on-female aggression, pathogens, and neutral scenes. Male-on-male aggression and pathogen primes were associated with increased preference for masculine traits, but the same effect emerged in the neutral condition. We show the increased preference for masculine traits was due to repeated exposure to these traits, not the priming images themselves. Images of male-on-female aggression...

Data from: Beyond novelty effect: a mixed-methods exploration into the motivation for long-term activity tracker use

Grace Shin, Yuanyuan Feng, Mohammad Hossein Jarrahi & Nicci Gafinowitz
Objectives: Activity trackers hold the promise to support people in managing their health through quantified measurements about their daily physical activities. Monitoring personal health with quantified activity tracker-generated data provides patients with an opportunity to self-manage their health. Many activity tracker user studies have been conducted within short time frames, however, which makes it difficult to discover the impact of the activity tracker’s novelty effect or the reasons for the device’s long-term use. This study...

Mouse substantia nigra responses to optogenetic stimulation of projections from striatum and globus pallidus

Ryan Phillips, Ian Rosner, Aryn Gittis & Jonathan Rubin
As a rodent basal ganglia (BG) output nucleus, the substantia nigra pars reticulata (SNr) is well positioned to impact behavior. SNr neurons receive GABAergic inputs from the striatum (direct pathway) and globus pallidus (GPe, indirect pathway). Dominant theories of action selection rely on these pathways' inhibitory actions. Yet, experimental results on SNr responses to these inputs are limited and include excitatory effects. Our study combines experimental and computational work to characterize, explain, and make predictions...

Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Minseung Choi, Diane P. Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger & Charles D. Laird
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity...

Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

Chathurani Ranathunge, Gregory L. Wheeler, Melody E. Chimahusky, Meaghan M. Kennedy, Jesse I. Morrison, Brian S. Baldwin, Andy D. Perkins & Mark E. Welch
The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted...

Data from: Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids?

Heather E. Dwyer, Marie Jasieniuk, Miki Okada & Arthur M. Shapiro
Gene flow and hybridization among species dramatically affect our understanding of the species as a biological unit, species relationships, and species adaptations. In North American Colias eurytheme and Colias eriphyle, there has been historical debate over the extent of hybridization occurring and the identity of phenotypically intermediate individuals as genetic hybrids. This study assesses the population structure of these two species to measure the extent of hybridization and the genetic identity of phenotypic intermediates as...

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