cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7924/r4dn45v9g
title: Data from: Drones and deep learning produce accurate and efficient monitoring of large-scale seabird colonies

description: Population monitoring in some colonial seabirds is often complicated by the large size of colonies, remote locations, and by close inter- and intra-species aggregation. While drones have been successfully used to monitor large inaccessible colonies, the vast amount of imagery collected introduces a data analysis bottleneck. Convolutional neural networks are evolving as a prominent means for object detection and can be applied to drone imagery for population monitoring. In this study, we explore the use of these technologies to increase capabilities for seabird monitoring by using convolutional neural networks to detect and enumerate Black-browed Albatross (Thalassarche melanophris) and Southern Rockhopper Penguins (Eudyptes c.chrysocome) at one of their largest breeding colonies, the Falkland (Malvinas) Islands. Our results show these techniques have great potential for seabird monitoring at significant and spatially complex colonies, producing accuracies of 97.66% and 87.16% with ninety percent of automated counts being within 5% of manual counts. The results of this study imply our methods are a viable population assessment tool, presenting many opportunities to reduce manual labor, cost, and human error.

This dataset contains all relevant drone imagery and associated training, testing, and validation labels for the creation of a convolutional neural network to detect seabirds.
DOI: 10.7924/r4rn36833
title: Data from: The cancer microbiome atlas (TCMA): A pan-cancer comparative analysis to distinguish organ-associated microbiota from contaminants

description: Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated with original TCGA samples. "Mixed-evidence"species can be further distinguished by gene copy and nucleotide variants. We thus present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to discovery of prognostic species and blood signatures of mucosal barrier injuries, and enabled systematic matched microbe-host multi-omics analyses, which will help guide future studies of the microbiome's role in human health and disease.
DOI: 10.7924/r4bk1dq8n
title: Data from: The control of colonic motility using electrical stimulation to modulate enteric neural circuitry

description: Electrical stimulation of the enteric nervous system (ENS) is an attractive approach to modify gastrointestinal transit. Colonic motor complexes (CMCs) occur with a periodic rhythm, but the ability to elicit a premature CMC depends, at least in part, upon the intrinsic refractory properties of the ENS, which are presently unknown. The objectives of this study were to record myoelectric complexes (MCs, the electrical correlates of CMCs) in the smooth muscle and (i) determine the refractory periods of MCs, (ii) inform and evaluate closed-loop stimulation to repetitively evoke MCs, and (iii) identify stimulation methods to suppress MC propagation. We dissected the colon from male and female C57BL/6 mice, preserving the integrity of intrinsic circuitry while removing the extrinsic nerves, and measured properties of spontaneous and evoked MCs in vitro. Hexamethonium abolished spontaneous and evoked MCs, confirming the necessary involvement of the ENS for electrically-evoked MCs.  Electrical stimulation reduced the mean interval between evoked and spontaneous CMCs (24.6 ± 3.5 vs 70.6 ± 15.7 s, p = 0.0002, n = 7). The absolute refractory period was 4.3 s (95% CI = 2.8 - 5.7 s, R2 = 0.7315, n = 8). Electrical stimulation lead to arrest of fluid distention-evoked propagating MC, and following cessation of stimulation propagation resumed at an increased velocity (n = 9). The timing parameters of electrical stimulation increased the rate of evoked MCs, including the duration of entrained MCs, and provide insights into timing considerations for designing neuromodulation strategies to treat colonic dysmotility.
DOI: 10.7924/r4gb24j1x
title: Data from: Range-wide variations in common milkweed traits and their effect on monarch larvae

description: ABSTRACT Premise. Leaf economic spectrum (LES) theory has historically been employed to inform vegetation models of ecosystem processes, but largely neglects intraspecific variation and biotic interactions. We attempt to integrate across environment-plant trait-herbivore interactions within a species at a range-wide scale. 

Methods. We measured traits in 53 populations spanning the range of common milkweed (Asclepias syriaca) and used a common garden to determine the role of environment in driving patterns of intraspecific variation. We used a feeding trial to determine the role of plant traits in monarch (Danaus plexippus) larval development. 

Results. Trait-trait relationships largely follow interspecific patterns in LES theory and persist in a common garden when individual traits change. Common milkweed shows intraspecific variation and biogeographic clines in traits. Clines do not persist in a common garden. Larvae ate more and grew larger when fed plants with more nitrogen. A longitudinal environmental gradient in precipitation corresponds to a resource gradient in plant nitrogen which produces a gradient in larvae performance. 

Conclusions. Biogeographic patterns in common milkweed traits can sometimes be predicted from LES, are largely driven by environmental conditions, and have consequences for monarch larval performance. Changes to nutrient dynamics of landscapes with common milkweed could potentially influence monarch population dynamics. We show how biogeographic trends in intraspecific variation can influence key ecological interactions, especially in common species with large distributions.
DOI: 10.7924/r4gq6z428
title: Data from: Distal conformational locks on ferrocene mechanophores guide reaction pathways for increased mechanochemical reactivity

description: When incorporated into polymeric materials, mechanophores can be used to produce strain-dependent covalent chemical responses, including stress-strengthening, stress-sensing and network remodeling. In general, it is desirable for mechanophores to be highly inert in the absence of force but highly reactive under applied tension. Metallocenes possess remarkable combinations of force-free stability and force-coupled reactivity, but the mechanistic basis of this reactivity remains largely unexplored. Here, we use single molecule force spectroscopy to probe the mechanical reactivity of a series of ferrocenophanes and elucidate the mechanistic factors that dictate their mechanochemical activity. The force-coupled rate of cyclopentadiene (Cp) dissociation among various ferrocene derivatives varies by several orders of magnitude at ~1 nN, and the differences in reactivity are not correlated with ring strain in the reactants, but the extent of rotational realignment of the two Cp ligands. Mechanophores with pulling points that are conformationally restricted by distal attachments to an eclipsing orientation are most labile, whereas conformationally unrestricted ligands reorient under force to effectively superpose "catch bond" like contributions onto the overall mechanically assisted dissociation reaction. The ability to program the mechanism of ferrocene dissociation to proceed through ligand "peeling", as opposed to the more conventional "shearing" mechanism of the parent ferrocene, leads to enhanced macroscopic, multi-responsive behavior including mechanochromism and force-induced crosslinking in ferrocenophane-containing polymers.
DOI: 10.7924/r44m97j8v
title: Data from: Lightning Initiation from Fast Negative Breakdown is Led by Positive Polarity Dominated Streamers

description: Evidence of positive polarity dominated streamers preceding fast negative breakdown and of simultaneous positive and negative polarity streamer development in lightning initiation is reported. Observations of lightning initiation in the form of fast negative breakdown have remained a puzzle since their discovery, because simulations of lightning initiation have shown that negative streamers are not produced in virgin air without simultaneous positive streamers. Here, high bandwidth (>200 MHz) and fast time resolution (<0.5 microseconds) very high frequency (VHF) interferometry is used to examine the detailed development of fast breakdown in the first several microseconds of the event. We find downward motion of the VHF emissions for the first 1-2 microseconds, even in events that quickly become dominated by negative breakdown. This indicates that positive streamer development forms first or at least simultaneously with negative streamers. Further evidence for this picture comes from observations of mixed fast breakdown, which begins and ends as fast positive breakdown but is interrupted by a burst of upward-moving negative streamer emission. The overall trajectory of the positive breakdown during such mixed events indicates that the positive streamers continuously propagate downward even during the burst of strong negative breakdown. These observations indicate that even when negative streamers dominate the overall VHF emissions, both positive and negative streamers are likely propagating simultaneously from the initiation point. These findings on the structure and dynamics of fast breakdown provide key new insight to our understanding of lightning initiation.
DOI: 10.7924/r4c53n875
title: Data and scripts from: A structure database and in silico spectral library for comprehensive suspect screening of per- and polyfluoroalkyl substances (PFASs) in environmental media by high-resolution mass spectrometry

description: Per and polyfluoroalkyl substances (PFASs) are an important class of organic pollutants. Many diverse PFASs are used in commerce and most are not amenable to conventional targeted chemical analysis due to lack of reference standards. Therefore, methods for elucidating the chemical structure of previously unreported or unexpected PFASs in the environment rely exten-sively on high-resolution mass spectrometry (HRMS). High-throughput structure identification by HRMS is hindered by a lack of PFAS molecular databases and tandem mass spectral libraries. Here we report a new approach for generating an envi-ronmentally-relevant PFAS molecular database constructed from curated structure lists and biotic/abiotic in silico predicted transformation products.  Further, we have generated a predicted tandem mass spectral library using computational mass spectrometry tools. Results demonstrate the utility of the generated database and approach for identifying PFASs in HRMS-enabled suspect- and non-target screening studies.
DOI: 10.7924/r4wd3x28b
title: Data and scripts from: A Bayesian approach for predicting photogrammetric uncertainty in morphometric measurements derived from UAS

description: Increasingly, drone-based photogrammetry has been used to measure size and body condition changes in marine megafauna. A broad range of platforms, sensors, and altimeters are being applied for these purposes, but there is no unified way to predict uncertainty associated with photogrammetric measurements across this methodological spectrum. As such, it is difficult to make robust comparisons across studies, disrupting collaborations amongst researchers using platforms with varying levels of measurement accuracy.

We used an experimental approach to train a Bayesian statistical model using a known-sized object floating at the water’s surface to quantify how measurement error scales with altitude for several different UAS platforms equipped with different cameras, focal length lenses, and altimeters. We then use the fitted model to predict the length distributions of unknown-sized humpback whales and assess how predicted uncertainty can affect quantities derived from photogrammetric measurements such as the age class of an animal.

This statistical framework jointly estimates errors from altitude and length measurements and accounts for altitudes measured with both barometers and laser altimeters while incorporating errors specific to each. This Bayesian model outputs a posterior predictive distribution of measurement uncertainty around length measurements and allows for the construction of credible intervals to define measurement uncertainty, which allows one to make probabilistic statements and stronger inferences pertaining to morphometric features critical for understanding life history patterns and potential impacts from anthropogenically altered habitats. 

The present study provides a robust and coherent methodology for determining measurement error associated with different UAS and sensor platforms and a model for predicting measurement uncertainty of unknown-sized objects, such as whales and other marine megafauna. This framework can guide researchers in determining the most appropriate UAS and sensor platforms needed to answer specific research questions, as well as facilitate collaboration amongst researchers collecting photogrammetric imagery with different levels of measurement accuracy.
DOI: 10.7924/r4b27x11m
title: Data and scripts from: Mechanism and function of root circumnutation

description: Early root growth is critical for plant establishment and survival. We have identified a molecular pathway required for helical root tip movement known as circumnutation. Here we report a multiscale investigation of the regulation and function of this phenomenon. We identify key cell signaling events comprising interaction of the ethylene, cytokinin, and auxin hormone signaling pathways. We identify the gene Oryza sativa HISTIDINE KINASE-1 (HK1), as well as the auxin influx carrier gene OsAUX1, as essential regulators of this process in rice. Robophysical modelling and growth challenge experiments indicate circumnutation is critical for seedling establishment in rocky soil, consistent with the long-standing hypothesis that root circumnutation facilitates growth past obstacles. Thus, the integration of robotics, physics and biology has elucidated the functional importance of root circumnutation and uncovered the molecular mechanisms underlying its regulation.
DOI: 10.7924/r4pg1qw8p
title: Data from: Coastal protection and blue carbon mapping for six mid-Atlantic states

description: Coastal habitats’ ability to store carbon and protect natural and human communities from hazards makes them valuable assets in state and community efforts to enhance coastal resilience and support climate mitigation. The Nicholas Institute collaborated with six eastern seaboard states (North Carolina, Virginia, Maryland, Delaware, New Jersey, and New York) on a U.S. Climate Alliance-funded project to prioritize coastal habitats based on their contributions to coastal protection and blue carbon storage. 

The Nicholas Institute team completed spatial modeling that considers current  coastal habitats and potential future changes to these habitats due to sea level rise.  We assess habitats’ ability to store carbon long-term and protect vulnerable ecological and human communities into the future.
DOI: 10.7924/r47d2xg50
title: Data and Code from: T Cell-Depleted Cultured Pediatric Thymus Tissue as a Model for Some Aspects of Human Age-Related Thymus Involution

description: This dataset contains the QuantiGene data and the code used to analyze it, as published in Hale, LP, et al. T Cell-Depleted Cultured Pediatric Thymus Tissue as a Model for Some Aspects of Human Age-Related Thymus Involution, GeroScience (accepted November 2020). 

Abstract: Human age-related thymus involution is characterized by loss of developing thymocytes and the thymic epithelial network that supports them, with replacement by adipose tissue. The mechanisms that drive these changes are difficult to study in vivo due to constant trafficking to and from the thymus. We hypothesized that the loss of thymocytes that occurs during human thymic organ cultures could model some aspects of thymus involution and begin to identify mechanisms that drive age related changes in the thymic microenvironment. Potential mechanistically important candidate molecules were initially identified by screening conditioned media from human thymus organ cultures using antibody microarrays. These candidates were further validated using cultured tissue extracts and conditioned media. Results were compared with gene expression studies from a panel of well-characterized (non-cultured) human thymus tissues from human donors aged 5 days to 78 years. L-selectin released into conditioned media was identified as a biomarker for the content of viable thymocytes within cultured thymus.

Levels of the cheamokines CCL21 and CXCL12, likely produced by surviving thymic epithelial cells, increased markedly in conditioned media as thymocytes were lost during culture. Native non-cultured thymus from adults older than 18 years also showed a strong trend toward increased CCL21 expression, in conjunction with significant decreases in thymocyte-related mRNAs compared with thymus from subjects younger than 18 years. Together, these findings demonstrate that use of postnatal human thymus organ cultures can model some aspects of human age-related thymic involution.
DOI: 10.7924/r4765hq57
title: Primary and recurrent (second-look surgery) serous epithelial ovarian cancers Illumina Infinium HumanMethylation450 BeadChip data

description: This dataset was generated from 16 primary and matched recurrent ovarian cancer tissue sets from patients with stage III/IV serous epithelial OC. The primary tumor specimens were collected at the time of initial debulking surgery. Recurrent tumor samples were obtained from the same patients during “second-look” surgeries. Samples were obtained and data was generated after patients provided written informed consent under protocols approved by the Duke University Institutional Review Board.
DOI: 10.7924/r4pn94v5h
title: Data from: Non-monotonic kilohertz frequency neural block thresholds arise from amplitude- and frequency-dependent charge imbalance

description: Reversible block of nerve conduction using kilohertz frequency electrical signals has substantial potential for treatment of disease. However, the ability to block nerve fibers selectively is limited by poor understanding of the relationship between waveform parameters and the nerve fibers that are blocked. Previous in vivo studies reported non-monotonic relationships between block signal frequency and block threshold, suggesting the potential for fiber-selective block. However, the mechanisms of non-monotonic block thresholds were unclear, and these findings were not replicated in a subsequent in vivo study. We used high-fidelity computational models and in vivo experiments in anesthetized rats to show that non-monotonic threshold-frequency relationships do occur, that they result from amplitude- and frequency-dependent charge imbalances that cause a shift between kilohertz frequency and direct current block regimes, and that these relationships can differ across fiber diameters such that smaller fibers can be blocked at lower thresholds than larger fibers. These results reconcile previous contradictory studies, clarify the mechanisms of interaction between kilohertz frequency and direct current block, and demonstrate the potential for selective block of small fiber diameters.
DOI: 10.7924/r4q23zg65
title: Data and scripts from: A structure database and in silico spectral library for comprehensive suspect screening of per- and polyfluoroalkyl substances (PFASs) in environmental media by high-resolution mass spectrometry

description: Per and polyfluoroalkyl substances (PFASs) are an important class of organic pollutants. Many diverse PFASs are used in commerce and most are not amenable to conventional targeted chemical analysis due to lack of reference standards. Therefore, methods for elucidating the chemical structure of previously unreported or unexpected PFASs in the environment rely exten-sively on high-resolution mass spectrometry (HRMS). High-throughput structure identification by HRMS is hindered by a lack of PFAS molecular databases and tandem mass spectral libraries. Here we report a new approach for generating an envi-ronmentally-relevant PFAS molecular database constructed from curated structure lists and biotic/abiotic in silico predicted transformation products.  Further, we have generated a predicted tandem mass spectral library using computational mass spectrometry tools. Results demonstrate the utility of the generated database and approach for identifying PFASs in HRMS-enabled suspect- and non-target screening studies.
DOI: 10.7924/r4ft8mt51
title: Research vessel Dan Moore station logs, 1968-1981

description: The R/V DAN MOORE, an 85 foot steel stern trawler, collected over 4,400 samples during service with the North Carolina Division of Marine Fisheries (NC DMF), 1968-1981.  The vessel’s purpose was to conduct applied research to enable the Division to manage and develop coastal fisheries resources for the benefit of all North Carolinians.  Objectives of individual cruises included gear tests, fish tagging, relative abundance and distribution surveys, biological investigations (i.e., age and growth), bottom type surveys, and many others.  Information collected consisted of location, environmental, and catch data.  Results of cruises were summarized in bulletins from 1968-1974.  Complete cruise reports describing methods and results were filed for the remaining cruises.
[Source of this blurb:    Biological Program Documentation
Program Series 700’s R/V Dan Moore Cruises
Masterfile:  NER.NMA.NMA700-1.DNMOORE
Biologist:  Frank Holland]
DOI: 10.7924/r41j9fq8z
title: Research vessel Dan Moore station logs, 1968-1981

description: The R/V DAN MOORE, an 85 foot steel stern trawler, collected over 4,400 samples during service with the North Carolina Division of Marine Fisheries (NC DMF), 1968-1981.  The vessel’s purpose was to conduct applied research to enable the Division to manage and develop coastal fisheries resources for the benefit of all North Carolinians.  Objectives of individual cruises included gear tests, fish tagging, relative abundance and distribution surveys, biological investigations (i.e., age and growth), bottom type surveys, and many others.  Information collected consisted of location, environmental, and catch data.  Results of cruises were summarized in bulletins from 1968-1974.  Complete cruise reports describing methods and results were filed for the remaining cruises.
[Source of this blurb:    Biological Program Documentation
Program Series 700’s R/V Dan Moore Cruises
Masterfile:  NER.NMA.NMA700-1.DNMOORE
Biologist:  Frank Holland]