cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1g8q3f4
title: Data from: Proximity to roads disrupts rodents’ contributions to seed dispersal services and subsequent recruitment dynamics

description: 1. Seed dispersal and subsequent recruitment dynamics play a crucially
 important role in regulating species coexistence and structuring tree
 diversity in diverse forests. Wildlife, which can dually shape the tree
 recruitment process by simultaneously functioning as natural enemies and
 seed dispersers, are undergoing widespread changes in population and
 behaviour due to the detrimental effects of expanding global road
 networks. However, the impact of these changes on recruitment dynamics
 through the alteration of seed dispersal processes remains understudied.
 2. Here, we assessed how roads affect animal-mediated recruitment dynamics
 from the seed to adult stages of trees using a ubiquitous vertebrate-seed
 model: rodents and acorns. To quantify the degree to which proximity to a
 road alters seed dispersal and regulates subsequent recruitment dynamics,
 we conducted seed dispersal and predation experiments, and investigated
 the natural recruitment of a dominant tree species (Quercus aliena) from
 September 2009 to July 2012 in a subtropical forest of central China. 3.
 Roads caused a decreased seed dispersal distance and increasing larder
 hoarding, demonstrating a weakened contribution of rodents to seed
 dispersal services. These patterns were stronger in the masting year than
 in the non-masting year. Correspondingly, seedlings, saplings, and adult
 trees had higher densities near roads than far from roads. Near roads,
 recruit transition rates (i.e., seedling-to-sapling and
 sapling-to-juvenile) were low, and the influential strength of conspecific
 adult density was weakened over these recruit transitions, indicating that
 space limitation and lottery competition, not conspecific negative
 density-dependent effects, approximately determined the near-road
 recruitment process. Furthermore, most adults near roads were young, and
 their ages matched the road ages. 4. Synthesis. Roads diminished
 animal-mediated seed dispersal services and disrupted subsequent
 recruitment dynamics in Q. aliena populations, thus weakening the key
 process promoting diversity in forest ecosystems. Given that these
 animal-regulated roles in recruitment dynamics are widespread stabilizing
 forces for tree coexistence, our findings suggest that the ubiquity of
 roads and their continued expansion will contribute to the increase in
 forests dominated by a relatively low number of species. Consequently, the
 growing expansion of road networks will ultimately cause profound changes
 in community composition and structure across diverse forests worldwide.
description: Rodent
 communityrodent community
 dataSeed
 fateseed fate
 dataRecruitment
 dynamicsrecruitment
 dataREADMEThis file explains all
 of the variables in each of the datasets that accompany: Chen W, Zhong J,
 Carson W, Tang Z, Xie Z, Sun S, Zhou Y. Proximity to roads disrupts
 rodents’ contributions to seed dispersal services and subsequent
 recruitment dynamics.
DOI: 10.6078/d1c88g
title: Confirmation of progressive plate motion during the Midcontinent Rift’s early magmatic stage from the Osler Volcanic Group, Ontario, Canada

description: As the supercontinent Rodinia was assembling ca. 1.1 billion years ago,
 there was extensive magmatism on at least five Proterozoic continents
 including the development of the North American Midcontinent Rift. New
 paleomagnetic data from 84 lava flows of the Osler Volcanic Group of the
 Midcontinent Rift reveal that there was a significant and progressive
 decrease in inclination between the initiation of extrusive volcanism in
 the region (ca. 1110 Ma) and ca. 1105 ± 2 Ma (during the “early stage” of
 rift development). Paleomagnetic poles can be calculated for the lower
 portion of the reversed Osler Volcanic Group (40.9°N, 218.6°E, A95 = 4.8°,
 N = 30) and the upper portion of the reversed Osler Volcanic Group
 (42.5°N, 201.6°E, A95 = 3.7°, N = 59; this pole can be assigned the age of
 ca. 1105 ± 2 Ma). This result is a positive test of the hypothesis that
 there was significant plate motion during the early stage of rift
 development. In addition to being a time of widespread volcanism on
 Laurentia and other continents, this interval of the late Mesoproterozoic
 was characterized by rapid paleogeographic change.
description: The 2014_Osler_data folder contains these files:
 Simpson_Island_alldata.xlsx: This excel spreadsheet has all of the
 specimen level data and details the flow mean calculations.
 SimpsonIsland_OslerData.csv: This csv file contains the flow (i.e. site)
 mean paleomagnetic data as well as the locations of the flows
 stratigraphically and geographically (lat, long is in WGS84).
 Halls1974_data.csv: This csv file contains data from the Halls (1974)
 study of the Osler Volcanics. Tauxe2009a_data.csv: This csv file contains
 data from the Tauxe and Kodama (2009) study of the North Shore Volcanic
 Group. The 2014_Osler_Manuscript folder contains the manuscript and figure
 files. The source .tex file and individual figure files are in the folder
 along with the compiled .pdf file. The 2014_Osler_Code folder contains an
 IPython notebook with all of the statistical data analysis and plotting
 for the manuscript. In addition to the IPython notebook, the folder
 contains the pmag.py, and pmagplotlib.py libraries of PmagPy version 2.206
 as well as a newly developed library IPmag.py that modifies some of the
 interactive programs of PmagPy for use in the IPython environment in
 addition to providing new functions. This folder also contains a PDF
 version of notebook to be viewed outside of the IPython that is the
 supporting online material to the G^3 manuscript. Note that the IPython
 notebook can also be viewed online as rendered html without an IPython
 installation at this link: http://nbviewer.ipython.org/urls/raw.github.com/Swanson-H...
DOI: 10.6078/d1ms3x
title: Fast Charging Tests

description: A series of tests were carried out in order to explore alternate charging
 protocols to the standard CCCV. Using such alternative protocols, it was
 possible to apply higher currents to achieve faster charging without cell
 degradation. In addition, baseline tests were carried out in order to
 study capacity fade.
description: First, several CCCV cycles were run at gradually increasing
 C-rates to examine behavior (particularly temperature increases) at higher
 C-rates. Then, MCC, CP-CV, and Boostcharge cycles were run at various
 C-rates. Additional 1C CCCV baseline capacity tests were run in order to
 examine capacity fade.
DOI: 10.6078/d1rg66
title: Pharmacogenomics Research Network: Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines
DOI: 10.15468/ac95eg
title: DFO Monthly GRDI Survey eDNA metabarcoding (16S) Iqaluit, Nunavut 2019

description: Environmental DNA (eDNA) is a non-invasive monitoring approach increasingly used to detect marine organisms; however, misunderstandings of the temporal variability in eDNA detection has limited its integration within management decisions. A clearer understanding of the periodicity (e.g., seasonality) and duration (e.g., weeks, months) of species eDNA detection is essential to optimize sampling design and data interpretation. As such, this study aims to provide a representative assessment of optimal eDNA detection windows across diverse taxonomic groups, primers, and geographic regions using eDNA metabarcoding. Coastal marine presence-absence eDNA data were collected along the Northwest Atlantic coast, in the Bay of Fundy, Scotian Shelf, and Baffin Island. eDNA detection window(s) were defined as unimodal, contiguous months having greater than 75% detection probability and were calculated for each taxon for each primer in each region. Most marine species exhibited short eDNA detection windows (1–2 months). The optimal sampling periods and durations were conserved among closely related species, highlighting the importance of considering biological traits when designing and interpreting eDNA studies. Additionally, primer choice influenced the optimal detection periods, with higher seasonal variation in community composition and detection rates using universal COI and 18S primers compared to fish 16S and 12S primers. These results demonstrate that ignoring seasonal variation may cause false negatives, inefficient sampling, and reduced data comparability across independent studies, emphasizing the need for temporal considerations when designing eDNA studies. Thus, we propose a set of guidelines aimed at the development of optimal sampling designs for coastal ecosystems and the interpretation of trends across datasets.This dataset is for the 16S mitochondrial gene in Iqaluit, Nunavut only; Results for the 18S, 12S and COI markers in Iqaluit are also available in OBIS.
DOI: 10.15468/kzmqxs
title: DFO Monthly GRDI Survey eDNA metabarcoding (12S) Iqaluit, Nunavut 2019

description: Environmental DNA (eDNA) is a non-invasive monitoring approach increasingly used to detect marine organisms; however, misunderstandings of the temporal variability in eDNA detection has limited its integration within management decisions. A clearer understanding of the periodicity (e.g., seasonality) and duration (e.g., weeks, months) of species eDNA detection is essential to optimize sampling design and data interpretation. As such, this study aims to provide a representative assessment of optimal eDNA detection windows across diverse taxonomic groups, primers, and geographic regions using eDNA metabarcoding. Coastal marine presence-absence eDNA data were collected along the Northwest Atlantic coast, in the Bay of Fundy, Scotian Shelf, and Baffin Island. eDNA detection window(s) were defined as unimodal, contiguous months having greater than 75% detection probability and were calculated for each taxon for each primer in each region. Most marine species exhibited short eDNA detection windows (1–2 months). The optimal sampling periods and durations were conserved among closely related species, highlighting the importance of considering biological traits when designing and interpreting eDNA studies. Additionally, primer choice influenced the optimal detection periods, with higher seasonal variation in community composition and detection rates using universal COI and 18S primers compared to fish 16S and 12S primers. These results demonstrate that ignoring seasonal variation may cause false negatives, inefficient sampling, and reduced data comparability across independent studies, emphasizing the need for temporal considerations when designing eDNA studies. Thus, we propose a set of guidelines aimed at the development of optimal sampling designs for coastal ecosystems and the interpretation of trends across datasets.This dataset is for the 12S mitochondrial gene in Iqaluit, Nunavut only; Results for the 18S, 16S and COI markers in Iqaluit are also available in OBIS.
DOI: 10.6078/d1cc74
title: The Evolution of Function within the Nudix Superfamily

description: The Nudix superfamily encompasses over 80,000 protein domains from all
 three domains of life. These proteins fall into four general functional
 classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine
 mismatch-specific adenine glycosylases (A/G-specific adenine
 glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as
 protein/protein interaction and transcriptional regulation. The largest
 group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase
 specificities. To understand the evolution of this vast number of
 activities, we assembled and analyzed experimental and structural data for
 205 Nudix proteins collected from the literature. We corrected erroneous
 functions or provided more appropriate descriptions for 53 annotations
 described in the Gene Ontology Annotation database in this family, and
 propose 275 new experimentally-based annotations. We manually constructed
 structure-guided sequence alignment of 78 Nudix proteins. Using the
 structural alignment as a seed, we then made an alignment of 347 “select”
 Nudix domains, curated from structurally determined, functionally
 characterized, or phylogenetically important Nudix domains. Based on our
 review of Nudix pyrophosphohydrolase structures and specificities, we
 further analyzed a loop region downstream of the Nudix hydrolase motif
 previously shown to contact the substrate molecule and possess known
 functional motifs. This loop region provides a potential structural basis
 for the functional radiation and evolution of substrate specificity within
 the hydrolase family. Finally, phylogenetic analyses of the 347 select
 protein domains and of the complete Nudix clan revealed general monophyly
 with regard to function and a few instances of probable homoplasy.
DOI: 10.6078/d1rp4h
title: Maternity Leave Educational Tool Evaluation

description: We developed an evidence-based maternity leave educational tool for
 working women in California using participatory design. We tested its
 short-term efficacy with a randomized controlled trial of pregnant
 English-speakers (n=155).
description: Participants in the intervention group received the educational
 tool, while control participants did not. This dataset contains data from
 a postpartum online survey of these participants, including data on
 prenatal and postpartum leave and reasons for taking/not taking leave.
 Intervention participants were asked if they read the tool, how they used
 the tool, and how helpful it was in planning their leave.
DOI: 10.7272/q6qj7f78
title: Monroe Monroe Group Videos
DOI: 10.15468/dl.mj3239
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dioscorea monadelpha"
 ]
}

 The dataset includes 163 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001865-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7272/q63r0qr4
title: Mentor Assessment Instrument validation study

description: Prospective survey study
DOI: 10.7272/q6c8276k
title: Alpha-1A Adrenergic Receptor in Rabbit Heart

description: The alpha-1A-adrenergic receptor (AR) subtype is associated with
 cardioprotective signaling in the mouse and human heart. The rabbit is
 useful for cardiac disease modeling, but data on the alpha-1A in the
 rabbit heart are limited. Our objective was to test for expression and
 function of the alpha-1A in rabbit heart. By quantitative real-time
 reverse transcription PCR (qPCR) on mRNA from left ventricular myocardium
 of adult male New Zealand White rabbits, the alpha-1B was 99% of total
 alpha-1-AR mRNA, with &lt;1% alpha-1A and alpha-1D, whereas alpha-1A
 mRNA was over 50% of total in brain and liver. Saturation radioligand
 binding identified ~4 fmol total alpha-1-ARs per mg myocardial protein,
 with 17% alpha-1A by competition with the selective antagonist
 5-methylurapidil. The alpha-1D was not detected by competition with
 BMY-7378, indicating that 83% of alpha-1-ARs were alpha-1B. In isolated
 left ventricle and right ventricle, the selective alpha-1A agonist A61603
 stimulated a negative inotropic effect, versus a positive inotropic effect
 with the nonselective alpha-1-agonist phenylephrine and the beta-agonist
 isoproterenol. Blood pressure assay in conscious rabbits using an
 indwelling aortic telemeter showed that A61603 by bolus intravenous dosing
 increased mean arterial pressure by 20 mm Hg at 0.14 μg/kg, 10-fold lower
 than norepinephrine, and chronic A61603 infusion by iPRECIO programmable
 micro Infusion pump did not increase BP at 22 μg/kg/d. A myocardial slice
 model useful in human myocardium and an anthracycline cardiotoxicity model
 useful in mouse were both problematic in rabbit. We conclude that alpha-1A
 mRNA is very low in rabbit heart, but the receptor is present by binding
 and mediates a negative inotropic response. Expression and function of the
 alpha-1A in rabbit heart differ from mouse and human, but the vasopressor
 response is similar to mouse.
description: Details in Plos One paper Fig 1. qPCR Fig 2. saturation and
 competition radioligand binding FIG 3. Contraction in isolated heart
 muscle FIG 4. Telemetry blood pressure and heart rate in vivo
DOI: 10.7272/q6bg2kwf
title: Provider counseling and provision of female condom in South Africa and Zimbabwe

description: Objectives: Female condoms are the only female-initiated HIV and pregnancy
 prevention technology currently available. We examined female condom
 counseling and provision among providers in South Africa and Zimbabwe,
 high HIV-prevalence countries. Design: Cross-sectional study using a
 nationally-representative survey. Setting: All facilities that provide
 family planning or HIV/STI services in the two countries. Participants:
 National probability sample of 1,444 nurses and physicians who provide
 family planning or HIV/STI services. Primary and secondary outcome
 measures: Female condom practices with different female patients,
 including adolescents, married women, women using hormonal contraception,
 and by HIV status. Using multivariable logistic analysis, we measured
 variations in condom counseling by provider characteristics. Results: Most
 providers reported offering female condoms (88%), but perceived a need for
 novel female barrier methods for HIV/STI prevention (85%). By patient
 type, providers reported less frequent female condom counseling of
 adolescents (55%), women using hormonal contraception (65%), and married
 women (66%), compared to unmarried (74%) or HIV-positive women (82%).
 Multivariable results showed providers in South Africa were less likely to
 counsel women on female condoms than in Zimbabwe (OR=0.48, 95% CI:
 0.35-0.68, p= 0.001). However, South African providers were more likely to
 counsel women on male condoms (OR=2.39, 95% CI: 1.57-3.65, p= 0.001).
 Nurses counseled patients on female condoms more frequently than
 physicians (OR=5.41, 95% CI: 3.26-8.98, p= 0.001). HIV training, family
 planning training, provider location (urban vs. rural), and facility type
 (hospital vs. clinic) were not associated with greater condom counseling.
 Conclusions: Female condoms were integrated into provider counseling and
 care, although providers reported a need for new female-initiated
 multipurpose prevention technologies, suggesting female condoms do not
 meet all patient/provider needs or are not adequately well-known or
 accessible. Providers should be included in HIV training efforts to raise
 awareness of new and existing products, and encouraged to educate all
 women.
description: Stata dataset
DOI: 10.7272/q6w66hpn
title: NEXUS Chest CT
DOI: 10.7272/q68g8hmp
title: Media coverage of nonsmoker only hiring policies

description: This SPSS dataset contains 1,159 records (from 1995-2013) representing the
 content of media items published in the US concerning employers who chose
 to hire only nonsmokers. The Excel spreadsheet contains a list of the
 titles, authors, publication sources, and publication dates of all the
 media items in the SPSS database.
description: There are 71 variables in the SPSS dataset that cover the
 characteristics of each media item, as well as the content.
DOI: 10.5519/qd.vdqqzd8g
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (8956 records)
DOI: 10.7272/q6d798bd
title: NODDI-PLOS-ONE-Chang et al 2015

description: Diffusion tensor imaging (DTI) studies of human brain development have
 consistently shown widespread, but nonlinearly increasing white matter
 anisotropy through childhood, adolescence, and into adulthood. However,
 despite its sensitivity to changes in tissue microstructure, DTI lacks the
 specificity to disentangle distinct microstructural features of white and
 gray matter. Neurite orientation dispersion and density imaging (NODDI) is
 a recently proposed multi-compartment biophysical model of brain
 microstructure that can estimate non-collinear properties of white matter,
 such as neurite orientation dispersion (OD) and neurite density (ND). In
 this study, we apply NODDI to 67 healthy controls aged 7-63 years to
 investigate changes of OD and ND with brain maturation, with comparison to
 standard DTI metrics. Using both region-of-interest and voxel-wise
 analyses, we find that ND exhibits striking increases over the studied age
 range following a logarithmic growth pattern, while OD rises following an
 exponential growth pattern. This novel finding is consistent with
 well-established age-related changes of FA over the lifespan that show
 growth during childhood and adolescence, plateau during early adulthood,
 and accelerating decay after the fourth decade of life. Our results
 suggest that the rise of FA during the first two decades of life is
 dominated by increasing ND, while the fall in FA after the fourth decade
 is driven by the exponential rise of OD that overcomes the slower
 increases of ND. Using partial least squares regression, we further
 demonstrate that NODDI better predicts chronological age than DTI.
 Finally, we show excellent test-retest reliability of NODDI metrics, with
 coefficients of variation below 5% in all measured regions of interest.
 Our results support the conclusion that NODDI reveals biologically
 specific characteristics of brain development that are more closely linked
 to the microstructural features of white matter than are the empirical
 metrics provided by DTI.
description: NODDI