cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d2547d7z6
title: Data from: Defining isoscapes in the Northeast Pacific as an index of ocean productivity

description: Aim: We modeled isoscapes in the Northeast Pacific using satellite-based
 data with the main objective of testing if isoscapes defined by a few key
 parameters can be used as a proxy for secondary productivity. Location:
 Northeast (NE) Pacific; 46 – 60⁰N and 125 – 165⁰W. Time period: From 1998
 to 2017 (ongoing). Major taxa studied: Zooplankton with a focus on large
 herbivores. Methods: Approximately 280 summer zooplankton samples were
 analyzed for Carbon (δ13C) and Nitrogen (δ15N) stable isotope (SI) ratios.
 Environmental conditions experienced by zooplankton organisms were
 extracted from satellite, in situ sensor and model databases. A
 generalized additive model approach was used to explain the spatial
 variability of δ13C and δ15N values and predict isoscapes. Results: Sea
 surface temperature (SST), sea level anomaly (SLA) and chlorophyll-a
 concentration emerged as the significant SI predictors. Modelled isoscapes
 reproduced patterns observed in δ13C and δ15N value distribution, such as
 a decrease from the coast to offshore. The contribution of eddies in
 enhancing local production in the open ocean was also well captured by the
 models. In the central part of the NE Pacific higher SI values were
 correlated with higher large copepod biomass measured by the North Pacific
 Continuous Plankton Recorder (CPR) survey. However, in the area off the
 coast of British Columbia (BC) high δ15N variability appeared to be
 associated with episodic intrusions of coastal waters demonstrating that
 caution is needed when interpreting sharp changes in SI ratios. Main
 conclusions: While the mechanisms driving SI ratio variability are
 complex, we demonstrated that a few parameters used as a proxy for some of
 these major mechanisms are able to successfully produce isoscape models.
 This approach was proven useful to provide a qualitative estimate of the
 secondary production, which can be particularly valuable in a region where
 few data are available.
description: Approximately 280 summer zooplankton samples were analyzed for
 Carbon (δ<sup>13</sup>C) and Nitrogen
 (δ<sup>15</sup>N) stable isotope (SI) ratios. Environmental
 conditions experienced by zooplankton organisms were extracted from
 satellite, in situ sensor and model databases. A generalized additive
 model approach was used to explain the spatial variability of
 δ<sup>13</sup>C and δ<sup>15</sup>N values and
 predict isoscapes.
description: We provide C and N isoscapes at zooplankton level for the NE
 Pacific for 1998-2017. The uncertainties associated with the predicted
 values are provided as well and should be considered when using the
 isoscape value. Please don't hesitate to contact the corresponding
 author for any questions that you might have about the isoscapes
 production and uses. See ReadMe file for data structure
 information.
DOI: 10.18112/openneuro.ds007338.v1.0.0
title: EEGEyeNet Dataset
DOI: 10.5061/dryad.z612jm67m
title: Impaired brain network architecture in Cushing’s disease based on graph theoretical analysis

description: Objective: To investigate the whole functional brain networks of Cushing
 disease (CD) patients about topological parameters compared with healthy
 control (NC). Further, we tested whether the small world and rich club
 organization were changed in CD patients compared with NC. Patients and
 Methods: Nineteen CD patients and twenty-two healthy control subjects,
 matched in age, gender, and education, underwent resting-state fMRI. Graph
 theoretical were used to calculated the functional brain networks
 organization of all participants and compare between CD and NC. Results:
 CD patients revealed higher global efficiency, less path length and
 cluster efficiency compared with healthy control. Additionally, small word
 organization was present in CD patients but higher than healthy control.
 Moreover, rich club connections, feeder connections and local connection
 were significantly decreased in CD patients. Conclusion: We demonstrated
 that functional brain networks were altered in CD patients compared with
 healthy control. Topological parameters of brain network can be served as
 a new biomarker of CD patients and help us understand the pathogenesis of
 ACTH at the whole brain level.
DOI: 10.5061/dryad.kprr4xh0m
title: Positive allosteric modulation of the α7 nicotinic acetylcholine receptor as a treatment for cognitive deficits after traumatic brain injury

description: Cognitive impairments are a common consequence of traumatic brain injury
 (TBI). The hippocampus is a subcortical structure that plays a key role in
 the formation of declarative memories and is highly vulnerable to TBI. The
 α7 nicotinic acetylcholine receptor (nAChR) is highly expressed in the
 hippocampus and reduced expression and function of this receptor are
 linked with cognitive impairments in Alzheimer’s disease and
 schizophrenia. Positive allosteric modulation of α7 nAChRs with AVL-3288
 enhances receptor currents and improves cognitive functioning in naïve
 animals and healthy human subjects. Therefore, we hypothesized that
 targeting the α7 nAChR with the positive allosteric modulator AVL-3288
 would enhance cognitive functioning in the chronic recovery period of TBI.
 To test this hypothesis, adult male Sprague Dawley rats received moderate
 parasagittal fluid-percussion brain injury or sham surgery. At 3 months
 after recovery, animals were treated with vehicle or AVL-3288 at 30 min
 prior to cue and contextual fear conditioning and the water maze task.
 Treatment of TBI animals with AVL-3288 rescued learning and memory
 deficits in water maze retention and working memory. AVL-3288 treatment
 also improved cue and contextual fear memory when tested at 24 hr and 1
 month after training, when TBI animals were treated acutely just during
 fear conditioning at 3 months post-TBI. Hippocampal atrophy but not
 cortical atrophy was reduced with AVL-3288 treatment in the chronic
 recovery phase of TBI. AVL-3288 application to acute hippocampal slices
 from animals at 3 months after TBI rescued basal synaptic transmission
 deficits and long-term potentiation (LTP) in area CA1. Our results
 demonstrate that AVL-3288 improves hippocampal synaptic plasticity, and
 learning and memory performance after TBI in the chronic recovery period.
 Enhancing cholinergic transmission through positive allosteric modulation
 of the α7 nAChR may be a novel therapeutic to improve cognition after TBI.
DOI: 10.15139/s3/mijkcv
title: Data Management and Sharing Plan for: Evaluating antibiotic tolerance in single cells with tandem single cell measurements of translation rate and transcriptomes

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.6078/d1p09w
title: Kinesin and dynein use distinct mechanisms to bypass obstacles

description: Kinesin-1 and cytoplasmic dynein are microtubule (MT) motors that
 transport intracellular cargos. It remains unclear how these motors move
 along MTs densely coated with obstacles of various sizes in the cytoplasm.
 Here, we tested the ability of single and multiple motors to bypass
 synthetic obstacles on MTs in vitro. Contrary to previous reports, we
 found that mammalian dynein is highly capable of bypassing obstacles.
 Human kinesin-1 motors fail to avoid obstacles, consistent with their
 inability to take sideways steps on to neighboring MT protofilaments.
 Kinesins overcome this limitation when working in teams, bypassing
 obstacles as effectively as multiple dyneins. Cargos driven by multiple
 kinesin or dyneins are also capable of rotating around the MT to bypass
 large obstacles. These results suggest that multiplicity of motors is
 required not only for transporting cargos over long distances and
 generating higher forces, but also for maneuvering of the cargos on
 obstacle-coated MT surfaces.
DOI: 10.5061/dryad.pnvx0k6h5
title: Reinforcement learning theory reveals the cognitive requirements for solving the cleaner fish market task

description: Learning is an adaptation that allows individuals to respond to
 environmental stimuli in ways that improve their reproductive outcomes.
 The degree of sophistication in learning mechanisms potentially explains
 variation in behavioural responses. Here, we present a model of learning
 that is inspired by documented intra- and interspecific variation in the
 performance in a simultaneous two-choice task, the ‘biological market
 task’. The task presents a problem that cleaner fish often face in nature:
 the decision of choosing between two client types; one that is willing to
 wait for inspection and one that may leave if ignored. The cleaners’
 choice hence influences the future availability of clients, i.e. it
 influences food availability. We show that learning the preference that
 maximizes food intake requires subjects to represent in their memory
 different combinations of pairs of client types rather than just
 individual client types. In addition, subjects need to account for future
 consequences of actions, either by estimating expected long-term reward or
 by experiencing a client leaving as a penalty (negative reward). Finally,
 learning is influenced by the absolute and relative abundance of client
 types. Thus, cognitive mechanisms and ecological conditions jointly
 explain intra and interspecific variation in the ability to learn the
 adaptive response.
description: All the data for the paper was generated by running individual
 based simulations written in c++ laguange. The code both for generating
 the data and for figure of the published article can be found in
 here: DOI:
 10.5281/zenodo.3361665 Files names starting
 with the identifier "FAA" correspond to Fully Aware Agents,
 while files named starting with "PAA" correspond to Partially
 Aware Agents. After the identifier, file names contain 7 numbers, each one
 preceeded by the information of the simulation they communicate. The first
 number gives the alpha parameter, it is followed by the word
 "alph". The second number provides the value used in parameter
 gamma. The third number correspond to the value of parameter tau (this
 parameter is only relevant for simulation run for algorithm SARSA). The
 fourth number provides the value for a boolean variable that determines
 whether penalty is used in the simulation. The fifth and sixth numbers
 give the value for the probability of a visitor, and the probability of a
 resident, respetively. Finally, the last number gives the seed used in the
 random number generator.  Columns, in the files, have
 headers that correspond to values or parameters in the models. All other
 parameter values can be found in the associated json files that are
 contained within the same folder.
DOI: 10.5061/dryad.tqjq2bvtc
title: Data from: Using functional and phylogenetic diversity to infer avian community assembly along elevational gradients

description: Aim We present the first global analysis of elevational gradients in
 functional and phylogenetic diversity of birds and test for signals of
 deterministic processes (i.e., environmental filtering and limiting
 similarity) in community assembly. Further, we examine for latitudinal
 effects in the strength of these processes. Location Forty-six elevational
 gradients across the globe. Time period Current (between 1924 and 2016)
 Major taxa Birds. Methods We systematically selected, compiled and
 analyzed published data on bird diversity along elevational gradients. For
 each gradient, we calculated functional and phylogenetic diversity across
 elevations and described the main patterns for each diversity metric.
 Then, we calculated standardized effect sizes (SES) of each metric and
 used these SES values to (1) test the signals of deterministic processes
 shaping assemblages across elevations and (2) to compare changes in
 within-mountain diversity, among mountains located at different latitudes.
 Results Birds displayed eight different patterns of functional and
 phylogenetic diversity across elevations, but no global pattern of
 increase or decrease was found. There is, however, a consistent global
 pattern of phylogenetic clustering, with mountain species being more
 closely related to each other at any given elevation. Latitude had a
 significant effect on within-mountain changes in functional and
 phylogenetic diversity across elevations, with more negative slopes
 (stronger decline in diversity metrics with increasing elevation) in
 tropical mountains. Main conclusions Our findings challenge the idea that
 the decline of functional and phylogenetic diversity with elevation is a
 general pattern, emphasizing the uniqueness of each mountain system. In
 spite of this great variability, we found a latitudinal effect in the
 patterns of within-mountain functional and phylogenetic dispersion of
 birds after controlling for effects of species richness. Environmental
 filtering, thus, may act differently in tropical and temperate mountains,
 and calls for more comparative studies on the mechanisms driving community
 assembly at different latitudes.
description: The file contains functional and phylogenetic diversity of bird
 assemblages in 46 mountain systems across the globe. Each metric is
 calculated for 100-m elevational bands (0-100, 100-200, 200-300,
 etc.). Bird raw data were extracted from published sources detailed in
 Appendix 1[see main text] and are available from the original source or
 from upon request from the main authors of these articles. 
description: Column headings are described in the first sheet of the
 file.
DOI: 10.5061/dryad.v41ns1rrf
title: Data from: Thermal variability and plasticity drive the outcome of a host-pathogen interaction

description: Variable, changing, climates may affect each participant in a biotic
 interaction differently. We explored the effects of temperature and
 plasticity on the outcome of a host-pathogen interaction to try to predict
 the outcomes of infection under fluctuating temperatures. We infected
 Gryllus veletis crickets with the entomopathogenic fungus Metarhizium
 brunneum under constant (6 °C, 12 °C, 18 °C or 25 °C) or fluctuating
 temperatures (6 °C to 18 °C or 6 °C to 25 °C). We also acclimated crickets
 and fungi to constant or fluctuating conditions. Crickets acclimated to
 fluctuating conditions survived best under constant conditions if paired
 with warm-acclimated fungus. Overall, matches and mismatches in thermal
 performance, driven by acclimation, determined host survival. Mismatched
 performance also determined differences in survival under different
 fluctuating thermal regimes: crickets survived best when fluctuating
 temperatures favoured their performance (6 °C to 25 °C), compared to
 fluctuations that favoured fungus performance (6 °C to 18 °C). Thus, we
 could predict the outcome of infection under fluctuating temperatures by
 averaging relative host-pathogen performance under constant temperatures,
 suggesting that it may be possible to predict responses to fluctuating
 temperatures for at least some biotic interactions.
DOI: 10.5061/dryad.44j0zpc8q
title: Striking centennial-scale changes in the population size of a threatened seabird

description: Many animal populations are under stress and declining. For numerous
 marine bird species, only recent or sparse monitoring data are available,
 lacking the appropriate temporal perspective needed to consider natural,
 long-term population dynamics when developing conservation strategies.
 Here we use a combination of established paleoenvironmental approaches to
 examine the millennial-scale dynamics of the world’s largest colony
 (representing ~50% of the global population) of the declining and
 vulnerable Leach’s Storm-petrel (Hydrobates leucorhous). By reconstructing
 the last ~1,700 years of the colony’s population trends, we corroborate
 recent surveys indicating rapid declines since the 1980s. More
 surprisingly, however, was that population size was smaller and has
 changed strikingly in the past, even prior to the introduction of human
 stressors. Our results challenge notions that very large colonies are
 generally stable in the absence of anthropogenic pressures and speak to an
 increasingly pressing need to better understand inter-colony movement and
 recruitment when inferring range- and species-wide trends. While the
 recently documented decline in storm-petrels clearly warrants conservation
 concern, we show that colony size was consistently much lower in the past
 and changed markedly in the absence of major anthropogenic activity. In
 response, we emphasize the need for enlarged protected area networks to
 maintain natural population cycles, coupled with continued research to
 identify the driver(s) of the current global seabird decline.
DOI: 10.25338/b8303j
title: Sex-specific evolution of relative leg size in Drosophila prolongata results from changes in the intersegmental coordination of tissue growth

description: Evolution of relative organ size is the most prolific source of
 morphological diversity, yet the underlying molecular mechanisms that
 modify growth control are largely unknown. Models where organ proportions
 have undergone recent evolutionary changes hold the greatest promise for
 understanding this process. Uniquely among Drosophila species, D.
 prolongata displays a dramatic, male-specific increase in the size of its
 forelegs relative to other legs. By comparing leg development between
 males and females of D. prolongata and its closest relative D. carrolli,
 we show that the exaggerated male forelegs are produced by a sex- and
 segment-specific increase in mitosis during the final larval instar.
 Intersegmental compensatory control, where smaller leg primordia grow at a
 faster rate, is observed in both species and sexes. However, the
 equlibrium growth rates that determine the final relative proportion
 between the first and second legs have shifted in male D. prolongata
 compared both to conspecific females and to D. carrolli. We suggest that
 the observed developmental changes that produce new adult proportions
 reflect an interplay between conserved growth coordination mechanisms and
 evolving organ-specific growth targets.
DOI: 10.5061/dryad.44j0zpc8r
title: Data from: Empirical evidence for the potential climate benefits of decarbonizing light vehicle transport in the U.S. with bioenergy from purpose-grown biomass with and without BECCS

description: Climate mitigation scenarios limiting global temperature increases to 1.5
 °C rely on decarbonizing vehicle transport with bioenergy production plus
 carbon capture and storage (BECCS), but climate impacts for producing
 different bioenergy feedstocks have not been directly compared
 experimentally nor for ethanol vs. electric light-duty vehicles. A field
 experiment at two Midwest U.S. sites on contrasting soils revealed that
 feedstock yields of seven potential bioenergy cropping systems varied
 substantially within sites but little between. Bioenergy produced per
 hectare reflected yields: miscanthus &gt; poplar &gt; switchgrass
 &gt; native grasses ≈ maize stover (residue) &gt; restored prairie
 ≈ early successional. Greenhouse gas emission intensities for ethanol
 vehicles ranged from 20 to -179 g CO2e MJ-1: maize stover &gt;&gt;
 miscanthus ≈ switchgrass ≈ native grasses ≈ poplar &gt; early
 successional ≥ restored prairie; direct climate benefits ranged from ~80%
 (stover) – 290% (restored prairie) reductions in CO2e compared to
 petroleum, and were similar for electric vehicles. With CCS, reductions in
 emission intensities ranged from 204% (stover) – 416% (restored prairie)
 for ethanol vehicles, and from 329 – 558% for electric vehicles, declining
 27% and 15%, respectively, once soil carbon equilibrates within several
 decades of establishment.  Extrapolation based on expected U.S.
 transportation energy use suggests that, once CCS potential is maximized
 with CO2 pipeline infrastructure, negative emissions from bioenergy with
 CCS for light-duty electric vehicles could capture &gt;900 Tg CO2e
 yr-1 in the U.S. In the future, as other renewable electricity sources
 become more important, electricity production from biomass would offset
 less fossil-fuel electricity, and the advantage of electric over ethanol
 vehicles would decrease proportionately.
description: Data collected as described in materials and methods.
description: See the readme file for a description of data in
 "dataset_gelfand_es&t.xlsx". The file
 "calculations_gelfand_est_corrected_v2_12.15.2022.xlsx" shows
 the assumptions, calculations, and extrapolations of these data and their
 location in the paper and supplemental information. This file contains the
 corrections described in https://doi.org/10.1021/acs.est.2c09013 published on 15 Dec 2022.
DOI: 10.6075/j0dz06nt
title: 3D scans of plant shoot architectures

description: 713 3D plant shoot architectures from 3 species (Tomato, Tobacco,
 Sorghum), scanned across multiple conditions (ambient light, high-heat,
 high-light, vegetative shade, drought), and through 20-30 developmental
 time-points. Also included are architectures of Arabidopsis wildtype
 (Columbia-0) and 10 genetic mutants.  Visualizations are
 available at: https://plant3d.navlakhalab.net/ Contact: Saket Navlakha
 (navlakha@salk.edu)
DOI: 10.5061/dryad.08kprr4xk
title: Autoantibodies against the prion protein in individuals with PRNP mutations

description: Objective. To determine whether naturally occurring
 autoantibodies against the prion protein are present in individuals with
 genetic prion disease mutations and controls, and if so, whether they are
 protective against prion disease.  Methods. In this
 case-control study, we collected 124 blood samples from individuals with a
 variety of pathogenicPRNPmutations and 78 control individuals with a
 positive family history of genetic prion disease but lacking
 disease-associatedPRNPmutations. Antibody reactivity was measured using an
 indirect ELISA for the detection of human IgG1-4 antibodies
 against wild-type human prion protein. Multivariate linear regression
 models were constructed to analyze differences in autoantibody reactivity
 between a) PRNPmutation carriers versus controls and b)
 asymptomatic versus symptomatic PRNPmutation carriers. Robustness
 of results was examined in matched cohorts. Results. We found
 that antibody reactivity was present in a subset of
 both PRNPmutation carriers and controls. Autoantibody levels were
 not influenced by PRNP mutation status nor clinical
 manifestation of prion disease. Post hocanalyses showed
 anti-PrPCautoantibody titers to be independent of personal history of
 autoimmune disease and other immunological disorders, as well
 as PRNPcodon 129 polymorphism. 
 Conclusions.Pathogenic PRNPvariants do not notably stimulate
 antibody-mediated anti-PrPCimmunity. Anti-PrPCIgG autoantibodies are not
 associated with the onset of prion disease. The presence of
 anti-PrPCautoantibodies in the general population without any
 disease-specific association suggests that relatively high titers of
 naturally occurring antibodies are well tolerated. Clinicaltrials.gov
 identifier NCT02837705.
DOI: 10.15468/dl.6xhjmf
title: Occurrence Download

description: A dataset containing 2393 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Norway",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nigritella nigra",
 "Year 2014-2026"
 ]
}

 The dataset includes 2393 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001933-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.