cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dc1s8h3
title: Data from: Inbreeding reduces long-term growth of Alpine ibex populations

description: Many studies document negative inbreeding effects on individuals, and
 conservation efforts to preserve rare species routinely employ strategies
 to reduce inbreeding. Despite this, there are few clear examples in nature
 of inbreeding decreasing the growth rates of populations, and the extent
 of population-level effects of inbreeding in the wild remains
 controversial. Here we take advantage of a long-term data set of 26
 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly 100
 years to show that inbreeding substantially reduced per capita population
 growth rates, particularly for populations in harsher environments.
 Populations with high average inbreeding (F ≈ 0.2) had population growth
 rates reduced by 71% compared to populations with no inbreeding. Our
 results show that inbreeding can have long-term demographic consequences
 even when environmental variation is large and deleterious alleles may
 have been purged during bottlenecks. Thus, efforts to guard against
 inbreeding effects in populations of endangered species have not been
 misplaced.
description: time series and allele
 frequency dataThe file contains data
 used to estimate the population growth rate (time series data) and
 inbreeding (allele frequency data).Inbreeding_Ibex_dataDryad_Bozzuto_etal_NEE2019.xlsxdata for custom R-codeData for custom R-code used for the regression analysis.ibexData.RDatacustom R-codeCustom R-code used for the regression analysisInbreeding_Ibex_Bozzuto_etal_NEE2019.r
DOI: 10.5061/dryad.45m46kp
title: Data from: The response of root traits to precipitation change of herbaceous species in temperate steppes

description: 1. Plasticity of root traits plays an important role in determining plant
 growth and survival under changing climate. Shift in precipitation is one
 of the most pertinent global change factors driving changes in structure
 and function of grasslands. However, few studies have focused on
 intra-specific variation of root traits in response to precipitation
 change under field conditions. 2. We conducted a 10-year simulated
 increased precipitation experiment in a temperate grassland and a 700-km
 regional scale transect along a precipitation gradients ranging from
 144.23 to 412.29 mm in northern China. The morphological, chemical and
 anatomical traits of the first two orders roots were measured on 15 common
 herbaceous species in the manipulation experiment and two regionally
 common species (Leymus chinensis, Artemisia frigida) along the
 precipitation gradients. 3. We found that most of the root traits of the
 herbaceous species exhibited no significant responses to water addition.
 The two regionally common species adjusted their root traits at sites with
 the annual precipitation lower than certain value, i.e., 250 mm and 160 mm
 for L. chinensis and A. frigida, respectively. These results indicate that
 root traits of the herbaceous species exhibit little plasticity in
 response to precipitation change, and that the adjustment of root traits
 occurs when the range of annual precipitation exceeds a certain
 thresholds. 4. Root traits of L. chinensis and A. frigida varied
 differently both in manipulation experiment and along the precipitation
 gradients. Root traits of L. chinensis were relatively constant, while A.
 frigida adjusted their morphological root traits in response to water
 addition. Moreover, L. chinensis showed higher specific root length and
 area, and root N contents at sites with annual precipitation lower than c.
 250 mm. In contrast, A. frigida displayed thicker roots with lower
 specific root length and area at sites with annual precipitation lower
 than c.160 mm. 5. Our results showed that root traits of herbaceous
 species in temperate grasslands exhibited little plasticity, and that
 different species have evolved diverse adaptive strategies in response to
 precipitation change. These novel findings may provide valuable
 information to predict responses of temperate grasslands to future climate
 change.
description: Data for Zhou et al.
 Functional EcologyThe data include root
 traits for grassland species under water addition and control conditions;
 root traits for two dominant species across precepitation gradients;
 annual precipitation across the research areas.Data Dryad-Zhou et al.
 Functional ecology.xls
DOI: 10.5061/dryad.q6t8k07
title: Data from: Sperm cryopreservation reduces offspring growth

description: Sperm cryopreservation is routinely used in reproductive medicine,
 livestock production, and wildlife management. Its effect on offspring
 performance is often assumed negligible, but this still remains to be
 confirmed in well controlled within-subject experiments. We use a
 vertebrate model that allows to experimentally separate parental and
 environmental effects to test whether sperm cryopreservation influences
 offspring phenotype under stress and non-stress conditions, and whether
 such effects are male-specific. Wild brown trout (Salmo trutta) were
 stripped for their gametes, and a portion of each male’s milt was
 cryopreserved. Then, 960 eggs were simultaneously fertilized with either
 non-cryopreserved or frozen-thawed semen and raised singly in the presence
 or absence of a pathogen. We found no significant effects of
 cryopreservation on fertilization rates, and no effects on growth,
 survival, nor pathogen resistance during the embryo stage. However,
 fertilization by cryopreserved sperm lead to significantly reduced larval
 growth after hatching. Males varied in genetic quality as determined from
 offspring performance, but effects of cryopreservation on larval growth
 were not male specific. We conclude that cryopreservation causes a
 reduction of offspring growth that is easily overlooked because it only
 manifests itself at later developmental stages when many other factors
 affect growth and survival, too.
description: Nusbaumer_CryoSpermThe 960 fertilized eggs, their association to blocks and sires, their assignments to treatment of sperm and exposure to pathogen, and the dependent variables: fertilization successful (yes/no) and mortality and growth measures.
DOI: 10.5061/dryad.n1kv40m
title: Data from: An automated approach to identifying search terms for systematic reviews using keyword co-occurrence networks

description: 1. Systematic review, meta-analysis, and other forms of evidence synthesis
 are critical to strengthen the evidence base concerning conservation
 issues and to answer ecological and evolutionary questions. Synthesis lags
 behind the pace of scientific publishing, however, due to time and
 resource costs which partial automation of evidence synthesis tasks could
 reduce. Additionally, current methods of retrieving evidence for synthesis
 are susceptible to bias towards studies with which researchers are
 familiar. In fields that lack standardized terminology encoded in an
 ontology, including ecology and evolution, research teams can
 unintentionally exclude articles from the review by omitting synonymous
 phrases in their search terms. 2. To combat these problems, we developed a
 quick, objective, reproducible method for generating search strategies
 that uses text mining and keyword co-occurrence networks to identify the
 most important terms for a review. The method reduces bias in search
 strategy development because it does not rely on a predetermined set of
 articles and can improve search recall by identifying synonymous terms
 that research teams might otherwise omit. 3. When tested against the
 search strategies used in published environmental systematic reviews, our
 method performs as well as the published searches and retrieves
 gold-standard hits that replicated versions of the original searches do
 not. Because the method is quasi-automated, the amount of time required to
 develop a search strategy, conduct searches, and assemble results is
 reduced from approximately 17-34 hours to under 2 hours. 4. To facilitate
 use of the method for environmental evidence synthesis, we implemented the
 method in the R package litsearchr, which also contains a suite of
 functions to improve efficiency of systematic reviews by automatically
 deduplicating and assembling results from separate databases.
description: Comparison of litsearchr
 performance to other methodsPerformance of search
 strategies developed with quasi-automated methods in comparison to
 conventional methods. Precision and recall data comes from the original
 publications for Sarol (2018), Belter et al. (2018) and Hausner et al.
 (2015). Data for the litsearchr performance comes from the separate file
 litsearchr precision and recall.xlsxlitsearchr precision and
 recallResults retrieved per
 database per search, used to measure the precision and recall of original,
 replicated, naive, and litsearchr searches for six reviews from
 Environmental Evidence.
DOI: 10.5061/dryad.cp75158
title: Data from: Vocal and locomotor coordination develops in association with the autonomic nervous system

description: In adult animals, movement and vocalizations are coordinated, sometimes
 facilitating, and at other times inhibiting, each other. What is missing
 is how these different domains of motor control become coordinated over
 the course of development. We investigated how postural-locomotor
 behaviors may influence vocal development, and the role played by
 physiological arousal during their interactions. Using infant marmoset
 monkeys, we densely sampled vocal, postural and locomotor behaviors and
 estimated arousal fluctuations from electrocardiographic measures of heart
 rate. We found that vocalizations matured sooner than postural and
 locomotor skills, and that vocal-locomotor coordination improved with age
 and during elevated arousal levels. These results suggest that
 postural-locomotor maturity is not required for vocal development to
 occur, and that infants gradually improve coordination between
 vocalizations and body movement through a process that may be facilitated
 by arousal level changes.
description: SupplementaryDatawithGuide_07_03_19
DOI: 10.15468/dl.7knpxg
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-65.04499 -31.54661,-65.25339 -32.09526,-64.87486 -32.25901,-64.39639 -31.738,-64.86848 -31.28929,-65.04499 -31.54661))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oxymycterus"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001828-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.96224rg
title: Data from: New ways to acquire resistance – Imperfect convergence in insect adaptations to a potent plant toxin

description: Evolution of insensitivity to the toxic effects of cardiac glycosides has
 become a model in the study of convergent evolution, as five taxonomic
 orders of insects use the same few similar amino acid substitutions in the
 otherwise highly conserved Na,K-ATPase α. We here show that insensitivity
 in pyrgomorphid grasshoppers evolved along a slightly divergent path. As
 in other lineages, duplication of the Na,K-ATPase α gene paved the way for
 subfunctionalization: one copy maintains the ancestral, sensitive state
 while the other copy is resistant. Nonetheless, in contrast to all other
 investigated insects, the grasshoppers’ resistant copy shows length
 variation by two amino acids in the first extracellular loop, the main
 part of the cardiac glycoside binding pocket. RT-qPCR analyses confirmed
 this copy is predominantly expressed in tissues exposed to the toxins,
 while the ancestral copy predominates in the nervous tissue. Functional
 tests with genetically engineered Drosophila Na,K-ATPases bearing the
 first extracellular loop of the pyrgomorphid genes showed the derived form
 to be highly resistant, while the ancestral state is sensitive. Thus, we
 report convergence in gene duplication and in the gene targets for toxin
 insensitivity, however the means to the phenotypic end have been novel in
 pyrgomorphid grasshoppers.
description: qPCR data for
 DryadRaw qPCR data as
 obtained from StepOne system and following analyses for both Na,K-ATPase
 genes of Phymateus aegrotus (identified from gut and nervous tissue) in
 brain, Malpighian tubules, midgut and hindgut tissue
 extractions.Na,K-ATPase_Inhibitionsassay_Data_for_DryadRaw data (absorbances) and final data (percentages) of phosphate released under varying concentrations of ouabain added to the assay buffer for engineered protein constructs mimicking the nervous tissue or gut form of the P.aegrotus Na,K-ATPase. As a comparison data for wild type Drosophila melanogaster Na,K-ATPase expressed in cell culture (to be published in Karageorgi et al., Nature 2019) and Schistocerca gregaria hind gut extracts (published by Petschenka et al. 2018, doi: 10.5061/dryad.fq064) are given.Assays_Data_for_Dryad.xlsx
DOI: 10.5061/dryad.bf08b1t
title: Data from: Allergenic pollen production across a large city for common ragweed (Ambrosia artemisiifolia)

description: Predictions of airborne allergenic pollen concentrations at fine spatial
 scales require information on source plant location and pollen production.
 Such data are lacking at the urban scale, largely because manually mapping
 allergenic pollen producing plants across large areas is infeasible.
 However, modest-sized field surveys paired with allometric equations,
 remote sensing, and habitat distribution models can predict where these
 plants occur and how much pollen they produce. In this study, common
 ragweed (Ambrosia artemisiifolia) was mapped in a field survey in Detroit,
 MI, USA. The relationship between ragweed presence and habitat-related
 variables derived from aerial imagery, LiDAR, and municipal data were used
 to create a habitat distribution model, which was then used to predict
 ragweed presence across the study area (392 km2). The relationship between
 inflorescence length and pollen production was used to predict pollen
 production in the city. Ragweed occurs in 1.7% of Detroit and total pollen
 production is 312 × 1012 pollen grains annually, but ragweed presence was
 highly heterogeneous across the city. Ragweed was predominantly found in
 in vacant lots (75%) and near demolished structures (48%), and had varying
 associations with land cover types (e.g., sparse vegetation, trees,
 pavement) detected by remote sensing. These findings also suggest several
 management strategies that could help reduce levels of allergenic pollen,
 including appropriate post-demolition management practices.
 Spatially-resolved predictions for pollen production will allow
 mechanistic modeling of airborne allergenic pollen and improved exposure
 estimates for use in epidemiological and other applications.
description: ragweed database for
 analysisDatabase including
 ragweed presence and each predictor variable (thinned to one cell per
 parcel and to 1 point per 16m2); this is the version used in the analysis.
 Variable descriptions are provided in the README file.ragweed_thinned_dataset.csvRasters of predictor variablesRasters that were included in the analysis. For descriptions of each raster see the README file associated with the ragweed database.dryad ragweed.zipunsupervised classification of NAIP 2016 imageryLarge raster of unsupervised classification of NAIP 2016 false color imagery.naip2016_fc_unsupclass.tifpredictionsPredicted ragweed presence (mean and standard deviation) and predicted ragweed pollen production (mean).
DOI: 10.5281/zenodo.18392620
title: CosmoPowerJAX emulators for matter power spectra

description: Matter power spectrum emulators for different cosmologies. These emulators were made using the CosmoPower-Jax package.

Includes full linear, full nonlinear, cb (cold matter + baryons) linear and nonlinear matter power spectrum, as well as emulators for s8 and fs8.



Supported models include:



- w0waCDM with 3 degenerate massive neutrinos

- w0waCDM with one massive neutrino


- w0waCDM with mass of the neutrino 0

- wCDM with 3 degenerate massive neutrinos

- wCDM with one massive neutrino



- wCDM with mass of the neutrino 0

- LCDM with 3 degenerate massive neutrinos




- LCDM with one massive neutrino

- LCDM with mass of the neutrinos 0
DOI: 10.5281/zenodo.18392621
title: CosmoPowerJAX emulators for matter power spectra

description: Matter power spectrum emulators for different cosmologies. These emulators were made using the CosmoPower-Jax package.

Includes full linear, full nonlinear, cb (cold matter + baryons) linear and nonlinear matter power spectrum, as well as emulators for s8 and fs8.



Supported models include:



- w0waCDM with 3 degenerate massive neutrinos

- w0waCDM with one massive neutrino


- w0waCDM with mass of the neutrino 0

- wCDM with 3 degenerate massive neutrinos

- wCDM with one massive neutrino



- wCDM with mass of the neutrino 0

- LCDM with 3 degenerate massive neutrinos




- LCDM with one massive neutrino

- LCDM with mass of the neutrinos 0
DOI: 10.5281/zenodo.17419824
title: Digitized Metadata of Solar Disk H-alpha Observations At Sacramento Peak Observatory

description: The dataset contains metadata (date and time of observations) extracted from the digitized (scanned) photographic images of solar disk observations in neutral hydrogen H-alpha spectral line made at the U.S. National Solar Observatory at Sacramento Peak during 1966-2002 (https://nispdata.nso.edu/ftp/flare_patrol_h_alpha_sp/).

Digitized text information is presented in a CSV table. The table includes the following columns:



Filename: string with the original file name;

Date: corrected date and time in the format YYYYMMDD_hhmmss;

Day: day number predicted by the CRNN model;

Month: month number inferred manually;

Year: year number inferred manually if month is given and predicted by the CRNN model otherwise;

Date_confidence: confidence in date digitization by the CRNN model;

Date_box_confidence: confidence in date bounding box predicted by the YOLO model;

Hour: hour number  predicted by the CRNN model;

Hour_confidence: confidence in hour digitization by the CRNN model;

Hour_box_confidence: confidence in hour bounding box predicted by the YOLO model;

Minutes: minutes number  predicted by the CRNN model;

Minutes_confidence: confidence in minutes digitization by the CRNN model;

Minutes_box_confidence: confidence in minutes bounding box predicted by the YOLO model;

Seconds: seconds number predicted by the CRNN model;

Seconds_confidence: confidence in seconds digitization by the CRNN model;

Seconds_box_confidence: confidence in seconds bounding box predicted by the YOLO model.


Note that the table contains empty cells in cases where the YOLO model did not find the corresponding text field.

Unknown dates and times are filled with 9999 for years and 99 for other values.

Description of the text detection and recognition methods is given in the paper DOI.

Source code of the models is on https://github.com/observethesun/halpha.
DOI: 10.5281/zenodo.18392561
title: Digitized Metadata of Solar Disk H-alpha Observations At Sacramento Peak Observatory

description: The dataset contains metadata (date and time of observations) extracted from the digitized (scanned) photographic images of solar disk observations in neutral hydrogen H-alpha spectral line made at the U.S. National Solar Observatory at Sacramento Peak during 1966-2002 (https://nispdata.nso.edu/ftp/flare_patrol_h_alpha_sp/).

Digitized text information is presented in a CSV table. The table includes the following columns:



Filename: string with the original file name;

Date: corrected date and time in the format YYYYMMDD_hhmmss;

Day: day number predicted by the CRNN model;

Month: month number inferred manually;

Year: year number inferred manually if month is given and predicted by the CRNN model otherwise;

Date_confidence: confidence in date digitization by the CRNN model;

Date_box_confidence: confidence in date bounding box predicted by the YOLO model;

Hour: hour number  predicted by the CRNN model;

Hour_confidence: confidence in hour digitization by the CRNN model;

Hour_box_confidence: confidence in hour bounding box predicted by the YOLO model;

Minutes: minutes number  predicted by the CRNN model;

Minutes_confidence: confidence in minutes digitization by the CRNN model;

Minutes_box_confidence: confidence in minutes bounding box predicted by the YOLO model;

Seconds: seconds number predicted by the CRNN model;

Seconds_confidence: confidence in seconds digitization by the CRNN model;

Seconds_box_confidence: confidence in seconds bounding box predicted by the YOLO model.


Note that the table contains empty cells in cases where the YOLO model did not find the corresponding text field.

Unknown dates and times are filled with 9999 for years and 99 for other values.

Description of the text detection and recognition methods is given in the paper DOI.

Source code of the models is on https://github.com/observethesun/halpha.
DOI: 10.5061/dryad.kg18b9c
title: Data from: Ultraviolet irradiation increases size of the first clutch but decreases longevity in a marine copepod

description: An important component of life history theory is understanding how natural
 variation arises in populations. Both endogenous and exogenous factors
 contribute to organism survival and reproduction, and therefore, it is
 important to understand how such factors are both beneficial and
 detrimental to population dynamics. One ecologically relevant factor that
 influences the life history of aquatic organisms is ultraviolet (UV)
 radiation. While the majority of research has focused on the potentially
 detrimental effects that UV radiation has on aquatic organisms, few
 studies have evaluated hormetic responses stimulated by radiation under
 select conditions. The goal of this study was to evaluate the impact of
 UV-A/B irradiation on life history characteristics in Tigriopus
 californicus copepods. After exposing copepods to UV-A/B irradiation
 (control, one, and three-hour UV treatments at 0.5 W/m2), we measured the
 impact of exposure on fecundity, reproductive effort, and longevity. We
 found that UV irradiation increased the size of the first clutch among all
 reproducing females in both the one and three-hour experimental groups and
 decreased longevity among all females that mated in the one-hour
 treatment. UV irradiation had no effect on the number of clutches females
 produced. These findings indicate a potential benefit of UV irradiation on
 reproductive performance early in life, although the same exposure came at
 a cost to longevity.
description: Heine et al., UV
 data