cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/agr-rf8-hkl
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bjm-g62-6rk
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vbj-6k7-bet
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ehz-1et-dfz
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mxw-1ph-q97
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xnp-xb3-ze0
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5281/zenodo.16946293
title: Comprehensive defect detection in mouse embryos and in the heart by combining automated phenotyping with novel population averages and atlases.

description: This data set is associated with the following publication:

Comprehensive defect detection in mouse embryos and in the heart by combining automated phenotyping with novel population averages and atlases.

DOI:

 

Contents



E12.5_Population_Average_16bit_5um.nrrd


16-bit E12.5 population average with a voxel size of 5 µm in NRRD format

 



E12.5_Atlas_5um.nrrd


E12.5 atlas with a voxel size of 5 µm in 8-bit NRRD format

 



E12.5_labels_5um.csv


Meta-data file for 5 µm E12.5 atlas

 



E12.5_stats_mask_5um.nrrd


E12.5 tight mask with a voxel size of 5 µm in 8-bit NRRD format

 



E12.5_fixed_mask_5um.nrrd


E12.5 rough mask with a voxel size of 5 µm in 8-bit NRRD format

 

Population average, atlas, atlas meta-data, and mask files are also provided at 7µm resolution for E12.5 and for stages E15.5 (14 µm), E17.5 (14 µm and 28 µm resolutions), and E18.5 isolated heart (4.95 µm).

The following LAMA configuration files are provided:



pop_avg_pairwise.toml


LAMA config file for creating a population average using the parallel_average_pairwise.py script

 



generate_data.toml


LAMA config file for registering wild type and mutant data to the population average

 



lama_stats.toml


LAMA config file for performing statistical analysis using the lama_stats script.

 



permutation_stats.yaml


LAMA config file for performing statistical analysis using the lama_permutation_stats script.
DOI: 10.5281/zenodo.16946294
title: Comprehensive defect detection in mouse embryos and in the heart by combining automated phenotyping with novel population averages and atlases.

description: This data set is associated with the following publication:

Comprehensive defect detection in mouse embryos and in the heart by combining automated phenotyping with novel population averages and atlases.

DOI:

 

Contents



E12.5_Population_Average_16bit_5um.nrrd


16-bit E12.5 population average with a voxel size of 5 µm in NRRD format

 



E12.5_Atlas_5um.nrrd


E12.5 atlas with a voxel size of 5 µm in 8-bit NRRD format

 



E12.5_labels_5um.csv


Meta-data file for 5 µm E12.5 atlas

 



E12.5_stats_mask_5um.nrrd


E12.5 tight mask with a voxel size of 5 µm in 8-bit NRRD format

 



E12.5_fixed_mask_5um.nrrd


E12.5 rough mask with a voxel size of 5 µm in 8-bit NRRD format

 

Population average, atlas, atlas meta-data, and mask files are also provided at 7µm resolution for E12.5 and for stages E15.5 (14 µm), E17.5 (14 µm and 28 µm resolutions), and E18.5 isolated heart (4.95 µm).

The following LAMA configuration files are provided:



pop_avg_pairwise.toml


LAMA config file for creating a population average using the parallel_average_pairwise.py script

 



generate_data.toml


LAMA config file for registering wild type and mutant data to the population average

 



lama_stats.toml


LAMA config file for performing statistical analysis using the lama_stats script.

 



permutation_stats.yaml


LAMA config file for performing statistical analysis using the lama_permutation_stats script.
DOI: 10.3535/awp-tek-pfd
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cv4-sqb-wp3
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/f2c-338-595
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/glq-mng-k2g
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.4tn48
title: Data from: Imperfect vaccination can enhance the transmission of highly virulent pathogens

description: Could some vaccines drive the evolution of more virulent pathogens?
 Conventional wisdom is that natural selection will remove highly lethal
 pathogens if host death greatly reduces transmission. Vaccines that keep
 hosts alive but still allow transmission could thus allow very virulent
 strains to circulate in a population. Here we show experimentally that
 immunization of chickens against Marek's disease virus enhances the
 fitness of more virulent strains, making it possible for hyperpathogenic
 strains to transmit. Immunity elicited by direct vaccination or by
 maternal vaccination prolongs host survival but does not prevent
 infection, viral replication or transmission, thus extending the
 infectious periods of strains otherwise too lethal to persist. Our data
 show that anti-disease vaccines that do not prevent transmission can
 create conditions that promote the emergence of pathogen strains that
 cause more severe disease in unvaccinated hosts.
description: Experiment
 1Data_and_R_code_for_Fig1_and_S1Fig1_and_S1.zipExperiment 2Data and R code for Fig2_and_S2Fig2_and_S2.zipExperiment 3Data and R code for Fig3_and_S3Fig3_and_S3.zipExperiment 4Data and R code for Fig 4Fig4.zip
DOI: 10.3535/4qc-4v6-5vy
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/srr-427-aml
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wdp-2b9-0w6
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/j0z-bad-5gs
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mb5-slx-62j
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nhb-dbr-gv8
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6ek-5tp-kvk
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9pz-kjh-1v6
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vxm-nzc-mxt
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.8753
title: Data from: Are pollination "syndromes" predictive? Asian dalechampia fit neotropical models

description: Using pollination-syndrome parameters and pollinator correlations with
 floral phenotype from the neotropics, we predicted that Dalechampia
 bidentata Blume (Euphorbiaceae) in southern China would be pollinated by
 female resin-collecting bees between 12 and 20 mm in length. Observations
 in southwestern Yunnan Province, China, revealed pollination by
 resin-collecting, female Megachile (Callomegachile) nr. faceta Bingham
 (Hymenoptera: Megachilidae). These bees, at 14 mm in length, were in the
 predicted size range, confirming the utility of syndromes and models
 developed in distant regions. Phenotypic-selection analyses and estimation
 of adaptive surfaces and adaptive accuracies together suggest that the
 blossoms of D. bidentata are well adapted to pollination by their most
 common floral visitors.
description: bract-gland
 selectionBee visitation to
 blossoms of Dalechampia bidentata in relation to area of resin gland and
 size of upper bracts.GSD-selection_femaleRate of contact with stigmas in relation to gland-stigma distance in blossoms with no male flowers open.GSD-selection_bisexual-bRate of bee contact with stigmas of Dalechampia bidentata in relation to the gland-stigma distance, bisexual blossoms.
DOI: 10.3535/nmc-ef1-p8d
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pdc-dq3-2we
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sva-8ve-m9d
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x28-dcs-x4b
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1dm-b1r-9bn
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7mv-w6n-gk0
title: Paralogania ex gr. martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/18e-avt-2xn
title: Paralogania martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ea8-5j9-s6n
title: Paralogania martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qdp-97c-nae
title: Paralogania martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v6a-09r-8ej
title: Paralogania martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.63p7r97
title: Data from: Using root traits to understand temporal changes in biodiversity effects in grassland mixtures.

description: Biodiversity-ecosystem functioning (BEF) studies typically show that
 species richness enhances community biomass, but the underlying mechanisms
 remain debated. Here, we combine metrics from BEF research that
 distinguish the contribution of dominant species (selection effects, SE)
 from those due to positive interactions such as resource partitioning
 (complementarity effects, CE) with a functional trait approach in an
 attempt to reveal the functional characteristics of species that drive
 community biomass in species mixtures. In a biodiversity experiment with
 16 plant species in monocultures, 4-species and 16-species mixtures, we
 used aboveground biomass to determine the relative contributions of CE and
 SE to biomass production in mixtures in the second, dry year of the
 experiment. We also measured root traits (specific root length, root
 length density, root tissue density and the deep root fraction) of each
 species in monocultures and linked the calculated community weighted mean
 (CWM) trait values and trait diversity of mixtures to CE and SE. In the
 second year of the experiment, community biomass, CE and SE increased
 compared to the first year. The contribution of SE to this positive effect
 was greater than that of CE. The increased contribution of SE was
 associated with root traits: SE increased most in communities with high
 abundance of species with deep, thick and dense roots. In contrast,
 changes in CE were not related to trait diversity or CWM trait values.
 Together, these results suggest that increased positive effects of species
 richness on community biomass in a dry year were mainly driven by
 increased dominance of deep-rooting species, supporting the insurance
 hypothesis of biodiversity. Positive CE indicates that other positive
 interactions did occur, but we did not find evidence that belowground
 resource partitioning or facilitation via root traits was important for
 community productivity in our biodiversity experiment.
description: Community performance
 and traitsPlot information,
 yielded biomass, calculated biodiversity effects and calculated root trait
 averages (community weighted means) and root trait diversity (Functional
 dispersion).root traits monocultures
 2015 per plotRoot traits measured in
 all monocultures in 2015 (0-50 cm depth).soil moisture data
 (TDR)Plot soil moisture
 (volumetric) during the drought in 2015, measured with a
 TDR.TDR
 data.csv
DOI: 10.3535/r24-emr-a73
title: Paralogania martinssoni (Gross, 1967)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.9dk62
title: Data from: The phylogenetic likelihood library

description: We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized
 application programming interface for developing likelihood-based
 phylogenetic inference and post-analysis software. The PLL implements
 appropriate data structures and functions that allow users to quickly
 implement common, error-prone, and labor-intensive tasks, such as
 likelihood calculations, model parameter as well as branch length
 optimization, and tree space exploration. The highly optimized and
 parallelized implementation of the phylogenetic likelihood function and a
 thorough documentation provide a framework for rapid development of
 scalable parallel phylogenetic software. By example of two
 likelihood-based phylogenetic codes we show that the PLL improves the
 sequential performance of current software by a factor of two to ten while
 requiring only one month of programming time for integration. We show
 that, when numerical scaling for preventing floating point underflow is
 enabled, the double precision likelihood calculations in the PLL are up to
 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with
 2,000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling
 enabled and required). The PLL is available at http://www.libpll.org under
 the GNU General Public License (GPL).
description: Supplementary
 MaterialOnline supplementary
 material supporting the main text. Contains three sections: 1)
 Experimental results when using the PThreads and MPI version of PLL 2)
 Details about the comparison with BEAGLE 3) TreeBase Matrix IDs used for
 assessing the performance of IQ-Treesuppl.pdf
DOI: 10.5061/dryad.jk353fs
title: Data from: Copepod respiration increases by 7% per degree °C increase in temperature: a meta-analysis

description: Exponential increase in respiration rate with increasing temperature in
 poikilotherms is well documented, however, the overall rate of change
 varies greatly across copepod taxa. Studies often report magnitude of
 change, but the rate of change in respiration across multiple temperatures
 is equivocal. We used 32 studies spanning 78 years of research and 50
 copepod species (three orders) to quantify percent increase in respiration
 rates per one-unit increase in temperature. We found that copepod
 respiration rates increased with temperature by 7% across three
 well-studied orders, Calanoida, Cyclopoida, and Harpacticoida. Neither
 food availability nor scaling respiration to copepod dry weight affected
 the rate of change of respiration rates. Studies using Winkler titration
 to measure oxygen consumption produced significantly larger percent
 changes in respiration, whereas newer methods such as fiber optics
 produced smaller effects. These results have far reaching implications,
 suggesting that copepods can adapt to increasing temperatures brought
 forth by climate change.
description: Copepod Meta-analysis
 Data: Temperature Effects on Copepod RespirationThis file contains data
 collected from the literature to conduct a formal meta-analysis
 quantifying percent change in copepod respiration rates per one-unit
 change in temperature. Study methodology, food availability, and the
 incorporation of dry weight into respiration measurements, were modeled as
 categorical moderators.Meta-analysis Data, Heine et
 al..xlsxMetaData, Heine et
 al.
DOI: 10.5061/dryad.718q8
title: Data from: Combined effects of retention forestry and prescribed burning on polypore fungi

description: 1. Retention forestry and prescribed burning aim to alleviate the negative
 effects of forestry on biodiversity by maintaining the structural elements
 of natural forests in managed forests. We present the long-term effects of
 these methods on polypore fungi, a taxonomic group that has been severely
 affected by forestry. 2. Using a 10-year, large-scale field experiment, we
 studied how prescribed burning and two different tree retention levels (10
 and 50 m3 ha−1) affect polypore fungi. We monitored polypore sporocarps on
 2767 individually marked trees four times over the study period: in the
 first autumn after the treatments, and again 2, 4 and 10 years after the
 treatments. 3. The number of polypore species and records initially
 increased rather slowly but showed a marked increasing trend towards the
 end of the 10-year monitoring period. After 2 years, the higher retention
 sites had an average 8·5 species and the low retention sites 4·5 species
 per site. After 4 years, the difference was 14 vs. 9 species and after 10
 years 26 vs. 19 species. Red-listed species were not found often on the
 trunks earlier than 10 years after the treatments. 4. Prescribed burning
 increased the number of polypore species and records along with time.
 Furthermore, 13 species favoured burned sites, while only six species
 favoured unburned sites, and the differences in the composition of species
 assemblages between burned and unburned sites were evident 10 years after
 the treatments. 5. Synthesis and applications. We show, for the first
 time, that retention trees can host rich polypore assemblages, and even
 some red-listed species, and, thus, be useful in conservation of forest
 biodiversity outside protected areas. Higher retention levels maintain
 more diverse polypore assemblages. Prescribed burning increases the
 positive effects of retention forestry by creating substrates that are
 typical in the early-successional natural forests.
description: Polypore fungi on
 retention treesData include fungi
 occurrences on individual trees in two retention levels in years 2003,2005
 and 2011.Dryad_Data_JAPPL-2014-01145A.xlsx
DOI: 10.5061/dryad.h234b36
title: Data from: Solitary ecology as a phenomenon extending beyond insular systems: exaptive evolution in Anolis lizards

description: The mechanisms driving phenotypic evolution have been of interest to
 biologists since Darwin. Ecological release—wherein adaptive evolution
 occurs following relaxation of constraining selective pressures—and
 environmental filtering—wherein exaptive traits allow colonization of a
 new area—have been studied in several insular cases. Anolis lizards, which
 may exist in solitude or sympatry with multiple congeners, are an
 excellent system for evaluating whether ecological release and
 environmental filtering are associated with phenotypic shifts across
 phylogenetic and geographical scales. Insular solitary Anolis exhibit
 phenotypic differentiation in body size and sexual size
 dimorphism—SSD—through exaptive and adaptive evolution, respectively. But,
 the generality of these effects has not yet been addressed. Here, we
 analyse the evolution of body size and SSD relative to sympatry in
 mainland Anolis. We found that mainland species co-occurring with few
 congeners exhibit uniform body size and greater SSD relative to other
 random mainland assemblages, consistent with the insular solitary pattern.
 The locations of evolutionary shifts for both traits do not coincide with
 evolutionary transitions to decreased levels of sympatry. These results
 are consistent with exaptive environmental filtering but not adaptive
 ecological release. Future studies should be conducted at local scales to
 evaluate the role of these factors in the evolution of solitary existence
 in mainland and island species.
description: anole_phylogenyPhylogeny of Anolis lizards from Poe et al. 2017Full_Codedataset_Anolisbody size, sexual size dimorphism, region and ecological state for Anolis lizards.DRYAD_dataset_FINAL_Upload.csv
DOI: 10.5061/dryad.4k03n
title: Data from: How do leaf trait values change spatially and temporally with light availability in a grassland diversity experiment?

description: Complementarity in light use might increase light exploitation and could
 be an important mechanism explaining the coexistence of multiple species
 in plant communities of increasing diversity. We measured vertical light
 profiles and leaf traits related to light acquisition and light use in 40
 mixtures of varying species richness (SR, 2, 4, 8 and 16) and functional
 group richness (FR, 1-4) in a large grassland biodiversity experiment at
 five different times during the growing season. Light attenuation within
 the canopy differed significantly among mixtures of varying SR at peak
 biomass, with 40% in 2-species mixtures and up to 80% in 16-species
 mixtures. In contrast, increasing SR did not affect light attenuation at
 the beginning of the growing season or during regrowth after mowing, when
 large fractions of incoming radiation reached the ground level. These
 patterns suggested the presence of highly variable light niches over space
 and time. Trait expression differed among functional groups (except
 specific leaf area (SLA)) and varied within the growing season. However,
 we found no direct effect of increased SR or FR on the expression of leaf
 traits, except for positive species richness-effects on SLA at peak
 biomass time. SLA and stomatal conductance increased and leaf dry matter
 content decreased at lower light at leaf height, while leaf greenness was
 independent of relative light availability. Dissimilarity of leaf traits
 (except SLA) at the community level increased with increasing SR. Thus,
 our results suggest that after accounting for light availability, which
 was driven by SR and time of year, variations in leaf trait expression
 within the grassland canopies did not depend on SR, but rather on
 functional group identity and time of year. Consequently, increased
 complementarity in light use at higher plant diversity is due to presence
 of more species with different leaf trait expression and trait variation
 in response to the actual light environment.
description: Leaf trait and light
 measurements Jena Experiment 2011The data folder
 comprises three csv-files with plant trait and light measurements
 conducted within the Jena Experiment in 2011. Information of each column
 is given in the header of each file.JENA.2011.Bachmann.zip