cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6031268.v1
title: MOESM2 of The FieldTrip-SimBio pipeline for EEG forward solutions

description: Additional file 2. Example dataset: tlaLeft.mat, mri.mat, segmentedmri.mat, elec_projected.mat. Example dataset as processed in "Source localization of SEP data" section. It contains: tlaLeft.mat—Preprocessed SEP data (cf. Fig. 4); mri.mat—MRI of the subject (cf. Fig. 5, left); segmentedmri.mat—Segmented MRI (cf. Fig. 5, middle); elec_projected.mat—Electrodes aligned to the surface of the headmodel (cf. Fig. 5, right).
DOI: 10.6084/m9.figshare.6031262
title: MOESM1 of The FieldTrip-SimBio pipeline for EEG forward solutions

description: Additional file 1. Sample matlab script fieldtrip_simbio.m. Example script for EEG source analysis using the FieldTrip-SimBio pipeline. Data preprocessing steps are included, but outcommented, use preprocessed data â tlaLeft.matâ from Additional file 2 instead.
DOI: 10.6084/m9.figshare.6031262.v1
title: MOESM1 of The FieldTrip-SimBio pipeline for EEG forward solutions

description: Additional file 1. Sample matlab script fieldtrip_simbio.m. Example script for EEG source analysis using the FieldTrip-SimBio pipeline. Data preprocessing steps are included, but outcommented, use preprocessed data â tlaLeft.matâ from Additional file 2 instead.
DOI: 10.6084/m9.figshare.6031259
title: Additional File 2:

description: Table S5.Â Significantly enriched DAVID GO annotation clusters forÂ three protein groups with different dN/dS estimates. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6031259.v1
title: Additional File 2:

description: Table S5.Â Significantly enriched DAVID GO annotation clusters forÂ three protein groups with different dN/dS estimates. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6031190
title: Genome-scale DNA sequence data and the evolutionary history of placental mammals

description: The genomic data set is comprised of the coding DNA sequences of 5162 loci from 90 vertebrate species, including 82 mammals. <br>cds_5162.zip: the cds datac12_5162.zip: the c12 data<br>The start codon ATG was not properly aligned in cds_5162.zip. This alignment error has been corrected and the new alignments were saved in cds_new.zip and c12_new.zip
DOI: 10.6084/m9.figshare.6031190.v2
title: Genome-scale DNA sequence data and the evolutionary history of placental mammals

description: The genomic data set is comprised of the coding DNA sequences of 5162 loci from 90 vertebrate species, including 82 mammals.
DOI: 10.6084/m9.figshare.6031190.v4
title: Genome-scale DNA sequence data and the evolutionary history of placental mammals

description: The genomic data set is comprised of the coding DNA sequences of 5162 loci from 90 vertebrate species, including 82 mammals. <br>cds_5162.zip: the cds datac12_5162.zip: the c12 data<br>The start codon ATG was not properly aligned in cds_5162.zip. This alignment error has been corrected and the new alignments were saved in cds_new.zip and c12_new.zip
DOI: 10.6084/m9.figshare.6031055
title: The Effect of Alignment Uncertainty, Substitution Models and Priors in Building and Dating the Mammal Tree of Life

description: The CDS sequences derived from Liu et al. (2017) were processed to remove potential low-quality regions and indels. The aligned DNA sequences were trimmed and the sequences corresponding to any unusually long terminal branches were removed. Finally, the first and second codon positions (C12) were extracted from 4 sets of alignments - before trimming (BT), after trimming (AT), filtered by the protocol of Irisarri et al. (FP), and further filtered by comparing ML trees with the reference tree (FM). The extracted C12 positions of the BT, AT, FP, and FM alignment were used here to assess uncertainty of alignments and its effect on gene trees, species trees, and divergence time estimation.
DOI: 10.6084/m9.figshare.6030848
title: A comparison of the effects of water-level policies on the availability of walleye spawning habitat in a boreal reservoir

description: Papenfuss JT, Cross T, Venturelli PA. 2018. A comparison of the effects of water-level policies on the availability of walleye spawning habitat in a boreal reservoir. Lake Reserv Manage. 34:321–333. Water levels in reservoirs can affect the quantity and quality of the habitat that is available for spawning fish and their eggs. We studied how a change in the water-level management policy (“rule curve”) in 2000 affected the availability of walleye (<i>Sander vitreus</i>) spawning habitat in 3 lakes (Kabetogama, Namakan, and Sand Point) that make up a large, boreal reservoir between Canada and the United States. According to observed water-level data, available spawning habitat on known Lake Kabetogama spawning sites increased 95% (<i>P</i> &lt; 0.01) with the 2000 rule curve, but did not change on Namakan or Sand Point lake spawning sites. However, when using modeled water-level data to control for confounding weather events, habitat availability at known spawning sites increased significantly (<i>P</i> &lt; 0.01) on all 3 lakes (179%, 92%, and 93%, respectively). Habitat availability improved because the 2000 rule curve increased mean spring water levels by 0.5 m, and water levels rose more slowly (2.2 vs. 3.0 cm/d) during egg incubation. Our findings suggest that, although water-level management on large reservoirs can be a challenge, carefully designed policies can improve walleye spawning habitat conditions and help to achieve fisheries management goals.
DOI: 10.6084/m9.figshare.6030848.v1
title: A comparison of the effects of water-level policies on the availability of walleye spawning habitat in a boreal reservoir

description: Papenfuss JT, Cross T, Venturelli PA. 2018. A comparison of the effects of water-level policies on the availability of walleye spawning habitat in a boreal reservoir. Lake Reserv Manage. 34:321–333. Water levels in reservoirs can affect the quantity and quality of the habitat that is available for spawning fish and their eggs. We studied how a change in the water-level management policy (“rule curve”) in 2000 affected the availability of walleye (<i>Sander vitreus</i>) spawning habitat in 3 lakes (Kabetogama, Namakan, and Sand Point) that make up a large, boreal reservoir between Canada and the United States. According to observed water-level data, available spawning habitat on known Lake Kabetogama spawning sites increased 95% (<i>P</i> &lt; 0.01) with the 2000 rule curve, but did not change on Namakan or Sand Point lake spawning sites. However, when using modeled water-level data to control for confounding weather events, habitat availability at known spawning sites increased significantly (<i>P</i> &lt; 0.01) on all 3 lakes (179%, 92%, and 93%, respectively). Habitat availability improved because the 2000 rule curve increased mean spring water levels by 0.5 m, and water levels rose more slowly (2.2 vs. 3.0 cm/d) during egg incubation. Our findings suggest that, although water-level management on large reservoirs can be a challenge, carefully designed policies can improve walleye spawning habitat conditions and help to achieve fisheries management goals.
DOI: 10.6084/m9.figshare.6030803
title: Theoretical ribosomal protein mass fingerprint of Oryzias latipes

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Oryzias latipes.<br></i><br>
DOI: 10.6084/m9.figshare.6030800
title: Theoretical ribosomal protein mass fingerprint of Ciona intestinalis

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Ciona intestinalis.</i><br><br>
DOI: 10.6084/m9.figshare.6030800.v1
title: Theoretical ribosomal protein mass fingerprint of Ciona intestinalis

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Ciona intestinalis.</i><br><br>
DOI: 10.6084/m9.figshare.6030794
title: Delayed plumage maturation explains differences in breeding performance of Saffron Finches

description: Theory predicts that, even within the same population, birds may vary their breeding investment with age. This may be due to an improvement in individual quality of old birds in body condition, foraging and in nesting experience. Birds commonly signal age and individual quality to potential mates and competitors through plumage colour. Young male and female breeders of Saffron Finches (<i>Sicalis flaveola</i>) have dull plumages that change to yellow with age. We asked whether older, yellow birds are in better condition and invest more in breeding than dull, younger birds. In southern Brazil, we monitored Saffron Finches breeding in nest-boxes over three breeding seasons. We found that yellow birds were in better condition: females had more furcular fat and males were heavier. Yellow parents bred earlier, had larger clutch sizes, shorter incubation periods, re-nested more and ultimately fledged twice as many offspring as dull parents. Egg mass, nestling mass and nest survival probability were similar between plumage colours. Female colour predicted clutch sizes and incubation periods better than male colour. Our results highlight the importance of accounting for female quality and reproductive investment decisions within the context of sexual selection.
DOI: 10.6084/m9.figshare.6030794.v1
title: Delayed plumage maturation explains differences in breeding performance of Saffron Finches

description: Theory predicts that, even within the same population, birds may vary their breeding investment with age. This may be due to an improvement in individual quality of old birds in body condition, foraging and in nesting experience. Birds commonly signal age and individual quality to potential mates and competitors through plumage colour. Young male and female breeders of Saffron Finches (<i>Sicalis flaveola</i>) have dull plumages that change to yellow with age. We asked whether older, yellow birds are in better condition and invest more in breeding than dull, younger birds. In southern Brazil, we monitored Saffron Finches breeding in nest-boxes over three breeding seasons. We found that yellow birds were in better condition: females had more furcular fat and males were heavier. Yellow parents bred earlier, had larger clutch sizes, shorter incubation periods, re-nested more and ultimately fledged twice as many offspring as dull parents. Egg mass, nestling mass and nest survival probability were similar between plumage colours. Female colour predicted clutch sizes and incubation periods better than male colour. Our results highlight the importance of accounting for female quality and reproductive investment decisions within the context of sexual selection.
DOI: 10.6084/m9.figshare.6030788
title: Australian house sparrow MAP file

description: This is the MAP file for the SNP data used in Andrew et al. (title: Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows).<br>This file includes the 162,299 SNPs after filtering, from the 200K SNP array. This file can be opened in PLINK with the associated PED file.
DOI: 10.6084/m9.figshare.6030788.v2
title: Australian house sparrow MAP file

description: This is the MAP file for the SNP data used in Andrew et al. (title: Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows).<br>This file includes the 162,299 SNPs after filtering, from the 200K SNP array. This file can be opened in PLINK with the associated PED file.
DOI: 10.6084/m9.figshare.6030788.v1
title: Australian house sparrow MAP file

description: This is the MAP file for the SNP data used in Andrew et al. (title: Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows).<br>This file includes the 162,299 SNPs after filtering, from the 200K SNP array. This file can be opened in PLINK with the associated PED file.
DOI: 10.6084/m9.figshare.6030782
title: Australian house sparrow PED file

description: This is the PED file for the SNP data used in Andrew et al. (title: Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows).<br>This file includes the 162,299 SNPs after filtering, from the 200K SNP array. This file can be opened in PLINK and other programs with the associated MAP file.<br>
DOI: 10.6084/m9.figshare.6030782.v1
title: Australian house sparrow PED file

description: This is the PED file for the SNP data used in Andrew et al. (title: Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows).<br>This file includes the 162,299 SNPs after filtering, from the 200K SNP array. This file can be opened in PLINK and other programs with the associated MAP file.<br>
DOI: 10.6084/m9.figshare.6030782.v2
title: Australian house sparrow PED file

description: This is the PED file for the SNP data used in Andrew et al. (title: Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows).<br>This file includes the 162,299 SNPs after filtering, from the 200K SNP array. This file can be opened in PLINK and other programs with the associated MAP file.<br>
DOI: 10.6084/m9.figshare.6030776
title: upload data.xlsx

description: Manuscript Title: Root diameter predicts the extramatrical hyphal exploration distance of the ectomycorrhizal fungal community<br>Journal: Ecosphere<br>Relative abundance of each exploration type across plots of all tree species.
DOI: 10.6084/m9.figshare.6030758
title: expression matrix

description: DESeq2 normalized read counts of nine Drosophila species
DOI: 10.6084/m9.figshare.6030743
title: annotation

description: updated annotation of nine Drosophila species
DOI: 10.6084/m9.figshare.6030758.v1
title: expression matrix

description: DESeq2 normalized read counts of nine Drosophila species
DOI: 10.6084/m9.figshare.6030743.v1
title: annotation

description: updated annotation of nine Drosophila species
DOI: 10.6084/m9.figshare.6030731
title: Exercise COE data mastersheet.xlsx

description: Understanding of physiological responses of organisms is typically based on data collected during an isolated event. Although many fundamental insights have been gained from these studies, evaluating the response to a single event ignores the fact that each individual has experienced a unique set of events throughout its life that may have altered its physiology. The idea that prior experiences can influence subsequent performance is known as a carry-over effect. Carry-over effects may explain much of the variation in performance found among individuals. For example, high physical activity has been shown to improve mitochondrial respiratory function and biogenesis and reduce oxidative stress and has been linked to improved health and longevity. In this study, we asked if the bioenergetic differences between active and inactive individuals carry over to impact performance in a subsequent reproductive event and alter a females' reproductive outcome. Female mice that had access to running wheel for a month before mating gave birth to a larger litter and weaned a heavier litter, indicating that high physical activity had a positive carry-over effect to reproduction. Mice that ran also displayed higher mitochondria respiration and biogenesis with no changes in endogenous antioxidant enzymes. These results provide a mechanistic framework for how the conditions that animals experience before breeding can impact reproductive outcomes.
DOI: 10.6084/m9.figshare.6030731.v1
title: Exercise COE data mastersheet.xlsx

description: Understanding of physiological responses of organisms is typically based on data collected during an isolated event. Although many fundamental insights have been gained from these studies, evaluating the response to a single event ignores the fact that each individual has experienced a unique set of events throughout its life that may have altered its physiology. The idea that prior experiences can influence subsequent performance is known as a carry-over effect. Carry-over effects may explain much of the variation in performance found among individuals. For example, high physical activity has been shown to improve mitochondrial respiratory function and biogenesis and reduce oxidative stress and has been linked to improved health and longevity. In this study, we asked if the bioenergetic differences between active and inactive individuals carry over to impact performance in a subsequent reproductive event and alter a females' reproductive outcome. Female mice that had access to running wheel for a month before mating gave birth to a larger litter and weaned a heavier litter, indicating that high physical activity had a positive carry-over effect to reproduction. Mice that ran also displayed higher mitochondria respiration and biogenesis with no changes in endogenous antioxidant enzymes. These results provide a mechanistic framework for how the conditions that animals experience before breeding can impact reproductive outcomes.
DOI: 10.6084/m9.figshare.6030656
title: Ecology shapes the evolutionary trade-off between predator avoidance and defence in coral reef butterflyfishes

description: The data include morphometric measurements of traits important in predator defence, detection and avoidance, and ecological classifications of foraging strategy and social behaviour. The datafile details the butterflyfish species examined, the number of specimens measured per species, the collections the specimens were loaned from and their catalogue numbers, the species-averaged morphometric measurements (mm), and the ecological data classifications of species' foraging strategies and social behaviour, with references.
DOI: 10.6084/m9.figshare.6030656.v1
title: Ecology shapes the evolutionary trade-off between predator avoidance and defence in coral reef butterflyfishes

description: The data include morphometric measurements of traits important in predator defence, detection and avoidance, and ecological classifications of foraging strategy and social behaviour. The datafile details the butterflyfish species examined, the number of specimens measured per species, the collections the specimens were loaned from and their catalogue numbers, the species-averaged morphometric measurements (mm), and the ecological data classifications of species' foraging strategies and social behaviour, with references.
DOI: 10.6084/m9.figshare.6030578
title: The cellular and molecular effects of the androgen receptor agonist, Cl-4AS-1, on breast cancer cells

description: <b>Purpose</b>: The androgen receptor (AR) has attracted attention in the treatment of breast cancer. Due to the undesirable side effects of AR agonists, attempts have been undertaken to develop selective AR modulators. One of these compounds is Cl-4AS-1. This study examined this compound more closely at the cellular and molecular levels. <b>Methods</b>: Three different breast cancer cell lines were utilized, namely the luminal MCF-7 cells, the molecular apocrine MDA-MB-453 cells, and the triple negative, basal MDA-MB-231 cells. <b>Results</b>: High and significant concordance between dihydrotestosterone (DHT) and Cl-4AS-1 in regulation of gene expression in MDA-MB-453 cells was found. However, some differences were noted including the expression of AR, which was upregulated by DHT, but not Cl-4AS-1. In addition, both DHT and Cl-4AS-1 caused a similar morphological change and reorganization of the actin structure of MDA-MB-453 cells into a mesenchymal phenotype. Treatment of cells with DHT resulted in induction of proliferation of MCF-7 and MDA-MB-453 cells, but no effect was observed on the growth of MDA-MB-231 cells. On the other hand, increasing doses of Cl-4AS-1 resulted in a dose-dependent inhibition on the growth of the three cell lines. This inhibition was a result of induction of apoptosis whereby Cl-4AS-1 caused a block in entry of cells into the S-phase followed by DNA degradation. <b>Conclusions</b>: These results indicate that although Cl-4AS-1 has characteristics of classical AR agonist, it has dissimilar properties that may make it useful in treating breast cancer.
DOI: 10.6084/m9.figshare.6030578.v1
title: The cellular and molecular effects of the androgen receptor agonist, Cl-4AS-1, on breast cancer cells

description: <b>Purpose</b>: The androgen receptor (AR) has attracted attention in the treatment of breast cancer. Due to the undesirable side effects of AR agonists, attempts have been undertaken to develop selective AR modulators. One of these compounds is Cl-4AS-1. This study examined this compound more closely at the cellular and molecular levels. <b>Methods</b>: Three different breast cancer cell lines were utilized, namely the luminal MCF-7 cells, the molecular apocrine MDA-MB-453 cells, and the triple negative, basal MDA-MB-231 cells. <b>Results</b>: High and significant concordance between dihydrotestosterone (DHT) and Cl-4AS-1 in regulation of gene expression in MDA-MB-453 cells was found. However, some differences were noted including the expression of AR, which was upregulated by DHT, but not Cl-4AS-1. In addition, both DHT and Cl-4AS-1 caused a similar morphological change and reorganization of the actin structure of MDA-MB-453 cells into a mesenchymal phenotype. Treatment of cells with DHT resulted in induction of proliferation of MCF-7 and MDA-MB-453 cells, but no effect was observed on the growth of MDA-MB-231 cells. On the other hand, increasing doses of Cl-4AS-1 resulted in a dose-dependent inhibition on the growth of the three cell lines. This inhibition was a result of induction of apoptosis whereby Cl-4AS-1 caused a block in entry of cells into the S-phase followed by DNA degradation. <b>Conclusions</b>: These results indicate that although Cl-4AS-1 has characteristics of classical AR agonist, it has dissimilar properties that may make it useful in treating breast cancer.
DOI: 10.6084/m9.figshare.6030572
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v1
title: All Figure Data

description: Experimental data for figures 3, 4 and 5.
DOI: 10.6084/m9.figshare.6030572.v2
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5.
DOI: 10.6084/m9.figshare.6030572.v3
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v4
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v5
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v6
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v7
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v9
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6030572.v8
title: Figure Data for "Surfing it own wave: hydroelastic migration of a particle near a membrane"

description: Experimental data for figures 3, 4 and 5; and movie for figure 1.
DOI: 10.6084/m9.figshare.6029801
title: Figure 5 Data

description: Experimental data for Figure 5.