Find research datasets worth reusing

Fig. 1 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 1. Development and reversion of the three morphological variables exposed to nine hours of hypoxia, followed by three hours of normoxia in Piaractus mesopotamicus. (a) lower lip, (b) maxillary, and (c) opercular valve. Capital letters above box plots indicate groups in multiple comparisons (Tukey's tests) after repeated measures ANOVA.

Fig. 4 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 4. Response curves of behavioral and respiratory variables of Piaractus mesopotamicus respect to dissolved oxygen gradient. Black arrow indicates inflection point given by the four parameters logistic function. The curve fitted to data points is not shown for horizontal and vertical movements due to the great dispersion.

Fig. 5 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 5. Comparisons of plasticity among behavioral (a), respiratoy (b) and morphological traits (c) of Piaractus mesopotamicus as measured by the coefficient of variation (CV) across the DO gradient. Capital letters above box plots indicate groups in multiple comparison Tukey's tests after a one way ANOVA. Names of traits as defined in the text.

Fig. 2 in Phenotypic plasticity associated to environmental hypoxia in the neotropical serrasalmid Piaractus mesopotamicus (Holmberg, 1887) (Characiformes: Serrasalmidae)

Fig. 2. Photographs showing increases in size of the three morphological traits of Piaractus mesopotamicus analyzed exposed to extreme hypoxia: (a) lower lip, (b) maxillary, and (c) opercular valve. White arrow indicates the area where the expansion of dermal tissue occurred.

opencc-by-4.0Jun 2021View details →

Differential associations between nucleotide polymorphisms and physiological traits in Norway spruce (Picea abies Karst.) provenances under contrasting water regimes

Three datasets are provided here, yielded by a study on drought-stressed and control (well-watered) seedlings of Norway spruce (Picea abies Karst.), coming from 5 provenances distributed along a steep altitudinal gradient from 550 to 1,280 m a.s.l. in central Slovakia: 1. physiological traits 2. double-digest restriction-site associated sequencing data (ddRAD) 3. nuclear microsatellite (nSSR) genotypes

opencc-by-4.0Jun 2010View details →

Image 1 in Parasitic associations of a threatened Sri Lankan rainforest rodent, Mus mayori pococki (Rodentia: Muridae)

Image 1. Photomicrographs of the intestinal parasitic eggs & the larva detected in faecal samples of Mus mayori.

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Phylogenetic signals in host-parasite associations for Neotropical bats and Nearctic desert rodents

Hosts and their parasites have strong ecological and evolutionary relationships, with hosts representing habitats and resources for parasites. In the present study, we use approaches developed to evaluate the statistical dependence of species trait values on phylogenetic relationships to determine whether host–parasite relationships (i.e. parasite infections) are contingent on host phylogeny. If host–parasite relationships are contingent on the ability of hosts to provide habitat or resources to parasites, and if host phylogeny is an effective surrogate for among-host variation in habitat and resource quality, host–parasite relationships should evince phylogenetic signals (i.e. be contingent on host phylogeny). Because the strength of ecological relationships between parasites and their hosts may affect the likelihood of phylogenetic signals occurring in host–parasite relationships, we hypothesized that (1) host specificity would be positively correlated with the strength of phylogenetic signals and (2) the strength of phylogenetic signals will be greater for parasites that rely more on their host throughout their life cycle. Analyses were conducted for ectoparasites from tropical bats and for ectoparasites, helminths, and coccidians from desert rodents. Phylogenetic signals were evaluated for parasite presence and for parasite prevalence. The frequency of phylogenetic signal occurrence was similar for parasite presence and prevalence, with a signal detected in 24–27% of cases at the species level and in 67% and 15% of cases at the genus level for parasites of bats and rodents, respectively. No differences in signal strength or the likelihood of detecting a signal existed between groups of parasites. Phylogenetic signal strength was correlated with host specificity, suggesting that mechanisms increasing host specificity also increase the likelihood of a phylogenetic signal in host use by parasites. Differences in the transmission mode did not affect signal strength or the likelihood of detecting a signal, indicating that variation in host switching opportunities associated with the transmission mode does not affect signal strength.

opencc-zeroDec 2014View details →

dryad40/100

Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms

In the United States, forest genetics research began over 100 years ago and loblolly pine breeding programs were established in the 1950s. However, the genetics underlying complex traits of loblolly pine remains to be discovered. To address this, adaptive and growth traits were measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.) population. Over 2.8 million single nucleotide polymorphism (SNP) markers detected from exome sequencing were used to test for single locus associations, SNP-SNP interactions and correlation of individual heterozygosity with phenotypic traits. A total of 36 SNP-trait associations were found for specific leaf area (5 SNPs), branch angle (2), crown width (3), stem diameter (4), total height (9), carbon isotope discrimination (4), nitrogen concentration (2), and pitch canker resistance traits (7). Eleven SNP-SNP interactions were found to be associated with branch angle (1 SNP-SNP interaction), crown width (2), total height (2), carbon isotope discrimination (2), nitrogen concentration (1), and pitch canker resistance (3). Non-additive effects imposed by dominance and epistasis account for a large fraction of the genetic variance for the quantitative traits. Genes that contain the identified SNPs have a wide spectrum of functions. Individual heterozygosity positively correlated with water use efficiency and nitrogen concentration. In conclusion, multiple effects identified in this study influence the performance of loblolly pines, provide resources for understanding the genetic control of complex traits, and have potential value for assessing with breeding through marker assisted selection and genomic selection.

opencc-zeroDec 2018View details →

dryad40/100

Data from: Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri

Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations. We analysed new SNP data of 444 plants with the same methodology (partial Mantel tests, PMTs) as in the original study and additionally with a latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41% (PMTs) and 51% (LFMM) were associated with environmental factors in the independent data set. However, only 5% (PMTs) and 15% (LFMM) of the associations showed the same environment–allele relationships as in the original study. In total, we found 11 genes (31%) containing the same association in the original and independent data set. These can be considered prime candidate genes for environmental adaptation at a broader geographical scale. Our results suggest that selection pressures in highly heterogeneous alpine environments vary locally and signatures of selection are likely to be population-specific. Thus, genotype-by-environment interactions underlying adaptation are more heterogeneous and complex than is often assumed, which might represent a problem when testing for adaptation at specific loci.

opencc-zeroDec 2015View details →

opencc-by-4.0Jun 2021View details →

/ourguy/ mentions and associated names on 4chan/pol/

Datasets related to the meme '<a href="https://knowyourmeme.com/memes/is-he-our-guy">/ourguy/</a>' on 4chan/pol/, used in <a href="https://doi.org/10.1177/14614448221078274">this paper</a>. The data are all derived from 4CAT, a tool that archives 4chan, and consist of the following: <ul> <li>ourguy_mentions_4chanpol_no_referrals.csv: Posts on 4chan/pol/ where either the body or subject text mentions one of the following: "our guy", "ourguy", "/our guy/", or "/ourguy/".</li> <li>ourguy_mentions_4chanpol.csv: The same dataset as the first, but here I also added posts that were replied-to with an implicit /ourguy/-referral in the original dataset (e.g. without a name - 'Yes, he's definitely /ourguy/'). I identified this by marking which posts were implicit referrals (for time reasons, I only did so for sanitised text that appeared twice or more). With the implicit referrals, I checked whether they started with two greater-than signs and an integer, representing a reply on 4chan (e.g. '>>12345678'). I extracted the posts numbers from these replies, queried them in 4CAT, and added the results to the above dataset. Finally, I deleted any duplicates.</li> <li>ourguy_counts.xlsx: Numbers for the amount of posts per month and day from the first dataset, with area graphs (hence the .xlsx).</li> <li>top_ourguys.csv: The top names of public figures associated to /ourguy/. I extracted these in two ways. First, I used SpaCy's language model for entity recognition to extract tokens recognised as a PERSON entity (in either the body or subject). I also used word collocations to extract names surrounding '/ourguy/' (window size of six). I then merged these and filtered out the valid names. I did not consider posts where three or more PERSON-entities were recognised to prevent spam from dominating. I also did not account for polysemy and separated surnames from given names so only one token remained.</li> <li>top_ourguys_month.csv: The same as top_ourguys.csv, but separated per month.</li> </ul> All data ranges from late November 2013 to 28 May 2020.

opencc-by-4.0Jun 2015View details →

Dataset and Code: Pain and sickness behavior associated with corneal lesions in dairy calves

This is the dataset and code for the analysis of sickness behaviors in calves within corneal lesions (IBK or pinkeye).

openmit-licenseOct 2015View details →

Code and Data associated to Salazar et al. (2015) MolEcol

This is the first release Abundance table, auxiliary data, phylogeny and code for the particle-attached and free-living prokaryotes detected in 30 globally distributed stations from the Malaspina 2010 Expedition. Corresponds to 16SrDNA amplicons Illumina-based sequencing. Associated to publication: Salazar G., Cornejo-Castillo F.M., Borrull E., Díez-Vives C., Lara E., Vaqué D., Arrieta J.M., Duarte C.M., Gasol J.M. and Acinas S.G. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. (2015) Molecular Ecology. doi:10.1111/mec.13419

opencc-zeroJan 2016View details →

Common Genetic Variants in FOXP2 are Not Associated with Individual Differences in Language Development

Three data sets used in” Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development” are provided.  The discovery data set was comprised of 834 children who were members of a Longitudinal sample and children who were members of a School sample.  Both samples are contained in the Iowa data set.  The Iowa data set contains a quantitative variable LCOMP that represents a composite z-score representing oral language ability.  The data set also identifies which sample the children belonged to and the allele calls for 13 tag SNPs located across FOXP2.  A second data file, ELVS, contains data from a separate sample of children who were used to test for replication of inconsistent evidence of an association between language and the SNP rs1916988.  The ELVS file provides a composite oral language score scaled in standard score units (mean=100, SD=15) and the genotype calls for the  SNP rs1916988.

opencc-zeroFeb 2016View details →

Example phenopacket containing one disease and two associations

This is an example of a nascent exchange format "Phenopacket". For more information, see github.com/phenopackets

opencc-zeroJul 2016View details →

Data and modeling results for publication: Landscape genetics indicate recently increased habitat fragmentation in African forest-associated chafers

<ul> <li>DNA sequences: cox1 and ITS1 alignments</li> <li>spatial records (in hypervolume archive)</li> <li>spatial principal component 1-3 used for hypervolume models (in hypervolume archive)</li> <li>Present and past species distribution models (SDMs): <ul> <li>biomod2 ensemble SDMs <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li>biomod2 SDMs for single PMIP3 models <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li>hypervolume SDMs</li> </ul> </li> <li>landscape connectivity models <ul> <li>circuitscape (for F0, F1, and F2)</li> <li>least cost corridors and paths (for F0, F1, and F2)</li> </ul> </li> </ul>

opencc-by-4.0Sep 2016View details →

Analog series-based scaffolds from ChEMBL with associated activity information

Reported is the activity information for the 12,294 analog series-based (ASB) scaffolds extracted from ChEMBL database. For each ASB scaffold structural and activity information for all analogs comprising the analog series is provoded.

FIGURES 1 – 8. Lopheucoila anastrephae. 1 in Eucoilinae species (Hymenoptera: Cynipoidea: Figitidae) parasitoids of fruitinfesting dipterous larvae in Brazil: identity, geographical distribution and host associations

FIGURES 1 – 8. Lopheucoila anastrephae. 1. Head, anterior view (183 x, 100 m); 2. Female antenna (58 x, 250 m); 3. Flagellomerous 1 and 2 of male (170 x, 100 m); 4. Pronotal plate (160 x, 100 m); 5. Head, mesosoma and anterior part of metasoma, lateral view (74 x, 250 m); 6. Mesosoma, dorsal view (172 x, 100 m); 7. Forewing (10 x, 0,5 mm); 8. Metacoxa (163 x, 100 m).

FIGURES 9 – 15. Tropideucoila weldi. 9 in Eucoilinae species (Hymenoptera: Cynipoidea: Figitidae) parasitoids of fruitinfesting dipterous larvae in Brazil: identity, geographical distribution and host associations

FIGURES 9 – 15. Tropideucoila weldi. 9. Head, anterior view (228 x, 100 m); 10. Female antenna (179 x, 100 m); 11. Pronotal plate (391 x, 20 m); 12. Mesosoma and anterior part of metasoma, lateral view (168 x, 100 m); 13. Head and mesosoma, dorsal view (215 x, 100 m); 14. Forewing (10 x, 0,25 mm); 15. Metacoxa (261 x, 100 m).

FIGURES 40 – 47. Trybliographa infuscata. 40 in Eucoilinae species (Hymenoptera: Cynipoidea: Figitidae) parasitoids of fruitinfesting dipterous larvae in Brazil: identity, geographical distribution and host associations

FIGURES 40 – 47. Trybliographa infuscata. 40. Head, anterior view (218 x, 100 m); 41. Female antenna (109 x, 100 m); 42. Flagellomerous 1 and 2 of male (182 x, 100 m); 43. Pronotal plate (568 x, 20 m); 44. Mesosoma and anterior part of metasoma, lateral view (161 x, 100 m); 45. Mesosoma, dorsal view (193 x, 100 m); 46. Forewing (10 x, 0,5 mm); 47. Metacoxa (161 x, 100 m).

FIGURES 32 39. A g anaspis pelleranoi. 32 in Eucoilinae species (Hymenoptera: Cynipoidea: Figitidae) parasitoids of fruitinfesting dipterous larvae in Brazil: identity, geographical distribution and host associations

FIGURES 32 39. A g anaspis pelleranoi. 32. Head, anterior view (170 x, 100 m); 33. Female antenna (97 x, 100 m); 34. Flagellomerous 1 and 2 of male (130 x, 100 m); 35. Pronotal plate (288 x, 100 m); 36. Head, mesosoma and anterior part of metasoma, lateral view (48 x, 250 m); 37. Mesosoma, dorsal view (64 x, 250 m); 38. Forewing (10 x, 0,5 mm); 39. Metacoxa (163 x, 100 m).