cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h9w0vt4k9
title: Pollution induces epigenetic effects that are stably transmitted across multiple generations

description: It has been hypothesised that the effects of pollutants on phenotypes can
 be passed to subsequent generations through epigenetic inheritance,
 affecting populations long after the removal of a pollutant. But there is
 still little evidence that pollutants can induce persistent epigenetic
 effects in animals. Here we show that low doses of commonly used
 pollutants induce genome-wide differences in cytosine methylation in the
 freshwater crustacean Daphnia pulex. Uniclonal populations were either
 continually exposed to pollutants or switched to clean water, and
 methylation was compared to control populations that did not experience
 pollutant exposure. While some direct changes to methylation were only
 present in the continually exposed populations, others were present in
 both the continually exposed and switched to clean water treatments,
 suggesting that these modifications had persisted for seven months
 (&gt; 15 generations). We also identified modifications which were
 only present in the populations that had switched to clean water,
 indicating a long-term legacy of pollutant exposure distinct from the
 persistent effects. Pollutant-induced differential methylation tended to
 occur at sites that were highly methylated in controls. Modifications that
 were observed in both continually and switched treatments were highly
 methylated in controls and showed reduced methylation in the treatments.
 On the other hand, modifications found just in the switched treatment
 tended to have lower levels of methylation in the controls and showed
 increase methylation in the switched treatment. In a second experiment we
 confirmed that sub-lethal doses of the same pollutants generate effects on
 life-histories for at least three generations following the removal of the
 pollutant. Our results demonstrate that even low doses of pollutants can
 induce transgenerational epigenetic effects that are stably transmitted
 over many generations. Persistent effects are likely to influence
 phenotypic development, which could contribute to the rapid adaptation, or
 extinction, of populations confronted by anthropogenic stressors.
description: Please refer to the article <em>"Pollution induces
 epigenetic effects that are stably transmitted across multiple
 generations"</em> for information about methods.
description: Please refer to the README file for information about data and R
 scripts.
DOI: 10.7280/d1bh77
title: Predictive coding and internal error correction in speech production

description: This is a project attempting to replicate and extend prior work that has
 used a tongue twister paradigm to i) demonstrate predictive coding in
 auditory cortex during speech, and ii) provide suggestive evidence of
 internal error correction in speech that implicates the posterior middle
 temporal gyrus. For previous work that this project is based on see:
 Okada, K., Matchin, W., & Hickok, G. (2018). Neural evidence for
 predictive coding in auditory cortex during speech production. Psychonomic
 Bulletin & Review, 25(1), 423-430. (2022-01-10). 
description: This dataset contains raw structural and functional MRI data and
 associated files necessary to analyze it. See Readme.txt for further
 information.
DOI: 10.5061/dryad.8gtht76qv
title: Over the hills and through the farms: Land use and topography influence genetic connectivity of northern leopard frog (Rana pipiens) in the Prairie Pothole Region

description: Context Agricultural land-use conversion has fragmented prairie wetland
 habitats in the Prairie Pothole Region (PPR), an area with one of the most
 wetland-dense regions in the world. This fragmentation can lead to
 negative consequences for wetland obligate organisms, heightening risk of
 local extinction and reducing evolutionary potential for populations to
 adapt to changing environments. Objectives This study models biotic
 connectivity of prairie-pothole wetlands using landscape genetic analyses
 of the northern leopard frog (Rana pipiens) to: (1) identify population
 structure and (2) determine landscape factors driving genetic
 differentiation and possibly leading to population fragmentation. Methods
 Frogs from 22 sites in the James River and Lake Oahe river basins in North
 Dakota were genotyped using Best-RAD sequencing at 2868 bi-allelic single
 nucleotide polymorphisms (SNPs). Population structure was assessed using
 STRUCTURE, DAPC, and fineSTRUCTURE. Circuitscape was used to model
 resistance values for ten landscape variables that could affect habitat
 connectivity. Results STRUCTURE results suggested a panmictic population,
 but other more sensitive clustering methods identified six spatially
 organized clusters. Circuit theory-based landscape resistance analysis
 suggested land use, including cultivated crop agriculture, and topography
 were the primary influences on genetic differentiation. Conclusions While
 the R. pipiens populations appear to have high gene flow, we found a
 difference in the patterns of connectivity between the eastern portion of
 our study area which was dominated by cultivated crop agriculture, versus
 the western portion where topographic roughness played a greater role.
 This information can help identify amphibian dispersal corridors and
 prioritize lands for conservation or restoration.
description: The files included in this repository are all provided in basic
 file formats (.txt and .asc). To run the analyses, the following
 open-source programs are needed: R (v4.1.3) https://cran.r-project.org/src/base/R-4/ STRUCTURE https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html fineRADstructure https://github.com/millanek/fineRADstructure Julia https://julialang.org/downloads/ COLONY https://www.zsl.org/science/software/colony NeEstimator http://www.molecularfisherieslaboratory.com.au/neestimator-software/
DOI: 10.5061/dryad.9p8cz8wj0
title: Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation

description: Integrin adhesion complexes (IACs) are integrin-based plasma
 membrane-associated compartments where cells sense environmental cues. The
 physical mechanisms and molecular interactions that mediate initial IAC
 formation are unclear. We found that both p130Cas (“Cas”) and Focal
 adhesion kinase (“FAK”) undergo liquid-liquid phase separation in
 vitrounder physiologic conditions. Cas- and FAK- driven phase separation
 is sufficient to reconstitute kindlin-dependent integrin
 clustering in vitro with recombinant mammalian
 proteins. In vitro condensates and IACs in mouse
 embryonic fibroblasts (MEFs) exhibit similar sensitivities to
 environmental perturbations including changes in temperature and pH.
 Furthermore, mutations that inhibit or enhance phase
 separation in vitro reduce or increase the number of
 IACs in MEFs, respectively. Finally, we find that the Cas and FAK pathways
 act synergistically to promote phase separation, integrin clustering, IAC
 formation and partitioning of key components in
 vitro and in cells. We propose that Cas- and FAK- driven phase
 separation provides an intracellular trigger for integrin clustering and
 nascent IAC formation.
DOI: 10.5061/dryad.cnp5hqc66
title: Fitness data for control autotomized and regenerated crabs Hemigrapsus nudus

description: The capacity of certain animals to regrow a lost appendage has been
 exploited as a powerful tool to study development. As a result, we now
 understand many of the proximate details of the regeneration process.
 Ironically, despite being one of the oldest studied developmental
 phenomena, regeneration is not often considered in the context of natural
 selection and evolution. Why do select species retain the capacity to shed
 and regrow body parts, whereas more derived lineages do not? We conducted
 a comprehensive study on the costs and benefits of autotomy and
 regeneration on Hemigrapsus nudus, the purple shore crab. In the realms of
 feeding and locomotion, regeneration restored fitness to what it otherwise
 would have been; autotomized animals showed decreases in feeding and
 locomotion, but regenerated animals performed no differently than intact
 crabs. However, for fecundity and male-male competition, regenerated
 animals had the lowest fitness compared to control and autotomized crabs.
 Our results raise the intriguing possibility that tradeoffs associated
 with reproduction may have led to the loss of regenerative abilities in
 derived lineages such as mammals and birds. Future work on the hundreds of
 species that regenerate lost body parts will reveal if and how this
 hypothesis can address the pervasive speculation plaguing the ultimate
 causes of regenerative losses.
DOI: 10.5061/dryad.sn02v6x5n
title: Low-pH seawater alters indirect interactions in rocky-shore tidepools

description: Ocean acidification is expected to degrade marine ecosystems, yet most
 studies focus on organismal-level impacts rather than ecological
 perturbations. Field studies are especially sparse, particularly ones
 examining shifts in direct and indirect consumer interactions. Here we
 address such connections within tidepool communities of rocky shores,
 focusing on a three-level food web involving the keystone sea star
 predator, Pisaster ochraceus, a common herbivorous
 snail, Tegula funebralis, and a macroalgal basal
 resource, Macrocystis pyrifera. We demonstrate that during
 nighttime low tides, experimentally manipulated declines in seawater pH
 suppress the antipredator behavior of snails, bolstering their grazing,
 and diminishing the top-down influence of predators on basal resources.
 This attenuation of top-down control is absent in pools maintained
 experimentally at higher pH. These findings suggest that as ocean
 acidification proceeds, shifts of behaviorally mediated links in food webs
 could change how cascading effects of predators manifest within marine
 communities.
DOI: 10.5061/dryad.pvmcvdnnj
title: Data from: Balancing food acquisition and predation risk drives demographic changes in snowshoe hare population cycles

description: Snowshoe hare cycles are one of the most prominent phenomena in ecology.
 Experimental studies point to predation as the dominant driving factor,
 but previous experiments combining food supplementation and predator
 removal produced unexplained multiplicative effects on density. We
 examined the potential interactive effects of food limitation and
 predation in causing hare cycles using an individual based
 food-supplementation experiment over-winter across three cycle phases that
 naturally varied in predation risk. Supplementation doubled over-winter
 survival with the largest effects occurring in the late increase phase.
 Although the proximate cause of mortality was predation, supplemented
 hares significantly decreased foraging time and selected for conifer
 habitat, potentially reducing their predation risk. Supplemented hares
 also lost less body mass which resulted in the production of larger
 leverets. Our results establish a mechanistic link between how foraging
 time, mass loss, and predation risk affect survival and reproduction,
 potentially driving demographic changes associated with hare cycles.
DOI: 10.5061/dryad.0cfxpnw47
title: Food restriction delays breeding and affects insulin-like growth factor-1, oxidative damage, and haematocrit value before egg-laying in female canaries

description: Environmental challenges, such as fluctuations in food availability, could
 influence reproductive investment. If resource availability is poor,
 individuals need to decide in which life-history process they invest more
 energy and vital compounds, which determine the cost of reproduction. In
 resource allocation, the physiological pathways have important roles. The
 aim of our study was to examine whether food availability influenced
 physiological traits (insulin-like growth factor-1 (IGF-1) concentration,
 antioxidant capacity (OXY), level of oxidative damage (ROM) and
 haematocrit value) prior to egg-laying in female canaries (Serinus
 canaria). We also tested whether these physiological traits were
 associated with traits reflecting the reproductive investment in egg
 macro- (egg mass and yolk mass) and micronutrient content (eggshell
 biliverdin- and protoporphyrin-based colouration). To test these questions
 we conducted a food restriction experiment with control and
 food-restricted (72% of control food) groups. Our study showed that
 food-restricted canary females delayed egg-laying and the physiological
 traits differed between the groups. At the pre-laying period, after 9-11
 days of treatment, a reduction in plasma IGF-1 concentration, ROM level,
 and haematocrit value was detected in the control group, whereas in the
 food-restricted group plasma IGF-1 concentration increased, while ROM
 level and haematocrit value did not change. Plasma level of OXY was not
 influenced by treatment or breeding period. Plasma concentration of IGF-1,
 haematocrit value and oxidative status before egg laying did not affect
 the egg characteristics. Our study highlights the importance of breeding
 stage when studying and interpreting the effects of food restriction on
 physiological traits of breeding birds. Moreover, our data suggest that
 nutritional limitation had an effect on the timing of egg-laying that
 could be mediated by changes in physiological variables.
DOI: 10.5517/ccdc.csd.cc2q2qfz
title: CCDC 2505061: Experimental Crystal Structure Determination

description: Related Article: Jayakumar Sekar, Yushu Jin, Sobi Asako, Laurean Ilies|2026|J. Am. Ceram. Soc.|148||doi:10.1021/jacs.5c21089
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.bzkh189bg
title: Data from: Territoriality modifies the effects of habitat complexity on animal behavior: a meta-analysis

description: Augmenting habitat complexity by adding structure has been used to
 increase the population density of some territorial species in the wild
 and to reduce aggression among captive animals.  However, it is
 unknown if all territorial species are affected similarly by habitat
 complexity, and whether these effects extend to non-territorial
 species.  We conducted a meta-analysis to compare the behavior of
 a wide range of territorial and non-territorial taxa in complex and open
 habitats to determine the effects of habitat complexity on 1) territory
 size, 2) population density, 3) rate and time spent on aggression, 4) rate
 and time devoted to foraging, 5) rate and time spent being active, 6)
 shyness/boldness, 7) survival rate, and 8) exploratory behavior. 
 Overall, all measures were significantly affected by habitat complexity,
 but the responses of territorial and non-territorial species
 differed.  As predicted, territorial species were less
 aggressive, had smaller territories and higher densities in complex
 habitats, whereas non-territorial species were more aggressive and did not
 differ in population density.  Territorial species were bolder
 but not more active in complex habitats, whereas non-territorial species
 were more active but not bolder. While the survival of non-territorial
 species increased in complex habitats, no such increase was observed for
 territorial species.  The increased safety from predators
 provided by complex habitats may have been balanced by the higher
 population densities and bolder behavior in territorial species.
  Our analysis suggests that territorial and non-territorial
 animals respond differently to habitat complexity, perhaps due to the
 strong reliance on visual cues by territorial animals.
description: This data is for a meta-analysis on the effects of territoriality
 on eight different behavioural variables: 1) territory size, 2) population
 density, 3) rate and time spent on aggression, 4) rate and time devoted to
 foraging, 5) rate and time spent being active, 6) shyness/boldness, 7)
 survival rate, and 8) exploratory behavior.  It consists of a mean value
 for a given behaviour in both an open and complex habitat, as well as the
 associated standard error, standard deviation, and number of data points
 obtained from published studies, and whether or not the species is
 territorial.
DOI: 10.25505/fiz.icsd.cc2przct
title: CSD 2495697: Experimental Crystal Structure Determination

description: Related Article: Xian-Juan Feng, Matej Bobnar, Alim Ormeci, Mohammad Mehmandoust, Marcus Schmidt, Bodo Böhme, Mitja Krnel, Michael Baitinger, Julia Maria Hübner|2026|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c05692
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc2ps0zh
title: CSD 2495747: Experimental Crystal Structure Determination

description: Related Article: Xian-Juan Feng, Matej Bobnar, Alim Ormeci, Mohammad Mehmandoust, Marcus Schmidt, Bodo Böhme, Mitja Krnel, Michael Baitinger, Julia Maria Hübner|2026|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c05692
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.0k6djhb1x
title: Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

description: Single cell RNA sequencing (scRNAseq) is a powerful technique that
 continues to expand across various biological applications. However,
 incomplete 3’ UTR annotations can impede single cell analysis resulting in
 genes that are partially or completely uncounted. Performing scRNAseq with
 incomplete 3’ UTR annotations can hinder the identification of cell
 identities and gene expression patterns and lead to erroneous biological
 inferences. We demonstrate that performing single cell isoform sequencing
 (ScISOr-Seq) in tandem with scRNAseq can rapidly improve 3' UTR
 annotations. Using threespine stickleback fish (Gasterosteus aculeatus),
 we show that gene models resulting from a minimal embryonic ScISOr-Seq
 dataset retained 26.1% greater scRNAseq reads than gene models from
 Ensembl alone. Furthermore, pooling our ScISOr-Seq isoforms with a
 previously published adult bulk Iso-Seq dataset from stickleback, and
 merging the annotation with the Ensembl gene models, resulted in a
 marginal improvement (+0.8%) over the ScISOr-Seq only dataset. In
 addition, isoforms identified by ScISOr-Seq included thousands of new
 splicing variants. The improved gene models obtained using ScISOr-Seq lead
 to successful identification of cell types and increased the reads
 identified of many genes in our scRNAseq stickleback dataset. Our work
 illuminates ScISOr-Seq as a cost-effective and efficient mechanism to
 rapidly annotate genomes for scRNAseq.
description: This dataset originates from an experiment where 70hpf embryos
 were dissociated into single cells then captured by the 10X Single Cell
 Genomics 3' Genome Expression mRNA-Seq prep with v3.1 NextGem
 chemistry. After capture, the library was split into two libraries, one
 was sequenced using illumina's NovaSeq 6000 and the other was
 sequenced by Pacbio Sequel 2. The single cell ISO sequencing (ScISOrSeq)
 was processed using PacBio's SMRT Analysis software, custom scripts
 (https://github.com/hopehealey/scISOseq_processing), cDNA cupcake, and SQANTI3. Additional sequencing data (from Naftaly, Pau, and White 2021) was also processed with PacBio's SMRT Analysis software, cDNA cupcake, and SQANTI3. The produced annotation file was merged with the stickleback annotation (BROAD S1: 104.1 database version, downloaded from Ensembl) using TAMA. The new annotations were tested with Cell Ranger to see how well they captured the generated stickleback scRNAseq reads.
description: We used raw sequncing data from Naftaly, Pau, and White
 (2021)'s paper to create
 the Supplementalfile3_Annotation2_Bulk_Iso_Seq, Supplementalfile4_Annotation3_Pooled_Iso_Seqs_merged_with_ensembl.gtf, and Supplementalfile5_Annotation4_Pooled_Iso_Seqs_merged_with_ensembl_for_cellranger.gtf annotations. Information on accessing the sequencing data from our experiment can be found in our manuscript (Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis in Genetics).
DOI: 10.25505/fiz.icsd.cc2pvzg0
title: CSD 2498583: Experimental Crystal Structure Determination

description: Related Article: Vidyanshu Mishra, Jinseong Kim, Jong-Hoon Lim, Manya Rishi, Joon Jang, Abishek K. Iyer|2026|Chem.Mater.|||doi:10.1021/acs.chemmater.5c02904
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.25505/fiz.icsd.cc2pvzh1
title: CSD 2498584: Experimental Crystal Structure Determination

description: Related Article: Vidyanshu Mishra, Jinseong Kim, Jong-Hoon Lim, Manya Rishi, Joon Jang, Abishek K. Iyer|2026|Chem.Mater.|||doi:10.1021/acs.chemmater.5c02904
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.