cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8310386
title: Data and Code for: Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America

description: This submission contains all the code and data necessary for reproducing 1) the dataset, 2) the main results, and 3) all supplemental analyses appearing in the manuscript titled: Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America (Ramirez-Parada, Park, Record, Davis, Ellison, and Mazer, 2023). A preprint of this manuscript can be accessed at: https://doi.org/10.21203/rs.3.rs-3131821/v1.


 


Extracting the compressed file will generate a folder titled "Project folder", containing sub-folders named "Data" and "R code". In order for the code to work, users need to preserve the folder structure of the code and data, as the R Markdown files in the "R code" folder have relative file paths that read and write data within the "Data" folder. Moving either would require re-writing the filepaths across Rmds for the code to run.



To replicate the results, the following R Markdowns must be run in sequence (once they have been run, the Rmds for supplemental analyses can be used in any order):



"1. Subsetting Dataset.Rmd"


This file processes a specimen dataset of ca. 2.3 million specimens that we assembled for this project (publicly available on Dryad: https://doi.org/10.25349/D9WP6S), filtering out duplicates, specimens out of the spatial scope of the PRISM data used for all analyses,  and subsetting to only those species represented by a minimum of 300 specimens. This filtering yields a dataset of 1,038,047 specimens in flower across 1,605 species.


For an in-depth description of the starting dataset, please refer to the "READ ME.txt" file within the "Project folder", and visit its corresponding Dryad repository (linked above).



"2. Main Analysis - Estimating S_space, S_time, and S_diff.Rmd"


This file uses the subset dataset produced by the previous Rmd to fit the varying-intercepts, varying-slopes model that produced the estimates of apparent plasticity and apparent adaptation underlying all main analyses. This Rmd exports a dataset of species-specific estimates of Sspace, Stime, and Sspace - Stime that is used to recreate Figures 2, 3, and 4 of the main text in the next step. This is the most time consuming R Markdown file to run, as each MCMC chain used to fit the model in Stan must be run on a dedicated processor (limiting the usefulness of parallel computation). Fitting the model using 3 MCMC chains, 1000 iterations for warmup, and 4000 iterations for sampling, took approximately 24 hours using an Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz processor.  


 


"3. Main Analysis - Figures 2, 3, and 4.Rmd"


Finally, this Rmd uses the dataset of species-specific estimates to conduct all analyses underlying Figures 2, 3, and 4, recreating each of these figures.


For detailed descriptions of all materials (code and data) and instructions for using them, please refer to the "READ ME.txt" file within "Project folder".
DOI: 10.5281/zenodo.8310387
title: Data and Code for: Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America

description: This submission contains all the code and data necessary for reproducing 1) the dataset, 2) the main results, and 3) all supplemental analyses appearing in the manuscript titled: Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America (Ramirez-Parada, Park, Record, Davis, Ellison, and Mazer, 2023). A preprint of this manuscript can be accessed at: https://doi.org/10.21203/rs.3.rs-3131821/v1.


 


Extracting the compressed file will generate a folder titled "Project folder", containing sub-folders named "Data" and "R code". In order for the code to work, users need to preserve the folder structure of the code and data, as the R Markdown files in the "R code" folder have relative file paths that read and write data within the "Data" folder. Moving either would require re-writing the filepaths across Rmds for the code to run.



To replicate the results, the following R Markdowns must be run in sequence (once they have been run, the Rmds for supplemental analyses can be used in any order):



"1. Subsetting Dataset.Rmd"


This file processes a specimen dataset of ca. 2.3 million specimens that we assembled for this project (publicly available on Dryad: https://doi.org/10.25349/D9WP6S), filtering out duplicates, specimens out of the spatial scope of the PRISM data used for all analyses,  and subsetting to only those species represented by a minimum of 300 specimens. This filtering yields a dataset of 1,038,047 specimens in flower across 1,605 species.


For an in-depth description of the starting dataset, please refer to the "READ ME.txt" file within the "Project folder", and visit its corresponding Dryad repository (linked above).



"2. Main Analysis - Estimating S_space, S_time, and S_diff.Rmd"


This file uses the subset dataset produced by the previous Rmd to fit the varying-intercepts, varying-slopes model that produced the estimates of apparent plasticity and apparent adaptation underlying all main analyses. This Rmd exports a dataset of species-specific estimates of Sspace, Stime, and Sspace - Stime that is used to recreate Figures 2, 3, and 4 of the main text in the next step. This is the most time consuming R Markdown file to run, as each MCMC chain used to fit the model in Stan must be run on a dedicated processor (limiting the usefulness of parallel computation). Fitting the model using 3 MCMC chains, 1000 iterations for warmup, and 4000 iterations for sampling, took approximately 24 hours using an Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz processor.  


 


"3. Main Analysis - Figures 2, 3, and 4.Rmd"


Finally, this Rmd uses the dataset of species-specific estimates to conduct all analyses underlying Figures 2, 3, and 4, recreating each of these figures.


For detailed descriptions of all materials (code and data) and instructions for using them, please refer to the "READ ME.txt" file within "Project folder".
DOI: 10.5281/zenodo.7040003
title: Leveraging Hardware Probes and Acceleration for Testing Heterogeneous Applications

description: The part of data and code for HFuzz: Leveraging Hardware Probes and Acceleration for Testing Heterogeneous Applications
DOI: 10.5281/zenodo.7040002
title: Leveraging Hardware Probes and Acceleration for Testing Heterogeneous Applications

description: The part of data and code for HFuzz: Leveraging Hardware Probes and Acceleration for Testing Heterogeneous Applications
DOI: 10.5281/zenodo.10214444
title: Data for DC Congruence Dashboard
DOI: 10.5281/zenodo.10214445
title: Data for DC Congruence Dashboard
DOI: 10.6084/m9.figshare.24650310
title: Data for: Shoenberger, T.W. & Fowler-Finn, K.D. Seasonal variation in the strength and consistency of tritrophic interactions among treehoppers, plants, and ants may favor generalist relationships. 2023. Arthropod Plant Interactions.

description: Abstract: Organisms interact with numerous species in their environment, and these interactionsAQ1 can influence a variety of social and ecological processes. Thus, temporal and spatial variation in species interactions is important for understanding the fitness consequences of multi-trophic relationships. Here, we investigate how tritrophic interactions between a host plant generalist sap-feeding insect, host plant species, and ant mutualists vary in a prairie habitat. We used field transects to quantify the abundances of three host plant species, three species of ants, and the treehopper Entylia carinata. We repeated the transects from Spring until late Fall to quantify seasonal changes in abundances, and across three years to investigate stability of tritrophic relationships across years. In the first year of the study, we also measured plant height. Finally, we characterized variation in the tending behavior inof the three species of ants. We found that certain plant-ant species combinations are more common than others. Furthermore, wWhile these tritrophic associations between plants, ants, and treehoppers changed seasonally, they were largely stable across years. Furthermore, Wwe found pervasive effects of ants on E. carinata, including E. carinata presence and abundance, E. carinata aggregation size and abundance, E. carinata nest presence and abundance, and E. carinata nest-tending behavior. Plant species had fewer effects, but affected E. carinata presence and abundance as well as the likelihood of E. carinata aggregations occurring on a plant. SFinally, significant seasonal changes in ant abundances and ant tending rates create dynamic temporal variation in tritrophic interactions. The patterns observed are likely to have significant effects on E. carinata populations, and—due to the importance of ant-treehopper mutualisms in local ecosystems—cascading effects on local communities.
DOI: 10.5281/zenodo.10214439
title: Dissertations on medieval Human Remains_Portugal

description: Databased build to be used in a publication - Alves-Cardoso, F; Belém, Inês. A portrait of Disease in Medieval Portugal: the contribution of paleopathology. 
Information on the manuscripts was retrieved from the Portuguese Open Access Scientific Repositories (RCAAP), in 2023.
DOI: 10.5281/zenodo.10214438
title: Dissertations on medieval Human Remains_Portugal

description: Databased build to be used in a publication - Alves-Cardoso, F; Belém, Inês. A portrait of Disease in Medieval Portugal: the contribution of paleopathology. 
Information on the manuscripts was retrieved from the Portuguese Open Access Scientific Repositories (RCAAP), in 2023.
DOI: 10.6084/m9.figshare.22272622
title: A Survey Of Burrows In The Drylands Of Southern California Dataset.

description: A burrow survey dataset comprised of two key measures: burrow location + burrow diameter. Data were collected within various-sized plots at different sites across Southern California.
DOI: 10.6084/m9.figshare.22272622.v4
title: A Survey Of Burrows In The Drylands Of Southern California Dataset.

description: A burrow survey dataset comprised of two key measures: burrow location + burrow diameter. Data were collected within various-sized plots at different sites across Southern California.
DOI: 10.6084/m9.figshare.22272622.v5
title: A Survey Of Burrows In The Drylands Of Southern California Dataset.

description: A burrow survey dataset comprised of two key measures: burrow location + burrow diameter. Data were collected within various-sized plots at different sites across Southern California.
DOI: 10.6084/m9.figshare.24270407
title: Overlap in synaptic neurological condition susceptibility pathways and the neural pannexin 1 interactome revealed by bioinformatics analyses

description: Many neurological conditions exhibit synaptic impairments, suggesting mechanistic convergence. Additionally, the pannexin 1 (PANX1) channel and signaling scaffold is linked to several of these neurological conditions and is an emerging regulator of synaptic development and plasticity; however, its synaptic pathogenic contributions are relatively unexplored. To this end, we explored connections between synaptic neurodevelopmental disorder and neurodegenerative disease susceptibility genes discovered by genome-wide association studies (GWASs), and the neural PANX1 interactome (483 proteins) identified from mouse Neuro2a (N2a) cells. To identify shared susceptibility genes, we compared synaptic suggestive GWAS candidate genes amongst autism spectrum disorders, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. To further probe PANX1 signaling pathways at the synapse, we used bioinformatics tools to identify PANX1 interactome signaling pathways and protein–protein interaction clusters. To shed light on synaptic disease mechanisms potentially linking PANX1 and these four neurological conditions, we performed additional cross-analyses between gene ontologies enriched for the PANX1 synaptic and disease-susceptibility gene sets. Finally, to explore the regional specificity of synaptic PANX1-neurological condition connections, we identified brain region-specific elevations of synaptic PANX1 interactome and GWAS candidate gene set transcripts. Our results confirm considerable overlap in risk genes for autism spectrum disorders and schizophrenia and identify potential commonalities in genetic susceptibility for neurodevelopmental disorders and neurodegenerative diseases. Our findings also pinpointed novel putative PANX1 links to synaptic disease-associated pathways, such as regulation of vesicular trafficking and proteostasis, warranting further validation.
DOI: 10.6084/m9.figshare.24270407.v1
title: Overlap in synaptic neurological condition susceptibility pathways and the neural pannexin 1 interactome revealed by bioinformatics analyses

description: Many neurological conditions exhibit synaptic impairments, suggesting mechanistic convergence. Additionally, the pannexin 1 (PANX1) channel and signaling scaffold is linked to several of these neurological conditions and is an emerging regulator of synaptic development and plasticity; however, its synaptic pathogenic contributions are relatively unexplored. To this end, we explored connections between synaptic neurodevelopmental disorder and neurodegenerative disease susceptibility genes discovered by genome-wide association studies (GWASs), and the neural PANX1 interactome (483 proteins) identified from mouse Neuro2a (N2a) cells. To identify shared susceptibility genes, we compared synaptic suggestive GWAS candidate genes amongst autism spectrum disorders, schizophrenia, Parkinson’s disease, and Alzheimer’s disease. To further probe PANX1 signaling pathways at the synapse, we used bioinformatics tools to identify PANX1 interactome signaling pathways and protein–protein interaction clusters. To shed light on synaptic disease mechanisms potentially linking PANX1 and these four neurological conditions, we performed additional cross-analyses between gene ontologies enriched for the PANX1 synaptic and disease-susceptibility gene sets. Finally, to explore the regional specificity of synaptic PANX1-neurological condition connections, we identified brain region-specific elevations of synaptic PANX1 interactome and GWAS candidate gene set transcripts. Our results confirm considerable overlap in risk genes for autism spectrum disorders and schizophrenia and identify potential commonalities in genetic susceptibility for neurodevelopmental disorders and neurodegenerative diseases. Our findings also pinpointed novel putative PANX1 links to synaptic disease-associated pathways, such as regulation of vesicular trafficking and proteostasis, warranting further validation.
DOI: 10.6084/m9.figshare.22904480
title: Non-canonical helical transitions and conformational switching are associated with characteristic flexibility and disorder indices in TRP and Kv channels

description: Structural evidence and much experimental data have demonstrated the presence of non-canonical helical substructures (π and 3<sub>10</sub>) in regions of great functional relevance both in TRP as in Kv channels. Through an exhaustive compositional analysis of the sequences underlying these substructures, we find that each of them is associated with characteristic local flexibility profiles, which in turn are implicated in significant conformational rearrangements and interactions with specific ligands. We found that α-to-π helical transitions are associated with patterns of local rigidity whereas α-to-3<sub>10</sub> transitions are mainly leagued with high local flexibility profiles. We also study the relationship between flexibility and protein disorder in the transmembrane domain of these proteins. By contrasting these two parameters, we located regions showing a sort of structural discrepancy between these similar but not identical protein attributes. Notably, these regions are presumably implicated in important conformational rearrangements during the gating in those channels. In that sense, finding these regions where flexibility and disorder are not proportional allows us to detect regions with potential functional dynamism. From this point of view, we highlighted some conformational rearrangements that occur during ligand binding events, the compaction, and refolding of the outer pore loops in several TRP channels, as well as the well-known S4 motion in Kv channels.
DOI: 10.6084/m9.figshare.22904480.v1
title: Non-canonical helical transitions and conformational switching are associated with characteristic flexibility and disorder indices in TRP and Kv channels

description: Structural evidence and much experimental data have demonstrated the presence of non-canonical helical substructures (π and 3<sub>10</sub>) in regions of great functional relevance both in TRP as in Kv channels. Through an exhaustive compositional analysis of the sequences underlying these substructures, we find that each of them is associated with characteristic local flexibility profiles, which in turn are implicated in significant conformational rearrangements and interactions with specific ligands. We found that α-to-π helical transitions are associated with patterns of local rigidity whereas α-to-3<sub>10</sub> transitions are mainly leagued with high local flexibility profiles. We also study the relationship between flexibility and protein disorder in the transmembrane domain of these proteins. By contrasting these two parameters, we located regions showing a sort of structural discrepancy between these similar but not identical protein attributes. Notably, these regions are presumably implicated in important conformational rearrangements during the gating in those channels. In that sense, finding these regions where flexibility and disorder are not proportional allows us to detect regions with potential functional dynamism. From this point of view, we highlighted some conformational rearrangements that occur during ligand binding events, the compaction, and refolding of the outer pore loops in several TRP channels, as well as the well-known S4 motion in Kv channels.
DOI: 10.26078/ad1d-7c7f
title: Data From: Root Distributions Predict Shrub-Steppe Responses to Precipitation Intensity

description: Precipitation events are becoming more intense around the world, changing the way water moves through soils and plants. Plant rooting strategies that sustain water uptake under these conditions are likely to become more abundant (e.g., shrub encroachment). Yet, it remains difficult to predict species responses to climate change because we typically do not know where active roots are located or how much water they absorb. Here, we applied a water tracer experiment to describe forb, grass, and shrub root distributions. These measurements were made in 8 m by 8 m field shelters with low or high precipitation intensity. We used tracer uptake data in a soil water flow model to estimate how much water respective plant root tissues absorb over time. In low precipitation intensity plots, deep shrub roots were estimated to absorb the most water (93 mm yr-1) and shrubs had the greatest aboveground cover (27%). Grass root distributions were estimated to absorb an intermediate amount of water (80 mm yr-1) and grasses had intermediate aboveground cover (18%). Forb root distributions were estimated to absorb the least water (79 mm yr-1) and had the least aboveground cover (12%). In high precipitation intensity plots, shrub and forb root distributions changed in ways that increased their water uptake relative to grasses, predicting the increased aboveground growth of shrubs and forbs in these plots. In short, water uptake caused by different rooting distributions predicted plant aboveground cover. Our results suggest that detailed descriptions of active plant root distributions can predict plant growth responses to climate change in arid and semi-arid ecosystems.
DOI: 10.26078/6170-d520
title: Molecular Dynamics Simulations of the Spontaneous Deformation and Auxetics Behavior During Tensile Test of a Nematic Liquid Crystal Elastomer Model

description: Nematic liquid crystal elastomers (LCEs) are advanced materials known for their shape-changing capability in response to external stimuli such as heat, light and electromagnetic fields. This makes them excellent candidates for applications like soft robotics and energy harvesting. While studies on their physical behavior have shed light on the complex nonlinear mechanics of LCEs, investigations through all-atom molecular dynamics (MD) simulations remain an underutilized avenue compared to experimental and theoretical analyses. This limited use is primarily due to the lack of well-established frameworks for conducting high-fidelity atomistic simulations of LCEs. To bridge this gap, we introduce an all-atom MD simulation framework based on the Polymer Consistent Force-Field (PCFF), which models the polymerization and crosslinking processes for a category of acrylate LCEs and captures their synthesis history- and composition-dependent properties. Our computational framework empowers us to simulate the spontaneous deformations and shape memory behavior upon temperature changes and enables us to observe the auxetic effect under elastic strains by generating models that closely replicate experimental findings. Moreover, this study not only validates the numerical models but opens up new avenues to explore the intricate behaviors of LCEs through their molecular structures and facilitate computational design advancements.
DOI: 10.5281/zenodo.10199638
title: Hourly Wind and Solar Generation Profiles at 1/8th Degree Resolution - wind 80m rcp85hotter 2080-2099

description: Please see the parent record at https://doi.org/10.5281/zenodo.10214348.
DOI: 10.5281/zenodo.10199639
title: Hourly Wind and Solar Generation Profiles at 1/8th Degree Resolution - wind 80m rcp85hotter 2080-2099

description: Please see the parent record at https://doi.org/10.5281/zenodo.10214348.
DOI: 10.5517/ccdc.csd.cc2b5gff
title: CCDC 2150204: Experimental Crystal Structure Determination

description: Related Article: Eloy  Pablo Gómez-Oliveira, Daniel Reinares-Fisac, Lina M. Aguirre-Díaz, Fátima Esteban-Betegón, Mercedes Pintado-Sierra, Enrique Gutiérrez-Puebla, Marta Iglesias, M. Ángeles Ph.D. Monge, Felipe Gándara|2022|Angew.Chem.,Int.Ed.|61|e202209335|doi:10.1002/anie.202209335
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: 10.5517/ccdc.csd.cc2bg2jf
title: CCDC 2158484: Experimental Crystal Structure Determination

description: Related Article: Peter Coburger, Fabio Masero, Victor Mougel, Hansjörg Grützmacher|2022|Angew.Chem.,Int.Ed.|61|e202211749|doi:10.1002/anie.202211749
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: 10.5517/ccdc.csd.cc28msb1
title: CCDC 2104383: Experimental Crystal Structure Determination

description: Related Article: John Kornfeind, James E. Allen, Taylor M. Keller, Fraser F. Fleming|2023|J.Org.Chem.|88|15947|doi:10.1021/acs.joc.3c02210
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.