cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25921/6gc5-ny03
title: NOAA/WDS Paleoclimatology - Neuwirth - Nordrhein-Westfalen/Oberbergisches drl03 - FASY - ITRDB GERM201

description: An improved understanding of the spatiotemporal climate/growth relationship of our forests is of particular importance for assessing the consequences of climate warming. A total of 67 stands of beech (Fagus sylvatica L.), pedunculate oak (Quercus robur L.), sessile oak (Quercus petraea (Matt.) Liebl.), Scots pine (Pinus sylvestris L.), and spruce (Picea abies Karst.) from sites located in the transition zone from the lowlands to the low mountain ranges of West Germany have been analysed. A combination of pointer year and cluster analysis was used to find groups with similar growth anomaly patterns over the 1941-2000 period. Shifted reaction patterns especially characterise differences in the growth behaviour of the clusters. These are controlled by different reactions to the climate conditions in winter and spring and are determined by a complex system of forcing factors. Results of this study reflect the enormous importance of the length of the growing season. Increasing the duration of the vegetation period climate warming can change the climate/growth relationship of trees, thereby confounding climate reconstructions which use tree rings. Since forcing factors have been detected that are more important than the tree species, we recommend the application of growth-specific approaches for the analysis of tree species' vulnerability to climate.
description: Purpose of Collection:
# climate/growth relationship NOAA Template Raw Measurements file added 2019-02-05.
DOI: 10.25921/6w5n-b680
title: NOAA/WDS Paleoclimatology - Luckman - Highwood Pass - PCEN - ITRDB CANA438

description: A new network of 21 Picea engelmannii Parry ex Engelm. ring-width chronologies was developed from tree-line sites in the Canadian Rockies. These chronologies range in length from 297 to 648 years (mean 423 years) and have mean sensitivities between 0.16 and 0.20 (mean 0.18), first-order autocorrelations between 0.73 and 0.88 (mean 0.83), and subsample signal strengths >0.85 for 246-494 years (mean 324 years). Mean intersite correlations (A.D. 1700-1982) for chronologies with expressed population signals >0.85 are 0.46 and 0.63 for standard and residual chronologies, respectively. Standard ring-width chronologies are, in general, positively correlated with summer temperatures and negatively correlated with spring and previous summer temperatures. A regional June-September temperature reconstruction for the Banff-Jasper region (BJR; A.D. 1715-1982) was developed using multiple regression of three significant principal components from 14 standard ring-width chronologies. The first principal component contains 55% of the total chronology variance. The model reconstructs 38% of summer temperature variance during the calibration period (1888-1982). The BJR is the first regional temperature reconstruction for this area based on ring-width data from a network of sites. The reconstructed temperature patterns are broadly similar to other regional estimates of past temperatures. Above-average summer temperatures occurred in the mid-20th century and the late 1700s - early 1800s. Most of the 19th century was unusually cold, with the coldest conditions in the late 19th century. Detailed differences between BJR and previously developed reconstructions lie well within 2 sigma confidence limits and may reflect differences in tree species, modelling techniques, spatial coverage, and the seasonal temperature parameter reconstructed.
description: NOAA Template Raw Measurements file added 2019-02-04.
DOI: 10.25921/6kgd-gw34
title: NOAA/WDS Paleoclimatology - Yang - Delingha GM - JUPR - ITRDB CHIN069

description: An annually resolved and absolutely dated ring-width chronology spanning 4,500 y has been constructed using subfossil, archaeological, and living-tree juniper samples from the northeastern Tibetan Plateau. The chronology represents changing mean annual precipitation and is most reliable after 1500 B.C. Reconstructed precipitation for this period displays a trend toward more moist conditions: the last 10-, 25-, and 50-y periods all appear to be the wettest in at least three and a half millennia. Notable historical dry periods occurred in the 4th century BCE and in the second half of the 15th century CE. The driest individual year reconstructed (since 1500 B.C.) is 1048 B.C., whereas the wettest is 2010. Precipitation variability in this region appears not to be associated with inferred changes in Asian monsoon intensity during recent millennia. The chronology displays a statistical association with the multidecadal and longer-term variability of reconstructed mean Northern Hemisphere temperatures over the last two millennia. This suggests that any further large-scale warming might be associated with even greater moisture supply in this region.
description: Purpose of Collection: 
# Climatology - precipitation NOAA Template Raw Measurements file added 2019-04-08. July 2024: Elevation added by WDS-Paleo using get_elev_point() from the elevatr R package with the AWS Terrain Tiles (aws) and WGS 84 reference frame.
DOI: 10.5281/zenodo.16648999
title: Project files provided as supporting information to the manuscript "Sequence- and supercoiling-dependent effects on the structural dynamics of DNA minicircles"

description: README file to the project files provided as supporting information to the manuscript.

Authors: Manuel Micheloni, Luca Tubiana, Raffaello Potestio, Lorenzo Petrolli

==================================

 

The main directory contains this readme file and two compressed archives: EqDNAMini.tar.gz and SynthBubble.tar.gz.





EqDNAMini.tar.gz includes MD simulations of a 672-bp DNA minicircle at six values superhelical densities. Each simulation scenario is stored in a separate subfolder named according to its superhelical density (i.e., Sigma_-0.1, Sigma_-0.08, Sigma_-0.06, Sigma_0, Sigma_0.06, and Sigma_0.1).

SynthBubble.tar.gz contains simulations of the DNA minicircle at a fixed superhelical density of –0.06, with synthetic DNA bubbles of different sizes enforced in the same supercoiled region. These simulations are organized in subfolders as B1, B2, B5, and B10, corresponding to bubble sizes of 1, 2, 5, and 10 bp, respectively.



Each subfolder (e.g., Sigma_* and B*) contains a data, input_structure and MD_scripts directory. 





The data directory includes three subfolders:



1.E: for each independent MD replica, the folder contains the internal energy data files of the DNA minicircle (both for the relaxation and the production run stage) and the pairwise energy contribution between complementary nucleotides in the DNA helix (production run only);

2.traj: it contains the MD trajectories of the DNA minicircle for each replica (both the relaxation and production run stage).



The /MD_scripts folder contains the scripts used to perform the molecular dynamics simulations.

The /input_structure folder contains the configuration and topology (in the oxDNA format) files used for each MD run. The DNA template used in all MD simulations is based on the work of Fogg and colleagues [1].



NOTE: Data files related to the relaxation stage of each simulation contain “Relax1” in their filenames, while files associated with the production run stage are labeled with “Relax2. For details about the simulation protocol employed in either stage, please refer to the main text of the work.

 

[1] Fogg, J.M., Judge, A.K., Stricker, E. et al. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 12, 5683 (2021). https://doi.org/10.1038/s41467-021-25936-2
DOI: 10.5281/zenodo.16648998
title: Project files provided as supporting information to the manuscript "Sequence- and supercoiling-dependent effects on the structural dynamics of DNA minicircles"

description: README file to the project files provided as supporting information to the manuscript.

Authors: Manuel Micheloni, Luca Tubiana, Raffaello Potestio, Lorenzo Petrolli

==================================

 

The main directory contains this readme file and two compressed archives: EqDNAMini.tar.gz and SynthBubble.tar.gz.





EqDNAMini.tar.gz includes MD simulations of a 672-bp DNA minicircle at six values superhelical densities. Each simulation scenario is stored in a separate subfolder named according to its superhelical density (i.e., Sigma_-0.1, Sigma_-0.08, Sigma_-0.06, Sigma_0, Sigma_0.06, and Sigma_0.1).

SynthBubble.tar.gz contains simulations of the DNA minicircle at a fixed superhelical density of –0.06, with synthetic DNA bubbles of different sizes enforced in the same supercoiled region. These simulations are organized in subfolders as B1, B2, B5, and B10, corresponding to bubble sizes of 1, 2, 5, and 10 bp, respectively.



Each subfolder (e.g., Sigma_* and B*) contains a data, input_structure and MD_scripts directory. 





The data directory includes three subfolders:



1.E: for each independent MD replica, the folder contains the internal energy data files of the DNA minicircle (both for the relaxation and the production run stage) and the pairwise energy contribution between complementary nucleotides in the DNA helix (production run only);

2.traj: it contains the MD trajectories of the DNA minicircle for each replica (both the relaxation and production run stage).



The /MD_scripts folder contains the scripts used to perform the molecular dynamics simulations.

The /input_structure folder contains the configuration and topology (in the oxDNA format) files used for each MD run. The DNA template used in all MD simulations is based on the work of Fogg and colleagues [1].



NOTE: Data files related to the relaxation stage of each simulation contain “Relax1” in their filenames, while files associated with the production run stage are labeled with “Relax2. For details about the simulation protocol employed in either stage, please refer to the main text of the work.

 

[1] Fogg, J.M., Judge, A.K., Stricker, E. et al. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 12, 5683 (2021). https://doi.org/10.1038/s41467-021-25936-2
DOI: 10.15468/dl.3w2rmb
title: Occurrence Download

description: A dataset containing 131878 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anser indicus"
 ]
}

 The dataset includes 131878 records from 369 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085733-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ktrr7c
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Carterornis castus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 144 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085780-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc6xqld
title: CCDC 206354: Experimental Crystal Structure Determination

description: Related Article: S.Jayanty, T.P.Radhakrishnan|2004|Chem.-Eur.J.|10|791|doi:10.1002/chem.200305123
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/cc6xqmf
title: CCDC 206355: Experimental Crystal Structure Determination

description: Related Article: S.Jayanty, T.P.Radhakrishnan|2004|Chem.-Eur.J.|10|791|doi:10.1002/chem.200305123
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/cc7hkfp
title: CCDC 223492: Experimental Crystal Structure Determination

description: Related Article: D.Sellmann, A.Hille, A.Rosler, F.W.Heinemann, M.Moll, G.Brehm, S.Schneider, M.Reiher, B.A.Hess, W.Bauer|2004|Chem.-Eur.J.|10|819|doi:10.1002/chem.200305499
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/cc7hkgq
title: CCDC 223493: Experimental Crystal Structure Determination

description: Related Article: D.Sellmann, A.Hille, A.Rosler, F.W.Heinemann, M.Moll, G.Brehm, S.Schneider, M.Reiher, B.A.Hess, W.Bauer|2004|Chem.-Eur.J.|10|819|doi:10.1002/chem.200305499
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/cc7hkhr
title: CCDC 223494: Experimental Crystal Structure Determination

description: Related Article: D.Sellmann, A.Hille, A.Rosler, F.W.Heinemann, M.Moll, G.Brehm, S.Schneider, M.Reiher, B.A.Hess, W.Bauer|2004|Chem.-Eur.J.|10|819|doi:10.1002/chem.200305499
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/cc7hkjs
title: CCDC 223495: Experimental Crystal Structure Determination

description: Related Article: D.Sellmann, A.Hille, A.Rosler, F.W.Heinemann, M.Moll, G.Brehm, S.Schneider, M.Reiher, B.A.Hess, W.Bauer|2004|Chem.-Eur.J.|10|819|doi:10.1002/chem.200305499
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/cc6xprj
title: CCDC 206328: Experimental Crystal Structure Determination

description: Related Article: J.Fornies, J.Gomez, E.Lalinde, M.T.Moreno|2004|Chem.-Eur.J.|10|888|doi:10.1002/chem.200304987
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/cc6xpsk
title: CCDC 206329: Experimental Crystal Structure Determination

description: Related Article: J.Fornies, J.Gomez, E.Lalinde, M.T.Moreno|2004|Chem.-Eur.J.|10|888|doi:10.1002/chem.200304987
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/cc6xptl
title: CCDC 206330: Experimental Crystal Structure Determination

description: Related Article: J.Fornies, J.Gomez, E.Lalinde, M.T.Moreno|2004|Chem.-Eur.J.|10|888|doi:10.1002/chem.200304987
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/cc6xpvm
title: CCDC 206331: Experimental Crystal Structure Determination

description: Related Article: J.Fornies, J.Gomez, E.Lalinde, M.T.Moreno|2004|Chem.-Eur.J.|10|888|doi:10.1002/chem.200304987
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/cc5z6bn
title: CCDC 177981: Experimental Crystal Structure Determination

description: Related Article: R.Fischer, J.Baumgartner, G.Kickelbick, K.Hassler, C.Marschner|2004|Chem.-Eur.J.|10|1021|doi:10.1002/chem.200305225
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/cc7c793
title: CCDC 219334: Experimental Crystal Structure Determination

description: Related Article: D.Leca, Kai Song, M.Amatore, L.Fensterbank, E.Lacote, M.Malacria|2004|Chem.-Eur.J.|10|906|doi:10.1002/chem.200305525
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: 10.15468/dl.j2vcd9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Eurypygiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((0 -20,10 -20,10 -10,0 -10,0 -20))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018752-251009101135966/datasets/export for details.
DOI: 10.5517/cc5z6cp
title: CCDC 177982: Experimental Crystal Structure Determination

description: Related Article: R.Fischer, J.Baumgartner, G.Kickelbick, K.Hassler, C.Marschner|2004|Chem.-Eur.J.|10|1021|doi:10.1002/chem.200305225
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/cc5z6dq
title: CCDC 177983: Experimental Crystal Structure Determination

description: Related Article: R.Fischer, J.Baumgartner, G.Kickelbick, K.Hassler, C.Marschner|2004|Chem.-Eur.J.|10|1021|doi:10.1002/chem.200305225
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/cc5z6fr
title: CCDC 177984: Experimental Crystal Structure Determination

description: Related Article: R.Fischer, J.Baumgartner, G.Kickelbick, K.Hassler, C.Marschner|2004|Chem.-Eur.J.|10|1021|doi:10.1002/chem.200305225
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/cc77vr1
title: CCDC 216093: Experimental Crystal Structure Determination

description: Related Article: M.G.Anorbe, M.S.Luth, M.Roitzsch, M.M.Cerda, P.Lax, G.Kampf, H.Sigel, B.Lippert|2004|Chem.-Eur.J.|10|1046|doi:10.1002/chem.200305509
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/cc7hyyl
title: CCDC 223880: Experimental Crystal Structure Determination

description: Related Article: F.Millange, C.Serre, J.Marrot, N.Gardant, F.Pelle, G.Ferey|2004|J.Mater.Chem.|14|642|doi:10.1039/b314343k
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/cc7b2m7
title: CCDC 218228: Experimental Crystal Structure Determination

description: Related Article: J.S.Figueroa, C.C.Cummins|2004|Angew.Chem.,Int.Ed.|43|984|doi:10.1002/anie.200352779
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/cc7b2n8
title: CCDC 218229: Experimental Crystal Structure Determination

description: Related Article: J.S.Figueroa, C.C.Cummins|2004|Angew.Chem.,Int.Ed.|43|984|doi:10.1002/anie.200352779
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/cc7b2p9
title: CCDC 218230: Experimental Crystal Structure Determination

description: Related Article: J.S.Figueroa, C.C.Cummins|2004|Angew.Chem.,Int.Ed.|43|984|doi:10.1002/anie.200352779
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.