cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8342158
title: The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi)

description: Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or “living fossils” when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi (“whip spiders”), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous “whips”). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils, which bears upon the ancestral range reconstruction for the group. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of “dark taxa”, and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy.
description: Funding provided by: Global Genome Initiative*
Crossref Funder Registry ID:
Award Number: GGI-Peer-2018-179

Funding provided by: Global Genome Initiative*
Crossref Funder Registry ID:
Award Number: GGI-Rolling-2018-200

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: IOS-2016141

Funding provided by: CAPES
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002322
Award Number: 88882.426372/2019-01

Funding provided by: CAPES
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002322
Award Number: 88887.631058/2021-00

Funding provided by: Binational Science Foundation*
Crossref Funder Registry ID:
Award Number: 2019216
DOI: 10.5281/zenodo.16627462
title: Dataset of Extracted Observable Benefits from Studies on the Adoption and Implementation of ISO/IEC 29110

description: This dataset contains the complete extraction table of observable benefits reported in primary studies on the adoption and implementation of the ISO/IEC 29110 standard. It was compiled as part of the systematic literature review presented in the article:

Contributions on the Adoption and Implementation of ISO/IEC 29110: A Systematic Literature Review

The dataset expands upon the information summarized in Tables 14–16 of the paper.

Each record includes:





Type of Benefit: Technical, economic, or organizational.




Category: Specific benefit classification.




Observable Benefit: Reported benefit in concise form.




Supporting Study: ID of the primary study in the SLR.




Excerpt/s (Literal Quote/s): Source text supporting the benefit.




Evidence Type: Management opinion, qualitative, or quantitative support.




Robustness: Assessment of evidence strength.




Justification: Rationale for robustness assessment.



By providing the full extraction data, the dataset promotes transparency and reproducibility, enabling other researchers to verify the classification, robustness assessment, and interpretation of each reported benefit.
DOI: 10.5281/zenodo.10702601
title: FESOM-REcoM model data: Predicting future distribution of Antarctic toothfish (Dissostichus mawsoni), with implications for Marine Protected Areas in the Southern Ocean

description: This data set belongs to "Predicting future distribution of Antarctic toothfish (Dissostichus mawsoni), with implications for Marine Protected Areas in the Southern Ocean" by Rebecca Konijnenberg, Cara Nissen, Casper Kraan, Jilda Cavacco, Peter Yates, Philippe Ziegler, and Katharina Teschke (in preparation). 

Contact for data set: cara.nissen@colorado.edu

The data provided here are post-processed from the raw FESOM1.4-REcoM2 model output which can be obtained at the World Data Center for Climate (WDCC): https://www.wdc-climate.de/ui/project?acronym=HighRes_highLat_SO

simA (historical simulation): https://doi.org/10.26050/WDCC/FESOM14-REcoM2_A_hist_vA_vCsimA-ssp126: https://doi.org/10.26050/WDCC/FESOM14-REcoM2_A_s126_vA_vCsimA-ssp245: https://doi.org/10.26050/WDCC/FESOM14-REcoM2_A_s245_vA_vCsimA-ssp370: https://doi.org/10.26050/WDCC/FESOM14-REcoM2_A_s370_vA_vCsimA-ssp585: https://doi.org/10.26050/WDCC/FESOM14-REcoM2_A_s585_vA_vCsimB (control simulation): https://doi.org/10.26050/WDCC/FESOM14-REcoM2_B_1921_cA_cC

Here, we provide decadal monthly climatologies of the following variables: sea-ice fraction, surface small-phytoplankton chlorophyll, surface diatom chlorophyll, as well as potential temperature, practical salinity and oxygen concentrations (all at the surface, at the bottom, at 100m, at 250m, at 500m, at 1000m, and at 1500m). For example, "tos" is temperature in ocean at surface", while "tob" is "temperature in ocean at bottom" (with bottom here being the deepest available model grid cell at each location).

We also provide the script used to re-grid the original model output to the regular 0.25° x 0.0625° mesh used in this study.
DOI: 10.5281/zenodo.15584210
title: Integrated multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of metastatic melanoma.

description: ABSTRACT. Background. We developed an integrated multi-omics analysis in metastatic melanoma (MM) cohorts to associate DNA methylation profiles with tumor progression, survival, response to adjuvant immunotherapy, structure of the tumor immune microenvironment and transcriptional programs of immunity and melanoma differentiation. Methods. Lesions (n=191) from a fully annotated, retrospective cohort of 165 AJCC 8th Stage III and IV melanoma patients (EPICA cohort) were characterized by reduced representation bisulfite sequencing, RNA sequencing, whole exome sequencing, quantitative immunohistochemistry and multiplex immunofluorescence analysis. The TCGA melanoma datasets were used for validation. Pre-therapy lesions (n=28) from a cohort of MM patients treated with adjuvant immune checkpoint blockade were characterized for the DNA methylation profile.  Impact of a DNMT inhibitor on DNA methylation and transcriptomic profiles of melanoma cell lines was investigated by EPIC arrays and Clariom S arrays. Results. Four tumor subsets (i.e. DEMethylated, LOW, INTermediate and CIMP) with progressively increasing levels of DNA methylation were identified in EPICA, TCGA MM and TCGA primary melanoma cohorts. EPICA patients with LOW methylation tumors exhibited a significantly longer survival and a lower progression rate to more advanced AJCC stages, compared to patients with CIMP tumors. In an adjuvant immune checkpoint blockade cohort, patients with DEM/LOW pre-therapy lesions showed significantly longer relapse-free survival compared to those with INT/CIMP lesions. RNA-seq data analysis revealed that LOW and CIMP EPICA tumors showed opposite activation of master molecules influencing prognostic target genes, and differential expression of immunotherapy response and melanoma differentiation signatures. Compared to CIMP tumors, LOW lesions showed enrichment for CD8+ TCF-1+ PD-1+ TIM-3- pre-exhausted and CD8+ TCF-1- PD-1+ TIM-3+ exhausted T cells, more frequent retention of HLA Class I antigens and a de-differentiated melanoma phenotype. The differentiation and immune-related transcriptional features associated with LOW vs CIMP lesions were tumor-intrinsic programs retained in-vitro by melanoma cell lines. Consistently, treatment of differentiated melanoma cell lines with a DNMT inhibitor induced global DNA de-methylation, promoted de-differentiation and upregulated viral mimicry and IFNG predictive signatures of immunotherapy response.  Conclusions. These results reveal the biological, prognostic and therapeutic relevance of DNA methylation classes in MM and support methylome targeting strategies for precision immunotherapy.
DOI: 10.5281/zenodo.14524844
title: EJP SensRes bi-directional reflectance of soils

description: Repository of the database of bi-directional soil spectral reflectance measurements and the corresponding physico-chemical variables for soil carbon estimation. 




Soil samples from the chemistry laboratory were prepared for the spectral measurements that were carried out using a full-range PSR-3500 spectrometer in the range 350-2500 nm. The spectral sensor was mounted on a robotic arm to perform a regular sampling strategy involving multiple viewing angles and different soil water contents.  




Three main datasets were compiled, and they are summarized in Table 1 in the related .doc document.
DOI: 10.5281/zenodo.15492702
title: Genomic liver profiling identifies hepatokines promoting tissue wasting in cancer cachexia
DOI: 10.5281/zenodo.15496149
title: Functional liver genomics identifies hepatokines promoting wasting in cancer cachexia
DOI: 10.5281/zenodo.15878143
title: PAMGuard Tutorial dataset (for review)

description: Dataset and tutorial for PAMGuard. 

This is a very basic PAMGuard tutorial which will introduce you to the following concepts:

1. Launching PAMGuard and selecting a configuration file2. Running the click detector and using Target Motion Analysis to localise sperm whale clicks3. Adding a whistle detector and detecting dolphin sounds4. Using different detectors for baleen whale sounds
DOI: 10.5281/zenodo.15879114
title: PAMGuard Tutorial dataset (for review)

description: Dataset and tutorial for PAMGuard. 

Also includes installers for Windows and Mac

This is a very basic PAMGuard tutorial which will introduce you to the following concepts:

1. Launching PAMGuard and selecting a configuration file2. Running the click detector and using Target Motion Analysis to localise sperm whale clicks3. Adding a whistle detector and detecting dolphin sounds4. Using different detectors for baleen whale sounds
DOI: 10.5281/zenodo.14002689
title: SERENA EJP SOIL: Soil organic carbon concentration map for the topsoil of Hungary (2016)

description: The internal EJP SOIL project SERENA contributed to the evaluation of soil multifunctionality aiming at providing assessment tools for land planning and soil policies at different scales. By co-working with relevant stakeholders, the project provided co-developed indicators and associated cookbooks to assess and map them, to report both on soil degradation, soil-based ecosystem services and their bundles, under actual conditions and for climate and land-use changes, at the regional, national, and European scales.

The data was prepared according to the methodology of SERENA SOC loss cookbook for the territory of Hungary. To compile the soil organic carbon map, soil organic carbon (0-30 cm, year 2016) data of the Hungarian Soil Information and Monitoring System (SIMS) were used, which are not publicly available. The selection of environmental covariates, which are then used to model and map SOC content, was based on the ‘scorpan’ model: (s) soil properties, (c) climate, (o) organisms, (r) relief, (p) parent material, (a) age and (n) spatial coordinates. The following covariates were used: soil type map of Hungary (Pásztor et al., 2018); long-term mean annual evapotranspiration, -evaporation, -precipitation, and -temperature (Szentimrey et al., 2007); CORINE Land Cover 2012; EU-DEM and derivatives; Geological map of Hungary (Gyalog & Síkhegyi, 2005). Random forest kriging (RFK, combination of the random forest machine learning algorithm and the kriging technique) was used for the prediction of the SOC concentration.
description: The data are derived from the calculation of indicators based on a standard methodology established as part of the EJP Soil SERENA programme. Please keep in mind that:



It is the result of a modelling exercise and does not necessarily reflect reality.

Despite the efforts made to provide reliable data, the results may contain inconsistencies, depending in particular on the raw data available and level of accuracy of the techniques chosen and their prior knowledge.

It is necessary to consider how the results have been obtained in order to decide on their relevance in relation to the intended purpose of reuse.

These results are interesting from a scientific point of view, but their use for environmental management and policy issues should be done keeping the previous aspects in mind and complementing when necessary the provided results with the best available data.


Finally, it is the responsibility of the users of this information to decide whether it is appropriate to use these data and whether the data meet their needs. The authors of this resource can in no way be held responsible for the results obtained from the use of this data.
DOI: 10.15468/dl.nh6t9a
title: Occurrence Download

description: A dataset containing 9434 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "TaxonKey is Podarcis muralis",
 "Year 2005-2025"
 ]
}

 The dataset includes 9434 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047434-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.16857.08803
title: Audio "Die Idee bei Platon. Das Enigma der Philosophie" - Audio of the lecture held at the Volkshochschule Meidling, Vienna within the Programme UMP-University Meets Public, 30th May 2012
DOI: 10.13140/rg.2.2.10637.72163
title: REDUCTION OF SHORT SHOTS BY OPTIMIZING INJECTION MOLDING PROCESS PARAMETERS
DOI: 10.13140/rg.2.2.18502.04169
title: Chapter 5 IPBES IAS Assessment Supplementary material 5.13 Case studies – role of national and international networks and
DOI: 10.13140/rg.2.2.16404.88960
title: Supplementary material 5.6. Species-based management technologies
DOI: 10.13140/rg.2.2.35698.68803
title: Supplementary material 5.8. International Standards for Phytosanitary Measures Supplement to section 5.3.1.2
DOI: 10.13140/rg.2.2.22329.34407
title: Chapter 5 IPBES IAS Assessment Supplementary material 5.5 Pathway management – prevention options
DOI: 10.5517/ccxmflj
title: CCDC 852828: Experimental Crystal Structure Determination

description: Related Article: Jieming Zhang, Zuiliang Chen, Hai-Hong Wu, Junliang Zhang|2012|Chem.Commun.|48|1817|doi:10.1039/c2cc16918e
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/ccxrrq3
title: CCDC 856986: Experimental Crystal Structure Determination

description: Related Article: T.J.Hebden, R.Schrock, M.K.Takase, P.Muller|2012|Chem.Commun.|48|1851|doi:10.1039/c2cc17634c
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/ccxhd81
title: CCDC 848943: Experimental Crystal Structure Determination

description: Related Article: Shi-Wen Chiu, Li-Yen Lin, Hao-Wu Lin, Yi-Hong Chen, Zheng-Yu Huang, Yu-Ting Lin, F.Lin, Yi-Hung Liu, Ken-Tsung Wong|2012|Chem.Commun.|48|1857|doi:10.1039/c2cc16390j
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/ccxrrr4
title: CCDC 856987: Experimental Crystal Structure Determination

description: Related Article: T.J.Hebden, R.Schrock, M.K.Takase, P.Muller|2012|Chem.Commun.|48|1851|doi:10.1039/c2cc17634c
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: 10.13140/rg.2.2.23613.84964
title: UW-Code
DOI: 10.5517/ccxcg6x
title: CCDC 845159: Experimental Crystal Structure Determination

description: Related Article: A.Lemmerer, J.Bernstein, M.A.Spackman|2012|Chem.Commun.|48|1883|doi:10.1039/c1cc15849j
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/ccxcg7y
title: CCDC 845160: Experimental Crystal Structure Determination

description: Related Article: A.Lemmerer, J.Bernstein, M.A.Spackman|2012|Chem.Commun.|48|1883|doi:10.1039/c1cc15849j
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/ccxh0r4
title: CCDC 848586: Experimental Crystal Structure Determination

description: Related Article: Nigel S. Simpkins,Ilias Pavlakos,Michael D. Weller,Louise Male|2013|Org.Biomol.Chem.|11|4957|doi:10.1039/C3OB40979A
description: Related Article: N.Simpkins, I.Pavlakos, L.Male|2012|Chem.Commun.|48|1958|doi:10.1039/c1cc16510k
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/ccq5xlc
title: CCDC 661093: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccq5xmd
title: CCDC 661094: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccq5xnf
title: CCDC 661095: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccq5xpg
title: CCDC 661096: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccq5xqh
title: CCDC 661097: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccq5xrj
title: CCDC 661098: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccq5xsk
title: CCDC 661099: Experimental Crystal Structure Determination

description: Related Article: A.Medina-Molner, B.Spingler|2012|Chem.Commun.|48|1961|doi:10.1039/c2cc16483c
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/ccvsthx
title: CCDC 798420: Experimental Crystal Structure Determination

description: Related Article: F.Bouillere, D.Feytens, D.Gori, R.Guillot, C.Kouklovsky, E.Miclet, V.Alezra|2012|Chem.Commun.|48|1982|doi:10.1039/c2cc16852a
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.