cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14626269
title: Hormone peptide data set

description: The data set including 5729 hormone peptide, 40 peptide drugs and 256 marketed preparations of these drugs. Each item has detailed notes, containing basic information, sequence, structure, activity, physics, and literature. We also added IC50, EC50, ED50 and information about whether to cross the blood-brain barrier into the activity information annotation.
DOI: 10.6084/m9.figshare.14626269.v2
title: Hormone peptide data set

description: The data set including 5729 hormone peptide, 40 peptide drugs and 256 marketed preparations of these drugs. Each item has detailed notes, containing basic information, sequence, structure, activity, physics, and literature. We also added IC50, EC50, ED50 and information about whether to cross the blood-brain barrier into the activity information annotation.
DOI: 10.6084/m9.figshare.14626269.v1
title: Hormone peptide data set

description: The data set including 5729 hormone peptide, 40 peptide drugs and 256 marketed preparations of these drugs. Each item has detailed notes, containing basic information, sequence, structure, activity, physics, and literature. We also added IC50, EC50, ED50 and information about whether to cross the blood-brain barrier into the activity information annotation.
DOI: 10.21227/nhea-gt59
title: KROCO

description: KROCO is an acronym for Kinesthetic Robot Contacts. The dataset consists of Learning from Demonstration (LfD, aka Programming by Demonstration (PbD)) samples that were collected via kinesthetic teaching. Each labeld sample is a contact-based (force-based) interaction with the environment.
DOI: 10.5519/qd.83i55unz
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2866 records)
DOI: 10.6084/m9.figshare.14626277.v1
title: Data for paper analysis and plotting. from Where is my hand in space? The internal model of gravity influences proprioception

description: Data used for main analyses in manuscript, including Constant and Variable errors With and Against Gravity in Upright and Tilted body postures. Constant errors at each hand angle for each participant for creating raincloud plots.
DOI: 10.5281/zenodo.4775388
title: Zooarchaeological database of early medieval Heumarkt (Cologne, Germany)

description: The site of Heumarkt (FB96.13) is located in the city center of Cologne, in North Rhine-Westphalia, western Germany. This database contains the zooarchaeological information of the inventory of the faunal materials recovered at the site (mainly from fills of sunken featured structures and dark-coloured layers), all hand-collected. The remains were recorded using Ossobook. There were almost 8000 fragments, of which we calculated approximately 3200 MNE (Minimum Number of Elements). The recorded data are: taxon, skeletal element, taphonomy (butchery marks, overal preservation, colour, etc.), and biometrical data. The majority of the remains are dated to the Merovingian (5th-7th c.), Carolingian (8th-9th c.), and Ottonian (end 9th-10th c.) periods. The assemblage is predominated by pig, followed by cattle, and with an increasing presence of sheep/goat over time. Other identified species are: equids, cat, dog, aurochs, red deer, roe deer, wolf?, fox, beaver, Anser sp., chicken, eel, common barbel, Percidae, Salmo sp., Cyprinidae and Bivalvia. We would like to thank Thomas Höltken, from the Römisch-Germanisches Museum Köln, and Eckhard Deschler-Erb, from the University of Cologne, for their collaboration. The faunal remains from Heumarkt were subject to previous analyses by H. Berke and J. Kokabi. These are the references for these works: Berke, H. 1997. Haustiere, Handwerker und Händler, vorläufige archäozoologische Ergebnisse der Ausgrabungen am Heumarkt in Köln. Kölner Jarhbuch 30: 405-413. Kokabi, J. 2001. Archäozoologische Untersuchung zu den Ausgrabungen Köln-Heumarkt. Kölner Jarhbuch 34: 841-873.
DOI: 10.5281/zenodo.4707456
title: Zooarchaeological database of early medieval Heumarkt (Cologne, Germany)

description: The site of Heumarkt (FB96.13) is located in the city center of Cologne, in North Rhine-Westphalia, western Germany. This database contains the zooarchaeological information of the inventory of the faunal materials recovered at the site (mainly from fills of sunken featured structures and dark-coloured layers), all hand-collected. The remains were recorded using Ossobook. There were almost 8000 fragments, of which we calculated approximately 3200 MNE (Minimum Number of Elements). The recorded data are: taxon, skeletal element, taphonomy (butchery marks, overal preservation, colour, etc.), and biometrical data. The majority of the remains are dated to the Merovingian (5th-7th c.), Carolingian (8th-9th c.), and Ottonian (end 9th-10th c.) periods. The assemblage is predominated by pig, followed by cattle, and with an increasing presence of sheep/goat over time. Other identified species are: equids, cat, dog, aurochs, red deer, roe deer, wolf?, fox, beaver, Anser sp., chicken, eel, common barbel, Percidae, Salmo sp., Cyprinidae and Bivalvia. We would like to thank Thomas Höltken, from the Römisch-Germanisches Museum Köln, and Eckhard Deschler-Erb, from the University of Cologne, for their collaboration. The faunal remains from Heumarkt were subject to previous analyses by H. Berke and J. Kokabi. These are the references for these works: Berke, H. 1997. Haustiere, Handwerker und Händler, vorläufige archäozoologische Ergebnisse der Ausgrabungen am Heumarkt in Köln. Kölner Jarhbuch 30: 405-413. Kokabi, J. 2001. Archäozoologische Untersuchung zu den Ausgrabungen Köln-Heumarkt. Kölner Jarhbuch 34: 841-873.
DOI: 10.5281/zenodo.3911187
title: Integrative approaches in nsCL/P

description: We here provide chromatin segmentation data based on previously generated raw data or chromatin immunoprecipitation followed by sequencing (ChIP-seq) data from human neural crest cells (hNCC, Rada-Iglesias et al. 2012 (GSE28874)) and cranial neural crest cells (cNCC, Prescott et al. 2015 (GSE70751)), which have been generated to be used for interpretation of common risk variation for orofacial clefting. Furthermore, this datasets contains a list of regions that are specifically active in NCC while not being active in craniofacial tissue, and vice versa. More details are provided in the Additional notes.
description: 1) cNCC_UCSC_ChromHMM.bed, and hNCC_UCSC_ChromHMM.bed.bed These files contain the chromatin segmentation data that was generated based on chromatin immunoprecipitation followed by sequrencing (CHiP-seq) data of different histone modifications captured in early human neural crest cells (hNCC, Rada-Iglesias et al. 2012 (GSE28874)) and cranial neural crest cells (cNCC, Prescott et al. 2015 (GSE70751)). While the histone marks H3K27ac, H3K4me1, H3K4me3 and H3K27me3 were directly measured in hNCC, additional histone marks (H3K9me3 and H3K36me3) were imputed using ChromImpute v1.0.1 (Ernst and Kellis, 2015) based on 127 cell types from Roadmap Epigenome Project (Roadmap Epigenomics Consortium et al. 2015) and the available chromatin marks in hNCC, cNCC and craniofacial tissue before chromatin segmentation. For the chromatin segmentation itself, we used the core 18 + H3K27ac model as implemented in ChromHMM (Ernst and Kellis, 2012). The files are provided in a genome browser compatible format. 2) CT_active_NCC_inactive.bed, and CT_act_NCC_inact_UCSC.bed These files contain specific active sites in NCC or CT. In the chromatin segmentation datasets, we filtered for active chromatin sites (Transcription starting sites (TSS), Enhancer or transcribed sites) in NCC that are repressed/quiet (Quiescent, Bivalent_TSS_poised_Enhancers, RepressedPolyComb sites, Heterochromatin) in CT and vice versa. For robust observations, we only trust in a chromatin state if it is present in both NCC samples (hNCC, cNCC), or in five of the six CT (Carnegie stage (CS) 13, CS14, CS15, CS17, CS20, 1 weeks post-conceptum) samples. To account for biases in length associated with batch-effects, active sites were only retained if they had a distance of ≥500 base pairs to any chromatin segment of opposite activity status in the other cell system/tissue. In the following, we combined the specific active chromatin sites with associations of our meta-analysis in cleft (MAiC) and topologically associating domain (TAD) data to filter for TADs with high density of strong associated genetic variants (PMAiC ≤ 5×10-05) in specific active chromatin sites at new and known nsCL/P GWAS risk loci.
DOI: 10.5281/zenodo.3911186
title: Integrative approaches in nsCL/P

description: We here provide chromatin segmentation data based on previously generated raw data or chromatin immunoprecipitation followed by sequencing (ChIP-seq) data from human neural crest cells (hNCC, Rada-Iglesias et al. 2012 (GSE28874)) and cranial neural crest cells (cNCC, Prescott et al. 2015 (GSE70751)), which have been generated to be used for interpretation of common risk variation for orofacial clefting. Furthermore, this datasets contains a list of regions that are specifically active in NCC while not being active in craniofacial tissue, and vice versa. More details are provided in the Additional notes.
description: 1) cNCC_UCSC_ChromHMM.bed, and hNCC_UCSC_ChromHMM.bed.bed These files contain the chromatin segmentation data that was generated based on chromatin immunoprecipitation followed by sequrencing (CHiP-seq) data of different histone modifications captured in early human neural crest cells (hNCC, Rada-Iglesias et al. 2012 (GSE28874)) and cranial neural crest cells (cNCC, Prescott et al. 2015 (GSE70751)). While the histone marks H3K27ac, H3K4me1, H3K4me3 and H3K27me3 were directly measured in hNCC, additional histone marks (H3K9me3 and H3K36me3) were imputed using ChromImpute v1.0.1 (Ernst and Kellis, 2015) based on 127 cell types from Roadmap Epigenome Project (Roadmap Epigenomics Consortium et al. 2015) and the available chromatin marks in hNCC, cNCC and craniofacial tissue before chromatin segmentation. For the chromatin segmentation itself, we used the core 18 + H3K27ac model as implemented in ChromHMM (Ernst and Kellis, 2012). The files are provided in a genome browser compatible format. 2) CT_active_NCC_inactive.bed, and CT_act_NCC_inact_UCSC.bed These files contain specific active sites in NCC or CT. In the chromatin segmentation datasets, we filtered for active chromatin sites (Transcription starting sites (TSS), Enhancer or transcribed sites) in NCC that are repressed/quiet (Quiescent, Bivalent_TSS_poised_Enhancers, RepressedPolyComb sites, Heterochromatin) in CT and vice versa. For robust observations, we only trust in a chromatin state if it is present in both NCC samples (hNCC, cNCC), or in five of the six CT (Carnegie stage (CS) 13, CS14, CS15, CS17, CS20, 1 weeks post-conceptum) samples. To account for biases in length associated with batch-effects, active sites were only retained if they had a distance of ≥500 base pairs to any chromatin segment of opposite activity status in the other cell system/tissue. In the following, we combined the specific active chromatin sites with associations of our meta-analysis in cleft (MAiC) and topologically associating domain (TAD) data to filter for TADs with high density of strong associated genetic variants (PMAiC ≤ 5×10-05) in specific active chromatin sites at new and known nsCL/P GWAS risk loci.
DOI: 10.25646/8527
title: Tagesdaten-CSV aus dem DIVI-Intensivregister

description: Die Tagesdaten-CSV entspricht einem Auszug der Daten des DIVI-Intensivregisters. Die Datei enthält eine Aggregation der aktuellsten Meldungen pro Landkreis. Es werden die aktuell gemeldeten Anzahlen der COVID-19 Intensivfälle sowie die gemeldeten intensivmedizinischen Behandlungskapazitäten angezeigt. Die Tagesdaten-CSV liefert dabei ausschließlich einen Blick auf die Daten gemäß dem Stand des betrachteten Tages. Die Daten sind im situationsbedingten Kontext aufbereitet, damit sind verschiedene Tagesdaten-CSVs u.U. nicht direkt miteinander vergleichbar. Die aktuellsten Meldungen werden im gewählten Betrachtungszeitfenster über alle Meldebereiche und Standorte aufsummiert. Weitere Informationen sind zu finden unter https://www.intensivregister.de/#/faq
DOI: 10.6084/m9.figshare.12852609.v1
title: The Test of Time: Using Historical Methods to Assess Models of Ecological Change on California’s Hardwood Rangelands

description: Geographers and environmental scientists use conceptual models to understand ecological processes and support management decisions. Most of these models are based on short-term experiments and field observations, which might not account for longer term forces that shape ecosystems over decades to centuries. How can scholars use historical sources and methods to improve conceptual models of ecological change? In this article, we present the results of a study that employed methods from environmental history and historical geography to assess three conceptual models that researchers have used to study ecological changes on California’s hardwood rangelands: the succession and climax, state and transition, and cyclical replacement models. The succession and climax model fared poorly at all spatial scales. The historical record contained substantial evidence to support the predictions of the state and transition model at the small spatial scale of the plot or field (0.1–100 ha) and the very large spatial scale of the hardwood rangeland bioregion (4 million ha). The cyclical replacement model performed well at the intermediate scale of the landscape or typical cattle ranch (100–10,000 ha). Historical data and methods hold considerable untapped potential for assessing, building on, and improving conceptual models of ecological change in geography and the environmental sciences.
DOI: 10.6084/m9.figshare.12852612
title: What’s in a Name? Undergraduate Student Perceptions of Geography, Environment, and Sustainability Key Words and Program Names

description: The academic discipline of geography, faced with increasing competition from cognate fields and declining undergraduate enrollments, continues to suffer an identity crisis. In recent decades, many geography programs have instituted department or degree name changes, or otherwise rebranded, without any evidence guiding these decisions. This study begins to build an evidence base for these decisions by presenting results from a survey of 4,388 undergraduates across four U.S. universities to understand how students rate key words that commonly appear in geography course descriptions and titles and phrases that comprise degree and department names. Undergraduates overwhelmingly and consistently preferred simple, thematic types of terms to those that sounded more technical or science oriented. Forms of the word <i>geography</i> were rated significantly lower than words or phrases containing <i>environment</i> and <i>sustainability</i>. Forms of geography that included the word <i>science</i> were rated particularly low. Student ratings varied by class standing, major, gender, high school location (United States vs. outside of the United States), whether the student had previously enrolled in a geography course, and self-perceived numeracy. Multivariable analysis revealed potential opportunities for targeted undergraduate recruiting and curricular development. This study is an important step toward reconciling contemporary student perceptions of geography and related fields with departmental identities and the disciplinary jargon often used in program and course descriptions. We offer a toolkit for implementing similar research at other institutions and ultimately helping geography programs recruit and retain the next generation of geographers.
DOI: 10.6084/m9.figshare.12852609
title: The Test of Time: Using Historical Methods to Assess Models of Ecological Change on California’s Hardwood Rangelands

description: Geographers and environmental scientists use conceptual models to understand ecological processes and support management decisions. Most of these models are based on short-term experiments and field observations, which might not account for longer term forces that shape ecosystems over decades to centuries. How can scholars use historical sources and methods to improve conceptual models of ecological change? In this article, we present the results of a study that employed methods from environmental history and historical geography to assess three conceptual models that researchers have used to study ecological changes on California’s hardwood rangelands: the succession and climax, state and transition, and cyclical replacement models. The succession and climax model fared poorly at all spatial scales. The historical record contained substantial evidence to support the predictions of the state and transition model at the small spatial scale of the plot or field (0.1–100 ha) and the very large spatial scale of the hardwood rangeland bioregion (4 million ha). The cyclical replacement model performed well at the intermediate scale of the landscape or typical cattle ranch (100–10,000 ha). Historical data and methods hold considerable untapped potential for assessing, building on, and improving conceptual models of ecological change in geography and the environmental sciences.
DOI: 10.6084/m9.figshare.12852612.v1
title: What’s in a Name? Undergraduate Student Perceptions of Geography, Environment, and Sustainability Key Words and Program Names

description: The academic discipline of geography, faced with increasing competition from cognate fields and declining undergraduate enrollments, continues to suffer an identity crisis. In recent decades, many geography programs have instituted department or degree name changes, or otherwise rebranded, without any evidence guiding these decisions. This study begins to build an evidence base for these decisions by presenting results from a survey of 4,388 undergraduates across four U.S. universities to understand how students rate key words that commonly appear in geography course descriptions and titles and phrases that comprise degree and department names. Undergraduates overwhelmingly and consistently preferred simple, thematic types of terms to those that sounded more technical or science oriented. Forms of the word <i>geography</i> were rated significantly lower than words or phrases containing <i>environment</i> and <i>sustainability</i>. Forms of geography that included the word <i>science</i> were rated particularly low. Student ratings varied by class standing, major, gender, high school location (United States vs. outside of the United States), whether the student had previously enrolled in a geography course, and self-perceived numeracy. Multivariable analysis revealed potential opportunities for targeted undergraduate recruiting and curricular development. This study is an important step toward reconciling contemporary student perceptions of geography and related fields with departmental identities and the disciplinary jargon often used in program and course descriptions. We offer a toolkit for implementing similar research at other institutions and ultimately helping geography programs recruit and retain the next generation of geographers.
DOI: 10.5281/zenodo.4775463
title: Replication package for: Conditional Superior Predictive Ability

description: The package contains the code and data necessary to reproduce the figures and talbes in Li, Liao and Quaedvlieg (forthcoming). "Conditional Superior Preditive Ability." Review of Economic Studies.
DOI: 10.5281/zenodo.4775523
title: Replication package for: Conditional Superior Predictive Ability

description: The package contains the code and data necessary to reproduce the figures and talbes in Li, Liao and Quaedvlieg (forthcoming). "Conditional Superior Preditive Ability." Review of Economic Studies.
DOI: 10.6084/m9.figshare.9976115
title: Lacertid trees

description: Phylogenetic trees (Maximum Likelihood tree and timetree) of lizards in the family Lacertidae.<br>
DOI: 10.6084/m9.figshare.9976115.v1
title: Lacertid trees

description: Phylogenetic trees (Maximum Likelihood tree and timetree) of lizards in the family Lacertidae.<br>
DOI: 10.6084/m9.figshare.14604537
title: Accipiter nisus potential microsatellite loci

description: Full library of potential microsatellite loci for Accipiter nisus.<br><br>Based on DNA from tissue samples of four specimens of A. nisus from Tenerife, Germany, Finland and Georgia. DNA digestion with restriction enzymes AluI, RsaI, and Hpy166II. Blunt ends were adenylated (+A) with Klenow (exo-) and dATP, and after heat inactivation of the Klenow (exo-), the reactions were supplemented with ATP to 1 mM and an Illumina Y-adaptor was ligated with T4 DNA ligase. Enrichment of the fragments for microsatellites by hybridisation to and magnetic capture of biotinylated repeat probes (representing two unique dimers, five unique trimers, seven unique tetramers and two unique pentamers), followed by amplification and barcoding by PCR, and sequencing on an Illumina MiSeq instrument (2 × 250 bp paired reads). SeqMan NGen (version 11) was used for raw read assembly, and the program msatcommander 1.0.8_beta (for Mac OSX) was employed to scan the assembly for microsatellite loci and automatically design primer pairs.<br>
DOI: 10.6084/m9.figshare.14604537.v1
title: Accipiter nisus potential microsatellite loci

description: Full library of potential microsatellite loci for Accipiter nisus.<br><br>Based on DNA from tissue samples of four specimens of A. nisus from Tenerife, Germany, Finland and Georgia. DNA digestion with restriction enzymes AluI, RsaI, and Hpy166II. Blunt ends were adenylated (+A) with Klenow (exo-) and dATP, and after heat inactivation of the Klenow (exo-), the reactions were supplemented with ATP to 1 mM and an Illumina Y-adaptor was ligated with T4 DNA ligase. Enrichment of the fragments for microsatellites by hybridisation to and magnetic capture of biotinylated repeat probes (representing two unique dimers, five unique trimers, seven unique tetramers and two unique pentamers), followed by amplification and barcoding by PCR, and sequencing on an Illumina MiSeq instrument (2 × 250 bp paired reads). SeqMan NGen (version 11) was used for raw read assembly, and the program msatcommander 1.0.8_beta (for Mac OSX) was employed to scan the assembly for microsatellite loci and automatically design primer pairs.<br>
DOI: 10.6084/m9.figshare.13079489.v2
title: MargazoglouEtAl_2020.zip

description: We present here the majority of the dataset used for the figures of the paper "Multistability of the Earth's Climate as a Problem of Stochastic Dynamics and of Data Science". Some datafiles are sufficient to reproduce directly the figures, while others are the raw data one needs to reproduce the figures using the methodologies described in the paper.<br><br>For more information, please contact Georgios Margazoglou at g.margazoglou@reading.ac.uk or Valerio Lucarini at v.lucarini@reading.ac.uk. Thank you!<br><br>
DOI: 10.6084/m9.figshare.8295815
title: Multigene data set (Nexus) and BI phylogenetic tree Uroplatus ebenaui group - partitioned by gene

description: Bayesian Inference tree of Madagascar leaf-tailed geckos in the Uroplatus ebenaui group, calculated using the program MrBayes, based on DNA sequences of four mitochondrial and one nuclear gene fragments, with a by-gene partition scheme. Along with Nexus file with original sequence data used.<br>
DOI: 10.6084/m9.figshare.8295815.v1
title: Multigene data set (Nexus) and BI phylogenetic tree Uroplatus ebenaui group - partitioned by gene

description: Bayesian Inference tree of Madagascar leaf-tailed geckos in the Uroplatus ebenaui group, calculated using the program MrBayes, based on DNA sequences of four mitochondrial and one nuclear gene fragments, with a by-gene partition scheme. Along with Nexus file with original sequence data used.<br>