cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.19nr2
title: Data from: How new concepts become universal scientific approaches – insights from citation network analysis of agent-based complex systems science

description: Progress in understanding and managing complex systems comprised of
 decision-making agents, such as cells, organisms, ecosystems, or
 societies, is—like many scientific endeavors—limited by disciplinary
 boundaries. These boundaries, however, are moving and can actively be made
 porous or even disappear. To study this process, we advanced an original
 bibliometric approach based on network analysis to track and understand
 the development of the model-based science of agent-based complex systems
 (ACS). We analyzed research citations between the two communities devoted
 to ACS research, namely agent-based (ABM) and individual-based modeling
 (IBM). Both terms refer to the same approach, yet the former is preferred
 in engineering and social sciences, while the latter prevails in natural
 sciences. This situation provided a unique case study for grasping how a
 new concept evolves distinctly across scientific domains and how to foster
 convergence into a universal scientific approach. The present analysis
 based on novel hetero-citation metrics revealed the historical development
 of ABM and IBM, confirmed their past disjointedness, and detected their
 progressive merger. The separation between these synonymous disciplines
 had silently opposed the free flow of knowledge among ACS practitioners
 and has thereby hindered the transfer of methodological advances and the
 emergence of general systems theories. A surprisingly small number of key
 publications sparked the ongoing fusion between ABM and IBM research.
 Beside reviews raising awareness of broad-spectrum issues, generic
 protocols for model formulation and boundary-transcending inference
 strategies were critical means of science integration. From the modeling
 viewpoint, the discovery of the unification of ABM and IBM demonstrates
 that a wide variety of systems substantiate the premise of ACS research
 that microscale behaviors of agents and system-level dynamics are
 inseparably bound.
description: Historical evolution of
 ACS literatureGenesis and evolution of
 the science of agent-based complex systems seen from the perspective of
 its citation network from 1990 to January 2016. The dynamic graph shows
 the temporal dynamics of the agent-based modeling (blue vertices) and
 individual-based modeling (red vertices) corpora. Vertices are positioned
 based on the ForceAtlas2 layout algorithm without vertex overlapping. The
 video uploaded here is a high-resolution version of the one provided
 alongside the manuscript.Vincenot 2018 - RSPB
 (HQ).mp4Bibliographic
 DatasetBibliographic dataset
 compiling all Scopus records relevant to Agent-based Complex Systems (ACS)
 science (i.e. the fields of agent-based and individual-based modelling).
 This dataset was post-processed and used to create a citation graph using
 the Diderot R package
 (https://cran.r-project.org/package=Diderot).RSPBVincenot-Dataset.csv
DOI: 10.5061/dryad.s46kt
title: Data from: Acute modulation of brain connectivity in Parkinson disease after Automatic Mechanical Peripheral Stimulation: a pilot study

description: Objective: The present study shows the results of a double-blind
 sham-controlled pilot trial to test whether measurable stimulus-specific
 functional connectivity changes exist after Automatic Mechanical
 Peripheral Stimulation (AMPS) in patients with idiopathic Parkinson
 Disease. Methods: Eleven patients (6 women and 5 men) with idiopathic
 Parkinson Disease underwent brain fMRI immediately before and after sham
 or effective AMPS. Resting state Functional Connectivity (RSFC) was
 assessed using the seed-ROI based analysis. Seed ROIs were positioned on
 basal ganglia, on primary sensory-motor cortices, on the supplementary
 motor areas and on the cerebellum. Individual differences for pre- and
 post-effective AMPS and pre- and post-sham condition were obtained and
 first entered in respective one-sample t-test analyses, to evaluate the
 mean effect of condition. Results: Effective AMPS, but not sham
 stimulation, induced increase of RSFC of the sensory motor cortex, nucleus
 striatum and cerebellum. Secondly, individual differences for both
 conditions were entered into paired group t-test analysis to rule out
 sub-threshold effects of sham stimulation, which showed stronger
 connectivity of the striatum nucleus with the right lateral occipital
 cortex and the cuneal cortex (max Z score 3.12) and with the right
 anterior temporal lobe (max Z score 3.42) and of the cerebellum with the
 right lateral occipital cortex and the right cerebellar cortex (max Z
 score 3.79). Conclusions: Our results suggest that effective AMPS acutely
 increases RSFC of brain regions involved in visuo-spatial and
 sensory-motor integration. Classification of Evidence: This study provides
 Class II evidence that automatic mechanical peripheral stimulation is
 effective in modulating brain functional connectivity of patients with
 Parkinson Disease at rest. Trial Registration: Clinical Trials.gov
 NCT01815281.
description: AMPS_Pilot_MRI
 dataAMPS_Pilot_MRIdata_be.rar
DOI: 10.5061/dryad.j3m73
title: Data from: Intramolecular hydrogen bonds in 1,4-dihydropyridine derivatives

description: 1,4- dihydropyridine (1,4-DHP) derivatives have been synthesized and
 characterized by 1H, 13C, 15N NMR spectroscopy, secondary H/D 13C isotope
 shifts, variable temperature 1H NMR experiments and quantum-chemical
 calculation. The intramolecular hydrogen-bonds NH•••O=C and CH•••O=C in
 these compounds were established by NMR and quantum-chemical studies. The
 downfield shift of the NH proton, accompanied by the upfield shift of the
 15N NMR signals, the shift to the higher wave numbers of the NH stretching
 vibration in the IR spectra and the increase of the 1J(15N,1H) values may
 indicate the shortening of the N-H bond length upon intramolecular
 NH•••O=C hydrogen bond formation.
description: Supplementary_fileNMR and quantum-chemical data
DOI: 10.5061/dryad.f6s22
title: Data from: Gene prediction and annotation in Penstemon (Plantaginaceae): a workflow for marker development from extremely low-coverage genome sequencing

description: Premise of the study: Penstemon (Plantaginaceae) is a large and diverse
 genus endemic to North America. However, determining the phylogenetic
 relationships among its 280 species has been difficult due to its recent
 evolutionary radiation. The development of a large, multilocus data set
 can help to resolve this challenge. Methods: Using both previously
 sequenced genomic libraries and our own low-coverage whole-genome shotgun
 sequencing libraries, we used the MAKER2 Annotation Pipeline to identify
 gene regions for the development of sequencing loci from six extremely
 low-coverage Penstemon genomes (∼0.005×−0.007×). We also compared this
 approach to BLAST searches, and conducted analyses to characterize
 sequence divergence across the species sequenced. Results: Annotations and
 gene predictions were successfully added to more than 10,000 contigs for
 potential use in downstream primer design. Primers were then designed for
 chloroplast, mitochondrial, and nuclear loci from these annotated
 sequences. MAKER2 identified longer gene regions in all six Penstemon
 genomes when compared with BLASTN and BLASTX searches. The average level
 of sequence divergence among the six species was 7.14%. Discussion:
 Combining bioinformatics tools into a workflow that produces annotations
 can be useful for creating potential phylogenetic markers from thousands
 of sequences even when genome coverage is extremely low and reference data
 are only available from distant relatives. Furthermore, the output from
 MAKER2 contains information about important gene features, such as exon
 boundaries, and can be easily integrated with visualization tools to
 facilitate the process of marker development.
description: Perl script for
 functional annotationsHit-desc.pl - Perl
 script for adding functional annotations to contigs using BLAST output
 (-outfmt 6). Note: This script uses regular expressions that are specific
 to targeting the accession numbers of our contigs and those that were used
 for BLAST searches. It is to be used as a reference for writing similar
 scripts for similar purposes but will not work as is for datasets other
 than our own. Requires an installation of BioPerl. Running too much BLAST
 output at once will kick you off of the NCBI server, so restrict the
 number of queries to ~500.Hit-desc.plPenstemonSNAP hidden Markov model parameter file used for Penstemon.Penstemon-MAKER-FuncAnnotsExcel spreadsheet of functional annotations added to MAKER2 structural annotations.MakerESTFASTA file of EST sequences used during MAKER2 runs.MakerProteinFASTA file of protein sequences used during MAKER2 runs.
DOI: 10.5061/dryad.3rg62
title: Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

description: This paper reports on SNP discovery in the Atlantic mackerel
 transcriptome, using next generation sequencing technologies and applying
 developed methodology already proven successful for the European anchovy.
 A total of 9,966 high quality transcriptome contigs were assembled, from
 which 951 putative SNPs were discovered. In all, 479 putative SNPs and
 1,624 simple sequence repeats (SSRs) suitable for genotyping were
 identified. A subset of 96 was selected for genotyping; from these, 80
 SNPs were considered polymorphic and reliably scored after genotyping of
 105 individuals from three locations in the Eastern Atlantic Ocean. These
 markers will be valuable for future studies on population genetic
 structure assessment and for product tracing.
description: SSR and SNP markers
 discovered for Atlantic mackerelSSRs: The 1,624 SSR
 markers detected in the Atlantic mackerel transcriptome. SSR names follow
 the format Ssco_[A]-[B] where [A] indicates the transcriptome contig where
 the SSR was detected and [B] indicates the number of SSR in the contig.
 SNPs:. The 80 validated SNPs sequences and their descriptive statistics.
 For each marker following information is provided: NCBI Submitter SNP (ss)
 accession numbers, reference and alternative alleles, call rate (%), minor
 allele frequency (MAF), global (pooling the three sampling locations)
 expected heterozygosity (He), global and per location deviation (p-value)
 from the Hardy-Weinberg equilibrium (HWE), and flanking sequence. SNP
 names follow the format [A]_[B] where [A] indicates the contig number and
 [B] indicates the SNP position in that contig. Target SNP is encoded in
 the sequence as [REF/ALT] where REF indicates the reference allele ALT
 indicates the alternative allele. * corresponds to p-value &lt; 0.0001.
 SIGN. means that at least 1 location is not in HWE for these markers. N.S.
 corresponds to not significant.dryad.xlsxAtlantic mackerel transcriptome sequence files (.sff)Atlantic mackerel genome sequence files (.fastq) for the 10 individuals analyzedAtlantic mackerel transcriptome assembly (.fasta)ssco_trans_filtered.fastaAtlantic mackerel T2T and G2T alignment files (.bam)alignments.zipAtlantic mackerel T2T and G2T variant files (.vcf)variants.zip
DOI: 10.5061/dryad.s38jv
title: Data from: Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at non coding sites

description: In Saccharomyces cerevisiae, the main yeast in wine fermentation, the
 opportunity to examine divergence at the molecular level between a
 domesticated lineage and its wild counterpart arose recently due to the
 identification of the closest relatives of wine strains, a wild population
 associated with Mediterranean oaks. Since genomic data is available for a
 considerable number of representatives belonging to both groups, we used
 population genomics to estimate the degree and distribution of nucleotide
 variation between wine yeasts and their closest wild relatives. We found
 widespread genome-wide divergence, particularly at non-coding sites,
 which, together with above average divergence in trans-acting DNA binding
 proteins, may suggest an important role for divergence at the level of
 transcriptional regulation. Nine outlier regions putatively under strong
 divergent selection were highlighted by a genome wide scan under stringent
 conditions. Several cases of introgressions originating in the sibling
 species S. paradoxus, were also identified in the Mediterranean oak
 population. FFZ1 and SSU1, mostly known for conferring sulphite resistance
 in wine yeasts, were among the introgressed genes, although not fixed.
 Because the introgressions detected in our study are not found in wine
 strains, we hypothesise that ongoing divergent ecological selection
 segregates the two forms between the different niches. Together, our
 results provide a first insight into the extent and kind of divergence
 between wine yeasts and their closest wild relatives.
description: Chromosome alignments of
 Wine and Mediterranean oaks populationsThis is a gzip/tar
 compressed data archive containing the chromosome alignments of Wine and
 Mediterranean oaks populations in fastA format.final-clean-wineAll-moAll.tgzAlignments of FZF1 coding regionThis is a gzip/tar compressed data archive with the alignments of the coding region of FZF1.FZF1_alignments.tgzPolymorphism analysis between the Mediterranean oak population and the wine populationThis is a gzip/tar compressed data archive containing the results of sharedPoly from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003). The archive contains results for each reference chromosome.libsequence_sharedpoly.tgzVariant Effect Predictor related filesThis is a gzip/tar compressed data archive containing the input and output files for the Variant Effect Predictor (VEP) related analyses. It also has a RepeatMasker results file, based on the sacCer3 reference genome, and a perl script "mask.repeatmasker.pl" to mask/exclude the VEP resultsVEP_input_output.tgz
DOI: 10.5517/ccdc.csd.cc2ph3y8
title: CCDC 2487190: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph3z9
title: CCDC 2487191: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.1hj3m
title: Data from: "Transcriptome sequences for Campanula gentilis" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015

description: In this report, we present the transcriptome of a single accession of
 Campanula gentilis Kovanda, obtained through the sequencing of both a
 normalized and a non-normalized cDNA library generated from stem and leaf
 tissue. The resources we provide include the raw sequence reads, the
 assembled contigs, the putative open reading frames, the contig/ORF
 annotations and the normalized as well as non-normalized expression
 levels.
description: Transcriptome
 contigsTranscriptome contigs
 obtained through the assembly of merged sequence read data sets from
 normalised and non-normalised cDNA librariestranscriptomeContigs.fastaBlastx annotation and expression levelsTranscriptomic contig Blastx-based annotations and expression levelsblastxAnnotationAndExpressionLevels.txtBlastp annotation and expression levelsTranscriptomic contig Blastp-based annotations and expression levelsblastpAnnotationAndExpressionLevels.txtTranscriptomic contig expression levelsExpression levels of the transcriptomic contigs based on the alignment of the non-normalised cDNA library sequence reads against the assembled transcriptome.nonNormalizedExpressionLevels.txtnormalizedExpressionLevelsExpression levels of the transcriptomic contigs after normalisation of the cDNA libraryBlastx-based annotation (green plants) and expression levelsTranscriptomic contig Blastx-based annotations using green-plant Swiss-prot accessions and expression levelsblastxExpressionLevels.txtBlastp annotation (green plants) and expression levelsTranscriptomic contig Blastp-based annotations using green-plant Swiss-prot accessions and expression levelsblastpExpressionLevels.txtTranscriptomic contig expression levels (no isoforms)Expression levels of the transcriptomic contigs (no isoforms) based on the alignment of the non-normalised cDNA library sequence reads against the assembled transcriptome.nonNormalizedExpressionLevels.txtTranscriptomic contig normalized expression levels (no isoforms)Expression levels of the transcriptomic contigs (no isoforms) after normalisation of the cDNA library.normalizedExpressionLevels.txtTranscriptome coding sequencesCoding sequences derived from the transcriptome contigs using TransDecoder softwaretranscriptomeORFs.cdsTranslated transcriptome coding sequencesAmino acid sequences obtained through translation of the transcriptome coding sequencestranscriptomeORFs.pep
DOI: 10.5517/ccdc.csd.cc2ph7s7
title: CCDC 2487309: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph7t8
title: CCDC 2487310: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph7v9
title: CCDC 2487311: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph7xc
title: CCDC 2487313: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph7yd
title: CCDC 2487314: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph80h
title: CCDC 2487316: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph81j
title: CCDC 2487317: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph82k
title: CCDC 2487318: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2ph83l
title: CCDC 2487319: Experimental Crystal Structure Determination

description: Related Article: Dongjing Hong|2025|CSD Communication|||
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.cc2phdzl
title: CCDC 2487470: Experimental Crystal Structure Determination

description: Related Article: Yunping Zhoujin, Michael Anim Safo, Navindra Keerthisinghe, Mark D. Smith, Sophya Garashchuk, Hans-Conrad zur Loye|2026|Solid State Sciences||108228|doi:10.1016/j.solidstatesciences.2026.108228
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.