cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2npmrr
title: CCDC 2463655: Experimental Crystal Structure Determination

description: Related Article: Muhammad S. Muhammad, Dilruba A. Popy, Hamza Shoukat, John M. Lane, Neeraj Rai, Vojtěch Vaněček, Zdeněk Remeš, Romana Kučerková, Vladimir Babin, Chenjia Mi, Yitong Dong, Mark D. Smith, Novruz G. Akhmedov, Daniel T. Glatzhofer, Bayram Saparov|2026|J.Am.Chem.Soc.|||doi:10.1021/jacs.5c20638
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.cc2nsww7
title: CCDC 2466790: Experimental Crystal Structure Determination

description: Related Article: Yan-Ting Hong, Ying Fan, Chao Huang, Bi-Xue Zhu|2026|Cryst.Growth Des.|||doi:10.1021/acs.cgd.5c01237
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.cc2nswx8
title: CCDC 2466791: Experimental Crystal Structure Determination

description: Related Article: Yan-Ting Hong, Ying Fan, Chao Huang, Bi-Xue Zhu|2026|Cryst.Growth Des.|||doi:10.1021/acs.cgd.5c01237
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.cc2nswzb
title: CCDC 2466793: Experimental Crystal Structure Determination

description: Related Article: Yan-Ting Hong, Ying Fan, Chao Huang, Bi-Xue Zhu|2026|Cryst.Growth Des.|||doi:10.1021/acs.cgd.5c01237
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.5k9s0
title: Data from: A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles

description: True crocodiles (Crocodylus) are the most broadly distributed,
 ecologically diverse, and species-rich crocodylian genus, comprising about
 half of extant crocodylian diversity and exhibiting a circumtropical
 distribution. Crocodylus traditionally has been viewed as an ancient group
 of morphologically conserved species that originated in Africa prior to
 continental breakup. In this study, these long-held notions about the
 temporal and geographic origin of Crocodylus are tested using DNA sequence
 data of 10 loci from 76 individuals representing all 23 crocodylian
 species. I infer a time-calibrated species tree of all Crocodylia and
 estimate the spatial pattern of diversification within Crocodylus. For the
 first time, a fully resolved phylogenetic estimate of all Crocodylia is
 well-supported. The results overturn traditional views of the evolution of
 Crocodylus by demonstrating that the true crocodiles are not
 "living-fossils" that originated in Africa. Rather, Crocodylus
 originated from an ancestor in the tropics of the Late Miocene
 Indo-Pacific, and rapidly radiated and dispersed around the globe during a
 period marked by mass extinctions of fellow crocodylians. The findings
 also reveal more diversity within the genus than is recognized by current
 taxonomy.
description: oaks2011_crocodyliaMulti-locus alignment of DNA sequences from 79 crocodylians in nexus format. Gene regions are specified as character sets.
DOI: 10.5517/ccdc.csd.cc2nsx0d
title: CCDC 2466794: Experimental Crystal Structure Determination

description: Related Article: Yan-Ting Hong, Ying Fan, Chao Huang, Bi-Xue Zhu|2026|Cryst.Growth Des.|||doi:10.1021/acs.cgd.5c01237
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.cc2nt4qc
title: CCDC 2467033: Experimental Crystal Structure Determination

description: Related Article: Shivam Meena, Deepika Thakur, Surya P Tripathi, Rahul Ranjan, Akhilesh Verma|2025|Chem.Commun.|||doi:10.1039/D5CC04935K
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.585t4
title: Data from: Medical-device recalls in the UK and the device-regulation process: retrospective review of safety notices and alerts

description: Background: Medical devices are used widely for virtually every disease
 and condition. Although devices are subject to regulation, the number of
 recalls, the clinical data requirements for regulation and the impact on
 patient safety are poorly understood. Methods: The authors defined a
 device using European directives and used publicly available information
 on the Medicines and Health Regulatory Authority website to determine the
 number of devices recalled from January 2006 to December 2010. Two
 reviewers independently assessed Field Safety Notices and Medical Device
 Alerts. The authors wrote to manufacturers to obtain further information
 and clinical data, and summarised data by year, Conformité Européenne
 classification, indication, and Food and Drug Administration recall system
 of severity. Results: In total, 2124 field safety notices were issued over
 the 5-year period, an increase of 1220% (62 in 2006 to 757 in 2010). 447
 Medical Device Alerts were issued in the same period, and 44% were
 assessed as a reasonable probability of causing serious adverse health
 consequences or death. The authors wrote to 192 manufacturers of withdrawn
 devices and received 101 (53%) replies; only four (2.1%) provided the
 clinical data the authors requested. A lack of available transparent data
 prevented full analyses of the safety impact. Of the highest-risk recalled
 devices, more than half were related to the cardiovascular system (25%) or
 musculoskeletal system (33%), and 88% (95% CI 80% to 97%) were assessed as
 a reasonable probability of causing serious adverse health consequences or
 death. For low-risk devices, the figure was 34% (95% CI 26% to 42%).
 Conclusion: The number of medical devices subject to recalls or warnings
 in the UK has risen dramatically. A substantial number of these devices
 may have caused serious adverse effects in patients and contributed to
 healthcare costs. Significant problems exist in the UK with a lack of
 access to transparent data and a registry of the highest-risk devices.
description: BMJ open Access MHRA
 Field Safety Notices 2006_2010Medical Device alert:
 Medical Device Alerts (MDAs) were introduced on 1 January 2003, to replace
 the previous types of safety warnings (Hazard notice, Safety notice,
 Device alert, Advice notice and Pacemaker technical note. Medical Device
 Alerts (MDAs) are the MHRA's prime means of communicating safety
 information to medical device users in health and social care. Each MDA is
 designated either for ‘Immediate action’ or ‘Action’. MDAs may also be
 used to provide updated information.MHRA Field safety
 notices_FDA 19_5_11
DOI: 10.5061/dryad.mf1sd
title: Data from: Who shares? Who doesn’t? Factors associated with openly archiving raw research data

description: Many initiatives encourage investigators to share their raw datasets in
 hopes of increasing research efficiency and quality. Despite these
 investments of time and money, we do not have a firm grasp of who openly
 shares raw research data, who doesn’t, and which initiatives are
 correlated with high rates of data sharing. In this analysis I use
 bibliometric methods to identify patterns in the frequency with which
 investigators openly archive their raw gene expression microarray datasets
 after study publication. Automated methods identified 11,603 articles
 published between 2000 and 2009 that describe the creation of gene
 expression microarray data. Associated datasets in best-practice
 repositories were found for 25% of these articles, increasing from less
 than 5% in 2001 to 30%-35% in 2007-2009. Accounting for sensitivity of the
 automated methods, approximately 45% of recent gene expression studies
 made their data publicly available. First-order factor analysis on 124
 diverse bibliometric attributes of the data creation articles revealed 15
 factors describing authorship, funding, institution, publication, and
 domain environments. In multivariate regression, authors were most likely
 to share data if they had prior experience sharing or reusing data, if
 their study was published in an open access journal or a journal with a
 relatively strong data sharing policy, or if the study was funded by a
 large number of NIH grants. Authors of studies on cancer and human
 subjects were least likely to make their datasets available. These results
 suggest research data sharing levels are still low and increasing only
 slowly, and data is least available in areas where it could make the
 biggest impact. Let’s learn from those with high rates of sharing to
 embrace the full potential of our research output.
description: Microarray publications
 and publication attributes157 columns of
 attributes for 11603 publications identified as creating gene expression
 microarray data. Tab delimited. Key: PubMed identifier (pmid). See stats.R
 for data cleaning steps and more details on variables. Data collected in
 January 2010 using code available at
 http://github.com/hpiwowar/pypubrawdata.txtJournal policy details for microarray dataData sharing policy details for journals that publish a lot of gene expression microarray data. Policy links, excerpts, and classifications (24 columns) for 156 journals. Some of these classifications are included as columns in rawdata.txt as journal policy attributes.journal_policies_microarray_data.csvStatistical analysis R scriptR script for data cleaning, statistical analysis, and graphics as presented in the paper. Takes rawdata.txt as input and loads helper_functions.R source.stats.RHelper R script functionsHelper functions loaded by stats.R for analysis and graphical output.helper_functions.R
DOI: 10.5061/dryad.vh3dm
title: Data from: Exploring the selective constraint on the sizes of insertions and deletions in 5’ untranslated regions in mammals

description: Background: Small insertions and deletions ("indels" with size ≦
 100 bp) whose lengths are not multiples of three (non-3n) are strongly
 constrained and depleted in protein-coding sequences. Such a constraint
 has never been reported in noncoding genomic regions. In
 5'untranslated regions (5'UTRs) in mammalian genomes, upstream
 start codons (uAUGs) and upstream open reading frames (uORFs) can regulate
 protein translation. The presence of non-3n indels in uORFs can
 potentially disrupt the functions of these regulatory elements. We thus
 hypothesize that natural selection disfavors non-3n indels in 5'UTRs
 when these regulatory elements are present. Results: We design the Indel
 Selection Index to measure the selective constraint on non-3n indels in
 5'UTRs. The index controls for the genomic compositions of the
 analyzed 5'UTRs and measures the probability of non-3n indel
 depletion downstream of uAUGs. By comparing the experimentally supported
 transcripts of human-mouse orthologous genes, we demonstrate that non-3n
 indels downstream of two types of uAUGs (alternative translation
 initiation sites and the uAUGs of coding sequence-overlapping uORFs) are
 underrepresented. The results hold well regardless of differences in
 alignment tool, gene structures between human and mouse, or the criteria
 in selecting alternatively spliced isoforms used for the analysis.
 Conclusions: To our knowledge, this is the first study to demonstrate
 selective constraints on non-3n indels in 5'UTRs. Such constraints
 may be associated with the regulatory functions of uAUGs/uORFs in
 translational regulation or the generation of protein isoforms. Our study
 thus brings a new perspective to the evolution of 5'UTRs in mammals.
description: alignment_human_mouseThe file involves the pairwise alignments in 5'UTRs of human and mouse genomes. The alignments were downloaded from the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/). The versions of the human and mouse genomes (hg18 and mm9, respectively) correspond to Ensembl release 54. The Ensembl IDs of genes, transcripts, and proteins were listed. Noted that unalignable regions between human and mouse have been excluded in the file. Noted that the Ensembl IDs include both human (the first 61592 rows) and mouse (after row no. 61592).
DOI: 10.15468/dl.yx2qj7
title: Occurrence Download

description: A dataset containing 26145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphibia",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26145 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001708-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6vq04
title: Data from: Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation

description: Ecological selection against hybrids between populations occupying
 different habitats might be an important component of reproductive
 isolation during the initial stages of speciation. The strength and
 directionality of this barrier to gene flow depends on the genetic
 architecture underlying divergence in ecologically relevant phenotypes. We
 here present line cross analyses of inheritance for two key
 foraging-related morphological traits involved in adaptive divergence
 between stickleback ecotypes residing parapatrically in lake and stream
 habitats within the Misty Lake watershed (Vancouver Island, Canada). One
 main finding is striking genetic dominance of the lake phenotype for body
 depth. Selection associated with this phenotype against first and later
 generation hybrids should therefore be asymmetric, hindering introgression
 from the lake to the stream population but not vice versa. Another main
 finding is that divergence in gill raker number is inherited additively
 and should therefore contribute symmetrically to reproductive isolation.
 Our study suggests that traits involved in adaptation might contribute to
 reproductive isolation qualitatively differently, depending on their mode
 of inheritance.
description: Individual landmarks
 Berner et al. 2011see "ReadMe Berner
 et al. 2011.txt"SexByFamilyConsensus
 landmarks Berner et al. 2011see "ReadMe Berner
 et al. 2011.txt"Individual data Berner
 et al. 2011see "ReadMe Berner
 et al. 2011.txt"SexByFamily data Berner
 et al. 2011see "ReadMe Berner
 et al. 2011.txt"ReadMe Berner et al.
 2011ReadMe file describing
 all four data files.
DOI: 10.5061/dryad.fv348
title: Data from: Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations

description: Currently there exists a limited knowledge on the extent of temporal
 variation in population genetic parameters of natural populations. Here we
 study the extent of temporal variation in population genetics by
 genotyping 151 genome-wide SNP markers polymorphic in 466 individuals
 collected from nine populations of the annual plant Arabidopsis thaliana
 during four years. Populations are located along an altitudinal climatic
 gradient from Mediterranean to subalpine environments in NE Spain, which
 has been shown to influence key demographic attributes and life-cycle
 adaptations. Genetically, A. thaliana populations were more variable
 across space than over time. Common multilocus genotypes were detected
 several years in the same population, whereas low-frequency multilocus
 genotypes appeared only one year. High-elevation populations were
 genetically poorer and more variable over time than low-elevation
 populations, which might be caused by a higher overall demographic
 instability at higher altitudes. Estimated effective population sizes were
 very low but also showed a significant decreasing trend with increasing
 altitude, suggesting a deeper impact of genetic drift at high-elevation
 populations. In comparison with single-year samplings, repeated genotyping
 over time captured substantially higher amount of genetic variation
 contained in A. thaliana populations. Furthermore, repeated genotyping of
 populations provided novel information on the genetic properties of A.
 thaliana populations and allowed hypothesizing on their underlying
 mechanisms. Therefore, including temporal genotyping programs into
 traditional population genetic studies can significantly increase our
 understanding of the dynamics of natural populations.
description: Arabidopsis_SNPsGenetic data from 239 SNPs in 507 individuals from 9 populations of Arabidopsis thaliana.
DOI: 10.5061/dryad.c1q30
title: Data from: Climatic forcing of Quaternary deep-sea benthic communities in the North Pacific Ocean

description: There is a growing evidence that changes in deep-sea benthic ecosystems
 are modulated by climate changes, but most evidence to date comes from the
 North Atlantic Ocean. Here we analyze new ostracod and published
 foraminiferal records for the last 250,000 years on Shatsky Rise in the
 North Pacific Ocean. Using linear models, we evaluate statistically the
 ability of environmental drivers (temperature, productivity, and
 seasonality of productivity) to predict changes in faunal diversity,
 abundance and composition. These microfossil data show
 glacial-interglacial shifts in overall abundances and species diversities
 that are low during glacial intervals and high during interglacials. These
 patterns replicate those previously documented in the North Atlantic
 Ocean, suggesting that the climatic forcing of the deep-sea ecosystem is
 widespread, and possibly global in nature. However, these results also
 reveal differences with prior studies that probably reflect the isolated
 nature of Shatsky Rise as a remote oceanic plateau. Ostracod assemblages
 on Shatsky Rise are highly endemic but of low diversity, consistent with
 the limited dispersal potential of these animals. Benthic foraminifera, by
 contrast, have much greater dispersal ability and their assemblages at
 Shatsky Rise show diversities typical for deep-sea faunas in other
 regions. Statistical analyses also reveal ostracod–foraminferal
 differences in relationships between environmental drivers and biotic
 change. Rarefied diversity is best explained as a hump-shaped function of
 surface productivity in ostracods, but as having a weak and positive
 relationship with temperature in foraminifera. Abundance shows a positive
 relationship with both productivity and seasonality of productivity in
 foraminifera, and a hump-shaped relationship in ostracods. Finally,
 species composition in ostracods is influenced by both temperature and
 productivity, but only a temperature effect is evident in foraminifera.
 Though complex in detail, the global-scale link between deep-sea
 ecosystems and Quaternary climate changes underscores the interaction
 between the physical and biological components of paleoceanographical
 research to better understand the history of the biosphere.
description: NGC104_RawCensus
 TextCensus data of NGC104
 ostracods (Raw census data) in plain text format.NGC104_RawCensus.txtNGC104_RawCensus ExcelCensus data of NGC104 ostracods (Raw census data) in Microsoft Excel format.NGC104_RawCensus.xlsNGC104_3movCensus TextThree-sample moving sums of the census dataset of NGC104 ostracods in plain text format.NGC104_3movCensus.txtNGC104_3movCensus ExcelThree-sample moving sums of the census dataset of NGC104 ostracods in Microsoft Excel format.NGC104_3movCensus.xlsYasuhara-STables PDFOnline Supplement Tables in PDF format.Yasuhara-STables.pdfYasuhara-STables WordOnline Supplement Tables in Microsoft Word format.Yasuhara-STables.docTable-S1Table-S2Table-S3Table-S4Table-S5Table-S6Table-S7Table-S8Table-S9
DOI: 10.5061/dryad.15nn2
title: Data from: Relationship between genetic distances and postzygotic reproductive isolation in diploid Fragaria (Rosaceae)

description: Studies of reproductive isolation are important for understanding
 speciation and species delimitation. We studied seven components of
 reproductive isolation at different taxonomic and geographical levels and
 their relationship with genetic distance in diploid Fragaria. Isolation
 was only evident between different taxa at later stages (post F1
 survivorship) not at the earlier ones of fruit and seed set, F1 seed
 germination and survivorship. Within F. vesca, isolation at the later
 stages was positively correlated with genetic distance, but this was not
 found at interspecific levels. The lack of isolation between F. vesca and
 the other species at the early stages provide the chance for hybrid
 formation, but high levels of infertility expressed among the offspring
 can lead to potentially opposing evolutionary outcomes. Within F. vesca,
 there was evidence of unexpected isolation promoting evolutionary
 diversification and incipient speciation. Reproductive isolation values
 between sympatric and allopatric species pairs were similar and indicate a
 lack of reinforcement in Fragaria. This, combined with the lack of
 correlation between genetic distance and isolation at interspecific levels
 shows that genetic distance is not always proportionally correlated with
 the degree of isolation in plants and suggests that evolutionary processes
 may be playing differently in plants compared to animals.
description: Dataset Reproductive
 fitness & genetic distances in diploid FragariaLevels of reproductive
 fitness & genetic distances in diploid Fragaria: 1) Variations in
 seven components of postzygotic reproductive fitness (initial fruit
 (berry) set, seed set, F1 hybrid seed germination, survivorship,
 flowering, fruit (berry) set and pollen sterility at three hierarchal
 taxonomic levels: • interspecific crosses level: between F. vesca (ssp.
 vesca) as maternal parent and four species of F. nubicola, F. viridis, F.
 daltoniana and F. nipponica; • inter-subspecific level between F. vesca
 ssp. vesca and F. vesca ssp. americana; • intra-subspecific level within
 F. vesca ssp. vesca (between F. vesca ssp. vesca, F. vesca ssp. vesca var.
 alba, and F. vesca ssp. vesca f. monophylla) 2) Variations in reproductive
 isolation between sympatric & allopatric species pairs: • Sympatry: F.
 vesca versus F. viridis; • Allopatric: F. vesca versus F. nubicola, F.
 daltoniana and F. nipponica 3) Genetic distance between diploid Fragaria
 based on RAPDs Nei's Distance (NTSYS-pc ver. 2.02) & ITS
 P-distance (using sequence data presented by Potter et al. 2005 in
 Genbank) in PAUP (ver. 4.0b10, Swofford, 2003).