cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4663t
title: Data from: Cooperative interactions between different classes of disordered proteins play a functional role in the nuclear pore complex of Baker's yeast

description: Nucleocytoplasmic transport is highly selective, efficient, and is
 regulated by a poorly understood mechanism involving hundreds of
 disordered FG nucleoporin proteins (FG nups) lining the inside wall of the
 nuclear pore complex (NPC). Previous research has concluded that FG nups
 in Baker's yeast (S. cerevisiae) are present in a bimodal
 distribution, with the ``Forest Model'' classifying FG nups as
 either di-block polymer like ``trees'' or single-block polymer
 like ``shrubs''. Using a combination of coarse-grained modeling
 and polymer brush modeling, the function of the di-block FG nups has been
 hypothesized in the Di-block Copolymer Brush Gate (DCBG) model to form a
 higher-order polymer brush architecture which can open and close to
 regulate transport across the NPC. Here we perform coarse grained
 simulations of the single-block FG nups which confirm that they have a
 single block polymer structure rather than the di-block structure of tree
 nups. Our molecular simulations also demonstrate that these single-block
 FG nups are likely cohesive, compact, collapsed coil polymers, implying
 that these FG nups are generally localized to their grafting location
 within the NPC. We find that adding a layer of single-block FG nups to the
 DCBG model increases the range of cargo sizes which are able to
 translocate the pore through a cooperative effect involving single-block
 and di-block FG nups. This effect can explain the puzzling connection
 between single-block FG nup deletion mutants in S. cerevisiae and the
 resulting failure of certain large cargo transport through the NPC.
 Facilitation of large cargo transport via single-block and di-block FG nup
 cooperativity in the nuclear pore could provide a model mechanism for
 designing future biomimetic pores of greater applicability.
description: XYZ molecular dynamics
 trajectory file for Nup42This is a CG MD
 simulation of Nup42 in Baker's Yeast.nup42-traj.xyz.zipXYZ molecular dynamics trajectory file for Nup49This is a CG MD simulation of Nup49 in Baker's Yeast.nup49-traj.xyz.zipXYZ molecular dynamics trajectory file for Nup57This is a CG MD simulation of Nup57 in Baker's Yeast.nup57-traj.xyz.zipContact probability for Nup57Contact probability for Nup57contact-prob_nup57.txtContact Probability for Nup49Contact Probability for Nup49contact-prob_nup49.txtContact Probability for Nup42Contact Probability for Nup42contact-prob_nup42.txt
DOI: 10.5061/dryad.f9n5qm1
title: Data from: Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

description: The Eneolithic Botai culture of the Central Asian steppes provides the
 earliest archaeological evidence for horse husbandry, ~5500 years ago, but
 the exact nature of early horse domestication remains controversial. We
 generated 42 ancient-horse genomes, including 20 from Botai. Compared to
 46 published ancient- and modern-horse genomes, our data indicate that
 Przewalski’s horses are the feral descendants of horses herded at Botai
 and not truly wild horses. All domestic horses dated from ~4000 years ago
 to present only show ~2.7% of Botai-related ancestry. This indicates that
 a massive genomic turnover underpins the expansion of the horse stock that
 gave rise to modern domesticates, which coincides with large-scale human
 population expansions during the Early Bronze Age.
description: ALL.beagle.gprobs.maf0genotype posterior probabilities of segregating sites with minor allele frequency filter of 0.01 (all individuals)ALL_maxmiss3.TransversionOnly.beagle.gzALL.beaglegenotype posterior probabilities of segregating sites (all individuals)ALL.0.0.treemix.gzchry_AllNoOut.1.fastaY-Chromosome alignment for male samples (without outgroup)chry_All.1.fasta.reducedY-Chromosome alignment for male samples (with Equus africanus somaliensis as outgroup)ALL_maxmiss3.TransversionOnly.noCAGT.beaglepseudo haploid sites (random sampling of one allele), transversions only and all C to A and G to T were removedALL_maxmiss3.TransversionOnly.beaglepseudo haploid sites (random sampling of one allele), only transversionsALL.0.0.treemix.gzcalled genotypes for all samples above 3.0X coverage
DOI: 10.5061/dryad.bt51g
title: Data from: The molecular trigger for high-speed wing beats in a bee

description: The high-frequency wing beat of higher-order insects is driven by
 self-sustained oscillations of constantly activated flight muscles.
 However, it remains unknown whether its underlying mechanism is based on
 flight muscle–specific features or on preexisting contractile functions.
 Here, we recorded x-ray diffraction movies, at a rate of 5000 frames per
 second, simultaneously from the two antagonistic flight muscles of
 bumblebees during wing beat. Signals that occurred at the right timing for
 triggering each wing-beat stroke were resolved in both muscles. The
 signals likely reflect stretch-induced myosin deformation, which would
 also enhance force in vertebrate muscles. The results suggest that insects
 use a refined preexisting force-enhancing mechanism for high-frequency
 wing beat, rather than developing a novel mechanism.
description: WingPositionAn Excel file containing data of wing angle of 9 bees.BeeXraydata_TiffBeeXrayIndiv_TiffReadMe_newA Readme file.
DOI: 10.5061/dryad.sn034
title: Data from: AftrRAD: a pipeline for accurate and efficient de novo assembly of RADseq data

description: An increase in studies using restriction site-associated DNA sequencing
 (RADseq) methods has led to a need for both the development and assessment
 of novel bioinformatic tools that aid in the generation and analysis of
 these data. Here, we report the availability of AftrRAD, a bioinformatic
 pipeline that efficiently assembles and genotypes RADseq data, and outputs
 these data in various formats for downstream analyses. We use simulated
 and experimental data sets to evaluate AftrRAD's ability to perform
 accurate de novo assembly of loci, and we compare its performance with two
 other commonly used programs, stacks and pyrad. We demonstrate that
 AftrRAD is able to accurately assemble loci, while accounting for indel
 variation among alleles, in a more computationally efficient manner than
 currently available programs. AftrRAD run times are not strongly affected
 by the number of samples in the data set, making this program a useful
 tool when multicore systems are not available for parallel processing, or
 when data sets include large numbers of samples.
description: Compare_Stacks_vs_AftrRADPerl script to compare AftrRAD loci to Stacks loci. Requires a series of output files that are listed in a comment at the beginning of the script. Note that this script must be run prior to running Compare_PyRAD_vs_AftrRAD.pl. Also note that both of these scripts are starting points for analysis, and that any loci identified as not shared among programs should be double-checked manually. For questions regarding these scripts, visit the AftrRAD Google group.Compare_PyRAD_vs_AftrRADPerl script to compare AftrRAD loci to PyRAD loci. Note that the Compare_Stacks_vs_AftrRAD.pl script must be run prior to running Compare_PyRAD_vs_AftrRAD.pl. Also note that both of these scripts are starting points for analysis, and that any loci identified as not shared among programs should be double-checked manually.Mallard DataFastq file containing data from mallard (Anas platyrhynchos) used in comparisons of AftrRAD, Stacks, and PyRAD.rad12_pool2_51bp.fastq.tar.gzRAD5_data.txt.tarFastq file containing data from eastern massasauga rattlesnake (Sistrurus catenatus) used in comparisons of AftrRAD, Stacks, and PyRAD.Rattlesnake_Barcode_InfoBarcode information for rattlesnake fastq dataset.Mallard_Barcode_InfoBarcode information for Mallard fastq dataset.
DOI: 10.5061/dryad.78kn3
title: Data from: Effects of trophy hunting leftovers on the ranging behaviour of large carnivores: a case study on spotted hyenas

description: Human-related food resources such as garbage dumps and feeding sites have
 been shown to significantly influence space use, breeding success and
 population dynamics in a variety of animal species. In contrast,
 relatively little is known on the effects of unpredictable sources of
 food, such as carcasses discarded by hunters, on carnivore species. We
 evaluated the effect of elephant carcasses, mainly deriving from trophy
 hunting, on the ranging and feeding behavior of spotted hyenas (Crocuta
 crocuta) in the Okavango Delta, Botswana. Using data from hyenas monitored
 before and during carcass availability via GPS radio-collars and camera
 traps, we investigated changes in ranging and feeding behavior over time.
 Carcass availability influenced hyenas’ ranging behavior for an average of
 10–12 days, after which their movements returned to patterns observed
 before carcass availability. In particular, we observed an increased
 spatial clustering of locations and reduced speeds (up to 15% less)
 between successive locations with carcass availability. Consistent feeding
 at carcasses during the first two weeks was typical, and some individuals
 fed from elephant carcasses for as long as 50 days. The impact and
 conservation value of hunting are often assessed based solely on the
 effects on the hunted species. Our results show that hunting remains can
 influence other species and suggest that such extra food could have
 important effects on critical life history processes and ultimately
 population dynamics. We recommend conservationists and wildlife managers
 evaluate management strategies and hunting practices regarding carcass
 disposal in order to incorporate the potential collateral impacts of
 hunting on non-hunted species in the same community.
description: hyena_locationsSpotted hyenas GPS locationselephant_carcassesElephant carcasses locationscamera trap pictureshyena camera trap pictures
DOI: 10.5061/dryad.2929bs2
title: Data from: A robust and tunable mitotic oscillator in artificial cells

description: Single-cell analysis is pivotal to deciphering complex phenomena like
 heterogeneity, bistability, and asynchronous oscillations, where a
 population ensemble cannot represent individual behaviors. Bulk cell-free
 systems, despite having unique advantages of manipulation and
 characterization of biochemical networks, lack the essential single-cell
 information to understand a class of out-of-steady-state dynamics
 including cell cycles. Here, by encapsulating Xenopus egg extracts in
 water-in-oil microemulsions, we developed artificial cells that are
 adjustable in sizes and periods, sustain mitotic oscillations for over 30
 cycles, and function in forms from the simplest cytoplasmic-only to the
 more complicated ones involving nuclear dynamics, mimicking real cells.
 Such innate flexibility and robustness make it key to studying clock
 properties like tunability and stochasticity. Our results also highlight
 energy as an important regulator of cell cycles. We demonstrate a simple,
 powerful, and likely generalizable strategy of integrating strengths of
 single-cell approaches into conventional in vitro systems to study complex
 clock functions.
description: Fig1C_raw.tifThis file, named “Fig1C_raw.tif”, contains raw image data for Figure 1C. It contains 4 channels, 8 zstacks, and 130 time points. The tif file can be read in Image J software.meta_fig2demeta_fig2de.mat is the data obtained by image processing without droplet area estimation. It is used for Figure 2D and 2E.meta_fig2fgmeta_fig2fg.mat is the data obtained by image processing with droplet area estimation. It is used for Fig 2F and 2G.
DOI: 10.5061/dryad.bp462
title: Data from: Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

description: The timing of the diversification of placental mammals relative to the
 Cretaceous–Paleogene (KPg) boundary mass extinction remains highly
 controversial. In particular, there have been seemingly irreconcilable
 differences in the dating of the early placental radiation not only
 between fossil-based and molecular datasets but also among molecular
 datasets. To help resolve this discrepancy, we performed genome-scale
 analyses using 4,388 loci from 90 taxa, including representatives of all
 extant placental orders and transcriptome data from flying lemurs
 (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning
 scheme, molecular clock model, and genic deviation from molecular clock
 assumptions, extensive sensitivity analyses recovered widely varying
 diversification scenarios for placental mammals from a given gene set,
 ranging from a deep Cretaceous origin and diversification to a scenario
 spanning the KPg boundary, suggesting that the use of suboptimal molecular
 clock markers and methodologies is a major cause of controversies
 regarding placental diversification timing. We demonstrate that
 reconciliation between molecular and paleontological estimates of
 placental divergence times can be achieved using the appropriate clock
 model and gene partitioning scheme while accounting for the degree to
 which individual genes violate molecular clock assumptions. A
 birth-death-shift analysis suggests that placental mammals underwent a
 continuous radiation across the KPg boundary without apparent interruption
 by the mass extinction, paralleling a genus-level radiation of
 multituberculates and ecomorphological diversification of both
 multituberculates and therians. These findings suggest that the KPg
 catastrophe evidently played a limited role in placental diversification,
 which, instead, was likely a delayed response to the slightly earlier
 radiation of angiosperms.
description: alignments of placental
 mammalsseq.zipmaximum likelihood gene treesmltree.zipmcmctreeThe 3867 genes are divided into five quintiles according to DVMC values from the lowest to the highest. Then, randomly drew 60, 100 and 200 genes from each quintile, and replicated this procedure three times for each of the three gene-sets. For each of the 60, 100, and 200 gene sets, five different gene partitioning schemes: no partition; five partitions; ten partitions; twenty partitions; and each single gene as a separate partition.
DOI: 10.5061/dryad.94pv1
title: Data from: Reinvestigation of Protelytron permianum (Insecta; Early Permian; USA) as an example for applying reflectance transformation imaging to insect imprint fossils

description: We reinvestigated the holotype of Protelytron permianum, one of the
 earliest putative stem-dermapteran (i.e. stem-earwig). We recurred to
 reflectance transformation imaging (RTI) to deliver exhaustive and
 interactive photographic data. We were able to ascertain the occurrence of
 broadenings located along veins of the hind wing vannus and forming an
 arc, as well as a series of radiating folds, alternatively concave and
 convex. Such an organization is diagnostic of Dermaptera, in which it is
 indicative of hind wing folding mechanisms, particularly elaborated in
 these insects. We provide a foldable, paper model of the hind wing. Based
 on the case presented herein we anticipate that RTI process will be a
 major upheaval in the documentation of fossil insects preserved as
 imprints.
description: Dryad
 datasetThanks for downloading
 this package. It is divided into three sub-packages, 1_softwares_set,
 2_RTI_set, and a 3_paper_model_set. ---- 1_softwares_set sub-package
 contains a number of files currently available at
 http://culturalheritageimaging.org/What_We_Offer/Downloads/. They are
 provided here to ensure long-term archiving, and reading of our dataset.
 In details, this sub-package contains: RTIbuilder_2_0_2_MacOs Installation
 package for RTIbuilder software under Mac operating system
 RTIbuilder_2_0_2_WinOs Installation package for RTIbuilder software under
 Windows operating system RTIViewer-1.1.0_MacOs Installation package for
 RTIviewer software under Mac operating system
 RTIViewerSetup-1.1.0-WinOs_x32 Installation package for RTIviewer software
 under Windows operating system, 32 bits RTIViewerSetup-1.1.0-WinOs_x64
 Installation package for RTIviewer software under Windows operating
 system, 64 bits ---- 2_RTI_set sub-package contains two *.rti files of the
 specimen YPM IP 001019 (b side; Yale Peabody Museum; holotype of
 Protelytron permianum, Lower Permian, USA), together with their associated
 bookmarks files. In details, this sub-package contains:
 YPM_IP_001019b_1overview This *.rti file is an overview of the complete
 specimen. The associated bookmarks file (*.xmp) is YPM_1019b_1overview_rti
 YPM_IP_001019b_2detailHW This *.rti file is a close-up view of the left
 hind wing of specimen. The associated bookmarks file (*.xmp) is
 YPM_1019b_2detailHW_rti ---- 3_paper_model_set This set contains our Fig.
 3 as pdf and a video tutorial providing guidelines on how to prepare and
 operate the paper model.Dryad
 set.zip
DOI: 10.34740/kaggle/dsv/11957028
title: Brain Tumor Dataset: Segmentation & Classification
DOI: 10.5061/dryad.c1951
title: Data from: Observed forest sensitivity to climate implies large changes in 21st century North American forest growth

description: Predicting long-term trends in forest growth requires accurate
 characterisation of how the relationship between forest productivity and
 climatic stress varies across climatic regimes. Using a network of over
 two million tree-ring observations spanning North America and a
 space-for-time substitution methodology, we forecast climate impacts on
 future forest growth. We explored differing scenarios of increased
 water-use efficiency (WUE) due to CO2-fertilisation, which we simulated as
 increased effective precipitation. In our forecasts: (1) climate change
 negatively impacted forest growth rates in the interior west and
 positively impacted forest growth along the western, southeastern and
 northeastern coasts; (2) shifting climate sensitivities offset positive
 effects of warming on high-latitude forests, leaving no evidence for
 continued ‘boreal greening’; and (3) it took a 72% WUE enhancement to
 compensate for continentally averaged growth declines under RCP 8.5. Our
 results highlight the importance of locally adapted forest management
 strategies to handle regional differences in growth responses to climate
 change.
description: Runs with 50%
 subsetsZipped folder containing
 subset of model outputs where 50% of data were used in fitting. The
 purpose of these runs were to estimate model uncertainty. See "Read
 Me.txt" for more information.50percent_runs.zipPrimary Zipped Folder of Outputs and ScriptsZipped folder containing subfolders with model outputs and R scripts. Please see "Read Me.txt" for more information.Supp_Data_PrimaryFolder.zip
DOI: 10.57841/casdc.0007099
title: 建立超导材料临界电流角度依赖性测试平台
DOI: 10.5061/dryad.sq67g
title: Data from: Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

description: Understanding the extreme variation among bacterial genomes remains an
 unsolved challenge in evolutionary biology, despite long-standing debate
 about the relative importance of natural selection, mutation, and random
 drift. A potentially important confounding factor is the variation in
 mutation rates between lineages and over evolutionary history, which has
 been documented in several species. Mutation accumulation experiments have
 shown that hypermutability can erode genomes over short timescales. These
 results, however, were obtained under conditions of extremely weak
 selection, casting doubt on their general relevance. Here, we circumvent
 this limitation by analyzing genomes from mutator populations that arose
 during a long-term experiment with Escherichia coli, in which populations
 have been adaptively evolving for &gt;50,000 generations. We develop
 an analytical framework to quantify the relative contributions of mutation
 and selection in shaping genomic characteristics, and we validate it using
 genomes evolved under regimes of high mutation rates with weak selection
 (mutation accumulation experiments) and low mutation rates with strong
 selection (natural isolates). Our results show that, despite sustained
 adaptive evolution in the long-term experiment, the signature of selection
 is much weaker than that of mutational biases in mutator genomes. This
 finding suggests that relatively brief periods of hypermutability can play
 an outsized role in shaping extant bacterial genomes. Overall, these
 results highlight the importance of genomic draft, in which strong linkage
 limits the ability of selection to purge deleterious mutations. These
 insights are also relevant to other biological systems evolving under
 strong linkage and high mutation rates, including viruses and cancer
 cells.
description: LTEE_NonMutator_MutationList.txtLTEE_MutationList.txtLTEE_MMR_MutationList.txtLTEE_MutT_MutationList.txtMAE_MutL_MutationListMAE_MutT_MutationListREL606_QuantitativeGenicDataK12_QuantitativeGenicDataall_mutations_k12_global_rank_new_ecoli_remove_ip_space.datMutation effect prediction with the independent site modelall_mutations_k12_global_rank_new_ecoli_remove_space.datMutation effect prediction with the DCA modelall_mutations_rel606_global_rank_new_ecoli_remove_ip_space.datMutation effect prediction with the independent site modelall_mutations_rel606_global_rank_new_ecoli_remove_space.datMutation effect prediction with the DCA modelNature_MutationListTable_K12_MAE_MutL_IND_DCA.txtTable_K12_MAE_MutT_IND_DCA.txtTable_REL606_LTEE_MMR_IND_DCA.txtTable_REL606_LTEE_MutT_IND_DCA.txtTable_REL606_LTEE_IND_DCA.txtTable_REL606_DivergenceED1a_restricted_IND_DCA.txtReadMeExplains the content of all files