cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3h061
title: Data from: Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation

description: Macrophage activation/polarization to distinct functional states is
 critically supported by metabolic shifts. How polarizing signals
 coordinate metabolic and functional reprogramming, and the potential
 implications for control of macrophage activation, remains poorly
 understood. Here we show that IL-4 signaling co-opts the Akt-mTORC1
 pathway to regulate Acly, a key enzyme in Ac-CoA synthesis, leading to
 increased histone acetylation and M2 gene induction. Only a subset of M2
 genes is controlled in this way, including those regulating cellular
 proliferation and chemokine production. Moreover, metabolic signals
 impinge on the Akt-mTORC1 axis for such control of M2 activation. We
 propose that Akt-mTORC1 signaling calibrates metabolic state to
 energetically demanding aspects of M2 activation, which may define a new
 role for metabolism in supporting macrophage activation.
description: 20150422-AC1-AC1809_S1_R1Mock rep120150422-AC2-AC1809_S2_R1Mock rep220150422-AC4-AC1809_S3_R1AKTinh rep120150422-AC5-AC1809_S4_R1AKTinh rep220150422-AC7-AC1809_S5_R1ACLYinh rep120150422-AC8-AC1809_S6_R1ACLYinh rep220150422-AC13-AC1809_S9_R1IL-4 rep120150422-AC14-AC1809_S10_R1IL-4 rep220150422-AC16-AC1809_S11_R1IL-4 AKTinh rep120150422-AC17-AC1809_S12_R1IL-4 AKTinh rep220150422-AC19-AC1809_S13_R1IL-4 ACLYinh rep120150422-AC20-AC1809_S14_R1IL-4 ACLYinh rep2
DOI: 10.5061/dryad.cv803rv
title: Data from: Mouse screen reveals multiple new genes underlying mouse and human hearing loss

description: Adult-onset hearing loss is very common but we know little about the
 underlying molecular pathogenesis, impeding development of therapies. We
 took a genetic approach to identify new molecules involved in hearing loss
 by screening a large cohort of newly-generated mouse mutants using a
 sensitive electrophysiological test, the auditory brainstem response. We
 review here the findings from this screen. Thirty-eight unexpected genes
 associated with raised thresholds were detected from our unbiased sample
 of 1,211 genes tested, suggesting extreme genetic heterogeneity. A wide
 range of auditory pathophysiologies was found, and some mutant lines
 showed normal development followed by deterioration of responses,
 revealing new molecular pathways involved in progressive hearing loss.
 Several of the genes were associated with the range of hearing thresholds
 in the human population and one, SPNS2, was involved in childhood
 deafness. The new pathways required for maintenance of hearing discovered
 by this screen present new therapeutic opportunities.
description: ABR_RESOURCE_InformationDocumenting the files and content of this mouse ABR resourceABR_RESOURCE_Mouse IDABR_RESOURCE_Annotation_M00013165_to_M00145618Data zip-file 1 of 19_M00145660_to_M00218577Data zip-file 2 of 19_M00218786_to_M00286920Data zip-file 3 of 19_M00286927_to_M00370330Data zip-file 4 of 19_M00371702_to_M00491851Data zip-file 5 of 19_M00491852_to_M00617707Data zip-file 6 of 19_M00617709_to_M00754249Data zip-file 7 of 19_M00754250_to_M00889693Data zip-file 8 of 19_M00889694_to_M01025210Data zip-file 9 of 19_M01025211_to_M01164518Data zip-file 10 of 19_M01164520_to_M01328136Data zip-file 11 of 19_M01328137_to_M01470166Data zip-file 12 of 19_M01470167_to_M01623523Data zip-file 13 of 19_M01623527_to_M01745797Data zip-file 14 of 19_M01745798_to_M01867451Data zip-file 15 of 19_M01867816_to_M02001583Data zip-file 16 of 19_M02001765_to_M02135571Data zip-file 17 of 19_M02135572_to_M02271105Data zip-file 18 of 19_M02271106_to_M02405362Data zip-file 19 of 19
DOI: 10.5061/dryad.ps319
title: Data from: Cyanobacteria maintain constant protein concentration despite genome copy-number variation

description: The cyanobacterium Synechococcus elongatus PCC 7942 has multiple copies of
 its single chromosome, and the copy number varies in individual cells,
 providing an ideal system to study the effect of genome copy-number
 variation on cell size and gene expression. Using single-cell fluorescence
 imaging, we found that protein concentration remained constant across
 individual cells regardless of genome copy number. Cell volume and the
 total protein amount from a single gene were both positively, linearly
 correlated with genome copy number, suggesting that changes in cell volume
 play an important role in buffering genome copy-number variance. This
 study provides a quantitative examination of gene expression regulation in
 cells with variable genome copies and sheds light on the compensation
 mechanisms for variance in genome copy number.
description: Read_meBbbJ23119_30uERaw images for the strain BbbJ23119::EYFP grown in default condition. Corresponding to data presented in Figure 1, Figure 2, Figure 1S and Figure 4S. Corresponding to 'BbbJ23119_30uE_r1' data in supplemental data and Table S1.BbbJ23119_DarkRaw images for strain BbbJ23119::EYFP after 24 h darkness. Corresponding to data presented in Figure 3, 'BbbJ23119_Dark' in supplemental data S1 and that in Table S1.BbbJ23119_Black.zipBbbJ23119_HighRaw images for strain BbbJ23119::EYFP strain grown under high light intensity (Figure S3). Corresponding to ‘BbbJ23119_High_r1’ in supplemental data S1 and Table S1.BbbJ23119_LowRaw images for strain BbbJ23119::EYFP strain grown under low light intensity (Figure 3). Corresponding to ‘BbbJ23119_Low_r1’ in supplemental data S1 and Table S1.BbbJ23119_minDRaw images for minD mutant strain with BbbJ23119::EYFP strain grown under default condition (Figure 4 and Figure S4). Corresponding to ‘BbbJ23119_minD_r1’ in supplemental data S1 and Table S1.pkaiBC_ZT6Raw images for strain pkaiBC::EYFP strain at ZT6, trough phase (Figure 1E and Figure S2). Corresponding to 'pkaiBC_ZT6_r1’ in supplemental data S1 and Table S1.pKaiBC_ZT6.zippkaiBC_ZT18Raw images for strain pkaiBC::EYFP strain at ZT18, peak phase (Figure 1E and Figure S2). Corresponding to 'pkaiBC_ZT18_r1’ in supplemental data S1 and Table S1.
DOI: 10.5061/dryad.ph715dd
title: Data from: Ecomorphological and phylogenetic controls on sympatry across extant bats

description: Aim: Macroecological patterns of sympatry can inform our understanding of
 how ecological and evolutionary processes govern species distributions.
 Following speciation, both intrinsic and extrinsic factors may determine
 how readily sympatry occurs. One possibility is that sympatry most readily
 occurs with ecological divergence, especially if broad-scale co-occurrence
 is mediated by niche differentiation. Time since divergence may also
 predict sympatry if hybridization and gene flow lead to the collapse of
 species boundaries between closely-related taxa. Here, we test for
 ecological and phylogenetic predictors of sympatry across the global
 radiation of extant bats. Location: Global Taxon: Bats (Order Chiroptera)
 Methods: We used a combination of linear mixed modeling, simulations, and
 maximum-likelihood modeling to test whether phylogenetic and
 ecomorphological divergence between species predict sympatry. We further
 assess how these relationships vary based on biogeographic realm. Results:
 We find that time since divergence does not predict sympatry in any
 biogeographic realm. Morphological divergence is negatively related to
 sympatry in the Neotropics, but shows no relationship with sympatry
 elsewhere. Main conclusions: We find that bats in most biogeographic
 realms co-occur at broad spatial scales regardless of phylogenetic
 similarity. Neotropical bats, however, appear to co-occur most readily
 when morphologically similar. To the extent that pairwise phylogenetic and
 morphological divergence reflect ecological differentiation, our results
 suggest that abiotic and environmental factors may be more important than
 species interactions in determining patterns of sympatry across bats.
description: Shi_etal_2018_JBI_data_code This compressed file contains all data and code associated with Shi et al. (2018), J. Biogeog. Shi_etal_2018.tgz   Appendices, tables, etc. referred to in the manuscript are most easily found in the much smaller .zip file - it is recommended to start there.
DOI: 10.5061/dryad.5vb1601
title: Data from: Genetic analysis identifies the missing parchment of New Zealand’s founding document, The Treaty of Waitangi.

description: Genetic analyses provide a powerful tool with which to identify the
 biological components of historical objects. Te Tiriti o Waitangi | The
 Treaty of Waitangi is New Zealand’s founding document, intended to be a
 partnership between the indigenous Māori and the British Crown. Here we
 focus on an archived piece of blank parchment that has been proposed to be
 the missing portion of the lower parchment of the Waitangi Sheet of the
 Treaty. However, its physical dimensions and characteristics are not
 consistent with this hypothesis. We perform genetic analyses on the
 parchment membranes of the Treaty, plus the blank piece of parchment. We
 find that all three parchments were made from ewes and that the blank
 parchment is highly likely to be a portion cut from the lower membrane of
 the Waitangi Sheet because they share identical whole mitochondrial
 genomes, including an unusual heteroplasmic site. We suggest that the
 differences in size and characteristics between the two pieces of
 parchment may have resulted from the Treaty’s exposure to water in the
 early 20th century and the subsequent repair work, light exposure during
 exhibition or the later conservation treatments in the 1970s and 80s. The
 blank piece of parchment will be valuable for comparison tests to study
 the effects of earlier treatments and to monitor the effects of long-term
 display on the Treaty.
description: Raw Illumina R1 reads
 for lower Waitangi parchmentCBBN1ANXX-2718-03-11-1_S14_L008_R1_001.fastq.gzRaw Illumina R2 reads for lower Waitangi parchmentCBBN1ANXX-2718-03-11-1_S14_L008_R2_001.fastq.gzRaw Illumina R1 reads for upper Waitangi parchmentCBBN1ANXX-2718-04-11-1_S15_L008_R1_001.fastq.gzRaw Illumina R2 reads for upper Waitangi parchmentCBBN1ANXX-2718-04-11-1_S15_L008_R2_001.fastq.gzRaw Illumina R1 reads for blank piece of parchmentCBBN1ANXX-2718-06-11-1_S17_L008_R1_001.fastq.gzRaw Illumina R2 reads for blank piece of parchmentCBBN1ANXX-2718-06-11-1_S17_L008_R2_001.fastq.gz
DOI: 10.5061/dryad.f3dn2
title: Data from: Complex genome evolution in A. coluzzii associated with increased insecticide usage in Mali

description: In certain cases, a species may have access to important genetic variation
 present in a related species via adaptive introgression. These novel
 alleles may interact with their new genetic background, resulting in
 unexpected phenotypes. In this study, we describe a selective sweep on
 standing variation on the X chromosome in the mosquito Anopheles coluzzii,
 a principal malaria vector in West Africa. This event may have been
 influenced by the recent adaptive introgression of the insecticide
 resistance gene known as kdr from the sister species Anopheles gambiae.
 Individuals carrying both kdr and a nearly fixed X-linked haplotype,
 encompassing at least four genes including the P450 gene CYP9K1 and the
 cuticular protein CPR125, have rapidly increased in relative frequency. In
 parallel, a reproductively isolated insecticide-susceptible A. gambiae
 population (Bamako form) has been driven to local extinction, likely due
 to strong selection from increased insecticide-treated bed net usage.
description: A. coluzzii variant
 fileThis file contains
 variants from all A. coluzzii individuals described in this study (plus a
 few others). See the README for the list of individual sample ID's
 from pre- and post-2006 samples that can be used with VCFtools to recreate
 the figures.Agam_normfilt_vcfs.vcf.gzSRP063464Illumina sequencing data for pre- and post-2006 A. coluzzii individuals from Selenkenyi, Mali.
DOI: 10.5061/dryad.q0d1n
title: Data from: Distributed rhythm generators underlie Caenorhabditis elegans forward locomotion

description: Coordinated rhythmic movements are ubiquitous in animal behavior. In many
 organisms, chains of neural oscillators underlie the generation of these
 rhythms. In C. elegans, locomotor wave generation has been poorly
 understood; in particular, it is unclear where in the circuit rhythms are
 generated, and whether there exists more than one such generator. We used
 optogenetic and ablation experiments to probe the nature of rhythm
 generation in the locomotor circuit. We found that multiple sections of
 forward locomotor circuitry are capable of independently generating
 rhythms. By perturbing different components of the motor circuit, we
 localize the source of secondary rhythms to cholinergic motor neurons in
 the midbody. Using rhythmic optogenetic perturbation, we demonstrate
 bidirectional entrainment of oscillations between different body regions.
 These results show that, as in many other vertebrates and invertebrates,
 the C. elegans motor circuit contains multiple oscillators that coordinate
 activity to generate behavior.
description: Data_IRsurgery_1Data_IRsurgery_2Data_IRsurgery_3Data_IRsurgery_4Data_IRsurgery_5Data_IRsurgery_6Data_IRsurgery_7_reviewContains replicates of VNC/DNC cut surgery at various location which were pooled with the data in Figure 7 at the review stage.Data_IRsurgery_8_reviewContains replicates of most conditions in the B-motor-neuron ablation experiments in Figure 4, which are now pooled with the original data.Data_MiniSOGData_MiniSOG_2_reviewContains optogenetic 2FU data from worms in which all DB and/or most VB motor neurons were ablated.Data_MiniSOG_3_reviewContains data from VNC-isolated worms in which all DB and/or most VB motor neurons were ablated.Data_Optogenetics_1Data_Optogenetics_2Data_Optogenetics_3Data_Optogenetics_4Data_Optogenetics_5Data_Optogenetics_6_reviewContains optogenetic 2FU experiments with vab-7 mutant wormsCodes_All_v4Matlab and C/C++ codes, updated after completing experiments requested in review. Includes instructions to compile StageBoost, the C++ code for the optogenetic targeting system.
DOI: 10.21227/ppfa-2g45
title: "Student Social Media Addiction Dataset (Egypt)"

description: "This data descriptor documents a  student survey dataset (N = 12,038)  for research and benchmarking on social media addiction among students in Egypt. The dataset is calibrated to match the marginal distributions and key latent correlations observed in an original anonymized survey sample."
DOI: 10.5061/dryad.233hb
title: Data from: Going with the flow: the role of ocean circulation in global marine ecosystems under a changing climate

description: Ocean warming, acidification, deoxygenation and reduced productivity are
 widely considered to be the major stressors to ocean ecosystems induced by
 emissions of CO2. However, an overlooked stressor is the change in ocean
 circulation in response to climate change. Strong changes in the intensity
 and position of the western boundary currents have already been observed,
 and the consequences of such changes for ecosystems are beginning to
 emerge. In this study, we address climatically induced changes in ocean
 circulation on a global scale but relevant to propagule dispersal for
 species inhabiting global shelf ecosystems, using a high resolution global
 ocean model run under the IPCC RCP 8.5 scenario. The ¼ degree model
 resolution allows improved regional realism of the ocean circulation
 beyond that of available CMIP5-class models. We use a Lagrangian approach
 forced by modelled ocean circulation to simulate the circulation pathways
 that disperse planktonic life stages. Based on trajectory backtracking, we
 identify present-day coastal retention, dominant flow and dispersal range
 for coastal regions at the global scale. Projecting into the future, we
 identify areas of the strongest projected circulation change and present
 regional examples with the most significant modifications in their
 dominant pathways. Climatically-induced changes in ocean circulation
 should be considered as an additional stressor of marine ecosystems in a
 similar way to ocean warming or acidification.
description: Asia and Oceania
 releasesThe dataset contains the
 particle tracking runs for the coastline of Asia and Oceania. 3 runs were
 carried out using the velocity field of three different decades: 2000-09,
 2050-59 and 2090-99 and released particles were tracked backwards in time
 for 12 months.Releases_Asia_Oceania.tar.gzReleases Europe and AfricaReleases_Europe_Africa.tar.gzReleases North AmericaReleases_Nth_America.tar.gzReleases South AmericaReleases_Sth_America.tar.gzMatlab script to extract each ASCIIdataA step by step procedure to extract trajectories from the datasetsExtract_ASCIIdata.mExplanation_ASCII_dataDescription of datasets content
DOI: 10.5061/dryad.6j58m7g
title: Data from: Species tree estimation using ddRADseq data from historical specimens confirms the monophyly of highly disjunct species of Chloropyron (Orobanchaceae)

description: Sequence data exist for only about 1/5 of plant species; therefore we are
 at risk of losing many branches of the tree of life even before they are
 placed into a molecular evolutionary context. This necessitates methods
 for phylogeny estimation of understudied, rare, and threatened taxa, which
 often forces researchers to utilize historical collections. The
 restriction site-associated DNA sequencing (RADseq) family of reduced
 representation sequence generation has provided a flexible and efficient
 method for the rapid generation of hundreds to tens of thousands of loci,
 and has recently seen adoption for phylogeny estimation. However, these
 methods have been primarily utilized with freshly collected or well
 preserved tissue. Here we sample all taxa of a genus of rare flowering
 plants, Chloropyron (Orobanchaceae), from herbarium sheets dating up to 25
 yr and use double digest restriction site-associated DNA sequencing
 (ddRADseq) to resolve intraspecific relationships. We find all species in
 Chloropyron to be monophyletic, with the inland taxon C. maritimum ssp.
 canescens sister to the rest of the coastal C. maritimum (ssp. maritimum +
 ssp. palustre), and the two distinct subspecies of C. molle to be each
 other’s closest relative with strong support. In addition, we demonstrate
 the utility of reduced representation libraries to address phylogenomic
 problems in a group of rare species and address pitfalls of accurately
 inferring relationships when the amount of missing data is large, as is
 often the case when using historical specimens and rare taxa.
description: Compressed
 berk1_R1_.fastqCompressed ddRAD
 libraryberk1_R1_.fastq.gzCompressed berk1_R2_.fastqCompressed ddRAD libraryberk1_R2_.fastq.gzCompressed cordy2_R1_.fastqCompressed ddRAD librarycordy2_R1_.fastq.gzCompressed cordy2_R2_.fastqCompressed ddRAD librarycordy2_R2_.fastq.gzCompressed RSA1Library_S2_L001_R1_001.fastqCompressed ddRAD libraryRSA1Library_S2_L001_R1_001.fastq.gzCompressed RSA1Library_S2_L001_R2_001.fastqCompressed ddRAD libraryRSA1Library_S2_L001_R2_001.fastq.gzAccession barcodesList of barcodes file for all accessions included in this study as well as some accessions not used but included on the same sequencing lane.all_barcodes.barcodes.txt
DOI: 10.5061/dryad.fn664f0
title: Data from: Decoding the influence of anticipatory states on visual perception in the presence of temporal distractors

description: Anticipatory states help prioritise relevant perceptual targets over
 competing distractor stimuli and amplify early brain responses to these
 targets. Here we combine electroencephalography recordings in humans with
 multivariate stimulus decoding to address whether anticipation also
 increases the amount of target identity information contained in these
 responses, and to ask how targets are prioritised over distractors when
 these compete in time. We show that anticipatory cues not only boost
 visual target representations, but also delay the interference on these
 target representations caused by temporally adjacent distractor
 stimuli—possibly marking a protective window reserved for high-fidelity
 target processing. Enhanced target decoding and distractor resistance are
 further predicted by the attenuation of posterior 8–14 Hz alpha
 oscillations. These findings thus reveal multiple mechanisms by which
 anticipatory states help prioritise targets from temporally competing
 distractors, and they highlight the potential of non-invasive multivariate
 electrophysiology to track cognitive influences on perception in
 temporally crowded contexts.
description: READMEs01s02s03s04s05s06s07s08s09s10s11s12s13s14s15s16s17s18s19s20s21s22s23s24s25s26s27s28s29s30
DOI: 10.5517/ccdc.csd.cc2nx491
title: CCDC 2469903: Experimental Crystal Structure Determination

description: Related Article: Hideyuki Takahashi, Hayato Kobayashi, Tadashi Kawasaki, Akiko Hori|2025|Chem.Lett.|54|upaf211|doi:10.1093/chemle/upaf211
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.cc2nxpy7
title: CCDC 2470450: Experimental Crystal Structure Determination

description: Related Article: Yangbin Jin, Yinwu Li, Mingda Li, Jiarui Li, Haobing Wang, Wanqing Wu, Zhuofeng Ke, Huanfeng Jiang|2026|J.Am.Chem.Soc.|||doi:10.1021/jacs.5c17010
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.cc2p7425
title: CCDC 2479506: Experimental Crystal Structure Determination

description: Related Article: Olaitan E. Oladipupo, David M. Muthama, Wilmer J. Andújar-Cruz, Ge Shi, Sanjit Das, Rifat Ara Masud, Aruzhan Abdikaiym, Caleb A. Buell, Isabella R. Mejia, Chandni S. Bhat, Emily A. Schmitt, Daniel I. Osaigbovo, Logan M. Whitt, Fengrui Qu, Colin G. Cameron, Sherri A. McFarland, Igor Fedin, Yonghyun Kim, Elizabeth T. Papish|2026|Organometallics|||doi:10.1021/acs.organomet.5c00305
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.cc2p7436
title: CCDC 2479507: Experimental Crystal Structure Determination

description: Related Article: Olaitan E. Oladipupo, David M. Muthama, Wilmer J. Andújar-Cruz, Ge Shi, Sanjit Das, Rifat Ara Masud, Aruzhan Abdikaiym, Caleb A. Buell, Isabella R. Mejia, Chandni S. Bhat, Emily A. Schmitt, Daniel I. Osaigbovo, Logan M. Whitt, Fengrui Qu, Colin G. Cameron, Sherri A. McFarland, Igor Fedin, Yonghyun Kim, Elizabeth T. Papish|2026|Organometallics|||doi:10.1021/acs.organomet.5c00305
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.