cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10255571.v1
title: The Bouba–Kiki Effect in Persons with Prelingual Auditory Deprivation

description: The “bouba–kiki effect” refers to the correspondence between arbitrary visual and auditory stimuli. Previous studies have demonstrated that neurodevelopmental conditions and sensory impairment affect subjects’ performance on the bouba–kiki task. This study examined the bouba–kiki effect in participants with severe-to-profound hearing loss. Sixteen participants with severe- to- profound hearing loss who were habilitated aurally and used oral language for everyday communication and 16 matched hearing peers were presented with the bouba–kiki task auditorily and orthographically. Verbal intelligence (Wechsler Adult Intelligence Scale – Third Edition) was determined for all participants and was similar in both groups. Our results demonstrate a reduced bouba–kiki effect in participants with severe-to-profound hearing loss compared to their hearing peers, though they performed above chance level. Moreover, the age at the first use of a hearing device was associated with participants’ performance on the bouba–kiki task in adulthood. Better performance was shown in participants who used a hearing device at infancy before 23 months of age. These results support a relationship between early auditory or linguistic deprivation, and performance on the bouba–kiki task, and are discussed in the light of the role of a sensitive period on the development of the effect. This study is the first to show that prelingual deafness affects cross-modal auditory–visual correspondence resulting in reduced sound symbolism.
DOI: 10.6084/m9.figshare.10255526.v2
title: Metadata record for: Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

description: This dataset contains key characteristics about the data described in the Data Descriptor Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.10255526.v1
title: Metadata record for: Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

description: This dataset contains key characteristics about the data described in the Data Descriptor Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.10253291
title: TOFF Data Release

description: The data release of behavioral, morphological, phenological, and physiological (BMPP) traits and associated environmental characteristics available in TOFF. Retrieved 2019-07-16.<br>The archive includes three files:<br>- The file Data_Release_TOFF_1.csv displays BMPP information- The file Data_Release_TOFF_2.csv displays environmental characteristic information- The file R-Script_TOFF_Data_Release.r displays the R-script used to produce the data release
DOI: 10.6084/m9.figshare.10253291.v1
title: TOFF Data Release

description: The data release of behavioral, morphological, phenological, and physiological (BMPP) traits and associated environmental characteristics available in TOFF. Retrieved 2019-07-16.<br>The archive includes three files:<br>- The file Data_Release_TOFF_1.csv displays BMPP information- The file Data_Release_TOFF_2.csv displays environmental characteristic information- The file R-Script_TOFF_Data_Release.r displays the R-script used to produce the data release
DOI: 10.6084/m9.figshare.10253291.v4
title: TOFF Data Release

description: The data release of behavioral, morphological, phenological, and physiological (BMPP) traits and associated environmental characteristics available in TOFF. Retrieved 2019-07-16.<br>The archive includes three files:<br>- The file Data_Release_TOFF_1.csv displays BMPP information- The file Data_Release_TOFF_2.csv displays environmental characteristic information- The file R-Script_TOFF_Data_Release.r displays the R-script used to produce the data release
DOI: 10.6084/m9.figshare.10253291.v3
title: TOFF Data Release

description: The data release of behavioral, morphological, phenological, and physiological (BMPP) traits and associated environmental characteristics available in TOFF. Retrieved 2019-07-16.<br>The archive includes three files:<br>- The file Data_Release_TOFF_1.csv displays BMPP information- The file Data_Release_TOFF_2.csv displays environmental characteristic information- The file R-Script_TOFF_Data_Release.r displays the R-script used to produce the data release
DOI: 10.6084/m9.figshare.10253219.v1
title: Thesaurus of TOFF

description: This file provides the definition of each behavioral, morphological, phenological, and physiological (BMPP) trait and environmental characteristic includes in the TOFF database. This thesaurus will be updated as TOFF progresses (see the last version at http://toff-project.univ-lorraine.fr).
DOI: 10.6084/m9.figshare.10253219.v2
title: Thesaurus of TOFF

description: This file provides the definition of each behavioral, morphological, phenological, and physiological (BMPP) trait and environmental characteristic includes in the TOFF database. This thesaurus will be updated as TOFF progresses (see the last version at http://toff-project.univ-lorraine.fr).
DOI: 10.6084/m9.figshare.10253219.v3
title: Thesaurus of TOFF

description: This file provides the definition of each behavioral, morphological, phenological, and physiological (BMPP) trait and environmental characteristic includes in the TOFF database. This thesaurus will be updated as TOFF progresses (see the last version at http://toff-project.univ-lorraine.fr).
DOI: 10.6084/m9.figshare.10253129
title: A diminutive species of emu (Casuariidae: Dromaiinae) from the late Miocene of the Northern Territory, Australia

description: A new, diminutive species of dromaiine casuariid, <i>Dromaius arleyekweke</i>, is described from dispersed skeletal elements from the late Miocene Waite Formation of the Northern Territory, Australia. Remains of <i>D. arleyekweke</i>, sp. nov., have been found from the Ongeva Local Fauna in the Alcoota Scientific Reserve, but most remains come from the stratigraphically lower Alcoota Local Fauna where they form part of a densely fossiliferous series of mingled bone beds. Previously, remains of the new species had been referred to the basal dromaiine genus, <i>Emuarius</i>, but phylogenetic appraisal of new specimens indicates that the species shared a more recent common ancestor with the extant <i>Dromaius novaehollandiae</i> than it did with the type species of <i>Emuarius</i>, <i>E. gidju</i>. Consequently, the new species is placed in the genus <i>Dromaius</i> as its oldest known member. Derived characters of <i>D. arleyekweke</i> that are shared with <i>D. novaehollandiae</i> to the exclusion of <i>E. gidju</i> include a distally flattened external condyle of the distal end of the tibiotarsus and a more elongate tarsometatarsus, with marked transverse compression of the midshaft and a weakly impressed median sulcus on trochlea metatarsi II. Casuariid evolution shows a trend of increasingly cursorial hind limb proportions on the emu lineage, but <i>D. arleyekweke</i> has a tarsometatarsus that is more elongate than that of <i>D. novaehollandiae</i>. This implies nonlinear evolution of cursoriality in dromaiines and that <i>D. arleyekweke</i> evolved extreme cursorial proportions independently of <i>D. novaehollandiae</i>, or that a high degree of cursoriality evolved early in <i>Dromaius</i> and was reversed in the Pliocene <i>D. ocypus</i>.
DOI: 10.6084/m9.figshare.10253129.v1
title: A diminutive species of emu (Casuariidae: Dromaiinae) from the late Miocene of the Northern Territory, Australia

description: A new, diminutive species of dromaiine casuariid, <i>Dromaius arleyekweke</i>, is described from dispersed skeletal elements from the late Miocene Waite Formation of the Northern Territory, Australia. Remains of <i>D. arleyekweke</i>, sp. nov., have been found from the Ongeva Local Fauna in the Alcoota Scientific Reserve, but most remains come from the stratigraphically lower Alcoota Local Fauna where they form part of a densely fossiliferous series of mingled bone beds. Previously, remains of the new species had been referred to the basal dromaiine genus, <i>Emuarius</i>, but phylogenetic appraisal of new specimens indicates that the species shared a more recent common ancestor with the extant <i>Dromaius novaehollandiae</i> than it did with the type species of <i>Emuarius</i>, <i>E. gidju</i>. Consequently, the new species is placed in the genus <i>Dromaius</i> as its oldest known member. Derived characters of <i>D. arleyekweke</i> that are shared with <i>D. novaehollandiae</i> to the exclusion of <i>E. gidju</i> include a distally flattened external condyle of the distal end of the tibiotarsus and a more elongate tarsometatarsus, with marked transverse compression of the midshaft and a weakly impressed median sulcus on trochlea metatarsi II. Casuariid evolution shows a trend of increasingly cursorial hind limb proportions on the emu lineage, but <i>D. arleyekweke</i> has a tarsometatarsus that is more elongate than that of <i>D. novaehollandiae</i>. This implies nonlinear evolution of cursoriality in dromaiines and that <i>D. arleyekweke</i> evolved extreme cursorial proportions independently of <i>D. novaehollandiae</i>, or that a high degree of cursoriality evolved early in <i>Dromaius</i> and was reversed in the Pliocene <i>D. ocypus</i>.
DOI: 10.6084/m9.figshare.10253048
title: Metabolomics Data Deposition from Cardiac metabolomic profile of the naked mole-rat—glycogen to the rescue

description: The African naked mole-rat (<i>Heterocephalus glaber</i>) is unique among mammals, displaying extreme longevity, resistance to cardiovascular disease and an ability to survive long periods of extreme hypoxia. The metabolic adaptations required for resistance to hypoxia are hotly debated and a recent report provides evidence that they are able to switch from glucose to fructose driven glycolysis in the brain. However, other systemic alterations in their metabolism are largely unknown. In the current study, a semi-targeted high resolution <sup>1</sup>H magnetic resonance spectroscopy (MRS) metabolomics investigation was performed on cardiac tissue from the naked mole-rat (NMR) and wild-type C57/BL6 mice to better understand these adaptations. A range of metabolic differences was observed in the NMR including increased lactate, consistent with enhanced rates of glycolysis previously reported, increased glutathione, suggesting increased resistance to oxidative stress and decreased succinate/fumarate ratio suggesting reduced oxidative phosphorylation and ROS production. Surprisingly, the most significant difference was an elevation of glycogen stores and glucose-1-phosphate resulting from glycogen turnover, that were completely absent in the mouse heart and above the levels found in the mouse liver. Thus, we identified a range of metabolic adaptations in the NMR heart that are relevant to their ability to survive extreme environmental pressures and metabolic stress. Our study underscores the plasticity of energetic pathways and the need for compensatory strategies to adapt in response to the physiological and pathological stress including ageing and ischaemic heart pathologies.
DOI: 10.6084/m9.figshare.10253051
title: Environmental variability in response to abrupt climatic change during the Last Glacial- Interglacial Transition (16–8 cal. ka BP): evidence from Mainland, Orkney

description: Supplementary Data 1: All raw data associated with this publication: raw pollen counts, charcoal data, Principal Curve and Rate of Change outputs and the age-model output
DOI: 10.6084/m9.figshare.10253048.v1
title: Metabolomics Data Deposition from Cardiac metabolomic profile of the naked mole-rat—glycogen to the rescue

description: The African naked mole-rat (<i>Heterocephalus glaber</i>) is unique among mammals, displaying extreme longevity, resistance to cardiovascular disease and an ability to survive long periods of extreme hypoxia. The metabolic adaptations required for resistance to hypoxia are hotly debated and a recent report provides evidence that they are able to switch from glucose to fructose driven glycolysis in the brain. However, other systemic alterations in their metabolism are largely unknown. In the current study, a semi-targeted high resolution <sup>1</sup>H magnetic resonance spectroscopy (MRS) metabolomics investigation was performed on cardiac tissue from the naked mole-rat (NMR) and wild-type C57/BL6 mice to better understand these adaptations. A range of metabolic differences was observed in the NMR including increased lactate, consistent with enhanced rates of glycolysis previously reported, increased glutathione, suggesting increased resistance to oxidative stress and decreased succinate/fumarate ratio suggesting reduced oxidative phosphorylation and ROS production. Surprisingly, the most significant difference was an elevation of glycogen stores and glucose-1-phosphate resulting from glycogen turnover, that were completely absent in the mouse heart and above the levels found in the mouse liver. Thus, we identified a range of metabolic adaptations in the NMR heart that are relevant to their ability to survive extreme environmental pressures and metabolic stress. Our study underscores the plasticity of energetic pathways and the need for compensatory strategies to adapt in response to the physiological and pathological stress including ageing and ischaemic heart pathologies.
DOI: 10.6084/m9.figshare.10253051.v1
title: Environmental variability in response to abrupt climatic change during the Last Glacial- Interglacial Transition (16–8 cal. ka BP): evidence from Mainland, Orkney

description: Supplementary Data 1: All raw data associated with this publication: raw pollen counts, charcoal data, Principal Curve and Rate of Change outputs and the age-model output
DOI: 10.6084/m9.figshare.10253063.v1
title: dataset

description: dataset of the study
DOI: 10.6084/m9.figshare.10253063.v3
title: dataset of the research

description: dataset of the study
DOI: 10.6084/m9.figshare.10253063.v2
title: ChiCTR-INR-17012089

description: dataset of the study
DOI: 10.6084/m9.figshare.10252949
title: List of predicted secreted proteins of M. enterolobii (genome V1, INRA/JKI)

description: Predicted Secretome of M. enterolobii genome (V1, INRA/JKI)<br><br>Strategy:<br>1. Use SignalP 4.0 that better discriminate between SP and N-terminal TM<br>Put the -m 'file' option to produce a FASTA with cleaved SP<br><br>signalp -f short -m MentV1-cleaved.fa -t euk MentV1.pep.fa &gt; MentV1.SP<br><br>--&gt; there are 6,065 proteins with a predicted SP.<br><br>2. Use TMHMM-2.0 to predict TMs on the cleaved FASTA sequences.<br><br>tmhmm --short MentV1-cleaved.fa &gt; MentV1-cleaved-TM-short.txt<br><br>--&gt; there are 1,092 proteins with a SP and at least one TM (that is not included within the SP).<br>Thus 4,973 proteins with SP and no TM.<br><br>3. Generate a list of sequences with predicted SP an no predicted TM<br>The accession numbers for the 4,973 proteins with SP and no TM is saved in MentV1.SP-no-TM.acc<br>
DOI: 10.6084/m9.figshare.10252919
title: A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea.

description: File S1: Bioinformatics methods, tools and pipelines used to generate gadMor_Celtic and other information complementing the materials and methods section can be found here. Table S1: Linkage map of gadMor_Celtic: SNPs, position in gadMor_Celtic, genetic linkage of male, female in centimorgan (cM) and SNP flank sequence from gadMor1 (NEAC). Table S2: Predicted function of open reading frames were found with TransDecoder and homology search using blastp against zebrafish and stickleback protein databases. Figure S1: Plots showing collinearity between genetic maps for males (red) and female (blue) and the frequency of a 258bp tandem repeat structure (histogram) predicted to be related to centromeres in all 23 chromosomes. Table S3: This contains the list of genes in LGs 1, 2, 7 and 12. File S2: The putative 258bp centromere repeat sequence.gadMor_celtic_repeat_Library.fa.txt - Repeat library<br><br>gadMor_Celtic.fa.txt -Genome assembly<br>
DOI: 10.6084/m9.figshare.10252964.v3
title: informed consent

description: informed consent information template without personal identify information of patients
DOI: 10.6084/m9.figshare.10252877
title: Dysregulated activities of proline-specific enzymes in septic shock patients (sepsis-2)_Vliegen et al_Raw data.sav

description: - Patients with septic shock (≥ 18 years) admitted to the ICU of the Radboud University Medical Center (Radboudumc, Nijmegen, the Netherlands).(Sepsis-2 criteria). Samples were available at 4 time points (days 1, 3, 5 and 7 after diagnosis). Collection of samples from septic shock patients was done in accordance with the applicable rules concerning the review of the Ethics Committee of UMC Radboud (CMO-nr: 2016/2923) and informed consent was given by the patient or his/her closest relative. - The non-septic shock ICU control group consisted of 22 consecutively admitted patients (≥ 18 years) undergoing major intracranial surgery (resection of a cerebral tumor or clipping of an aneurysm) who were admitted to the ICU of the Antwerp University Hospital for postoperative monitoring. All ICU control patients gave written informed consent and the study was approved by the Ethics Committee of the Antwerp University Hospital/ University of Antwerp (Amendment 17/10/119 ref. B300201732219). The study was performed in accordance with the Declaration of Helsinki.- DPP4 activity was measured colorimetrically using Gly-Pro-pNA, FAP and PREP were measured fluorimetrically using Z-Gly-Pro-AMC, PRCP was measured using a RP-HPLC method with Z-Pro-Phe.- Cytokines were measured using a Luminex assay.<br>
DOI: 10.6084/m9.figshare.10252847
title: Freshwater common reeds in the Yellow River Delta responding to salt stress_CK

description: Freshwater common reed (F) in Yellow River Delta responding to salt stress. F0 (0 mmol/L NaCl treatment)：F10, F20, F29.<br>
DOI: 10.6084/m9.figshare.10252772
title: PDB files for UGT1A1 mutants

description: <pre>UGT1A1_mutants.zip file contains PDB files with names UGT1A1_G71R, UGT1A1_F83L, UGT1A1_P229L, UGT1A1_P229Q, UGT1A1_L233R, UGT1A1_I294T, UGT1A1_I322V, UGT1A1_R336L, UGT1A1_H376R, UGT1A1_P387S, UGT1A1_N400D, and UGT1A1_W461R. Each PDB file is the last frame from 10000-ps molecular dynamics simulation of human UGT1A1 with the respective mutations.</pre>
DOI: 10.6084/m9.figshare.10252847.v1
title: Freshwater common reeds in the Yellow River Delta responding to salt stress_CK

description: Freshwater common reed (F) in Yellow River Delta responding to salt stress. F0 (0 mmol/L NaCl treatment)：F10, F20, F29.<br>
DOI: 10.6084/m9.figshare.10252877.v1
title: Raw_data_PLOS ONE.sav

description: - Patients with septic shock (≥ 18 years) admitted to the ICU of the Radboud University Medical Center (Radboudumc, Nijmegen, the Netherlands).(Sepsis-2 criteria). Samples were available at 4 time points (days 1, 3, 5 and 7 after diagnosis). Collection of samples from septic shock patients was done in accordance with the applicable rules concerning the review of the Ethics Committee of UMC Radboud (CMO-nr: 2016/2923) and informed consent was given by the patient or his/her closest relative. - The non-septic shock ICU control group consisted of 22 consecutively admitted patients (≥ 18 years) undergoing major intracranial surgery (resection of a cerebral tumor or clipping of an aneurysm) who were admitted to the ICU of the Antwerp University Hospital for postoperative monitoring. All ICU control patients gave written informed consent and the study was approved by the Ethics Committee of the Antwerp University Hospital/ University of Antwerp (Amendment 17/10/119 ref. B300201732219). The study was performed in accordance with the Declaration of Helsinki.- DPP4 activity was measured colorimetrically using Gly-Pro-pNA, FAP and PREP were measured fluorimetrically using Z-Gly-Pro-AMC, PRCP was measured using a RP-HPLC method with Z-Pro-Phe.- Cytokines were measured using a Luminex assay.<br>
DOI: 10.6084/m9.figshare.10252748
title: Overview_Microscopy data_files

description: Excel file summarising all the informations related to microscopy data deposited.
DOI: 10.6084/m9.figshare.10252748.v1
title: Overview_Microscopy data_files

description: Excel file summarising all the informations related to microscopy data deposited.
DOI: 10.6084/m9.figshare.10252694
title: MSR_20191105.csv

description: A dataset of mass-specific respiration rate of terrestrial vegetation worldwide.
DOI: 10.6084/m9.figshare.10252715
title: Unique and redundant roles of SOX2 and SOX17 in regulating the germ cell tumor fate

description: Embryonal carcinomas (ECs) and seminomas are testicular germ cell tumors. ECs display expression of SOX2, while seminomas display expression of SOX17. In somatic differentiation, SOX17 drives endodermal cell fate. However, seminomas lack expression of endoderm markers, but show features of pluripotency. Here, we use chromatin immunoprecipitation sequencing to report and compare the binding pattern of SOX17 in seminoma-like TCam-2 cells to SOX17 in somatic cells and SOX2 in EC-like 2102EP cells. In seminoma-like cells, SOX17 was detected at canonical (SOX2/OCT4), compressed (SOX17/OCT4) and noncomposite SOXmotifs. SOX17 regulates TFAP2C, PRDM1 and PRDM14, therebymaintaining latent pluripotency and suppressing somatic differentiation. In contrast, in somatic cells canonicalmotifs are rarely bound by SOX17. In sum, only 12%of SOX17-binding sites overlap in seminoma-like and somatic cells. This illustrates that binding site choice is highly dynamic and cell type specific. Deletion of SOX17 in seminoma-like cells resulted in loss of pluripotency,marked by a reduction of OCT4 protein level and loss of alkaline phosphatase activity. Furthermore, we found that in EC-like cells SOX2 regulates pluripotency-associated genes,most likely by partneringwith OCT4. In conclusion, SOX17 (in seminomas) functionally replaces SOX2 (in ECs) tomaintain expression of the pluripotency cluster.
DOI: 10.6084/m9.figshare.10252673
title: Data file from The effects of anthropogenic noise on animals: a meta-analysis

description: Anthropogenic noise has become a major global pollutant and studies have shown that noise can affect animals. However, such single studies cannot provide holistic quantitative assessments on the potential effects of noise across species. Using a multi-level phylogenetically controlled meta-analysis, we provide the first holistic quantitative analysis on the effects of anthropogenic noise. We found that noise affects many species of amphibians, arthropods, birds, fish mammals, molluscs and reptilians. Interestingly, phylogeny contributes only little to the variation in response to noise. Thus, the effects of anthropogenic noise can be explained by the majority of species responding to noise rather than a few species being particularly sensitive to noise. Consequently, anthropogenic noise must be considered as a serious form of environmental change and pollution as it affects both aquatic and terrestrial species. Our analyses provide the quantitative evidence necessary for legislative bodies to regulate this environmental stressor more effectively.