cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10249001.v1
title: MarsWRF output for southern summer solstice in Gale Crater, needed to calculate Renno et al. [1998] Dust Devil Activity and intermediate variables.

description: This netCDF file of 7 sols of output from the MarsWRF atmospheric model includes all variables needed to calculate Renno et al. [1998]'s "Dust devil activity" in Gale Crater, Mars, for southern summer solstice (Ls~270°). The dust devil activity predicts the amount of convective and dust devil activity based on the thermodynamic environment. <br><br>Variables included are: lon (longitude in deg E), lat (latitude in deg N), ddac (dust devil activity), hfx(sensible heat flux in W/m2), ls (areocentric solar longitude), ltst (local true solar time in hours), omb (vertical thermodynamic efficiency), pbh (planetary boundary layer height in m), psrf (surface pressure in Pa), ptop (pressure at boundary layer top in Pa), rho (near-surface air density in kg/m3), t1_5 (air temperature at 1.5m above the surface in K), tsk (surface air temperature in K), ust (drag velocity, u*, in m/s).<br><br>These data are used to produce Figures (especially Figures 2-5, 7-8, and S2-4) in the paper “Convective vortex and dust devil predictions for Gale Crater over three Mars years and comparison with MSL-REMS observations” - JGR-Planets, 2019 - by C. E. Newman, H. Kahanpää, M. I. Richardson, G. M. Martinez, A. Vicente-Retortillo and M. Lemmon<br><br><br>
DOI: 10.6084/m9.figshare.10249796.v1
title: MarsWRF output for southern fall equinox in Gale Crater, needed to calculate Renno et al. [1998] Dust Devil Activity and intermediate variables.

description: This netCDF file of 7 sols of output from the MarsWRF atmospheric model includes all variables needed to calculate Renno et al. [1998]'s "Dust devil activity" in Gale Crater, Mars, for southern fall equinox (Ls~0°). The dust devil activity predicts the amount of convective and dust devil activity based on the thermodynamic environment.<br>Variables included are: lon (longitude in deg E), lat (latitude in deg N), ddac (dust devil activity), hfx(sensible heat flux in W/m2), ls (areocentric solar longitude), ltst (local true solar time in hours), omb (vertical thermodynamic efficiency), pbh (planetary boundary layer height in m), psrf (surface pressure in Pa), ptop (pressure at boundary layer top in Pa), rho (near-surface air density in kg/m3), t1_5 (air temperature at 1.5m above the surface in K), tsk (surface air temperature in K), ust (drag velocity, u*, in m/s).<br>These data are used to produce Figures (especially Figures 8 and Supplementary Figures S2-4) in the paper “Convective vortex and dust devil predictions for Gale Crater over three Mars years and comparison with MSL-REMS observations” - JGR-Planets, 2019 - by C. E. Newman, H. Kahanpää, M. I. Richardson, G. M. Martinez, A. Vicente-Retortillo and M. Lemmon
DOI: 10.6084/m9.figshare.10250297.v1
title: MarsWRF output for southern winter solstice in Gale Crater, needed to calculate Renno et al. [1998] Dust Devil Activity and intermediate variables.

description: This netCDF file of 7 sols of output from the MarsWRF atmospheric model includes all variables needed to calculate Renno et al. [1998]'s "Dust devil activity" in Gale Crater, Mars, for southern winter solstice (Ls~90°). The dust devil activity predicts the amount of convective and dust devil activity based on the thermodynamic environment. <br><br>Variables included are: lon (longitude in deg E), lat (latitude in deg N), ddac (dust devil activity), hfx(sensible heat flux in W/m2), ls (areocentric solar longitude), ltst (local true solar time in hours), omb (vertical thermodynamic efficiency), pbh (planetary boundary layer height in m), psrf (surface pressure in Pa), ptop (pressure at boundary layer top in Pa), rho (near-surface air density in kg/m3), t1_5 (air temperature at 1.5m above the surface in K), tsk (surface air temperature in K), ust (drag velocity, u*, in m/s).<br><br>These data are used to produce Figures (especially Figures 8 and S2-4) in the paper “Convective vortex and dust devil predictions for Gale Crater over three Mars years and comparison with MSL-REMS observations” - JGR-Planets, 2019 - by C. E. Newman, H. Kahanpää, M. I. Richardson, G. M. Martinez, A. Vicente-Retortillo and M. Lemmon<br><br><br>
DOI: 10.6084/m9.figshare.10248932
title: BDE-db: A collection of 290,664 Homolytic Bond Dissociation Enthalpies for Small Organic Molecules

description: A database of 290,664 bond dissociation energies for small molecules (10 or fewer heavy atoms) consisting of C, H, O, or N atoms. Enthalpy calculations were carried out using the M06-2X/def2-TZVP functional / basis set using Gaussian 16. Reported BDEs are in kcal/mol.
DOI: 10.6084/m9.figshare.10248821
title: Alsheikh AJ-Supplemental Table S1.xlsx

description: Complete List of Gene Expression data.
DOI: 10.6084/m9.figshare.10248818
title: Detection and comparative analysis of cutaneous bacterial communities of farmed and wild <i>Rana dybowskii</i> (Amphibia: Anura)

description: <i>Rana dybowskii</i> Gunther, 1876 is a dominant amphibian species in northeast China. In order to understand the composition and structure of the cutaneous bacterial communities of farmed and wild <i>R. dybowskii</i>, two experimental groups (farmed and wild) were investigated in this study. Following DNA extraction, the V3-V4 hypervariable region of the 16S rRNA gene was targeted and analyzed by high-throughput sequencing. The cutaneous bacterial community diversity was investigated and compared through analysis of alpha and beta diversity. A total of 524,852 valid sequences and 1,023 operational taxonomic units (OTUs) were obtained from these two experimental groups. The number of shared OTUs was 333, while there were 603 unique OTUs in the farmed group and 87 unique OTUs in the wild group. The Chao, ACE and Shannon indices of the farmed group were significantly higher than those of the wild group (<i>p</i> R. dybowskii exhibited significant differences. This study provides a theoretical basis for comprehensively understanding the composition and abundance of bacteria on the skin of farmed and wild <i>R. dybowskii</i>, which helps to develop its breeding industry and gain economic benefits.
DOI: 10.6084/m9.figshare.10248821.v1
title: Alsheikh AJ-Supplemental Table S1.xlsx

description: Complete List of Gene Expression data.
DOI: 10.6084/m9.figshare.10248818.v1
title: Detection and comparative analysis of cutaneous bacterial communities of farmed and wild <i>Rana dybowskii</i> (Amphibia: Anura)

description: <i>Rana dybowskii</i> Gunther, 1876 is a dominant amphibian species in northeast China. In order to understand the composition and structure of the cutaneous bacterial communities of farmed and wild <i>R. dybowskii</i>, two experimental groups (farmed and wild) were investigated in this study. Following DNA extraction, the V3-V4 hypervariable region of the 16S rRNA gene was targeted and analyzed by high-throughput sequencing. The cutaneous bacterial community diversity was investigated and compared through analysis of alpha and beta diversity. A total of 524,852 valid sequences and 1,023 operational taxonomic units (OTUs) were obtained from these two experimental groups. The number of shared OTUs was 333, while there were 603 unique OTUs in the farmed group and 87 unique OTUs in the wild group. The Chao, ACE and Shannon indices of the farmed group were significantly higher than those of the wild group (<i>p</i> R. dybowskii exhibited significant differences. This study provides a theoretical basis for comprehensively understanding the composition and abundance of bacteria on the skin of farmed and wild <i>R. dybowskii</i>, which helps to develop its breeding industry and gain economic benefits.
DOI: 10.6084/m9.figshare.10248788
title: Phrase annotations from Phase synchronization varies systematically with linguistic structure composition

description: Computation in neuronal assemblies is putatively reflected in the excitatory and inhibitory cycles of activation distributed throughout the brain. In speech and language processing, coordination of these cycles resulting in phase synchronization has been argued to reflect the integration of information on different timescales (e.g. segmenting acoustics signals to phonemic and syllabic representations; (Giraud and Poeppel 2012 <i>Nat. Neurosci.</i> <b>15</b>, 511. (doi:10.1038/nn.3063)). A natural extension of this claim is that phase synchronization functions similarly to support the inference of more abstract higher-level linguistic structures (Martin 2016 <i>Front. Psychol.</i> <b>7</b>, 120; Martin and Doumas 2017 <i>PLoS Biol</i>. <b>15</b>, e2000663. (doi:10.1371/journal.pbio.2000663); Martin and Doumas. 2019 <i>Curr. Opin. Behav. Sci.</i> <b>29</b>, 77–83. (doi:10.1016/j.cobeha.2019.04.008)). Hale <i>et al</i>. (Hale <i>et al</i>. 2018 Finding syntax in human encephalography with beam search. (http://arxiv.org/abs/1806.04127) showed that syntactically driven parsing decisions predict EEG responses in the time domain; here we ask whether phase synchronization in the form of either inter-trial phrase coherence or cross-frequency coupling (CFC) between high-frequency (i.e. gamma) bursts and lower-frequency carrier signals (i.e. delta, theta), changes as the linguistic structures of compositional meaning (<i>viz</i>., bracket completions, as denoted by the onset of words that complete phrases) accrue. We use a naturalistic story-listening EEG dataset from Hale <i>et al</i>. to assess the relationship between linguistic structure and phase alignment. We observe increased phase synchronization as a function of phrase counts in the delta, theta, and gamma bands, especially for function words. A more complex pattern emerged for CFC as phrase count changed, possibly related to the lack of a one-to-one mapping between ‘size’ of linguistic structure and frequency band—an assumption that is tacit in recent frameworks. These results emphasize the important role that phase synchronization, desynchronization, and thus, inhibition, play in the construction of compositional meaning by distributed neural networks in the brain.This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
DOI: 10.6084/m9.figshare.10248788.v1
title: Phrase annotations from Phase synchronization varies systematically with linguistic structure composition

description: Computation in neuronal assemblies is putatively reflected in the excitatory and inhibitory cycles of activation distributed throughout the brain. In speech and language processing, coordination of these cycles resulting in phase synchronization has been argued to reflect the integration of information on different timescales (e.g. segmenting acoustics signals to phonemic and syllabic representations; (Giraud and Poeppel 2012 <i>Nat. Neurosci.</i> <b>15</b>, 511. (doi:10.1038/nn.3063)). A natural extension of this claim is that phase synchronization functions similarly to support the inference of more abstract higher-level linguistic structures (Martin 2016 <i>Front. Psychol.</i> <b>7</b>, 120; Martin and Doumas 2017 <i>PLoS Biol</i>. <b>15</b>, e2000663. (doi:10.1371/journal.pbio.2000663); Martin and Doumas. 2019 <i>Curr. Opin. Behav. Sci.</i> <b>29</b>, 77–83. (doi:10.1016/j.cobeha.2019.04.008)). Hale <i>et al</i>. (Hale <i>et al</i>. 2018 Finding syntax in human encephalography with beam search. (http://arxiv.org/abs/1806.04127) showed that syntactically driven parsing decisions predict EEG responses in the time domain; here we ask whether phase synchronization in the form of either inter-trial phrase coherence or cross-frequency coupling (CFC) between high-frequency (i.e. gamma) bursts and lower-frequency carrier signals (i.e. delta, theta), changes as the linguistic structures of compositional meaning (<i>viz</i>., bracket completions, as denoted by the onset of words that complete phrases) accrue. We use a naturalistic story-listening EEG dataset from Hale <i>et al</i>. to assess the relationship between linguistic structure and phase alignment. We observe increased phase synchronization as a function of phrase counts in the delta, theta, and gamma bands, especially for function words. A more complex pattern emerged for CFC as phrase count changed, possibly related to the lack of a one-to-one mapping between ‘size’ of linguistic structure and frequency band—an assumption that is tacit in recent frameworks. These results emphasize the important role that phase synchronization, desynchronization, and thus, inhibition, play in the construction of compositional meaning by distributed neural networks in the brain.This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
DOI: 10.6084/m9.figshare.10248779
title: Single-trial derived measures aligned with phrase annotations from Phase synchronization varies systematically with linguistic structure composition

description: Computation in neuronal assemblies is putatively reflected in the excitatory and inhibitory cycles of activation distributed throughout the brain. In speech and language processing, coordination of these cycles resulting in phase synchronization has been argued to reflect the integration of information on different timescales (e.g. segmenting acoustics signals to phonemic and syllabic representations; (Giraud and Poeppel 2012 <i>Nat. Neurosci.</i> <b>15</b>, 511. (doi:10.1038/nn.3063)). A natural extension of this claim is that phase synchronization functions similarly to support the inference of more abstract higher-level linguistic structures (Martin 2016 <i>Front. Psychol.</i> <b>7</b>, 120; Martin and Doumas 2017 <i>PLoS Biol</i>. <b>15</b>, e2000663. (doi:10.1371/journal.pbio.2000663); Martin and Doumas. 2019 <i>Curr. Opin. Behav. Sci.</i> <b>29</b>, 77–83. (doi:10.1016/j.cobeha.2019.04.008)). Hale <i>et al</i>. (Hale <i>et al</i>. 2018 Finding syntax in human encephalography with beam search. (http://arxiv.org/abs/1806.04127) showed that syntactically driven parsing decisions predict EEG responses in the time domain; here we ask whether phase synchronization in the form of either inter-trial phrase coherence or cross-frequency coupling (CFC) between high-frequency (i.e. gamma) bursts and lower-frequency carrier signals (i.e. delta, theta), changes as the linguistic structures of compositional meaning (<i>viz</i>., bracket completions, as denoted by the onset of words that complete phrases) accrue. We use a naturalistic story-listening EEG dataset from Hale <i>et al</i>. to assess the relationship between linguistic structure and phase alignment. We observe increased phase synchronization as a function of phrase counts in the delta, theta, and gamma bands, especially for function words. A more complex pattern emerged for CFC as phrase count changed, possibly related to the lack of a one-to-one mapping between ‘size’ of linguistic structure and frequency band—an assumption that is tacit in recent frameworks. These results emphasize the important role that phase synchronization, desynchronization, and thus, inhibition, play in the construction of compositional meaning by distributed neural networks in the brain.This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
DOI: 10.6084/m9.figshare.10248779.v1
title: Single-trial derived measures aligned with phrase annotations from Phase synchronization varies systematically with linguistic structure composition

description: Computation in neuronal assemblies is putatively reflected in the excitatory and inhibitory cycles of activation distributed throughout the brain. In speech and language processing, coordination of these cycles resulting in phase synchronization has been argued to reflect the integration of information on different timescales (e.g. segmenting acoustics signals to phonemic and syllabic representations; (Giraud and Poeppel 2012 <i>Nat. Neurosci.</i> <b>15</b>, 511. (doi:10.1038/nn.3063)). A natural extension of this claim is that phase synchronization functions similarly to support the inference of more abstract higher-level linguistic structures (Martin 2016 <i>Front. Psychol.</i> <b>7</b>, 120; Martin and Doumas 2017 <i>PLoS Biol</i>. <b>15</b>, e2000663. (doi:10.1371/journal.pbio.2000663); Martin and Doumas. 2019 <i>Curr. Opin. Behav. Sci.</i> <b>29</b>, 77–83. (doi:10.1016/j.cobeha.2019.04.008)). Hale <i>et al</i>. (Hale <i>et al</i>. 2018 Finding syntax in human encephalography with beam search. (http://arxiv.org/abs/1806.04127) showed that syntactically driven parsing decisions predict EEG responses in the time domain; here we ask whether phase synchronization in the form of either inter-trial phrase coherence or cross-frequency coupling (CFC) between high-frequency (i.e. gamma) bursts and lower-frequency carrier signals (i.e. delta, theta), changes as the linguistic structures of compositional meaning (<i>viz</i>., bracket completions, as denoted by the onset of words that complete phrases) accrue. We use a naturalistic story-listening EEG dataset from Hale <i>et al</i>. to assess the relationship between linguistic structure and phase alignment. We observe increased phase synchronization as a function of phrase counts in the delta, theta, and gamma bands, especially for function words. A more complex pattern emerged for CFC as phrase count changed, possibly related to the lack of a one-to-one mapping between ‘size’ of linguistic structure and frequency band—an assumption that is tacit in recent frameworks. These results emphasize the important role that phase synchronization, desynchronization, and thus, inhibition, play in the construction of compositional meaning by distributed neural networks in the brain.This article is part of the theme issue ‘Towards mechanistic models of meaning composition’.
DOI: 10.6084/m9.figshare.10248713
title: Dataset for PeerJ rhino monitoring paper

description: This dataset is a collection of variables, morphometrics, derived from rhino footprints using JMP software from SAS. The morphometrics are different combinations of lengths, angles and areas. Each row describes the variables from one footprint, and for each animal trail several footprints are collected to describe the characteristics that make the footprints from that animal unique
DOI: 10.6084/m9.figshare.10248572
title: Fig. S8E_DNA_BJ1_NPC.zip

description: 3D DNA-FISH microscopy images related to Fig. S8E (Number of associated file: 14)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248542
title: Fig. S8E_DNA_BJ1_ESC.zip

description: 3D DNA-FISH microscopy images related to Fig.S8E (Number of associated file: 19)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248572.v1
title: Fig. S8E_DNA_BJ1_NPC.zip

description: 3D DNA-FISH microscopy images related to Fig. S8E (Number of associated file: 14)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248530
title: Fig. S7B_RNA_JB1-delta site-c2-cl4_NPC.zip

description: RNA-FISH microscopy images related to Fig.S7B (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248506
title: Fig. S7A_BJ1-delta site-c2-cl1_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248512
title: Fig. S7A_BJ1-delta site-c2-cl28_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248518
title: Fig. S7B_RNA_JB1-WT_NPC.zip

description: RNA-FISH microscopy images related to Fig.S7B (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248530.v1
title: Fig. S7B_RNA_JB1-delta site-c2-cl4_NPC.zip

description: RNA-FISH microscopy images related to Fig.S7B (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248497
title: Fig. S7A_BJ1-WT_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248506.v1
title: Fig. S7A_BJ1-delta site-c2-cl1_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248518.v1
title: Fig. S7B_RNA_JB1-WT_NPC.zip

description: RNA-FISH microscopy images related to Fig.S7B (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248482
title: Fig. S7A_JB1-delta site-c2-cl4_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”<br>
DOI: 10.6084/m9.figshare.10248494
title: Fig. S7A_JB1-delta site-c2-cl15_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.10248482.v1
title: Fig. S7A_JB1-delta site-c2-cl4_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”<br>
DOI: 10.6084/m9.figshare.10248467
title: Fig. S7A_JB1-WT_NPC.zip

description: Immunofluorescence staining microscopy images related to Fig.S7A (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”<br>