cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6783479.v1
title: Compromised phagosome maturation underlies RPE pathology in cell culture and whole animal models of Smith-Lemli-Opitz Syndrome

description: Treatment of rats with the cholesterol pathway inhibitor AY9944 produces an animal model of Smith-Lemli-Opitz syndrome (SLOS), an autosomal recessive disease caused by defective cholesterol synthesis. This SLOS rat model undergoes progressive and irreversible degeneration of the neural retina, with associated pathological features of the retinal pigmented epithelium (RPE). Here, we provide further insights into the mechanism involved in the RPE pathology. In the SLOS rat model, markedly increased RPE apical autofluorescence is observed, compared to untreated animals, which correlates with increased levels of A2E and other bisretinoids. Utilizing cultured human induced pluripotent stem cell (iPSC)- derived SLOS RPE cells, we found significantly elevated steady-state levels of 7-dehydrocholesterol (7DHC) and decreased cholesterol levels (key biochemical hallmarks of SLOS). Western blot analysis revealed altered levels of the macroautophagy/autophagy markers MAP1LC3B-II and SQSTM1/p62, and build-up of ubiquitinated proteins. Accumulation of immature autophagosomes was accompanied by inefficient degradation of phagocytized, exogenously supplied retinal rod outer segments (as evidenced by persistence of the C-terminal 1D4 epitope of RHO [rhodopsin]) in SLOS RPE compared to iPSC-derived normal human control. SLOS RPE cells exhibited lysosomal pH levels and CTSD activity within normal physiological limits, thus discounting the involvement of perturbed lysosomal function. Furthermore, 1D4-positive phagosomes that accumulated in the RPE in both pharmacological and genetic rodent models of SLOS failed to fuse with lysosomes. Taken together, these observations suggest that defective phagosome maturation underlies the observed RPE pathology. The potential relevance of these findings to SLOS and the requirement of cholesterol for phagosome maturation are discussed.
DOI: 10.6084/m9.figshare.6771938
title: Data for: Homogenization of species composition and species association networks are decoupled

description: These data are used in Li et al. 2018 GEB. Rare species with &lt;6 observations have been removed. Row names are in the format of site_sampleEvent(whenAvailable)_quadrat.<br>Please cite: Li, D, T Poisot, DM Waller, B Baiser. In press. Homogenization of species composition and species association networks are decoupled. Global Ecology and Biogeography. https://doi.org/10.1111/geb.12825
DOI: 10.6084/m9.figshare.6771938.v1
title: Data for: Homogenization of species composition and species association networks are decoupled

description: These data are used in Li et al. 2018 GEB. Rare species with &lt;6 observations have been removed. Row names are in the format of site_sampleEvent(whenAvailable)_quadrat.<br>Please cite: Li, D, T Poisot, DM Waller, B Baiser. In press. Homogenization of species composition and species association networks are decoupled. Global Ecology and Biogeography.
DOI: 10.6084/m9.figshare.6771755
title: NMR Data from Urine Samples

description: NMR Data from Urine Samples
DOI: 10.6084/m9.figshare.6771758
title: NMR Data from Pancreas Tissues

description: NMR Data from Pancreas Tissues
DOI: 10.6084/m9.figshare.6771758.v1
title: NMR Data from Pancreas Tissues

description: NMR Data from Pancreas Tissues
DOI: 10.6084/m9.figshare.6771728
title: NMR Data from Fecal Samples

description: NMR Data from Fecal Samples
DOI: 10.6084/m9.figshare.6771755.v1
title: NMR Data from Urine Samples

description: NMR Data from Urine Samples
DOI: 10.6084/m9.figshare.6771692
title: NMR Data from Blood Samples

description: NMR Data from Blood Samples
DOI: 10.5517/ccdc.csd.cc20xxpk
title: CCDC 1874839: Experimental Crystal Structure Determination

description: Related Article: Qiong Wu, Yue Song, Ruotong Liu, Rui Wang, Wenjie Mei, Weiming Chen, Huanglan Yang, Xicheng Wang|2020|Bioorg.Chem.|102|104074|doi:10.1016/j.bioorg.2020.104074
DOI: 10.6084/m9.figshare.6771728.v1
title: NMR Data from Fecal Samples

description: NMR Data from Fecal Samples
DOI: 10.5517/ccdc.csd.cc21fwn1
title: CCDC 1890183: Experimental Crystal Structure Determination

description: Related Article: Jiadong Hu, Yu-Qi Gao, Dongyang Xu, Le Chen, Wen Wen, Yi Hou, Lu Chen, Weiqing Xie|2020|Chem.Commun.|56|10018|doi:10.1039/D0CC04424E
DOI: 10.5517/ccdc.csd.cc223k4x
title: CCDC 1910038: Experimental Crystal Structure Determination

description: Related Article: Qiong Wu, Yue Song, Ruotong Liu, Rui Wang, Wenjie Mei, Weiming Chen, Huanglan Yang, Xicheng Wang|2020|Bioorg.Chem.|102|104074|doi:10.1016/j.bioorg.2020.104074
DOI: 10.6084/m9.figshare.6771635
title: A mesopelagic ctenophore representing a new family, with notes on family-level taxonomy in Ctenophora: Vampyroctena delmarvensis gen. nov. sp. nov.

description: Data matrices, tree files, and assembled transcriptomes from Townsend et al. (2020)
DOI: 10.6084/m9.figshare.6771635.v1
title: A mesopelagic ctenophore representing a new family, with notes on family-level taxonomy in Ctenophora: Vampyroctena delmarvensis gen. nov. sp. nov.

description: Data matrices, tree files, and assembled transcriptomes from Townsend et al. (2020)
DOI: 10.5517/ccdc.csd.cc23pd3b
title: CCDC 1956971: Experimental Crystal Structure Determination

description: Related Article: Julien Braire, Vincent Dorcet, Joëlle Vidal, Claudia Lalli, François Carreaux|2020|Org.Biomol.Chem.|18|6042|doi:10.1039/D0OB01386B
DOI: 10.6084/m9.figshare.6768509
title: Distribution of Land Grants (30-year interval, 17th-18th c.)

description: The series of maps register the distribution of land grants in the town of Curitiba in the seventeenth and eighteenth centuries. Each frame shows the plots of land granted in a 30-year interval, advancing 10 years for the next frame. The set also contains an animation of the frames.
DOI: 10.5517/ccdc.csd.cc24kmkx
title: CCDC 1983149: Experimental Crystal Structure Determination

description: Related Article: Lu Yang, Lan Qin, Yong Dou, Daopeng Zhang, Zhen Zhou, Suna Wang|2020|CrystEngComm|22|5411|doi:10.1039/D0CE00678E
DOI: 10.6084/m9.figshare.6768506
title: Distribution of Land Grants (cumulative, 17th-18th c.)

description: The series of maps register the distribution of land grants in the town of Curitiba in the seventeenth and eighteenth centuries. Each frame shows the plots of land granted up to a certain decade. The set also contains an animation of the frames.<br>
DOI: 10.6084/m9.figshare.6768506.v1
title: Distribution of Land Grants (cumulative, 17th-18th c.)

description: The series of maps register the distribution of land grants in the town of Curitiba in the seventeenth and eighteenth centuries. Each frame shows the plots of land granted up to a certain decade. The set also contains an animation of the frames.<br>
DOI: 10.6084/m9.figshare.6768509.v1
title: Distribution of Land Grants (30-year interval, 17th-18th c.)

description: The series of maps register the distribution of land grants in the town of Curitiba in the seventeenth and eighteenth centuries. Each frame shows the plots of land granted in a 30-year interval, advancing 10 years for the next frame. The set also contains an animation of the frames.
DOI: 10.5517/ccdc.csd.cc24z68m
title: CCDC 1995230: Experimental Crystal Structure Determination

description: Related Article: Andrei Nesmelov, David Lee, Christopher Bejger, Margaret Kocherga, Zachary Lyles, Madeline K. Greenier, Ashley Ariel Vitallo, Ghallia Kaouk, Daniel S. Jones, Thomas A. Schmedake|2020|Chem.Commun.|56|9846|doi:10.1039/D0CC02767G
DOI: 10.5517/ccdc.csd.cc2525m2
title: CCDC 1998093: Experimental Crystal Structure Determination

description: Related Article: Luan F. Diniz, Paulo S. Carvalho Jr, Sarah A. C. Pena, José E. Gonçalves, Mateus A.C. Souza, José D. de Souza Filho, Lucius F. O. Bomfim Filho, Chris H.J. Franco, Renata Diniz, Christian Fernandes|2020|Int.J.Pharm.|587|119694|doi:10.1016/j.ijpharm.2020.119694
DOI: 10.6084/m9.figshare.6768494
title: Differentially expressed miRNAs in nephron progenitors

description: miRNAs with a miRDeep2 count of above 10 across all samples were analysed by DESeq2, and differentially expressed miRNAs were ranked according to padj.
DOI: 10.5517/ccdc.csd.cc2525p4
title: CCDC 1998095: Experimental Crystal Structure Determination

description: Related Article: Luan F. Diniz, Paulo S. Carvalho Jr, Sarah A. C. Pena, José E. Gonçalves, Mateus A.C. Souza, José D. de Souza Filho, Lucius F. O. Bomfim Filho, Chris H.J. Franco, Renata Diniz, Christian Fernandes|2020|Int.J.Pharm.|587|119694|doi:10.1016/j.ijpharm.2020.119694
DOI: 10.6084/m9.figshare.6768494.v1
title: Differentially expressed miRNAs in nephron progenitors

description: miRNAs with a miRDeep2 count of above 10 across all samples were analysed by DESeq2, and differentially expressed miRNAs were ranked according to padj.
DOI: 10.5517/ccdc.csd.cc253v9g
title: CCDC 1999695: Experimental Crystal Structure Determination

description: Related Article: Upasana Gulati, Srishti Rawat, Diwan S. Rawat|2020|Tetrahedron Lett.|61|152304|doi:10.1016/j.tetlet.2020.152304
DOI: 10.6084/m9.figshare.6768479
title: Analysis

description: Data sets for metabolomics paper
DOI: 10.5517/ccdc.csd.cc2574n7
title: CCDC 2002868: Experimental Crystal Structure Determination

description: Related Article: Jun-Cheng Jin, Ya-Jie Zhu, Jun Li, Ying-Lao Zhang, Cheng-Gen Xie|2020|Inorg.Chem.Commun.|119|108062|doi:10.1016/j.inoche.2020.108062
DOI: 10.6084/m9.figshare.6768449
title: Table1

description: Set of reactant pairs predicted by the method reaCTS. We are providing the concordant and discordant pairs, and the statistic confidence for each pair.
DOI: 10.6084/m9.figshare.6768449.v1
title: Table1

description: Set of reactant pairs predicted by the method reaCTS. We are providing the concordant and discordant pairs, and the statistic confidence for each pair.
DOI: 10.6084/m9.figshare.6768479.v1
title: Analysis

description: Data sets for metabolomics paper
DOI: 10.6084/m9.figshare.6768446
title: Comparison of Sightings of Indigenous Group and Expeditions of Portuguese Explorers (1500-1800)

description: The series of maps compares the data from the Curt Nimuendajú's "Mapa Etno-histórico" and Afonso Taunay's "Mapa das Bandeiras Paulistas," chronicling the contentious relationship between these groups.
DOI: 10.5517/ccdc.csd.cc25bd20
title: CCDC 2005981: Experimental Crystal Structure Determination

description: Related Article: Vivian Lioret, Yoann Rousselin, Richard A. Decréau|2020|Dyes Pigm.|183|108696|doi:10.1016/j.dyepig.2020.108696
DOI: 10.6084/m9.figshare.6768446.v1
title: Comparison of Sightings of Indigenous Group and Expeditions of Portuguese Explorers (1500-1800)

description: The series of maps compares the data from the Curt Nimuendajú's "Mapa Etno-histórico" and Afonso Taunay's "Mapa das Bandeiras Paulistas," chronicling the contentious relationship between these groups.
DOI: 10.25377/sussex.6757292
title: Dataset: jackknife maps for research paper: A comparative fMRI meta-analysis of altruistic and strategic decisions to give

description: Data for paper appearing in NeuroImage, published online September 2018 (abstract below). More data related to this publication is available in separate datasets in the same collection, DOIs:Thresholded maps: https://doi.org/10.25377/sussex.6756890Unthresholded maps: https://doi.org/10.25377/sussex.6756899Peaks: https://doi.org/10.25377/sussex.6756872<br>These maps show the number of repeats in a "jackknife" analysis that voxels remained significant in. A jackknife analysis runs a meta-analysis as many times as there are studies, leaving one study out each time. This gives a measure of reliability. For all maps, maximum replicability would show as a value of 12.<br>These maps are in .nii format so can be opened in many neuroimaging viewers. If you do not have a viewer installed, one free option is MRIcron which can be downloaded from www.nitrc.org/projects/mricron. They can also be viewed online through NeuroVault, see the third link in "references" below.<br><br>Links to the paper can be found in the references section below: 1) On NeuroImage 2) Open access version on the Social Decision Lab website.<br><b>Publication abstract:</b>The decision to share resources is fundamental for cohesive societies. Humans can be motivated to give for many reasons. Some generosity incurs a definite cost, with no extrinsic reward to the act, but instead provides intrinsic satisfaction (labelled here as ‘altruistic’ giving). Other giving behaviours are done with the prospect of improving one's own situation via reciprocity, reputation, or public good (labelled here as ‘strategic’ giving). These contexts differ in the source, certainty, and timing of rewards as well as the inferences made about others' mental states. We executed a combined statistical map and coordinate-based fMRI meta-analysis of decisions to give (36 studies, 1150 participants). Methods included a novel approach for accommodating variable signal dropout between studies in meta-analysis. Results reveal consistent, cross-paradigm neural correlates of each decision type, commonalities, and informative differences. Relative to being selfish, altruistic and strategic giving activate overlapping reward networks. However, strategic decisions showed greater activity in striatal regions than altruistic choices. Altruistic giving, more than strategic, activated subgenual anterior cingulate cortex (sgACC). Ventromedial prefrontal cortex (vmPFC) is consistently involved during generous decisions and processing across a posterior to anterior axis differentiates the altruistic/strategic context. Posterior vmPFC was preferentially recruited during altruistic decisions. Regions of the ‘social brain’ showed distinct patterns of activity between choice types, reflecting the different use of theory of mind in the two contexts. We provide the consistent neural correlates of decisions to give, and show that many will depend on the source of incentives.
DOI: 10.5517/ccdc.csd.cc25blns
title: CCDC 2006185: Experimental Crystal Structure Determination

description: Related Article: Euan N. Bassey, Joseph A. M. Paddison, Evan N. Keyzer, Jeongjae Lee, Pascal Manuel, Ivan da Silva, Siân E. Dutton, Clare P. Grey, Matthew J. Cliffe|2020|Inorg.Chem.|59|11627|doi:10.1021/acs.inorgchem.0c01478
DOI: 10.25377/sussex.6757292.v1
title: Dataset: jackknife maps for research paper: A comparative fMRI meta-analysis of altruistic and strategic decisions to give

description: Data for paper appearing in NeuroImage, published online September 2018 (abstract below). More data related to this publication is available in separate datasets in the same collection, DOIs:Thresholded maps: https://doi.org/10.25377/sussex.6756890Unthresholded maps: https://doi.org/10.25377/sussex.6756899Peaks: https://doi.org/10.25377/sussex.6756872<br>These maps show the number of repeats in a "jackknife" analysis that voxels remained significant in. A jackknife analysis runs a meta-analysis as many times as there are studies, leaving one study out each time. This gives a measure of reliability. For all maps, maximum replicability would show as a value of 12.<br>These maps are in .nii format so can be opened in many neuroimaging viewers. If you do not have a viewer installed, one free option is MRIcron which can be downloaded from www.nitrc.org/projects/mricron. They can also be viewed online through NeuroVault, see the third link in "references" below.<br><br>Links to the paper can be found in the references section below: 1) On NeuroImage 2) Open access version on the Social Decision Lab website.<br><b>Publication abstract:</b>The decision to share resources is fundamental for cohesive societies. Humans can be motivated to give for many reasons. Some generosity incurs a definite cost, with no extrinsic reward to the act, but instead provides intrinsic satisfaction (labelled here as ‘altruistic’ giving). Other giving behaviours are done with the prospect of improving one's own situation via reciprocity, reputation, or public good (labelled here as ‘strategic’ giving). These contexts differ in the source, certainty, and timing of rewards as well as the inferences made about others' mental states. We executed a combined statistical map and coordinate-based fMRI meta-analysis of decisions to give (36 studies, 1150 participants). Methods included a novel approach for accommodating variable signal dropout between studies in meta-analysis. Results reveal consistent, cross-paradigm neural correlates of each decision type, commonalities, and informative differences. Relative to being selfish, altruistic and strategic giving activate overlapping reward networks. However, strategic decisions showed greater activity in striatal regions than altruistic choices. Altruistic giving, more than strategic, activated subgenual anterior cingulate cortex (sgACC). Ventromedial prefrontal cortex (vmPFC) is consistently involved during generous decisions and processing across a posterior to anterior axis differentiates the altruistic/strategic context. Posterior vmPFC was preferentially recruited during altruistic decisions. Regions of the ‘social brain’ showed distinct patterns of activity between choice types, reflecting the different use of theory of mind in the two contexts. We provide the consistent neural correlates of decisions to give, and show that many will depend on the source of incentives.
DOI: 10.6084/m9.figshare.6756836
title: Tables from: "Natural selection on the Arabidopsis thaliana genome in present and future climates"

description: Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. Current assessments of the risks associated with climate change, however, do not typically take into account that natural selection can dramatically impact the genetic makeup of populations. We made use of extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection at the genetic level. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant proportion of this selection over variants could be predicted from the climate (mis)match between experimental sites and the geographic areas where variants are found (R2=29-52%). Field-validated predictions across the species range indicated that Mediterranean and Western Siberia populations — at the edges of the species' environmental limits — currently experience the strongest climate-driven selection, and Central Europeans the weakest. With rapidly increasing droughts and rising temperatures in Europe, we forecast a wave of directional selection moving North, putting many native A. thaliana populations at evolutionary risk.<br>
DOI: 10.6084/m9.figshare.6756845
title: penA sequences_Yahara2018MGenNgo

description: Amino acid sequences of the penA alleles in Figure 2, penA V variants in Figure 3, and the ESC-susceptible reference strain FA1090 are summarized as a supplementary fasta file
DOI: 10.6084/m9.figshare.6756845.v2
title: penA sequences_Yahara2018MGenNgo

description: Amino acid sequences of the penA alleles in Figure 2, penA V variants in Figure 3, and the ESC-susceptible reference strain FA1090 are summarized as a supplementary fasta file
DOI: 10.6084/m9.figshare.6756836.v1
title: Tables from: "A map of climate change-driven natural selection in Arabidopsis thaliana "

description: Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. Current assessments of the risks associated with climate change, however, do not typically take into account that natural selection can dramatically impact the genetic makeup of populations. We made use of extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection at the genetic level. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant proportion of this selection over variants could be predicted from the climate (mis)match between experimental sites and the geographic areas where variants are found (R2=29-52%). Field-validated predictions across the species range indicated that Mediterranean and Western Siberia populations — at the edges of the species' environmental limits — currently experience the strongest climate-driven selection, and Central Europeans the weakest. With rapidly increasing droughts and rising temperatures in Europe, we forecast a wave of directional selection moving North, putting many native A. thaliana populations at evolutionary risk.<br>
DOI: 10.6084/m9.figshare.6756845.v1
title: penA sequences

description: Amino acid sequences of the penA alleles in Figure 2, penA V variants in Figure 3, and the ESC-susceptible reference strain FA1090 are summarized as a supplementary fasta file
DOI: 10.6084/m9.figshare.6756731
title: nr blast results for assembly contigs not hitting ref

description: nr blast results for assembly contigs not hitting ref
DOI: 10.6084/m9.figshare.6756797
title: mt assembly

description: mt assembly
DOI: 10.6084/m9.figshare.6756731.v1
title: nr blast results for assembly contigs not hitting ref

description: nr blast results for assembly contigs not hitting ref
DOI: 10.6084/m9.figshare.6756797.v1
title: mt assembly

description: mt assembly
DOI: 10.6084/m9.figshare.6756728
title: Transcriptomic characterization of the human habenula highlights drug metabolism and the neuroimmune system

description: Supplement data and tables for "Transcriptomic characterization of the human habenula highlights drug metabolism and the neuroimmune system" by Dr. Bernard Le Foll and Leon French.<br>Supplement tables:1 - Genome-wide probe-level results for the lateral habenula2 - Genome-wide probe-level results for the medial habenula3 - Estimated relative cell-type proportions4 - Complete gene ontology results for the lateral habenula5 - Complete gene ontology results for the medial habenula6 - Complete DisGeNet results for the lateral habenula7 - Complete DisGeNet results for the medial habenula
DOI: 10.6084/m9.figshare.6756725
title: kh 128

description: kh 128<br>
DOI: 10.6084/m9.figshare.6756635
title: Matlab code to produce the figures from Three-dimensional time-domain scattering of waves in the marginal ice zone

description: Three-dimensional scattering of ocean surface waves in the marginal ice zone (MIZ) is determined in the time-domain. The solution is found using spectral analysis of the linear operator for the Boltzmann equation. The method to calculate the scattering kernel that arises in the Boltzmann model from the single floe solution is also presented along with new identities for the far-field scattering, which can be used to validate the single floe solution. The spectrum of the operator is computed, and it is shown to have a universal structure under a special non-dimensionalization. This universal structure implies that under a scaling wave scattering in the MIZ has similar properties for a large range of ice types and wave periods. A scattering theory solution using fast Fourier transforms is given to find the solution for directional incident wave packets. A numerical solution method is also given using the split-step method and this is used to validate the spectral solution. Numerical calculations of the evolution of a typical wave field are presented.This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
DOI: 10.6084/m9.figshare.6756725.v1
title: kh 128

description: kh 128<br>