cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20407609
title: Supplementary Data 4.xlsx from A genetic model for <i>in vivo</i> proximity labelling of the mammalian secretome

description: Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a <i>BirA*G3</i> mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labelling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and healthy and diseased adult states.
DOI: 10.6084/m9.figshare.20407609.v1
title: Supplementary Data 4.xlsx from A genetic model for <i>in vivo</i> proximity labelling of the mammalian secretome

description: Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a <i>BirA*G3</i> mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labelling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and healthy and diseased adult states.
DOI: 10.6084/m9.figshare.20407612
title: Supplementary Data 2.xlsx from A genetic model for <i>in vivo</i> proximity labelling of the mammalian secretome

description: Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a <i>BirA*G3</i> mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labelling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and healthy and diseased adult states.
DOI: 10.6084/m9.figshare.20407612.v1
title: Supplementary Data 2.xlsx from A genetic model for <i>in vivo</i> proximity labelling of the mammalian secretome

description: Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a <i>BirA*G3</i> mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labelling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and healthy and diseased adult states.
DOI: 10.6084/m9.figshare.20407572
title: Capital_Invet_CHN_datasbase

description: This dataset records capital investment (based on the newly increased fixed assets from National Statistics Bureau of China) for 31 provinces in China, during the period of 1995-2017. The capital investment are disaggregated into three types of assets, i.e., equipment, residential structures, and non-residential structures, according to WORLDKLEMS. Detailed procedures to create the datase have been documented in:<em>Ye, Q., Krol, M.S., Shan, Y.*, Schyns, J.F., Berger, M. and Hubacek, K.* Allocating capital-associated CO2 emissions along full lifespan of capital investments helps re-assessing emission responsibilities. (in submission)</em> You are more than welcome to contact the authors if you meet any problems or have any questions regarding the dataset.
DOI: 10.6084/m9.figshare.20407596
title: MCE-Octocoral-microalgae

description: setting up Github project "<strong>MCE-Octocoral-microalgae"</strong>
DOI: 10.6084/m9.figshare.20407623
title: supplementary materials.zip from Extending Goldberg’s method to parameterize and control the geometry of Goldberg polyhedra

description: Goldberg polyhedra have been widely studied across multiple fields, as their distinctive pattern can lead to many useful applications. Their topology can be determined using Goldberg’s method through generating topologically equivalent structures, named cages. However, the geometry of Goldberg polyhedra remains underexplored. This study extends Goldberg’s framework to a new method that can systematically determine the topology and effectively control the geometry of Goldberg polyhedra based on the initial shapes of cages. In detail, we first parameterize the cage’s geometry under specified topology and polyhedral symmetry; then, we manipulate the predefined independent variables through optimization to achieve the user-defined geometric properties. The benchmark problem of finding equilateral Goldberg polyhedra is solved to demonstrate the effectiveness of the proposed method. Using this method, we have successfully achieved nearly exact spherical Goldberg polyhedra, with all vertices on a sphere and all faces being planar under extremely low numerical errors. Such results serve as strong numerical evidence for the existence of this new type of Goldberg polyhedra. Furthermore, we iteratively perform <i>k</i>-means clustering and optimization to significantly reduce the number of different edge lengths to benefit the cost reduction for architectural and engineering applications.
DOI: 10.6084/m9.figshare.20407623.v1
title: supplementary materials.zip from Extending Goldberg’s method to parameterize and control the geometry of Goldberg polyhedra

description: Goldberg polyhedra have been widely studied across multiple fields, as their distinctive pattern can lead to many useful applications. Their topology can be determined using Goldberg’s method through generating topologically equivalent structures, named cages. However, the geometry of Goldberg polyhedra remains underexplored. This study extends Goldberg’s framework to a new method that can systematically determine the topology and effectively control the geometry of Goldberg polyhedra based on the initial shapes of cages. In detail, we first parameterize the cage’s geometry under specified topology and polyhedral symmetry; then, we manipulate the predefined independent variables through optimization to achieve the user-defined geometric properties. The benchmark problem of finding equilateral Goldberg polyhedra is solved to demonstrate the effectiveness of the proposed method. Using this method, we have successfully achieved nearly exact spherical Goldberg polyhedra, with all vertices on a sphere and all faces being planar under extremely low numerical errors. Such results serve as strong numerical evidence for the existence of this new type of Goldberg polyhedra. Furthermore, we iteratively perform <i>k</i>-means clustering and optimization to significantly reduce the number of different edge lengths to benefit the cost reduction for architectural and engineering applications.
DOI: 10.6084/m9.figshare.20407629
title: Supplemental.Rmd from Artificial light impacts the mate success of female fireflies

description: Statistical analyses of mate success and movement data; R notebook
DOI: 10.6084/m9.figshare.20407629.v1
title: Supplemental.Rmd from Artificial light impacts the mate success of female fireflies

description: Statistical analyses of mate success and movement data; R notebook
DOI: 10.6084/m9.figshare.20407632
title: P_obscurellus.xlsx from Artificial light impacts the mate success of female fireflies

description: P. obscurellus mate success data from laboratory and field studies
DOI: 10.6084/m9.figshare.20407632.v1
title: P_obscurellus.xlsx from Artificial light impacts the mate success of female fireflies

description: P. obscurellus mate success data from laboratory and field studies
DOI: 10.6084/m9.figshare.20407635
title: movement.xlsx from Artificial light impacts the mate success of female fireflies

description: P. pyralis and P. marginellus mark-recapture data from field
DOI: 10.6084/m9.figshare.20407635.v1
title: movement.xlsx from Artificial light impacts the mate success of female fireflies

description: P. pyralis and P. marginellus mark-recapture data from field
DOI: 10.6084/m9.figshare.20407638.v1
title: P_greeni.csv from Artificial light impacts the mate success of female fireflies

description: P. greeni binary choice data from field
DOI: 10.6084/m9.figshare.20407641.v1
title: Supplemental.docx from Artificial light impacts the mate success of female fireflies

description: Supplemental figures and text
DOI: 10.6084/m9.figshare.20407638
title: P_greeni.csv from Artificial light impacts the mate success of female fireflies

description: P. greeni binary choice data from field
DOI: 10.6084/m9.figshare.20407641
title: Supplemental.docx from Artificial light impacts the mate success of female fireflies

description: Supplemental figures and text
DOI: 10.6084/m9.figshare.19165280.v4
title: mb.final.repeat-sort-mask.fa

description: mb-genome
DOI: 10.14469/hpc/10757
title: bis methylene atrop, saddle=1, G = 918.566079

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10758
title: bis methylene atrop, saddle=2 IRC, D2h symmetry

description: Gaussian 16 (C01) calculation
DOI: 10.14469/hpc/10759
title: bis methylene atrop, saddle=2 OH, G = -918.563390

description: Gaussian 16 (C01) calculation
DOI: 10.6084/m9.figshare.20407686
title: Data from Humpback whale song revolutions continue to spread from the central into the eastern South Pacific

description: Raw song transcripts supporting this article.
DOI: 10.6084/m9.figshare.20338089.v1
title: allen_brain.h5ad

description: Anndata format of the adult mouse brain atlas generated by reasearchers the Allen institute (Tasic et al.), together with inferred cell type colocalization information, as described in Dimitrov et al, 2022. <br> <br> Tasic, B. et al. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat. Neurosci. 19, 335–346 (2016). <br> Dimitrov, D., Türei, D., Garrido-Rodriguez, M., Burmedi, P.L., Nagai, J.S., Boys, C., Ramirez Flores, R.O., Kim, H., Szalai, B., Costa, I.G. and Valdeolivas, A., 2022. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. <em>Nature Communications</em>, <em>13</em>(1), pp.1-13.
DOI: 10.6084/m9.figshare.20407707.v1
title: Supporting Data and Code from Spatial selectivity in adaptation to gaze direction

description: A person's focus of attention is conveyed by the direction of their eyes and face, providing a simple visual cue fundamental to social interaction. A growing body of research examines the visual mechanisms that encode the direction of another person's gaze as we observe them. Here we investigate the <i>spatial receptive field properties</i> of these mechanisms, by testing the spatial selectivity of sensory adaptation to gaze direction. Human observers were adapted to faces with averted gaze presented in one visual hemifield, then tested in their perception of gaze direction for faces presented in the same or opposite hemifield. Adaptation caused strong, repulsive perceptual aftereffects, but only for faces presented in the same hemifield as the adapter. This occurred even though adapting and test stimuli were in the same external location across saccades. Hence, there was clear evidence for <i>retinotopic</i> adaptation and a relative lack of either <i>spatiotopic</i> or <i>spatially invariant</i> adaptation. These results indicate that adaptable representations of gaze direction in the human visual system have retinotopic spatial receptive fields. This strategy of coding others' direction of gaze with positional specificity relative to one's own eye position may facilitate key functions of gaze perception, such as socially cued shifts in visual attention.
DOI: 10.6084/m9.figshare.20407707
title: Supporting Data and Code from Spatial selectivity in adaptation to gaze direction

description: A person's focus of attention is conveyed by the direction of their eyes and face, providing a simple visual cue fundamental to social interaction. A growing body of research examines the visual mechanisms that encode the direction of another person's gaze as we observe them. Here we investigate the <i>spatial receptive field properties</i> of these mechanisms, by testing the spatial selectivity of sensory adaptation to gaze direction. Human observers were adapted to faces with averted gaze presented in one visual hemifield, then tested in their perception of gaze direction for faces presented in the same or opposite hemifield. Adaptation caused strong, repulsive perceptual aftereffects, but only for faces presented in the same hemifield as the adapter. This occurred even though adapting and test stimuli were in the same external location across saccades. Hence, there was clear evidence for <i>retinotopic</i> adaptation and a relative lack of either <i>spatiotopic</i> or <i>spatially invariant</i> adaptation. These results indicate that adaptable representations of gaze direction in the human visual system have retinotopic spatial receptive fields. This strategy of coding others' direction of gaze with positional specificity relative to one's own eye position may facilitate key functions of gaze perception, such as socially cued shifts in visual attention.
DOI: 10.5281/zenodo.6945311
title: Deleted Upload

description: Deleted upload.
DOI: 10.5281/zenodo.6605376
title: Deleted Upload

description: Deleted upload.
DOI: 10.6084/m9.figshare.20338536.v1
title: TNBC Data from Wu et al, 2021

description: Anndata format of the TNBC data set generated by Wu et al, 2021, together with inferred cytokine activity, as described in Dimitrov et al, 2022.<br> <br> <br> Wu, S.Z., Al-Eryani, G., Roden, D.L., Junankar, S., Harvey, K., Andersson, A., Thennavan, A., Wang, C., Torpy, J.R., Bartonicek, N. and Wang, T., 2021. A single-cell and spatially resolved atlas of human breast cancers. <em>Nature genetics</em>, <em>53</em>(9), pp.1334-1347.<br> <br> Dimitrov, D., Türei, D., Garrido-Rodriguez, M., Burmedi, P.L., Nagai, J.S., Boys, C., Ramirez Flores, R.O., Kim, H., Szalai, B., Costa, I.G. and Valdeolivas, A., 2022. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. <em>Nature Communications</em>, <em>13</em>(1), pp.1-13.
DOI: 10.6084/m9.figshare.20407647.v1
title: Effect of feed enriched by products formulated from coconut water, palm sap sugar, and mushroom on the chemical composition of feed and carcass, growth performance, body indices, and gut micromorphology of giant gourami, Osphronemus goramy (Lacepède, 1801), juveniles

description: <strong>Background:</strong> Giant gourami (Osphronemus goramy Lacepede, 1801) is a freshwater species of Indonesia's most important commercial fish, and most of the giant gourami is produced by aquaculture. The first purpose of this investigation is to determine the effect of various newly formulated products on the amino acid composition of the diet and whole-body carcass. The second aim is to analysed the impact of newly formulated products on the growth performance, body indices, and gut micromorphology. <strong>Methods:</strong> A total of 1.0 litres of palm sap sugar solution and 2.0 litres of mature coconut water were formulated. Each 1.0-litre product formulated was added to 2 g of Aspergillus niger (labeled CP2), 2 g of Rhizopus oligosporus (labeled CP3), and 2 g of Saccharomyces cerevisiae (labeled CP4). Commercial aquafeed to which freshwater was added was labeled CP1 (placebo). Aquafeed was added to CP1 and supplemented with CP2, CP3, and CP4 (labeled KP1, KP2, KP3, and KP4 diets). Their dosage was 150 ml/kg of feed. Juvenile giant gourami (initial weight 50 ± 0.25 g and length 13.2 ± 0.07 cm) were reared in triplicate net frames (2 m × 1 m × 1 m; water volume 1.5 m3/frame nets) in a freshwater concrete pond. The juveniles were randomly distributed at a stocking density of 30 juveniles/net. <strong>Results:</strong> Results support our hypothesis that different product formulations have a significant effect (P &lt; 0.05) on aquafeed nutrition and the whole-body carcass, growth indices, fish feed efficiency, and gut micromorphology of giant gourami juveniles. The KP3 diet contains a higher concentration of amino acids, which increased the growth rate, feed efficiency, and carcass quality more than the other diets that we tested. <strong>Conclusion:</strong> Diet KP3 contains higher total amino acids in diets and carcasses and gives the better growth of giant gourami.
DOI: 10.6084/m9.figshare.20407728
title: Tests for expression changes in key candidate genes from Ageing desexualizes the <i>Drosophila</i> brain transcriptome

description: Here we report of changes in gene expression of genes in the sex determination and nutrient sensing pathway.
DOI: 10.6084/m9.figshare.20407728.v1
title: Tests for expression changes in key candidate genes from Ageing desexualizes the <i>Drosophila</i> brain transcriptome

description: Here we report of changes in gene expression of genes in the sex determination and nutrient sensing pathway.
DOI: 10.6084/m9.figshare.20407764
title: html files (2 files) from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: codes for the sequence analyses performed in R
DOI: 10.6084/m9.figshare.20407767
title: SM1_H1-MYF5.fasta from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: Sequence alignment for H1-Myf5
DOI: 10.6084/m9.figshare.20407767.v1
title: SM1_H1-MYF5.fasta from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: Sequence alignment for H1-Myf5
DOI: 10.6084/m9.figshare.20407770.v1
title: SM3_HOX10.fasta from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: Sequence alignment for Hox10
DOI: 10.6084/m9.figshare.20407773
title: html files (2 files) from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: codes for the sequence analyses performed in R
DOI: 10.6084/m9.figshare.20407773.v1
title: html files (2 files) from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: codes for the sequence analyses performed in R
DOI: 10.6084/m9.figshare.20407770
title: SM3_HOX10.fasta from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: Sequence alignment for Hox10
DOI: 10.6084/m9.figshare.20407776
title: SM2_table.xlsx from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: information for sequences downloaded from public repositories
DOI: 10.6084/m9.figshare.20407779.v1
title: SM4_HOXA10_DNA.fasta from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: Sequence alignment for HoxA10
DOI: 10.6084/m9.figshare.20407776.v1
title: SM2_table.xlsx from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: information for sequences downloaded from public repositories
DOI: 10.6084/m9.figshare.20407779
title: SM4_HOXA10_DNA.fasta from What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda

description: Sequence alignment for HoxA10
DOI: 10.6084/m9.figshare.20338089.v2
title: allen_brain.h5ad

description: Anndata format of the adult mouse brain atlas generated by reasearchers the Allen institute (Tasic et al.), together with inferred cell type colocalization information, as described in Dimitrov et al, 2022. <br> <br> Tasic, B. et al. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat. Neurosci. 19, 335–346 (2016). <br> Dimitrov, D., Türei, D., Garrido-Rodriguez, M., Burmedi, P.L., Nagai, J.S., Boys, C., Ramirez Flores, R.O., Kim, H., Szalai, B., Costa, I.G. and Valdeolivas, A., 2022. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. <em>Nature Communications</em>, <em>13</em>(1), pp.1-13.
DOI: 10.34740/kaggle/dsv/4010343
title: YouTube Daily