cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5325541
title: Antarctic Seasonal Spatial Pressure Reconstructions, 1905-2013

description: .zip files of the spatial pressure reconstructions. These cover the domain of 60-90S, seasonally. Two datasets are available: those based on the original station reconstructions, and those based on the pseudo station reconstructions. The data are on a 80km x 80km Cartesian grid, centered over the South Pole.The creators of the dataset suggest:1) Using the original spatial reconstruction for DJF, and the pseudo spatial reconstructions for other seasons.2) Caution interpreting variability and change away from the continent in the dataset, especially around 60S in all seasons, and in the Amundsen and Bellingshausen Seas in seasons outside of austral summer.<br>In addition, we have uploaded a .nc file (wrf_latlon_80km.nc) that contains the latitude / longitude information that will be needed to reference the mapping needed for plotting and analyzing the reconstructions in such software as NCL.
DOI: 10.6084/m9.figshare.5325574.v1
title: Supplementary_DarwinCore

description: This file includes the meta data of the specimens from Supplementary file 1, using the template provided by GBIF for upload using the Integrated Publishing Toolkit (https://www.gbif.org/news/82852/new-darwin-core-spreadsheet-templates-simplify-data-preparation-and-publishing).
DOI: 10.6084/m9.figshare.5325370
title: Protease dead separase inhibits chromosome segregation and RAB-11 vesicle trafficking

description: Separase cleaves cohesin to allow chromosome segregation. Separase also regulates cortical granule exocytosis and vesicle trafficking during cytokinesis, both of which involve RAB-11. We investigated whether separase regulates exocytosis through a proteolytic or non-proteolytic mechanism. In <i>C. elegans</i>, protease-dead separase (SEP-1<sup>PD</sup>::GFP) is dominant negative. Consistent with its role in cohesin cleavage, SEP-1<sup>PD</sup>::GFP causes chromosome segregation defects. As expected, partial depletion of cohesin rescues this defect, confirming that SEP-1<sup>PD</sup>::GFP acts through a substrate trapping mechanism. SEP-1<sup>PD</sup>::GFP causes cytokinetic defects that are synergistically exacerbated by depletion of the t-SNARE SYX-4. Furthermore, SEP-1<sup>PD</sup>::GFP delays furrow ingression, causes an accumulation of RAB-11 vesicles at the cleavage furrow site and delays the exocytosis of cortical granules during anaphase I. Depletion of <i>syx-4</i> further enhanced RAB-11::mCherry and SEP-1<sup>PD</sup>::GFP plasma membrane accumulation during cytokinesis, while depletion of cohesin had no effect. In contrast, centriole disengagement appears normal in SEP-1<sup>PD</sup>::GFP embryos, indicating that chromosome segregation and vesicle trafficking are more sensitive to inhibition by the inactive protease. These findings suggest that separase cleaves an unknown substrate to promote the exocytosis of RAB-11 vesicles and paves the way for biochemical identification of substrates.
DOI: 10.6084/m9.figshare.5325541.v1
title: Antarctic Seasonal Spatial Reconstructions, 1905-2013

description: .zip files of the spatial pressure reconstructions. These cover the domain of 60-90S, seasonally. Two datasets are available: those based on the original station reconstructions, and those based on the pseudo station reconstructions.The creators of the dataset suggest:1) Using the original spatial reconstruction for DJF, and the pseudo spatial reconstructions for other seasons.2) Caution interpreting variability and change away from the continent in the dataset, especially around 60S in all seasons, and in the Amundsen and Bellingshausen Seas in seasons outside of austral summer.
DOI: 10.6084/m9.figshare.5325367.v2
title: Bayesian Approximate Kernel Regression With Variable Selection

description: Nonlinear kernel regression models are often used in statistics and machine learning because they are more accurate than linear models. Variable selection for kernel regression models is a challenge partly because, unlike the linear regression setting, there is no clear concept of an effect size for regression coefficients. In this article, we propose a novel framework that provides an effect size analog for each explanatory variable in Bayesian kernel regression models when the kernel is shift-invariant—for example, the Gaussian kernel. We use function analytic properties of shift-invariant reproducing kernel Hilbert spaces (RKHS) to define a linear vector space that: (i) captures nonlinear structure, and (ii) can be projected onto the original explanatory variables. This projection onto the original explanatory variables serves as an analog of effect sizes. The specific function analytic property we use is that shift-invariant kernel functions can be approximated via random Fourier bases. Based on the random Fourier expansion, we propose a computationally efficient class of Bayesian approximate kernel regression (BAKR) models for both nonlinear regression and binary classification for which one can compute an analog of effect sizes. We illustrate the utility of BAKR by examining two important problems in statistical genetics: genomic selection (i.e., phenotypic prediction) and association mapping (i.e., inference of significant variants or loci). State-of-the-art methods for genomic selection and association mapping are based on kernel regression and linear models, respectively. BAKR is the first method that is competitive in both settings. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5325370.v1
title: Protease Dead Separase Inhibits Chromosome Segregation and RAB-11 Vesicle Trafficking

description: Separase cleaves cohesin to allow chromosome segregation. Separase also regulates cortical granule exocytosis and vesicle trafficking during cytokinesis, both of which involve RAB-11. We investigated whether separase regulates exocytosis through a proteolytic or non-proteolytic mechanism. In <i>C. elegans</i>, protease-dead separase (SEP-1<sup>PD</sup>::GFP) is dominant negative. Consistent with its role in cohesin cleavage, SEP-1<sup>PD</sup>::GFP causes chromosome segregation defects. As expected, partial depletion of cohesin rescues this defect, confirming that SEP-1<sup>PD</sup>::GFP acts through a substrate trapping mechanism. SEP-1<sup>PD</sup>::GFP causes cytokinetic defects that is synergistically exacerbated by depletion of the t-SNARE SYX-4. Furthermore, SEP-1<sup>PD</sup>::GFP delays furrow ingression, causes an accumulation of RAB-11 vesicles at the cleavage furrow site and delays the exocytosis of cortical granules during anaphase I. Depletion of <i>syx-4</i> further enhanced RAB-11::mCherry and SEP-1<sup>PD</sup>::GFP plasma membrane accumulation during cytokinesis, while depletion of cohesin had no effect. In contrast, centriole disengagement appears normal in SEP-1<sup>PD</sup>::GFP embryos, indicating that chromosome segregation and vesicle trafficking are more sensitive to inhibition by the inactive protease. These findings suggest that separase cleaves an unknown substrate to promote the exocytosis of RAB-11 vesicles and paves the way for biochemical identification of substrates.
DOI: 10.6084/m9.figshare.5325367.v1
title: Bayesian Approximate Kernel Regression with Variable Selection

description: Nonlinear kernel regression models are often used in statistics and machine learning because they are more accurate than linear models. Variable selection for kernel regression models is a challenge partly because, unlike the linear regression setting, there is no clear concept of an effect size for regression coefficients. In this paper, we propose a novel framework that provides an effect size analog for each explanatory variable in Bayesian kernel regression models when the kernel is shift-invariant — for example, the Gaussian kernel. We use function analytic properties of shift-invariant reproducing kernel Hilbert spaces (RKHS) to define a linear vector space that: (i) captures nonlinear structure, and (ii) can be projected onto the original explanatory variables. This projection onto the original explanatory variables serves as an analog of effect sizes. The specific function analytic property we use is that shift-invariant kernel functions can be approximated via random Fourier bases. Based on the random Fourier expansion, we propose a computationally efficient class of Bayesian approximate kernel regression (BAKR) models for both nonlinear regression and binary classification for which one can compute an analog of effect sizes. We illustrate the utility of BAKR by examining two important problems in statistical genetics: genomic selection (i.e. phenotypic prediction) and association mapping (i.e. inference of significant variants or loci). State-of-the-art methods for genomic selection and association mapping are based on kernel regression and linear models, respectively. BAKR is the first method that is competitive in both settings.
DOI: 10.6084/m9.figshare.5325541.v2
title: Antarctic Seasonal Spatial Pressure Reconstructions, 1905-2013

description: .zip files of the spatial pressure reconstructions. These cover the domain of 60-90S, seasonally. Two datasets are available: those based on the original station reconstructions, and those based on the pseudo station reconstructions.The creators of the dataset suggest:1) Using the original spatial reconstruction for DJF, and the pseudo spatial reconstructions for other seasons.2) Caution interpreting variability and change away from the continent in the dataset, especially around 60S in all seasons, and in the Amundsen and Bellingshausen Seas in seasons outside of austral summer.
DOI: 10.6084/m9.figshare.5325370.v3
title: Protease dead separase inhibits chromosome segregation and RAB-11 vesicle trafficking

description: Separase cleaves cohesin to allow chromosome segregation. Separase also regulates cortical granule exocytosis and vesicle trafficking during cytokinesis, both of which involve RAB-11. We investigated whether separase regulates exocytosis through a proteolytic or non-proteolytic mechanism. In <i>C. elegans</i>, protease-dead separase (SEP-1<sup>PD</sup>::GFP) is dominant negative. Consistent with its role in cohesin cleavage, SEP-1<sup>PD</sup>::GFP causes chromosome segregation defects. As expected, partial depletion of cohesin rescues this defect, confirming that SEP-1<sup>PD</sup>::GFP acts through a substrate trapping mechanism. SEP-1<sup>PD</sup>::GFP causes cytokinetic defects that are synergistically exacerbated by depletion of the t-SNARE SYX-4. Furthermore, SEP-1<sup>PD</sup>::GFP delays furrow ingression, causes an accumulation of RAB-11 vesicles at the cleavage furrow site and delays the exocytosis of cortical granules during anaphase I. Depletion of <i>syx-4</i> further enhanced RAB-11::mCherry and SEP-1<sup>PD</sup>::GFP plasma membrane accumulation during cytokinesis, while depletion of cohesin had no effect. In contrast, centriole disengagement appears normal in SEP-1<sup>PD</sup>::GFP embryos, indicating that chromosome segregation and vesicle trafficking are more sensitive to inhibition by the inactive protease. These findings suggest that separase cleaves an unknown substrate to promote the exocytosis of RAB-11 vesicles and paves the way for biochemical identification of substrates.
DOI: 10.6084/m9.figshare.5325370.v2
title: Protease dead separase inhibits chromosome segregation and RAB-11 vesicle trafficking

description: Separase cleaves cohesin to allow chromosome segregation. Separase also regulates cortical granule exocytosis and vesicle trafficking during cytokinesis, both of which involve RAB-11. We investigated whether separase regulates exocytosis through a proteolytic or non-proteolytic mechanism. In <i>C. elegans</i>, protease-dead separase (SEP-1<sup>PD</sup>::GFP) is dominant negative. Consistent with its role in cohesin cleavage, SEP-1<sup>PD</sup>::GFP causes chromosome segregation defects. As expected, partial depletion of cohesin rescues this defect, confirming that SEP-1<sup>PD</sup>::GFP acts through a substrate trapping mechanism. SEP-1<sup>PD</sup>::GFP causes cytokinetic defects that are synergistically exacerbated by depletion of the t-SNARE SYX-4. Furthermore, SEP-1<sup>PD</sup>::GFP delays furrow ingression, causes an accumulation of RAB-11 vesicles at the cleavage furrow site and delays the exocytosis of cortical granules during anaphase I. Depletion of <i>syx-4</i> further enhanced RAB-11::mCherry and SEP-1<sup>PD</sup>::GFP plasma membrane accumulation during cytokinesis, while depletion of cohesin had no effect. In contrast, centriole disengagement appears normal in SEP-1<sup>PD</sup>::GFP embryos, indicating that chromosome segregation and vesicle trafficking are more sensitive to inhibition by the inactive protease. These findings suggest that separase cleaves an unknown substrate to promote the exocytosis of RAB-11 vesicles and paves the way for biochemical identification of substrates.
DOI: 10.6084/m9.figshare.5325361
title: N-3 PUFAs induce inflammatory tolerance by formation of KEAP1-containing SQSTM1/p62-bodies and activation of NFE2L2

description: Inflammation is crucial in the defense against infections but must be tightly controlled to limit detrimental hyperactivation. Our diet influences inflammatory processes and omega-3 polyunsaturated fatty acids (n-3 PUFAs) have known anti-inflammatory effects. The balance of pro- and anti-inflammatory processes is coordinated by macrophages and macroautophagy/autophagy has recently emerged as a cellular process that dampens inflammation. Here we report that the n-3 PUFA docosahexaenoic acid (DHA) transiently induces cytosolic speckles of the autophagic receptor SQSTM1/p62 (sequestosome 1) (described as SQSTM1/p62-bodies) in macrophages. We suggest that the formation of SQSTM1/p62-bodies represents a fast mechanism of NFE2L2/Nrf2 (nuclear factor, erythroid 2 like 2) activation by recruitment of KEAP1 (kelch like ECH associated protein 1). Further, the autophagy receptor TAX1BP1 (Tax1 binding protein 1) and ubiquitin-editing enzyme TNFAIP3/A20 (TNF α induced protein 3) could be identified in DHA-induced SQSTM1/p62-bodies. Simultaneously, DHA strongly dampened the induction of pro-inflammatory genes including <i>CXCL10</i> (C-X-C motif chemokine ligand 10) and we suggest that formation of SQSTM1/p62-bodies and activation of NFE2L2 leads to tolerance towards selective inflammatory stimuli. Finally, reduced CXCL10 levels were related to the improved clinical outcome in n-3 PUFA-supplemented heart-transplant patients and we propose CXCL10 as a robust marker for the clinical benefits mobilized by n-3 PUFA supplementation.
DOI: 10.6084/m9.figshare.5325361.v1
title: N-3 PUFAs induce inflammatory tolerance by formation of KEAP1-containing SQSTM1/p62-bodies and activation of NFE2L2

description: Inflammation is crucial in the defense against infections but must be tightly controlled to limit detrimental hyperactivation. Our diet influences inflammatory processes and omega-3 polyunsaturated fatty acids (n-3 PUFAs) have known anti-inflammatory effects. The balance of pro- and anti-inflammatory processes is coordinated by macrophages and macroautophagy/autophagy has recently emerged as a cellular process that dampens inflammation. Here we report that the n-3 PUFA docosahexaenoic acid (DHA) transiently induces cytosolic speckles of the autophagic receptor SQSTM1/p62 (sequestosome 1) (described as SQSTM1/p62-bodies) in macrophages. We suggest that the formation of SQSTM1/p62-bodies represents a fast mechanism of NFE2L2/Nrf2 (nuclear factor, erythroid 2 like 2) activation by recruitment of KEAP1 (kelch like ECH associated protein 1). Further, the autophagy receptor TAX1BP1 (Tax1 binding protein 1) and ubiquitin-editing enzyme TNFAIP3/A20 (TNF α induced protein 3) could be identified in DHA-induced SQSTM1/p62-bodies. Simultaneously, DHA strongly dampened the induction of pro-inflammatory genes including <i>CXCL10</i> (C-X-C motif chemokine ligand 10) and we suggest that formation of SQSTM1/p62-bodies and activation of NFE2L2 leads to tolerance towards selective inflammatory stimuli. Finally, reduced CXCL10 levels were related to the improved clinical outcome in n-3 PUFA-supplemented heart-transplant patients and we propose CXCL10 as a robust marker for the clinical benefits mobilized by n-3 PUFA supplementation.
DOI: 10.6084/m9.figshare.5325355
title: Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase

description: Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes. Our sequence analysis reveals that archaeal TSs possess all zinc chelating residues to bind a metal ion that are lacking in the structurally characterized homologs. Phylogenetic analysis suggests that TSs with an N-terminal zinc ribbon likely represents the ancestral state of the enzyme while TSs without a zinc ribbon must have diverged later in specific lineages. The zinc ribbon and its N- and C-terminal extensions are important for enzyme stability, activity and regulation. It is likely that the zinc ribbon domain is involved in higher order oligomerization or mediating interactions with other biomolecules leading to formation of larger metabolic complexes.
DOI: 10.6084/m9.figshare.5325355.v1
title: Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase

description: Threonine synthase (TS) catalyzes the terminal reaction in the biosynthetic pathway of threonine and requires pyridoxal phosphate as a cofactor. TSs share a common catalytic domain with other fold type II PALP dependent enzymes. TSs are broadly grouped into two classes based on their sequence, quaternary structure, and enzyme regulation. We report the presence of a novel zinc ribbon domain in the N-terminal region preceding the catalytic core in TS. The zinc ribbon domain is present in TSs belonging to both classes. Our sequence analysis reveals that archaeal TSs possess all zinc chelating residues to bind a metal ion that are lacking in the structurally characterized homologs. Phylogenetic analysis suggests that TSs with an N-terminal zinc ribbon likely represents the ancestral state of the enzyme while TSs without a zinc ribbon must have diverged later in specific lineages. The zinc ribbon and its N- and C-terminal extensions are important for enzyme stability, activity and regulation. It is likely that the zinc ribbon domain is involved in higher order oligomerization or mediating interactions with other biomolecules leading to formation of larger metabolic complexes.
DOI: 10.6084/m9.figshare.5325343
title: Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice

description: The SPO11-generated DNA double-strand breaks (DSBs) that initiate meiotic recombination occur non-randomly across genomes, but mechanisms shaping their distribution and repair remain incompletely understood. Here, we expand on recent studies of nucleotide-resolution DSB maps in mouse spermatocytes. We find that trimethylation of histone H3 lysine 36 around DSB hotspots is highly correlated, both spatially and quantitatively, with trimethylation of H3 lysine 4, consistent with coordinated formation and action of both PRDM9-dependent histone modifications. In contrast, the DSB-responsive kinase ATM contributes independently of PRDM9 to controlling hotspot activity, and combined action of ATM and PRDM9 can explain nearly two-thirds of the variation in DSB frequency between hotspots. DSBs were modestly underrepresented in most repetitive sequences such as segmental duplications and transposons. Nonetheless, numerous DSBs form within repetitive sequences in each meiosis and some classes of repeats are preferentially targeted. Implications of these findings are discussed for evolution of PRDM9 and its role in hybrid strain sterility in mice. Finally, we document the relationship between mouse strain-specific DNA sequence variants within PRDM9 recognition motifs and attendant differences in recombination outcomes. Our results provide further insights into the complex web of factors that influence meiotic recombination patterns.
DOI: 10.6084/m9.figshare.5325340
title: Odor concentration series electrophysiology data

description: This is a dataset collected to determine whether early responses of mitral/tufted cells in the OB provide information about odor identity that generalizes across concentrations.<br>
DOI: 10.6084/m9.figshare.5326603.v8
title: Solving the velocity field for a 2-D incompressible flow in the case of constant viscosity using both Navier-Stokes equation and stream function approaches

description: Two different 2-D incompressible flow problems with constant viscosities were investigated. The first problem was a fluid with constant density driven by the boundary condition. The time evolution of pressure and velocity was solved with the Navier-Stokes equation. Using different experimental materials, the result showed that reducing the viscosity affects the flow patterns and increases the time needed to reach the steady state. The second problem was a buoyancy driven flow in a vertical gravity field for a density structure with two vertical layers. The instantaneous velocity field as the flow starts was solved with the stream function – vorticity formulation. The maximum magnitude of the velocity field increases linearly with gravity and density contrast, but decreases inversely with viscosity. Finite element and finite difference approaches produced consistent solutions with only small differences. The accuracy of the two methods needs to be further investigated. The discrepancy did not reduce at all when the grid number was increased to twice of the default setting for both methods.
DOI: 10.6084/m9.figshare.5325340.v1
title: Odor concentration series electrophysiology data

description: This is a dataset collected to determine whether early responses of mitral/tufted cells in the OB provide information about odor identity that generalizes across concentrations.<br>
DOI: 10.6084/m9.figshare.5325310
title: Optogenetic Masking of olfactory system

description: Behavioral dataset for optogenetic during an odor concentration task.<br>The data can be loaded using Python software found at https://github.com/c-wilson/behavior_tools.<br>