cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5285872.v1
title: Age-related differences in left ventricular structure and function between healthy men and women

description: <b>Objectives:</b> Cardiovascular function generally decreases with age, but whether this decrease differs between men and women is unclear. Our aims were twofold: (1) to investigate age-related sex differences in left ventricular (LV) structure, function and mechanics, and (2) to compare these measures between pre- and postmenopausal women in the middle-aged group. <b>Methods:</b> Resting echocardiography was performed in a cross-sectional sample of 82 healthy adults (14 young men, 19 middle-aged men, 15 young women, 34 middle-aged women: 15 premenopausal and 19 postmenopausal). Two-way ANOVAs were used to examine sex × age interactions, and <i>t</i>-tests to compare pre- and postmenopausal women (<i>α &lt;</i> 0.1). <b>Results:</b> Normalized LV mass, stroke volume and end-diastolic volume were significantly lower in middle-aged than young men, but this difference was smaller between middle-aged and young women. Peak systolic apical mechanics were significantly greater in middle-aged men than in middle-aged women, but not between young men and women. Postmenopausal women had significantly lower LV relaxation and mechanics (torsion, twisting velocity and apical circumferential strain rates) compared with middle-aged premenopausal women. <b>Conclusion:</b> Our cross-sectional findings suggest that the hearts of men and women may age differently, with men displaying greater differences in LV volumes accompanied by differences in apical mechanics.
DOI: 10.6084/m9.figshare.5285965.v3
title: Research data supporting "Microbial mineralization of cellulose in frozen soils"

description: Research data supporting "Microbial mineralization of cellulose in frozen soils". The files uploaded contain solid state and liquid state NMR data in TOPSPIN, Bruker format. A word document contains the NMR_data_key information.<br>An Excel file summarizes the data from NMR and GC experiments and is the base of the figures generated for the manuscript.<br>
DOI: 10.6084/m9.figshare.5286019.v4
title: SQLite database with MGI mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 14 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.<br>This is like mouse_genes.sqlite, but just with the records with source=="MGI" and taking just one of each of the duplicate records for a gene.
DOI: 10.6084/m9.figshare.5285818
title: DiverseGenome-AllvAll-cluster_HMMs

description: Generated by all vs. all blast of 34 eukaryote genomes, followed by mcl clustering, alignment of proteins in each cluster, and generation of HMMs from each alignment.
DOI: 10.6084/m9.figshare.5286019.v5
title: SQLite database with MGI mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 14 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.<br>This is like mouse_genes.sqlite, but just with the records with source=="MGI" and taking just one of each of the duplicate records for a gene.
DOI: 10.6084/m9.figshare.5285809
title: Supplementary data 02 - experimental from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for experimental analysis
DOI: 10.6084/m9.figshare.5285815
title: Supplementary data 03 - survival from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for survival analysis
DOI: 10.6084/m9.figshare.5285809.v1
title: Supplementary data 02 - experimental from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for experimental analysis
DOI: 10.6084/m9.figshare.5285815.v1
title: Supplementary data 03 - survival from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for survival analysis
DOI: 10.6084/m9.figshare.5285818.v1
title: DiverseGenome-AllvAll-cluster_HMMs

description: Generated by all vs. all blast of 34 eukaryote genomes, followed by mcl clustering, alignment of proteins in each cluster, and generation of HMMs from each alignment.
DOI: 10.6084/m9.figshare.5285806
title: Supplementary data 04 - infanticide from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for infanticide analysis
DOI: 10.6084/m9.figshare.5285806.v1
title: Supplementary data 04 - infanticide from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for infanticide analysis
DOI: 10.6084/m9.figshare.5285791
title: Data from Detection of Allee effects in marine fishes: analytical biases generated by data availability and model selection

description: The demographic Allee effect, or depensation, implies positive association between <i>per capita</i> population growth rate and population size at low abundances, thereby lowering growth ability of sparse populations. This can have far-reaching consequences on population recovery ability and colonization success. In the context of marine fishes, there is a widespread perception that Allee effects are rare or non-existent. However, studies that have failed to detect Allee effects in marine fishes have suffered from several fundamental methodological and data limitations. In the present study, we challenge the prevailing perception about the rarity of Allee effects by analysing nine populations of Atlantic herring (<i>Clupea harengus</i>), using Bayesian statistical methods. We find that populations of the same species can show either strong evidence for Allee effects or compensation. We explicitly demonstrate how the evidence for Allee effects is strongly provisional on observations made at low population abundances. We contrast our statistical approach with previous attempts to detect Allee effects and illustrate methodological issues that can lead to erroneous conclusions about the nature of population dynamics at low abundance. The present study demonstrates that there is no substantive scientific basis to support the perception that Allee effects are rare or non-existent in marine fishes.
DOI: 10.6084/m9.figshare.5285788
title: Supplementary data 01 - correlative from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for correlative analysis
DOI: 10.6084/m9.figshare.5285791.v1
title: Data from Detection of Allee effects in marine fishes: analytical biases generated by data availability and model selection

description: The demographic Allee effect, or depensation, implies positive association between <i>per capita</i> population growth rate and population size at low abundances, thereby lowering growth ability of sparse populations. This can have far-reaching consequences on population recovery ability and colonization success. In the context of marine fishes, there is a widespread perception that Allee effects are rare or non-existent. However, studies that have failed to detect Allee effects in marine fishes have suffered from several fundamental methodological and data limitations. In the present study, we challenge the prevailing perception about the rarity of Allee effects by analysing nine populations of Atlantic herring (<i>Clupea harengus</i>), using Bayesian statistical methods. We find that populations of the same species can show either strong evidence for Allee effects or compensation. We explicitly demonstrate how the evidence for Allee effects is strongly provisional on observations made at low population abundances. We contrast our statistical approach with previous attempts to detect Allee effects and illustrate methodological issues that can lead to erroneous conclusions about the nature of population dynamics at low abundance. The present study demonstrates that there is no substantive scientific basis to support the perception that Allee effects are rare or non-existent in marine fishes.
DOI: 10.6084/m9.figshare.5285788.v1
title: Supplementary data 01 - correlative from Effects of early-life competition and maternal nutrition on telomere lengths in wild meerkats

description: Data for correlative analysis
DOI: 10.6084/m9.figshare.5285701
title: Identification of the actual coding region for polyamine oxidase 6 from rice (OsPAO6) and its partial characterization

description: Polyamines (PA) in plant play roles in growth and development and in responses to environmental stresses. The family of polyamine oxidases (PAO) contributes to a balanced homeostasis of PAs catalyzing two different reactions, terminal catabolic (TC) and back-conversion (BC) pathway, in PA catabolism. From the seven PAOs encoded by the rice genome (OsPAO1 – OsPAO7) OsPAO6 could so far not be characterized due to failure in obtaining the coding cDNA based on accessions in the genomic databases. We report cloning and characterization of the correct OsPAO6 cDNA with a length of 1,742 bp. The 1,491 bp long open reading frame codes for a 497-amino acid protein from nine exons. The protein which has 92% identity to OsPAO7 localizes to plasma membrane.
DOI: 10.6084/m9.figshare.5285701.v1
title: Identification of the actual coding region for polyamine oxidase 6 from rice (OsPAO6) and its partial characterization

description: Polyamines (PA) in plant play roles in growth and development and in responses to environmental stresses. The family of polyamine oxidases (PAO) contributes to a balanced homeostasis of PAs catalyzing two different reactions, terminal catabolic (TC) and back-conversion (BC) pathway, in PA catabolism. From the seven PAOs encoded by the rice genome (OsPAO1 – OsPAO7) OsPAO6 could so far not be characterized due to failure in obtaining the coding cDNA based on accessions in the genomic databases. We report cloning and characterization of the correct OsPAO6 cDNA with a length of 1,742 bp. The 1,491 bp long open reading frame codes for a 497-amino acid protein from nine exons. The protein which has 92% identity to OsPAO7 localizes to plasma membrane.
DOI: 10.6084/m9.figshare.5285665
title: PTPN22 regulates NLRP3-mediated IL1B secretion in an autophagy-dependent manner

description: A variant within the gene locus encoding PTPN22 (protein tyrosine phosphatase, non-receptor type 22) emerged as an important risk factor for auto-inflammatory disorders, including rheumatoid arthritis, systemic lupus erythematosus and type 1 diabetes, but at the same time protects from Crohn disease, one of the 2 main forms of inflammatory bowel diseases. We have previously shown that loss of PTPN22 results in decreased NLRP3 (NLR family pyrin domain containing 3) activation and that this effect is mediated via enhanced NLRP3 phosphorylation. However, it is unclear how phosphorylation of NLRP3 mediates its inhibition. Here, we demonstrate that loss of macroautophagy/autophagy abrogates the inhibitory effect on NLRP3 activation observed upon loss of PTPN22. Phosphorylated, but not nonphosphorylated NLRP3 is found in autophagosomes, indicating that NLRP3 phosphorylation mediates its inactivation via promoting sequestration into phagophores, the precursors to autophagosomes. This finding shows that autophagy and NLRP3 inflammasome activation are connected, and that PTPN22 plays a key role in the regulation of those 2 pathways. Given its role in inflammatory disorders, PTPN22 might be an attractive therapeutic target, and understanding the cellular mechanisms modulated by PTPN22 is of crucial importance.
DOI: 10.6084/m9.figshare.5285656
title: Supplementary Material for: Electrical Potential of Leaping Eels

description: When approached by a large, partially submerged conductor, electric eels <i>(Electrophorus electricus)</i> will often defend themselves by leaping from the water to directly shock the threat. Presumably, the conductor is interpreted as an approaching terrestrial or semiaquatic animal. In the course of this defensive behavior, eels first make direct contact with their lower jaw and then rapidly emerge from the water, ascending the conductor while discharging high-voltage volleys. In this study, the equivalent circuit that develops during this behavior was proposed and investigated. First, the electromotive force and internal resistance of four electric eels were determined. These values were then used to estimate the resistance of the water volume between the eel and the conductor by making direct measurements of current with the eel and water in the circuit. The resistance of the return path from the eel's lower jaw to the main body of water was then determined, based on voltage recordings, for each electric eel at the height of the defensive leap. Finally, the addition of a hypothetical target for the leaping defense was considered as part of the circuit. The results suggest the defensive behavior efficiently directs electrical current through the threat, producing an aversive and deterring experience by activating afferents in potential predators.
DOI: 10.6084/m9.figshare.5285665.v2
title: PTPN22 regulates NLRP3-mediated IL1B secretion in an autophagy-dependent manner

description: A variant within the gene locus encoding PTPN22 (protein tyrosine phosphatase, non-receptor type 22) emerged as an important risk factor for auto-inflammatory disorders, including rheumatoid arthritis, systemic lupus erythematosus and type 1 diabetes, but at the same time protects from Crohn disease, one of the 2 main forms of inflammatory bowel diseases. We have previously shown that loss of PTPN22 results in decreased NLRP3 (NLR family pyrin domain containing 3) activation and that this effect is mediated via enhanced NLRP3 phosphorylation. However, it is unclear how phosphorylation of NLRP3 mediates its inhibition. Here, we demonstrate that loss of macroautophagy/autophagy abrogates the inhibitory effect on NLRP3 activation observed upon loss of PTPN22. Phosphorylated, but not nonphosphorylated NLRP3 is found in autophagosomes, indicating that NLRP3 phosphorylation mediates its inactivation via promoting sequestration into phagophores, the precursors to autophagosomes. This finding shows that autophagy and NLRP3 inflammasome activation are connected, and that PTPN22 plays a key role in the regulation of those 2 pathways. Given its role in inflammatory disorders, PTPN22 might be an attractive therapeutic target, and understanding the cellular mechanisms modulated by PTPN22 is of crucial importance.
DOI: 10.6084/m9.figshare.5285656.v1
title: Supplementary Material for: Electrical Potential of Leaping Eels

description: When approached by a large, partially submerged conductor, electric eels <i>(Electrophorus electricus)</i> will often defend themselves by leaping from the water to directly shock the threat. Presumably, the conductor is interpreted as an approaching terrestrial or semiaquatic animal. In the course of this defensive behavior, eels first make direct contact with their lower jaw and then rapidly emerge from the water, ascending the conductor while discharging high-voltage volleys. In this study, the equivalent circuit that develops during this behavior was proposed and investigated. First, the electromotive force and internal resistance of four electric eels were determined. These values were then used to estimate the resistance of the water volume between the eel and the conductor by making direct measurements of current with the eel and water in the circuit. The resistance of the return path from the eel's lower jaw to the main body of water was then determined, based on voltage recordings, for each electric eel at the height of the defensive leap. Finally, the addition of a hypothetical target for the leaping defense was considered as part of the circuit. The results suggest the defensive behavior efficiently directs electrical current through the threat, producing an aversive and deterring experience by activating afferents in potential predators.
DOI: 10.6084/m9.figshare.5285665.v1
title: PTPN22 regulates NLRP3-mediated IL1B secretion in an autophagy dependent manner

description: A variant within the gene locus encoding PTPN22 (protein tyrosine phosphatase, non-receptor type 22) emerged as an important risk factor for auto-inflammatory disorders, including rheumatoid arthritis, systemic lupus erythematosus and type 1 diabetes, but at the same time protects from Crohn disease, one of the 2 main forms of inflammatory bowel diseases. We have previously shown that loss of PTPN22 results in decreased NLRP3 (NLR family pyrin domain containing 3) activation and that this effect is mediated via enhanced NLRP3 phosphorylation. However, it is unclear how phosphorylation of NLRP3 mediates its inhibition. Here, we demonstrate that loss of macroautophagy/autophagy abrogates the inhibitory effect on NLRP3 activation observed upon loss of PTPN22. Phosphorylated, but not nonphosphorylated NLRP3 is found in autophagosomes, indicating that NLRP3 phosphorylation mediates its inactivation via promoting sequestration into phagophores, the precursors to autophagosomes. This finding shows that autophagy and NLRP3 inflammasome activation are connected, and that PTPN22 plays a key role in the regulation of those 2 pathways. Given its role in inflammatory disorders, PTPN22 might be an attractive therapeutic target, and understanding the cellular mechanisms modulated by PTPN22 is of crucial importance.
DOI: 10.6084/m9.figshare.5285635
title: Data Caching for Where and What.xlsx

description: Excel file of data used in analyses. Data is a measure of how much squirrels overlapped caches by nut type under different experimental conditions.
DOI: 10.6084/m9.figshare.5285512
title: How to make your research open access? For free and legally.

description: The infographic shows how to achieve 100% Open Access for free and legally.
DOI: 10.6084/m9.figshare.5285521
title: Gridded bathymetry of the Baker-Martinez fjord complex (Chile, 48°S) v1

description: <b>UPDATE:</b> <b>version 2 of the bathymetric map is available at Marine Geoscience Data System</b> <br>(www.marine-geo.org/tools/search/entry.php?id=ChileanFjords_Piret)<br><br>We present a bathymetric map of the Baker-Martinez fjord complex (Chile, 48⁰S) constructed from multiple data sets: multibeam echosounder data of Baker channel (Harada et al., 2008) and of Steffen fjord and Baker river delta (Vandekerkhove & Bertrand, 2016), single beam echosounder data of Jorge Montt fjord (Rivera et al., 2012, Moffat, 2014 and additional data from C. Moffat) and individual bathymetry points from two SHOA nautical charts (SHOA, 2001, 2008). The heterogeneous data with distinct spatial resolution was gridded using the kriging method (3.6 arc-second resolution) in Surfer from Golden Software. We intend to update this map when new datasets become available. The deepest basin of Baker channel (73.8°W) reaches depths of 1075 m below sea level (BSL). To the west, the channel has depths ranging from 450 to 750 m BSL. Martinez channel is between 200 and 440 m deep in its eastern part and reaches depths of 535 m BSL to the west. The bullseye effect in Martinez channel is a mere artefact of the gridding procedure as there is only sparse bathymetric data available in that area. The deepest and largest basin (1405 m BSL and approx. 10 km wide) is located in Messier channel. All the channels are flanked by steep slopes (20 – 40°). Transverse ridges are present throughout the fjord complex, creating separated sub-basins (e.g. north of the deepest basin in Messier channel, in the center of Baker channel at 74.35°W). The fjord becomes shallower (200 – 300m BSL) towards its mouth in the Gulf of Penas. This bathymetric map is intended for regional oceanographic and geological research projects. <b>References:</b> Harada, N. and the shipboard scientific party, 2008. MIRAI cruise report MR06-04 Leg 3, Japan Agency for Marine Earth Science and Technology, Yokosuka, 176 pp. Moffat, C., 2014. Wind-driven modulation of warm water supply to a proglacial fjord, Jorge Montt Glacier, Patagonia. Geophysical Research Letters, <i>41</i>, 1–8. Rivera, A., Koppes, M.N., Bravo, C., Aravena, J.C., 2012. Little Ice Age advance and retreat of Glaciar Jorge Montt, Chilean Patagonia. Climate of the Past, 8, 403–414. SHOA (Servicio Hidrográfico y Oceanográfico de la Armada de Chile), 2001. "Canal Baker y Puertos Adyacentes (Canal Baker)", 6<sup>th</sup> ed., sheet 9100, 1:200 000, Mercator projection. SHOA (Servicio Hidrográfico y Oceanográfico de la Armada de Chile), 2008. “Acceso Norte a Canal Messier – Boca de Canales a Isla Van Der Meulen”, 2nd ed., sheet 9300, 1:100 000, Mercator projection. Vandekerkhove, E., Bertrand, S., 2016. Expedition report Paleo-GLOFs and HYDROPROX, 13 pp.
DOI: 10.6084/m9.figshare.5285521.v1
title: Gridded bathymetry of the Baker-Martinez fjord complex (Chile, 48°S) v1

description: We present a bathymetric map of the Baker-Martinez fjord complex (Chile, 48⁰S) constructed from multiple data sets: multibeam echosounder data of Baker channel (Harada et al., 2008) and of Steffen fjord and Baker river delta (Vandekerkhove & Bertrand, 2016), single beam echosounder data of Jorge Montt fjord (Rivera et al., 2012, Moffat, 2014 and additional data from C. Moffat) and individual bathymetry points from two SHOA nautical charts (SHOA, 2001, 2008). The heterogeneous data with distinct spatial resolution was gridded using the kriging method (3.6 arc-second resolution) in Surfer from Golden Software. We intend to update this map when new datasets become available. The deepest basin of Baker channel (73.8°W) reaches depths of 1075 m below sea level (BSL). To the west, the channel has depths ranging from 450 to 750 m BSL. Martinez channel is between 200 and 440 m deep in its eastern part and reaches depths of 535 m BSL to the west. The bullseye effect in Martinez channel is a mere artefact of the gridding procedure as there is only sparse bathymetric data available in that area. The deepest and largest basin (1405 m BSL and approx. 10 km wide) is located in Messier channel. All the channels are flanked by steep slopes (20 – 40°). Transverse ridges are present throughout the fjord complex, creating separated sub-basins (e.g. north of the deepest basin in Messier channel, in the center of Baker channel at 74.35°W). The fjord becomes shallower (200 – 300m BSL) towards its mouth in the Gulf of Penas. This bathymetric map is intended for regional oceanographic and geological research projects. <b>References:</b> Harada, N. and the shipboard scientific party, 2008. MIRAI cruise report MR06-04 Leg 3, Japan Agency for Marine Earth Science and Technology, Yokosuka, 176 pp. Moffat, C., 2014. Wind-driven modulation of warm water supply to a proglacial fjord, Jorge Montt Glacier, Patagonia. Geophysical Research Letters, <i>41</i>, 1–8. Rivera, A., Koppes, M.N., Bravo, C., Aravena, J.C., 2012. Little Ice Age advance and retreat of Glaciar Jorge Montt, Chilean Patagonia. Climate of the Past, 8, 403–414. SHOA (Servicio Hidrográfico y Oceanográfico de la Armada de Chile), 2001. "Canal Baker y Puertos Adyacentes (Canal Baker)", 6<sup>th</sup> ed., sheet 9100, 1:200 000, Mercator projection. SHOA (Servicio Hidrográfico y Oceanográfico de la Armada de Chile), 2008. “Acceso Norte a Canal Messier – Boca de Canales a Isla Van Der Meulen”, 2nd ed., sheet 9300, 1:100 000, Mercator projection. Vandekerkhove, E., Bertrand, S., 2016. Expedition report Paleo-GLOFs and HYDROPROX, 13 pp.