cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7967958
title: Proposed catalytic mechanism of mAMCase.

description: This directory contains all files required to analyze the proposed catalytic mechanism of mouse AMCase at pH 2.0 and 6.5 presented in <strong>Figure 6</strong> in the manuscript Díaz et al.<em> </em>(2023). Structure models were analyzed using PyMOL. Figures were compiled using PerkinElmer ChemDraw and Adobe Illustrator. Files included in this directory: <strong>Figures</strong> - contains ChemDraw file for the proposed catalytic mechanism schematic, PNGs of each step of the proposed catalytic mechanism at pH 2.0 and 6.5, and a GIF of the entire proposed catalytic mechanism at pH 2.0 and 6.5. <strong>PyMOL</strong> - contains all structure models, PyMOL script, and PyMOL session used to generate <strong>Figure 6</strong>. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7967955
title: Proposed catalytic mechanism of mAMCase.

description: This directory contains all files required to analyze the proposed catalytic mechanism of mouse AMCase at pH 2.0 and 6.5 presented in <strong>Figure 6</strong> in the manuscript Díaz et al.<em> </em>(2023). Structure models were analyzed using PyMOL. Figures were compiled using PerkinElmer ChemDraw and Adobe Illustrator. Files included in this directory: <strong>Figures</strong> - contains ChemDraw file for the proposed catalytic mechanism schematic, PNGs of each step of the proposed catalytic mechanism at pH 2.0 and 6.5, and a GIF of the entire proposed catalytic mechanism at pH 2.0 and 6.5. <strong>PyMOL</strong> - contains all structure models, PyMOL script, and PyMOL session used to generate <strong>Figure 6</strong>. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7758815
title: Ringer analysis of mAMCase structures

description: This directory contains all files required to analyze the mouse AMCase structures using Ringer as presented in <strong>Supplemental Figure 7</strong> in the manuscript Díaz et al.<em> </em>(2023). Structures were analyzed using Ringer. Ringer data was analyzed using Python. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>8fXX</strong> - Ringer output files for each mAMCase structure reported. <strong>Figures</strong><br> - contains .PNG files of Ringer plots for Asp136, Asp138, and Glu140 of each chain of each structure reported. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7758814
title: Ringer analysis of mAMCase structures

description: This directory contains all files required to analyze the mouse AMCase structures using Ringer as presented in <strong>Supplemental Figure 7</strong> in the manuscript Díaz et al.<em> </em>(2023). Structures were analyzed using Ringer. Ringer data was analyzed using Python. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>8fXX</strong> - Ringer output files for each mAMCase structure reported. <strong>Figures</strong><br> - contains .PNG files of Ringer plots for Asp136, Asp138, and Glu140 of each chain of each structure reported. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7905863
title: pKa of GH18 chitinases in the inactive and active conformation

description: This directory contains all files required to plot the theoretical pKa of D1, D2, and E from mouse AMCase, human AMCase, and other GH18 chitinases presented in <strong>Figure 4</strong> and <strong>Supplemental Figure 4 </strong>of Díaz et al.<em> </em>(2023). Structure models were analyzed using PyMOL. Data was analyzed using Graphpad Prism. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>Figures</strong> - contains PDFs of Graphpad plots for the pKa of human AMCase, mouse AMCase, and GH18 chitinases D2 in the <em>active </em>or <em>inactive </em>conformation. <strong>PDB2PQR</strong> - contains all log files from PDB2PQR sorted by data type (mouse AMCase <em>active</em> and <em>inactive </em>D2, human AMCase <em>active</em> and <em>inactive </em>D2, and GH18 chitinase <em>active</em> and <em>inactive </em>D2). <strong>PyMOL</strong> - contains PyMOL script and session file for each data type (mouse AMCase <em>active</em> and <em>inactive </em>D2, human AMCase <em>active</em> and <em>inactive </em>D2, and GH18 chitinase <em>active</em> and <em>inactive </em>D2) shown in <strong>Figure 4</strong>. <strong>Reference Models</strong> - contains all structure models shown in <strong>Figure 4</strong>. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7905862
title: pKa of GH18 chitinases in the inactive and active conformation

description: This directory contains all files required to plot the theoretical pKa of D1, D2, and E from mouse AMCase, human AMCase, and other GH18 chitinases presented in <strong>Figure 4</strong> and <strong>Supplemental Figure 4 </strong>of Díaz et al.<em> </em>(2023). Structure models were analyzed using PyMOL. Data was analyzed using Graphpad Prism. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>Figures</strong> - contains PDFs of Graphpad plots for the pKa of human AMCase, mouse AMCase, and GH18 chitinases D2 in the <em>active </em>or <em>inactive </em>conformation. <strong>PDB2PQR</strong> - contains all log files from PDB2PQR sorted by data type (mouse AMCase <em>active</em> and <em>inactive </em>D2, human AMCase <em>active</em> and <em>inactive </em>D2, and GH18 chitinase <em>active</em> and <em>inactive </em>D2). <strong>PyMOL</strong> - contains PyMOL script and session file for each data type (mouse AMCase <em>active</em> and <em>inactive </em>D2, human AMCase <em>active</em> and <em>inactive </em>D2, and GH18 chitinase <em>active</em> and <em>inactive </em>D2) shown in <strong>Figure 4</strong>. <strong>Reference Models</strong> - contains all structure models shown in <strong>Figure 4</strong>. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5066/p9qt5vc1
title: GPS telemetry of Florida manatees and riverine water temperatures from southwest Florida 2002-2015

description: These data represent 1) GPS telemetry of 40 Florida manatees from 2002 through 2008, covering southwest Florida from Charlotte Harbor to Florida Bay, and 2) water temperature readings from 10 riverine sites in the Everglades region of southwest Florida using Onset dataloggers from 2008 through 2015.
DOI: 10.6073/pasta/60edabfbfd85c623fce05822befaa071
title: Temporal and spatial changes of the abundance and species composition of phytoplankton in the California Current from samples collected aboard CalCOFI cruises from summer 1996 through 2022.

description: The abundances of 385 taxonomic categories of phytoplankton (species where possible) are presented for the 26.5 -year period beginning with summer, 1996 and concluding with autumn 2022. There were four cruises per year. Samples were water samples collected from the second depth, which was designed to sample the mixed layer when a mixed layer existed, generally between 5m - 15m. Before counting, samples from single stations were pooled into four regions: NE (northern inshore), SE (southern inshore), Alley (the region of the California Current) and Offshore (Central Pacific). Pooled samples were enumerated with an inverted microscope. The species data are presented by seven major taxonomic categories followed by the sums of those major taxa. The species codes are defined in the table metadata.
DOI: 10.25345/c5f18sr28
title: MassIVE MSV000092105 - Mus musculus brown adipose tissue histone proteoforms
title: Histones were isolated from brown adipose tissue and liver from mice housed at 28, 22, or 8 C. Quantitative top- or middle-down approaches were used to quantitate histone H4 and H3.2 proteoforms. See published article for complimentary RNA-seq and RRBS datasets.
DOI: 10.6084/m9.figshare.23297758
title: Data_for_manuscript_submission.zip from Adoption of alternative life cycles in a parasitic trematode is linked to microbiome differences

description: For parasites with complex multi-host life cycles, the facultative truncation of the cycle represents an adaptation to challenging conditions for transmission. However, why certain individuals are capable of abbreviating their life cycle while other conspecifics are not remained poorly understood. Here, we test whether conspecific trematodes that either follow the normal three-host life cycle or skip their final host by reproducing precociously (via progenesis) in an intermediate host differ in the composition of their microbiomes. Characterization of bacterial communities based on sequencing of the V4 hypervariable region of the 16S SSU rRNA gene revealed that the same bacterial taxa occur in both normal and progenetic individuals, independent of host identity and temporal variation. However, all bacterial phyla recorded in our study, and two-thirds of bacterial families, differed in abundance between the two morphs, with some achieving higher abundance in the normal morph and others in the progenetic morph. Although the evidence is purely correlative, our results reveal a weak association between microbiome differences and intraspecific plasticity in life cycle pathways. Advances in functional genomics and experimental microbiome manipulation will allow future tests of the significance of these findings.
DOI: 10.6084/m9.figshare.23297758.v1
title: Data_for_manuscript_submission.zip from Adoption of alternative life cycles in a parasitic trematode is linked to microbiome differences

description: For parasites with complex multi-host life cycles, the facultative truncation of the cycle represents an adaptation to challenging conditions for transmission. However, why certain individuals are capable of abbreviating their life cycle while other conspecifics are not remained poorly understood. Here, we test whether conspecific trematodes that either follow the normal three-host life cycle or skip their final host by reproducing precociously (via progenesis) in an intermediate host differ in the composition of their microbiomes. Characterization of bacterial communities based on sequencing of the V4 hypervariable region of the 16S SSU rRNA gene revealed that the same bacterial taxa occur in both normal and progenetic individuals, independent of host identity and temporal variation. However, all bacterial phyla recorded in our study, and two-thirds of bacterial families, differed in abundance between the two morphs, with some achieving higher abundance in the normal morph and others in the progenetic morph. Although the evidence is purely correlative, our results reveal a weak association between microbiome differences and intraspecific plasticity in life cycle pathways. Advances in functional genomics and experimental microbiome manipulation will allow future tests of the significance of these findings.
DOI: 10.5066/p98c25sk
title: Manatee tracking, sighting and environmental data from the Northern Gulf of Mexico, 2013-2019

description: Data sets collected for manatee movement and habitat research in the Northern Gulf of Mexico from 2013-2019. These include manatee GPS tracking, manatee sightings, aquatic vegetation from manatee use areas, and environmental data (salinity and bathymetry at vegetation sampling sites).
DOI: 10.5281/zenodo.7967954
title: Protein-ligand interactions between mAMCase and chitin.

description: This directory contains all files to analyze mouse AMCase-ligand interactions as presented in <strong>Supplemental Figure 6</strong> in the manuscript Díaz et al.<em> </em>(2023). Structure models were analyzed in PyMOL. Figures were compiled using Adobe Illustrator. Contact: Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7967953
title: Protein-ligand interactions between mAMCase and chitin.

description: This directory contains all files to analyze mouse AMCase-ligand interactions as presented in <strong>Supplemental Figure 6</strong> in the manuscript Díaz et al.<em> </em>(2023). Structure models were analyzed in PyMOL. Figures were compiled using Adobe Illustrator. Contact: Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.6073/pasta/0a34c37143b03a881816e82609c2bba1
title: MCR LTER: Coral Reef: Asynchrony in coral community structure contributes to reef‑scale community stability, data for Srednick et al., Nature 2023

description: These data were generated in support of the manuscript: Srednick G, Davis K, and Edmunds P, Nature To evaluate whether spatial insurance effects are important on coral reefs, we explored variation over 2006–2019 in coral community structure and environmental conditions in Moorea, French Polynesia. We studied coral community structure at a single site with fringing, back reef, and fore reef habitats, and used this system to explore associations among community asynchrony, asynchrony of environmental conditions, and community stability. The daily range in seawater temperature among habitats suggests it could be a factor contributing to the variation in coral community structure. Wave-forced seawater flow facilitated larval exchange among connected habitats, differing in strength among years, and accentuated periodic connectivity among habitats at 1-7 year intervals. At this site, connected habitats harboring taxonomically similar coral assemblages and exhibiting asynchronous population dynamics can provide insurance against extirpation and may promote community stability. If these effects apply at larger spatial scale, then among-habitat community asynchrony is likely to play an important role in determining reef-wide coral community resilience. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
DOI: 10.6084/m9.figshare.23297771
title: Optic Tract ROIs and reference curves in MNI space Drawn using Yeh atlas: <em>Yeh, FC. Population-based tract-to-region connectome of the human brain and its hierarchical topology. Nat Commun 13, 4933 (2022). https://doi.org/10.1038/s41467-022-32595-4</em>

description: Optic Tract ROIs and reference curves in MNI space for use in tractometry. Still being worked on, may be updated in the future.
DOI: 10.5281/zenodo.7996176
title: IODP Expedition 369 Stratigraphic Correlation

description: Affine and splice files created for stratigraphic correlation.
DOI: 10.5281/zenodo.7996175
title: IODP Expedition 369 Stratigraphic Correlation

description: Affine and splice files created for stratigraphic correlation.
DOI: 10.5281/zenodo.8007765
title: IODP Expedition 369 Stratigraphic Correlation

description: Affine and splice files created for stratigraphic correlation.
DOI: 10.6084/m9.figshare.22259743.v1
title: *=BASE DE DATOS LATENCIA PARA R.csv

description: Dataset accompanying the manuscript "EVIDENCE OF LONG-TERM ALLOCENTRIC SPATIAL MEMORY IN THE TERRESTRIAL HERMIT CRAB Coenobita compressus" ID: character code that uniquely identifies each hermit crab with a numeric label (1-18) and respective holding tank (A, B or C). FASE: indicates the phase of the experimental procedures (F1, visible reward, F2, hidden reward, F4, no reward) ENSAYO: number of trials in each phase HORAS: indicates the time of a particular trial (0 - 72 hours) LATENCIA: numeric, time difference in seconds between the beginning of the trial and the time the crab reached the tray
DOI: 10.6084/m9.figshare.22266400.v1
title: *=BASE DE DATOS PERMANENCIA PARA R

description: Dataset accompanying the manuscript "EVIDENCE OF LONG-TERM ALLOCENTRIC SPATIAL MEMORY IN THE TERRESTRIAL HERMIT CRAB Coenobita compressus" <br> Organismo: character code that uniquely identifies each hermit crab with a numeric label (1-18) and respective holding tank (A, B or C). Cuadrante1: percentage of time spent in quadrant 1 Cuadrante2: percentage of time spent in quadrant 2 Cuadrante3: percentage of time spent in quadrant 3 Cuadrante4: percentage of time spent in quadrant 4 Plataforma: percentage of time spent in the tray’s former place spot ENSAYO:indicates the time of a particular trial (24, 48, 72 hours) <br>
DOI: 10.5517/ccdc.csd.cc2f2skw
title: CCDC 2237008: Experimental Crystal Structure Determination

description: Related Article: Kono Sasaki, Daisuke Saito, Masaki Yoshida, Fuka Tanaka, Atsushi Kobayashi, Kazuki Sada, Masako Kato|2023|Chem.Commun.|59|6745|doi:10.1039/D3CC01525D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f5gtx
title: CCDC 2239589: Experimental Crystal Structure Determination

description: Related Article: Eleanor Dodd, Simon J. Coles, Terry L. Threlfall, Liam Oliver|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f5mbl
title: CCDC 2239729: Experimental Crystal Structure Determination

description: Related Article: Eleanor Dodd, Simon J. Coles, Terry L. Threlfall|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f5mjs
title: CCDC 2239735: Experimental Crystal Structure Determination

description: Related Article: Eleanor Dodd, Simon J. Coles, Terry L. Threlfall, Liam Oliver|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f5p4g
title: CCDC 2239785: Experimental Crystal Structure Determination

description: Related Article: Gilles Stebens, Arthur Semmelmaier, Arberi Salihi, Burkhard Butschke|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f5qdr
title: CCDC 2239824: Experimental Crystal Structure Determination

description: Related Article: Eleanor Dodd, Simon J. Coles, Terry L. Threlfall|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f6bnn
title: CCDC 2240421: Experimental Crystal Structure Determination

description: Related Article: Eleanor Dodd, Simon J. Coles, Terry L. Threlfall, Philip Adler|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f6kks
title: CCDC 2240635: Experimental Crystal Structure Determination

description: Related Article: Wolfgang Imhof, Helmar Görls|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ff9ry
title: CCDC 2247120: Experimental Crystal Structure Determination

description: Related Article: Yuliya A. Bryleva, Vladislav Yu. Komarov, Ludmila A. Glinskaya, Alexander V. Artem'ev, Maria P. Davydova, Mariana I. Rakhmanova, Denis G. Samsonenko|2023|New J.Chem.|47|10446|doi:10.1039/D3NJ01119D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.