cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24026588.v1
title: Spectral Clustering, Bayesian Spanning Forest, and Forest Process

description: Spectral clustering views the similarity matrix as a weighted graph, and partitions the data by minimizing a graph-cut loss. Since it minimizes the across-cluster similarity, there is no need to model the distribution within each cluster. As a result, one reduces the chance of model misspecification, which is often a risk in mixture model-based clustering. Nevertheless, compared to the latter, spectral clustering has no direct ways of quantifying the clustering uncertainty (such as the assignment probability), or allowing easy model extensions for complicated data applications. To fill this gap, we propose the Bayesian forest model as a generative graphical model for spectral clustering. This is motivated by our discovery that the posterior connecting matrix in a forest model has almost the same leading eigenvectors, as the ones used by normalized spectral clustering. To induce a distribution for the forest, we develop a “forest process” as a graph extension to the urn process, while we carefully characterize the differences in the partition probability. We derive a simple Markov chain Monte Carlo algorithm for posterior estimation, and demonstrate superior performance compared to existing algorithms. We illustrate several model-based extensions useful for data applications, including high-dimensional and multi-view clustering for images. Supplementary materials for this article are available online.
DOI: 10.5066/p9rc44vo
title: Airborne magnetic and radiometric survey, western Arkansas, 2022

description: This publication provides digital flight line data for a high-resolution magnetic and radiometric survey over part of western Arkansas. The airborne geophysical survey was funded by the USGS National Cooperative Geologic Mapping Program. The survey covers a rectangular area 91.55 by 92.15 kilometers (km) over the transition between the Ouachita Mountains and Ozark Plateau physiographic provinces and includes 31,006 line-km of magnetic and radiometric data. Data were collected from a fixed-wing aircraft flown at a median terrain clearance of 170 meters (m) above topography along north-south flight lines spaced at 300-m intervals. Tie lines were flown in an east-west direction every 3,000 m. Data were collected by EON Geosciences Inc. under contract with the USGS using a fixed-wing aircraft with a magnetometer mounted in the tail stinger and a fully calibrated gamma-ray spectrometer. The survey operated out of the Branson, Missouri airport from April of 2022 to May of 2022. Files that are available in this publication include flight line data for the magnetic survey, flight line data for the radiometric survey and a report describing the survey parameters, field operations, quality control and data reduction procedures. A zip file is provided that contains the contractor's deliverable products that includes Geosoft databases and grids for this magnetic and radiometric survey and the report describing the survey and data reduction. These products can be accessed using the free software Geosoft Viewer or the commercial Oasis Montaj software.
DOI: 10.5066/p9dsog9r
title: North Lake Mechant Landbridge Restoration (TE-44): 2021 land-water classification

description: The Louisiana State Legislature created the Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) in order to conserve, restore, create and enhance Louisiana's coastal wetlands. The wetland restoration plans developed pursuant to these acts specifically require an evaluation of the effectiveness of each coastal wetlands restoration project in achieving long-term solutions to arresting coastal wetlands loss. This data set includes mosaicked aerial photographs for the North Lake Mechant Landbridge Restoration (TE-44) project for 2021. This data is used as a basemap land-water classification. It also serves as a visual tool for project managers to help them identify any obvious problems or land loss within their project boundary. To better evaluate the effectiveness of restoration efforts, a land-water classification is performed on specific CWPPRA sites to help assess landscape changes.
DOI: 10.25345/c5416t91t
title: MassIVE MSV000093002 - An inhibitor/anti-inhibitor system controls the activity of lytic transglycosylase MltF in Pseudomonas aeruginosa
title: Most bacterial cell envelopes contain a cell wall layer made of peptidoglycan. The synthesis of new peptidoglycan is critical for cell growth, division and morphogenesis, and is also coordinated with peptidoglycan hydrolysis to accommodate the new material. However, the enzymes that cleave peptidoglycan must be carefully controlled to avoid autolysis. In recent years, some control mechanisms have begun to emerge, although there are many more questions than answers for how most cell wall hydrolases are regulated. Here, we report a novel cell wall hydrolase control mechanism in Pseudomonas aeruginosa, which we discovered during our characterization of a mutant sensitive to the overproduction of a secretin protein. The mutation affected an uncharacterized Sel1-like repeat protein encoded by the PA3978 locus. In addition to the secretin-sensitivity phenotype, PA3978 disruption also increased resistance to a b-lactam antibiotic used in the clinic. Affinity purification followed by mass spectrometry on the C-terminal flag tagged PA3978 protein revealed that PA3978 binds to the lytic transglycosylase MltF. In vitro and In vivo analysis revealed that the binding occurs on the catalytic domain of the lytic transglycosylase MltF and inhibits its activity. We also discovered another interaction partner of PA3978 encoded by the PA5502 locus. The phenotypes of a deltaPA5502 mutant suggested that PA5502 interferes with the inhibitory function of PA3978 towards MltF, and we confirmed that activity for PA5502 in vitro. Therefore, PA3978 and PA5502 form an inhibitor/anti-inhibitor system that controls MltF activity. We propose to name these proteins IltA (inhibitor of lytic transglycosylase) and LiiA (lytic transglycosylase inhibitor, inhibitor). The mass spectrometry raw files and search results for the affinity purification of PA3978 are deposited here.
DOI: 10.5281/zenodo.8393576
title: The numbers from 1 to 6

description: Data of the paper "The numbers from 1 to 6"
DOI: 10.6084/m9.figshare.24222907
title: Dataset from UPLC-MS analysis of lipids in human sperm

description: The lipidomic profiles of human sperm under varying physiological conditions were determined using UPLC-MS based on the mass-to-charge ratio (m/z) and retention time (RT).
DOI: 10.6084/m9.figshare.24222907.v1
title: Raw data from UPLC-MS analysis of lipids in human sperm

description: The lipidomic profiles of human sperm under varying physiological conditions were determined using UPLC-MS based on the mass-to-charge ratio (m/z) and retention time (RT).
DOI: 10.6084/m9.figshare.24222907.v2
title: Dataset from UPLC-MS analysis of lipids in human sperm

description: The lipidomic profiles of human sperm under varying physiological conditions were determined using UPLC-MS based on the mass-to-charge ratio (m/z) and retention time (RT).
DOI: 10.18112/openneuro.ds004785.v1.0.0
title: EEG data for paper titled - Precise cortical contributions to feedback sensorimotor control during reactive balance
DOI: 10.5281/zenodo.8384719
title: Gradients 5 - TN412 - Nutrients from Underway

description: These Simons Collaboration on Ocean Processes and Ecology (SCOPE) data products were produced by the University of Hawaiʻi at Mānoa with support from the Simons Foundation. This dataset was collected on the R/V Thompson during the Gradients V cruise which departed from San Diego, CA and ended in Honolulu, HI. A transect was performed on the 140 degree longitude line from roughly 16 degrees N to 4 degrees S before heading to Honolulu. All organic and inorganic nutrients are analyzed in unfiltered seawater that was sampled from the underway uncontaminated seawater system into HDPE or polypropylene bottles and immediately frozen. Silicate, phosphate and nitrate+nitrite are determined colormetrically on a SEAL Analytical Autoanalyzer (AA3 with HR detectors), with the exception of nitrate+nitrite that is &lt;0.5umol/L, which is analyzed by chemiluminescence. Total phosphorus (TP) and total nitrogen (TN) are determined by analysis of phosphate and nitrate, respectively, after oxidation by high-intensity ultraviolet light. Total organic phosphorus and total organic nitrogen are determined by subtracting background PO4 and NO3+NO2 from TP and TN, respectively. Time is in UTC.
DOI: 10.5281/zenodo.8384720
title: Gradients 5 - TN412 - Nutrients from Underway

description: These Simons Collaboration on Ocean Processes and Ecology (SCOPE) data products were produced by the University of Hawaiʻi at Mānoa with support from the Simons Foundation. This dataset was collected on the R/V Thompson during the Gradients V cruise which departed from San Diego, CA and ended in Honolulu, HI. A transect was performed on the 140 degree longitude line from roughly 16 degrees N to 4 degrees S before heading to Honolulu. All organic and inorganic nutrients are analyzed in unfiltered seawater that was sampled from the underway uncontaminated seawater system into HDPE or polypropylene bottles and immediately frozen. Silicate, phosphate and nitrate+nitrite are determined colormetrically on a SEAL Analytical Autoanalyzer (AA3 with HR detectors), with the exception of nitrate+nitrite that is &lt;0.5umol/L, which is analyzed by chemiluminescence. Total phosphorus (TP) and total nitrogen (TN) are determined by analysis of phosphate and nitrate, respectively, after oxidation by high-intensity ultraviolet light. Total organic phosphorus and total organic nitrogen are determined by subtracting background PO4 and NO3+NO2 from TP and TN, respectively. Time is in UTC.
DOI: 10.6084/m9.figshare.23664546
title: Fig 6, SFig 7.xlsx

description: Figure 6, and Supplementary Figure 7 data from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.23983032
title: Fig 4.xlsx

description: Figure 4 data from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.23983032.v1
title: Fig 4.xlsx

description: Figure 4 data from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.5281/zenodo.8393591
title: other

description: Data of the paper "Other"
DOI: 10.5281/zenodo.8393575
title: other

description: Data of the paper "Other"
DOI: 10.6084/m9.figshare.23664543
title: Fig 3.xlsx

description: Figure 3 data from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.23664543.v1
title: Fig 3.xlsx

description: Figure 3 data from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.23638839
title: Fig 5, SFig 6.xlsx

description: Data from Figure 5 and Supplementary Figure 6 of "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.23638839.v1
title: Fig 5, SFig 6.xlsx

description: Data from Figure 5 and Supplementary Figure 6 of "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.22003/xfel.eu-data-003777-00
title: High-resolution measurements of the electronic response of materials from the visible to extreme ultraviolet
DOI: 10.22003/xfel.eu-data-003375-00
title: Structure and Function of Heme Dioxygenases
DOI: 10.22003/xfel.eu-data-004036-00
title: 2D crystals of bacterial spore coat proteins
DOI: 10.22003/xfel.eu-data-004423-00
title: Characterization of early intermediates in the photoactivation pathway of a bacterial adenylate cyclase
DOI: 10.22003/xfel.eu-data-004491-00
title: Towards understanding heating mechanisms of warm dense matter using short pulse laser
DOI: 10.22003/xfel.eu-data-004079-00
title: Uncovering the nature of ultrafast lattice dynamics driving polaron formation in bismuth vanadate films for artificial photosynthesis
DOI: 10.22003/xfel.eu-data-004099-00
title: Structure Determination of Crystalline and Quasiperiodic Designer DNA Molecular Scaffolds with XFEL Pulses
DOI: 10.22003/xfel.eu-data-004502-00
title: Deciphering the half-reductive reaction mechanism of a human flavoprotein by TR-SFX with Minimized Sample Consumption at the EuXFEL
DOI: 10.6084/m9.figshare.22782959.v1
title: Fig 2, SFig 3.xlsx

description: Data from Figure 2 and Supplementary Figure 3 of "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.22782959
title: Fig 2, SFig 3.xlsx

description: Data from Figure 2 and Supplementary Figure 3 of "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.22714417
title: Fig 1D-G, SFig 2.xlsx

description: Data from Figure 1D-G and Supplementary Figure 2 in "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.22714417.v1
title: Fig 1D-G, SFig 2.xlsx

description: Data from Figure 1D-G and Supplementary Figure 2 in "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.22714327
title: Fig 1A,B + SFig 1.xlsx

description: Data from Figure 1A,B and Supplemental Figure 1 from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.6084/m9.figshare.22714327.v1
title: Fig 1A,B + SFig 1.xlsx

description: Data from Figure 1A,B and Supplemental Figure 1 from "Sexual differentiation of neural mechanisms of stress sensitivity during puberty".
DOI: 10.5281/zenodo.7079778
title: Data and Code for "An updated end-to-end ecosystem model of the Northern California Current"

description: This upload contains all data and code for "An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves", submitted to PLOS ONE. Manuscript abstract is pasted below: The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (<em>Oncorhynchus tshawytscha</em>) and southern resident killer whales (<em>Orcinus orca</em>). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 100-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.
DOI: 10.5281/zenodo.7806546
title: Data and Code for "An updated end-to-end ecosystem model of the Northern California Current"

description: This upload contains all data and code for "An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves", submitted to PLOS ONE. Manuscript abstract is pasted below: The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (<em>Oncorhynchus tshawytscha</em>) and southern resident killer whales (<em>Orcinus orca</em>). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 100-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.
DOI: 10.5281/zenodo.7951097
title: Data and Code for "An updated end-to-end ecosystem model of the Northern California Current"

description: This upload contains all data and code for "An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves", submitted to PLOS ONE. Manuscript abstract is pasted below: The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (<em>Oncorhynchus tshawytscha</em>) and southern resident killer whales (<em>Orcinus orca</em>). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 100-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.
DOI: 10.5281/zenodo.8015467
title: Data and Code for "An updated end-to-end ecosystem model of the Northern California Current"

description: This upload contains all data and code for "An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves", submitted to PLOS ONE. Manuscript abstract is pasted below: The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (<em>Oncorhynchus tshawytscha</em>) and southern resident killer whales (<em>Orcinus orca</em>). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 100-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.