cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10257740
title: Serine-129 phosphorylation of a-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function

description: Phosphorylation of a-synuclein at the Serine-129 site (a-syn Ser129P) is an established pathologic hallmark of synucleinopathies and a therapeutic target. In physiologic states, only a small fraction of a-syn is phosphorylated at this site, and most studies have focused on the pathologic roles of this post-translational modification. We found that unlike wild-type (WT) a-syn which is widely expressed throughout the brain, the overall pattern of a-syn Ser129P is restricted, suggesting intrinsic regulation. Surprisingly, preventing Ser129P blocked activity-dependent synaptic attenuation by a-syn – thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments Ser129P, which is a trigger for protein-protein interactions that are necessary for mediating a-syn function at the synapse. AlphaFold2-driven modeling and membrane-binding simulations suggest a scenario where Ser129P induces conformational changes that facilitate interactions with binding partners. Our experiments offer a new conceptual platform for investigating the role of Ser129 in synucleinopathies, with implications for drug-development. 
description: Data associated with https://doi.org/10.1101/2022.12.22.521485
DOI: 10.5281/zenodo.10257850
title: Serine-129 phosphorylation of a-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function

description: Phosphorylation of a-synuclein at the Serine-129 site (a-syn Ser129P) is an established pathologic hallmark of synucleinopathies and a therapeutic target. In physiologic states, only a small fraction of a-syn is phosphorylated at this site, and most studies have focused on the pathologic roles of this post-translational modification. We found that unlike wild-type (WT) a-syn which is widely expressed throughout the brain, the overall pattern of a-syn Ser129P is restricted, suggesting intrinsic regulation. Surprisingly, preventing Ser129P blocked activity-dependent synaptic attenuation by a-syn – thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments Ser129P, which is a trigger for protein-protein interactions that are necessary for mediating a-syn function at the synapse. AlphaFold2-driven modeling and membrane-binding simulations suggest a scenario where Ser129P induces conformational changes that facilitate interactions with binding partners. Our experiments offer a new conceptual platform for investigating the role of Ser129 in synucleinopathies, with implications for drug-development. 
description: Data associated with https://doi.org/10.1101/2022.12.22.521485
DOI: 10.25573/data.23676900
title: SHARAD Studies of Total Electron Content at Mars

description: Data supporting analysis and publication of SHARAD studies of the Total Electron Content of the Ionosphere of Mars.The text file: tec_fraction_250km_80613_10S_90S_90E_270E.txt contains averaged values of the TEC variation from an along-track best fit with solar zenith angle. This is a list of latitude, longitude, and TEC variation about unity for mean values within a 250-km diameter circle about cells centered 0.5 degrees apart. SHARAD data through orbit 80613 were used.The image file coverage_south_80613.jpg is a color map of the number of SHARAD tracks crossing a 250-diameter cell within the map. The lowest color values correspond to 8 tracks. Black areas fall below this cutoff.
DOI: 10.25345/c50c4sw3f
title: MassIVE MSV000093561 - High-Throughput Glycan Profiling of Human Serum IgG Subclasses Using Parallel Reaction Monitoring Peptide Bond Fragmentation of Glycopeptides and Microflow LC-MS
title: We described a targeted method based on MnESI-MS platform to characterize N-glycosylation profile in IgG subclasses in human serum. The peptide bond fragmentation of glycopeptides were used for distiguising IgG3 and IgG4 which share identical mass and retention time.
DOI: 10.25390/caryinstitute.22184062.v2
title: Data and code associated with: Gora, E.M., Schnitzer, S.A., Bitzer, P.M., Burchfield, J.C., Gutierrez, C. and Yanoviak, S.P. (2023), Lianas increase lightning-caused disturbance severity in a tropical forest. New Phytol, 238: 1865-1875

description: <b>Abstract:</b>Lightning is an important agent of plant mortality and disturbance in forests. Lightning-caused disturbance is highly variable in terms of its area of effect and disturbance severity (i.e., tree damage and death), but we do not know how this variation is influenced by forest structure and plant composition. We used a novel lightning detection system to quantify how lianas influenced the severity and spatial extent (i.e., area) of lightning disturbance using 78 lightning strikes in central Panama. The local density of lianas (measured as liana basal area) was positively associated with the number of trees killed and damaged by lightning, and patterns of plant damage indicated that this occurred because lianas facilitated more electrical connections from large to small trees. Liana presence, however, did not increase the area of the disturbance. Thus, lianas increased the severity of lightning disturbance by facilitating damage to additional trees without influencing the footprint of the disturbance. These findings indicate that lianas spread electricity to damage and kill understory trees that otherwise would survive a strike. As liana abundance increases in tropical forests, their negative effects on tree survival with respect to the severity of lightning-related tree damage and death is likely to increase.<b>File list:</b>current_transfer_bystrike.csvperstrike_lianas_chars.csvGora_etal_2023_ReadMe.csv - contains metadata for CSV files, including variable definitions.electric_current_transfer.Rlianas_predict_lightning.R<br>
DOI: 10.25390/caryinstitute.22184062
title: Data and code associated with: Gora, E.M., Schnitzer, S.A., Bitzer, P.M., Burchfield, J.C., Gutierrez, C. and Yanoviak, S.P. (2023), Lianas increase lightning-caused disturbance severity in a tropical forest. New Phytol, 238: 1865-1875

description: <b>Abstract:</b>Lightning is an important agent of plant mortality and disturbance in forests. Lightning-caused disturbance is highly variable in terms of its area of effect and disturbance severity (i.e., tree damage and death), but we do not know how this variation is influenced by forest structure and plant composition. We used a novel lightning detection system to quantify how lianas influenced the severity and spatial extent (i.e., area) of lightning disturbance using 78 lightning strikes in central Panama. The local density of lianas (measured as liana basal area) was positively associated with the number of trees killed and damaged by lightning, and patterns of plant damage indicated that this occurred because lianas facilitated more electrical connections from large to small trees. Liana presence, however, did not increase the area of the disturbance. Thus, lianas increased the severity of lightning disturbance by facilitating damage to additional trees without influencing the footprint of the disturbance. These findings indicate that lianas spread electricity to damage and kill understory trees that otherwise would survive a strike. As liana abundance increases in tropical forests, their negative effects on tree survival with respect to the severity of lightning-related tree damage and death is likely to increase.<b>File list:</b>current_transfer_bystrike.csvperstrike_lianas_chars.csvGora_etal_2023_ReadMe.csv - contains metadata for CSV files, including variable definitions.electric_current_transfer.Rlianas_predict_lightning.R<br>
DOI: 10.25390/caryinstitute.22184062.v1
title: Data and code associated with: Evan M. Gora, Stefan A. Schnitzer, Phillip M. Bitzer, Jeffrey C. Burchfield, Cesar Gutierrez, and Stephen P. Yanoviak. In press. Lianas increase lightning-caused disturbance severity in a tropical forest. New Phytologist

description: These files are associated with, Evan M. Gora, Stefan A. Schnitzer, Phillip M. Bitzer, Jeffrey C. Burchfield, Cesar Gutierrez, and Stephen P. Yanoviak. <em>In press.</em> Lianas increase lightning-caused disturbance severity in a tropical forest. New Phytologist. <strong>Abstract:</strong> Lightning is an important agent of plant mortality and disturbance in forests. Lightning-caused disturbance is highly variable in terms of its area of effect and disturbance severity (i.e., tree damage and death), but we do not know how this variation is influenced by forest structure and plant composition. We used a novel lightning detection system to quantify how lianas influenced the severity and spatial extent (i.e., area) of lightning disturbance using 78 lightning strikes in central Panama. The local density of lianas (measured as liana basal area) was positively associated with the number of trees killed and damaged by lightning, and patterns of plant damage indicated that this occurred because lianas facilitated more electrical connections from large to small trees. Liana presence, however, did not increase the area of the disturbance. Thus, lianas increased the severity of lightning disturbance by facilitating damage to additional trees without influencing the footprint of the disturbance. These findings indicate that lianas spread electricity to damage and kill understory trees that otherwise would survive a strike. As liana abundance increases in tropical forests, their negative effects on tree survival with respect to the severity of lightning-related tree damage and death is likely to increase. <strong>File list:</strong> current_transfer_bystrike.csv perstrike_lianas_chars.csv Gora_etal_2023_ReadMe.csv - contains metadata for CSV files, including variable definitions. electric_current_transfer.R lianas_predict_lightning.R <br>
DOI: 10.6084/m9.figshare.24729954
title: System Identification of Interaction Network in Insect Group Flights by Cross Correlation

description: Despite significant communication and processing limitations, flying insects frequently demonstrate coordinated flight in crowded assemblies. Identifying the feedback mechanisms that enable these maneuvers remains a challenging task. This study experimentally records multiple flying insects induced to chase a moving vertical visual stimulus, and a cross-correlation based system identification method is developed to identify their interaction networks. Modeling the interaction network as a series of pairwise-directed graphs, the adjacency matrix weights are identified serially by indexing agent wise through temporal cross correlation. The induced matrix 2 norm, in and out-degree weight sum, and degree distributions are then computed for 1000 examples of recorded interaction networks to reveal aggregate trends. The results show a consistency in topological neighbor choice, with 68\% of agents limiting their connectivity to 2-4 agents. Information sharing among insects (as measured by adjacency matrix norm) grows in direct proportion to group size. The degree distribution obeys a power law distribution, consistent with scale free networks. Numerous examples of insect pairs sharing similar velocities were also identified. The interaction network identification implementation and findings can help in the understanding swarm models for insects in cluttered group flight as well as identifying neighbor-relative feedback control strategies for engineered air vehicles.
DOI: 10.6084/m9.figshare.24729954.v1
title: System Identification of Interaction Network in Insect Group Flights by Cross Correlation

description: Despite significant communication and processing limitations, flying insects frequently demonstrate coordinated flight in crowded assemblies. Identifying the feedback mechanisms that enable these maneuvers remains a challenging task. This study experimentally records multiple flying insects induced to chase a moving vertical visual stimulus, and a cross-correlation based system identification method is developed to identify their interaction networks. Modeling the interaction network as a series of pairwise-directed graphs, the adjacency matrix weights are identified serially by indexing agent wise through temporal cross correlation. The induced matrix 2 norm, in and out-degree weight sum, and degree distributions are then computed for 1000 examples of recorded interaction networks to reveal aggregate trends. The results show a consistency in topological neighbor choice, with 68\% of agents limiting their connectivity to 2-4 agents. Information sharing among insects (as measured by adjacency matrix norm) grows in direct proportion to group size. The degree distribution obeys a power law distribution, consistent with scale free networks. Numerous examples of insect pairs sharing similar velocities were also identified. The interaction network identification implementation and findings can help in the understanding swarm models for insects in cluttered group flight as well as identifying neighbor-relative feedback control strategies for engineered air vehicles.
DOI: 10.5066/p98ltter
title: MODFLOW-2005 and MODPATH models in support of groundwater flow model investigation of water resources at Chaco Culture National Historical Park

description: Situated in a remote corner of northwestern New Mexico, Chaco Culture National Historical Park (CCNHP) was once the center of a sophisticated social, political and architectural civilization with a 50,000-square mile sphere of influence. The park protects the greatest concentration of Chacoan historical sites in the American Southwest and is arguably the most significant prehistoric site in North America. Following decades of unsuccessful attempts to develop usable near-surface water sources, the National Park Service constructed a 3,100-foot deep well into the Gallup Sandstone aquifer in 1972, providing the park with the first reliable drinking water source since it was established in 1907. The ~100-foot thick Gallup Sandstone is sandwiched between thick confining sequences of the lower-permeability Mancos Shale. Both the Mancos Shale and the Gallup Sandstone are part of the San Juan Basin and critically, both units have long been targeted for oil and natural gas development. Groundwater-flow (MODFLOW-2005) and advective transport (MODPATH) models of the Mancos Shale and Gallup Sandstone units in the vicinity of CCNHP were created in order to determine groundwater-flow paths to the park well, and to test how potential hydraulic fracturing operations could influence the well. This USGS data release contains input and output files for the model simulations documented in the associated model report (https://doi.org/10.3133/sir20235097). In total, 204 groundwater-flow and 206 particle-tracking simulations were performed.
DOI: 10.5281/zenodo.10251835
title: Data from: Role of mass transport in electrochemical carbon dioxide reduction to methanol using immobilized cobalt phthalocyanine

description: Cell files.zip

.dwg files of the pocket for the cathode and anode chamber. 
.dwg files of the gasket design
Experimental data.zip (>60 experiments)

Chronoamperometry data
Each experiment has a mpr and txt file. The .mpr file can be read by EC-lab software, while the txt file has the raw data.
H-NMR data
Each experiment has its own folder, then another folder with the experiment number. Within that experiment number folder is .fid file needed to view the H-NMR data. 
Gas Chromatography data 
Each experiment has its own folder. the files can be opened using SRI proprietary software. There are also .log files which contain the results of each experiment as the raw data. 
description: This material is based on work performed by the Liquid Sunlight Alliance, which is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Fuels from Sunlight Hub under Award Number DE-SC0021266. TC acknowledges fellowship support from the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program. The SCGSR program is administered by the Oak Ridge Institute for Science and Education for the DOE under contract number DE‐SC0014664. AJK acknowledges funding from the National Science Foundation Graduate Research Fellowship under Grant No. DGE 2146752.
DOI: 10.5281/zenodo.10251836
title: Data from: Role of mass transport in electrochemical carbon dioxide reduction to methanol using immobilized cobalt phthalocyanine

description: Cell files.zip

.dwg files of the pocket for the cathode and anode chamber. 
.dwg files of the gasket design
Experimental data.zip (>60 experiments)

Chronoamperometry data
Each experiment has a mpr and txt file. The .mpr file can be read by EC-lab software, while the txt file has the raw data.
H-NMR data
Each experiment has its own folder, then another folder with the experiment number. Within that experiment number folder is .fid file needed to view the H-NMR data. 
Gas Chromatography data 
Each experiment has its own folder. the files can be opened using SRI proprietary software. There are also .log files which contain the results of each experiment as the raw data. 
description: This material is based on work performed by the Liquid Sunlight Alliance, which is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Fuels from Sunlight Hub under Award Number DE-SC0021266. TC acknowledges fellowship support from the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program. The SCGSR program is administered by the Oak Ridge Institute for Science and Education for the DOE under contract number DE‐SC0014664. AJK acknowledges funding from the National Science Foundation Graduate Research Fellowship under Grant No. DGE 2146752.
DOI: 10.25345/c5vm4377r
title: MassIVE MSV000093562 - Comparison of glycopeptide to released glycan abundances and the influence of glycopeptide charge state on N-linked glycosylation of IgG antibodies
title: We report the comparison of mass-spectral-based abundances of tryptic glycopeptides with fluorescence abundances of released labeled glycans, both derived from therapeutic monoclonal antibodies. These proteins were selected for their very high purities, which assures the origin of all observed released glycans. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances over a dynamic range of 500. The primary glycoforms derived from Rituximab, NISTmAb, Evolocumab, and Infliximab were high mannose and biantennary complex galactosylated and fucosylated and, in some cases, sialylated N-glycans. Except for Evolucumab, in-source ions derived from the loss of HexNAc or HexNAc and hexose sugars to HexNAc(4)Hex(4)Fuc(1) glycoform are prominent for other therapeutic IgGs. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances across all mAb samples over a dynamic range of 500. Different charge states of human IgG-derived glycopeptides containing a wider variety of abundant attached glycans were also investigated closely to examine the effect of charge state on ion abundances. These results confirmed and refined results for the therapeutic proteins, clearly revealing a linear dependence of relative glycopeptide abundance on the mass of the glycan, with higher charge states favoring higher mass glycans. Overall, our findings indicate that the mass-spectrometry-based bottom-up approach can provide results as accurate as those of glycan release studies while revealing the origin of each attached glycan. These site-specific relative abundances are conveniently displayed and compared using previously described Glycopeptide Abundance Distribution Spectra GADS representations.
DOI: 10.5517/ccdc.csd.cc2c9kz7
title: CCDC 2183949: Experimental Crystal Structure Determination

description: Related Article: Zhenkai Lei, Fei Xue, Bin Wang, Shijie Wang, Yu Xia, Yonghong Zhang, Weiwei Jin, Chenjiang Liu|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.cc2c9l09
title: CCDC 2183950: Experimental Crystal Structure Determination

description: Related Article: Zhenkai Lei, Fei Xue, Bin Wang, Shijie Wang, Yu Xia, Yonghong Zhang, Weiwei Jin, Chenjiang Liu|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: 10.34740/kaggle/dsv/7114277
title: TMF Business Process Framework Dataset for Neo4j
DOI: 10.5281/zenodo.10206478
title: Experimental and theoretical analysis of ultrafast electron diffraction (UED) data for acetylacetone

description: Here, in two archives with data for ultrafast electron diffraction (UED) study of the acetylacetone.

AcAc_UED_theoretical.zip contains the results of theoretical simulations.
AcAc_UED_experimental.zip contains raw and processed experimental data and scripts for data processing.
Within each of the ZIP archives, the README files provide information on the actual data content within.
DOI: 10.5281/zenodo.10206479
title: Experimental and theoretical analysis of ultrafast electron diffraction (UED) data for acetylacetone

description: Here, in two archives with data for ultrafast electron diffraction (UED) study of the acetylacetone.

AcAc_UED_theoretical.zip contains the results of theoretical simulations.
AcAc_UED_experimental.zip contains raw and processed experimental data and scripts for data processing.
Within each of the ZIP archives, the README files provide information on the actual data content within.
DOI: 10.5281/zenodo.10109654
title: Data from: Importance of Site Diversity and Connectivity in Electrochemical CO reduction on Cu

description: Microkinetic Modeling

Contains raw ipynb files to generate graphs used in this work
EC-Lab Potentiosat Data

Contains potentiostat I-V data, organized in folder by date of acquisition
Mass flow and product quantification

Mass flow measurements, gas chromatography, and nuclear magnetic resonance spectroscopy
Overview of all experiments

Spreadsheets listing all experiments
Cell Design

Files for the 1 cm2 gas diffusion electrodes used in this work.
description: This work was supported by the Clean Energy Manufacturing Program, U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division, in under Contract No. DE-AC02-05CH11231. Research on microkinetic modeling was supported as part of the Center for Closing the Carbon Cycle, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences (BES), under Award Number DE-SC0023427.