cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4231/ya7s-h420
title: LG MJ1 Vent Cap CT Scans

description: &lt;p&gt;&lt;strong&gt;Purpose:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Computed tomography (CT) scans of an LG MJ1 18650 vent cap assembly were conducted to analyze the geometry and structure of  the vent cap assembly including key safety devices, such as: the current interrupt device (CID) and burst disk.  The bundled data files may be used to inspect the vent cap assembly and take measurements of geometric features.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Method:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The following excerpt is from the paper by Li et al. [1]:&lt;/p&gt;

&lt;blockquote&gt;... CT scans were conducted using an X50 industrial X-ray inspection system from North Star Imaging (NSI).  The CT scans had spatial resolution of 16.6&mu;m.  3D renderings of the CT scans were created with a filtered back projection algorithm using ex-X CT Software from North Star Imaging.   The 3D rendering dimensions were calibrated by scanning a reference standard with the same scan parameters and were viewed using efX-CT Lite v. 2.0.5.0 software. ... CT scans were conducted for three different states of failure: intact (normal operation), CID activated, and vent activated.&lt;/blockquote&gt;

&lt;p&gt;&lt;strong&gt;Quick Start Guide:&lt;/strong&gt;&lt;/p&gt;

&lt;ol&gt;
 &lt;li&gt;Download bundle&lt;/li&gt;
 &lt;li&gt;Open executable file for one of three operational states: intact, CID activated, or vent activated&lt;/li&gt;
 &lt;li&gt;Use &quot;X&quot;, &quot;Y&quot;, or &quot;Z&quot; keys to change viewing plane&lt;/li&gt;
 &lt;li&gt;Use spacebar to toggle between viewing window and scan data&lt;/li&gt;
 &lt;li&gt;Use mouse left-click and drag to rotate plane&lt;/li&gt;
 &lt;li&gt;Use mouse wheel to move viewing plane through the volume&lt;/li&gt;
 &lt;li&gt;Use the histogram tool to improve contrast and brightness&lt;/li&gt;
 &lt;li&gt;Extract 2D slices to make measurements of length, diameter, angle, etc.&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;&lt;strong&gt;REFERENCES:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;[1] Li, W., Crompton, K. R., Hacker, C., &amp; Ostanek, J. K. (2020). Comparison of Current Interrupt Device and Vent Design for 18650 Format Lithium-ion Battery Caps. &lt;em&gt;Journal of Energy Storage&lt;/em&gt;, 32, 101890. doi:&lt;a href="https://doi.org/10.1016/j.est.2020.101890" target="_blank"&gt;10.1016/j.est.2020.101890&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;DISTRIBUTION STATEMENT A.&lt;/strong&gt; Approved for public release: distribution unlimited.&lt;/p&gt;

&lt;p&gt; &lt;/p&gt;
description: This dataset includes computed tomography (CT) scans of the positive terminal assembly from a commercial lithium-ion battery (model: LG INR18650 MJ1).
DOI: 10.4231/v87t-4x79
title: Positions of known ICRs/gDMRs with respect to peaks in plots of ZFBS-morph-overlap density in the mouse genome

description: &lt;p&gt;In mammalian genomes, a subset of genes is imprinted to produce parent-of-origin-specific expression.  This process is regulated by ICRs/gDMRs.  Previously, I demonstrated that in the mouse genome, the ICRs/gDMRs often encompass clusters of a set of composite-DNA-elements known as ZFBS-morph overlaps.  These elements  are CpG-rich.  They consist of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes.  In order to facilitate the detection of such clusters, a publication offered a dataset for displaying the density of ZFBS-morph overlaps in the built mm9 of the mouse genome.  You can access and download this dataset via &lt;em&gt;Purdue University Research Repository&lt;/em&gt; doi:10.4231/R7W37TJH (&lt;a href="https://purr.purdue.edu/publications/2961/1"&gt;https://purr.purdue.edu/publications/2961/1&lt;/a&gt;).  The goal of the project is to create a framework for &lt;em&gt;de&lt;/em&gt; &lt;em&gt;novo&lt;/em&gt; discovery of candidate ICRs and imprinted genes. &lt;/p&gt;

&lt;p&gt;To investigate the validity of my strategy, initially I obtained snapshots of peak positions in plots of the entire chromosomal DNA sequences.  The plots were displayed with respect to known ICRs/gDMRs and results of ChIPs (chromatin (immunoprecipitation assays) performed using mouse embryonic stem cells (ESCs) E14.  I obtained the experimental data &lt;em&gt;via&lt;/em&gt; a link listed in the GEO series GSE77444 &mdash;Riso et al. &lt;em&gt;Nucleic Acids Res&lt;/em&gt; 44, &lt;a href="tel:8165-8178"&gt;8165-8178&lt;/a&gt; (2016).  From the extensive experimental datasets, I selected the track displaying the genomic positions of the known ICRs/gDMRs, and tracks displaying results of ChIPs corresponding to ZFP57, KAP1, and H3K9me3.  You can access and download these plots &lt;em&gt;via&lt;/em&gt; &lt;em&gt;Purdue University Research Repository &lt;/em&gt;doi:10.4231/32C9-G644 (&lt;a href="https://purr.purdue.edu/publications/3493/1"&gt;https://purr.purdue.edu/publications/3493/1&lt;/a&gt;).&lt;/p&gt;

&lt;p&gt;Here, I provide a series of snapshots, showing closeup views of peak-positions in the density-plots, with respect to the known ICRs/gDMRs and results of ChIPs.  These plots clearly demonstrate that peaks in plots correctly located the known ICRs/gDMRs with respect to experimental results.  You can access a PDF of the images by clicking on download &ndash;on the top right-side of this page. &lt;/p&gt;

&lt;p&gt;If you observe anomalies on this page and if you encounter a problem with downloading the bed file, please contact bina@ purdue.edu&lt;/p&gt;
description: Supplementary material for the publication entitled “Simultaneous discovery of candidate imprinted genes and Imprinting Control Regions in the mouse genome” Bina M., and Wyss P.
bioRxiv doi: https://doi.org/10.1101/780551 (2019).
DOI: 10.4231/p800-nm47
title: Data for: Warm temperatures increase population growth of a non-native defoliator and inhibit demographic responses by parasitoids

description: &lt;p&gt;Changes in thermal regimes that disparately affect hosts and parasitoids could release hosts from biological control. When multiple natural enemy species share a host, shifts in host-parasitoid dynamics could depend on whether natural enemies interact antagonistically versus synergistically. We investigated how biotic and abiotic factors influence the population ecology of larch casebearer (&lt;i&gt;Coleophora laricella&lt;/i&gt;), a non-native pest, and two imported parasitoids, &lt;i&gt;Agathis pumila &lt;/i&gt;and &lt;i&gt;Chrysocharis laricinellae&lt;/i&gt;, by analyzing (i) temporal dynamics in defoliation from 1962-2018 and (ii) historical, branch-level data on densities of larch casebearer and parasitism rates by the two imported natural enemies from 1972-1995. Analyses of defoliation indicated that, prior to the introduction of parasitoids (1962 to ~1980), larch casebearer outbreaks occurred in 2 to 6 year cycles. This pattern was followed by a &gt;15-year period during which populations were at low, apparently stable densities undetectable via aerial surveys, presumably under control from parasitoids. However, since the late 1990s and despite the persistence of both parasitoids, outbreaks exhibiting unstable dynamics have occurred. Analyses of branch-level data indicated that growth of casebearer populations, &lt;i&gt;A. pumila &lt;/i&gt;populations, and within-casebearer densities of &lt;i&gt;Ch. laricinellae&lt;/i&gt; &ndash; a generalist whose population dynamics are likely also influenced by use of alternative hosts &ndash; were inhibited by density-dependence, with high intraspecific densities in one year slowing growth into the next. Casebearer population growth was also inhibited by parasitism from &lt;i&gt;A. pumila&lt;/i&gt;, but not &lt;i&gt;Ch. &lt;/i&gt;&lt;i&gt;laricinellae&lt;/i&gt;, and increased with warmer autumnal temperatures. Growth of &lt;i&gt;A. pumila &lt;/i&gt;populations and within-casebearer densities of&lt;i&gt; Ch. laricinellae &lt;/i&gt;increased with casebearer densities but decreased with warmer annual maximum temperatures. Moreover, parasitism by &lt;i&gt;A. pumila &lt;/i&gt;was associated with increased growth of within-casebearer densities of &lt;i&gt;Ch. laricinellae &lt;/i&gt;without adverse effects on its own demographics, indicating a synergistic interaction between these parasitoids. Our results indicate that warming can be associated with opposing effects between trophic levels, with deleterious effects of warming on one natural enemy species&lt;i&gt; &lt;/i&gt;potentially being exacerbated by similar impacts on another. Coupling of such parasitoid responses with positive responses of hosts to warming might have contributed to the return of casebearer outbreaks to North America.&lt;/p&gt;
description: Abundance of larch casebearer (larvae, adults) on western larch in Oregon and Washington (1972-1995) along with parasitism rates from two imported biological control agents.
DOI: 10.5281/zenodo.17981608
title: The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance

description: The kink-turn is a recurrent RNA structural motif that induces a sharp bend (kink) in the A-form RNA helix. It is defined by key structural features, including consecutive sheared AG base pairs, an A-minor interaction, and multiple base–sugar interactions. An accurate representation of these densely packed noncanonical interactions by molecular dynamics simulations poses a significant challenge for contemporary force fields (FFs). Here, we present extended simulations of the ribosomal kink-turn 7 (Kt-7) from H.m., the so-called “consensual” kink-turn, using a broad spectrum of pair-additive and polarizable RNA FFs. None of the tested FFs manage to flawlessly describe all of the structural features of the Kt-7 although several FFs provide rather acceptable results and should not cause problems in simulations of larger RNAs containing a kink-turn. On aggregate, the widely used OL3 (ff99bsc0χOL3) and polarizable AMOEBA FFs achieve the best performance for this motif. Interestingly, some more recently parametrized FF variants struggle to describe the Kt-7’s tertiary A-minor interaction – a ubiquitous tertiary contact in RNA. This raises some concerns about the broader applicability of these FFs and suggests that they may be overfitted to small model systems, such as RNA tetranucleotides. In some cases, irreversible unkinking of the entire kink-turn motif can also be observed. The kink-turn motif is highly sensitive to variations in RNA FFs, and we strongly recommend its inclusion in training and benchmarking data sets as an important regression test to improve the robustness and accuracy of RNA FF parametrization.

This deposition contains the manuscript files as well as the data necessary to reproduce main text and SI images and tables, and TOC, in accordance with the funding rules.
DOI: 10.5281/zenodo.17981609
title: The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance

description: The kink-turn is a recurrent RNA structural motif that induces a sharp bend (kink) in the A-form RNA helix. It is defined by key structural features, including consecutive sheared AG base pairs, an A-minor interaction, and multiple base–sugar interactions. An accurate representation of these densely packed noncanonical interactions by molecular dynamics simulations poses a significant challenge for contemporary force fields (FFs). Here, we present extended simulations of the ribosomal kink-turn 7 (Kt-7) from H.m., the so-called “consensual” kink-turn, using a broad spectrum of pair-additive and polarizable RNA FFs. None of the tested FFs manage to flawlessly describe all of the structural features of the Kt-7 although several FFs provide rather acceptable results and should not cause problems in simulations of larger RNAs containing a kink-turn. On aggregate, the widely used OL3 (ff99bsc0χOL3) and polarizable AMOEBA FFs achieve the best performance for this motif. Interestingly, some more recently parametrized FF variants struggle to describe the Kt-7’s tertiary A-minor interaction – a ubiquitous tertiary contact in RNA. This raises some concerns about the broader applicability of these FFs and suggests that they may be overfitted to small model systems, such as RNA tetranucleotides. In some cases, irreversible unkinking of the entire kink-turn motif can also be observed. The kink-turn motif is highly sensitive to variations in RNA FFs, and we strongly recommend its inclusion in training and benchmarking data sets as an important regression test to improve the robustness and accuracy of RNA FF parametrization.

This deposition contains the manuscript files as well as the data necessary to reproduce main text and SI images and tables, and TOC, in accordance with the funding rules.
DOI: 10.4231/fv6t-nq34
title: Data for: Effects of terrestrial transport corridors and associated landscape context on invasion by forest plants

description: &lt;p&gt;The construction, use, and maintenance of roads and railroads (terrestrial transport corridors, TTCs) facilitate spread of invasive plants, but the distances at which plants spread away from TTCs, and how that process is mediated by landscape context, is not well understood. We analyzed data from 44,000+ forest inventory plots in the eastern USA to investigate how invasive richness, defined as the number of invasive plant species per ~672 m&lt;sup&gt;2&lt;/sup&gt; plot, is influenced by distance from the nearest TTC, surrounding land use type, and ecological province using a generalized linear model framework. Invasive richness in forests decreased as distance from the nearest TTC increased. Directly adjacent to TTCs, there were an estimated 1.4 &plusmn; 0.01 SE invasive plant species per plot compared to 0.7 &plusmn; 0.01 and 0.2 &plusmn; 0.01 species at 1 km and 3 km, respectively, away from the nearest TTC. Invasive richness was highest on plots associated with a combination of agriculture/development (2.1 &plusmn; 0.03 species per plot) and in the Midwest Broadleaf Forest province (2.1 &plusmn; 0.06). Our macroscale analysis also demonstrated that rates of decay in invasive richness away from TTCs was mediated by the types of land use and ecological provinces within which plots were located. The influences of TTCs and associated activities (e.g., construction, travel) on invasive plant richness were widespread across forests of the eastern USA, but the relative importance of TTCs for facilitating spread appear to be highly context dependent.&lt;/p&gt;

&lt;p&gt; &lt;/p&gt;

&lt;p&gt; &lt;/p&gt;
description: Data characterizing the number of invasive plants on Forest Inventory and Analysis (USDA Forest Service) plots across the eastern USA.
DOI: 10.4231/0m14-ey38
title: Data Sets for: Quantifying the Impacts of Compound Extremes on Agriculture and Irrigation Water Demand

description: &lt;p&gt;Here, we combine a high-resolution weather product (PRISM) with fine-scale outputs of a hydrologic model (WBM) to construct functional indicators of compound hydroclimatic extremes for agriculture. Data for US counties for 1981-2015. The main variables are: degree days above 29C; degree days from 10C to 29C; seasonal mean volumetric soil moisture; seasonal mean soil moisture fraction; seasonal mean evapotranspiration; cumulative precipitation; corn irrigated area share; and metrics for the daily interaction of heat and soil moisture. &lt;/p&gt;
description: Metrics of heat stress, water stress, and compound extremes for agriculture for US counties for 1981-2015.
DOI: 10.4231/q07d-j369
title: Model Code for: Quantifying the Impacts of Compound Extremes on Agriculture and Irrigation Water Demand

description: &lt;p&gt;The code will estimate 1) the marginal impacts of heat stress on crop yields; 2) the marginal impact of daily soil moisture extremes on crop yields, and 3) the conditional marginal impact of heat and soil moisture on crop yields. This code can be used for studying the impacts of compound extremes on agriculture. The code generates figures and tables too.&lt;/p&gt;
description: This Stata code estimates a model to investigate the impacts of compound extremes, water stress, and heat stress on crop yields. It requires "soilMoistureData.dta".
DOI: 10.4231/h3n7-qb39
title: Summer Science Program in Biochemistry - Characterization of the Cdc14 phosphatase homolog from Aspergillus flavus

description: &lt;p&gt;&lt;meta charset="utf-8" /&gt;&lt;/p&gt;

&lt;p dir="ltr"&gt;&lt;b id="docs-internal-guid-090cab9b-7fff-5e25-3883-add11f337df7"&gt;The Research Project in SSP Biochemistry&lt;/b&gt;&lt;/p&gt;

&lt;p&gt;Cdc14 enzymes have been reported to be required for normal plant infection by several plant pathogen species. In the SSP Biochemistry program, research groups of 3 participants each purify and characterize the Cdc14 homolog encoded by a different plant fungal pathogen species. Each group is initially given the gene sequence for the putative Cdc14 homolog from a phytopathogenic fungus. Their overall goal is to determine if this protein would be a suitable target for development of a novel fungicide to protect crops from pathogens. They first use bioinformatic tools to generate a hypothesis about the function of the protein encoded by their gene sequence. Then, they use a recombinant plasmid to overexpress their protein in &lt;em&gt;E. coli&lt;/em&gt; and purify it using nickel affinity chromatography. They characterize steady-state kinetic properties and substrate specificity of their enzymes and compare the results to previously characterized Cdc14 from the model fungal species &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; (ScCdc14), for which structural information is available. They then design an assay to test inhibition of their enzyme by a series of compounds originally identified as&lt;em&gt; in vitro&lt;/em&gt; inhibitors of ScCdc14. They choose the best one, perform computational docking to predict how it might bind to the homology-based structural model of their enzyme&rsquo;s active site that they previously generated, and finally hypothesize about ways to optimize their inhibitor structure to improve binding and specificity by taking advantage of known features of Cdc14 substrates. In the end they conclude whether or not the active site substrate specificity is conserved enough to justify using the ScCdc14 structure as a model for designing inhibitors to their enzyme. In this publication, the biochemical results and the homology based structural modeling of the Cdc14 homolog from &lt;em&gt;Aspergillus flavus&lt;/em&gt; are presented.&lt;/p&gt;
description: In SSP Biochemistry, high school participants conduct group research projects to characterize the Cdc14 phosphatase homolog from a phytopathogenic fungus and explore its potential as a novel antifungal target to protect crops from disease.
DOI: 10.4231/fmy9-6966
title: Metadata for alfalfa varieties and experimental lines 1986 to 1999

description: &lt;p&gt;The alfalfa variety metadata file contains descriptors and characteristic of over 2900 alfalfa varieties and experimental lines used in these variety trials. The data were aggregated from the Alfalfa Variety Performance Database originally compiled in 2000 by Daniel W. Wiersma and Wayne G. Hartman (doi: &lt;a href="https://doi.org/10.4231/PHKH-4334" rel="external" target="_blank"&gt;10.4231/PHKH-4334)&lt;/a&gt;. Three companion data files also extracted from the database contain the yield (doi: &lt;a href="https://doi.org/10.4231/Y31N-5R10" rel="external" target="_blank"&gt;10.4231/Y31N-5R10)&lt;/a&gt;, forage quality (doi: &lt;a href="https://doi.org/10.4231/02PR-9H36" rel="external" target="_blank"&gt;10.4231/02PR-9H36)&lt;/a&gt;, and stand persistence data (doi: &lt;a href="https://doi.org/10.4231/KK4K-QD96" rel="external" target="_blank"&gt;10.4231/KK4K-QD96)&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;Characteristics of alfalfa varieties and experimental lines in this dataset include variety name, business and marketing information, agronomic information such as fall dormancy, grazing tolerance, and winterhardiness ratings, and pest tolerance information including pathogen and insect resistance ratings. These ratings were determined using Standardized Tests developed by the North American Alfalfa Improvement Conference (&lt;a href="http://NAAIC.org"&gt;NAAIC.org&lt;/a&gt;). Details of each test can be found as a PDF file archived at the NAAIC web site (&lt;a href="https://www.naaic.org/resource/stdtests.php"&gt;https://www.naaic.org/resource/stdtests.php&lt;/a&gt;).&lt;/p&gt;
description: A compiled dataset of the metadata for alfalfa varieties and experimental lines from the Alfalfa Variety Performance Database 1986 to 1999.
DOI: 10.4231/02pr-9h36
title: Genetic and environmental variation in alfalfa forage quality from variety testing experiments conducted in North America between 1986 and 1999

description: &lt;p&gt;The dataset contains forage quality data from alfalfa variety tests conducted by researchers in the US from 1986 through 1999. All trials measured forage yield, while a subset also measured stand persistence; these data are also available in PURR. The data were aggregated from the Alfalfa Variety Performance Database originally compiled in 2000 by Daniel W. Wiersma and Wayne G. Hartman (doi: &lt;a href="https://doi.org/10.4231/PHKH-4334" rel="external" target="_blank"&gt;10.4231/PHKH-4334)&lt;/a&gt;. The database was used to analyze long-term trends in genetic improvement of alfalfa yield, quality, and agronomic performance.&lt;/p&gt;

&lt;p&gt;The forage quality file contains cultivar- and harvest-specific forage quality and corresponding yield data. It is organized by Trial, and includes trial-specific spatial (state, latitude, longitude, elevation), and temporal (year of trial, harvest number, harvest date, planting date) details. Finally, when available soil type and statistics are also provided. A companion dataset contains the characteristics of these alfalfa varieties (doi: &lt;a href="https://doi.org/10.4231/FMY9-6966" rel="external" target="_blank"&gt;10.4231/FMY9-6966)&lt;/a&gt;.&lt;/p&gt;
description: The dataset contains data used to analyze genetic and environmental effects on alfalfa forage quality and corresponding forage yield. Data were compiled from variety tests conducted by University researchers in the US and Canada from 1986 through...
DOI: 10.4231/kk4k-qd96
title: Genetic and environmental variation in alfalfa stand persistence from variety testing experiments conducted in North America between 1986 and 1999

description: &lt;p&gt;The dataset contains stand persistence data from alfalfa variety tests conducted by University researchers in the US and Canada from 1986 through 1999. All trails measured forage yield, and some trials also measured forage quality; these data are also available in PURR. The data are aggregated from the Alfalfa Variety Performance Database originally compiled in 2000 by Daniel W. Wiersma and Wayne G. Hartman (doi: &lt;a href="https://doi.org/10.4231/PHKH-4334" rel="external" target="_blank"&gt;10.4231/PHKH-4334)&lt;/a&gt;. This database was used to analyze long-term trends in genetic improvement of alfalfa yield and persistence across a broad range of environments&lt;/p&gt;

&lt;p&gt;The stand persistence file contains cultivar-specific stand data reported for some, but not all experiments. Units for stand data are percent of a full stand, as judged by the person conducting the experiment. Variation in this subjective judgment over time and space may be present in the data. Stand estimates were generally measured near the end of the experiment. Data are organized by variety and include trial-specific spatial (state, latitude, longitude, elevation), and temporal (year of trial, harvest number, harvest date, planting date) details. Finally, when available soil type and experimental design are also provided. A companion dataset contains the characteristics of these alfalfa varieties (doi: &lt;a href="https://doi.org/10.4231/FMY9-6966" target="_blank"&gt;10.4231/FMY9-6966)&lt;/a&gt;.&lt;/p&gt;
description: The dataset contains data used to analyze genetic and environmental effects on alfalfa stand persistence. Data were compiled from alfalfa varieties tests conducted by University researchers in the US and Canada from 1986 through 1999.