cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4231/3cd8-ha69
title: Elasticity operator toolkit with embedded fracture sets

description: &lt;p&gt;Elasticity operator toolkit programmed in both Python or Matlab to perform 3D rotation on the elasticity stiffness or compliance and embed arbitrary oriented linear slip deformation (LSD) fracture sets.&lt;/p&gt;

&lt;p&gt;Key Components Python:  &lt;/p&gt;

&lt;ul&gt;
 &lt;li&gt;&lt;em&gt;&lt;strong&gt;stiffnessoperator.py&lt;/strong&gt;&lt;/em&gt;: This script contain a python class StiffnessMatrix, which is constructed with up to 21 elasticity constant C&lt;sub&gt;IJ&lt;/sub&gt;. The class has various methods to perform rotation and transformation between elasticity stiffness and compliance. More information can be found with the comments.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Key Components Matlab: &lt;/p&gt;

&lt;ul&gt;
 &lt;li&gt;&lt;strong&gt;&lt;em&gt;dipdir_dip_2dcm.ENU.m&lt;/em&gt;&lt;/strong&gt;:  This program outputs a set of Euler angles and the corresponding direction cosine rotation matrix for a plane defined by its dip direction (or azimuth) as measured clockwise looking down from geographic N and the dip angle both in degrees.  Note that the global co-ordinate frame is taken to be E-N-Up.    This is first used to obtain the direction cosine matrix dcm.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;More detailed information can be found in &lt;em&gt;&lt;strong&gt;README_Fracture_Calculations.docx&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;
description: Elasticity operator toolkit programmed in both Python or Matlab to perform 3D rotation on the elasticity stiffness or compliance and embed arbitrary oriented linear slip deformation (LSD) fracture sets.
DOI: 10.4231/fd22-9d96
title: Understanding disease-associated metabolic changes in human colon epithelial cells using iColonEpithelium metabolic reconstruction

description: &lt;p&gt;Background: The human colon epithelium is crucial for metabolic interactions with gut microbiota, which mediates influence of dietary inputs on host metabolism. Colonic epithelial cells have distinct metabolic properties essential for maintaining homeostasis, whose disturbances are associated with inflammatory bowel disease (IBD). However, metabolism of colon epithelium and its interactions with the gut microbiota at the cellular level remains poorly understood.&lt;/p&gt;

&lt;p&gt;Method: We analyzed transcriptome data of 188 healthy human colon epithelium samples from the GEO database to build the draft reconstruction of colonic epithelial cells based on the generic human metabolic reconstruction, Recon3D. It was further refined with metabolic reactions and genes specific to colon epithelium and its specificity was tested with metabolic tasks essential to colonic epithelial cells. We used colon carcinoma (Caco-2) cell line for validating findings related to short chain fatty acids and amino acids.&lt;/p&gt;

&lt;p&gt;Results: The iColonEpithelium reconstruction consisted of 6551 reactions, 1820 metabolites and 1961 genes. It can achieve essential colonic epithelial cell metabolic functions, like beta-oxidation of butyrate and acetate and tryptophan metabolism. We used it to predict metabolic changes in two case studies: ulcerative colitis (UC) and Crohn&rsquo;s diseases (CD). &lt;/p&gt;

&lt;p&gt;Conclusion and application: We present the first manually curated metabolic reconstruction of human colonic epithelial cells, namely iColonEpithelium, which captures the metabolic signatures of the cell. Ongoing integration of iColonEpithelium with gut microbiome models and multi-omics data will provide deeper insights into the role of colonic epithelial cells in the host-microbiome interactions. It will contribute to predicting dietary effects on host-microbiome metabolism and the metabolic alterations associated with various gut-related disorders.&lt;/p&gt;
description: Codes for the construction of iColomEpithelium and analysis of case studies
DOI: 10.4231/rntj-4v21
title: Physiological and behavioral responses to novel saline conditions in an invasive treefrog

description: &lt;p&gt;Salinity can be an environmental stressor for anurans, as their highly permeable skin makes them prone to osmotic stress when exposed to saline conditions. However, certain anuran species have colonized areas near saltwater habitats, suggesting an ability to acclimate to saline conditions. Here, we evaluated physiological and behavioral responses to saline conditions in adult Cuban treefrogs (&lt;em&gt;Osteopilus septentrionalis&lt;/em&gt;), an invasive anuran found throughout Florida. To examine their response to salinity, adult frogs were maintained in two treatments simulating a freshwater (0.5 ppt) or brackish (8.0 ppt) environment for six weeks. To assess their physiological response to this potential stressor, all frogs were submerged in a brackish solution to quantify individual weight change every two weeks. We found that frogs maintained in brackish solution lost more weight at weeks two and six when compared to week zero, suggesting that salinity may be an environmental stressor for Cuban treefrogs. Yet, the weight change at week four was similar to the pre-exposure period, which may indicate that constant exposure to salinity may alter their physiological response to saline conditions. To supplement the physiological analyses, we investigated avoidance behavior towards saline conditions by offering individuals a choice between freshwater or brackish environments. Our results showed that Cuban treefrogs chose freshwater environments more frequently and may thus avoid saline ones. This study reveals that salinity may induce plastic and avoidance responses in Cuban treefrogs, potentially allowing them to expand their range into areas typically stressful for most anurans. &lt;/p&gt;
description: This study evaluates physiological and behavioral responses to saline conditions in the Cuban treefrog (Osteopilus septentrionalis), an invasive anuran distributed throughout Florida.
DOI: 10.4231/qneq-wg69
title: Invasive Species Identification from High-resolution 4-band Multispectral Imagery - Data

description: &lt;p&gt;Invasive tree species pose major threats to various ecosystems, and their accurate identification and mapping are vital to the development of effective management strategies. Many invasive species demonstrate unique phenological characteristics that are visually identifiable through remote sensing. Previous species identification research relies heavily on the fusion of multiple remote sensing data sources, and are highly constricted in spatial scale.  Here, we used high resolution, single instance, 4-band aerial imagery acquired during the blooming season to identify and map Callery pear (&lt;em&gt;Pyrus calleryana&lt;/em&gt;) across all five New York City Boroughs (~1,188 km&lt;sup&gt;2&lt;/sup&gt;) in urban, suburban, and non-developed environments.  We compared traditional pixel-based filtering models against U-Net based convolutional neural networks (CNN).  The U-Net CNN greatly outperformed the traditional pixel-based models, achieving a precision, recall, and F1 score of 86.9%, 89.5%, and 88.2% respectively compared to a performance of 47.2%, 52.7%, and 49.8% for the best of the pixel-based models.  We also greatly improved CNN performance through the introduction of negative training data, specifically in non-urban areas.  We show an effective deep learning strategy for identifying and mapping canopy coverage of Callery pear, which provides a base map for monitoring and management of Callery pear in the Greater New York City Metropolitan Area.  More importantly, the method can be readily applicable to the mapping of Callery pear in other regions or other invasive species with unique phenological characteristics given the availability of punctual, high-resolution, multispectral imagery. &lt;/p&gt;
description: Data associated with invasive species (Callery Pear) identification in the greater New York City metropolitan area.
DOI: 10.4231/vh4y-fz82
title: Connected Truck Speeds on U.S. Interstates During Total Solar Eclipse 2024

description: &lt;p&gt;This dataset provides 4,989 records of hourly mile-hours of congestion (speeds operating below 45 mph) observed on interstate routes in 13 US States that the total solar eclipse of April 8, 2024 passed over. The dataset contains records for a 16-day period from March 25 through April 9, 2024 which includes the day of the eclipse.&lt;/p&gt;

&lt;p&gt;The video illustrates the use of connected truck data for monitoring freeway mobility for a 12-hour period from noon to midnight on the day of the eclipse for approximately 97,000 directional miles of interstate routes.  The path of the eclipse along with totality and partial eclipse times for cities sourced from NASA&rsquo;s Scientific Visualization Studio are overlayed on the map for context.&lt;/p&gt;

&lt;p&gt;The dataset consists of the following attributes:&lt;/p&gt;

&lt;ol&gt;
 &lt;li&gt;hour_of: timestamp in UTC representing start of hour&lt;/li&gt;
 &lt;li&gt;state: 2-letter abbreviation for US State&lt;/li&gt;
 &lt;li&gt;mhc &ndash; mile-hours of congestion&lt;br /&gt;
  &lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;A timelapse video showing connected truck speeds along U.S. Interstates for a 12 hour period from 12 PM to 12 AM eastern daylight time on Monday April 8, 2024 can be found at the following link - https://www.youtube.com/watch?v=e1zs2XSA9Tk&lt;/p&gt;
description: A visualization of connected truck data along U.S. Interstates for a 12 hour period from 12 PM to 12 AM eastern daylight time on Monday, April 8, 2024 within the contiguous United States.
DOI: 10.4231/e328-zs60
title: Tandem Mass Spectrometry for Assessment of IDH Mutation Status in Human Glioma

description: &lt;p&gt;Glioma is a malignant brain tumor. In some gliomas, mutations in isocitrate dehydrogenase (IDH) result in an abnormal accumulation of a unique biomarker called 2-hydroxyglutarate (2HG). Here, we performed two different tandem mass spectrometry measurements to detect IDH mutations in human glioma smears. Product-ion scanning and multiple reaction monitoring (MRM) were performed using desorption electrospray ionization (DESI) to assess mutation status of IDH. The intensity of 2HG was recorded against glutamate (Glu) as the reference biomarker. With both methods, a clear separation between IDH-mutant (mut) and IDH-wildtype (wt) samples (&lt;i&gt;p&lt;/i&gt; &lt; 0.0001) was observed despite the short analysis time. DESI tandem mass spectrometry demonstrates potential as an intraoperative diagnostic tool to delineate tumor boundaries and improve patient outcomes.&lt;/p&gt;
description: This data includes tandem mass spectrometry results from human glioma to detect isocitrate dehydrogenase (IDH) mutations. Product-ion scanning and multiple reaction monitoring (MRM) were done using a linear ion trap (LIT) and a triple quadrupole (TQ).
DOI: 10.4231/tt0f-kh40
title: A deep learning neural network to extract of P- and S-wave transit times from Vertical Seismic Profile (VSP)

description: &lt;p&gt;This work was motivated by our need to repetitively determine thousands of transit times from ensembles of forward modelled CSG&rsquo;s for use in a minimization inversion that focusses on obtaining in situ anisotropic elastic constants. By leveraging the capabilities of a deep learning neural network, specifically a three-layer U-net architecture with PyTorch, this could significantly reduce the labor intensity for similar inversion problem with good accuracy. Note: the current implementation has been trained exclusively on a specific complex 3D geological model with two contrasting rock types in a noise-free environment.&lt;/p&gt;
description: This archive contains the training dataset and the Python code to train a deep learning neural net that aims to extract separately P and S wave arrival transit times from synthetic common shot gathers (CSG) in a deviated borehole geometry.
DOI: 10.4231/gmqs-dj89
title: West African Heat Low Climatology and Comparison with Dry Tropical Cyclones

description: &lt;p&gt;Heat-lows are low pressure systems that have been qualitatively compared to dry tropical cyclones (TCs) given their low-level cyclonic circulation which is co-located with strong surface sensible heat fluxes. Many transient heat-lows in West Africa are likely associated with dry African Easterly Waves (AEWs). This work examines the climatology of West African heat-lows and their relationship to TCs by extending potential intensity (PI) over land. Using ERA5 reanalysis, we calculate PI over land from sensible heat flux and land surface roughness and use pre-existing data of tracked dry low-pressure systems to create composite West African heat-lows during Summer. PI spatial distribution correlates well with that of heat-low tracks and closely matches the peak heat-low wind speeds. The asymmetric and baroclinic structure of heat-low composites and the lack of marked diurnal cycles suggest that West African heat-lows are likely dominated by the traditional mixed baroclinic barotropic energy pathways of dry AEWs&lt;/p&gt;
description: This repository contains the data files and scripts required to recreate the figures for Kruskie et al. 2024 (in review), which examines the climatology of heat lows in West Africa and their relationship to tropical cyclones using potential...
DOI: 10.4231/183a-m656
title: Measuring reach, engagement, and use with penetration studies method: The impact of an animated jerrycan storage video after country-wide scaling in Ghana, Kenya, and Nigeria

description: &lt;p&gt;During the COVID-19 pandemic, a study was conducted in three USAID Feed the Future countries Ghana, Nigeria, and Kenya to address postharvest loss using a mass-distributed educational animation. The video is a 5-minute animated video that demonstrates how to preserve cowpeas in jerrycans after harvest while avoiding insect damage. The processes for preparing the cowpea for the technique are explained in the video, which was overlaid with various local languages in the three countries to provide access to farmers with language challenges.The study aimed to measure the reach, engagement, and self-reported use of the animation, translating it into approximately 100 languages and disseminating it through partner-developed virtual and traditional in-person channels. Surveys in randomly selected villages revealed that 42.1% of respondents had seen the video, 93.2% understood it, 90.3% could explain it, and 58.1% had used the techniques. These data were extrapolated to estimate a broader impact, projecting potential viewership at 13.2 million, comprehension at 12.4 million, ability to explain at 12.1 million, and usage at 9.0 million.&lt;/p&gt;

&lt;p&gt;The study demonstrated high engagement and practical application of the video&#39;s techniques, with regional variations. The strategic partnerships and flexible distribution channels were crucial to the video&#39;s effectiveness. The results highlight that mass-scale messaging for improved food security is possible during crises. This study prompts further investigation into the potential of animated videos to fill gaps in agricultural extension services, even in non-crisis times. The success during the COVID-19 pandemic suggests that similar strategies could be effective in addressing other crises, such as climate change, to tackle universal problems like food security. Future research should explore achieving similar results without the urgency of a crisis.&lt;/p&gt;
description: Study on postharvest loss in Ghana, Kenya, & Nigeria using the jerrycan storage video technique. Estimated 13.2M viewers across regions. Significant engagement & practical application noted.
DOI: 10.4231/jy1d-ff09
title: ABAQUS Code for the Simulation of Transverse Impact Loading of Topologically Interlocked Material Systems

description: &lt;h4&gt;A series of files for the execution of finite element simulations of the transverse impact loading of topologically interlocked assemblies are provided and can be executed with the finite element code ABAQUS (or similar).&lt;/h4&gt;

&lt;div class="pub-content"&gt;
&lt;p&gt;In all files the following structure is present:&lt;/p&gt;

&lt;p&gt;-- For each part of the assembly (frame, indenter, building block), a definition of nodes (*node) and sets of nodes (*nset), elements (*element) and set of elements (*elset) is provided.&lt;/p&gt;

&lt;p&gt;-- Instances of parts are defined an placed in the assembly at position according to the assembly plan.&lt;/p&gt;

&lt;p&gt;-- Parts frame and indenter are defined as rigid bodies (*rigid body) . Building blocks as linear elastic (*elastic).&lt;/p&gt;

&lt;p&gt;-- Boundary conditions and constraints are defined (*boundary)&lt;/p&gt;

&lt;p&gt;-- Surfaces (*surface), surface behavior (*surface behavior) and contact interactions (*contact) are given.&lt;/p&gt;

&lt;p&gt;-- An explicit FE solution is used (*dynamic, explicit)&lt;/p&gt;

&lt;p&gt;-- Computed values are recorded (*node output, *energy output, *element output)&lt;/p&gt;

&lt;p&gt;ABAQUS inp file for a 20 by 20 assembly of hexagonal scutoids, coefficient of friction 0.0: HexScutoid20x20.inp&lt;/p&gt;

&lt;p&gt;ABAQUS inp file for a 21 by 21 assembly of hexagonal scutoids, coefficient of friction 0.0: HexScutoid21x21.inp&lt;/p&gt;

&lt;p&gt;ABAQUS inp file for a 20 by 20 assembly of pentagonal scutoids, coefficient of friction 0.0: PentagonScutoid20x20.inp&lt;/p&gt;

&lt;p&gt;ABAQUS inp file for a 21 by 21 assembly of pentagonal scutoids, coefficient of friction 0.0: PentagonScutoid21x21.inp&lt;/p&gt;

&lt;p&gt;ABAQUS inp file for a 20 by 20 assembly of tetrahedra, coefficient of friction 0.0: Tetrahedron20x20.inp&lt;/p&gt;

&lt;p&gt;ABAQUS inp file for a 21 by 21 assembly of tetrahedra, coefficient of friction 0.0: Tetrahedron21x21.inp&lt;/p&gt;

&lt;p&gt;This work was supported by NSF Award 16622177.&lt;/p&gt;
&lt;/div&gt;
description: This data set contains input files for the FE code ABAQUS the simulation and analysis of transverse impact loading of Topologically Interlocked Material systems.
DOI: 10.4231/s34e-8n27
title: Simulations, data, and scripts for New correlations for the interphase drag in the two-fluid model of gas-liquid flows through packed-bed reactors

description: &lt;p&gt;Two sets of simulation files are zipped into individual archives and named as &quot;Teflon_packing.zip&quot; and &quot;Glass_packing.zip&quot; corresponding to all simulations for each type of packed-bed reactor packing material in NASA&#39;s Packed Bed Reactor Experiment (PBRE). Within each zipped archive, there are many simulation case files corresponding to different inlet gas and liquid flow rates as per NASA&#39;s PBRE, organized as subfolders and vie the subfolder names. These case files can be used to rerun the simulations using ANSYS Fluent 2022R1. Some selected output data files, which allows the user to identify the simulation that this data corresponds to in the manuscript, are also included.&lt;/p&gt;

&lt;p&gt;Post-processing was done using ANSYS Fluent to generate pressure drop data, which was tabulated in an Excel spreadsheet. This data was plotted using MATLAB R2019a. The archive &quot;Math_model_figs.zip&quot; contains the data, spreadsheet, and MATLAB scripts.&lt;/p&gt;

&lt;p&gt;Inferences based on these simulations and data, and a discussion of their meaning/implications, can be found in the manuscript &quot;New correlations for the interphase drag in the two-fluid model of gas-liquid flows through packed-bed reactors&quot; by Nagrani, Marconnet &amp; Christov (2024), available as a preprint at &lt;a href="https://arxiv.org/abs/2202.11704" rel="nofollow noopener noreferrer noopener noreferrer" target="_blank"&gt;https://arxiv.org/abs/2409.10674&lt;/a&gt;.&lt;/p&gt;
description: Zip files containing simulations, data, and post-processing scripts, used to generate the figures in the manuscript "New correlations for the interphase drag in the two-fluid model of gas-liquid flows through packed-bed reactors" by Nagrani, et al.
DOI: 10.4231/gjk2-vb81
title: Exploring CDK2-Ligand Interactions Using the Effective Fragment Potential Method and Molecular Dynamics Simulations

description: &lt;p&gt;This archive contains the structure and topology files necessary for running molecular dynamics (MD) simulations of 10 CDK2-ligand complexes. The structure of the CDK2 receptor used corresponds to the inactive conformation. For the CDK2-62K complex (4fkw directory), the archive includes cluster analysis results and the solvation shell structure file for the largest cluster. Additionally, for this specific case,  EFP parameter files and the corresponding LibEFP input and output files are provided. &lt;/p&gt;

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

&lt;p&gt;The archive also contains the hybrid EFP parameter files of capped amino acids obtained from the structural data corresponding to set B for each of the the 7 ligands analyzed in the main paper. &lt;/p&gt;
description: The Effective Fragment Potential (EFP) method is applied to structures derived from classical Molecular Dynamics (MD) simulations to investigate protein-ligand interactions of CDK2-ligand complexes.
DOI: 10.4231/dtjt-ks98
title: Young and older adults prioritize walking efficiency or walking stability based on environmental risk

description: &lt;p&gt;This work demonstrates how humans exploit the mechanics of their bodies to achieve specific movement goals. While this phenomenon is well-known in sports (e.g., modulation of body postures to increase jump height or length in high jump or long jump, or to control the number of twists and somersaults while diving), we demonstrate that the same principle is applicable in an activity of daily living &ndash; walking and stepping over an obstacle. Our results motivate the investigation of the effects of aging and pathology on this ability, and how any decrements could underlie mobility issues in these populations.&lt;/p&gt;

&lt;p&gt;Humans reuse the body&rsquo;s mechanical energy at the end of one step to achieve forward progression during the subsequent step, thereby reducing the energy required for walking. This is achieved by harnessing the passive instability of the upright human posture. Here we test the novel hypothesis that humans manipulate passive anterior-posterior (AP) stability by actively modulating the placement of each foot for each step to either achieve energy-efficient gait or to improve stability when balance is threatened.&lt;/p&gt;

&lt;p&gt;We computed the AP margin of stability, which quantifies the passive dynamic stability of gait, for multiple steps as healthy young (N=25) and older adults (N=23) walked on a clear and on an obstructed walkway. Participants in both age groups used passive dynamics to achieve energy-efficient gait for all but one step; when crossing the obstacle with the leading limb, AP margin of stability was increased and indicated cautious gait, reflecting the greater threat to balance arising from a potential trip. Furthermore, AP margin of stability increased while approaching the obstacle, indicating that humans proactively manipulated the passive dynamics to meet the demands of the locomotor task. The step length and the center of mass motion co-varied to maintain the AP margin of stability for all steps in both tasks at the specific values for each step. Older adults were more cautious than the young adults, showing higher margin of stability while approaching and crossing the obstacle. However, aging did not impair the ability to maintain  the desired margin of stability at various steps. We conclude that humans actively regulate step length to maintain specific levels of passive stability for each step during unobstructed and obstructed gait.&lt;/p&gt;
description: Margin of stability (MOS) and MOS synergy indices that quantify coordination between the step length and the body's motion as healthy young and older adults approach and cross an obstacle. Code to generate figures from data.