Please direct any questions regarding the data, data collection, methods used in the administration of this survey and/or the summarization of responses provided in this document (or the corresponding report) to Julie Wernert at Indiana University, jwernert@iu.edu.
Here we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modelling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts.
This dataset documents the outcomes of a research project where we identified, analyzed, and described a set of existing ethics-focused methods designed to support design research and practice for a range of audiences (such as technology and design researchers and practitioners, and educators). The final dataset includes 63 ethics-focused methods, describing the intended audience(s), format of guidance, interaction qualities, utilization of existing knowledge or concepts, implementation opportunities within design processes, and the "core" or "script" of the method.
The purpose of this study was to examine how IMW affects the sensory and affective components of dyspnea, exercise performance, and NIRS-derived metaboreflex effects during a cycling time to exhaustion test. Additionally, to augment the ventilatory response for better elucidation of the cardiorespiratory effects of IMW, we added hypoxia as an intervention. Using both normoxic and hypoxic conditions, our hypotheses were: 1) both sensory and affective components of dyspnea would be attenuated following IMW in each condition, 2) the extent of skeletal muscle deoxygenation (i.e., a NIRS-derived surrogate for the metaboreflex) in the leg would be reduced after IMW in each condition, and 3) participants’ time to exhaustion would be prolonged following IMW in each condition.
The purpose of this study was to examine how IMW affects the sensory and affective components of dyspnea, exercise performance, and NIRS-derived metaboreflex effects during a cycling time to exhaustion test. Additionally, to augment the ventilatory response for better elucidation of the cardiorespiratory effects of IMW, we added hypoxia as an intervention. Using both normoxic and hypoxic conditions, our hypotheses were: 1) both sensory and affective components of dyspnea would be attenuated following IMW in each condition, 2) the extent of skeletal muscle deoxygenation (i.e., a NIRS-derived surrogate for the metaboreflex) in the leg would be reduced after IMW in each condition, and 3) participants’ time to exhaustion would be prolonged following IMW in each condition.
The data set consists of movement kinematic data from 92 participants that are neurotypical or have certain neurodevelopmental disorders (Autism, Attention Deficit/Hyperactivity Disorder, and their comorbidity). The data is of roughly 100 trials of a reaching paradigm per participant. The raw data consists of the linear acceleration (a), the roll (R), pitch (P), and yaw (Y), and the rate of change of the roll, pitch, and yaw.
Description of the data and file structure.
There are three primary folders: Data, Matlab Code, and the Deep Learning Code., Data:
Each folder corresponds to one participant. Inside is their motion data (sensor_data.csv) and a file describing their diagnosis and severity (diagnosis.txt). The columns of the csv are: a in x, a in y, a in z, dR/dt, dP/dt, dY/dt, R, P, Y
The diagnosis.txt file contains two lines: the first is their diagnosis (ASD, ADHD, A^2, NT), the second is their severity (HF for high functioning, MF for mid functioning, LF for low functioning, and NA for not applicable)., Matlab Code:
Information on how to analyze participants can be found in README.txt file within the folder.
The Matlab code was written and run on MATLAB_R2023b. The signal processing toolbox is required., and Deep Learning Code:
Information on how to perform the deep learning analysis can be found in README.txt file within the folder.
The deep learning code is written in Python3 and relies on PyTorch.
K. Doctor, C. McKeever, A. Phadnis, D. Wu, J. Nurnberger Jr., M. Plawecki, & J.V. Jose. Deep learning and statistical millisecond motor assessments of neurodevelopmental disorders. Science, In Submission.
Title:
Deep Learning and statistical millisecond motor assessments of neurodevelopmental disorders
The data set consists of movement kinematic data from 92 participants that are neurotypical or have certain neurodevelopmental disorders (Autism, Attention Deficit/Hyperactivity Disorder, and their comorbidity). The data is of roughly 100 trials of a reaching paradigm per participant. The raw data consists of the linear acceleration (a), the roll (R), pitch (P), and yaw (Y), and the rate of change of the roll, pitch, and yaw.
Description of the data and file structure.
There are three primary folders: Data, Matlab Code, and the Deep Learning Code., Data:
Each folder corresponds to one participant. Inside is their motion data (sensor_data.csv) and a file describing their diagnosis and severity (diagnosis.txt). The columns of the csv are: a in x, a in y, a in z, dR/dt, dP/dt, dY/dt, R, P, Y
The diagnosis.txt file contains two lines: the first is their diagnosis (ASD, ADHD, A^2, NT), the second is their severity (HF for high functioning, MF for mid functioning, LF for low functioning, and NA for not applicable)., Matlab Code:
Information on how to analyze participants can be found in README.txt file within the folder.
The Matlab code was written and run on MATLAB_R2023b. The signal processing toolbox is required., and Deep Learning Code:
Information on how to perform the deep learning analysis can be found in README.txt file within the folder.
The deep learning code is written in Python3 and relies on PyTorch.
K. Doctor, C. McKeever, A. Phadnis, D. Wu, J. Nurnberger Jr., M. Plawecki, & J.V. Jose. Deep learning and statistical millisecond motor assessments of neurodevelopmental disorders. Science, In Submission.
Title:
Deep Learning and statistical millisecond motor assessments of neurodevelopmental disorders
Data for this research study were collected and assembled in the attached Excel file. These data were subsequently analyzed for the manuscript using GraphPad Prism version 9.0.0 (Prism, San Diego, CA) statistical software.
Data for this research study were collected and assembled in the attached Excel file. These data were subsequently analyzed for the manuscript using GraphPad Prism version 9.0.0 (Prism, San Diego, CA) statistical software.
As part of a study to make food policy recommendations to the City of Indianapolis, this component of the study was concerned with assessing the food environment of SNAP retailers across the city. This survey was carried out to understand food access in Indianapolis, especially when such access concerns marginalized residents.
Citation to related publication:
Title:
2021 Store Survey Dataset of SNAP Retailers in Indianapolis, IN
As part of a study to make food policy recommendations to the City of Indianapolis, this component of the study was concerned with assessing the food environment of SNAP retailers across the city. This survey was carried out to understand food access in Indianapolis, especially when such access concerns marginalized residents.
CIFASD (Collaborative Initiative on Fetal Alcohol Spectrum Disorders) is a multisite consortium supported by the National Institute on Alcohol Abuse and Alcoholism (NIAAA). The purpose of this consortium is to inform and develop effective interventions and treatment approaches for Fetal Alcohol Spectrum Disorders (FASD), through multidisciplinary research involving basic, behavioral, and clinical investigators and projects. We hope to develop an infrastructure to foster collaboration and coordinate basic, clinical, and translational research on FASD., Data were collected across multiple grant cycles spanning 2003 – present. For data from 2003-2022 (Phases 1-4), please go to https://cifasd.org/data-sharing/ to request these CIFASD data. Data from 2022 (Phase 5) and beyond are deposited into the NIAAA Data Archive ( https://www.niaaa.nih.gov/research/niaaa-data-archive). , CIFASD investigators designed and implemented the study and/or provided data but did not necessarily participate in the analysis or writing of this report. A list of CIFASD investigators and projects can be found at https://cifasd.org/research/ . , and CIFASD has received support from NIAAA under award numbers: U01AA014786, U01AA014790, U01AA014809, U01AA014812, U01AA014829, U01AA014834, U01AA014835, U01AA017120, U01AA017122, U01AA017123, U01AA017124, U01AA021651, U01AA026101, U01AA026102, U01AA026103, U01AA026104, U01AA026108, U01AA030164, U01AA030185, U01AA030187, U24AA014811, U24AA014815, U24AA014818, U24AA014828, U24AA014830, U24AA030169, UH2AA026106, UH2AA026109, UH2AA029050, UH2AA029056, UH2AA029062, and UH2AA030186.
This dataset was generated from experiments using purified materials. Experiments were designed to study phase separation of SARS-CoV-2 Nucleocapsid protein.
Soil geochemical analysis was performed using samples from around the US. The sampling and analysis protocols differ by data source (this is available at www.mapmyenvironment.com). The data in this table is soil lead concentration in parts per million binned by municipality in which it was collected.
Rare Earth Elements (REE) phosphates (monazite, xenotime, and rhabdophane) are critical REE-bearing minerals typically formed in hydrothermal and magmatic ore deposits. The ther-modynamic properties of those REE minerals are crucial to understanding the solubility, speciation, and transport of REE complexes. However, the reported standard state Gibbs free energy of for-mation (∆Gof) for these minerals in the literature vary up to 25 kJ mol−1. Here, we present linear free energy relationships that allow the evaluation and estimation of the ∆Gof values at 25 °C and 1 bar for the three minerals from the ionic radius (rREE3+) and the non-solvation Gibbs energy contribution to the REE3+ aqua ion (∆Gon, REE3+): ∆Gof, monazite – 399.71 rREE3+ = 1.0059 ∆Gon, REE3+ – 2522.51; ∆Gof, xenotime – 344.08 rREE3+ = 0.9909 ∆Gon, REE3+ – 2451.53; ∆Gof, rhabdophane – 416.17 rREE3+ = 1.0067 ∆Gon, REE3+ – 2688.86. Moreover, based on the new dataset derived for REE end-members, we re-fitted the binary Margules parameter (W) from previous theoretical calculations into linear correlations: W + 0.00204 ∆Go'n, monazite = 39.3549 ∆V + 0.0641; W + 0.00255 ∆Go'n, xenotime = 25.4885 ∆V – 0.0062. The internally con-sistent thermodynamic properties of these REE phosphates are incorporated into the computer program SUPCRTBL, which is freely available at the site https://models.earth.indiana.edu.
Citation to related publication:
Title:
Recommended standard thermodynamic dataset of monazite, xenotime, and rhabdophane
Rare Earth Elements (REE) are critical minerals (metals) for the transition from fossil fuels to renewable and clean energy. Accurate thermodynamic properties of REE minerals and other crystalline solids are crucial for geochemical modeling of the solubility, speciation, and transport of REE in ore formation, extraction, chemical processing, and recycling processes. However, the Gibbs free energies of formation (∆Gof, REEX) for these solids from different sources vary by 10s kJ/mol. We applied the Sverjensky linear free energy relationship (LFER) to evaluate their internal consistency and predict the unavailable ∆Gof of the REE solids. By considering both the effects of ionic radius size and corresponding aqueous ion properties, the Sverjensky LFER,
allows estimates with much accuracy and precision. Here, rREEZ+ represents the Shannon-Prewitt ionic radii (Å) of REEZ+, and ∆Gon, REEZ+ denotes the non-solvation contribution to the ∆Gof of the aqueous REEZ+ ion. X represents the remainder of the compounds. In this study, the parameters aREEX, bREEX, and βREEX were regressed from ∆Gof compilations in the literature for 13 isostructural families. Based on these linear relationships, we recommend a set of internally consistent ∆Gof, REEX for 119 end-members of REE oxides, hydroxides, chlorides, fluorides, carbonates, hydrous carbonates, and ferrites. These ∆Gof, REEX are combined with experimental or predicted values of So, Vo, and Cpo from the literature and incorporated into a new SUPCRT database, which allows the calculations of thermodynamic properties to high P-T conditions (e.g., up to 1000 oC and 5 kb). The log Ksp of REE solid dissociation reactions were incorporated into a modified USGS program PHREEQC for calculations of speciation, solubility, and reactive transport. These thermodynamic databases will also be incorporated into the MINES database to be used together with the GEMS code package in the future.
Citation to related publication:
Title:
Linear correlations of Gibbs free energy for rare earth element oxide, hydroxide, chloride, fluoride, carbonate, and ferrite minerals and crystalline solids
We recommend a set of internally consistent ΔGof, REEX for 119 end-members of REE oxides, hydroxides, chlorides, fluorides, carbonates, hydrous carbonates, and ferrites. These ΔGof, REEX are combined with experimental or predicted values of So, Vo, and Cpo from the literature and incorporated into a new SUPCRT database, which allows the calculations of thermodynamic properties to high P-T conditions (e.g., up to 1000 oC and 5 kb). The log Ksp of REE solid dissociation reactions were incorporated into a modified USGS program PHREEQC for calculations of speciation, solubility, and reactive transport. These thermodynamic databases will also be incorporated into the MINES database to be used together with the GEMS code package in the future.
Citation to related publication:
Title:
Linear correlations of Gibbs free energy for rare earth element oxide, hydroxide, chloride, fluoride, carbonate, and ferrite minerals and crystalline solids
To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D.
MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 100 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size.
Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
This zip file contains WAV-audio files and annotations. The recordings were produced using a digital audio recorder (ZOOM H6) and can be listened to using any sound software that can play WAV-audio files. The annotations can be viewed and edited by the ELAN software packages. ELAN ( https://tla.mpi.nl/tools/tla-tools/elan/) is a professional tool for the creation of complex annotations of video and audio resources. Download the dataset using the link below.
Download the software applications and data used for the 2017 Student Cluster Competition by clicking the URLs below: Model for Prediction Across Scales (MPAS); Born seismic imaging tool; MrBayes program for Bayesian inference and model choice; LAMMPS molecular dynamics (MD) code. Note that download times may vary.
Accompanying dataset to the protocol published in Methods in Molecular Biology. Click on the PURL link below in the "External Files" section to download the dataset.
Citation to related publication:
Title:
Bioinformatics Analysis of Top-Down Mass Spectrometry Data
To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D. MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 3/2 100 3/2 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size. Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
Supporting datasets for drill-down topic modeling workflow described in "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library." PLOS ONE. https://doi.org/10.1371/journal.pone.0184188
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Title:
Supporting Data for "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library"
The evigene_corn2016 archive package contains a complete, reconstructed gene set of Zea mays, corn plant, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Title:
Genes of Zea mays, corn plant reconstructed with EvidentialGene
The evigene_wasp_nasvit2012 archive package contains a complete, reconstructed gene set of Nasonia vitripennis, jewel wasp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Title:
Genes of Nasonia vitripennis, jewel wasp reconstructed with EvidentialGene
The evigene_catfish2013 archive package contains a complete, reconstructed gene set of Ictalurus punctatus, catfish, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Title:
Genes of Ictalurus punctatus, catfish reconstructed with EvidentialGene
Quantitative measurement of intact alpha-synuclein proteoforms from post-mortem control and Parkinson's disease brain tissue by intact protein mass spectrometry
The evigene_locust_locumig2013 archive package contains a complete, reconstructed gene set of Locusta migratoria migratoria, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Title:
Genes of Locusta migratoria migratoria reconstructed with EvidentialGene
