The two major components of this supplement are packaged as two separate UNIX tar files available through links below. The two tar file names are:
(1) ModelConstructionDetails.tar - this contains the pdf file with the text (file name SupplementText.pdf) describing the technical details of how the 3D model was constructed. The package also contains a directory called Figures that contain five interactive figures. The SupplementText.pdf file contains links to these files that will resolve only if the files are left in that directory. There is also a small README text file to make the set of files more self contained.
(2) DataSupplement.tar - this is the package of data files that form the data supplement. The organization of the files in the package and file descriptions are described in the pdf file with the name DataSupplementDescription.pdf. That file can also be accessed directly from the link below.
Citation to related publication:
Title:
Electronic Supplement to “A Unified Three-dimensional Model of the Lithospheric Structure at the Subduction Corner in Southeast Alaska: Summary Results from STEEP”
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.
Citation to related publication:
Title:
Genes of Nasonia vitripennis, jewel wasp reconstructed with EvidentialGene
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
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"
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
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
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.
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.
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
The IU collection of these (mostly) former Soviet Red Army topographic maps came to us from the duplicate map room of the Library of Congress Map Collection. While by no means complete, this collection is a fine addition to our existing international map holdings. These maps have a great story to tell: some carry the stamp from both the University of Berlin and the University of Bonn Geography Departments, some are stamped "Captured Map", some carry the ID of the CIA Map Library or the Bureau of Geographic Names, and still others are hand-annotated. They are in a variety of conditions (paper, laminated, photographically reproduced in color or black and white, plasticized, or muslin-backed). The collection ranges from around 1880-1945 with a geographic extent mostly centered around Eastern Europe and Western Russia.
This subcollection contains Russian Military Topographic Maps in the 1:100,000 scale. The IU collection of these (mostly) former Soviet Red Army topographic maps came to us from the duplicate map room of the Library of Congress Map Collection. While by no means complete, this collection is a fine addition to our existing international map holdings. These maps have a great story to tell: some carry the stamp from both the University of Berlin and the University of Bonn Geography Departments, some are stamped "Captured Map", some carry the ID of the CIA Map Library or the Bureau of Geographic Names, and still others are hand-annotated. They are in a variety of conditions (paper, laminated, photographically reproduced in color or black and white, plasticized, or muslin-backed). The collection ranges from around 1880-1945 with a geographic extent mostly centered around Eastern Europe and Western Russia.
This subcollection contains Russian Military Topographic Maps in the 1:25,000 scale. The IU collection of these (mostly) former Soviet Red Army topographic maps came to us from the duplicate map room of the Library of Congress Map Collection. While by no means complete, this collection is a fine addition to our existing international map holdings. These maps have a great story to tell: some carry the stamp from both the University of Berlin and the University of Bonn Geography Departments, some are stamped "Captured Map", some carry the ID of the CIA Map Library or the Bureau of Geographic Names, and still others are hand-annotated. They are in a variety of conditions (paper, laminated, photographically reproduced in color or black and white, plasticized, or muslin-backed). The collection ranges from around 1880-1945 with a geographic extent mostly centered around Eastern Europe and Western Russia.
This subcollection contains Russian Military Topographic Maps in the 1:50,000 scale. The IU collection of these (mostly) former Soviet Red Army topographic maps came to us from the duplicate map room of the Library of Congress Map Collection. While by no means complete, this collection is a fine addition to our existing international map holdings. These maps have a great story to tell: some carry the stamp from both the University of Berlin and the University of Bonn Geography Departments, some are stamped "Captured Map", some carry the ID of the CIA Map Library or the Bureau of Geographic Names, and still others are hand-annotated. They are in a variety of conditions (paper, laminated, photographically reproduced in color or black and white, plasticized, or muslin-backed). The collection ranges from around 1880-1945 with a geographic extent mostly centered around Eastern Europe and Western Russia.
Sanborn Fire Insurance Maps were made for the interests of fire insurance companies, but because they are detailed, building-by-building depictions of most urban areas, they are useful for many kinds of research.
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
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
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
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.
This dataset was generated from experiments using purified materials. Experiments were designed to study phase separation of SARS-CoV-2 Nucleocapsid protein.
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.
