71 Works

High-throughput sequencing (HTS) data of plasmid library subjected to Cas12a cleavage

Karthik Murugan, Dipali Sashital, Arun Seetharam & Andrew Severin
Cas12a (formerly Cpf1) is an RNA-guided endonuclease in the CRISPR-Cas immune system that can be easily programmed for genome editing. To understand the native cleavage specificity and cleavage activity of Cas12a, we employed high-throughput in vitro cleavage assays using a plasmid library (pLibrary). We tested the cleavage activity of three Cas12a orthologs – FnCas12a, LbCas12a and AsCas12a. For each Cas12a ortholog, we used three different crRNA sequences and corresponding target libraries (pLibrary), referred to as...

High-throughput sequencing (HTS) data of plasmid library subjected to Cas12a cleavage

Karthik Murugan, Dipali Sashital, Arun Seetharam & Andrew Severin
Cas12a (formerly Cpf1) is an RNA-guided endonuclease in the CRISPR-Cas immune system that can be easily programmed for genome editing. To understand the native cleavage specificity and cleavage activity of Cas12a, we employed high-throughput in vitro cleavage assays using a plasmid library (pLibrary). We tested the cleavage activity of three Cas12a orthologs – FnCas12a, LbCas12a and AsCas12a. For each Cas12a ortholog, we used three different crRNA sequences and corresponding target libraries (pLibrary), referred to as...

Effect of crop rotation on weed biomass and density literature summary

Virginia Nichols, David Weisberger & Matt Liebman
The dataset consists of data extracted from a systematic search of peer-reviewed literature using ISI Web of Knowledge (WoS). Searches were conducted using the following Boolean strings: ("crop rotation*" OR "crop sequence*" OR "multiple cropping*") AND (management* OR control*) AND ("weed biomass*" OR "weed density*" OR "weed seed bank*") NOT (orchard* OR vineyard* OR agroforestry*) ("crop rotation*" OR "crop sequence*" OR "multiple cropping*" OR “organic”) AND (management* OR control*) AND ("weed biomass*" OR "weed density*"...

Effect of crop rotation on weed biomass and density literature summary

Virginia Nichols, David Weisberger & Matt Liebman
The dataset consists of data extracted from a systematic search of peer-reviewed literature using ISI Web of Knowledge (WoS). Searches were conducted using the following Boolean strings: ("crop rotation*" OR "crop sequence*" OR "multiple cropping*") AND (management* OR control*) AND ("weed biomass*" OR "weed density*" OR "weed seed bank*") NOT (orchard* OR vineyard* OR agroforestry*) ("crop rotation*" OR "crop sequence*" OR "multiple cropping*" OR “organic”) AND (management* OR control*) AND ("weed biomass*" OR "weed density*"...

Effect of crop rotation on weed biomass and density literature summary

Virginia Nichols, David Weisberger & Matt Liebman
The dataset consists of data extracted from a systematic search of peer-reviewed literature using ISI Web of Knowledge (WoS). Searches were conducted using the following Boolean strings: ("crop rotation*" OR "crop sequence*" OR "multiple cropping*") AND (management* OR control*) AND ("weed biomass*" OR "weed density*" OR "weed seed bank*") NOT (orchard* OR vineyard* OR agroforestry*) ("crop rotation*" OR "crop sequence*" OR "multiple cropping*" OR “organic”) AND (management* OR control*) AND ("weed biomass*" OR "weed density*"...

Heterologous expression of maize Fatty Acid Elongase (FAE) components in yeast - growth analysis

Alexis Campbell, Kenna Stenback, Basil J. Nikolau, M. Ann Perera & Trang Hoang
Fatty acids of more than 18-carbons, generally known as very long chain fatty acids (VLCFAs) are essential for eukaryotic cell viability, and uniquely in terrestrial plants they are the precursors of the cuticular lipids that form the organism’s outer barrier to the environment. VLCFAs are synthesized by fatty acid elongase (FAE), which is an integral membrane enzyme system with multiple components. The genetic complexity of the FAE system, and its membrane association has hampered the...

Observation of η-Al41Sm5 reveals motif-aware structural evolution in Al-Sm alloys

Zhuo Ye, Fanqiang Meng, Feng Zhang, Yang Sun, Lin Yang, Shihuai Zhou, Ralph Napolitano, Mikhail Mendelev, Ryan Ott, Matt Kramer, Cai-Zhuang Wang & Kai-Ming Ho
Using an effective genetic algorithm, we uncover the structure of a metastable Al41Sm5 phase that supplements its family sharing similar short-range orders. The phase evolves upon heating an amorphous Al-9.7at.%Sm ribbon, produced by melt-spinning. The dynamical phase selection is discussed with respect to the structural connections between the short-range packing motifs in the amorphous precursor and those observed in the selected phases. This dataset includes information such as the crystal structure of Al41Sm5, the short-range...

Land Use and Cropping Recommendations For Various Soil Types in Iowa, 1937-1938.

John F. Obrycki
This dataset was transcribed and analyzed to support an in-press article which will be published in the Journal of Soil and Water Conservation in Nov/Dec 2018.

The dataset contains transcribed tables from the county pamphlets “How To Use Your Soil And Keep It Too” distributed by county agricultural planning committees in 1937/1938. There are 90 pamphlets available. One table was included in each pamphlet and was titled “Land Use and Cropping Recommendations For Various Soil Types.”...

Evidence of improved reporting of swine vaccination trials in the post-REFLECT statement publication period.

Cesar-August Amorim-Moura, Sarah C. Totton, Jan M. Sargeant, Terri L. O’Sullivan, Daniel C. L. Linhares & Annette O'Connor
The objective of this study was to describe the proportion of reporting the method used to assign study units to treatment groups; the proportion of reporting a random allocation approach; the proportion of reporting 18 REFLECT items; and the proportion of having a low risk-of-bias assessment in swine vaccination trial studies published after the REFLECT statement, compared to studies published before. The study population was 61 studies which evaluated vaccines targeted at pathogens affecting swine...

Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) Collection

Gaurav Kandoi & Julie A. Dickerson
The files for this project have been split into three separate download packages:
- Predictions- Scripts- Datasets
Each package has a copy of the readme file which covers all three packages.
Alternative Splicing produces multiple mRNA isoforms of a gene which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, very little has been done to assign functions at the mRNA isoform level. Functional networks, where the...

Formation of Multilayer Cu Islands Embedded beneath the Surface of Graphite: Characterization and Fundamental Insights

Ann Lii-Rosales, Yong Han, James W. Evans, Dapeng Jing, Yinghui Zhou, Michael C. Tringides, Minsung Kim, Cai-Zhuang Wang & Patricia A. Thiel
The file contains raw scanning tunneling microscopy (STM) images and x-ray photoelectron spectroscopy (XPS) spectra. To view and process STM images, the user can use a software called WSxM. To view XPS spectra, the program CASA XPS is recommended. The STM and XPS data uploaded herein are used to generate figures in the published paper, which can be found in J. Phys. Chem. C 2018, 122, 4454-4469.

Reverse-Engineering of Graphene on Metal Surfaces: A Case Study of Embedded Ruthenium

Ann Lii-Rosales, Yong Han, Ka Man Yu, Dapeng Jing, Nathaniel Anderson, David Vaknin, Michael C. Tringides, James W. Evans, Michael S. Altman & Patricia A. Thiel
Using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy, we show that Ru forms metallic nanoislands on graphite, covered by a graphene monolayer. These islands are air-stable, contain 2-4 layers of Ru, and have diameters on the order of 10 nm. To produce these nanoislands two conditions must be met during synthesis. The graphite surface must be ion bombarded, and subsequently held at elevated temperature (1000-1180 K) during Ru deposition. A coincidence lattice...

(111) single crystal NaAu2 images, parameters, and data

Deborah Schlagel, Matthew Besser, Chad Yuen, Holly Walen, Emma Kwolek, Patricia A. Thiel & Thomas A. Lograsso
These are the original images, parameter files, and data for the figures in the manuscript “Bulk Single Crystal Growth and Sample Surface Preparation of Catalytic NaAu2” submitted to Journal of Alloys and Compounds.
Figure 1 is images of phases that were found in the crystal growth.
Figure 2 is two theta vs intensity x-ray diffraction scans of bulk powder and of an oriented crystal face after different treatments.
Figure 3 is a Laue diffraction image...

Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) Collection

Julie Dickerson & Gaurav Kandoi
The files for this project have been split into three separate download packages:
- Predictions- Scripts- Datasets
Each package has a copy of the readme file which covers all three packages.
Alternative Splicing produces multiple mRNA isoforms of a gene which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, very little has been done to assign functions at the mRNA isoform level. Functional networks, where the...

Productivity and diversity of annually harvested reconstructed prairie communities database

Farnaz Kordbacheh, Meghann Jarchow, Lydia English & Matt Liebman
This data supports an accepted article that will be published in Journal of Applied Ecology in Jan 2019.Matt Liebman (mliebman@iastate.edu) is the corresponding author for the article.
Productivity and diversity of annually harvested reconstructed prairie communities database was compiled to test whether the long-term maintenance of biodiversity can be achieved alongside substantial productivity in fertilized mixed-species prairie. Using this database, we report how NPK fertilizer application, precipitation, and time affected the species composition and productivity...

Squeezed Nanocrystals: Equilibrium Configuration of Metal Clusters Embedded Beneath the Surface of a Layered Material

Scott E. Julien, Ann Lii-Rosales, Kai-Tak Wan, Yong Han, Michael C. Tringides, James W. Evans & Patricia A. Thiel
Shapes of functional metallic nanocrystals, typically synthesized either free in solution or supported on surfaces, are key for controlling properties. Here, we consider a novel new class of metallic nanocrystals, copper clusters embedded near the surface of graphite, which can be considered a model system for metals embedded beneath surfaces of layered materials, or beneath supported membranes. We develop a continuum elasticity (CE) model for the equilibrium shape of these islands, and compare its predictions...

Productivity and diversity of annually harvested reconstructed prairie communities database

Farnaz Kordbacheh, Meghann Jarchow, Lydia English & Matt Liebman
This data supports an accepted article that will be published in Journal of Applied Ecology in Jan 2019.Matt Liebman (mliebman@iastate.edu) is the corresponding author for the article.
Productivity and diversity of annually harvested reconstructed prairie communities database was compiled to test whether the long-term maintenance of biodiversity can be achieved alongside substantial productivity in fertilized mixed-species prairie. Using this database, we report how NPK fertilizer application, precipitation, and time affected the species composition and productivity...

Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) Collection

Gaurav Kandoi & Julie Dickerson
The files for this project have been split into three separate download packages:
- Predictions- Scripts- Datasets
Each package has a copy of the readme file which covers all three packages.
Alternative Splicing produces multiple mRNA isoforms of a gene which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, very little has been done to assign functions at the mRNA isoform level. Functional networks, where the...

Shoot Apical Meristem (SAM) Diversity Panel Genetic Markers and Map

Aaron Kusmec, Xianran Li, Cheng-Ting Yeh, Jianming Yu, Michael Scanlon & Patrick Schnable
Imputed and phased single nucleotide polymorphisms (SNPs) for 370 maize inbred lines from the Shoot Apical Meristem (SAM) Diversity Panel. SNPs were derived from RNA-seq, genotyping-by-sequencing (GBS), and tunable GBS (tGBS). SNPs are in VCF4.1 format. A csv file contains genetic map information for the SNPs.

Evidence of improved reporting of swine vaccination trials in the post-REFLECT statement publication period.

Cesar-August Amorim-Moura, Sarah C. Totton, Jan M. Sargeant, Terri L. O’Sullivan, Daniel C. L. Linhares & Annette O'Connor
The objective of this study was to describe the proportion of reporting the method used to assign study units to treatment groups; the proportion of reporting a random allocation approach; the proportion of reporting 18 REFLECT items; and the proportion of having a low risk-of-bias assessment in swine vaccination trial studies published after the REFLECT statement, compared to studies published before. The study population was 61 studies which evaluated vaccines targeted at pathogens affecting swine...

Direct Observation of Early Stages of Growth of Multilayered DNA-templated Au-Pd-Au Core-Shell Nanoparticles in Liquid Phase video files

Nabraj Bhattarai & Tanya Prozorov
Video 1 is a screen recording of Pd shell growth on several Au nanoparticles imaged in liquid phase in situ.
The times of actual image acquisition can be noted by a notably slower scanning speed.
The recording is sped up 4 times to compress the file.
Video 2 is a screen recording of early stages of Au-Pd-Au nanostar formation imaged in liquid phase in situ.
The initial Au-Pd nanocube is located in a close proximity...

Distributed shear apparatus experiments using semi-brittle analog Carbopol Ultrez 21

Thomas Birren & Jacqueline Reber
Journal of Geophysical Research - Solid EarthTitle: The impact of rheology on the transition from stick-slip to creep in a semi-brittle analog (Published)Authors: Thomas Birren and Jacqueline E. ReberAffiliation: Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA 50011
This data set contains distributed shear apparatus experiments using semi-brittle analog, Carbopol Ultrez 21 at concentrations of 1, 2, and 3 wt.%. Measurements of pulling force and displacement show the slip behavior of the material...

Heterologous expression of maize Fatty Acid Elongase (FAE) components in yeast - fatty acid analysis

Alexis Campbell, Basil J. Nikolau, M. Ann Perera, Kenna Stenback & Trang Hoang
Fatty acids of more than 18-carbons, generally known as very long chain fatty acids (VLCFAs) are essential for eukaryotic cell viability, and uniquely in terrestrial plants they are the precursors of the cuticular lipids that form the organism’s outer barrier to the environment. VLCFAs are synthesized by fatty acid elongase (FAE), which is an integral membrane enzyme system with multiple components. The genetic complexity of the FAE system, and its membrane association has hampered the...

Direct Observation of Early Stages of Growth of Multilayered DNA-templated Au-Pd-Au Core-Shell Nanoparticles in Liquid Phase

Nabraj Bhattarai & Tanya Prozorov
This collection includes both the data files and the video files that support the publication Direct Observation of Early Stages of Growth of Multilayered DNA-templated Au-Pd-Au Core-Shell Nanoparticles in Liquid Phase (forthcoming).

Distributed shear apparatus experiments using semi-brittle analog Carbopol Ultrez 21

Thomas Birren & Jacqueline Reber
Journal of Geophysical Research - Solid EarthTitle: The impact of rheology on the transition from stick-slip to creep in a semi-brittle analog (Published)Authors: Thomas Birren and Jacqueline E. ReberAffiliation: Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA 50011
This data set contains distributed shear apparatus experiments using semi-brittle analog, Carbopol Ultrez 21 at concentrations of 1, 2, and 3 wt.%. Measurements of pulling force and displacement show the slip behavior of the material...

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