Engineered Membrane Vesicle Production via oprF or oprI Deletion Has Distinct Phenotypic Effects in Pseudomonas putida - raw data for replicates
raw data for replicates for https://pubs.acs.org/doi/full/10.1021/acssynbio.5c00171
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raw data for replicates for https://pubs.acs.org/doi/full/10.1021/acssynbio.5c00171
Raw Mass Spectrometry data generated for the manuscript "Rubisco kinetic acclimation at the holoenzyme level." It characterizes the stoichiometry of Rubisco subunits in different Rubisco samples.
Raw data for publication: Moni Qiande and Fredy Altpeter. 2025. Comparing four heat-inducible promoters in stably transformed sugarcane regarding spatial and temporal control of transgene expression reveals candidates to drive stem preferred transgene expression. Frontiers in Plant Science (accepted for publication).
Raw LC–MS data files in mzML format obtained from isotopic feeding experiments in Aconitum plicatum callus cultures. Samples fed with L-serine (2,3,3-D3,¹⁵N) were acquired at a resolution of 500,000 to allow resolution of the nitrogen isotopologue. Control samples were re-acquired at the same resolution for comparison.
Raw data for publication: Viet Dang Cao, Baskaran Kannan, Guangbin Luo, Hui Liu, John Shanklin, and Fredy Altpeter. 2023. Triacylglycerol, total fatty acid and biomass accumulation of metabolically engineered energycane grown under field conditions. GCB-Bioenergy (accepted for publication).
For a detailed description of the database of which this record is only one part, please see the HarDWR meta-record. In order to hold a water right in the western United States, an entity, (e.g., an individual, corporation, municipality, sovereign government, or non-profit) must register a physical document with the state's water regulatory agency. State water agencies each maintain their own database containing all registered water right documents within the state, along with relevant metadata such as the point of diversion and place of use of the water. All western U.S. states have digitized their individual water rights databases, along with the geospatial data describing the spatial units where water rights are managed. Each state maintains and provides their own water rights data in accordance with individual state regulations and standards. We collected water rights databases from 11 western United States states either by downloading them from publicly accessible web portals, or by contacting state water management representatives; detailed descriptions of where and when the data was collected is provided in the README.txt, as well as Lisk et al.(in review). This collection of data are those raw water rights. Each state formats their data differently, meaning that file types, field availability, and names vary from state to state. Note, the data provided here reflects the state of the water rights databases at the time we collected the data; updates have likely occurred in many states. Some pieces of information are common among all states. These are: priority date, volume or flow of water allowed by the right, stated water use of the right, and some means of identifying the geography and source of the water pertaining to the right - typically the coordinates of the Point of Diversion (PoD) of a waterbody or well. Arizona regulates water in a different way than the other 10 states. Outside of some relatively small critical agricultural areas called Active Management Areas (AMAs), Arizona does not maintain any water rights. However, the state does require registration of surface and groundwater pumping devices, which includes disclosing the mechanical specifics of the devices. We used these records as a proxy for water rights. Each state, and their respective water right authorities, have made their water right records available for non-commercial reference uses. In addition, the states make no guarantees as to the completeness, accuracy, or timeliness of their respective databases, let alone the modifications which we, the authors of this paper, have made to the collected records. None of the states should be held liable for using this data outside of its intended use. In addition, the following states have requested specifically worded disclaimers to be included with their data. Colorado: "The data made available here has been modified for use from its original source, which is the State of Colorado. THE STATE OF COLORADO MAKES NO REPRESENTATIONS OR WARRANTY AS TO THE COMPLETENESS, ACCURACY, TIMELINESS, OR CONTENT OF ANY DATA MADE AVAILABLE THROUGH THIS SITE. THE STATE OF COLORADO EXPRESSLY DISCLAIMS ALL WARRANTIES, WHETHER EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED WARRANTIES OF MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE. The data is subject to change as modifications and updates are complete. It is understood that the information contained in the Web feed is being used at one's own risk." Montana: "The Montana State Library provides this product/service for informational purposes only. The Library did not produce it for, nor is it suitable for legal, engineering, or surveying purposes. Consumers of this information should review or consult the primary data and information sources to ascertain the viability of the information for their purposes. The Library provides these data in good faith but does not represent or warrant its accuracy, adequacy, or completeness. In no event shall the Library be liable for any incorrect results or analysis; any direct, indirect, special, or consequential damages to any party; or any lost profits arising out of or in connection with the use or the inability to use the data or the services provided. The Library makes these data and services available as a convenience to the public, and for no other purpose. The Library reserves the right to change or revise published data and/or services at any time." Oregon: "This product is for informational purposes and may not have been prepared for, or be suitable for legal, engineering, or surveying purposes. Users of this information should review or consult the primary data and information sources to ascertain the usability of the information." The available data is provided as a series of compressed files, which each containing the full data collected from each state. Some of the files have been renamed, to more easily know which state the data belongs to. The file renaming was also required as some files from different states had the same name. In other cases, the data for a state has been placed in a folder indicating which state it belongs to - as the state organized its data by selected subregions. Below is a brief description of the format of the collected data from each state. ArizonaRights_StatementOfClaimants: A folder containing a database of interconnected CSV files. The soc_erd.pdf file contains a visual flowchart of how the various files are connected, beginning with SOC_MAIN.csv in the center of the page. ArizonaRights_SurfaceWaterRightsData: A folder containing a database of a single Shapefile and 10 associated CSVs. SurfaceWater.pdf contains a visual flowchart of how the various files are connected, beginning with ADWR_SW_APPL_REGRY.csv. ArizonaRights_Well55Registry: A folder containing a database of a single Shapefile and 59 associated CSVs. Wells55.pdf contains a visual flowchart of how the various files are connected, beginning with WellRegistry.shp. CaliforniaRights_eWRIMS_directDatabase: A folder containing a collection of four "series" Microsoft Excel files, as either XLS or XLSX. The four "series": byCounty, byEntity (what type of legal entity holds the right), byUse (stated water use), and byWatershed, are various methods by which the California water rights are organized within the state's database. However, it was observed that by only collecting a single series, not all water rights were being provided. So, essentially, the majority of records within each "series" are copies of each other, with each "series" containing some unique records. ColoradoRights_NetAmounts: A folder containing 78 CSV files, with one file per Colorado Water District. IdahoRights_PointOfDiversion: A Shapefile containing the Points of Diversion for the entire state of Idaho. IdahoRights_PlaceOfUse: A Shapefile containing the Place of Use polygons for the entire state of Idaho. MontanaRights_WaterRights: A Geodatabase file containing the Points of Diversion and Places of Use for the entire state of Montana. The name of the Points of Diversion Feature Layer within the Geodatabase is "WRDIV", and the name of the Places of Use Feature Layer is "WRPOU". NevadaRights_POD_Sites: A Shapefile containing the Points of Diversion for the entire state of Nevada. NewMexicoRights_Points_of_Diversion: A Shapefile containing the Points of Diversion for the entire state of New Mexico. OregonRights_state_shp: A folder containing 36 Shapefiles and are split between "pod" (Point of Diversion) and "pou" (Place of Use) for each water management basin within Oregon. In other words, each basin has one "pod" file and one "pou" file. The "pod" files are point shapes, and the "pou" files are polygons. UtahRights_Points_of_Diversion: A Shapefile containing the Points of Diversion for the entire state of Utah. WashingtonRights_WaterDiversions_ECY_NHD: A Geodatabase file containing both the Points of Diversion for the entire state of Washington. The name of the Feature Layer within the Geodatabase is "WaterDiversions_ECY_NHD". WyomingRights: A folder containing four subdirectories, one for each Wyoming Water Division. Each Division directory includes a varying number of subdirectories for each Wyoming Water District. Each District folder contains two copies of the Point of Diversion records for that area, with one copying being in CSV and one copy in Microsoft Excel XLS format.
A dataset within the Harmonized Database of Western U.S. Water Rights (HarDWR). For a detailed description of the database, please see the meta-record v2.0. Changelog v2.0 - Switched source data from collecting records from each state independently to using the WestDAAT dataset v1.0 - Initial public release Description In order to hold a water right in the western United States, an entity, (e.g., an individual, corporation, municipality, sovereign government, or non-profit) must register a physical document with the state's water regulatory agency. State water agencies each maintain their own database containing all registered water right documents within the state, along with relevant metadata such as the point of diversion and place of use of the water. All western U.S. states have digitized their individual water rights databases, as well as geospatial data defining the areas in which water rights are managed. Each state maintains and provides their own water rights data in accordance with individual state regulations and standards. In addition, while all states make their water rights publicly available, each provides their records in unique formats, meaning that file types, field availability, and terms vary from state to state. This leads to additional challenges to managing resources which cross state lines, or conducting consistent multi-state water analyses. For the first version of HarDWR, we collected the water rights databases from 11 Western States of the United States. In order to preform regional analyses with the collected data, the raw records had to be harmonized into one single format. The Water Data Exchange (WaDE) is a program dedicated to the sharing of water-related data for the Western U.S. in a singular consistent format. Created by the Western States Water Council (WSWC) to facilitate the collection and dissemination of water data among WSWC's member states and the public, WaDE provides an important service for those interested in water resource planning and management in their focus region. Of the services which WaDE provides, the one of the most interesting is the WestDAAT dataset, which is a collection of water rights data provided by the 18 WSWC member states that have been standardized into a single format, much like we had done on a more limited scale with HarDWR v1. For this version of HarDWR we decided to use WestDAAT, specifically a snapshot created in Feburary 2024, as our water rights source data. A full explanation of the benefits gained from this switch can be found in the description of the updated Harmonized Water Rights Records v2.0, but in short it has allowed us to focus more of our efforts on answering research questions and gaining a more realistic understanding of how water rights are allocated. For more information on how the data for WestDAAT was collected, please see the WaDE data summary. Terms of Use While WaDE works directly with the state agencies to collect and standardize the water rights records, the ultimate authority for the water rights data remains the individual states. Each state, and their respective water right authorities, have made their water right records available for non-commercial reference uses. In addition, the states make no guarantees as to the completeness, accuracy, or timeliness of their respective databases, let alone the modifications which we, the authors of this paper, have made to the collected records. None of the states should be held liable for using this data outside of its intended use. As several of the states update their water rights databases daily, the information provided here is not the latest possible, and should not be used for legal purposes. WestDAAT itself has irregular updates. Additional questions about the data the source states provided should be directed to the respective state agencies (see methods.csv and organization.csv files described below). In addition, although data was presented here was not collected directly from the states, several states requested specifically worked disclaimers when sharing their data. These disclaimers are included here as an acknowledgement from where the water rights data is primarily sourced. Colorado: "The data made available here has been modified for use from its original source, which is the State of Colorado. THE STATE OF COLORADO MAKES NO REPRESENTATIONS OR WARRANTY AS TO THE COMPLETENESS, ACCURACY, TIMELINESS, OR CONTENT OF ANY DATA MADE AVAILABLE THROUGH THIS SITE. THE STATE OF COLORADO EXPRESSLY DISCLAIMS ALL WARRANTIES, WHETHER EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED WARRANTIES OF MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE. The data is subject to change as modifications and updates are complete. It is understood that the information contained in the Web feed is being used at one's own risk." Montana: "The Montana State Library provides this product/service for informational purposes only. The Library did not produce it for, nor is it suitable for legal, engineering, or surveying purposes. Consumers of this information should review or consult the primary data and information sources to ascertain the viability of the information for their purposes. The Library provides these data in good faith but does not represent or warrant its accuracy, adequacy, or completeness. In no event shall the Library be liable for any incorrect results or analysis; any direct, indirect, special, or consequential damages to any party; or any lost profits arising out of or in connection with the use or the inability to use the data or the services provided. The Library makes these data and services available as a convenience to the public, and for no other purpose. The Library reserves the right to change or revise published data and/or services at any time." Oregon: "This product is for informational purposes and may not have been prepared for, or be suitable for legal, engineering, or surveying purposes. Users of this information should review or consult the primary data and information sources to ascertain the usability of the information." File Descriptions The unmodified February, 2024 WestDAAT snapshot is composed of nine files. Below is a brief description of each file, as well as how they were utilized for HarDWR. WaDEDataDictionaryTerms.xlsx: As the file's name implies, this is a data dictionary for all of the below named files. This file describes the column names for each of the following files, with the exception of citation.txt which does not have any columns. The descriptions for each file are divided by tab,with the same name as their associated file, within this document. allocationamount.csv: The "main" file of the group, it contains the water right records for each state. Of particular note, each water right is broken down into one or more water allocations. Allocations may be withdrawn from one or more locations, or even multiple allocations associated with a particular location. This is a more subtle and realistic representation of how water is used than what was available in the first version of HarDWR. For the records from some states, this can mean that multiple allocations listed under a single right will appear as rows within this file. citation.txt: A combination of contact information for WaDE personnel, disclaimer about how the data should be used, and guidelines for citing WestDAAT. methods.csv: A file describing the source and method by which WaDE collected water rights data from each state. organization.csv: A file listing the water rights authoritative agencies for each state. sites.csv: This file provides the geographic, and other descriptors, of the physical location of allocations, called 'sites'. To reiterate, it is possible for one allocation to be associated with multiple sites, as well as one site to be associated with multiple allocations. The two descriptors which we were most interested in where the site's coordinates, as well as whether the site was classified as a Point of Diversion (POD) or a Place of Use (POU). As a general rule, PODs are geographic points, while POUs are areas typically represented as property boundaries or irregularly shaped polygons. sites_pouGeometry.csv: For those allocations with a POU site, this file contains the defining points for the associated polygons. variables.csv: A file describing the units in which an allocation's water amount is reported within WestDAAT. This information is essentially a repeat of the 'AllocationFlow_CFS' and 'AllocationVolume_AF' columns within allocationamount.csv, at least for our purposes. watersources: This file describes the source of water from which each site extracts from. For our purposes, this table was used to determine whether the water came from Surface Water, Groundwater, or Unspecified Water.
Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.
Accurate positioning of vehicles is a critical element of autonomous and connected vehicle systems. Most of other studies heavily focused on enhancing simultaneous localization and mapping (SLAM) methods, i.e., constructing or updating a map of an unknown environment and tracking an object within the map. This paper provides a method that can, in addition to existing SLAM or relevant methods, enhance the raw measurements of position and distance. The basic idea of this study is to identify and update the error distribution of each data source by combining all available information. A Bayesian approach was incorporated to estimate and update the error distribution of individual data sources or sensors. The proposed method can be conducted in real-time environments, and a self-learning scheme determines whether enough data has been collected to further improve the accuracy of such measurements. The simulated experiments show that the proposed model noticeably improves the accuracy of position and distance measurements. Especially, the estimated biases of position coordinates and distance measures are very close to the biases of true error distributions, with the R-squared over 0.98. A similar approach can also be utilized to enhance accuracy of other sensors or measurements in connected vehicle or relevant systems, where multi-data sources are available.
We investigate the feasibility of using deep learning techniques, in the form of a one-dimensional convolutional neural network (1D-CNN), for the extraction of signals from the raw waveforms produced by the individual channels of liquid argon time projection chamber (LArTPC) detectors. A minimal generic LArTPC detector model is developed to generate realistic noise and signal waveforms used to train and test the 1D-CNN, and evaluate its performance on low-level signals. We demonstrate that our approach overcomes the inherent shortcomings of traditional cut-based methods by extending sensitivity to signals with ADC values below their imposed thresholds. This approach exhibits great promise in enhancing the capabilities of future generation neutrino experiments like DUNE to carry out their low-energy neutrino physics programs.
Disclosed herein is a method of making polymerizable bio-based monomers containing one phenolic hydroxyl group which has been derivatized to provide at least one polymerizable functional group which is an ethylenically unsaturated functional group (such as a [meth]acrylate group), where the precursors of the polymerizable bio-based monomers are derived from raw lignin-containing biomass. Also disclosed herein are bio-based copolymers prepared from such bio-based monomers and a co-monomer, and methods of making and using such bio-based copolymers. In particular, the bio-based copolymers can be used as pressure sensitive adhesives, binders, and polymer electrolytes.
This is a microgravity dataset from the Utah FORGE site near Milford, Utah. This composite dataset was updated in October, 2021 and contains data from December 17th, 2018 through September 24th, 2021. The data includes the GPS location of the measurement, date of the measurement, name of the station, relative difference in gravity, and coordinates of the station. This data was generated by the Utah Geological Survey.
This submission contains the original, unprocessed data from the 2023 Large Amplitude Motion Platform (LAMP) testing of NREL's Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC). This data serves as a companion to MHKDR #520. Data was collected using NREL's Modular Ocean Data AcQuisition (MODAQ) system in TDMS format. Specifications of TDMS files can be found on the NI website. The TDMS files have been separated into zip files corresponding to either Drivetrain, Hydraulic, or Electric configuration runs representing the respective test cases that were run. The drivetrain runs were used to characterize the drivetrain only (no pump or generator). The Hydraulic runs represent the configuration when the seawater pump is installed, and the Electric runs represents the configuration when the generator is installed. The following sub-categories of data are included for each type: - DW - Deep water (monochromatic sine wave) profile (not run in drivetrain configuration) - Heave - Heave only (monochromatic sine wave) profile - Heave_NoRO (hydraulic configuration only) - Heave_ACC (hydraulic configuration only) - IR - Surge and heave irregular wave profile (not run in drivetrain configuration) - RW - Heave only profile created from real world encoder data (not run in drivetrain configuration) Reference documents: - "HERO WEC Lamp Test Run Log.xlsx": contains specifications for each test run - "Lamp Data Description.docx": provides detailed information about data types and processing methods For those interested in the processed data the authors have created a separate submission, MHKDR #520, linked below. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.
10 hours chronoamperometry (CA) testing under 1 sun illumination and constant bias at -0.6 V vs RHE, the corresponding Faradaic efficiency reveals a self-improving nature of GaN, inset: CA testing on bare Si for 5 hours under 1 sun illumination and -0.6 V vs RHE, this bare Si photocathode rapidly drops down to < 0.05 mA/cm2 within an hour. Both CA testing performed in 0.5 M H2SO4 (pH=0.4).
Accelerated CA testing on bare epilayer Si/GaN photocathode at constant bias of -0.6 V vs RHE under 3.5 sun illumination for 150 hours in 0.5 M H2SO4 (pH=0.4)
Intermittent chronoamperometry (CA) testing was performed on Si/GaN photocathode in hourly manner. The LSV scan at 0 hour, 1 hour CA, 2 hours CA, 3 hours CA, 4 hours CA, 6 hours CA, 8 hours CA and 10 hours CA were recorded to track the changes of the photoelectrochemica (PEC) performance of the photocathode. The scan range was set to be 0V vs open circuit voltage (Eoc) to -0.7V vs RHE. Test was performed under one sun illumination in 0.5M H2SO4 (pH=0.4).
Fig1d results were obtained using a 3-electrode configuration with IrOx as the counter electrode and saturated calomel electrode as the reference electrode. Two Si/GaN photocathodes were compared. Sample #1 (named as S#1) was the as-received sample, and sample #2 (named as S#2) was CA tested for 4 hours under same testing conditions described in Fig.1a. The PEC performance (J-V curve) was recorded for both samples. Then a photodeposition of Pt was performed on both samples, each loading time was set to be 5 minutes, then the J-V curve was recorded to track the changes of the performance. The Pt photodeposition was stopped until the J-V curve won't shift (the maximum onset potential was achieved). The results show that, S#1 needs at least 20 minutes of Pt photodeposition to achieve its best PEC performance while S#2, which is after CA testing, only needs 5 minutes of Pt photodeposition to achieve its best PEC performance.
Photoconductive atomic force microscopy (PC-AFM) measurements were conducted on Si/GaN samples. PeakForce TUNA mode was used to acquire the morphology and current simultaneously. A PtIr conductive probe with spring constant of 2.8 Nm-1 was used for the scanning. A white light source was used to illuminate the surface during the acquisition. Line scan extracting the topography and photocurrent from a as-received Si/GaN sample. The topography mapping is 2 × 2 µm2. The sample bias was 0.4V and this photoconductive AFM measurement was performed under white light front illumination with an angle.