1
|
Wan H, Ganguli S, Mohankumar NM, Jain M, Wilson K, Anderson D. Projected income data under different shared socioeconomic pathways for Washington state. Sci Data 2024; 11:85. [PMID: 38238323 PMCID: PMC10796341 DOI: 10.1038/s41597-023-02906-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024] Open
Abstract
High-resolution income projections under different Shared Socioeconomic Pathways (SSPs) are essential for the climate change research communities to devise climate change adaptation and mitigation strategies. To generate income projections for Washington state, we obtain state-level GDP per capita projections and convert them into projected annual household income. The resulting state-level income projections are subsequently downscaled to the census block-level based on the Longitudinal Origin-Destination Employment Statistics (LODES) dataset. For accuracy assessment, we downscale historical income data from state- level to block- and block group-level and compare the downscaled results against the actual income data from LODES. County-level accuracy assessment is also conducted based on American Community Survey. The results demonstrate a good agreement (Average R2 of 0.67, 0.8, and 0.99 for block-, block group-, and county-level, respectively) between the downscaled income data and the reference data, thereby validating the methodology employed. Our approach is applicable to other states for income projections, which can be utilized by a broader audience, including those involved in demographic analysis, economic research, and urban planning.
Collapse
Affiliation(s)
- Heng Wan
- Earth Systems Predictability & Resiliency Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Sumitrra Ganguli
- Economics, Policy & Institutional Support Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Milan Jain
- Optimization & Control Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kyle Wilson
- Economics, Policy & Institutional Support Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - David Anderson
- Risk & Environmental Assessment Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| |
Collapse
|
2
|
Muller SE, Prange MP, Lu Z, Rosenthal WS, Bilbrey JA. An open database of computed bulk ternary transition metal dichalcogenides. Sci Data 2023; 10:336. [PMID: 37253748 DOI: 10.1038/s41597-023-02103-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/24/2023] [Indexed: 06/01/2023] Open
Abstract
We present a dataset of structural relaxations of bulk ternary transition metal dichalcogenides (TMDs) computed via plane-wave density functional theory (DFT). We examined combinations of up to two chalcogenides with seven transition metals from groups 4-6 in octahedral (1T) or trigonal prismatic (2H) coordination. The full dataset consists of 672 unique stoichiometries, with a total of 50,337 individual configurations generated during structural relaxation. Our motivations for building this dataset are (1) to develop a training set for the generation of machine and deep learning models and (2) to obtain structural minima over a range of stoichiometries to support future electronic analyses. We provide the dataset as individual VASP xml files as well as all configurations encountered during relaxations collated into an ASE database with the corresponding total energy and atomic forces. In this report, we discuss the dataset in more detail and highlight interesting structural and electronic features of the relaxed structures.
Collapse
Affiliation(s)
- Scott E Muller
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Micah P Prange
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Zexi Lu
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Jenna A Bilbrey
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| |
Collapse
|
3
|
Woo J, Williams SM, Markillie LM, Feng S, Tsai CF, Aguilera-Vazquez V, Sontag RL, Moore RJ, Hu D, Mehta HS, Cantlon-Bruce J, Liu T, Adkins JN, Smith RD, Clair GC, Pasa-Tolic L, Zhu Y. High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip. Nat Commun 2021; 12:6246. [PMID: 34716329 PMCID: PMC8556371 DOI: 10.1038/s41467-021-26514-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/12/2021] [Indexed: 12/22/2022] Open
Abstract
Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to <30 nL and increases capacity to >240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.
Collapse
Affiliation(s)
- Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Victor Aguilera-Vazquez
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Hardeep S Mehta
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joshua Cantlon-Bruce
- Scienion AG, Volmerstraße 7, 12489, Berlin, Germany
- Cellenion SASU, 60 Avenue Rockefeller, Bâtiment BioSerra2, 69008, Lyon, France
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| |
Collapse
|
4
|
Yu J, Zhou Y, Engelhard M, Zhang Y, Son J, Liu S, Zhu Z, Yu XY. In situ molecular imaging of adsorbed protein films in water indicating hydrophobicity and hydrophilicity. Sci Rep 2020; 10:3695. [PMID: 32111945 PMCID: PMC7048838 DOI: 10.1038/s41598-020-60428-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 02/03/2020] [Indexed: 01/21/2023] Open
Abstract
In situ molecular imaging of protein films adsorbed on a solid surface in water was realized by using a vacuum compatible microfluidic interface and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Amino acid fragments from such hydrated protein films are observed and identified in the positive ion mode and the results are in agreement with reported works on dry protein films. Moreover, water clusters from the hydrated protein films have been observed and identified in both the positive and negative ion mode for a series protein films. Thus, the detailed composition of amino acids and water molecules in the hydrated protein films can be characterized, and the protein water microstructures can be revealed by the distinct three-dimensional spatial distribution reconstructed from in situ liquid ToF-SIMS molecular imaging. Furthermore, spectral principal component analysis of amino acid fragment peaks and water cluster peaks provides unique insights into the water cluster distribution, hydrophilicity, and hydrophobicity of hydrated adsorbed protein films in water.
Collapse
Affiliation(s)
- Jiachao Yu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210096, China
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Department of Chemistry, School of Science, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yufan Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Mark Engelhard
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Yuchen Zhang
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jiyoung Son
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Songqin Liu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 210096, China.
| | - Zihua Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Xiao-Ying Yu
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| |
Collapse
|