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Kumar A, Kumar S, Potter A, Gilja S, Liou D, Yang CF. OA02.04 Multimodal Management of T4 N2 Non-small-cell Lung Cancer with Additional Ipsilateral Pulmonary Nodules. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Ball J, Pastor AO, Liou D, Dickey E. Hot money: Illuminating the financing of high-carbon infrastructure in the developing world. iScience 2021; 24:103358. [PMID: 34841224 PMCID: PMC8605337 DOI: 10.1016/j.isci.2021.103358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 12/05/2022] Open
Abstract
Major infrastructure financiers will have to significantly decarbonize their investments to meet mounting promises to cut carbon emissions to “net-zero” by mid-century. We provide new details about those needed shifts. Using two World Bank databases of infrastructure projects throughout the developing world, and applying a methodology for imputing the projects' likely future carbon output, we assess the emissions profile of power-plant projects executed from 2018 through 2020 — the three years immediately preceding the spate of net-zero pledges. We find that approximately half the generation executed in those years is too carbon-intensive to align with keeping Earth's average temperature from exceeding 1.5°C above pre-industrial levels, largely because of the prevalence of new natural-gas–fired power plants. We also find new evidence of host countries' agency in shaping carbon trajectories: Much of the climate-misaligned financing is not foreign but domestic. And we find different institutions are financing infrastructure portfolios with significantly differing carbon intensities. New data yields insights on climate impact of developing-world infrastructure finance 52% of power generation added in developing world from 2018 through 2020 is climate-misaligned Climate benefits of falling coal financing eclipsed by surging natural-gas financing Much high-carbon developing-world finance comes from domestic, not foreign, investors
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Affiliation(s)
- Jeffrey Ball
- Steyer-Taylor Center for Energy Policy and Finance, Stanford University, Stanford, CA, USA
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Weber N, Liou D, Dommer J, MacMenamin P, Quiñones M, Misner I, Oler AJ, Wan J, Kim L, Coakley McCarthy M, Ezeji S, Noble K, Hurt DE. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics 2018; 34:1411-1413. [PMID: 29028892 PMCID: PMC5905584 DOI: 10.1093/bioinformatics/btx617] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 02/05/2023] Open
Abstract
Motivation Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. Availability and implementation https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele. Contact darrell.hurt@nih.gov.
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Affiliation(s)
- Nick Weber
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Liou
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Dommer
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Philip MacMenamin
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariam Quiñones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian Misner
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joe Wan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lewis Kim
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Meghan Coakley McCarthy
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Ezeji
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karlynn Noble
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darrell E Hurt
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Van Doorslaer K, Li Z, Xirasagar S, Maes P, Kaminsky D, Liou D, Sun Q, Kaur R, Huyen Y, McBride AA. The Papillomavirus Episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res 2017; 45:D499-D506. [PMID: 28053164 PMCID: PMC5210616 DOI: 10.1093/nar/gkw879] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/22/2016] [Indexed: 11/13/2022] Open
Abstract
The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algorithm to determine whether a newly sequenced virus is novel. PaVE also now contains an image library containing gross clinical and histopathological images of papillomavirus infected lesions. Database URL: https://pave.niaid.nih.gov/.
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Affiliation(s)
- Koenraad Van Doorslaer
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Zhiwen Li
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Piet Maes
- KU Leuven, Department of Microbiology and Immunology, Laboratory for Clinical Virology, Rega Institute for Medical Research, 3000 Leuven, Belgium
| | - David Kaminsky
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - David Liou
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Qiang Sun
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Ramandeep Kaur
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Yentram Huyen
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
| | - Alison A McBride
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 209892, USA
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Chuang GY, Liou D, Kwong PD, Georgiev IS. NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences. Nucleic Acids Res 2014; 42:W64-71. [PMID: 24782517 PMCID: PMC4086065 DOI: 10.1093/nar/gku318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/25/2014] [Accepted: 04/02/2014] [Indexed: 11/14/2022] Open
Abstract
Delineation of the antigenic site, or epitope, recognized by an antibody can provide clues about functional vulnerabilities and resistance mechanisms, and can therefore guide antibody optimization and epitope-based vaccine design. Previously, we developed an algorithm for antibody-epitope prediction based on antibody neutralization of viral strains with diverse sequences and validated the algorithm on a set of broadly neutralizing HIV-1 antibodies. Here we describe the implementation of this algorithm, NEP (Neutralization-based Epitope Prediction), as a web-based server. The users must supply as input: (i) an alignment of antigen sequences of diverse viral strains; (ii) neutralization data for the antibody of interest against the same set of antigen sequences; and (iii) (optional) a structure of the unbound antigen, for enhanced prediction accuracy. The prediction results can be downloaded or viewed interactively on the antigen structure (if supplied) from the web browser using a JSmol applet. Since neutralization experiments are typically performed as one of the first steps in the characterization of an antibody to determine its breadth and potency, the NEP server can be used to predict antibody-epitope information at no additional experimental costs. NEP can be accessed on the internet at http://exon.niaid.nih.gov/nep.
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Affiliation(s)
| | - David Liou
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Gangi A, Liou D, Barmparas G, Hotz H, Donovan S, Ley E. Trauma in the Intoxicated Bicyclist. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Barmparas G, Liou D, Lee D, Fierro N, Lu J, Ley E. Clostridium Difficile Colitis Increases The Risk For Venous Thromboembolism. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Barmparas G, Liou D, Lu J, Eng J, Lee D, Fierro N, Ley E. Risk Of Abdominal Abscess Following Elective And Traumatic Splenectomy. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.1047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Liou D, Barmparas G, Chung R, Ley E, Margulies D, Salim A, Bukur M. Work Hour Reduction: Still Room for Improvement. J Surg Res 2013. [DOI: 10.1016/j.jss.2012.10.870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Short S, Liou D, Singer M, Margulies D, Bukur M, Salim A, Ley E. Insurance Type, Not Race, Predicts Mortality After Pediatric Trauma. J Surg Res 2013. [DOI: 10.1016/j.jss.2012.10.721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Liou D, Singer M, Melo N, Chung R, Bukur M, Margulies D, Salim A, Ley E. Emergency Department Blood Transfusion of Greater Than Two Units Predicts Increased Mortality. J Surg Res 2013. [DOI: 10.1016/j.jss.2012.10.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Short S, Liou D, Singer M, Margulies D, Bukur M, Salim A, Ley E. Teenage Gender Impacts Mortality After Traumatic Brain Injury. J Surg Res 2013. [DOI: 10.1016/j.jss.2012.10.520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Liou D, Contento IR. Usefulness of psychosocial theory variables in explaining fat-related dietary behavior in Chinese Americans: association with degree of acculturation. J Nutr Educ 2001; 33:322-31. [PMID: 12031170 DOI: 10.1016/s1499-4046(06)60354-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To determine the usefulness of variables from psychosocial models of health behavior in explaining fat-related dietary behavior among a sample of Chinese Americans. DESIGN A survey questionnaire was administered to a convenience sample of Chinese Americans and analyzed for descriptive statistics and relationships among variables. SUBJECTS/SETTINGS Participants were 600 healthy individuals, ranging from 25 to 70 years of age, living in New York City. VARIABLES MEASURED Demographic factors, degree of acculturation, food preferences, and 13 social psychological scales derived from the Theory of Planned Behavior, the Healthy Belief Model, and Social Cognitive Theory. Dependent measures assessed were intention to reduce dietary fat and behaviors related to the selection of reduced-fat diets. STATISTICAL ANALYSES Descriptive statistics, Pearsons' correlation coefficients, t-tests, one-way analyses of variance, and multiple regression analyses were used. RESULTS Attitude, overall health concern, and self-efficacy accounted for 58% of the variance in behavioral intention for the entire sample. Attitude, perceived barriers, and self-efficacy accounted for 19% of the variance in the prediction of dietary fat reduction behaviors. In general, a gradient was seen in the increased predictiveness of each regression model by degree of acculturation of the immigrants to American culture: predictiveness (R2) for behavior ranged from 15% for the least to 34% for the most acculturated. Acculturation was significantly related to declines in the influence of habit and of social norms. These effects were not seen by length of residency. IMPLICATIONS Nutrition educators should assess the degree of acculturation of groups with whom they work and recognize that the degree of acculturation impacts the relative importance of various psychosocial variables in fat reduction behaviors.
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Affiliation(s)
- D Liou
- Department of Human Ecology, Montclair State University, Upper Montclair, New Jersey 07043, USA.
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