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  • 1
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
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  • 2
    In: Bulletin of the American Meteorological Society, American Meteorological Society, Vol. 101, No. 7 ( 2020-07), p. E968-E987
    Abstract: The National Oceanic and Atmospheric Administration’s (NOAA) Sensing Hazards with Operational Unmanned Technology (SHOUT) project evaluated the ability of observations from high-altitude unmanned aircraft to improve forecasts of high-impact weather events like tropical cyclones or mitigate potential degradation of forecasts in the event of a future gap in satellite coverage. During three field campaigns conducted in 2015 and 2016, the National Aeronautics and Space Administration (NASA) Global Hawk, instrumented with GPS dropwindsondes and remote sensors, flew 15 missions sampling 6 tropical cyclones and 3 winter storms. Missions were designed using novel techniques to target sampling regions where high model forecast uncertainty and a high sensitivity to additional observations existed. Data from the flights were examined in real time by operational forecasters, assimilated in operational weather forecast models, and applied postmission to a broad suite of data impact studies. Results from the analyses spanning different models and assimilation schemes, though limited in number, consistently demonstrate the potential for a positive forecast impact from the observations, both with and without a gap in satellite coverage. The analyses with the then-operational modeling system demonstrated large forecast improvements near 15% for tropical cyclone track at a 72-h lead time when the observations were added to the otherwise complete observing system. While future decisions regarding use of the Global Hawk platform will include budgetary considerations, and more observations are required to enhance statistical significance, the scientific results support the potential merit of the observations. This article provides an overview of the missions flown, observational approach, and highlights from the completed and ongoing data impact studies.
    Type of Medium: Online Resource
    ISSN: 0003-0007 , 1520-0477
    Language: Unknown
    Publisher: American Meteorological Society
    Publication Date: 2020
    detail.hit.zdb_id: 2029396-3
    detail.hit.zdb_id: 419957-1
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  • 3
    In: Bulletin of the American Meteorological Society, American Meteorological Society, Vol. 101, No. 9 ( 2020-09), p. 775-778
    Type of Medium: Online Resource
    ISSN: 0003-0007 , 1520-0477
    Language: Unknown
    Publisher: American Meteorological Society
    Publication Date: 2020
    detail.hit.zdb_id: 2029396-3
    detail.hit.zdb_id: 419957-1
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  • 4
    In: Earth's Future, American Geophysical Union (AGU), Vol. 6, No. 1 ( 2018-01), p. 80-102
    Abstract: The current climate observing system cannot address the range of important scientific and societally important climate issues. A significantly expanded climate observing system could address major science questions and meet important societal needs. Careful independent testing can evaluate whether proposed systems can address critical observing needs. Future investments in climate observations offer large societal benefits and economic return on investments.
    Type of Medium: Online Resource
    ISSN: 2328-4277 , 2328-4277
    URL: Issue
    Language: English
    Publisher: American Geophysical Union (AGU)
    Publication Date: 2018
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 2_Supplement_2 ( 2023-01-15), p. PR012-PR012
    Abstract: Pancreatic ductal adenocarcinoma (PDAc) remains a resistant malignancy with dismal outcomes. Early diagnosis, systemic treatment, and complete resection are interdependently essential in improving survival. But even with these interventions, 20-30% of patients will experience a metastatic recurrence within six months of surgery. This “rapid recurrence” (rrPDAc) is devastating and poorly understood, contributing to the nihilism surrounding pancreatic cancer. Overlapping etiologies of these metastatic lesions are possible. They include occult synchronous metastases, as well as disseminated metachronous lesions, both of which we hypothesize may be affected by systemic and microenvironmental changes that occur due to surgical intervention. In human rrPDAc primary tumors, we have identified increased expression of Myc-targets and differences in elements of the tumor immune microenvironment when compared to long-term non-recurrers, in the absence of substantial clinical differences. We describe a novel mouse model of immune competent, surgically resected human PDAc that models rapid recurrence compared to control mice. Our lab has developed an inducible, p48-Cre-recombinase driven LSL-KrasG12D/+ LSL-ROSA-MYC+/+ mouse model that reproducibly develops ADM to PanIN to PDAc lesions that highly recapitulate human carcinogenesis. Lesions lose Smad4 expression progressively, a feature associated with metastatic phenotypes of human PDAc, and also metastasize to the liver. Considering the role MYC plays in regulation of the immune microenvironment, we hypothesized that lines derived from this model would perform well in a model of rapid recurrence. We derived several cell lines from these tumors and implanted them orthotopically in syngeneic mice, monitoring tumor development over fourteen days with ultrasound. Mice were then subjected to takedown (‘pre-op’, n = 5), anesthesia-only controls (n = 17), sham surgical incision (n = 11), and distal pancreatectomy (n = 14). No micro-metastases were identified in livers of the ‘preop’ controls. Mice were tracked via twice-weekly trans-abdominal ultrasound. Surgically resected and sham surgery mice developed metastases a median of 10 days earlier than controls (p = 0.008), suggesting that surgical intervention perturbs the development of metastatic lesions. Furthermore, we have demonstrated that circulating tumor cells may be isolated from the portal venous drainage of these mice, allowing for a novel resource in studying pre-, intra-, and metastatic-compartments of tumor. This model will allow for investigation into rrPDAc and the role surgery may play in exacerbation of metastasis. Citation Format: Patrick J. Worth, Isabel A. English, Jackie M. Phipps, Jason M. Link, Ellen M. Langer, Motoyuki Tsuda, Colin Daniel, Carl Pelz, Jonathan Brody, Brett C. Sheppard, Rosalie C. Sears. A novel, immune-competent, Myc-dependent murine model of rapid metastatic recurrence of pancreatic cancer after resection [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr PR012.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 6
    In: SSRN Electronic Journal, Elsevier BV
    Type of Medium: Online Resource
    ISSN: 1556-5068
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
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  • 7
    Online Resource
    Online Resource
    American Meteorological Society ; 2017
    In:  Journal of Applied Meteorology and Climatology Vol. 56, No. 12 ( 2017-12), p. 3211-3228
    In: Journal of Applied Meteorology and Climatology, American Meteorological Society, Vol. 56, No. 12 ( 2017-12), p. 3211-3228
    Abstract: Observing systems consisting of a finite number of in situ monitoring stations can provide high-quality measurements with the ability to quality assure both the instruments and the data but offer limited information over larger geographic areas. This paper quantifies the spatial coverage represented by a finite set of monitoring stations by using global data—data that are possibly of lower resolution and quality. For illustration purposes, merged satellite temperature data from Microwave Sounding Units are used to estimate the representativeness of the Global Climate Observing System Reference Upper-Air Network (GRUAN). While many metrics exist for evaluating the representativeness of a site, the ability to have highly accurate monthly averaged data is essential for both trend detection and climatology evaluation. The calculated correlations of the monthly averaged upper-troposphere satellite-derived temperatures over the GRUAN stations with all other pixels around the globe show that the current 9 certified GRUAN stations have moderate correlations ( r ≥ 0.7) for approximately 10% of the earth, but an expanded network incorporating another 15 stations would result in moderate correlations for just over 60% of the earth. This analysis indicates that the value of additional stations can be quantified by using historical, satellite, or model data and can be used to reveal critical gaps in current monitoring capabilities. Evaluating the value of potential additional stations and prioritizing their initiation can optimize networks. The expansion of networks can be evaluated in a manner that allows for optimal benefit on the basis of optimization theory and economic analyses.
    Type of Medium: Online Resource
    ISSN: 1558-8424 , 1558-8432
    RVK:
    Language: Unknown
    Publisher: American Meteorological Society
    Publication Date: 2017
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  • 8
    In: Atmospheric Chemistry and Physics, Copernicus GmbH, Vol. 17, No. 24 ( 2017-12-20), p. 15069-15093
    Abstract: Abstract. Sensors on satellites provide unprecedented understanding of the Earth's climate system by measuring incoming solar radiation, as well as both passive and active observations of the entire Earth with outstanding spatial and temporal coverage. A common challenge with satellite observations is to quantify their ability to provide well-calibrated, long-term, stable records of the parameters they measure. Ground-based intercomparisons offer some insight, while reference observations and internal calibrations give further assistance for understanding long-term stability. A valuable tool for evaluating and developing long-term records from satellites is the examination of data from overlapping satellite missions. This paper addresses how the length of overlap affects the ability to identify an offset or a drift in the overlap of data between two sensors. Ozone and temperature data sets are used as examples showing that overlap data can differ by latitude and can change over time. New results are presented for the general case of sensor overlap by using Solar Radiation and Climate Experiment (SORCE) Spectral Irradiance Monitor (SIM) and Solar Stellar Irradiance Comparison Experiment (SOLSTICE) solar irradiance data as an example. To achieve a 1 % uncertainty in estimating the offset for these two instruments' measurement of the Mg II core (280 nm) requires approximately 5 months of overlap. For relative drift to be identified within 0.1 % yr−1 uncertainty (0.00008 W m−2 nm−1 yr−1), the overlap for these two satellites would need to be 2.5 years. Additional overlap of satellite measurements is needed if, as is the case for solar monitoring, unexpected jumps occur adding uncertainty to both offsets and drifts; the additional length of time needed to account for a single jump in the overlap data may be as large as 50 % of the original overlap period in order to achieve the same desired confidence in the stability of the merged data set. Results presented here are directly applicable to satellite Earth observations. Approaches for Earth observations offer additional challenges due to the complexity of the observations, but Earth observations may also benefit from ancillary observations taken from ground-based and in situ sources. Difficult choices need to be made when monitoring approaches are considered; we outline some attempts at optimizing networks based on economic principles. The careful evaluation of monitoring overlap is important to the appropriate application of observational resources and to the usefulness of current and future observations.
    Type of Medium: Online Resource
    ISSN: 1680-7324
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2017
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  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2020
    In:  Cancer Research Vol. 80, No. 22_Supplement ( 2020-11-15), p. IA-06-IA-06
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 22_Supplement ( 2020-11-15), p. IA-06-IA-06
    Abstract: Crosstalk between tumor cells and the tumor microenvironment contributes critically to tumor initiation, tumor progression, and therapeutic response. The tumor microenvironment (TME) is composed of multiple cell types (e.g. fibroblast, vascular, and immune cells) that are temporally and spatially dynamic. Stromal cells in the TME respond not only to the growing tumor cells, but are also affected by concurrent changes in the accessibility and composition of the extracellular matrix (ECM), signaling molecules, nutrients and oxygen. Together, the interactions of tumor cells and stromal cells regulates the tumor phenotype and, ultimately, affects patient outcomes. As more is understood about the dynamic relationship of multiple cell types in the tumor microenvironment, it has become clear that better models of human cancer are needed. In order to understand the impact of heterotypic crosstalk on tumor behaviors such as initiation, progression, and response to therapies, we recently developed heterotypic, scaffold-free tissue models of advanced cancer using an extrusion-based bioprinter system. Multiple cell types including cancer cells, fibroblasts, endothelial cells, mesenchymal stem cells, and immune cells can be incorporated into bioprinted tissues with defined spatial architecture, and the system is compatible with patient-derived cells. Within these structures, cells exhibit a tissue-like cellular density, deposit ECM, and self-organize to form complex structures, as illustrated by formation of nascent endothelial networks. Cell intrinsic, extrinsic, and spatial phenotypes, including cell survival, cell proliferation, differentiation state, ECM deposition, and cellular migration, can be assessed within these tissues following exposure to extrinsic signals or therapies. Our current work is focused in three main areas. First, we aim to understand the signaling between tumor and stromal cell types in early cancer development that contributes to malignant progression. Second, we are working to understand the influence of fibroblast heterogeneity on tumor cell phenotypes, using genetic or non-genetic perturbagens to alter fibroblast activation. Finally, we are building tissues comprising patient-derived cells to understand how the microenvironment influences therapeutic response. Together, our work demonstrates that bioprinted tumor tissues recapitulate many aspects of in vivo neoplastic tissues, and provides a manipulable model system to interrogate molecular mechanisms of tumor development, progression, and treatment response. Citation Format: Ellen M Langer, Brittany L Allen-Petersen, Isabel A English, Jason M Link, Rosalie C Sears. Heterotypic 3D bioprinted tissues to study pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr IA-06.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 10
    In: Earth and Space Science, Wiley, Vol. 5, No. 5 ( 2018-05), p. 176-196
    Abstract: We completed OSSEs to study the impacts of satellite and dropsonde data on global‐average and storm‐specific forecasts Removing satellite data degrades global average forecasts; adding dropsondes over a large idealized region mitigates this degradation Targeted dropsondes usually improve forecasts of three winter storms compared to a loss of satellite data, but results are case dependent
    Type of Medium: Online Resource
    ISSN: 2333-5084 , 2333-5084
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2807271-6
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