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  • 1
    In: GeroScience, Springer Science and Business Media LLC, Vol. 44, No. 3 ( 2022-06), p. 1641-1655
    Abstract: Prolonging survival in good health is a fundamental societal goal. However, the leading determinants of disability-free survival in healthy older people have not been well established. Data from ASPREE, a bi-national placebo-controlled trial of aspirin with 4.7 years median follow-up, was analysed. At enrolment, participants were healthy and without prior cardiovascular events, dementia or persistent physical disability. Disability-free survival outcome was defined as absence of dementia, persistent disability or death. Selection of potential predictors from amongst 25 biomedical, psychosocial and lifestyle variables including recognized geriatric risk factors, utilizing a machine-learning approach. Separate models were developed for men and women. The selected predictors were evaluated in a multivariable Cox proportional hazards model and validated internally by bootstrapping. We included 19,114 Australian and US participants aged ≥65 years (median 74 years, IQR 71.6–77.7). Common predictors of a worse prognosis in both sexes included higher age, lower Modified Mini-Mental State Examination score, lower gait speed, lower grip strength and abnormal (low or elevated) body mass index. Additional risk factors for men included current smoking, and abnormal eGFR. In women, diabetes and depression were additional predictors. The biased-corrected areas under the receiver operating characteristic curves for the final prognostic models at 5 years were 0.72 for men and 0.75 for women. Final models showed good calibration between the observed and predicted risks. We developed a prediction model in which age, cognitive function and gait speed were the strongest predictors of disability-free survival in healthy older people. Trial registration Clinicaltrials.gov (NCT01038583)
    Type of Medium: Online Resource
    ISSN: 2509-2715 , 2509-2723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 2
    Online Resource
    Online Resource
    Association for the Advancement of Artificial Intelligence (AAAI) ; 2022
    In:  Proceedings of the International AAAI Conference on Web and Social Media Vol. 16 ( 2022-05-31), p. 1208-1217
    In: Proceedings of the International AAAI Conference on Web and Social Media, Association for the Advancement of Artificial Intelligence (AAAI), Vol. 16 ( 2022-05-31), p. 1208-1217
    Abstract: A collection of over 3000 pages of emails sent by Anthony Fauci and his staff were released in an effort to understand the United States government response to the COVID-19 pandemic. In this paper, we describe how the original PDF document of emails was translated into a resource consisting of json files that make many future studies easy. We include examples for how to convert this email information into a network, a hypergraph, a temporal sequence, and a tensor for subsequent analysis, and discuss use cases and benefits in analyzing the data in these different derived formats. These resources are broadly useful for future research and pedagogical uses in terms of human and system behavioral interactions.
    Type of Medium: Online Resource
    ISSN: 2334-0770 , 2162-3449
    Language: Unknown
    Publisher: Association for the Advancement of Artificial Intelligence (AAAI)
    Publication Date: 2022
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  • 3
    Online Resource
    Online Resource
    Frontiers Media SA ; 2023
    In:  Frontiers in Veterinary Science Vol. 10 ( 2023-9-14)
    In: Frontiers in Veterinary Science, Frontiers Media SA, Vol. 10 ( 2023-9-14)
    Abstract: Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica ( S . Derby, S . Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S . Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson’s and Shannon’s indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.
    Type of Medium: Online Resource
    ISSN: 2297-1769
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
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  • 4
    Online Resource
    Online Resource
    Wiley ; 2010
    In:  Risk Analysis Vol. 30, No. 2 ( 2010-02), p. 224-235
    In: Risk Analysis, Wiley, Vol. 30, No. 2 ( 2010-02), p. 224-235
    Type of Medium: Online Resource
    ISSN: 0272-4332 , 1539-6924
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2010
    detail.hit.zdb_id: 2001458-2
    SSG: 25
    SSG: 3,6
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  • 5
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2023
    In:  Cancer Research Vol. 83, No. 7_Supplement ( 2023-04-04), p. 4606-4606
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 4606-4606
    Abstract: We previously demonstrated that upregulation of A20 in TNBC subtype in response to TNFα protects these cells from cytotoxic cell death by upregulating HSP70 protein and maintaining EMT/CSC phenotype. In contrast, luminal MCF7 or ZR75-1 cells display approximately 70% apoptosis when treated with TNFα. Overexpression of A20 in luminal cells not only protected them from TNFα-induced cytotoxicity by upregulating HSP70 and EMT/CSC phenotype, but also exhibited aggressive metastatic properties in mouse xenograft models. We determined that TNFα-induced HSP70 upregulation in TNBC cell lines was dependent on A20 de-ubiquitinase activity that protected its degradation. Interestingly, our preliminary findings also suggested that A20 protein upregulation may be dependent on HSP70 chaperone activity. We show significant overexpression of HSP70 and A20 proteins in 4T1 cell line when treated with TNFα or chemotherapeutic agents. However, A20 expression is significantly reduced when we block HSP70 activity in cells treated with TNFα or chemotherapeutic agents (Docetaxel-DTX or Doxorubicin-DOX). We proposed that A20 transcriptional upregulation upon TNFα stimulation leads to suppression of E3-ligase and accumulation of HSP70 which then stabilizes A20 with chaperone activity. Based on our reasoning, we performed the LIMBO chaperone binding assay which predicted A20 being the potential HSP70 client protein. Furthermore, we show that A20/HSP70 pathway attracts tumor-infiltrating lymphocytes (TILs) while inducing the accumulation of immunosuppressive MDSCs in syngeneic mouse models. Interestingly, pulmonary DTCs as well as the immune infiltrates from 4T1 tumor-bearing mice exhibited significantly higher HSP70 expression. Therefore, targeting HSP70 will have a dual activity on tumors and MDSCs and thus it may potentiate the efficacy of immunotherapy in preclinical models of breast cancer. As previously reported, murine 4T1 tumors fail to respond to check point inhibitors. We reasoned that this may be an appropriate model to test the efficacy of HSP70 inhibitor, JG-231. Expectedly, there was no difference in tumor growth and metastasis between control and anti-PDL1 treated animals, however, combination of anti-PDL1 antibody with JG-231 and chemotherapy (cyclophosphamide-CTX) significantly reduced primary tumor growth ( & gt;10 fold) and eliminated metastasis. Collectively, our pilot experiments provide a strong rationale for testing our hypothesis and may lead to a rapid translation into the clinical utility. Citation Format: Fulya Koksalar Alkan, Justin Wilson, Elayne Benson, Tulshi Patel, Virginia McEvoy, Nate Francois, Emma Nguyen, Hilmi Kaan Alkan, Ahmed Chadli, Jason Gestwicki, Hasan Korkaya. Heat shock proteins in immunosuppressive tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4606.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 4600-4600
    Abstract: Despite the advances in early diagnostics and therapeutics, women with metastatic breast cancer have limited treatment options. Women with TNBC, who constitute 15-20% of breast cancer patients, are often diagnosed with aggressive/metastatic disease. Advanced studies implicated immunosuppressive tumor microenvironment (TME) in aggressive/metastatic properties of TNBC subtype. Alternatively activated immature myeloid cells including tumor-associated macrophages (TAM), tumor-associated neutrophils (TAN), tumor-associated dendritic cells (TADC) and myeloid derived suppressor cells (MDSC) constitute a major component of TME. However, anti-tumorigenic microenvironment is also reported and that may have clinical relevance in early TNBC patients. Therefore, our hypothesis is that myeloid cells polarize to become immunosuppressive and infiltrate tumors and pre-metastatic niches in patients with advanced disease, while patients with early TNBCs may elicit anti-tumor immune response eliminating disseminated tumor cells (DTC). The utilization of syngeneic immunocompetent mouse models has contributed to our current understanding of immunosuppressive or immunomodulatory TME. Using these models, we have demonstrated that tumor dissemination and growth at metastatic sites is facilitated by MDSC’s. Emerging technologies; single cell RNA sequencing (scRNA-Seq), mass cytometry (CyTOF) or cellular indexing of transcriptomes and epitopes sequencing (CITE-Seq) has been powerful platforms for detailed characterization of tumors and TME compartments. We performed scRNA-Seq and CyTOF analyses of the myeloid cell populations of tumors and spleens from metastatic 4T1 and non-invasive EMT6 tumor-bearing mice. Tumors and spleens from 4T1 tumor-bearing mice exhibited a marked expansion of myeloid cell subsets that are characterized by the expression of immunosuppressive as well as progenitor markers. On the contrary, indicated tissues from EMT6 mice were enriched in NK cells, T and B lymphocytes and they were lacking immunosuppressive myeloid cell subsets. Furthermore, we identified a distinct differentiation pattern of immature myeloid cell subsets from neutrophil progenitors (NP) in 4T1 tumor-bearing mice. Using the murine TNBC models in syngeneic mice, we provide evidence that early TNBC tumors may elicit anti-tumor immune responses and thus the survival outcome in those patients is substantially increased after complete surgical resection of the primary tumors. Whereas immunosuppressive tumor microenvironment contributes to the poor overall survival in patients with advanced TNBCs. Therefore, identifying an anti-tumor immune signature in early TNBC patients may be utilized as a clinical biomarker before surgical intervention as well as improve the survival outcome. Citation Format: Hasan Korkaya, Elayne Benson, Fulya Koksalar Alkan, Justin Wilson, Tulshi Patel, Hilmi K. Alkan, Virginia McEvoy, Nika Shekastehband, Nate Francois, Huidong Shi, Catherine C. Hedrick. Phenotypic & functional diversity of tumor associated neutrophils in murine breast tumor models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4600.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 7
    In: International Journal of Wildland Fire, CSIRO Publishing, Vol. 15, No. 3 ( 2006), p. 319-
    Abstract: Space and airborne sensors have been used to map area burned, assess characteristics of active fires, and characterize post-fire ecological effects. Confusion about fire intensity, fire severity, burn severity, and related terms can result in the potential misuse of the inferred information by land managers and remote sensing practitioners who require unambiguous remote sensing products for fire management. The objective of the present paper is to provide a comprehensive review of current and potential remote sensing methods used to assess fire behavior and effects and ecological responses to fire. We clarify the terminology to facilitate development and interpretation of comprehensible and defensible remote sensing products, present the potential and limitations of a variety of approaches for remotely measuring active fires and their post-fire ecological effects, and discuss challenges and future directions of fire-related remote sensing research.
    Type of Medium: Online Resource
    ISSN: 1049-8001
    Language: English
    Publisher: CSIRO Publishing
    Publication Date: 2006
    SSG: 12
    SSG: 23
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  • 8
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2021
    In:  Science Advances Vol. 7, No. 28 ( 2021-07-09)
    In: Science Advances, American Association for the Advancement of Science (AAAS), Vol. 7, No. 28 ( 2021-07-09)
    Abstract: Hypergraphs are a natural modeling paradigm for networked systems with multiway interactions. A standard task in network analysis is the identification of closely related or densely interconnected nodes. We propose a probabilistic generative model of clustered hypergraphs with heterogeneous node degrees and edge sizes. Approximate maximum likelihood inference in this model leads to a clustering objective that generalizes the popular modularity objective for graphs. From this, we derive an inference algorithm that generalizes the Louvain graph community detection method, and a faster, specialized variant in which edges are expected to lie fully within clusters. Using synthetic and empirical data, we demonstrate that the specialized method is highly scalable and can detect clusters where graph-based methods fail. We also use our model to find interpretable higher-order structure in school contact networks, U.S. congressional bill cosponsorship and committees, product categories in copurchasing behavior, and hotel locations from web browsing sessions.
    Type of Medium: Online Resource
    ISSN: 2375-2548
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
    detail.hit.zdb_id: 2810933-8
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  • 9
    Online Resource
    Online Resource
    Open Publishing Association ; 2017
    In:  Electronic Proceedings in Theoretical Computer Science Vol. 251 ( 2017-7-25), p. 221-235
    In: Electronic Proceedings in Theoretical Computer Science, Open Publishing Association, Vol. 251 ( 2017-7-25), p. 221-235
    Type of Medium: Online Resource
    ISSN: 2075-2180
    URL: Issue
    Language: English
    Publisher: Open Publishing Association
    Publication Date: 2017
    detail.hit.zdb_id: 2577794-4
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  • 10
    In: Gut Microbes, Informa UK Limited, Vol. 15, No. 1 ( 2023-12-31)
    Type of Medium: Online Resource
    ISSN: 1949-0976 , 1949-0984
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2023
    detail.hit.zdb_id: 2575755-6
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