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Article ; Online: Model for Interpreting Discordant SARS-CoV-2 Diagnostic Test Results.

Egbelowo, Oluwaseun F / Fox, Spencer J / Gibson, Graham C / Meyers, Lauren Ancel

2024 Volume 30, Issue 2, Page(s) 388–391

Abstract: We devised a model to interpret discordant SARS-CoV-2 test results. We estimate that, during March 2020-May 2022, a patient in the United States who received a positive rapid antigen test result followed by a negative nucleic acid test result had only a ... ...

Abstract	We devised a model to interpret discordant SARS-CoV-2 test results. We estimate that, during March 2020-May 2022, a patient in the United States who received a positive rapid antigen test result followed by a negative nucleic acid test result had only a 15.4% (95% CI 0.6%-56.7%) chance of being infected.
MeSH term(s)	Humans ; United States/epidemiology ; SARS-CoV-2 ; COVID-19/diagnosis ; COVID-19 Testing ; Diagnostic Tests, Routine ; Sensitivity and Specificity
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid3002.230200
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Article ; Online: Real time monitoring of COVID-19 intervention effectiveness through contact tracing data

Graham C. Gibson / Spencer Woody / Emily James / Minda Weldon / Spencer J. Fox / Lauren Ancel Meyers / Darlene Bhavnani

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 9

Abstract: Abstract Communities worldwide have used vaccines and facemasks to mitigate the COVID-19 pandemic. When an individual opts to vaccinate or wear a mask, they may lower their own risk of becoming infected as well as the risk that they pose to others while ... ...

Abstract	Abstract Communities worldwide have used vaccines and facemasks to mitigate the COVID-19 pandemic. When an individual opts to vaccinate or wear a mask, they may lower their own risk of becoming infected as well as the risk that they pose to others while infected. The first benefit–reducing susceptibility–has been established across multiple studies, while the second–reducing infectivity–is less well understood. Using a new statistical method, we estimate the efficacy of vaccines and facemasks at reducing both types of risks from contact tracing data collected in an urban setting. We find that vaccination reduced the risk of onward transmission by 40.7% [95% CI 25.8–53.2%] during the Delta wave and 31.0% [95% CI 19.4–40.9%] during the Omicron wave and that mask wearing reduced the risk of infection by 64.2% [95% CI 5.8–77.3%] during the Omicron wave. By harnessing commonly-collected contact tracing data, the approach can broadly provide timely and actionable estimates of intervention efficacy against a rapidly evolving pathogen.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Real time monitoring of COVID-19 intervention effectiveness through contact tracing data.

Gibson, Graham C / Woody, Spencer / James, Emily / Weldon, Minda / Fox, Spencer J / Meyers, Lauren Ancel / Bhavnani, Darlene

Scientific reports

2023 Volume 13, Issue 1, Page(s) 9371

Abstract: Communities worldwide have used vaccines and facemasks to mitigate the COVID-19 pandemic. When an individual opts to vaccinate or wear a mask, they may lower their own risk of becoming infected as well as the risk that they pose to others while infected. ...

Abstract	Communities worldwide have used vaccines and facemasks to mitigate the COVID-19 pandemic. When an individual opts to vaccinate or wear a mask, they may lower their own risk of becoming infected as well as the risk that they pose to others while infected. The first benefit-reducing susceptibility-has been established across multiple studies, while the second-reducing infectivity-is less well understood. Using a new statistical method, we estimate the efficacy of vaccines and facemasks at reducing both types of risks from contact tracing data collected in an urban setting. We find that vaccination reduced the risk of onward transmission by 40.7% [95% CI 25.8-53.2%] during the Delta wave and 31.0% [95% CI 19.4-40.9%] during the Omicron wave and that mask wearing reduced the risk of infection by 64.2% [95% CI 5.8-77.3%] during the Omicron wave. By harnessing commonly-collected contact tracing data, the approach can broadly provide timely and actionable estimates of intervention efficacy against a rapidly evolving pathogen.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/prevention & control ; Contact Tracing ; Pandemics ; Vaccination
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-35892-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interpreting discordant SARS-CoV-2 diagnostic test results

Egbelowo, Oluwaseun F / Fox, Spencer J / Gibson, Graham C / Meyers, Lauren Ancel

medRxiv

Abstract: We introduce a model to interpret discordant SARS-CoV-2 test results and estimate that an individual receiving a positive rapid antigen test followed by a negative Nucleic Acid Amplification Test had only a 12-24% chance of being infected in the United ... ...

Abstract	We introduce a model to interpret discordant SARS-CoV-2 test results and estimate that an individual receiving a positive rapid antigen test followed by a negative Nucleic Acid Amplification Test had only a 12-24% chance of being infected in the United States from March 2020 to May 2022.
Keywords	covid19
Language	English
Publishing date	2023-02-10
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.02.07.23285547
Database	COVID19

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Article ; Online: Using stable isotopes to track hydrological processes at an oil sands mine, Alberta, Canada

Spencer J. Chad / S. Lee Barbour / Jeffrey J. McDonnell / John J. Gibson

Journal of Hydrology: Regional Studies, Vol 40, Iss , Pp 101032- (2022)

2022

Abstract: Study region: This study was conducted at an oil sands operation in the Athabasca Oil Sands Region (AOSR), northeastern Alberta, Canada. The mine comprises open pit excavation of bituminous sands at two sites (Mildred Lake, ML, and Aurora North, AN), ... ...

Abstract	Study region: This study was conducted at an oil sands operation in the Athabasca Oil Sands Region (AOSR), northeastern Alberta, Canada. The mine comprises open pit excavation of bituminous sands at two sites (Mildred Lake, ML, and Aurora North, AN), with a single hot-water extraction circuit connecting extraction plants at each mine. Study focus: Water samples were collected and analyzed regularly over an eight-year period to establish inventories of site-wide water isotope signatures including seasonal and interannual changes in the recycle water circuit, and to permit future application of an isotope balance model to constrain poorly quantified processes such as evaporation losses, dewatering of tailings, and tailings pond connectivity of the recycle water circuit. New hydrological insights for the region: Sampling of precipitation inputs over an 8-year period was used to constrain a local meteoric water line for the area. Differences in evaporative isotopic enrichment of tailings ponds at ML and AN are attributed to use of Athabasca River makeup water at the former site versus basal dewatering sources at the latter, with similar atmospheric controls at both. A conceptual model is developed summarizing temporal variations in water balance and isotopic signatures within the recycle water circuit, including accurate simulation of the unique isotopic enrichment of cooling tower blowdown. This study provides foundational evidence for application of stable isotope mass balance to monitor and improve industrial water use efficiency and management.
Keywords	Isotope hydrology ; Deuterium ; Oxygen-18 ; Isotope mass balance ; Oil sands ; Mine water management ; Physical geography ; GB3-5030 ; Geology ; QE1-996.5
Subject code	550
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Disproportionate impacts of COVID-19 in a large US city.

Spencer J Fox / Emily Javan / Remy Pasco / Graham C Gibson / Briana Betke / José L Herrera-Diestra / Spencer Woody / Kelly Pierce / Kaitlyn E Johnson / Maureen Johnson-León / Michael Lachmann / Lauren Ancel Meyers

PLoS Computational Biology, Vol 19, Iss 6, p e

2023 Volume 1011149

Abstract: COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but ... ...

Abstract	COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021 and fine-grain infection hospitalization rates, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 23.7% (95% CrI: 22.5-24.8%) infection rate and 29.4% (95% CrI: 28.0-31.0%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (11.2% [95% CrI: 10.3-12.0%] vs 25.1% [95% CrI: 23.7-26.4%]), but more likely to be hospitalized (1,965 per 100,000 vs 376 per 100,000) and have their infections reported (53% [95% CrI: 49-57%] vs 28% [95% CrI: 27-30%]). We used a mixed effect poisson regression model to estimate disparities in infection and reporting rates as a function of social vulnerability. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 60%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. Our results suggest that further public health efforts are needed to mitigate local COVID-19 disparities and that the CDC's social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.
Keywords	Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using stable isotopes to track hydrological processes at an oil sands mine, Alberta, Canada

Chad, Spencer J. / Barbour, S. Lee / McDonnell, Jeffrey J. / Gibson, John J.

Journal of Hydrology: Regional Studies. 2022 Apr., v. 40 p.101032-

2022

Abstract: This study was conducted at an oil sands operation in the Athabasca Oil Sands Region (AOSR), northeastern Alberta, Canada. The mine comprises open pit excavation of bituminous sands at two sites (Mildred Lake, ML, and Aurora North, AN), with a single hot- ...

Abstract	This study was conducted at an oil sands operation in the Athabasca Oil Sands Region (AOSR), northeastern Alberta, Canada. The mine comprises open pit excavation of bituminous sands at two sites (Mildred Lake, ML, and Aurora North, AN), with a single hot-water extraction circuit connecting extraction plants at each mine. Water samples were collected and analyzed regularly over an eight-year period to establish inventories of site-wide water isotope signatures including seasonal and interannual changes in the recycle water circuit, and to permit future application of an isotope balance model to constrain poorly quantified processes such as evaporation losses, dewatering of tailings, and tailings pond connectivity of the recycle water circuit. Sampling of precipitation inputs over an 8-year period was used to constrain a local meteoric water line for the area. Differences in evaporative isotopic enrichment of tailings ponds at ML and AN are attributed to use of Athabasca River makeup water at the former site versus basal dewatering sources at the latter, with similar atmospheric controls at both. A conceptual model is developed summarizing temporal variations in water balance and isotopic signatures within the recycle water circuit, including accurate simulation of the unique isotopic enrichment of cooling tower blowdown. This study provides foundational evidence for application of stable isotope mass balance to monitor and improve industrial water use efficiency and management.
Keywords	dewatering ; evaporation ; hydrology ; isotopic enrichment ; lakes ; models ; oils ; rivers ; stable isotopes ; water use efficiency ; Alberta ; Isotope hydrology ; Deuterium ; Oxygen-18 ; Isotope mass balance ; Oil sands ; Mine water management ; Tailings management
Language	English
Dates of publication	2022-04
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	2814784-4
ISSN	2214-5818
ISSN	2214-5818
DOI	10.1016/j.ejrh.2022.101032
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Disproportionate impacts of COVID-19 in a large US city.

Fox, Spencer J / Javan, Emily / Pasco, Remy / Gibson, Graham C / Betke, Briana / Herrera-Diestra, José L / Woody, Spencer / Pierce, Kelly / Johnson, Kaitlyn E / Johnson-León, Maureen / Lachmann, Michael / Meyers, Lauren Ancel

PLoS computational biology

2023 Volume 19, Issue 6, Page(s) e1011149

Abstract	COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021 and fine-grain infection hospitalization rates, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 23.7% (95% CrI: 22.5-24.8%) infection rate and 29.4% (95% CrI: 28.0-31.0%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (11.2% [95% CrI: 10.3-12.0%] vs 25.1% [95% CrI: 23.7-26.4%]), but more likely to be hospitalized (1,965 per 100,000 vs 376 per 100,000) and have their infections reported (53% [95% CrI: 49-57%] vs 28% [95% CrI: 27-30%]). We used a mixed effect poisson regression model to estimate disparities in infection and reporting rates as a function of social vulnerability. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 60%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. Our results suggest that further public health efforts are needed to mitigate local COVID-19 disparities and that the CDC's social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Ethnicity ; Hospitalization ; Public Health
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011149
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Breast Tumor Metastasis and Its Microenvironment: It Takes Both Seed and Soil to Grow a Tumor and Target It for Treatment.

Bonni, Shirin / Brindley, David N / Chamberlain, M Dean / Daneshvar-Baghbadorani, Nima / Freywald, Andrew / Hemmings, Denise G / Hombach-Klonisch, Sabine / Klonisch, Thomas / Raouf, Afshin / Shemanko, Carrie Simone / Topolnitska, Diana / Visser, Kaitlyn / Vizeacoumar, Franco J / Wang, Edwin / Gibson, Spencer B

Cancers

2024 Volume 16, Issue 5

Abstract: Metastasis remains a major challenge in treating breast cancer. Breast tumors metastasize to organ-specific locations such as the brain, lungs, and bone, but why some organs are favored over others remains unclear. Breast tumors also show heterogeneity, ... ...

Abstract	Metastasis remains a major challenge in treating breast cancer. Breast tumors metastasize to organ-specific locations such as the brain, lungs, and bone, but why some organs are favored over others remains unclear. Breast tumors also show heterogeneity, plasticity, and distinct microenvironments. This contributes to treatment failure and relapse. The interaction of breast cancer cells with their metastatic microenvironment has led to the concept that primary breast cancer cells act as seeds, whereas the metastatic tissue microenvironment (TME) is the soil. Improving our understanding of this interaction could lead to better treatment strategies for metastatic breast cancer. Targeted treatments for different subtypes of breast cancers have improved overall patient survival, even with metastasis. However, these targeted treatments are based upon the biology of the primary tumor and often these patients' relapse, after therapy, with metastatic tumors. The advent of immunotherapy allowed the immune system to target metastatic tumors. Unfortunately, immunotherapy has not been as effective in metastatic breast cancer relative to other cancers with metastases, such as melanoma. This review will describe the heterogeneic nature of breast cancer cells and their microenvironments. The distinct properties of metastatic breast cancer cells and their microenvironments that allow interactions, especially in bone and brain metastasis, will also be described. Finally, we will review immunotherapy approaches to treat metastatic breast tumors and discuss future therapeutic approaches to improve treatments for metastatic breast cancer.
Language	English
Publishing date	2024-02-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers16050911
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Article ; Online: Elevated expression of interleukin 16 in chronic lymphocytic leukemia is associated with disease burden and abnormal immune microenvironment.

Wu, Xun / Thisdelle, Jordan / Hou, Sen / Fajardo-Despaigne, J Ernesto / Gibson, Spencer B / Johnston, James B / Dawe, David E / Banerji, Versha / Marshall, Aaron J

Leukemia research

2023 Volume 131, Page(s) 107315

Abstract: Interleukin-16 (IL-16) is a novel biomarker that has been implicated in many cancers as well as inflammatory diseases. In this study, we examined plasma levels of 30 cytokines and chemokines in chronic lymphocytic leukemia (CLL) and monoclonal B cell ... ...

Abstract	Interleukin-16 (IL-16) is a novel biomarker that has been implicated in many cancers as well as inflammatory diseases. In this study, we examined plasma levels of 30 cytokines and chemokines in chronic lymphocytic leukemia (CLL) and monoclonal B cell lymphocytosis (MBL) patients, and examined their association with disease stage, CLL biomarkers and T cell subsets. Interleukin 16 (IL-16) was identified as a relatively uncharacterized cytokine significantly elevated in CLL patients compared to healthy controls and MBL patients. Plasma levels of IL-16 were significantly elevated by Rai stage 0, increased by Rai stage 3-4, correlated strongly with lymphocyte count and were decreased after Ibrutinib treatment. CLL cells expressed IL-16 mRNA and spontaneously secreted IL-16 in vitro. CLL cells express IL-16 mRNA at significantly higher levels in lymphoid tissues than blood, and we observed that IL-16 release was increased in co-cultures of CLL and autologous CD4 + T cells. Elevated plasma IL-16 levels were associated with abnormalities in the immune microenvironment including multiple inflammatory cytokines and chemokines and expansion of type 1 follicular helper T cells. Taken together, our results identify IL-16 as a novel biomarker in CLL with potential functional roles in cellular interactions between CLL cells and T cells.
MeSH term(s)	Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/therapy ; Interleukin-16 ; Lymphocyte Count ; Lymphocytosis ; Cost of Illness ; Tumor Microenvironment
Chemical Substances	Interleukin-16
Language	English
Publishing date	2023-05-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752396-8
ISSN	1873-5835 ; 0145-2126
ISSN (online)	1873-5835
ISSN	0145-2126
DOI	10.1016/j.leukres.2023.107315
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