NAU publications by SHERC
Faculty & staff publications
NAU faculty and staff have the opportunity to publish their findings and knowledge as authors. SHERC has many researchers that have been cited multiple times in major publications for their great work. The Southwest Health Equity Research Collaborative has accumulated all faculty publications into one, easy to navigate database.
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Williamson, Heather J; Chief, Carmenlita; Jiménez, Dulce; Begay, Andria; Milner, Trudie F; Sullivan, Shevaun; Torres, Emma; Remiker, Mark; Longorio, Alexandra Elvira Samarron; Sabo, Samantha; Teufel-Shone, Nicolette I Voices of Community Partners: Perspectives Gained from Conversations of Community-Based Participatory Research Experiences Journal Article International Journal of Environmental Research and Public Health, 2020. @article{Williamson2020, title = {Voices of Community Partners: Perspectives Gained from Conversations of Community-Based Participatory Research Experiences}, author = {Heather J. Williamson and Carmenlita Chief and Dulce Jiménez and Andria Begay and Trudie F. Milner and Shevaun Sullivan and Emma Torres and Mark Remiker and Alexandra Elvira Samarron Longorio and Samantha Sabo and Nicolette I. Teufel-Shone}, url = {https://www.mdpi.com/1660-4601/17/14/5245}, doi = {10.3390/ijerph1745245}, year = {2020}, date = {2020-07-21}, journal = {International Journal of Environmental Research and Public Health}, abstract = {Community-based participatory research (CBPR) has been documented as an effective approach to research with underserved communities, particularly with racial and ethnic minority groups. However, much of the literature promoting the use of CBPR with underserved communities is written from the perspective of the researchers and not from the perspective of the community partner. The purpose of this article is to capture lessons learned from the community partners’insight gained through their experiences with CBPR. A multi-investigator consensus method was used to qualitatively code the transcripts of a CBPR story-telling video series. Seven major themes were identified: (1) expectations for engaging in research, (2) cultural humility, (3) respecting the partnership, (4) open communication, (5) genuine commitment, (6) valuing strengths and recognizing capacities, and (7) collaborating to yield meaningful results. The themes drawn from the community partner’s voice align with the tenets of CBPR advanced in the academic literature.More opportunities to include the community voice when promoting CBPR should be undertaken to help introduce the concepts to potential community partners who may be research cautious.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Community-based participatory research (CBPR) has been documented as an effective approach to research with underserved communities, particularly with racial and ethnic minority groups. However, much of the literature promoting the use of CBPR with underserved communities is written from the perspective of the researchers and not from the perspective of the community partner. The purpose of this article is to capture lessons learned from the community partners’insight gained through their experiences with CBPR. A multi-investigator consensus method was used to qualitatively code the transcripts of a CBPR story-telling video series. Seven major themes were identified: (1) expectations for engaging in research, (2) cultural humility, (3) respecting the partnership, (4) open communication, (5) genuine commitment, (6) valuing strengths and recognizing capacities, and (7) collaborating to yield meaningful results. The themes drawn from the community partner’s voice align with the tenets of CBPR advanced in the academic literature.More opportunities to include the community voice when promoting CBPR should be undertaken to help introduce the concepts to potential community partners who may be research cautious. |
Lindly, Olivia J; Martin, Alison J; Lally, Kathryn Community Mental Health Journal, 2020. @article{Lindly2020, title = {A Profile of Care Coordination, Missed School Days, and Unmet Needs Among Oregon Children With Special Health Care Needs With Behavioral and Mental Health Conditions}, author = {Olivia J Lindly and Alison J Martin and Kathryn Lally}, url = {https://doi.org/10.1007/s10597-020-00609-4}, doi = {10.1007/s10597-020-00609-4}, year = {2020}, date = {2020-04-01}, journal = {Community Mental Health Journal}, abstract = {To inform Oregon's Title V needs assessment activities, we aimed to (1) characterize the state's subpopulation of children with special health care needs (CSHCN) with behavioral and mental health conditions (B/MHC) and (2) determine associations of care coordination with missed school days and unmet needs for this subpopulation. We analyzed 2009-2010 National Survey of Children with Special Health Care Needs data on 736 Oregon CSHCN < 18 years, including 418 CSHCN with B/MHC. Among Oregon CSHCN with B/MHC: 48.9% missed ≥ 4 school days, 25% had ≥ 1 unmet health services need, and 14.8% had ≥ 1 unmet family support services need. Care coordination was associated with lower adjusted odds of ≥ 1 unmet health services need but was not significantly associated with missed school days or unmet family support services need. The approach to identify Oregon CSHCN with B/MHC may be adopted by other states endeavoring to improve health for this vulnerable subpopulation}, keywords = {}, pubstate = {published}, tppubtype = {article} } To inform Oregon's Title V needs assessment activities, we aimed to (1) characterize the state's subpopulation of children with special health care needs (CSHCN) with behavioral and mental health conditions (B/MHC) and (2) determine associations of care coordination with missed school days and unmet needs for this subpopulation. We analyzed 2009-2010 National Survey of Children with Special Health Care Needs data on 736 Oregon CSHCN < 18 years, including 418 CSHCN with B/MHC. Among Oregon CSHCN with B/MHC: 48.9% missed ≥ 4 school days, 25% had ≥ 1 unmet health services need, and 14.8% had ≥ 1 unmet family support services need. Care coordination was associated with lower adjusted odds of ≥ 1 unmet health services need but was not significantly associated with missed school days or unmet family support services need. The approach to identify Oregon CSHCN with B/MHC may be adopted by other states endeavoring to improve health for this vulnerable subpopulation |
Stout, Nicole L; Brown, Justin C; Schwartz, Anna L; Marshall, Timothy F; Campbell, Anna M; Nekhlyudov, Larissa; Zucker, David S; Basen-Engquist, Karen M; Campbell, Grace; Meyerhardt, Jeffrey; Cheville, Andrea L; Covington, Kelley R; Ligibel, Jennifer A; Sokolof, Jonas M; Schmitz, Kathryn H; Alfano, Catherine M An exercise oncology clinical pathway: Screening and referral for personalized interventions Journal Article American Cancer Society Journals, 2020. @article{Stout2020, title = {An exercise oncology clinical pathway: Screening and referral for personalized interventions}, author = {Nicole L Stout and Justin C Brown and Anna L Schwartz and Timothy F Marshall and Anna M Campbell and Larissa Nekhlyudov and David S Zucker and Karen M Basen-Engquist and Grace Campbell and Jeffrey Meyerhardt and Andrea L Cheville and Kelley R Covington and Jennifer A Ligibel and Jonas M Sokolof and Kathryn H Schmitz and Catherine M Alfano}, url = {https://acsjournals.onlinelibrary.wiley.com/doi/abs/10.1002/cncr.32860}, doi = {10.1002/cncr.32860}, year = {2020}, date = {2020-03-25}, journal = {American Cancer Society Journals}, abstract = {This article presents a clinical screening and referral framework to enable health care professionals to guide individuals with cancer to safe and effective exercise programs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This article presents a clinical screening and referral framework to enable health care professionals to guide individuals with cancer to safe and effective exercise programs. |
Pearson, Talima; Sahl, Jason; Hepp, Crystal; Handady, Karthik; Hornstra, Heidie; Vazquez, Adam J; Mayo, Erik Settles Mark; Kaestli, Mirjam; Williamson, Heather; Price, Erin P; Sarovich, Derek S; Cook, James M; Wolken, Spenser R; Bowen, Richard; Tuanyok, Apichai; Foster, Jeffrey; Drees, Keven P; Kidd, Timothy J; Bell, Scott C; Currie, Bart J; Keim, Paul PLoS Pathogens, 2020. @article{Pearson2020, title = {Pathogen to Commensal? Longitudinal Within-Host Population Dynamics, Evolution, and Adaptation During a Chronic >16-year Burkholderia Pseudomallei Infection}, author = {Talima Pearson and Jason Sahl and Crystal Hepp and Karthik Handady and Heidie Hornstra and Adam J. Vazquez and Erik Settles Mark Mayo and Mirjam Kaestli and Heather Williamson and Erin P. Price and Derek S. Sarovich and James M. Cook and Spenser R. Wolken and Richard Bowen and Apichai Tuanyok and Jeffrey Foster and Keven P. Drees and Timothy J. Kidd and Scott C. Bell and Bart J. Currie and Paul Keim}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008298}, doi = {10.1371/journal.ppat.100829}, year = {2020}, date = {2020-03-05}, journal = {PLoS Pathogens}, abstract = {Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host. |
Cocking, Jill Hager; Deberg, Michael; Schupp, Jim; Sahl, Jason; Wiggins, Kristin; Porty, Ariel; Hornstra, Heidie M; Hepp, Crystal; Jardine, Claire; Furstenau, Tara N; Schulte-Hostedde, Albrecht; Fofanov, Viacheslav Y; Pearson, Talima Selective Whole Genome Amplification and Sequencing of Coxiella Burnetii Directly From Environmental Samples Journal Article Genomics, 112 (2), pp. 1872-1878, 2020. @article{Cocking2020, title = {Selective Whole Genome Amplification and Sequencing of Coxiella Burnetii Directly From Environmental Samples}, author = {Jill Hager Cocking and Michael Deberg and Jim Schupp and Jason Sahl and Kristin Wiggins and Ariel Porty and Heidie M. Hornstra and Crystal Hepp and Claire Jardine and Tara N. Furstenau and Albrecht Schulte-Hostedde and Viacheslav Y. Fofanov and Talima Pearson}, url = {https://www.sciencedirect.com/science/article/pii/S0888754319302058?via%3Dihub}, doi = {10.1016/j.ygeno.2019.10.02}, year = {2020}, date = {2020-03-01}, journal = {Genomics}, volume = {112}, number = {2}, pages = {1872-1878}, abstract = {Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations. |
Pinto, Bronson I; Cruz, Nathan D; Lujan, Oscar R; Propper, Catherine R; Kellar, Robert S In Vitro Scratch Assay to Demonstrate Effects of Arsenic on Skin Cell Migration Journal Article Jove, 144 , 2020. @article{Pinto2020, title = {In Vitro Scratch Assay to Demonstrate Effects of Arsenic on Skin Cell Migration}, author = {Bronson I Pinto and Nathan D Cruz and Oscar R Lujan and Catherine R Propper and Robert S Kellar}, url = {https://www.jove.com/video/58838/in-vitro-scratch-assay-to-demonstrate-effects-arsenic-on-skin-cell}, doi = {10.3791/58838}, year = {2020}, date = {2020-02-23}, journal = {Jove}, volume = {144}, abstract = {Understanding the physiologic mechanisms of wound healing has been the focus of ongoing research for many years. This research directly translates into changes in clinical standards used for treating wounds and decreasing morbidity and mortality for patients. Wound healing is a complex process that requires strategic cell and tissue interaction and function. One of the many critically important functions of wound healing is individual and collective cellular migration. Upon injury, various cells from the blood, surrounding connective, and epithelial tissues rapidly migrate to the wound site by way of chemical and/or physical stimuli. This migration response can largely dictate the outcomes and success of a healing wound. Understanding this specific cellular function is important for translational medicine that can lead to improved wound healing outcomes. Here, we describe a protocol used to better understand cellular migration as it pertains to wound healing, and how changes to the cellular environment can significantly alter this process. In this example study, dermal fibroblasts were grown in media supplemented with fetal bovine serum (FBS) as monolayer cultures in tissue culture flasks. Cells were aseptically transferred into tissue culture treated 12-well plates and grown to 100% confluence. Upon reaching confluence, the cells in the monolayer were vertically scratched using a p200 pipet tip. Arsenic diluted in culture media supplemented with FBS was added to individual wells at environmentally relevant doses ranging 0.1-10 μM. Images were captured every 4 hours (h) over a 24 h period using an inverted light microscope to observe cellular migration (wound closure). Images were individually analyzed using image analysis software, and percent wound closure was calculated. Results demonstrate that arsenic slows down wound healing. This technique provides a rapid and inexpensive first screen for evaluation of the effects of contaminants on wound healing.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding the physiologic mechanisms of wound healing has been the focus of ongoing research for many years. This research directly translates into changes in clinical standards used for treating wounds and decreasing morbidity and mortality for patients. Wound healing is a complex process that requires strategic cell and tissue interaction and function. One of the many critically important functions of wound healing is individual and collective cellular migration. Upon injury, various cells from the blood, surrounding connective, and epithelial tissues rapidly migrate to the wound site by way of chemical and/or physical stimuli. This migration response can largely dictate the outcomes and success of a healing wound. Understanding this specific cellular function is important for translational medicine that can lead to improved wound healing outcomes. Here, we describe a protocol used to better understand cellular migration as it pertains to wound healing, and how changes to the cellular environment can significantly alter this process. In this example study, dermal fibroblasts were grown in media supplemented with fetal bovine serum (FBS) as monolayer cultures in tissue culture flasks. Cells were aseptically transferred into tissue culture treated 12-well plates and grown to 100% confluence. Upon reaching confluence, the cells in the monolayer were vertically scratched using a p200 pipet tip. Arsenic diluted in culture media supplemented with FBS was added to individual wells at environmentally relevant doses ranging 0.1-10 μM. Images were captured every 4 hours (h) over a 24 h period using an inverted light microscope to observe cellular migration (wound closure). Images were individually analyzed using image analysis software, and percent wound closure was calculated. Results demonstrate that arsenic slows down wound healing. This technique provides a rapid and inexpensive first screen for evaluation of the effects of contaminants on wound healing. |
Kumar, Amit; Rivera-Hernandez, Maricruz; Karmarkar, Amol M; Chou, Lin-Na; Kuo, Yong-Fang; Baldwin, Julie A; Panagiotou, Orestis A; Burke, Robert E; Ottenbacher, Kenneth J Social and Health-Related Factors Associated With Enrollment in Medicare Advantage Plans in Older Adults Journal Article Journal of the American Geriatrics Society, 68 (2), pp. 313-320, 2020. @article{Kumar2020, title = {Social and Health-Related Factors Associated With Enrollment in Medicare Advantage Plans in Older Adults}, author = {Amit Kumar and Maricruz Rivera-Hernandez and Amol M. Karmarkar and Lin-Na Chou and Yong-Fang Kuo and Julie A. Baldwin and Orestis A. Panagiotou and Robert E. Burke and Kenneth J. Ottenbacher}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/jgs.16202}, doi = {10.1111/jgs.16202}, year = {2020}, date = {2020-02-01}, journal = {Journal of the American Geriatrics Society}, volume = {68}, number = {2}, pages = {313-320}, abstract = {Among Mexican American older adults, FFS enrollees were more likely to be born in Mexico, speak Spanish, have lower levels of education, and have more disability than MA enrollees. Older adults with a larger number of limitations of instrumental activities of daily living (odds ratio [OR] = .50; 95% confidence interval [CI] = .26‐.98) and more social support (OR = .70; 95% CI = .45‐.98) were less likely to switch from FFS to MA compared with older adults with no limitations and less social support. Additionally, older adults living in counties with a greater number of MA plans were more likely to switch from FFS to MA (OR = 2.1; 95% CI = 1.45‐3.16), compared with counties with a lower number of MA plans. In counties with a higher number of MA plans, older adults with more social support had lower odds of switching from FFS to MA (OR = .48; 95% CI = .28‐.82) compared with older adults with less social support.Compared with those enrolled in MA, older Mexican American adults enrolled in Medicare FFS are more socioeconomically disadvantaged and more likely to demonstrate poor health status. Stronger social support and increased physical limitations were strongly associated with less frequent switching from FFS to MA plans. Additionally, increased availability of MA plans at the county level is a significant driver of enrollment in MA plans. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Among Mexican American older adults, FFS enrollees were more likely to be born in Mexico, speak Spanish, have lower levels of education, and have more disability than MA enrollees. Older adults with a larger number of limitations of instrumental activities of daily living (odds ratio [OR] = .50; 95% confidence interval [CI] = .26‐.98) and more social support (OR = .70; 95% CI = .45‐.98) were less likely to switch from FFS to MA compared with older adults with no limitations and less social support. Additionally, older adults living in counties with a greater number of MA plans were more likely to switch from FFS to MA (OR = 2.1; 95% CI = 1.45‐3.16), compared with counties with a lower number of MA plans. In counties with a higher number of MA plans, older adults with more social support had lower odds of switching from FFS to MA (OR = .48; 95% CI = .28‐.82) compared with older adults with less social support.Compared with those enrolled in MA, older Mexican American adults enrolled in Medicare FFS are more socioeconomically disadvantaged and more likely to demonstrate poor health status. Stronger social support and increased physical limitations were strongly associated with less frequent switching from FFS to MA plans. Additionally, increased availability of MA plans at the county level is a significant driver of enrollment in MA plans. |
Camplain, Ricky; Camplain, Carolyn; II, Robert Trotter T; Pro, George; Sabo, Samantha; Eaves, Emery; Peoples, Marie; Baldwin, Julie A Racial/Ethnic Differences in Drug- and Alcohol-Related Arrest Outcomes in a Southwest County From 2009 to 2018 Journal Article American Journal of Public Health, 110 (S1), pp. 585-592, 2020. @article{Camplain2020, title = {Racial/Ethnic Differences in Drug- and Alcohol-Related Arrest Outcomes in a Southwest County From 2009 to 2018}, author = {Ricky Camplain and Carolyn Camplain and Robert T. Trotter II and George Pro and Samantha Sabo and Emery Eaves and Marie Peoples and Julie A. Baldwin}, url = {https://doi.org/10.2105/AJPH.2019.305409}, doi = {10.2105/AJPH.2019.305409}, year = {2020}, date = {2020-01-22}, journal = {American Journal of Public Health}, volume = {110}, number = {S1}, pages = {585-592}, abstract = {Among misdemeanor drug- and alcohol-related arrests, American Indian/Alaska Native (AI/AN; adjusted odds ratio [AOR] = 3.60; 95% confidence interval [CI] = 3.32, 3.90), Latino (AOR = 1.53; 95% CI = 1.35, 1.73), and Black persons (AOR = 1.28; 95% CI = 1.05, 1.55) were more likely than White persons to be booked into jail as opposed to cited and released. AI/AN (AOR = 10.77; 95% CI = 9.40, 12.35), Latino (AOR = 2.63; 95% CI = 2.12, 3.28), and Black persons (AOR = 1.84; 95% CI = 1.19, 2.84) also were more likely than White persons to be convicted and serve time for their misdemeanor charges. Results were similar for felony drug- and alcohol-related arrests aggregated and stratified. Conclusions. Our results suggest that race/ethnicity is associated with outcomes in drug-related arrests and that overrepresentation of racial/ethnic minorities in the criminal justice system cannot be attributed to greater use of drugs and alcohol in general. More than 60% of criminal justice–involved individuals are racial/ethnic minorities, even though these groups make up just 30% of the US population.1,2 Black, Latino, and American Indian/Alaska Native (AI/AN) persons are more likely to be incarcerated compared with White persons,1–3 and police interactions among racial/ethnic minorities are more likely to result in arrest, even after accounting for arrest decision-making by police.4 Of more than 10.5 million arrests made across the United States in 2017, 15% were drug-related, and 9% involved driving while intoxicated with alcohol.5 The War on Drugs has been credited with creating policies that significantly contribute to racial/ethnic and socioeconomic disparities in drug arrests,6 further embedding racial/ethnic disparities within the criminal justice system. Racial/ethnic minorities continue to be more likely than White individuals to be incarcerated for nonviolent substance-related offenses7,8 and imprisoned for drug charges.9 With regard to alcohol, racial/ethnic minorities are more likely to experience negative consequences, such as arrest and detainment for drinking, potentially because of perceived racial discrimination and racial/ethnic stigma.10 The Southwest United States, for example, has a long history of overrepresentation of AI/AN persons in the justice system2 specifically for alcohol-related offenses,11 yet AI/AN people in the Southwest have higher alcohol abstention rates than in the general population.12 Importantly, inherent bias toward AI/AN persons by law enforcement has been reported in towns that are in close proximity to tribal nations (i.e., border towns),13 presumably a more common occurrence than on tribal lands or in non–border towns. However, research on criminal justice outcomes among AI/AN individuals is limited. Although it is clear that racial/ethnic minorities are overrepresented in the criminal justice system, it is less clear how outcomes at different points of interactions with the criminal justice system, including entry into the system, prosecution and pretrial services, adjudication, sentencing and sanctions, and corrections,14 differ by race/ethnicity, specifically for drug- and alcohol-related offenses. Thus, we aimed to estimate the association between race/ethnicity and arrest outcomes among individuals arrested for drug- or alcohol-related reasons in a rural Southwest US county (the county) from 2009 to 2018.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Among misdemeanor drug- and alcohol-related arrests, American Indian/Alaska Native (AI/AN; adjusted odds ratio [AOR] = 3.60; 95% confidence interval [CI] = 3.32, 3.90), Latino (AOR = 1.53; 95% CI = 1.35, 1.73), and Black persons (AOR = 1.28; 95% CI = 1.05, 1.55) were more likely than White persons to be booked into jail as opposed to cited and released. AI/AN (AOR = 10.77; 95% CI = 9.40, 12.35), Latino (AOR = 2.63; 95% CI = 2.12, 3.28), and Black persons (AOR = 1.84; 95% CI = 1.19, 2.84) also were more likely than White persons to be convicted and serve time for their misdemeanor charges. Results were similar for felony drug- and alcohol-related arrests aggregated and stratified. Conclusions. Our results suggest that race/ethnicity is associated with outcomes in drug-related arrests and that overrepresentation of racial/ethnic minorities in the criminal justice system cannot be attributed to greater use of drugs and alcohol in general. More than 60% of criminal justice–involved individuals are racial/ethnic minorities, even though these groups make up just 30% of the US population.1,2 Black, Latino, and American Indian/Alaska Native (AI/AN) persons are more likely to be incarcerated compared with White persons,1–3 and police interactions among racial/ethnic minorities are more likely to result in arrest, even after accounting for arrest decision-making by police.4 Of more than 10.5 million arrests made across the United States in 2017, 15% were drug-related, and 9% involved driving while intoxicated with alcohol.5 The War on Drugs has been credited with creating policies that significantly contribute to racial/ethnic and socioeconomic disparities in drug arrests,6 further embedding racial/ethnic disparities within the criminal justice system. Racial/ethnic minorities continue to be more likely than White individuals to be incarcerated for nonviolent substance-related offenses7,8 and imprisoned for drug charges.9 With regard to alcohol, racial/ethnic minorities are more likely to experience negative consequences, such as arrest and detainment for drinking, potentially because of perceived racial discrimination and racial/ethnic stigma.10 The Southwest United States, for example, has a long history of overrepresentation of AI/AN persons in the justice system2 specifically for alcohol-related offenses,11 yet AI/AN people in the Southwest have higher alcohol abstention rates than in the general population.12 Importantly, inherent bias toward AI/AN persons by law enforcement has been reported in towns that are in close proximity to tribal nations (i.e., border towns),13 presumably a more common occurrence than on tribal lands or in non–border towns. However, research on criminal justice outcomes among AI/AN individuals is limited. Although it is clear that racial/ethnic minorities are overrepresented in the criminal justice system, it is less clear how outcomes at different points of interactions with the criminal justice system, including entry into the system, prosecution and pretrial services, adjudication, sentencing and sanctions, and corrections,14 differ by race/ethnicity, specifically for drug- and alcohol-related offenses. Thus, we aimed to estimate the association between race/ethnicity and arrest outcomes among individuals arrested for drug- or alcohol-related reasons in a rural Southwest US county (the county) from 2009 to 2018. |
Mousavi, Sajad; Fotoohinasab, Atiyeh; Afghah, Fatemeh Single-modal and multi-modal false arrhythmia alarm reduction using attention-based convolutional and recurrent neural networks Journal Article PLoS One, 15 (1), 2020. @article{Mousavi2020, title = {Single-modal and multi-modal false arrhythmia alarm reduction using attention-based convolutional and recurrent neural networks}, author = {Sajad Mousavi and Atiyeh Fotoohinasab and Fatemeh Afghah}, url = {https://pubmed.ncbi.nlm.nih.gov/31923226/}, doi = {10.1371/journal.pone.0226990}, year = {2020}, date = {2020-01-10}, journal = {PLoS One}, volume = {15}, number = {1}, abstract = {This study proposes a deep learning model that effectively suppresses the false alarms in the intensive care units (ICUs) without ignoring the true alarms using single- and multi- modal biosignals. Most of the current work in the literature are either rule-based methods, requiring prior knowledge of arrhythmia analysis to build rules, or classical machine learning approaches, depending on hand-engineered features. In this work, we apply convolutional neural networks to automatically extract time-invariant features, an attention mechanism to put more emphasis on the important regions of the segmented input signal(s) that are more likely to contribute to an alarm, and long short-term memory units to capture the temporal information presented in the signal segments. We trained our method efficiently using a two-step training algorithm (i.e., pre-training and fine-tuning the proposed network) on the dataset provided by the PhysioNet computing in cardiology challenge 2015. The evaluation results demonstrate that the proposed method obtains better results compared to other existing algorithms for the false alarm reduction task in ICUs. The proposed method achieves a sensitivity of 93.88% and a specificity of 92.05% for the alarm classification, considering three different signals. In addition, our experiments for 5 separate alarm types leads significant results, where we just consider a single-lead ECG (e.g., a sensitivity of 90.71%, a specificity of 88.30%, an AUC of 89.51 for alarm type of Ventricular Tachycardia arrhythmia).}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study proposes a deep learning model that effectively suppresses the false alarms in the intensive care units (ICUs) without ignoring the true alarms using single- and multi- modal biosignals. Most of the current work in the literature are either rule-based methods, requiring prior knowledge of arrhythmia analysis to build rules, or classical machine learning approaches, depending on hand-engineered features. In this work, we apply convolutional neural networks to automatically extract time-invariant features, an attention mechanism to put more emphasis on the important regions of the segmented input signal(s) that are more likely to contribute to an alarm, and long short-term memory units to capture the temporal information presented in the signal segments. We trained our method efficiently using a two-step training algorithm (i.e., pre-training and fine-tuning the proposed network) on the dataset provided by the PhysioNet computing in cardiology challenge 2015. The evaluation results demonstrate that the proposed method obtains better results compared to other existing algorithms for the false alarm reduction task in ICUs. The proposed method achieves a sensitivity of 93.88% and a specificity of 92.05% for the alarm classification, considering three different signals. In addition, our experiments for 5 separate alarm types leads significant results, where we just consider a single-lead ECG (e.g., a sensitivity of 90.71%, a specificity of 88.30%, an AUC of 89.51 for alarm type of Ventricular Tachycardia arrhythmia). |
Camplain, Ricky; Pinn, Travis A; Williamson, Heather J; Pro, George; Becenti, Lyle; Bret, James; Luna, Crystal; Baldwin, Julie A Adaptation of the System for Observing Play and Recreation in Communities (SOPARC) for the Measurement of Physical Activity in Jail Settings Journal Article Int Journal of Environ Res Public Health, 17 (1), pp. 349, 2020. @article{Camplain2020b, title = {Adaptation of the System for Observing Play and Recreation in Communities (SOPARC) for the Measurement of Physical Activity in Jail Settings}, author = {Ricky Camplain and Travis A. Pinn and Heather J. Williamson and George Pro and Lyle Becenti and James Bret and Crystal Luna and Julie A. Baldwin}, url = {https://pubmed.ncbi.nlm.nih.gov/31947914/}, doi = {10.3390/ijerph17010349}, year = {2020}, date = {2020-01-04}, journal = {Int Journal of Environ Res Public Health}, volume = {17}, number = {1}, pages = {349}, abstract = {Over 9 million people are incarcerated in jail each year, but physical activity has not been assessed among incarcerated populations. Measuring physical activity in the jail setting is complicated as current physical activity measurement tools are not designed for use inside jail facilities. Therefore, we adapted an evidence-based physical activity measurement tool, the System for Observing Play and Recreation in Communities (SOPARC), to assess physical activity within a jail facility. SOPARC was designed to obtain observational information on physical activity of individuals. The study team created a protocol for SOPARC for use in jail facilities. Unlike the original SOPARC, access to recreation time in jail required prior scheduling. Target areas were unnecessary as recreation spaces were enclosed. The adapted SOPARC protocol for jails included start and end times, the number of individuals that attended, and recreation time users' physical activity levels, footwear, outerwear, uniform color, and use of mobility assistive devices. The use of SOPARC in the jail setting requires adaptation to adequately capture physical activity data among incarcerated individuals. Accurately measuring physical activity among incarcerated individuals and the environment in which they are active may allow for future development and testing of physical activity interventions in jail facilities. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Over 9 million people are incarcerated in jail each year, but physical activity has not been assessed among incarcerated populations. Measuring physical activity in the jail setting is complicated as current physical activity measurement tools are not designed for use inside jail facilities. Therefore, we adapted an evidence-based physical activity measurement tool, the System for Observing Play and Recreation in Communities (SOPARC), to assess physical activity within a jail facility. SOPARC was designed to obtain observational information on physical activity of individuals. The study team created a protocol for SOPARC for use in jail facilities. Unlike the original SOPARC, access to recreation time in jail required prior scheduling. Target areas were unnecessary as recreation spaces were enclosed. The adapted SOPARC protocol for jails included start and end times, the number of individuals that attended, and recreation time users' physical activity levels, footwear, outerwear, uniform color, and use of mobility assistive devices. The use of SOPARC in the jail setting requires adaptation to adequately capture physical activity data among incarcerated individuals. Accurately measuring physical activity among incarcerated individuals and the environment in which they are active may allow for future development and testing of physical activity interventions in jail facilities. |
Pearson, Talima; Barger, Steven; Lininger, Monica; Wayment, Heidi; Hepp, Crystal; Villa, Francisco; Tucker-Morgan, Karen; Kyman, Shari; Cabrera, Melissa; Hurtado, Kevin; Menard, Ashley; Fulbright, Kelly; Wood, Colin; Mbegbu, Mimi; Zambrano, Yesenia; Fletcher, Annette; Medina-Rodriguez, Sarah; Manone, Mark; Aguirre, Amanda; Milner, Trudie; II, Robert Trotter T Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study Journal Article JMIR Research Protocols, 8 (9), 2019. @article{T2019, title = {Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study}, author = {Talima Pearson and Steven Barger and Monica Lininger and Heidi Wayment and Crystal Hepp and Francisco Villa and Karen Tucker-Morgan and Shari Kyman and Melissa Cabrera and Kevin Hurtado and Ashley Menard and Kelly Fulbright and Colin Wood and Mimi Mbegbu and Yesenia Zambrano and Annette Fletcher and Sarah Medina-Rodriguez and Mark Manone and Amanda Aguirre and Trudie Milner and Robert T. Trotter II}, year = {2019}, date = {2019-09-27}, journal = {JMIR Research Protocols}, volume = {8}, number = {9}, abstract = {Health care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce S aureus transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact S aureus carriage and transmission, either as risk or as protective factors. This study is designed to evaluate ethnic-specific prevalence of S aureus carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of S aureus strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of S aureus reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of S aureus carriage and transmission.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Health care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce S aureus transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact S aureus carriage and transmission, either as risk or as protective factors. This study is designed to evaluate ethnic-specific prevalence of S aureus carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of S aureus strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of S aureus reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of S aureus carriage and transmission. |
Greene, Joshua R; Merrett, Kahla L; Heyert, Alexanndra J; Simmons, Lucas F; Migliori, Camille M; Vogt, Kristen C; Castro, Rebeca S; Phillips, Paul D; Baker, Joseph L; Lindberg, Gerrick E; Fox, David T; Sesto, Rico Del E; Koppisch, Andrew T Scope and efficacy of the broad-spectrum topical antiseptic choline geranate Journal Article PLoS One, 14 (9), 2019. @article{Greene2019, title = {Scope and efficacy of the broad-spectrum topical antiseptic choline geranate}, author = {Joshua R Greene and Kahla L Merrett and Alexanndra J Heyert and Lucas F Simmons and Camille M Migliori and Kristen C Vogt and Rebeca S Castro and Paul D Phillips and Joseph L Baker and Gerrick E Lindberg and David T Fox and Rico E Del Sesto and Andrew T Koppisch}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222211}, doi = {10.1371/journal.pone.0222211}, year = {2019}, date = {2019-09-17}, journal = {PLoS One}, volume = {14}, number = {9}, abstract = {Choline geranate (also described as Choline And GEranic acid, or CAGE) has been developed as a novel biocompatible antiseptic material capable of penetrating skin and aiding the transdermal delivery of co-administered antibiotics. The antibacterial properties of CAGE were analyzed against 24 and 72 hour old biofilms of 11 clinically isolated ESKAPE pathogens (defined as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp, respectively), including multidrug resistant (MDR) isolates. CAGE was observed to eradicate in vitro biofilms at concentrations as low as 3.56 mM (0.156% v:v) in as little as 2 hours, which represents both an improved potency and rate of biofilm eradication relative to that reported for most common standard-of-care topical antiseptics in current use. In vitro time-kill studies on 24 hour old Staphylococcus aureus biofilms indicate that CAGE exerts its antibacterial effect upon contact and a 0.1% v:v solution reduced biofilm viability by over three orders of magnitude (a 3log10 reduction) in 15 minutes. Furthermore, disruption of the protective layer of exopolymeric substances in mature biofilms of Staphylococcus aureus by CAGE (0.1% v:v) was observed in 120 minutes. Insight into the mechanism of action of CAGE was provided with molecular modeling studies alongside in vitro antibiofilm assays. The geranate ion and geranic acid components of CAGE are predicted to act in concert to integrate into bacterial membranes, affect membrane thinning and perturb membrane homeostasis. Taken together, our results show that CAGE demonstrates all properties required of an effective topical antiseptic and the data also provides insight into how its observed antibiofilm properties may manifest.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Choline geranate (also described as Choline And GEranic acid, or CAGE) has been developed as a novel biocompatible antiseptic material capable of penetrating skin and aiding the transdermal delivery of co-administered antibiotics. The antibacterial properties of CAGE were analyzed against 24 and 72 hour old biofilms of 11 clinically isolated ESKAPE pathogens (defined as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp, respectively), including multidrug resistant (MDR) isolates. CAGE was observed to eradicate in vitro biofilms at concentrations as low as 3.56 mM (0.156% v:v) in as little as 2 hours, which represents both an improved potency and rate of biofilm eradication relative to that reported for most common standard-of-care topical antiseptics in current use. In vitro time-kill studies on 24 hour old Staphylococcus aureus biofilms indicate that CAGE exerts its antibacterial effect upon contact and a 0.1% v:v solution reduced biofilm viability by over three orders of magnitude (a 3log10 reduction) in 15 minutes. Furthermore, disruption of the protective layer of exopolymeric substances in mature biofilms of Staphylococcus aureus by CAGE (0.1% v:v) was observed in 120 minutes. Insight into the mechanism of action of CAGE was provided with molecular modeling studies alongside in vitro antibiofilm assays. The geranate ion and geranic acid components of CAGE are predicted to act in concert to integrate into bacterial membranes, affect membrane thinning and perturb membrane homeostasis. Taken together, our results show that CAGE demonstrates all properties required of an effective topical antiseptic and the data also provides insight into how its observed antibiofilm properties may manifest. |
Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R; Bokulich, Nicholas A; Abnet, Christian C; Al-Ghalith, Gabriel A; Alexander, Harriet; Alm, Eric J; Arumugam, Manimozhiyan; Asnicar, Francesco; Bai, Yang; Bisanz, Jordan E; Bittinger, Kyle; Brejnrod, Asker; Brislawn, Colin J; Brown, Titus C; Callahan, Benjamin J; Caraballo-Rodríguez, Andrés Mauricio; Chase, John; Cope, Emily K; Silva, Ricardo Da; Diener, Christian; Dorrestein, Pieter C; Douglas, Gavin M; Durall, Daniel M; Duvallet, Claire; Edwardson, Christian F; Ernst, Madeleine; Estaki, Mehrbod; Fouquier, Jennifer; Gauglitz, Julia M; Gibbons, Sean M; Gibson, Deanna L; Gonzalez, Antonio; Gorlick, Kestrel; Guo, Jiarong; Hillmann, Benjamin; Holmes, Susan; Holste, Hannes; Huttenhower, Curtis; Huttley, Gavin A; Janssen, Stefan; Jarmusch, Alan K; Jiang, Lingjing; Kaehler, Benjamin D; Kang, Kyo Bin; Keefe, Christopher R; Keim, Paul; Kelley, Scott T; Knights, Dan; Koester, Irina; Kosciolek, Tomasz; Kreps, Jorden; Langille, Morgan G I; Lee, Joslynn; Ley, Ruth; Liu, Yong-Xin; Loftfield, Erikka; Lozupone, Catherine; Maher, Massoud; Marotz, Clarisse; Martin, Bryan D; McDonald, Daniel; McIver, Lauren J; Melnik, Alexey V; Metcalf, Jessica L; Morgan, Sydney C; Morton, Jamie T; Naimey, Ahmad Turan; Navas-Molina, Jose A; Nothias, Louis Felix; Orchanian, Stephanie B; Pearson, Talima; Peoples, Samuel L; Petras, Daniel; Preuss, Mary Lai; Pruesse, Elmar; Rasmussen, Lasse Buur; Rivers, Adam; II, Michael Robeson S; Rosenthal, Patrick; Segata, Nicola; Shaffer, Michael; Shiffer, Arron; Sinha, Rashmi; Song, Se Jin; Spear, John R; Swafford, Austin D; Thompson, Luke R; Torres, Pedro J; Trinh, Pauline; Tripathi, Anupriya; Turnbaugh, Peter J; Ul-Hasan, Sabah; van der Hooft, Justin J J; Vargas, Fernando; Vázquez-Baeza, Yoshiki; Vogtmann, Emily; von Hippel, Max; Walters, William; Wan, Yunhu; Wang, Mingxun; Warren, Jonathan; Weber, Kyle C; Williamson, Charles H D; Willis, Amy D; Xu, Zhenjiang Zech; Zaneveld, Jesse R; Zhang, Yilong; Zhu, Qiyun; Knight, Rob; Caporaso, Gregory J Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2 Journal Article Nature Biotechnology, 37 (8), pp. 852-857, 2019. @article{Bolyen2019, title = {Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2}, author = {Evan Bolyen and Jai Ram Rideout and Matthew R Dillon and Nicholas A Bokulich and Christian C Abnet and Gabriel A Al-Ghalith and Harriet Alexander and Eric J Alm and Manimozhiyan Arumugam and Francesco Asnicar and Yang Bai and Jordan E Bisanz and Kyle Bittinger and Asker Brejnrod and Colin J Brislawn and C Titus Brown and Benjamin J Callahan and Andrés Mauricio Caraballo-Rodríguez and John Chase and Emily K Cope and Ricardo Da Silva and Christian Diener and Pieter C Dorrestein and Gavin M Douglas and Daniel M Durall and Claire Duvallet and Christian F Edwardson and Madeleine Ernst and Mehrbod Estaki and Jennifer Fouquier and Julia M Gauglitz and Sean M Gibbons and Deanna L Gibson and Antonio Gonzalez and Kestrel Gorlick and Jiarong Guo and Benjamin Hillmann and Susan Holmes and Hannes Holste and Curtis Huttenhower and Gavin A Huttley and Stefan Janssen and Alan K Jarmusch and Lingjing Jiang and Benjamin D Kaehler and Kyo Bin Kang and Christopher R Keefe and Paul Keim and Scott T Kelley and Dan Knights and Irina Koester and Tomasz Kosciolek and Jorden Kreps and Morgan G I Langille and Joslynn Lee and Ruth Ley and Yong-Xin Liu and Erikka Loftfield and Catherine Lozupone and Massoud Maher and Clarisse Marotz and Bryan D Martin and Daniel McDonald and Lauren J McIver and Alexey V Melnik and Jessica L Metcalf and Sydney C Morgan and Jamie T Morton and Ahmad Turan Naimey and Jose A Navas-Molina and Louis Felix Nothias and Stephanie B Orchanian and Talima Pearson and Samuel L Peoples and Daniel Petras and Mary Lai Preuss and Elmar Pruesse and Lasse Buur Rasmussen and Adam Rivers and Michael S Robeson II and Patrick Rosenthal and Nicola Segata and Michael Shaffer and Arron Shiffer and Rashmi Sinha and Se Jin Song and John R Spear and Austin D Swafford and Luke R Thompson and Pedro J Torres and Pauline Trinh and Anupriya Tripathi and Peter J Turnbaugh and Sabah Ul-Hasan and Justin J J van der Hooft and Fernando Vargas and Yoshiki Vázquez-Baeza and Emily Vogtmann and Max von Hippel and William Walters and Yunhu Wan and Mingxun Wang and Jonathan Warren and Kyle C Weber and Charles H D Williamson and Amy D Willis and Zhenjiang Zech Xu and Jesse R Zaneveld and Yilong Zhang and Qiyun Zhu and Rob Knight and J Gregory Caporaso}, url = {https://www.nature.com/articles/s41587-019-0209-9}, doi = {10.1038/s41587-019-0209-9}, year = {2019}, date = {2019-08-09}, journal = {Nature Biotechnology}, volume = {37}, number = {8}, pages = {852-857}, abstract = {Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease1 and medical treatment2; how microorganisms affect the health of the planet3; and the nascent exploration of the medical4, forensic5, environmental6 and agricultural7 applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite8, metaproteome9 or metatranscriptome profiles.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease1 and medical treatment2; how microorganisms affect the health of the planet3; and the nascent exploration of the medical4, forensic5, environmental6 and agricultural7 applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite8, metaproteome9 or metatranscriptome profiles. |
Ghazanfari, Behzad; Afghah, Fatemeh; Najarian, Kayvan; Mousavi, Sajad; Gryak, Jonathan; Todd, James An Unsupervised Feature Learning Approach to Reduce False Alarm Rate in ICUs Journal Article Conf Proc IEEE Eng Med Biol Soc., pp. 349-353, 2019. @article{Ghazanfari2019, title = {An Unsupervised Feature Learning Approach to Reduce False Alarm Rate in ICUs}, author = {Behzad Ghazanfari and Fatemeh Afghah and Kayvan Najarian and Sajad Mousavi and Jonathan Gryak and James Todd}, url = {https://ieeexplore.ieee.org/document/8857034}, doi = {0.1109/EMBC.2019.8857034}, year = {2019}, date = {2019-07-23}, journal = {Conf Proc IEEE Eng Med Biol Soc.}, pages = {349-353}, abstract = {The high rate of false alarms in intensive care units (ICUs) is one of the top challenges of using medical technology in hospitals. These false alarms are often caused by patients' movements, detachment of monitoring sensors, or different sources of noise and interference that impact the collected signals from different monitoring devices. In this paper, we propose a novel set of high-level features based on unsupervised feature learning technique in order to effectively capture the characteristics of different arrhythmia in electrocardiogram (ECG) signal and differentiate them from irregularity in signals due to different sources of signal disturbances. This unsupervised feature learning technique, first extracts a set of low-level features from all existing heart cycles of a patient, and then clusters these segments for each individual patient to provide a set of prominent high-level features. The objective of the clustering phase is to enable the classification method to differentiate between the high-level features extracted from normal and abnormal cycles (i.e., either due to arrhythmia or different sources of distortions in signal) in order to put more attention to the features extracted from abnormal portion of the signal that contribute to the alarm.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The high rate of false alarms in intensive care units (ICUs) is one of the top challenges of using medical technology in hospitals. These false alarms are often caused by patients' movements, detachment of monitoring sensors, or different sources of noise and interference that impact the collected signals from different monitoring devices. In this paper, we propose a novel set of high-level features based on unsupervised feature learning technique in order to effectively capture the characteristics of different arrhythmia in electrocardiogram (ECG) signal and differentiate them from irregularity in signals due to different sources of signal disturbances. This unsupervised feature learning technique, first extracts a set of low-level features from all existing heart cycles of a patient, and then clusters these segments for each individual patient to provide a set of prominent high-level features. The objective of the clustering phase is to enable the classification method to differentiate between the high-level features extracted from normal and abnormal cycles (i.e., either due to arrhythmia or different sources of distortions in signal) in order to put more attention to the features extracted from abnormal portion of the signal that contribute to the alarm. |
Camplain, Ricky; Warren, Meghan; Baldwin, Julie A; Camplain, Carolyn; Fofanov, Viacheslav Y; II, Robert Trotter T Epidemiology of Incarceration: Characterizing Jail Incarceration for Public Health Research Journal Article Epidemiology, 30 (4), pp. 561-568, 2019. @article{Camplain2019, title = {Epidemiology of Incarceration: Characterizing Jail Incarceration for Public Health Research}, author = {Ricky Camplain and Meghan Warren and Julie A Baldwin and Carolyn Camplain and Viacheslav Y Fofanov and Robert T Trotter II}, url = {https://journals.lww.com/epidem/Fulltext/2019/07000/Epidemiology_of_Incarceration__Characterizing_Jail.14.aspx}, doi = {10.1097/EDE.0000000000001021}, year = {2019}, date = {2019-07-01}, journal = {Epidemiology}, volume = {30}, number = {4}, pages = {561-568}, abstract = {Background: Each year, 9 million individuals cycle in and out of jails. The under-characterization of incarceration as an exposure poses substantial challenges to understanding how varying levels of exposure to jail may affect health. Thus, we characterized levels of jail incarceration including recidivism, number of incarcerations, total and average number of days incarcerated, and time to reincarceration. Methods: We created a cohort of 75,203 individuals incarcerated at the Coconino County Detention Facility in Flagstaff, Arizona, from 2001 to 2018 from jail intake and release records. Results: The median number of incarcerations during the study period was one (interquartile range [IQR] = 1-2). Forty percent of individuals had >1 incarceration. The median length of stay for first observed incarcerations was 1 day (IQR = 0-5). The median total days incarcerated was 3 (IQR = 1-23). Average length of stay increased by number of incarcerations. By 18 months, 27% of our sample had been reincarcerated. Conclusion: Characteristics of jail incarceration have been largely left out of public health research. A better understanding of jail incarcerations can help design analyses to assess health outcomes of individuals incarcerated in jail. Our study is an early step in shaping an understanding of jail incarceration as an exposure for future epidemiologic research. See video abstract at, http://links.lww.com/EDE/B536.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Each year, 9 million individuals cycle in and out of jails. The under-characterization of incarceration as an exposure poses substantial challenges to understanding how varying levels of exposure to jail may affect health. Thus, we characterized levels of jail incarceration including recidivism, number of incarcerations, total and average number of days incarcerated, and time to reincarceration. Methods: We created a cohort of 75,203 individuals incarcerated at the Coconino County Detention Facility in Flagstaff, Arizona, from 2001 to 2018 from jail intake and release records. Results: The median number of incarcerations during the study period was one (interquartile range [IQR] = 1-2). Forty percent of individuals had >1 incarceration. The median length of stay for first observed incarcerations was 1 day (IQR = 0-5). The median total days incarcerated was 3 (IQR = 1-23). Average length of stay increased by number of incarcerations. By 18 months, 27% of our sample had been reincarcerated. Conclusion: Characteristics of jail incarceration have been largely left out of public health research. A better understanding of jail incarcerations can help design analyses to assess health outcomes of individuals incarcerated in jail. Our study is an early step in shaping an understanding of jail incarceration as an exposure for future epidemiologic research. See video abstract at, http://links.lww.com/EDE/B536. |
Bartee, David; Sanders, Sara; Phillips, Paul D; Harrison, Mackenzie J; Koppisch, Andrew T; Meyers, Caren Freel L Enamide Prodrugs of Acetyl Phosphonate Deoxy-d-xylulose-5-phosphate Synthase Inhibitors as Potent Antibacterial Agents Journal Article ACS Infect. Dis, 5 (3), pp. 406-417, 2019. @article{Bartee2019, title = {Enamide Prodrugs of Acetyl Phosphonate Deoxy-d-xylulose-5-phosphate Synthase Inhibitors as Potent Antibacterial Agents}, author = {David Bartee and Sara Sanders and Paul D Phillips and Mackenzie J Harrison and Andrew T Koppisch and Caren L Freel Meyers}, url = {https://pubs.acs.org/doi/10.1021/acsinfecdis.8b00307}, doi = {10.1021/acsinfecdis.8b00307}, year = {2019}, date = {2019-05-08}, journal = {ACS Infect. Dis}, volume = {5}, number = {3}, pages = {406-417}, abstract = {To fight the growing threat of antibiotic resistance, new antibiotics are required that target essential bacterial processes other than protein, DNA/RNA, and cell wall synthesis, which constitute the majority of currently used antibiotics. 1-Deoxy-d-xylulose-5-phosphate (DXP) synthase is a vital enzyme in bacterial central metabolism, feeding into the de novo synthesis of thiamine diphosphate, pyridoxal phosphate, and essential isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. While potent and selective inhibitors of DXP synthase in vitro activity have been discovered, their antibacterial activity is modest. To improve the antibacterial activity of selective alkyl acetylphosphonate (alkylAP) inhibitors of DXP synthase, we synthesized peptidic enamide prodrugs of alkylAPs inspired by the natural product dehydrophos, a prodrug of methyl acetylphosphonate. This prodrug strategy achieves dramatic increases in activity against Gram-negative pathogens for two alkylAPs, butyl acetylphosphonate and homopropargyl acetylphosphonate, decreasing minimum inhibitory concentrations against Escherichia coli by 33- and nearly 2000-fold, respectively. Antimicrobial studies and LC-MS/MS analysis of alkylAP-treated E. coli establish that the increased potency of prodrugs is due to increased accumulation of alkylAP inhibitors of DXP synthase via transport of the prodrug through the OppA peptide permease and subsequent amide hydrolysis. This work demonstrates the promise of targeting DXP synthase for the development of novel antibacterial agents.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To fight the growing threat of antibiotic resistance, new antibiotics are required that target essential bacterial processes other than protein, DNA/RNA, and cell wall synthesis, which constitute the majority of currently used antibiotics. 1-Deoxy-d-xylulose-5-phosphate (DXP) synthase is a vital enzyme in bacterial central metabolism, feeding into the de novo synthesis of thiamine diphosphate, pyridoxal phosphate, and essential isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. While potent and selective inhibitors of DXP synthase in vitro activity have been discovered, their antibacterial activity is modest. To improve the antibacterial activity of selective alkyl acetylphosphonate (alkylAP) inhibitors of DXP synthase, we synthesized peptidic enamide prodrugs of alkylAPs inspired by the natural product dehydrophos, a prodrug of methyl acetylphosphonate. This prodrug strategy achieves dramatic increases in activity against Gram-negative pathogens for two alkylAPs, butyl acetylphosphonate and homopropargyl acetylphosphonate, decreasing minimum inhibitory concentrations against Escherichia coli by 33- and nearly 2000-fold, respectively. Antimicrobial studies and LC-MS/MS analysis of alkylAP-treated E. coli establish that the increased potency of prodrugs is due to increased accumulation of alkylAP inhibitors of DXP synthase via transport of the prodrug through the OppA peptide permease and subsequent amide hydrolysis. This work demonstrates the promise of targeting DXP synthase for the development of novel antibacterial agents. |
Mousavi, Sajad; Afghah, Fatemeh; Acharya, U.Rajendra SleepEEGNet: Automated sleep stage scoring with sequence to sequence deep learning approach Journal Article PLoS One, 14 (5), 2019. @article{Mousavi2019, title = {SleepEEGNet: Automated sleep stage scoring with sequence to sequence deep learning approach}, author = {Sajad Mousavi and Fatemeh Afghah and U.Rajendra Acharya}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216456}, doi = {10.1371/journal.pone.0216456}, year = {2019}, date = {2019-05-07}, journal = {PLoS One}, volume = {14}, number = {5}, abstract = {Electroencephalogram (EEG) is a common base signal used to monitor brain activities and diagnose sleep disorders. Manual sleep stage scoring is a time-consuming task for sleep experts and is limited by inter-rater reliability. In this paper, we propose an automatic sleep stage annotation method called SleepEEGNet using a single-channel EEG signal. The SleepEEGNet is composed of deep convolutional neural networks (CNNs) to extract time-invariant features, frequency information, and a sequence to sequence model to capture the complex and long short-term context dependencies between sleep epochs and scores. In addition, to reduce the effect of the class imbalance problem presented in the available sleep datasets, we applied novel loss functions to have an equal misclassified error for each sleep stage while training the network. We evaluated the performance of the proposed method on different single-EEG channels (i.e., Fpz-Cz and Pz-Oz EEG channels) from the Physionet Sleep-EDF datasets published in 2013 and 2018. The evaluation results demonstrate that the proposed method achieved the best annotation performance compared to current literature, with an overall accuracy of 84.26%, a macro F1-score of 79.66% and κ = 0.79. Our developed model can be applied to other sleep EEG signals and aid the sleep specialists to arrive at an accurate diagnosis}, keywords = {}, pubstate = {published}, tppubtype = {article} } Electroencephalogram (EEG) is a common base signal used to monitor brain activities and diagnose sleep disorders. Manual sleep stage scoring is a time-consuming task for sleep experts and is limited by inter-rater reliability. In this paper, we propose an automatic sleep stage annotation method called SleepEEGNet using a single-channel EEG signal. The SleepEEGNet is composed of deep convolutional neural networks (CNNs) to extract time-invariant features, frequency information, and a sequence to sequence model to capture the complex and long short-term context dependencies between sleep epochs and scores. In addition, to reduce the effect of the class imbalance problem presented in the available sleep datasets, we applied novel loss functions to have an equal misclassified error for each sleep stage while training the network. We evaluated the performance of the proposed method on different single-EEG channels (i.e., Fpz-Cz and Pz-Oz EEG channels) from the Physionet Sleep-EDF datasets published in 2013 and 2018. The evaluation results demonstrate that the proposed method achieved the best annotation performance compared to current literature, with an overall accuracy of 84.26%, a macro F1-score of 79.66% and κ = 0.79. Our developed model can be applied to other sleep EEG signals and aid the sleep specialists to arrive at an accurate diagnosis |
de Heer, Hendrik; Kinslow, Brian; Lane, Taylor; Tuckman, Ron; Warren, Meghan Only 1 in 10 Patients Told to Lose Weight Seek Help From a Health Professional: A Nationally Representative Sample Journal Article American Journal of Health Promotion, 2019. @article{deHeer2019, title = {Only 1 in 10 Patients Told to Lose Weight Seek Help From a Health Professional: A Nationally Representative Sample}, author = {Hendrik de Heer and Brian Kinslow and Taylor Lane and Ron Tuckman and Meghan Warren}, url = {https://journals.sagepub.com/doi/10.1177/0890117119839904}, doi = {10.1177/0890117119839904}, year = {2019}, date = {2019-03-28}, journal = {American Journal of Health Promotion}, abstract = {Receiving weight loss advice from a health-care provider has been associated with more weight loss efforts and greater odds of achieving weight loss. However, whether patients seek help from their provider or other health professional with weight loss after receiving advice from them to lose weight is largely unknown.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Receiving weight loss advice from a health-care provider has been associated with more weight loss efforts and greater odds of achieving weight loss. However, whether patients seek help from their provider or other health professional with weight loss after receiving advice from them to lose weight is largely unknown. |
Parsons, Michelle Anne; Barger, Steven D The US Mortality Crisis: An Examination of Non-Hispanic White Mortality and Morbidity in Yavapai County, Arizona Journal Article Journal of Community Health, 44 , pp. 661-667, 2019. @article{Parsons2019, title = {The US Mortality Crisis: An Examination of Non-Hispanic White Mortality and Morbidity in Yavapai County, Arizona}, author = {Michelle Anne Parsons and Steven D Barger}, url = {https://link.springer.com/article/10.1007/s10900-019-00648-3}, doi = {10.1007/s10900-019-00648-3}, year = {2019}, date = {2019-03-15}, journal = {Journal of Community Health}, volume = {44}, pages = {661-667}, abstract = {Midlife non-Hispanic white mortality in the United States is rising, particularly in small metro and rural counties. This article responds to calls for county-level studies. We examine social determinants of morbidity and mortality among adult non-Hispanic whites in Yavapai County, Arizona, as part of an integrative study. We report overall mortality trends in Yavapai County using CDC Wonder data and then examine social determinants of reported physical health and mental distress in Yavapai County data using 6 years (2011-2016) of the Arizona Behavioral Risk Factor Surveillance System (BRFSS). The BRFSS includes 1,024 non-Hispanic white respondents aged 25-64. We also present data from the recently established Yavapai County Overdose Fatality Review Board (YCOFRB). Mortality trends indicate that suicide and drug and alcohol-related mortality have all increased since 1999. These increases affect all 5-year age groups from 25 to 64 and both men and women. BRFSS data show that low education and unemployment, but not number of children or home ownership, are significantly associated with worse reported health and frequent mental distress in multivariate analyses. The YCOFRB point to the importance of homelessness and mental health. The mortality crisis in Yavapai County is not restricted to midlife or to drug-related deaths. The unemployed and those with low levels of education are particularly at risk. There is a need for integrative approaches that use local data to elucidate social determinants of morbidity and mortality and to reveal structural determinants.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Midlife non-Hispanic white mortality in the United States is rising, particularly in small metro and rural counties. This article responds to calls for county-level studies. We examine social determinants of morbidity and mortality among adult non-Hispanic whites in Yavapai County, Arizona, as part of an integrative study. We report overall mortality trends in Yavapai County using CDC Wonder data and then examine social determinants of reported physical health and mental distress in Yavapai County data using 6 years (2011-2016) of the Arizona Behavioral Risk Factor Surveillance System (BRFSS). The BRFSS includes 1,024 non-Hispanic white respondents aged 25-64. We also present data from the recently established Yavapai County Overdose Fatality Review Board (YCOFRB). Mortality trends indicate that suicide and drug and alcohol-related mortality have all increased since 1999. These increases affect all 5-year age groups from 25 to 64 and both men and women. BRFSS data show that low education and unemployment, but not number of children or home ownership, are significantly associated with worse reported health and frequent mental distress in multivariate analyses. The YCOFRB point to the importance of homelessness and mental health. The mortality crisis in Yavapai County is not restricted to midlife or to drug-related deaths. The unemployed and those with low levels of education are particularly at risk. There is a need for integrative approaches that use local data to elucidate social determinants of morbidity and mortality and to reveal structural determinants. |
Ofili, Elizabeth O; Tchounwou, Paul B; Fernandez-Repollet, Emma; Yanagihara, Richard; Akintobi, Tabia H; Lee, Jae E; Malouhi, Mohamad; Jr, Solomon Garner T; Hayes, Traci T; Baker, Almelida R; 2nd, Andrew Dent L; Abdelrahim, Muna; Rollins, Latrice; Chang, Sandra P; Sy, Angela; Hernandez, Brenda Y; Bullard, Pamela L; Jr, Richard Noel J; Shiramizu, Bruce; Hedges, Jerris R; Berry, Marla J; Bond, Vincent C; Lima, Maria F; Mokuau, Noreen; Kirken, Robert A; Cruz-Correa, Marcia; Sarpong, Daniel F; Vadgama, Jaydutt; Yates, Clayton; Kahn, Shafiq A; Soliman, Karam F; Perry, George; Pezzano, Mark; Luciano, Carlos A; Barnett, Edwina M; Oyekan, Adebayo; Kumar, Deepak; Norris, Keith C Ethnicity and Disease, 29 (1), 2019. @article{Ofili2019, title = {The Research Centers in Minority Institutions (RCMI) Translational Research Network: Building and Sustaining Capacity for Multi-Site Basic Biomedical, Clinical and Behavioral Research}, author = {Elizabeth O Ofili and Paul B Tchounwou and Emma Fernandez-Repollet and Richard Yanagihara and Tabia H Akintobi and Jae E Lee and Mohamad Malouhi and Solomon T Garner Jr and Traci T Hayes and Almelida R Baker and Andrew L Dent 2nd and Muna Abdelrahim and Latrice Rollins and Sandra P Chang and Angela Sy and Brenda Y Hernandez and Pamela L Bullard and Richard J Noel Jr and Bruce Shiramizu and Jerris R Hedges and Marla J Berry and Vincent C Bond and Maria F Lima and Noreen Mokuau and Robert A Kirken and Marcia Cruz-Correa and Daniel F Sarpong and Jaydutt Vadgama and Clayton Yates and Shafiq A Kahn and Karam F Soliman and George Perry and Mark Pezzano and Carlos A Luciano and M Edwina Barnett and Adebayo Oyekan and Deepak Kumar and Keith C Norris}, url = {https://www.ethndis.org/edonline/index.php/ethndis/article/view/1066}, doi = {10.18865/ed.29.S1.135}, year = {2019}, date = {2019-02-21}, journal = {Ethnicity and Disease}, volume = {29}, number = {1}, abstract = {The Research Centers in Minority Institutions (RCMI) program was established by the US Congress to support the development of biomedical research infrastructure at minority-serving institutions granting doctoral degrees in the health professions or in a health-related science. RCMI institutions also conduct research on diseases that disproportionately affect racial and ethnic minorities (ie, African Americans/Blacks, American Indians and Alaska Natives, Hispanics, Native Hawaiians and Other Pacific Islanders), those of low socioeconomic status, and rural persons. Quantitative metrics, including the numbers of doctoral science degrees granted to underrepresented students, NIH peer-reviewed research funding, peer-reviewed publications, and numbers of racial and ethnic minorities participating in sponsored research, demonstrate that RCMI grantee institutions have made substantial progress toward the intent of the Congressional legislation, as well as the NIH/NIMHD-linked goals of addressing workforce diversity and health disparities. Despite this progress, nationally, many challenges remain, including persistent disparities in research and career development awards to minority investigators. The continuing underrepresentation of minority investigators in NIH-sponsored research across multiple disease areas is of concern, in the face of unrelenting national health inequities. With the collaborative network support by the RCMI Translational Research Network (RTRN), the RCMI community is uniquely positioned to address these challenges through its community engagement and strategic partnerships with non-RCMI institutions. Funding agencies can play an important role by incentivizing such collaborations, and incorporating metrics for research funding that address underrepresented populations, workforce diversity and health equity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Research Centers in Minority Institutions (RCMI) program was established by the US Congress to support the development of biomedical research infrastructure at minority-serving institutions granting doctoral degrees in the health professions or in a health-related science. RCMI institutions also conduct research on diseases that disproportionately affect racial and ethnic minorities (ie, African Americans/Blacks, American Indians and Alaska Natives, Hispanics, Native Hawaiians and Other Pacific Islanders), those of low socioeconomic status, and rural persons. Quantitative metrics, including the numbers of doctoral science degrees granted to underrepresented students, NIH peer-reviewed research funding, peer-reviewed publications, and numbers of racial and ethnic minorities participating in sponsored research, demonstrate that RCMI grantee institutions have made substantial progress toward the intent of the Congressional legislation, as well as the NIH/NIMHD-linked goals of addressing workforce diversity and health disparities. Despite this progress, nationally, many challenges remain, including persistent disparities in research and career development awards to minority investigators. The continuing underrepresentation of minority investigators in NIH-sponsored research across multiple disease areas is of concern, in the face of unrelenting national health inequities. With the collaborative network support by the RCMI Translational Research Network (RTRN), the RCMI community is uniquely positioned to address these challenges through its community engagement and strategic partnerships with non-RCMI institutions. Funding agencies can play an important role by incentivizing such collaborations, and incorporating metrics for research funding that address underrepresented populations, workforce diversity and health equity. |
2020 |
Williamson, Heather J; Chief, Carmenlita; Jiménez, Dulce; Begay, Andria; Milner, Trudie F; Sullivan, Shevaun; Torres, Emma; Remiker, Mark; Longorio, Alexandra Elvira Samarron; Sabo, Samantha; Teufel-Shone, Nicolette I Voices of Community Partners: Perspectives Gained from Conversations of Community-Based Participatory Research Experiences Journal Article International Journal of Environmental Research and Public Health, 2020. @article{Williamson2020, title = {Voices of Community Partners: Perspectives Gained from Conversations of Community-Based Participatory Research Experiences}, author = {Heather J. Williamson and Carmenlita Chief and Dulce Jiménez and Andria Begay and Trudie F. Milner and Shevaun Sullivan and Emma Torres and Mark Remiker and Alexandra Elvira Samarron Longorio and Samantha Sabo and Nicolette I. Teufel-Shone}, url = {https://www.mdpi.com/1660-4601/17/14/5245}, doi = {10.3390/ijerph1745245}, year = {2020}, date = {2020-07-21}, journal = {International Journal of Environmental Research and Public Health}, abstract = {Community-based participatory research (CBPR) has been documented as an effective approach to research with underserved communities, particularly with racial and ethnic minority groups. However, much of the literature promoting the use of CBPR with underserved communities is written from the perspective of the researchers and not from the perspective of the community partner. The purpose of this article is to capture lessons learned from the community partners’insight gained through their experiences with CBPR. A multi-investigator consensus method was used to qualitatively code the transcripts of a CBPR story-telling video series. Seven major themes were identified: (1) expectations for engaging in research, (2) cultural humility, (3) respecting the partnership, (4) open communication, (5) genuine commitment, (6) valuing strengths and recognizing capacities, and (7) collaborating to yield meaningful results. The themes drawn from the community partner’s voice align with the tenets of CBPR advanced in the academic literature.More opportunities to include the community voice when promoting CBPR should be undertaken to help introduce the concepts to potential community partners who may be research cautious.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Community-based participatory research (CBPR) has been documented as an effective approach to research with underserved communities, particularly with racial and ethnic minority groups. However, much of the literature promoting the use of CBPR with underserved communities is written from the perspective of the researchers and not from the perspective of the community partner. The purpose of this article is to capture lessons learned from the community partners’insight gained through their experiences with CBPR. A multi-investigator consensus method was used to qualitatively code the transcripts of a CBPR story-telling video series. Seven major themes were identified: (1) expectations for engaging in research, (2) cultural humility, (3) respecting the partnership, (4) open communication, (5) genuine commitment, (6) valuing strengths and recognizing capacities, and (7) collaborating to yield meaningful results. The themes drawn from the community partner’s voice align with the tenets of CBPR advanced in the academic literature.More opportunities to include the community voice when promoting CBPR should be undertaken to help introduce the concepts to potential community partners who may be research cautious. |
Lindly, Olivia J; Martin, Alison J; Lally, Kathryn Community Mental Health Journal, 2020. @article{Lindly2020, title = {A Profile of Care Coordination, Missed School Days, and Unmet Needs Among Oregon Children With Special Health Care Needs With Behavioral and Mental Health Conditions}, author = {Olivia J Lindly and Alison J Martin and Kathryn Lally}, url = {https://doi.org/10.1007/s10597-020-00609-4}, doi = {10.1007/s10597-020-00609-4}, year = {2020}, date = {2020-04-01}, journal = {Community Mental Health Journal}, abstract = {To inform Oregon's Title V needs assessment activities, we aimed to (1) characterize the state's subpopulation of children with special health care needs (CSHCN) with behavioral and mental health conditions (B/MHC) and (2) determine associations of care coordination with missed school days and unmet needs for this subpopulation. We analyzed 2009-2010 National Survey of Children with Special Health Care Needs data on 736 Oregon CSHCN < 18 years, including 418 CSHCN with B/MHC. Among Oregon CSHCN with B/MHC: 48.9% missed ≥ 4 school days, 25% had ≥ 1 unmet health services need, and 14.8% had ≥ 1 unmet family support services need. Care coordination was associated with lower adjusted odds of ≥ 1 unmet health services need but was not significantly associated with missed school days or unmet family support services need. The approach to identify Oregon CSHCN with B/MHC may be adopted by other states endeavoring to improve health for this vulnerable subpopulation}, keywords = {}, pubstate = {published}, tppubtype = {article} } To inform Oregon's Title V needs assessment activities, we aimed to (1) characterize the state's subpopulation of children with special health care needs (CSHCN) with behavioral and mental health conditions (B/MHC) and (2) determine associations of care coordination with missed school days and unmet needs for this subpopulation. We analyzed 2009-2010 National Survey of Children with Special Health Care Needs data on 736 Oregon CSHCN < 18 years, including 418 CSHCN with B/MHC. Among Oregon CSHCN with B/MHC: 48.9% missed ≥ 4 school days, 25% had ≥ 1 unmet health services need, and 14.8% had ≥ 1 unmet family support services need. Care coordination was associated with lower adjusted odds of ≥ 1 unmet health services need but was not significantly associated with missed school days or unmet family support services need. The approach to identify Oregon CSHCN with B/MHC may be adopted by other states endeavoring to improve health for this vulnerable subpopulation |
Stout, Nicole L; Brown, Justin C; Schwartz, Anna L; Marshall, Timothy F; Campbell, Anna M; Nekhlyudov, Larissa; Zucker, David S; Basen-Engquist, Karen M; Campbell, Grace; Meyerhardt, Jeffrey; Cheville, Andrea L; Covington, Kelley R; Ligibel, Jennifer A; Sokolof, Jonas M; Schmitz, Kathryn H; Alfano, Catherine M An exercise oncology clinical pathway: Screening and referral for personalized interventions Journal Article American Cancer Society Journals, 2020. @article{Stout2020, title = {An exercise oncology clinical pathway: Screening and referral for personalized interventions}, author = {Nicole L Stout and Justin C Brown and Anna L Schwartz and Timothy F Marshall and Anna M Campbell and Larissa Nekhlyudov and David S Zucker and Karen M Basen-Engquist and Grace Campbell and Jeffrey Meyerhardt and Andrea L Cheville and Kelley R Covington and Jennifer A Ligibel and Jonas M Sokolof and Kathryn H Schmitz and Catherine M Alfano}, url = {https://acsjournals.onlinelibrary.wiley.com/doi/abs/10.1002/cncr.32860}, doi = {10.1002/cncr.32860}, year = {2020}, date = {2020-03-25}, journal = {American Cancer Society Journals}, abstract = {This article presents a clinical screening and referral framework to enable health care professionals to guide individuals with cancer to safe and effective exercise programs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This article presents a clinical screening and referral framework to enable health care professionals to guide individuals with cancer to safe and effective exercise programs. |
Pearson, Talima; Sahl, Jason; Hepp, Crystal; Handady, Karthik; Hornstra, Heidie; Vazquez, Adam J; Mayo, Erik Settles Mark; Kaestli, Mirjam; Williamson, Heather; Price, Erin P; Sarovich, Derek S; Cook, James M; Wolken, Spenser R; Bowen, Richard; Tuanyok, Apichai; Foster, Jeffrey; Drees, Keven P; Kidd, Timothy J; Bell, Scott C; Currie, Bart J; Keim, Paul PLoS Pathogens, 2020. @article{Pearson2020, title = {Pathogen to Commensal? Longitudinal Within-Host Population Dynamics, Evolution, and Adaptation During a Chronic >16-year Burkholderia Pseudomallei Infection}, author = {Talima Pearson and Jason Sahl and Crystal Hepp and Karthik Handady and Heidie Hornstra and Adam J. Vazquez and Erik Settles Mark Mayo and Mirjam Kaestli and Heather Williamson and Erin P. Price and Derek S. Sarovich and James M. Cook and Spenser R. Wolken and Richard Bowen and Apichai Tuanyok and Jeffrey Foster and Keven P. Drees and Timothy J. Kidd and Scott C. Bell and Bart J. Currie and Paul Keim}, url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008298}, doi = {10.1371/journal.ppat.100829}, year = {2020}, date = {2020-03-05}, journal = {PLoS Pathogens}, abstract = {Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host. |
Cocking, Jill Hager; Deberg, Michael; Schupp, Jim; Sahl, Jason; Wiggins, Kristin; Porty, Ariel; Hornstra, Heidie M; Hepp, Crystal; Jardine, Claire; Furstenau, Tara N; Schulte-Hostedde, Albrecht; Fofanov, Viacheslav Y; Pearson, Talima Selective Whole Genome Amplification and Sequencing of Coxiella Burnetii Directly From Environmental Samples Journal Article Genomics, 112 (2), pp. 1872-1878, 2020. @article{Cocking2020, title = {Selective Whole Genome Amplification and Sequencing of Coxiella Burnetii Directly From Environmental Samples}, author = {Jill Hager Cocking and Michael Deberg and Jim Schupp and Jason Sahl and Kristin Wiggins and Ariel Porty and Heidie M. Hornstra and Crystal Hepp and Claire Jardine and Tara N. Furstenau and Albrecht Schulte-Hostedde and Viacheslav Y. Fofanov and Talima Pearson}, url = {https://www.sciencedirect.com/science/article/pii/S0888754319302058?via%3Dihub}, doi = {10.1016/j.ygeno.2019.10.02}, year = {2020}, date = {2020-03-01}, journal = {Genomics}, volume = {112}, number = {2}, pages = {1872-1878}, abstract = {Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations. |
Pinto, Bronson I; Cruz, Nathan D; Lujan, Oscar R; Propper, Catherine R; Kellar, Robert S In Vitro Scratch Assay to Demonstrate Effects of Arsenic on Skin Cell Migration Journal Article Jove, 144 , 2020. @article{Pinto2020, title = {In Vitro Scratch Assay to Demonstrate Effects of Arsenic on Skin Cell Migration}, author = {Bronson I Pinto and Nathan D Cruz and Oscar R Lujan and Catherine R Propper and Robert S Kellar}, url = {https://www.jove.com/video/58838/in-vitro-scratch-assay-to-demonstrate-effects-arsenic-on-skin-cell}, doi = {10.3791/58838}, year = {2020}, date = {2020-02-23}, journal = {Jove}, volume = {144}, abstract = {Understanding the physiologic mechanisms of wound healing has been the focus of ongoing research for many years. This research directly translates into changes in clinical standards used for treating wounds and decreasing morbidity and mortality for patients. Wound healing is a complex process that requires strategic cell and tissue interaction and function. One of the many critically important functions of wound healing is individual and collective cellular migration. Upon injury, various cells from the blood, surrounding connective, and epithelial tissues rapidly migrate to the wound site by way of chemical and/or physical stimuli. This migration response can largely dictate the outcomes and success of a healing wound. Understanding this specific cellular function is important for translational medicine that can lead to improved wound healing outcomes. Here, we describe a protocol used to better understand cellular migration as it pertains to wound healing, and how changes to the cellular environment can significantly alter this process. In this example study, dermal fibroblasts were grown in media supplemented with fetal bovine serum (FBS) as monolayer cultures in tissue culture flasks. Cells were aseptically transferred into tissue culture treated 12-well plates and grown to 100% confluence. Upon reaching confluence, the cells in the monolayer were vertically scratched using a p200 pipet tip. Arsenic diluted in culture media supplemented with FBS was added to individual wells at environmentally relevant doses ranging 0.1-10 μM. Images were captured every 4 hours (h) over a 24 h period using an inverted light microscope to observe cellular migration (wound closure). Images were individually analyzed using image analysis software, and percent wound closure was calculated. Results demonstrate that arsenic slows down wound healing. This technique provides a rapid and inexpensive first screen for evaluation of the effects of contaminants on wound healing.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding the physiologic mechanisms of wound healing has been the focus of ongoing research for many years. This research directly translates into changes in clinical standards used for treating wounds and decreasing morbidity and mortality for patients. Wound healing is a complex process that requires strategic cell and tissue interaction and function. One of the many critically important functions of wound healing is individual and collective cellular migration. Upon injury, various cells from the blood, surrounding connective, and epithelial tissues rapidly migrate to the wound site by way of chemical and/or physical stimuli. This migration response can largely dictate the outcomes and success of a healing wound. Understanding this specific cellular function is important for translational medicine that can lead to improved wound healing outcomes. Here, we describe a protocol used to better understand cellular migration as it pertains to wound healing, and how changes to the cellular environment can significantly alter this process. In this example study, dermal fibroblasts were grown in media supplemented with fetal bovine serum (FBS) as monolayer cultures in tissue culture flasks. Cells were aseptically transferred into tissue culture treated 12-well plates and grown to 100% confluence. Upon reaching confluence, the cells in the monolayer were vertically scratched using a p200 pipet tip. Arsenic diluted in culture media supplemented with FBS was added to individual wells at environmentally relevant doses ranging 0.1-10 μM. Images were captured every 4 hours (h) over a 24 h period using an inverted light microscope to observe cellular migration (wound closure). Images were individually analyzed using image analysis software, and percent wound closure was calculated. Results demonstrate that arsenic slows down wound healing. This technique provides a rapid and inexpensive first screen for evaluation of the effects of contaminants on wound healing. |
Kumar, Amit; Rivera-Hernandez, Maricruz; Karmarkar, Amol M; Chou, Lin-Na; Kuo, Yong-Fang; Baldwin, Julie A; Panagiotou, Orestis A; Burke, Robert E; Ottenbacher, Kenneth J Social and Health-Related Factors Associated With Enrollment in Medicare Advantage Plans in Older Adults Journal Article Journal of the American Geriatrics Society, 68 (2), pp. 313-320, 2020. @article{Kumar2020, title = {Social and Health-Related Factors Associated With Enrollment in Medicare Advantage Plans in Older Adults}, author = {Amit Kumar and Maricruz Rivera-Hernandez and Amol M. Karmarkar and Lin-Na Chou and Yong-Fang Kuo and Julie A. Baldwin and Orestis A. Panagiotou and Robert E. Burke and Kenneth J. Ottenbacher}, url = {https://onlinelibrary.wiley.com/doi/full/10.1111/jgs.16202}, doi = {10.1111/jgs.16202}, year = {2020}, date = {2020-02-01}, journal = {Journal of the American Geriatrics Society}, volume = {68}, number = {2}, pages = {313-320}, abstract = {Among Mexican American older adults, FFS enrollees were more likely to be born in Mexico, speak Spanish, have lower levels of education, and have more disability than MA enrollees. Older adults with a larger number of limitations of instrumental activities of daily living (odds ratio [OR] = .50; 95% confidence interval [CI] = .26‐.98) and more social support (OR = .70; 95% CI = .45‐.98) were less likely to switch from FFS to MA compared with older adults with no limitations and less social support. Additionally, older adults living in counties with a greater number of MA plans were more likely to switch from FFS to MA (OR = 2.1; 95% CI = 1.45‐3.16), compared with counties with a lower number of MA plans. In counties with a higher number of MA plans, older adults with more social support had lower odds of switching from FFS to MA (OR = .48; 95% CI = .28‐.82) compared with older adults with less social support.Compared with those enrolled in MA, older Mexican American adults enrolled in Medicare FFS are more socioeconomically disadvantaged and more likely to demonstrate poor health status. Stronger social support and increased physical limitations were strongly associated with less frequent switching from FFS to MA plans. Additionally, increased availability of MA plans at the county level is a significant driver of enrollment in MA plans. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Among Mexican American older adults, FFS enrollees were more likely to be born in Mexico, speak Spanish, have lower levels of education, and have more disability than MA enrollees. Older adults with a larger number of limitations of instrumental activities of daily living (odds ratio [OR] = .50; 95% confidence interval [CI] = .26‐.98) and more social support (OR = .70; 95% CI = .45‐.98) were less likely to switch from FFS to MA compared with older adults with no limitations and less social support. Additionally, older adults living in counties with a greater number of MA plans were more likely to switch from FFS to MA (OR = 2.1; 95% CI = 1.45‐3.16), compared with counties with a lower number of MA plans. In counties with a higher number of MA plans, older adults with more social support had lower odds of switching from FFS to MA (OR = .48; 95% CI = .28‐.82) compared with older adults with less social support.Compared with those enrolled in MA, older Mexican American adults enrolled in Medicare FFS are more socioeconomically disadvantaged and more likely to demonstrate poor health status. Stronger social support and increased physical limitations were strongly associated with less frequent switching from FFS to MA plans. Additionally, increased availability of MA plans at the county level is a significant driver of enrollment in MA plans. |
Camplain, Ricky; Camplain, Carolyn; II, Robert Trotter T; Pro, George; Sabo, Samantha; Eaves, Emery; Peoples, Marie; Baldwin, Julie A Racial/Ethnic Differences in Drug- and Alcohol-Related Arrest Outcomes in a Southwest County From 2009 to 2018 Journal Article American Journal of Public Health, 110 (S1), pp. 585-592, 2020. @article{Camplain2020, title = {Racial/Ethnic Differences in Drug- and Alcohol-Related Arrest Outcomes in a Southwest County From 2009 to 2018}, author = {Ricky Camplain and Carolyn Camplain and Robert T. Trotter II and George Pro and Samantha Sabo and Emery Eaves and Marie Peoples and Julie A. Baldwin}, url = {https://doi.org/10.2105/AJPH.2019.305409}, doi = {10.2105/AJPH.2019.305409}, year = {2020}, date = {2020-01-22}, journal = {American Journal of Public Health}, volume = {110}, number = {S1}, pages = {585-592}, abstract = {Among misdemeanor drug- and alcohol-related arrests, American Indian/Alaska Native (AI/AN; adjusted odds ratio [AOR] = 3.60; 95% confidence interval [CI] = 3.32, 3.90), Latino (AOR = 1.53; 95% CI = 1.35, 1.73), and Black persons (AOR = 1.28; 95% CI = 1.05, 1.55) were more likely than White persons to be booked into jail as opposed to cited and released. AI/AN (AOR = 10.77; 95% CI = 9.40, 12.35), Latino (AOR = 2.63; 95% CI = 2.12, 3.28), and Black persons (AOR = 1.84; 95% CI = 1.19, 2.84) also were more likely than White persons to be convicted and serve time for their misdemeanor charges. Results were similar for felony drug- and alcohol-related arrests aggregated and stratified. Conclusions. Our results suggest that race/ethnicity is associated with outcomes in drug-related arrests and that overrepresentation of racial/ethnic minorities in the criminal justice system cannot be attributed to greater use of drugs and alcohol in general. More than 60% of criminal justice–involved individuals are racial/ethnic minorities, even though these groups make up just 30% of the US population.1,2 Black, Latino, and American Indian/Alaska Native (AI/AN) persons are more likely to be incarcerated compared with White persons,1–3 and police interactions among racial/ethnic minorities are more likely to result in arrest, even after accounting for arrest decision-making by police.4 Of more than 10.5 million arrests made across the United States in 2017, 15% were drug-related, and 9% involved driving while intoxicated with alcohol.5 The War on Drugs has been credited with creating policies that significantly contribute to racial/ethnic and socioeconomic disparities in drug arrests,6 further embedding racial/ethnic disparities within the criminal justice system. Racial/ethnic minorities continue to be more likely than White individuals to be incarcerated for nonviolent substance-related offenses7,8 and imprisoned for drug charges.9 With regard to alcohol, racial/ethnic minorities are more likely to experience negative consequences, such as arrest and detainment for drinking, potentially because of perceived racial discrimination and racial/ethnic stigma.10 The Southwest United States, for example, has a long history of overrepresentation of AI/AN persons in the justice system2 specifically for alcohol-related offenses,11 yet AI/AN people in the Southwest have higher alcohol abstention rates than in the general population.12 Importantly, inherent bias toward AI/AN persons by law enforcement has been reported in towns that are in close proximity to tribal nations (i.e., border towns),13 presumably a more common occurrence than on tribal lands or in non–border towns. However, research on criminal justice outcomes among AI/AN individuals is limited. Although it is clear that racial/ethnic minorities are overrepresented in the criminal justice system, it is less clear how outcomes at different points of interactions with the criminal justice system, including entry into the system, prosecution and pretrial services, adjudication, sentencing and sanctions, and corrections,14 differ by race/ethnicity, specifically for drug- and alcohol-related offenses. Thus, we aimed to estimate the association between race/ethnicity and arrest outcomes among individuals arrested for drug- or alcohol-related reasons in a rural Southwest US county (the county) from 2009 to 2018.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Among misdemeanor drug- and alcohol-related arrests, American Indian/Alaska Native (AI/AN; adjusted odds ratio [AOR] = 3.60; 95% confidence interval [CI] = 3.32, 3.90), Latino (AOR = 1.53; 95% CI = 1.35, 1.73), and Black persons (AOR = 1.28; 95% CI = 1.05, 1.55) were more likely than White persons to be booked into jail as opposed to cited and released. AI/AN (AOR = 10.77; 95% CI = 9.40, 12.35), Latino (AOR = 2.63; 95% CI = 2.12, 3.28), and Black persons (AOR = 1.84; 95% CI = 1.19, 2.84) also were more likely than White persons to be convicted and serve time for their misdemeanor charges. Results were similar for felony drug- and alcohol-related arrests aggregated and stratified. Conclusions. Our results suggest that race/ethnicity is associated with outcomes in drug-related arrests and that overrepresentation of racial/ethnic minorities in the criminal justice system cannot be attributed to greater use of drugs and alcohol in general. More than 60% of criminal justice–involved individuals are racial/ethnic minorities, even though these groups make up just 30% of the US population.1,2 Black, Latino, and American Indian/Alaska Native (AI/AN) persons are more likely to be incarcerated compared with White persons,1–3 and police interactions among racial/ethnic minorities are more likely to result in arrest, even after accounting for arrest decision-making by police.4 Of more than 10.5 million arrests made across the United States in 2017, 15% were drug-related, and 9% involved driving while intoxicated with alcohol.5 The War on Drugs has been credited with creating policies that significantly contribute to racial/ethnic and socioeconomic disparities in drug arrests,6 further embedding racial/ethnic disparities within the criminal justice system. Racial/ethnic minorities continue to be more likely than White individuals to be incarcerated for nonviolent substance-related offenses7,8 and imprisoned for drug charges.9 With regard to alcohol, racial/ethnic minorities are more likely to experience negative consequences, such as arrest and detainment for drinking, potentially because of perceived racial discrimination and racial/ethnic stigma.10 The Southwest United States, for example, has a long history of overrepresentation of AI/AN persons in the justice system2 specifically for alcohol-related offenses,11 yet AI/AN people in the Southwest have higher alcohol abstention rates than in the general population.12 Importantly, inherent bias toward AI/AN persons by law enforcement has been reported in towns that are in close proximity to tribal nations (i.e., border towns),13 presumably a more common occurrence than on tribal lands or in non–border towns. However, research on criminal justice outcomes among AI/AN individuals is limited. Although it is clear that racial/ethnic minorities are overrepresented in the criminal justice system, it is less clear how outcomes at different points of interactions with the criminal justice system, including entry into the system, prosecution and pretrial services, adjudication, sentencing and sanctions, and corrections,14 differ by race/ethnicity, specifically for drug- and alcohol-related offenses. Thus, we aimed to estimate the association between race/ethnicity and arrest outcomes among individuals arrested for drug- or alcohol-related reasons in a rural Southwest US county (the county) from 2009 to 2018. |
Mousavi, Sajad; Fotoohinasab, Atiyeh; Afghah, Fatemeh Single-modal and multi-modal false arrhythmia alarm reduction using attention-based convolutional and recurrent neural networks Journal Article PLoS One, 15 (1), 2020. @article{Mousavi2020, title = {Single-modal and multi-modal false arrhythmia alarm reduction using attention-based convolutional and recurrent neural networks}, author = {Sajad Mousavi and Atiyeh Fotoohinasab and Fatemeh Afghah}, url = {https://pubmed.ncbi.nlm.nih.gov/31923226/}, doi = {10.1371/journal.pone.0226990}, year = {2020}, date = {2020-01-10}, journal = {PLoS One}, volume = {15}, number = {1}, abstract = {This study proposes a deep learning model that effectively suppresses the false alarms in the intensive care units (ICUs) without ignoring the true alarms using single- and multi- modal biosignals. Most of the current work in the literature are either rule-based methods, requiring prior knowledge of arrhythmia analysis to build rules, or classical machine learning approaches, depending on hand-engineered features. In this work, we apply convolutional neural networks to automatically extract time-invariant features, an attention mechanism to put more emphasis on the important regions of the segmented input signal(s) that are more likely to contribute to an alarm, and long short-term memory units to capture the temporal information presented in the signal segments. We trained our method efficiently using a two-step training algorithm (i.e., pre-training and fine-tuning the proposed network) on the dataset provided by the PhysioNet computing in cardiology challenge 2015. The evaluation results demonstrate that the proposed method obtains better results compared to other existing algorithms for the false alarm reduction task in ICUs. The proposed method achieves a sensitivity of 93.88% and a specificity of 92.05% for the alarm classification, considering three different signals. In addition, our experiments for 5 separate alarm types leads significant results, where we just consider a single-lead ECG (e.g., a sensitivity of 90.71%, a specificity of 88.30%, an AUC of 89.51 for alarm type of Ventricular Tachycardia arrhythmia).}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study proposes a deep learning model that effectively suppresses the false alarms in the intensive care units (ICUs) without ignoring the true alarms using single- and multi- modal biosignals. Most of the current work in the literature are either rule-based methods, requiring prior knowledge of arrhythmia analysis to build rules, or classical machine learning approaches, depending on hand-engineered features. In this work, we apply convolutional neural networks to automatically extract time-invariant features, an attention mechanism to put more emphasis on the important regions of the segmented input signal(s) that are more likely to contribute to an alarm, and long short-term memory units to capture the temporal information presented in the signal segments. We trained our method efficiently using a two-step training algorithm (i.e., pre-training and fine-tuning the proposed network) on the dataset provided by the PhysioNet computing in cardiology challenge 2015. The evaluation results demonstrate that the proposed method obtains better results compared to other existing algorithms for the false alarm reduction task in ICUs. The proposed method achieves a sensitivity of 93.88% and a specificity of 92.05% for the alarm classification, considering three different signals. In addition, our experiments for 5 separate alarm types leads significant results, where we just consider a single-lead ECG (e.g., a sensitivity of 90.71%, a specificity of 88.30%, an AUC of 89.51 for alarm type of Ventricular Tachycardia arrhythmia). |
Camplain, Ricky; Pinn, Travis A; Williamson, Heather J; Pro, George; Becenti, Lyle; Bret, James; Luna, Crystal; Baldwin, Julie A Adaptation of the System for Observing Play and Recreation in Communities (SOPARC) for the Measurement of Physical Activity in Jail Settings Journal Article Int Journal of Environ Res Public Health, 17 (1), pp. 349, 2020. @article{Camplain2020b, title = {Adaptation of the System for Observing Play and Recreation in Communities (SOPARC) for the Measurement of Physical Activity in Jail Settings}, author = {Ricky Camplain and Travis A. Pinn and Heather J. Williamson and George Pro and Lyle Becenti and James Bret and Crystal Luna and Julie A. Baldwin}, url = {https://pubmed.ncbi.nlm.nih.gov/31947914/}, doi = {10.3390/ijerph17010349}, year = {2020}, date = {2020-01-04}, journal = {Int Journal of Environ Res Public Health}, volume = {17}, number = {1}, pages = {349}, abstract = {Over 9 million people are incarcerated in jail each year, but physical activity has not been assessed among incarcerated populations. Measuring physical activity in the jail setting is complicated as current physical activity measurement tools are not designed for use inside jail facilities. Therefore, we adapted an evidence-based physical activity measurement tool, the System for Observing Play and Recreation in Communities (SOPARC), to assess physical activity within a jail facility. SOPARC was designed to obtain observational information on physical activity of individuals. The study team created a protocol for SOPARC for use in jail facilities. Unlike the original SOPARC, access to recreation time in jail required prior scheduling. Target areas were unnecessary as recreation spaces were enclosed. The adapted SOPARC protocol for jails included start and end times, the number of individuals that attended, and recreation time users' physical activity levels, footwear, outerwear, uniform color, and use of mobility assistive devices. The use of SOPARC in the jail setting requires adaptation to adequately capture physical activity data among incarcerated individuals. Accurately measuring physical activity among incarcerated individuals and the environment in which they are active may allow for future development and testing of physical activity interventions in jail facilities. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Over 9 million people are incarcerated in jail each year, but physical activity has not been assessed among incarcerated populations. Measuring physical activity in the jail setting is complicated as current physical activity measurement tools are not designed for use inside jail facilities. Therefore, we adapted an evidence-based physical activity measurement tool, the System for Observing Play and Recreation in Communities (SOPARC), to assess physical activity within a jail facility. SOPARC was designed to obtain observational information on physical activity of individuals. The study team created a protocol for SOPARC for use in jail facilities. Unlike the original SOPARC, access to recreation time in jail required prior scheduling. Target areas were unnecessary as recreation spaces were enclosed. The adapted SOPARC protocol for jails included start and end times, the number of individuals that attended, and recreation time users' physical activity levels, footwear, outerwear, uniform color, and use of mobility assistive devices. The use of SOPARC in the jail setting requires adaptation to adequately capture physical activity data among incarcerated individuals. Accurately measuring physical activity among incarcerated individuals and the environment in which they are active may allow for future development and testing of physical activity interventions in jail facilities. |
2019 |
Pearson, Talima; Barger, Steven; Lininger, Monica; Wayment, Heidi; Hepp, Crystal; Villa, Francisco; Tucker-Morgan, Karen; Kyman, Shari; Cabrera, Melissa; Hurtado, Kevin; Menard, Ashley; Fulbright, Kelly; Wood, Colin; Mbegbu, Mimi; Zambrano, Yesenia; Fletcher, Annette; Medina-Rodriguez, Sarah; Manone, Mark; Aguirre, Amanda; Milner, Trudie; II, Robert Trotter T Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study Journal Article JMIR Research Protocols, 8 (9), 2019. @article{T2019, title = {Health Disparities in Staphylococcus aureus Transmission and Carriage in a Border Region of the United States Based on Cultural Differences in Social Relationships: Protocol for a Survey Study}, author = {Talima Pearson and Steven Barger and Monica Lininger and Heidi Wayment and Crystal Hepp and Francisco Villa and Karen Tucker-Morgan and Shari Kyman and Melissa Cabrera and Kevin Hurtado and Ashley Menard and Kelly Fulbright and Colin Wood and Mimi Mbegbu and Yesenia Zambrano and Annette Fletcher and Sarah Medina-Rodriguez and Mark Manone and Amanda Aguirre and Trudie Milner and Robert T. Trotter II}, year = {2019}, date = {2019-09-27}, journal = {JMIR Research Protocols}, volume = {8}, number = {9}, abstract = {Health care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce S aureus transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact S aureus carriage and transmission, either as risk or as protective factors. This study is designed to evaluate ethnic-specific prevalence of S aureus carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of S aureus strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of S aureus reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of S aureus carriage and transmission.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Health care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce S aureus transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact S aureus carriage and transmission, either as risk or as protective factors. This study is designed to evaluate ethnic-specific prevalence of S aureus carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of S aureus strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of S aureus reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of S aureus carriage and transmission. |
Greene, Joshua R; Merrett, Kahla L; Heyert, Alexanndra J; Simmons, Lucas F; Migliori, Camille M; Vogt, Kristen C; Castro, Rebeca S; Phillips, Paul D; Baker, Joseph L; Lindberg, Gerrick E; Fox, David T; Sesto, Rico Del E; Koppisch, Andrew T Scope and efficacy of the broad-spectrum topical antiseptic choline geranate Journal Article PLoS One, 14 (9), 2019. @article{Greene2019, title = {Scope and efficacy of the broad-spectrum topical antiseptic choline geranate}, author = {Joshua R Greene and Kahla L Merrett and Alexanndra J Heyert and Lucas F Simmons and Camille M Migliori and Kristen C Vogt and Rebeca S Castro and Paul D Phillips and Joseph L Baker and Gerrick E Lindberg and David T Fox and Rico E Del Sesto and Andrew T Koppisch}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222211}, doi = {10.1371/journal.pone.0222211}, year = {2019}, date = {2019-09-17}, journal = {PLoS One}, volume = {14}, number = {9}, abstract = {Choline geranate (also described as Choline And GEranic acid, or CAGE) has been developed as a novel biocompatible antiseptic material capable of penetrating skin and aiding the transdermal delivery of co-administered antibiotics. The antibacterial properties of CAGE were analyzed against 24 and 72 hour old biofilms of 11 clinically isolated ESKAPE pathogens (defined as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp, respectively), including multidrug resistant (MDR) isolates. CAGE was observed to eradicate in vitro biofilms at concentrations as low as 3.56 mM (0.156% v:v) in as little as 2 hours, which represents both an improved potency and rate of biofilm eradication relative to that reported for most common standard-of-care topical antiseptics in current use. In vitro time-kill studies on 24 hour old Staphylococcus aureus biofilms indicate that CAGE exerts its antibacterial effect upon contact and a 0.1% v:v solution reduced biofilm viability by over three orders of magnitude (a 3log10 reduction) in 15 minutes. Furthermore, disruption of the protective layer of exopolymeric substances in mature biofilms of Staphylococcus aureus by CAGE (0.1% v:v) was observed in 120 minutes. Insight into the mechanism of action of CAGE was provided with molecular modeling studies alongside in vitro antibiofilm assays. The geranate ion and geranic acid components of CAGE are predicted to act in concert to integrate into bacterial membranes, affect membrane thinning and perturb membrane homeostasis. Taken together, our results show that CAGE demonstrates all properties required of an effective topical antiseptic and the data also provides insight into how its observed antibiofilm properties may manifest.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Choline geranate (also described as Choline And GEranic acid, or CAGE) has been developed as a novel biocompatible antiseptic material capable of penetrating skin and aiding the transdermal delivery of co-administered antibiotics. The antibacterial properties of CAGE were analyzed against 24 and 72 hour old biofilms of 11 clinically isolated ESKAPE pathogens (defined as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp, respectively), including multidrug resistant (MDR) isolates. CAGE was observed to eradicate in vitro biofilms at concentrations as low as 3.56 mM (0.156% v:v) in as little as 2 hours, which represents both an improved potency and rate of biofilm eradication relative to that reported for most common standard-of-care topical antiseptics in current use. In vitro time-kill studies on 24 hour old Staphylococcus aureus biofilms indicate that CAGE exerts its antibacterial effect upon contact and a 0.1% v:v solution reduced biofilm viability by over three orders of magnitude (a 3log10 reduction) in 15 minutes. Furthermore, disruption of the protective layer of exopolymeric substances in mature biofilms of Staphylococcus aureus by CAGE (0.1% v:v) was observed in 120 minutes. Insight into the mechanism of action of CAGE was provided with molecular modeling studies alongside in vitro antibiofilm assays. The geranate ion and geranic acid components of CAGE are predicted to act in concert to integrate into bacterial membranes, affect membrane thinning and perturb membrane homeostasis. Taken together, our results show that CAGE demonstrates all properties required of an effective topical antiseptic and the data also provides insight into how its observed antibiofilm properties may manifest. |
Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R; Bokulich, Nicholas A; Abnet, Christian C; Al-Ghalith, Gabriel A; Alexander, Harriet; Alm, Eric J; Arumugam, Manimozhiyan; Asnicar, Francesco; Bai, Yang; Bisanz, Jordan E; Bittinger, Kyle; Brejnrod, Asker; Brislawn, Colin J; Brown, Titus C; Callahan, Benjamin J; Caraballo-Rodríguez, Andrés Mauricio; Chase, John; Cope, Emily K; Silva, Ricardo Da; Diener, Christian; Dorrestein, Pieter C; Douglas, Gavin M; Durall, Daniel M; Duvallet, Claire; Edwardson, Christian F; Ernst, Madeleine; Estaki, Mehrbod; Fouquier, Jennifer; Gauglitz, Julia M; Gibbons, Sean M; Gibson, Deanna L; Gonzalez, Antonio; Gorlick, Kestrel; Guo, Jiarong; Hillmann, Benjamin; Holmes, Susan; Holste, Hannes; Huttenhower, Curtis; Huttley, Gavin A; Janssen, Stefan; Jarmusch, Alan K; Jiang, Lingjing; Kaehler, Benjamin D; Kang, Kyo Bin; Keefe, Christopher R; Keim, Paul; Kelley, Scott T; Knights, Dan; Koester, Irina; Kosciolek, Tomasz; Kreps, Jorden; Langille, Morgan G I; Lee, Joslynn; Ley, Ruth; Liu, Yong-Xin; Loftfield, Erikka; Lozupone, Catherine; Maher, Massoud; Marotz, Clarisse; Martin, Bryan D; McDonald, Daniel; McIver, Lauren J; Melnik, Alexey V; Metcalf, Jessica L; Morgan, Sydney C; Morton, Jamie T; Naimey, Ahmad Turan; Navas-Molina, Jose A; Nothias, Louis Felix; Orchanian, Stephanie B; Pearson, Talima; Peoples, Samuel L; Petras, Daniel; Preuss, Mary Lai; Pruesse, Elmar; Rasmussen, Lasse Buur; Rivers, Adam; II, Michael Robeson S; Rosenthal, Patrick; Segata, Nicola; Shaffer, Michael; Shiffer, Arron; Sinha, Rashmi; Song, Se Jin; Spear, John R; Swafford, Austin D; Thompson, Luke R; Torres, Pedro J; Trinh, Pauline; Tripathi, Anupriya; Turnbaugh, Peter J; Ul-Hasan, Sabah; van der Hooft, Justin J J; Vargas, Fernando; Vázquez-Baeza, Yoshiki; Vogtmann, Emily; von Hippel, Max; Walters, William; Wan, Yunhu; Wang, Mingxun; Warren, Jonathan; Weber, Kyle C; Williamson, Charles H D; Willis, Amy D; Xu, Zhenjiang Zech; Zaneveld, Jesse R; Zhang, Yilong; Zhu, Qiyun; Knight, Rob; Caporaso, Gregory J Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2 Journal Article Nature Biotechnology, 37 (8), pp. 852-857, 2019. @article{Bolyen2019, title = {Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2}, author = {Evan Bolyen and Jai Ram Rideout and Matthew R Dillon and Nicholas A Bokulich and Christian C Abnet and Gabriel A Al-Ghalith and Harriet Alexander and Eric J Alm and Manimozhiyan Arumugam and Francesco Asnicar and Yang Bai and Jordan E Bisanz and Kyle Bittinger and Asker Brejnrod and Colin J Brislawn and C Titus Brown and Benjamin J Callahan and Andrés Mauricio Caraballo-Rodríguez and John Chase and Emily K Cope and Ricardo Da Silva and Christian Diener and Pieter C Dorrestein and Gavin M Douglas and Daniel M Durall and Claire Duvallet and Christian F Edwardson and Madeleine Ernst and Mehrbod Estaki and Jennifer Fouquier and Julia M Gauglitz and Sean M Gibbons and Deanna L Gibson and Antonio Gonzalez and Kestrel Gorlick and Jiarong Guo and Benjamin Hillmann and Susan Holmes and Hannes Holste and Curtis Huttenhower and Gavin A Huttley and Stefan Janssen and Alan K Jarmusch and Lingjing Jiang and Benjamin D Kaehler and Kyo Bin Kang and Christopher R Keefe and Paul Keim and Scott T Kelley and Dan Knights and Irina Koester and Tomasz Kosciolek and Jorden Kreps and Morgan G I Langille and Joslynn Lee and Ruth Ley and Yong-Xin Liu and Erikka Loftfield and Catherine Lozupone and Massoud Maher and Clarisse Marotz and Bryan D Martin and Daniel McDonald and Lauren J McIver and Alexey V Melnik and Jessica L Metcalf and Sydney C Morgan and Jamie T Morton and Ahmad Turan Naimey and Jose A Navas-Molina and Louis Felix Nothias and Stephanie B Orchanian and Talima Pearson and Samuel L Peoples and Daniel Petras and Mary Lai Preuss and Elmar Pruesse and Lasse Buur Rasmussen and Adam Rivers and Michael S Robeson II and Patrick Rosenthal and Nicola Segata and Michael Shaffer and Arron Shiffer and Rashmi Sinha and Se Jin Song and John R Spear and Austin D Swafford and Luke R Thompson and Pedro J Torres and Pauline Trinh and Anupriya Tripathi and Peter J Turnbaugh and Sabah Ul-Hasan and Justin J J van der Hooft and Fernando Vargas and Yoshiki Vázquez-Baeza and Emily Vogtmann and Max von Hippel and William Walters and Yunhu Wan and Mingxun Wang and Jonathan Warren and Kyle C Weber and Charles H D Williamson and Amy D Willis and Zhenjiang Zech Xu and Jesse R Zaneveld and Yilong Zhang and Qiyun Zhu and Rob Knight and J Gregory Caporaso}, url = {https://www.nature.com/articles/s41587-019-0209-9}, doi = {10.1038/s41587-019-0209-9}, year = {2019}, date = {2019-08-09}, journal = {Nature Biotechnology}, volume = {37}, number = {8}, pages = {852-857}, abstract = {Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease1 and medical treatment2; how microorganisms affect the health of the planet3; and the nascent exploration of the medical4, forensic5, environmental6 and agricultural7 applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite8, metaproteome9 or metatranscriptome profiles.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease1 and medical treatment2; how microorganisms affect the health of the planet3; and the nascent exploration of the medical4, forensic5, environmental6 and agricultural7 applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite8, metaproteome9 or metatranscriptome profiles. |
Ghazanfari, Behzad; Afghah, Fatemeh; Najarian, Kayvan; Mousavi, Sajad; Gryak, Jonathan; Todd, James An Unsupervised Feature Learning Approach to Reduce False Alarm Rate in ICUs Journal Article Conf Proc IEEE Eng Med Biol Soc., pp. 349-353, 2019. @article{Ghazanfari2019, title = {An Unsupervised Feature Learning Approach to Reduce False Alarm Rate in ICUs}, author = {Behzad Ghazanfari and Fatemeh Afghah and Kayvan Najarian and Sajad Mousavi and Jonathan Gryak and James Todd}, url = {https://ieeexplore.ieee.org/document/8857034}, doi = {0.1109/EMBC.2019.8857034}, year = {2019}, date = {2019-07-23}, journal = {Conf Proc IEEE Eng Med Biol Soc.}, pages = {349-353}, abstract = {The high rate of false alarms in intensive care units (ICUs) is one of the top challenges of using medical technology in hospitals. These false alarms are often caused by patients' movements, detachment of monitoring sensors, or different sources of noise and interference that impact the collected signals from different monitoring devices. In this paper, we propose a novel set of high-level features based on unsupervised feature learning technique in order to effectively capture the characteristics of different arrhythmia in electrocardiogram (ECG) signal and differentiate them from irregularity in signals due to different sources of signal disturbances. This unsupervised feature learning technique, first extracts a set of low-level features from all existing heart cycles of a patient, and then clusters these segments for each individual patient to provide a set of prominent high-level features. The objective of the clustering phase is to enable the classification method to differentiate between the high-level features extracted from normal and abnormal cycles (i.e., either due to arrhythmia or different sources of distortions in signal) in order to put more attention to the features extracted from abnormal portion of the signal that contribute to the alarm.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The high rate of false alarms in intensive care units (ICUs) is one of the top challenges of using medical technology in hospitals. These false alarms are often caused by patients' movements, detachment of monitoring sensors, or different sources of noise and interference that impact the collected signals from different monitoring devices. In this paper, we propose a novel set of high-level features based on unsupervised feature learning technique in order to effectively capture the characteristics of different arrhythmia in electrocardiogram (ECG) signal and differentiate them from irregularity in signals due to different sources of signal disturbances. This unsupervised feature learning technique, first extracts a set of low-level features from all existing heart cycles of a patient, and then clusters these segments for each individual patient to provide a set of prominent high-level features. The objective of the clustering phase is to enable the classification method to differentiate between the high-level features extracted from normal and abnormal cycles (i.e., either due to arrhythmia or different sources of distortions in signal) in order to put more attention to the features extracted from abnormal portion of the signal that contribute to the alarm. |
Camplain, Ricky; Warren, Meghan; Baldwin, Julie A; Camplain, Carolyn; Fofanov, Viacheslav Y; II, Robert Trotter T Epidemiology of Incarceration: Characterizing Jail Incarceration for Public Health Research Journal Article Epidemiology, 30 (4), pp. 561-568, 2019. @article{Camplain2019, title = {Epidemiology of Incarceration: Characterizing Jail Incarceration for Public Health Research}, author = {Ricky Camplain and Meghan Warren and Julie A Baldwin and Carolyn Camplain and Viacheslav Y Fofanov and Robert T Trotter II}, url = {https://journals.lww.com/epidem/Fulltext/2019/07000/Epidemiology_of_Incarceration__Characterizing_Jail.14.aspx}, doi = {10.1097/EDE.0000000000001021}, year = {2019}, date = {2019-07-01}, journal = {Epidemiology}, volume = {30}, number = {4}, pages = {561-568}, abstract = {Background: Each year, 9 million individuals cycle in and out of jails. The under-characterization of incarceration as an exposure poses substantial challenges to understanding how varying levels of exposure to jail may affect health. Thus, we characterized levels of jail incarceration including recidivism, number of incarcerations, total and average number of days incarcerated, and time to reincarceration. Methods: We created a cohort of 75,203 individuals incarcerated at the Coconino County Detention Facility in Flagstaff, Arizona, from 2001 to 2018 from jail intake and release records. Results: The median number of incarcerations during the study period was one (interquartile range [IQR] = 1-2). Forty percent of individuals had >1 incarceration. The median length of stay for first observed incarcerations was 1 day (IQR = 0-5). The median total days incarcerated was 3 (IQR = 1-23). Average length of stay increased by number of incarcerations. By 18 months, 27% of our sample had been reincarcerated. Conclusion: Characteristics of jail incarceration have been largely left out of public health research. A better understanding of jail incarcerations can help design analyses to assess health outcomes of individuals incarcerated in jail. Our study is an early step in shaping an understanding of jail incarceration as an exposure for future epidemiologic research. See video abstract at, http://links.lww.com/EDE/B536.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Each year, 9 million individuals cycle in and out of jails. The under-characterization of incarceration as an exposure poses substantial challenges to understanding how varying levels of exposure to jail may affect health. Thus, we characterized levels of jail incarceration including recidivism, number of incarcerations, total and average number of days incarcerated, and time to reincarceration. Methods: We created a cohort of 75,203 individuals incarcerated at the Coconino County Detention Facility in Flagstaff, Arizona, from 2001 to 2018 from jail intake and release records. Results: The median number of incarcerations during the study period was one (interquartile range [IQR] = 1-2). Forty percent of individuals had >1 incarceration. The median length of stay for first observed incarcerations was 1 day (IQR = 0-5). The median total days incarcerated was 3 (IQR = 1-23). Average length of stay increased by number of incarcerations. By 18 months, 27% of our sample had been reincarcerated. Conclusion: Characteristics of jail incarceration have been largely left out of public health research. A better understanding of jail incarcerations can help design analyses to assess health outcomes of individuals incarcerated in jail. Our study is an early step in shaping an understanding of jail incarceration as an exposure for future epidemiologic research. See video abstract at, http://links.lww.com/EDE/B536. |
Bartee, David; Sanders, Sara; Phillips, Paul D; Harrison, Mackenzie J; Koppisch, Andrew T; Meyers, Caren Freel L Enamide Prodrugs of Acetyl Phosphonate Deoxy-d-xylulose-5-phosphate Synthase Inhibitors as Potent Antibacterial Agents Journal Article ACS Infect. Dis, 5 (3), pp. 406-417, 2019. @article{Bartee2019, title = {Enamide Prodrugs of Acetyl Phosphonate Deoxy-d-xylulose-5-phosphate Synthase Inhibitors as Potent Antibacterial Agents}, author = {David Bartee and Sara Sanders and Paul D Phillips and Mackenzie J Harrison and Andrew T Koppisch and Caren L Freel Meyers}, url = {https://pubs.acs.org/doi/10.1021/acsinfecdis.8b00307}, doi = {10.1021/acsinfecdis.8b00307}, year = {2019}, date = {2019-05-08}, journal = {ACS Infect. Dis}, volume = {5}, number = {3}, pages = {406-417}, abstract = {To fight the growing threat of antibiotic resistance, new antibiotics are required that target essential bacterial processes other than protein, DNA/RNA, and cell wall synthesis, which constitute the majority of currently used antibiotics. 1-Deoxy-d-xylulose-5-phosphate (DXP) synthase is a vital enzyme in bacterial central metabolism, feeding into the de novo synthesis of thiamine diphosphate, pyridoxal phosphate, and essential isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. While potent and selective inhibitors of DXP synthase in vitro activity have been discovered, their antibacterial activity is modest. To improve the antibacterial activity of selective alkyl acetylphosphonate (alkylAP) inhibitors of DXP synthase, we synthesized peptidic enamide prodrugs of alkylAPs inspired by the natural product dehydrophos, a prodrug of methyl acetylphosphonate. This prodrug strategy achieves dramatic increases in activity against Gram-negative pathogens for two alkylAPs, butyl acetylphosphonate and homopropargyl acetylphosphonate, decreasing minimum inhibitory concentrations against Escherichia coli by 33- and nearly 2000-fold, respectively. Antimicrobial studies and LC-MS/MS analysis of alkylAP-treated E. coli establish that the increased potency of prodrugs is due to increased accumulation of alkylAP inhibitors of DXP synthase via transport of the prodrug through the OppA peptide permease and subsequent amide hydrolysis. This work demonstrates the promise of targeting DXP synthase for the development of novel antibacterial agents.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To fight the growing threat of antibiotic resistance, new antibiotics are required that target essential bacterial processes other than protein, DNA/RNA, and cell wall synthesis, which constitute the majority of currently used antibiotics. 1-Deoxy-d-xylulose-5-phosphate (DXP) synthase is a vital enzyme in bacterial central metabolism, feeding into the de novo synthesis of thiamine diphosphate, pyridoxal phosphate, and essential isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate. While potent and selective inhibitors of DXP synthase in vitro activity have been discovered, their antibacterial activity is modest. To improve the antibacterial activity of selective alkyl acetylphosphonate (alkylAP) inhibitors of DXP synthase, we synthesized peptidic enamide prodrugs of alkylAPs inspired by the natural product dehydrophos, a prodrug of methyl acetylphosphonate. This prodrug strategy achieves dramatic increases in activity against Gram-negative pathogens for two alkylAPs, butyl acetylphosphonate and homopropargyl acetylphosphonate, decreasing minimum inhibitory concentrations against Escherichia coli by 33- and nearly 2000-fold, respectively. Antimicrobial studies and LC-MS/MS analysis of alkylAP-treated E. coli establish that the increased potency of prodrugs is due to increased accumulation of alkylAP inhibitors of DXP synthase via transport of the prodrug through the OppA peptide permease and subsequent amide hydrolysis. This work demonstrates the promise of targeting DXP synthase for the development of novel antibacterial agents. |
Mousavi, Sajad; Afghah, Fatemeh; Acharya, U.Rajendra SleepEEGNet: Automated sleep stage scoring with sequence to sequence deep learning approach Journal Article PLoS One, 14 (5), 2019. @article{Mousavi2019, title = {SleepEEGNet: Automated sleep stage scoring with sequence to sequence deep learning approach}, author = {Sajad Mousavi and Fatemeh Afghah and U.Rajendra Acharya}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216456}, doi = {10.1371/journal.pone.0216456}, year = {2019}, date = {2019-05-07}, journal = {PLoS One}, volume = {14}, number = {5}, abstract = {Electroencephalogram (EEG) is a common base signal used to monitor brain activities and diagnose sleep disorders. Manual sleep stage scoring is a time-consuming task for sleep experts and is limited by inter-rater reliability. In this paper, we propose an automatic sleep stage annotation method called SleepEEGNet using a single-channel EEG signal. The SleepEEGNet is composed of deep convolutional neural networks (CNNs) to extract time-invariant features, frequency information, and a sequence to sequence model to capture the complex and long short-term context dependencies between sleep epochs and scores. In addition, to reduce the effect of the class imbalance problem presented in the available sleep datasets, we applied novel loss functions to have an equal misclassified error for each sleep stage while training the network. We evaluated the performance of the proposed method on different single-EEG channels (i.e., Fpz-Cz and Pz-Oz EEG channels) from the Physionet Sleep-EDF datasets published in 2013 and 2018. The evaluation results demonstrate that the proposed method achieved the best annotation performance compared to current literature, with an overall accuracy of 84.26%, a macro F1-score of 79.66% and κ = 0.79. Our developed model can be applied to other sleep EEG signals and aid the sleep specialists to arrive at an accurate diagnosis}, keywords = {}, pubstate = {published}, tppubtype = {article} } Electroencephalogram (EEG) is a common base signal used to monitor brain activities and diagnose sleep disorders. Manual sleep stage scoring is a time-consuming task for sleep experts and is limited by inter-rater reliability. In this paper, we propose an automatic sleep stage annotation method called SleepEEGNet using a single-channel EEG signal. The SleepEEGNet is composed of deep convolutional neural networks (CNNs) to extract time-invariant features, frequency information, and a sequence to sequence model to capture the complex and long short-term context dependencies between sleep epochs and scores. In addition, to reduce the effect of the class imbalance problem presented in the available sleep datasets, we applied novel loss functions to have an equal misclassified error for each sleep stage while training the network. We evaluated the performance of the proposed method on different single-EEG channels (i.e., Fpz-Cz and Pz-Oz EEG channels) from the Physionet Sleep-EDF datasets published in 2013 and 2018. The evaluation results demonstrate that the proposed method achieved the best annotation performance compared to current literature, with an overall accuracy of 84.26%, a macro F1-score of 79.66% and κ = 0.79. Our developed model can be applied to other sleep EEG signals and aid the sleep specialists to arrive at an accurate diagnosis |
de Heer, Hendrik; Kinslow, Brian; Lane, Taylor; Tuckman, Ron; Warren, Meghan Only 1 in 10 Patients Told to Lose Weight Seek Help From a Health Professional: A Nationally Representative Sample Journal Article American Journal of Health Promotion, 2019. @article{deHeer2019, title = {Only 1 in 10 Patients Told to Lose Weight Seek Help From a Health Professional: A Nationally Representative Sample}, author = {Hendrik de Heer and Brian Kinslow and Taylor Lane and Ron Tuckman and Meghan Warren}, url = {https://journals.sagepub.com/doi/10.1177/0890117119839904}, doi = {10.1177/0890117119839904}, year = {2019}, date = {2019-03-28}, journal = {American Journal of Health Promotion}, abstract = {Receiving weight loss advice from a health-care provider has been associated with more weight loss efforts and greater odds of achieving weight loss. However, whether patients seek help from their provider or other health professional with weight loss after receiving advice from them to lose weight is largely unknown.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Receiving weight loss advice from a health-care provider has been associated with more weight loss efforts and greater odds of achieving weight loss. However, whether patients seek help from their provider or other health professional with weight loss after receiving advice from them to lose weight is largely unknown. |
Parsons, Michelle Anne; Barger, Steven D The US Mortality Crisis: An Examination of Non-Hispanic White Mortality and Morbidity in Yavapai County, Arizona Journal Article Journal of Community Health, 44 , pp. 661-667, 2019. @article{Parsons2019, title = {The US Mortality Crisis: An Examination of Non-Hispanic White Mortality and Morbidity in Yavapai County, Arizona}, author = {Michelle Anne Parsons and Steven D Barger}, url = {https://link.springer.com/article/10.1007/s10900-019-00648-3}, doi = {10.1007/s10900-019-00648-3}, year = {2019}, date = {2019-03-15}, journal = {Journal of Community Health}, volume = {44}, pages = {661-667}, abstract = {Midlife non-Hispanic white mortality in the United States is rising, particularly in small metro and rural counties. This article responds to calls for county-level studies. We examine social determinants of morbidity and mortality among adult non-Hispanic whites in Yavapai County, Arizona, as part of an integrative study. We report overall mortality trends in Yavapai County using CDC Wonder data and then examine social determinants of reported physical health and mental distress in Yavapai County data using 6 years (2011-2016) of the Arizona Behavioral Risk Factor Surveillance System (BRFSS). The BRFSS includes 1,024 non-Hispanic white respondents aged 25-64. We also present data from the recently established Yavapai County Overdose Fatality Review Board (YCOFRB). Mortality trends indicate that suicide and drug and alcohol-related mortality have all increased since 1999. These increases affect all 5-year age groups from 25 to 64 and both men and women. BRFSS data show that low education and unemployment, but not number of children or home ownership, are significantly associated with worse reported health and frequent mental distress in multivariate analyses. The YCOFRB point to the importance of homelessness and mental health. The mortality crisis in Yavapai County is not restricted to midlife or to drug-related deaths. The unemployed and those with low levels of education are particularly at risk. There is a need for integrative approaches that use local data to elucidate social determinants of morbidity and mortality and to reveal structural determinants.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Midlife non-Hispanic white mortality in the United States is rising, particularly in small metro and rural counties. This article responds to calls for county-level studies. We examine social determinants of morbidity and mortality among adult non-Hispanic whites in Yavapai County, Arizona, as part of an integrative study. We report overall mortality trends in Yavapai County using CDC Wonder data and then examine social determinants of reported physical health and mental distress in Yavapai County data using 6 years (2011-2016) of the Arizona Behavioral Risk Factor Surveillance System (BRFSS). The BRFSS includes 1,024 non-Hispanic white respondents aged 25-64. We also present data from the recently established Yavapai County Overdose Fatality Review Board (YCOFRB). Mortality trends indicate that suicide and drug and alcohol-related mortality have all increased since 1999. These increases affect all 5-year age groups from 25 to 64 and both men and women. BRFSS data show that low education and unemployment, but not number of children or home ownership, are significantly associated with worse reported health and frequent mental distress in multivariate analyses. The YCOFRB point to the importance of homelessness and mental health. The mortality crisis in Yavapai County is not restricted to midlife or to drug-related deaths. The unemployed and those with low levels of education are particularly at risk. There is a need for integrative approaches that use local data to elucidate social determinants of morbidity and mortality and to reveal structural determinants. |
Ofili, Elizabeth O; Tchounwou, Paul B; Fernandez-Repollet, Emma; Yanagihara, Richard; Akintobi, Tabia H; Lee, Jae E; Malouhi, Mohamad; Jr, Solomon Garner T; Hayes, Traci T; Baker, Almelida R; 2nd, Andrew Dent L; Abdelrahim, Muna; Rollins, Latrice; Chang, Sandra P; Sy, Angela; Hernandez, Brenda Y; Bullard, Pamela L; Jr, Richard Noel J; Shiramizu, Bruce; Hedges, Jerris R; Berry, Marla J; Bond, Vincent C; Lima, Maria F; Mokuau, Noreen; Kirken, Robert A; Cruz-Correa, Marcia; Sarpong, Daniel F; Vadgama, Jaydutt; Yates, Clayton; Kahn, Shafiq A; Soliman, Karam F; Perry, George; Pezzano, Mark; Luciano, Carlos A; Barnett, Edwina M; Oyekan, Adebayo; Kumar, Deepak; Norris, Keith C Ethnicity and Disease, 29 (1), 2019. @article{Ofili2019, title = {The Research Centers in Minority Institutions (RCMI) Translational Research Network: Building and Sustaining Capacity for Multi-Site Basic Biomedical, Clinical and Behavioral Research}, author = {Elizabeth O Ofili and Paul B Tchounwou and Emma Fernandez-Repollet and Richard Yanagihara and Tabia H Akintobi and Jae E Lee and Mohamad Malouhi and Solomon T Garner Jr and Traci T Hayes and Almelida R Baker and Andrew L Dent 2nd and Muna Abdelrahim and Latrice Rollins and Sandra P Chang and Angela Sy and Brenda Y Hernandez and Pamela L Bullard and Richard J Noel Jr and Bruce Shiramizu and Jerris R Hedges and Marla J Berry and Vincent C Bond and Maria F Lima and Noreen Mokuau and Robert A Kirken and Marcia Cruz-Correa and Daniel F Sarpong and Jaydutt Vadgama and Clayton Yates and Shafiq A Kahn and Karam F Soliman and George Perry and Mark Pezzano and Carlos A Luciano and M Edwina Barnett and Adebayo Oyekan and Deepak Kumar and Keith C Norris}, url = {https://www.ethndis.org/edonline/index.php/ethndis/article/view/1066}, doi = {10.18865/ed.29.S1.135}, year = {2019}, date = {2019-02-21}, journal = {Ethnicity and Disease}, volume = {29}, number = {1}, abstract = {The Research Centers in Minority Institutions (RCMI) program was established by the US Congress to support the development of biomedical research infrastructure at minority-serving institutions granting doctoral degrees in the health professions or in a health-related science. RCMI institutions also conduct research on diseases that disproportionately affect racial and ethnic minorities (ie, African Americans/Blacks, American Indians and Alaska Natives, Hispanics, Native Hawaiians and Other Pacific Islanders), those of low socioeconomic status, and rural persons. Quantitative metrics, including the numbers of doctoral science degrees granted to underrepresented students, NIH peer-reviewed research funding, peer-reviewed publications, and numbers of racial and ethnic minorities participating in sponsored research, demonstrate that RCMI grantee institutions have made substantial progress toward the intent of the Congressional legislation, as well as the NIH/NIMHD-linked goals of addressing workforce diversity and health disparities. Despite this progress, nationally, many challenges remain, including persistent disparities in research and career development awards to minority investigators. The continuing underrepresentation of minority investigators in NIH-sponsored research across multiple disease areas is of concern, in the face of unrelenting national health inequities. With the collaborative network support by the RCMI Translational Research Network (RTRN), the RCMI community is uniquely positioned to address these challenges through its community engagement and strategic partnerships with non-RCMI institutions. Funding agencies can play an important role by incentivizing such collaborations, and incorporating metrics for research funding that address underrepresented populations, workforce diversity and health equity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Research Centers in Minority Institutions (RCMI) program was established by the US Congress to support the development of biomedical research infrastructure at minority-serving institutions granting doctoral degrees in the health professions or in a health-related science. RCMI institutions also conduct research on diseases that disproportionately affect racial and ethnic minorities (ie, African Americans/Blacks, American Indians and Alaska Natives, Hispanics, Native Hawaiians and Other Pacific Islanders), those of low socioeconomic status, and rural persons. Quantitative metrics, including the numbers of doctoral science degrees granted to underrepresented students, NIH peer-reviewed research funding, peer-reviewed publications, and numbers of racial and ethnic minorities participating in sponsored research, demonstrate that RCMI grantee institutions have made substantial progress toward the intent of the Congressional legislation, as well as the NIH/NIMHD-linked goals of addressing workforce diversity and health disparities. Despite this progress, nationally, many challenges remain, including persistent disparities in research and career development awards to minority investigators. The continuing underrepresentation of minority investigators in NIH-sponsored research across multiple disease areas is of concern, in the face of unrelenting national health inequities. With the collaborative network support by the RCMI Translational Research Network (RTRN), the RCMI community is uniquely positioned to address these challenges through its community engagement and strategic partnerships with non-RCMI institutions. Funding agencies can play an important role by incentivizing such collaborations, and incorporating metrics for research funding that address underrepresented populations, workforce diversity and health equity. |
2018 |
Teufel-Shone, Nicolette I; Schwartz, Anna L; Hardy, Lisa J; de Heer, Hendrik D; Williamson, Heather J; Dunn, Dorothy J; Polingyumptewa, Kellen; Chief, Carmenlita Supporting New Community-Based Participatory Research Partnerships Journal Article International Journal of Environmental Research and Public Health, 16 (1), 2018. @article{Teufel-Shone2018, title = {Supporting New Community-Based Participatory Research Partnerships}, author = {Nicolette I Teufel-Shone and Anna L Schwartz and Lisa J Hardy and Hendrik D de Heer and Heather J Williamson and Dorothy J Dunn and Kellen Polingyumptewa and Carmenlita Chief}, url = {Polingyumptewa and Carmenlita Chief https://doi.org/10.3390/ijerph16010044}, doi = {10.3390/ijerph16010044}, year = {2018}, date = {2018-12-25}, journal = {International Journal of Environmental Research and Public Health}, volume = {16}, number = {1}, abstract = {Marginalized communities have a documented distrust of research grounded in negative portrayals in the academic literature. Yet, trusted partnerships, the foundation for Community-Based Participatory Research (CBPR), require time to build the capacity for joint decision-making, equitable involvement of academically trained and community investigators, and co-learning. Trust can be difficult to develop within the short time between a funding opportunity announcement and application submission. Resources to support community- and academic-based investigators' time to discuss contexts, concerns, integration of expertise and locally acceptable research designs and data collection are limited. The National Institutes of Health (NIH) funded Center for American Indian Resilience and the Southwest Health Equity Research Collaborative have implemented an internal funding mechanism to support community and academic-based investigators' travel cost and time to discuss complementary areas of interest and skills and to decide if moving forward with a partnership and a collaborative grant proposal would be beneficial to the community. The rationale and administration of this Community-Campus Partnership Support (CCPS) Program are described and four examples of supported efforts are provided. Centers and training programs frequently fund pilot grants to support junior investigators and/or exploratory research. This CCPS mechanism should be considered as precursor to pilot work, to stimulate partnership building without the pressure of an approaching grant application deadline. }, keywords = {}, pubstate = {published}, tppubtype = {article} } Marginalized communities have a documented distrust of research grounded in negative portrayals in the academic literature. Yet, trusted partnerships, the foundation for Community-Based Participatory Research (CBPR), require time to build the capacity for joint decision-making, equitable involvement of academically trained and community investigators, and co-learning. Trust can be difficult to develop within the short time between a funding opportunity announcement and application submission. Resources to support community- and academic-based investigators' time to discuss contexts, concerns, integration of expertise and locally acceptable research designs and data collection are limited. The National Institutes of Health (NIH) funded Center for American Indian Resilience and the Southwest Health Equity Research Collaborative have implemented an internal funding mechanism to support community and academic-based investigators' travel cost and time to discuss complementary areas of interest and skills and to decide if moving forward with a partnership and a collaborative grant proposal would be beneficial to the community. The rationale and administration of this Community-Campus Partnership Support (CCPS) Program are described and four examples of supported efforts are provided. Centers and training programs frequently fund pilot grants to support junior investigators and/or exploratory research. This CCPS mechanism should be considered as precursor to pilot work, to stimulate partnership building without the pressure of an approaching grant application deadline. |
Trotter, Robert T; Lininger, Monica R; Camplain, Ricky; Fofanov, Viacheslav Y; Camplain, Carolyn; Baldwin, Julie A International Journal of Environmental Research and Public Health, 15 (11), 2018. @article{Trotter2018, title = {A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations}, author = {Robert T Trotter and Monica R Lininger and Ricky Camplain and Viacheslav Y Fofanov and Carolyn Camplain and Julie A Baldwin}, url = {https://doi.org/10.3390/ijerph15112500}, doi = {10.3390/ijerph15112500}, year = {2018}, date = {2018-11-08}, journal = {International Journal of Environmental Research and Public Health}, volume = {15}, number = {11}, abstract = {The environmental health status of jail populations in the United States constitutes a significant public health threat for prisoners and the general population. The ecology of jails creates a dynamic condition in relation to general population health due to the concentrated potential exposure to infectious diseases, difficult access to treatment for chronic health conditions, interruption in continuity of care for serious behavioral health conditions, as well as on-going issues for the prevention and treatment of substance abuse disorders. This paper reports on elements of a cross-sectional survey embedded in a parent project, "Health Disparities in Jail Populations." The overall project includes a comprehensive secondary data analysis of the health status of county jail populations, along with primary data collection that includes a cross-sectional health and health care services survey of incarcerated individuals, coupled with collection of biological samples to investigate infectious disease characteristics of a county jail population. This paper reports on the primary results of the survey data collection that indicate that this is a population with complex and interacting co-morbidities, as well as significant health disparities compared to the general population.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The environmental health status of jail populations in the United States constitutes a significant public health threat for prisoners and the general population. The ecology of jails creates a dynamic condition in relation to general population health due to the concentrated potential exposure to infectious diseases, difficult access to treatment for chronic health conditions, interruption in continuity of care for serious behavioral health conditions, as well as on-going issues for the prevention and treatment of substance abuse disorders. This paper reports on elements of a cross-sectional survey embedded in a parent project, "Health Disparities in Jail Populations." The overall project includes a comprehensive secondary data analysis of the health status of county jail populations, along with primary data collection that includes a cross-sectional health and health care services survey of incarcerated individuals, coupled with collection of biological samples to investigate infectious disease characteristics of a county jail population. This paper reports on the primary results of the survey data collection that indicate that this is a population with complex and interacting co-morbidities, as well as significant health disparities compared to the general population. |
Trotter, Robert T; Lininger, Monica R; Camplain, Ricky; Fofanov, Viacheslav Y; Camplain, Carolyn; Baldwin, Julie A International Journal of Environmental Research and Public Health, 15 (11), 2018. @article{Trotter2018b, title = {A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations}, author = {Robert T Trotter and Monica R Lininger and Ricky Camplain and Viacheslav Y Fofanov and Carolyn Camplain and Julie A Baldwin }, url = {https://www.mdpi.com/1660-4601/15/11/2500}, doi = {10.3390/ijerph15112500}, year = {2018}, date = {2018-11-08}, journal = {International Journal of Environmental Research and Public Health}, volume = {15}, number = {11}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Trotter, Robert T; Camplain, Ricky; Eaves, Emery R; Fofanov, Viacheslav Y; Dmitrieva, Natalia O; Hepp1, Crystal M; Warren, Meghan; Barrios, Brianna A; Pagel, Nicole; Mayer, Alyssa; Baldwin, Julie A Health Disparities and Converging Epidemics in Jail Populations: Protocol for a Mixed-Methods Study Journal Article JMIR Research Protocols, 7 (10), 2018. @article{Trotter24.1, title = {Health Disparities and Converging Epidemics in Jail Populations: Protocol for a Mixed-Methods Study}, author = {Robert T Trotter and Ricky Camplain and Emery R Eaves and Viacheslav Y Fofanov and Natalia O Dmitrieva and Crystal M Hepp1 and Meghan Warren and Brianna A Barrios and Nicole Pagel and Alyssa Mayer and Julie A Baldwin}, doi = {10.2196/10337}, year = {2018}, date = {2018-10-24}, journal = {JMIR Research Protocols}, volume = {7}, number = {10}, abstract = {Incarcerated populations have increased in the last 20 years and >12 million individuals cycle in and out of jails each year. Previous research has predominately focused on the prison population. However, a substantial gap exists in understanding the health, well-being, and health care utilization patterns in jail populations. This pilot study has 5 main objectives: (1) define recidivists of the jail system, individuals characterized by high incarceration rates; (2) describe and compare the demographic and clinical characteristics of incarcerated individuals; (3) identify jail-associated health disparities; (4) estimate associations between incarceration and health; and (5) describe model patterns in health care and jail utilization. To date, we have permission to link data across acquired databases. We have initiated data transfer, protection, and initial assessment of the 6 secondary databases. Of 199 inmates consented and enrolled, we have permission from 97.0% (193/199) to access and link electronic medical and incarceration records to their survey responses, and 95.0% (189/199) of interviewed inmates have given nasal and buccal swabs for analysis of S. aureus and the dental microbiome.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Incarcerated populations have increased in the last 20 years and >12 million individuals cycle in and out of jails each year. Previous research has predominately focused on the prison population. However, a substantial gap exists in understanding the health, well-being, and health care utilization patterns in jail populations. This pilot study has 5 main objectives: (1) define recidivists of the jail system, individuals characterized by high incarceration rates; (2) describe and compare the demographic and clinical characteristics of incarcerated individuals; (3) identify jail-associated health disparities; (4) estimate associations between incarceration and health; and (5) describe model patterns in health care and jail utilization. To date, we have permission to link data across acquired databases. We have initiated data transfer, protection, and initial assessment of the 6 secondary databases. Of 199 inmates consented and enrolled, we have permission from 97.0% (193/199) to access and link electronic medical and incarceration records to their survey responses, and 95.0% (189/199) of interviewed inmates have given nasal and buccal swabs for analysis of S. aureus and the dental microbiome. |
Varadaraj, Archana; Magdaleno, Carina; Mythreye, Karthikeyan Deoxycholate Fractionation of Fibronectin (FN) and Biotinylation Assay to Measure Recycled FN Fibrils in Epithelial Cells Journal Article Bio-protocol, 8 (16), 2018. @article{Varadaraj2018, title = {Deoxycholate Fractionation of Fibronectin (FN) and Biotinylation Assay to Measure Recycled FN Fibrils in Epithelial Cells}, author = {Archana Varadaraj and Carina Magdaleno and Karthikeyan Mythreye}, url = {https://bio-protocol.org/e2972}, doi = {10.21769/BioProtoc.2972}, year = {2018}, date = {2018-08-20}, journal = {Bio-protocol}, volume = {8}, number = {16}, abstract = {Fibronectin (FN) is an extracellular matrix protein that is secreted by many cell types and binds predominantly to the cell surface receptor Integrin α5β1. Integrin α5β1 binding initiates the step-wise assembly of FN into fibrils, a process called fibrillogenesis. We and several others have demonstrated critical effects of fibrillogenesis on cell migration and metastasis. While immunostaining and microscopy methods help visualize FN incorporation into fibrils, with each fibril being at least 3 μm in length, the first study that developed a method to biochemically fractionate FN to quantify fibril incorporated FN was published by Jean Schwarzbauer's group in 1996. Our protocol was adapted from the original publication, and has been tested on multiple cell types including as shown here in MCF10A mammary epithelial and Caki-1 renal cancer epithelial cells. Using two detergent extractions, cellular FN is separated into detergent insoluble or fibril incorporated FN and soluble FN or unincorporated fractions. To determine whether fibrillogenesis utilizes a recycled pool of FN, we have used a Biotin labeled FN (FN-Biotin) recycling assay, that has been modified from a previous study. Using a combination of the recycling assay and deoxycholate fractionation methods, one can quantitatively demonstrate the extent of fibrillogenesis in cells under different experimental conditions and determine the source of FN for fibrillogenesis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fibronectin (FN) is an extracellular matrix protein that is secreted by many cell types and binds predominantly to the cell surface receptor Integrin α5β1. Integrin α5β1 binding initiates the step-wise assembly of FN into fibrils, a process called fibrillogenesis. We and several others have demonstrated critical effects of fibrillogenesis on cell migration and metastasis. While immunostaining and microscopy methods help visualize FN incorporation into fibrils, with each fibril being at least 3 μm in length, the first study that developed a method to biochemically fractionate FN to quantify fibril incorporated FN was published by Jean Schwarzbauer's group in 1996. Our protocol was adapted from the original publication, and has been tested on multiple cell types including as shown here in MCF10A mammary epithelial and Caki-1 renal cancer epithelial cells. Using two detergent extractions, cellular FN is separated into detergent insoluble or fibril incorporated FN and soluble FN or unincorporated fractions. To determine whether fibrillogenesis utilizes a recycled pool of FN, we have used a Biotin labeled FN (FN-Biotin) recycling assay, that has been modified from a previous study. Using a combination of the recycling assay and deoxycholate fractionation methods, one can quantitatively demonstrate the extent of fibrillogenesis in cells under different experimental conditions and determine the source of FN for fibrillogenesis. |
Pinto, Bronson I; Lujan, Oscar R; Ramos, Stephan A; Propper, Catherine R; Kellar, Robert S Estrogen Mitigates the Negative Effects of Arsenic Contamination in an In Vitro Wound Model Journal Article Applied In Vitro Toxicology, 4 (1), 2018. @article{Pinto2018, title = {Estrogen Mitigates the Negative Effects of Arsenic Contamination in an In Vitro Wound Model}, author = {Bronson I Pinto and Oscar R Lujan and Stephan A Ramos and Catherine R Propper and Robert S Kellar}, url = {https://www.liebertpub.com/doi/10.1089/aivt.2017.0020}, doi = {10.1089/aivt.2017.0020}, year = {2018}, date = {2018-03-01}, journal = {Applied In Vitro Toxicology}, volume = {4}, number = {1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |