1,007 results on '"Lee, Alexandra"'
Search Results
2. Efficacy and Effectiveness of Mobile Health Technologies for Facilitating Physical Activity in Adolescents: Scoping Review
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Lee, Alexandra M, Chavez, Sarah, Bian, Jiang, Thompson, Lindsay A, Gurka, Matthew J, Williamson, Victoria G, and Modave, François
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Information technology ,T58.5-58.64 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundIncreasing physical activity (PA) levels in adolescents aged 12 to 18 years is associated with prevention of unhealthy weight gain and improvement in cardiovascular fitness. The widespread availability of mobile health (mHealth) and wearable devices offers self-monitoring and motivational features for increasing PA levels and improving adherence to exercise programs. ObjectiveThe aim of this scoping review was to identify the efficacy or effectiveness of mHealth intervention strategies for facilitating PA among adolescents aged 12 to 18 years. MethodsWe conducted a systematic search for peer-reviewed studies published between 2008 and 2018 in the following electronic databases: PubMed, Google Scholar, PsychINFO, or SportDiscus. The search terms used included mHealth or “mobile health” or apps, “physical activity” or exercise, children or adolescents or teens or “young adults” or kids, and efficacy or effectiveness. Articles published outside of the date range (July 2008 to October 2018) and non-English articles were removed before abstract review. Three reviewers assessed all abstracts against the inclusion and exclusion criteria. Any uncertainties or differences in opinion were discussed as a group. The inclusion criteria were that the studies should (1) have an mHealth component, (2) target participants aged between 12 and 18 years, (3) have results on efficacy or effectiveness, and (4) assess PA-related outcomes. Reviews, abstracts only, protocols without results, and short message service text messaging–only interventions were excluded. We also extracted potentially relevant papers from reviews. At least 2 reviewers examined all full articles for fit with the criteria and extracted data for analysis. Data extracted from selected studies included study population, study type, components of PA intervention, and PA outcome results. ResultsOverall, 126 articles were initially identified. Reviewers pulled 18 additional articles from excluded review papers. Only 18 articles were passed onto full review, and 16 were kept for analysis. The included studies differed in the sizes of the study populations (11-607 participants), locations of the study sites (7 countries), study setting, and study design. Overall, 5 mHealth intervention categories were identified: website, website+wearable, app, wearable+app, and website+wearable+app. The most common measures reported were subjective weekly PA (4/13) and objective daily moderate-to-vigorous PA (5/13) of the 19 different PA outcomes assessed. Furthermore, 5 of 13 studies with a control or comparison group showed a significant improvement in PA outcomes between the intervention group and the control or comparison group. Of those 5 studies, 3 permitted isolation of mHealth intervention components in the analysis. ConclusionsPA outcomes for adolescents improved over time through mHealth intervention use; however, the lack of consistency in chosen PA outcome measures, paucity of significant outcomes via between-group analyses, and the various study designs that prevent separating the effects of intervention components calls into question their true effect.
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- 2019
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3. Mobile Device Accuracy for Step Counting Across Age Groups
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Modave, François, Guo, Yi, Bian, Jiang, Gurka, Matthew J, Parish, Alice, Smith, Megan D, Lee, Alexandra M, and Buford, Thomas W
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Information technology ,T58.5-58.64 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundOnly one in five American meets the physical activity recommendations of the Department of Health and Human Services. The proliferation of wearable devices and smartphones for physical activity tracking has led to an increasing number of interventions designed to facilitate regular physical activity, in particular to address the obesity epidemic, but also for cardiovascular disease patients, cancer survivors, and older adults. However, the inconsistent findings pertaining to the accuracy of wearable devices for step counting needs to be addressed, as well as factors known to affect gait (and thus potentially impact accuracy) such as age, body mass index (BMI), or leading arm. ObjectiveWe aim to assess the accuracy of recent mobile devices for counting steps, across three different age groups. MethodsWe recruited 60 participants in three age groups: 18-39 years, 40-64 years, and 65-84 years, who completed two separate 1000 step walks on a treadmill at a self-selected speed between 2 and 3 miles per hour. We tested two smartphones attached on each side of the waist, and five wrist-based devices worn on both wrists (2 devices on one wrist and 3 devices on the other), as well as the Actigraph wGT3X-BT, and swapped sides between each walk. All devices were swapped dominant-to-nondominant side and vice-versa between the two 1000 step walks. The number of steps was recorded with a tally counter. Age, sex, height, weight, and dominant hand were self-reported by each participant. ResultsAmong the 60 participants, 36 were female (60%) and 54 were right-handed (90%). Median age was 53 years (min=19, max=83), median BMI was 24.1 (min=18.4, max=39.6). There was no significant difference in left- and right-hand step counts by device. Our analyses show that the Fitbit Surge significantly undercounted steps across all age groups. Samsung Gear S2 significantly undercounted steps only for participants among the 40-64 year age group. Finally, the Nexus 6P significantly undercounted steps for the group ranging from 65-84 years. ConclusionsOur analysis shows that apart from the Fitbit Surge, most of the recent mobile devices we tested do not overcount or undercount steps in the 18-39-year-old age group, however some devices undercount steps in older age groups. This finding suggests that accuracy in step counting may be an issue with some popular wearable devices, and that age may be a factor in undercounting. These results are particularly important for clinical interventions using such devices and other activity trackers, in particular to balance energy requirements with energy expenditure in the context of a weight loss intervention program.
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- 2017
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4. Hospice Quality, Race, and Disenrollment in Hospice Enrollees With Dementia
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Hunt, Lauren J, Gan, Siqi, Smith, Alexander K, Aldridge, Melissa D, Boscardin, W John, Harrison, Krista L, James, Jennifer E, Lee, Alexandra K, and Yaffe, Kristine
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Health Services and Systems ,Health Sciences ,Aging ,Health Services ,Clinical Research ,United States ,Aged ,Female ,Humans ,Aged ,80 and over ,Male ,Hospices ,Retrospective Studies ,Medicare ,Academies and Institutes ,Dementia ,Hospice Care ,dementia ,disenrollment ,health services ,hospice quality ,racial disparities ,Clinical Sciences ,Nursing ,Public Health and Health Services ,Gerontology ,Health services and systems - Abstract
Background: Racial and ethnic minoritized people with dementia (PWD) are at high risk of disenrollment from hospice, yet little is known about the relationship between hospice quality and racial disparities in disenrollment among PWD. Objective: To assess the association between race and disenrollment between and within hospice quality categories in PWD. Design/Setting/Subjects: Retrospective cohort study of 100% Medicare beneficiaries 65+ enrolled in hospice with a principal diagnosis of dementia, July 2012-December 2017. Race and ethnicity (White/Black/Hispanic/Asian and Pacific Islander [AAPI]) was assessed with the Research Triangle Institute (RTI) algorithm. Hospice quality was assessed with the publicly-available Consumer Assessment of Healthcare Providers and Systems (CAHPS) survey item on overall hospice rating, including a category for hospices exempt from public reporting (unrated). Results: The sample included 673,102 PWD (mean age 86, 66% female, 85% White, 7.3% Black, 6.3% Hispanic, 1.6% AAPI) enrolled in 4371 hospices nationwide. Likelihood of disenrollment was higher in hospices in the lowest quartile of quality ratings (vs. highest quartile) for both White (adjusted odds ratio [AOR] 1.12 [95% confidence interval 1.06-1.19]) and minoritized PWD (AOR range 1.2-1.3) and was substantially higher in unrated hospices (AOR range 1.8-2.0). Within both low- and high-quality hospices, minoritized PWD were more likely to be disenrolled compared with White PWD (AOR range 1.18-1.45). Conclusions: Hospice quality predicts disenrollment, but does not fully explain disparities in disenrollment for minoritized PWD. Efforts to improve racial equity in hospice should focus both on increasing equity in access to high-quality hospices and improving care for racial minoritized PWD in all hospices.
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- 2023
5. The Growing Role of Technology in the Care of Older Adults With Diabetes.
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Huang, Elbert, Sinclair, Alan, Conlin, Paul, Cukierman-Yaffe, Tali, Hirsch, Irl, Huisingh-Scheetz, Megan, Kahkoska, Anna, Laffel, Lori, Lee, Alexandra, Lee, Sei, Lipska, Kasia, Meneilly, Graydon, Pandya, Naushira, Peek, Monica, Peters, Anne, Pratley, Richard, Sherifali, Diana, Toschi, Elena, Umpierrez, Guillermo, Weinstock, Ruth, and Munshi, Medha
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Humans ,Aged ,Diabetes Mellitus ,Blood Glucose ,Caregivers ,Insulin Infusion Systems ,Costs and Cost Analysis - Abstract
The integration of technologies such as continuous glucose monitors, insulin pumps, and smart pens into diabetes management has the potential to support the transformation of health care services that provide a higher quality of diabetes care, lower costs and administrative burdens, and greater empowerment for people with diabetes and their caregivers. Among people with diabetes, older adults are a distinct subpopulation in terms of their clinical heterogeneity, care priorities, and technology integration. The scientific evidence and clinical experience with these technologies among older adults are growing but are still modest. In this review, we describe the current knowledge regarding the impact of technology in older adults with diabetes, identify major barriers to the use of existing and emerging technologies, describe areas of care that could be optimized by technology, and identify areas for future research to fulfill the potential promise of evidence-based technology integrated into care for this important population.
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- 2023
6. The Epidemiology of Smoking in Older Adults: A National Cohort Study.
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Hunt, Lauren, Covinsky, Kenneth, Cenzer, Irena, Espejo, Edie, Boscardin, W, Leutwyler, Heather, Lee, Alexandra, and Cataldo, Janine
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epidemiology ,geriatrics ,public health ,smoking ,Humans ,Female ,Aged ,Aged ,80 and over ,Middle Aged ,Male ,Cohort Studies ,Retrospective Studies ,Smoking Cessation ,Smokers ,Smoking - Abstract
BACKGROUND: Older smokers account for the greatest tobacco-related morbidity and mortality in the USA, while quitting smoking remains the single most effective preventive health intervention for reducing the risk of smoking-related illness. Yet, knowledge about patterns of smoking and smoking cessation in older adults is lacking. OBJECTIVE: Assess trends in prevalence of cigarette smoking between 1998 and 2018 and identify patterns and predictors of smoking cessation in US older adults. DESIGN: Retrospective cohort study PARTICIPANTS: Individuals aged 55+ enrolled in the nationally representative Health and Retirement Study, 1998-2018 MAIN MEASURES: Current smoking was assessed with the question: Do you smoke cigarettes now? Quitting smoking was defined as having at least two consecutive waves (between 2 and 4 years) in which participants who were current smokers in 1998 reported they were not currently smoking in subsequent waves. KEY RESULTS: Age-adjusted smoking prevalence decreased from 15.9% in 1998 (95% confidence interval (CI) 15.2, 16.7) to 11.2% in 2018 (95% CI 10.4, 12.1). Among 2187 current smokers in 1998 (mean age 64, 56% female), 56% of those living to age 90 had a sustained period of smoking cessation. Smoking less than 10 cigarettes/day was strongly associated with an increased likelihood of quitting smoking (subdistribution hazard ratio 2.3; 95% CI 1.9, 2.8), compared to those who smoked more than 20 cigarettes/day. CONCLUSIONS: Smoking prevalence among older persons has declined and substantial numbers of older smokers succeed in quitting smoking for a sustained period. These findings highlight the need for continued aggressive efforts at tobacco cessation among older persons.
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- 2023
7. New psychotropic medication use among Medicare beneficiaries with dementia after hospital discharge.
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Growdon, Matthew E, Gan, Siqi, Yaffe, Kristine, Lee, Alexandra K, Anderson, Timothy S, Muench, Ulrike, Boscardin, W John, and Steinman, Michael A
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Humans ,Dementia ,Anticonvulsants ,Hypnotics and Sedatives ,Antipsychotic Agents ,Psychotropic Drugs ,Antidepressive Agents ,Patient Discharge ,Retrospective Studies ,Aged ,Aged ,80 and over ,Hospitals ,Medicare ,United States ,Female ,Male ,dementia ,hospitalization ,prescribing ,psychotropics ,Aging ,Clinical Research ,Acquired Cognitive Impairment ,Brain Disorders ,Mental Health ,Neurosciences ,Medical and Health Sciences ,Geriatrics - Abstract
BackgroundHospitalizations among people with dementia (PWD) may precipitate behavioral changes, leading to the psychotropic medication use despite adverse outcomes and limited efficacy. We sought to determine the incidence of new psychotropic medication use among community-dwelling PWD after hospital discharge and, among new users, the proportion with prolonged use.MethodsThis was a retrospective cohort study using a 20% random sample of Medicare claims in 2017, including hospitalized PWD with traditional and Part D Medicare who were 68 years or older. The primary outcome was incident prescribing at discharge of psychotropics including antipsychotics, sedative-hypnotics, antiepileptics, and antidepressants. This was defined as new prescription fills (i.e., from classes not used in 180 days preadmission) within 7 days of hospital or skilled nursing facility discharge. Prolonged use was defined as the proportion of new users who continued to fill newly prescribed medications beyond 90 days of discharge.ResultsThe cohort included 117,022 hospitalized PWD with a mean age of 81 years; 63% were female. Preadmission, 63% were using at least 1 psychotropic medication; 10% were using medications from ≥3 psychotropic classes. These included antidepressants (44% preadmission), antiepileptics (29%), sedative-hypnotics (21%), and antipsychotics (11%). The proportion of PWD discharged from the hospital with new psychotropics ranged from 1.9% (antipsychotics) to 2.9% (antiepileptics); 6.6% had at least one new class started. Among new users, prolonged use ranged from 36% (sedative-hypnotics) to 63% (antidepressants); across drug classes, prolonged use occurred in 51%. Predictors of newly initiated psychotropics included length of stay (≥median vs. ConclusionsHospitalized PWD have a high prevalence of preadmission psychotropic medication use; against this baseline, discharge from the hospital with new psychotropics is relatively uncommon. Nevertheless, prolonged use of newly initiated psychotropics occurs in a substantial proportion of this population.
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- 2023
8. The Coming of Age of Nucleic Acid Vaccines during COVID-19
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Rando, Halie M., Lordan, Ronan, Kolla, Likhitha, Sell, Elizabeth, Lee, Alexandra J., Wellhausen, Nils, Naik, Amruta, Kamil, Jeremy P., Consortium, COVID-19 Review, Gitter, Anthony, and Greene, Casey S.
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Quantitative Biology - Biomolecules - Abstract
In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing SARS-CoV-2 pandemic has made the importance of such efforts especially clear. New biotechnological advances in vaccinology allow for recent advances that provide only the nucleic acid building blocks of an antigen, eliminating many safety concerns. During the COVID-19 pandemic, these DNA and RNA vaccines have facilitated the development and deployment of vaccines at an unprecedented pace. This success was attributable at least in part to broader shifts in scientific research relative to prior epidemics; the genome of SARS-CoV-2 was available as early as January 2020, facilitating global efforts in the development of DNA and RNA vaccines within two weeks of the international community becoming aware of the new viral threat. Additionally, these technologies that were previously only theoretical are not only safe but also highly efficacious. Although historically a slow process, the rapid development of vaccines during the COVID-19 crisis reveals a major shift in vaccine technologies. Here, we provide historical context for the emergence of these paradigm-shifting vaccines. We describe several DNA and RNA vaccines and in terms of their efficacy, safety, and approval status. We also discuss patterns in worldwide distribution. The advances made since early 2020 provide an exceptional illustration of how rapidly vaccine development technology has advanced in the last two decades in particular and suggest a new era in vaccines against emerging pathogens.
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- 2022
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9. Glucagon-like peptide-1 receptor agonists reverse nerve morphological abnormalities in diabetic peripheral neuropathy
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Dhanapalaratnam, Roshan, Issar, Tushar, Lee, Alexandra T. K., Poynten, Ann M., Milner, Kerry-Lee, Kwai, Natalie C. G., and Krishnan, Arun V.
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- 2024
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10. Application of Traditional Vaccine Development Strategies to SARS-CoV-2
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Rando, Halie M., Lordan, Ronan, Lee, Alexandra J., Naik, Amruta, Wellhausen, Nils, Sell, Elizabeth, Kolla, Likhitha, Consortium, COVID-19 Review, Gitter, Anthony, and Greene, Casey S.
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Quantitative Biology - Other Quantitative Biology - Abstract
Over the past 150 years, vaccines have revolutionized the relationship between people and disease. During the COVID-19 pandemic, technologies such as mRNA vaccines have received attention due to their novelty and successes. However, more traditional vaccine development platforms have also yielded important tools in the worldwide fight against the SARS-CoV-2 virus. A variety of approaches have been used to develop COVID-19 vaccines that are now authorized for use in countries around the world. In this review, we highlight strategies that focus on the viral capsid and outwards, rather than on the nucleic acids inside. These approaches fall into two broad categories: whole-virus vaccines and subunit vaccines. Whole-virus vaccines use the virus itself, either in an inactivated or attenuated state. Subunit vaccines contain instead an isolated, immunogenic component of the virus. Here, we highlight vaccine candidates that apply these approaches against SARS-CoV-2 in different ways. In a companion manuscript, we review the more recent and novel development of nucleic-acid based vaccine technologies. We further consider the role that these COVID-19 vaccine development programs have played in prophylaxis at the global scale. Well-established vaccine technologies have proved especially important to making vaccines accessible in low- and middle-income countries. Vaccine development programs that use established platforms have been undertaken in a much wider range of countries than those using nucleic-acid-based technologies, which have been led by wealthy Western countries. Therefore, these vaccine platforms, though less novel from a biotechnological standpoint, have proven to be extremely important to the management of SARS-CoV-2.
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- 2022
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11. Severe hypoglycemia and falls in older adults with diabetes: The Diabetes & Aging Study.
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Moffet, Howard, Huang, Elbert, Liu, Jennifer, Parker, Melissa, Lipska, Kasia, Laiteerapong, Neda, Grant, Richard, Lee, Alexandra, and Karter, Andrew
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aging ,diabetes mellitus ,falls ,patient-reported outcomes ,survey - Abstract
OBJECTIVE: To estimate rates of severe hypoglycemia and falls among older adults with diabetes and evaluate their association. RESEARCH DESIGN AND METHODS: Survey in an age-stratified, random sample adults with diabetes age 65-100 years; respondents were asked about severe hypoglycemia (requiring assistance) and falls in the past 12 months. Prevalence ratios (adjusted for age, sex, race/ethnicity) estimated the increased risk of falls associated with severe hypoglycemia. RESULTS: Among 2,158 survey respondents, 79 (3.7%) reported severe hypoglycemia, of whom 68 (86.1%) had no ED visit or hospitalization for hypoglycemia. Falls were reported by 847 (39.2%), of whom 745 (88.0%) had no fall documented in outpatient or inpatient records. Severe hypoglycemia was associated with a 70% greater prevalence of falls (adjusted prevalence ratio = 1.7 (95% CI, 1.3-2.2)). CONCLUSION: While clinical documentation of events likely reflects severity or care-seeking behavior, severe hypoglycemia and falls are common, under-reported life-threatening events.
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- 2023
12. Exploring the Relations of Academic Self-Handicapping with Achievement Goals among Urban, Underrepresented Minority, Middle School Students
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Lee, Alexandra A., Fleck, Bethany, and Richmond, Aaron S.
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There is a need to investigate motivational constructs for students traditionally underrepresented in educational research. In this study, we measured academic self-handicapping behavior, achievement goal orientations, and achievement in math and literacy in 327 urban, middle school students. Moderated mediation regression analyses were conducted to examine whether the relation of prior achievement with self-handicapping behavior was explained by achievement goals and whether these relations depended on underrepresented minority student status (URM). It was found that URM status moderated the relation of achievement with self-handicapping and that performance goals explained these relations in literacy, but not in math. Educational systems might consider these findings as a starting point for interventions to decrease self-handicapping behavior to support URM students' academic motivation.
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- 2021
13. Do functional status and Medicare claims data improve the predictive accuracy of an electronic health record mortality index? Findings from a national Veterans Affairs cohort
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Deardorff, William James, Jing, Bocheng, Jeon, Sun Y, Boscardin, W John, Lee, Alexandra K, Fung, Kathy Z, and Lee, Sei J
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Health Services and Systems ,Health Sciences ,Aging ,Patient Safety ,Prevention ,Clinical Research ,Networking and Information Technology R&D (NITRD) ,Health Services ,Good Health and Well Being ,Activities of Daily Living ,Aged ,Aged ,80 and over ,Cohort Studies ,Electronic Health Records ,Female ,Functional Status ,Humans ,Male ,Medicare ,Retrospective Studies ,United States ,United States Department of Veterans Affairs ,Veterans ,Functional status ,Physical function ,Medicare data ,Mortality prediction model ,Clinical Sciences ,Human Movement and Sports Sciences ,Geriatrics ,Clinical sciences ,Health services and systems ,Public health - Abstract
BackgroundElectronic health record (EHR) prediction models may be easier to use in busy clinical settings since EHR data can be auto-populated into models. This study assessed whether adding functional status and/or Medicare claims data (which are often not available in EHRs) improves the accuracy of a previously developed Veterans Affairs (VA) EHR-based mortality index.MethodsThis was a retrospective cohort study of veterans aged 75 years and older enrolled in VA primary care clinics followed from January 2014 to April 2020 (n = 62,014). We randomly split participants into development (n = 49,612) and validation (n = 12,402) cohorts. The primary outcome was all-cause mortality. We performed logistic regression with backward stepwise selection to develop a 100-predictor base model using 854 EHR candidate variables, including demographics, laboratory values, medications, healthcare utilization, diagnosis codes, and vitals. We incorporated functional measures in a base + function model by adding activities of daily living (range 0-5) and instrumental activities of daily living (range 0-7) scores. Medicare data, including healthcare utilization (e.g., emergency department visits, hospitalizations) and diagnosis codes, were incorporated in a base + Medicare model. A base + function + Medicare model included all data elements. We assessed model performance with the c-statistic, reclassification metrics, fraction of new information provided, and calibration plots.ResultsIn the overall cohort, mean age was 82.6 years and 98.6% were male. At the end of follow-up, 30,263 participants (48.8%) had died. The base model c-statistic was 0.809 (95% CI 0.805-0.812) in the development cohort and 0.804 (95% CI 0.796-0.812) in the validation cohort. Validation cohort c-statistics for the base + function, base + Medicare, and base + function + Medicare models were 0.809 (95% CI 0.801-0.816), 0.811 (95% CI 0.803-0.818), and 0.814 (95% CI 0.807-0.822), respectively. Adding functional status and Medicare data resulted in similarly small improvements among other model performance measures. All models showed excellent calibration.ConclusionsIncorporation of functional status and Medicare data into a VA EHR-based mortality index led to small but likely clinically insignificant improvements in model performance.
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- 2022
14. Fingerstick glucose monitoring by cognitive impairment status in Veterans Affairs nursing home residents with diabetes.
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Nguyen, Brian, Deardorff, William, Jing, Bocheng, Lee, Sei, Shi, Ying, and Lee, Alexandra
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cognitive impairment ,dementia ,diabetes ,fingerstick ,nursing home ,Humans ,Aged ,Nursing Homes ,Blood Glucose ,Veterans ,Blood Glucose Self-Monitoring ,Diabetes Mellitus ,Metformin ,Cognitive Dysfunction - Abstract
BACKGROUND: Guidelines recommend nursing home (NH) residents with cognitive impairment receive less intensive glycemic treatment and less frequent fingerstick monitoring. Our objective was to determine whether current practice aligns with guideline recommendations by examining fingerstick frequency in Veterans Affairs (VA) NH residents with diabetes across cognitive impairment levels. METHODS: We identified VA NH residents with diabetes aged ≥65 residing in VA NHs for >30 days between 2016 and 2019. Residents were grouped by cognitive impairment status based on the Cognitive Function Scale: cognitively intact, mild impairment, moderate impairment, and severe impairment. We also categorized residents into mutually exclusive glucose-lowering medication (GLM) categories: (1) no GLMs, (2) metformin only, (3) sulfonylureas/other GLMs (+/- metformin but no insulin), (4) long-acting insulin (+/- oral/other GLMs but no short-acting insulin), and (5) any short-acting insulin. Our outcome was mean daily fingersticks on day 31 of NH admission. RESULTS: Among 13,637 NH residents, mean age was 75 years and mean hemoglobin A1c was 7.0%. The percentage of NH residents on short-acting insulin varied by cognitive status from 22.7% in residents with severe cognitive impairment to 33.9% in residents who were cognitively intact. Mean daily fingersticks overall on day 31 was 1.50 (standard deviation = 1.73). There was a greater range in mean fingersticks across GLM categories compared to cognitive status. Fingersticks ranged widely across GLM categories from 0.39 per day (no GLMs) to 3.08 (short-acting insulin), while fingersticks ranged slightly across levels of cognitive impairment from 1.11 (severe cognitive impairment) to 1.59 (cognitively intact). CONCLUSION: NH residents receive frequent fingersticks regardless of level of cognitive impairment, suggesting that cognitive status is a minor consideration in monitoring decisions. Future studies should determine whether decreasing fingersticks in NH residents with moderate/severe cognitive impairment can reduce burdens without compromising safety.
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- 2022
15. A comprehensive prognostic tool for older adults: Predicting death, ADL disability, and walking disability simultaneously.
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Diaz-Ramirez, L, Boscardin, W, Lee, Sei, Smith, Alexander, and Lee, Alexandra
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disability ,mortality ,prediction ,Activities of Daily Living ,Aged ,Disability Evaluation ,Disabled Persons ,Humans ,Independent Living ,Prognosis ,Walking - Abstract
BACKGROUND: Many clinical and financial decisions for older adults depend on the future risk of disability and mortality. Prognostic tools for long-term disability risk in a general population are lacking. We aimed to create a comprehensive prognostic tool that predicts the risk of mortality, of activities of daily living (ADL) disability, and walking disability simultaneously using the same set of variables. METHODS: We conducted a longitudinal analysis of the nationally-representative Health and Retirement Study (HRS). We included community-dwelling adults aged ≥70 years who completed a core interview in the 2000 wave of HRS, with follow-up through 2018. We evaluated 40 predictors encompassing demographics, diseases, physical functioning, and instrumental ADLs. We applied novel methods to optimize three models simultaneously while prioritizing variables that take less time to ascertain during backward stepwise elimination. The death prediction model used Cox regression and both the models for walking disability and for ADL disability used Fine and Gray competing-risk regression. We examined calibration plots and generated optimism-corrected statistics of discrimination using bootstrapping. To simulate unavailable patient data, we also evaluated models excluding one or two variables from the final model. RESULTS: In 6646 HRS participants, 2662 developed walking disability, 3570 developed ADL disability, and 5689 died during a median follow-up of 9.5 years. The final prognostic tool had 16 variables. The optimism-corrected integrated area under the curve (iAUC) was 0.799 for mortality, 0.685 for walking disability, and 0.703 for ADL disability. At each percentile of predicted mortality risk, there was a substantial spread in the predicted risks of walking disability and ADL disability. Discrimination and calibration remained good even when missing one or two predictors from the model. This model is now available on ePrognosis (https://eprognosis.ucsf.edu/alexlee.php) CONCLUSIONS: Given the variability in disability risk for people with similar mortality risks, using individualized risks of disabilities may inform clinical and financial decisions for older adults.
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- 2022
16. Do performance goals and fixed mindset explicate the relations between stereotype threat and achievement? Examining differences between racially marginalized and White students in STEM
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Lee, Alexandra A., Totonchi, Delaram A., Priniski, Stacy J., Lee, Minhye, Perez, Tony, and Linnenbrink-Garcia, Lisa
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- 2024
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17. Using genome-wide expression compendia to study microorganisms
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Lee, Alexandra J., Reiter, Taylor, Doing, Georgia, Oh, Julia, Hogan, Deborah A., and Greene, Casey S.
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Quantitative Biology - Quantitative Methods - Abstract
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity for gaining a systems level understanding of the transcriptional responses that influence phenotypes. Variety in experimental design is particularly important for studying microbes, where the transcriptional responses integrate many signals and demonstrate plasticity across strains including response to what nutrients are available and what microbes are present. Advances in high-throughput measurement technology have made it feasible to construct compendia for many microbes. In this review we discuss how these compendia are constructed and analyzed to reveal transcriptional patterns.
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- 2022
18. Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post–COVID-19 syndrome
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Jia, Xiaolin, Cao, Shu, Lee, Alexandra S, Manohar, Monali, Sindher, Sayantani B, Ahuja, Neera, Artandi, Maja, Blish, Catherine A, Blomkalns, Andra L, Chang, Iris, Collins, William J, Desai, Manisha, Din, Hena Naz, Do, Evan, Fernandes, Andrea, Geng, Linda N, Rosenberg-Hasson, Yael, Mahoney, Megan Ruth, Glascock, Abigail L, Chan, Lienna Y, Fong, Sharon Y, Consortium, CLIAHUB, Biohub, Chan Zuckerberg, Phelps, Maira, Raeber, Olivia, Group, Stanford COVID-19 Biobank Study, Purington, Natasha, Röltgen, Katharina, Rogers, Angela J, Snow, Theo, Wang, Taia T, Solis, Daniel, Vaughan, Laura, Verghese, Michelle, Maecker, Holden, Wittman, Richard, Puri, Rajan, Kistler, Amy, Yang, Samuel, Boyd, Scott D, Pinsky, Benjamin A, Chinthrajah, Sharon, and Nadeau, Kari C
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Biomedical and Clinical Sciences ,Clinical Sciences ,Prevention ,Lung ,Clinical Research ,Infectious Diseases ,Good Health and Well Being ,COVID-19 ,Humans ,Immunoglobulin G ,SARS-CoV-2 ,Post-Acute COVID-19 Syndrome ,CLIAHUB Consortium ,Chan Zuckerberg Biohub ,Stanford COVID-19 Biobank Study Group ,Immunoglobulins ,Infectious disease ,Biomedical and clinical sciences ,Health sciences - Abstract
BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points that remain elusive.METHODSAdult SARS-CoV-2 reverse transcription PCR-positive (RT-PCR-positive) patients were recruited at Stanford from March 2020 to February 2021. Study participants were seen for in-person visits at diagnosis and every 1-3 months for up to 1 year after diagnosis; they completed symptom surveys and underwent blood draws and nasal swab collections at each visit.RESULTSOur cohort (n = 617) ranged from asymptomatic to critical COVID-19 infections. In total, 40% of participants reported at least 1 symptom associated with COVID-19 six months after diagnosis. Median time from diagnosis to first resolution of all symptoms was 44 days; median time from diagnosis to sustained symptom resolution with no recurring symptoms for 1 month or longer was 214 days. Anti-nucleocapsid IgG level in the first week after positive RT-PCR test and history of lung disease were associated with time to sustained symptom resolution. COVID-19 disease severity, ethnicity, age, sex, and remdesivir use did not affect time to sustained symptom resolution.CONCLUSIONWe found that all disease severities had a similar risk of developing post-COVID-19 syndrome in an ethnically diverse population. Comorbid lung disease and lower levels of initial IgG response to SARS-CoV-2 nucleocapsid antigen were associated with longer symptom duration.TRIAL REGISTRATIONClinicalTrials.gov, NCT04373148.FUNDINGNIH UL1TR003142 CTSA grant, NIH U54CA260517 grant, NIEHS R21 ES03304901, Sean N Parker Center for Allergy and Asthma Research at Stanford University, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative, Sunshine Foundation, Crown Foundation, and Parker Foundation.
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- 2022
19. A Mixed-Methods Exploration of Mastery Goal Support in 7th-Grade Science Classrooms
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Liu, Pei Pei, McKinney, David, Lee, Alexandra A., Schmidt, Jennifer A., Marchand, Gwen C., and Linnenbrink-Garcia, Lisa
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Mastery goal structures, which communicate value for developing deeper understanding, are an important classroom support for student motivation and engagement, especially in the context of science learning aligned with the Next Generation Science Standards. Prior research has identified key dimensions of goal structures, but a more nuanced examination of the variability of teacher-enacted and student-perceived goal structures within and across classrooms is needed. Using a concurrent mixed-methods approach, we developed case studies of how three 7th-grade science teachers enacted different goal structures while teaching the same chemistry unit and how their students perceived these goal structures. Student perceptions were largely consistent with our observational analysis and suggested that a positive social climate and autonomy support are important elements of mastery goal structure. However, balancing socio-emotional support with sufficient academic rigor may be especially important for students with high levels of mastery goal orientation and self-efficacy in science. Implications for research include the need for further research linking classroom stimuli to variability in perceived goal structure, especially across students with different motivational characteristics. Implications for practice include strategies for science teachers to promote perceptions of a mastery goal focus in students, particularly through feedback and recognition practices.
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- 2023
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20. Communally Engaged Educational Psychology: A Philosophy of Engagement
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Gray, DeLeon L., Lee, Alexandra A., Harris-Thomas, Brooke, Ali, Joanna N., and Allah, Kia J.
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In this article, we provide guidance for educational psychologists who want to advance equity-focused school policies and practices through engaged scholarship. We conceptualize a philosophy of engagement and describe how it can facilitate psychologists' efforts to address the social conditions of people from historically marginalized communities. Using our own philosophy of engagement as a case in point (which we refer to as communally engaged educational psychology), we share stories that showcase opportunities for roles that scholars can play in supporting education decision-makers and community members. Specifically, we illustrate that communal engagement involves building a tribe; identifying pockets of affirmation; establishing communal incubators; and leveraging existing networks to disseminate stories emerging from partnership activities. We then offer a roadmap for putting communal engagement into action by remixing Anderman's (2011) ten challenges for educational psychologists. We conclude with a discussion of the tensions and difficulties scholars may need to navigate when enacting a philosophy of engagement.
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- 2023
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21. Structural basis of homodimerization of the JNK scaffold protein JIP2 and its heterodimerization with JIP1
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Mariño Pérez, Laura, Ielasi, Francesco S., Lee, Alexandra, Delaforge, Elise, Juyoux, Pauline, Tengo, Maud, Davis, Roger J., Palencia, Andrés, and Jensen, Malene Ringkjøbing
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- 2024
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22. Propensity weighted analysis of chemical venous thromboembolism prophylaxis agents in isolated severe traumatic brain injury: An EAST sponsored multicenter study
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Ratnasekera, Asanthi M., Seng, Sirivan S., Kim, Daniel, Ji, Wenyan, Jacovides, Christina L., Kaufman, Elinore J., Sadek, Hannah M., Perea, Lindsey L., Poloni, Christina Monaco, Shnaydman, Ilya, Lee, Alexandra Jeongyoon, Sharp, Victoria, Miciura, Angela, Trevizo, Eric, Rosenthal, Martin G., Lottenberg, Lawrence, Zhao, William, Keininger, Alicia, Hunt, Michele, Cull, John, Balentine, Chassidy, Egodage, Tanya, Mohamed, Aleem T., Kincaid, Michelle, Doris, Stephanie, Cotterman, Robert, Seegert, Sara, Jacobson, Lewis E., Williams, Jamie, Moncrief, Melissa, Palmer, Brandi, Mentzer, Caleb, Tackett, Nichole, Hranjec, Tjasa, Dougherty, Thomas, Morrissey, Shawna, Donatelli-Seyler, Lauren, Rushing, Amy, Tatebe, Leah C., Nevill, Tiffany J., Aboutanos, Michel B., Hamilton, David, Redmond, Diane, Cullinane, Daniel C., Falank, Carolyne, McMellen, Mark, Duran, Chris, Daniels, Jennifer, Ballow, Shana, Schuster, Kevin M., and Ferrada, Paula
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- 2024
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23. The humanitarian architect
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Lee, Alexandra and Barrie, Andrew
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- 2011
24. Predicting Life Expectancy to Target Cancer Screening Using Electronic Health Record Clinical Data
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Lee, Alexandra K, Jing, Bocheng, Jeon, Sun Y, Boscardin, W John, and Lee, Sei J
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Health Services and Systems ,Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Health Services ,Patient Safety ,Breast Cancer ,Prevention ,Digestive Diseases ,Colo-Rectal Cancer ,Clinical Research ,Aging ,Cancer ,Good Health and Well Being ,Aged ,Colorectal Neoplasms ,Early Detection of Cancer ,Electronic Health Records ,Female ,Humans ,Life Expectancy ,Male ,Middle Aged ,Retrospective Studies ,Clinical Sciences ,General & Internal Medicine ,Clinical sciences ,Health services and systems ,Public health - Abstract
BackgroundGuidelines recommend breast and colorectal cancer screening for older adults with a life expectancy >10 years. Most mortality indexes require clinician data entry, presenting a barrier for routine use in care. Electronic health records (EHR) are a rich clinical data source that could be used to create individualized life expectancy predictions to identify patients for cancer screening without data entry.ObjectiveTo develop and internally validate a life expectancy calculator from structured EHR data.DesignRetrospective cohort study using national Veteran's Affairs (VA) EHR databases.PatientsVeterans aged 50+ with a primary care visit during 2005.Main measuresWe assessed demographics, diseases, medications, laboratory results, healthcare utilization, and vital signs 1 year prior to the index visit. Mortality follow-up was complete through 2017. Using the development cohort (80% sample), we used LASSO Cox regression to select ~100 predictors from 913 EHR data elements. In the validation cohort (remaining 20% sample), we calculated the integrated area under the curve (iAUC) and evaluated calibration.Key resultsIn 3,705,122 patients, the mean age was 68 years and the majority were male (97%) and white (85%); nearly half (49%) died. The life expectancy calculator included 93 predictors; age and gender most strongly contributed to discrimination; diseases also contributed significantly while vital signs were negligible. The iAUC was 0.816 (95% confidence interval, 0.815, 0.817) with good calibration.ConclusionsWe developed a life expectancy calculator using VA EHR data with excellent discrimination and calibration. Automated life expectancy prediction using EHR data may improve guideline-concordant breast and colorectal cancer screening by identifying patients with a life expectancy >10 years.
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- 2022
25. SARS-CoV-2 RNAemia predicts clinical deterioration and extrapulmonary complications from COVID-19
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Ram-Mohan, Nikhil, Kim, David, Zudock, Elizabeth J, Hashemi, Marjan M, Tjandra, Kristel C, Rogers, Angela J, Blish, Catherine A, Nadeau, Kari C, Newberry, Jennifer A, Quinn, James V, O’Hara, Ruth, Ashley, Euan, Nguyen, Hien, Jiang, Lingxia, Hung, Paul, Blomkalns, Andra L, Yang, Samuel, Mann, Rosen, Visweswaran, Anita, Ranganath, Thanmayi, Roque, Jonasel, Manohar, Monali, Din, Hena Naz, Kumar, Komal, Jee, Kathryn, Noon, Brigit, Anderson, Jill, Fay, Bethany, Schreiber, Donald, Zhao, Nancy, Vergara, Rosemary, McKechnie, Julia, Wilk, Aaron, de la Parte, Lauren, Dantzler, Kathleen Whittle, Ty, Maureen, Kathale, Nimish, Rustagi, Arjun, Martinez-Colon, Giovanny, Ivison, Geoff, Pi, Ruoxi, Lee, Maddie, Brewer, Rachel, Hollis, Taylor, Baird, Andrea, Ugur, Michele, Bogusch, Drina, Nahass, George R, Haider, Kazim, Tran, Kim Quyen Thi, Simpson, Laura, Tal, Michal, Chang, Iris, Do, Evan, Fernandes, Andrea, Lee, Alexandra S, Ahuja, Neera, Snow, Theo, and Krempski, James
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Biomedical and Clinical Sciences ,Clinical Sciences ,Lung ,Pneumonia ,Infectious Diseases ,Emerging Infectious Diseases ,Clinical Research ,4.1 Discovery and preclinical testing of markers and technologies ,Detection ,screening and diagnosis ,Good Health and Well Being ,Stanford COVID-19 Biobank Study Group ,RNAemia ,SARS-CoV-2 ,digital PCR ,extrapulmonary complications ,severity prediction ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundThe determinants of coronavirus disease 2019 (COVID-19) disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterized relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNAemia and disease severity, clinical deterioration, and specific EPCs.MethodsWe used quantitative and digital polymerase chain reaction (qPCR and dPCR) to quantify SARS-CoV-2 RNA from plasma in 191 patients presenting to the emergency department with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterized the role of RNAemia in predicting clinical severity and EPCs using elastic net regression.ResultsOf SARS-CoV-2-positive patients, 23.0% (44 of 191) had viral RNA detected in plasma by dPCR, compared with 1.4% (2 of 147) by qPCR. Most patients with serial measurements had undetectable RNAemia within 10 days of symptom onset, reached maximum clinical severity within 16 days, and symptom resolution within 33 days. Initially RNAemic patients were more likely to manifest severe disease (odds ratio, 6.72 [95% confidence interval, 2.45-19.79]), worsening of disease severity (2.43 [1.07-5.38]), and EPCs (2.81 [1.26-6.36]). RNA loads were correlated with maximum severity (r = 0.47 [95% confidence interval, .20-.67]).ConclusionsdPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Because many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.
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- 2022
26. Ten Quick Tips for Deep Learning in Biology
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Lee, Benjamin D., Gitter, Anthony, Greene, Casey S., Raschka, Sebastian, Maguire, Finlay, Titus, Alexander J., Kessler, Michael D., Lee, Alexandra J., Chevrette, Marc G., Stewart, Paul Allen, Britto-Borges, Thiago, Cofer, Evan M., Yu, Kun-Hsing, Carmona, Juan Jose, Fertig, Elana J., Kalinin, Alexandr A., Signal, Beth, Lengerich, Benjamin J., Triche Jr, Timothy J., and Boca, Simina M.
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Quantitative Biology - Other Quantitative Biology ,Computer Science - Machine Learning - Abstract
Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others., Comment: 23 pages, 2 figures
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- 2021
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27. Approximate Bayesian Computation for an Explicit-Duration Hidden Markov Model of COVID-19 Hospital Trajectories
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Visani, Gian Marco, Lee, Alexandra Hope, Nguyen, Cuong, Kent, David M., Wong, John B., Cohen, Joshua T., and Hughes, Michael C.
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Statistics - Applications ,Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
We address the problem of modeling constrained hospital resources in the midst of the COVID-19 pandemic in order to inform decision-makers of future demand and assess the societal value of possible interventions. For broad applicability, we focus on the common yet challenging scenario where patient-level data for a region of interest are not available. Instead, given daily admissions counts, we model aggregated counts of observed resource use, such as the number of patients in the general ward, in the intensive care unit, or on a ventilator. In order to explain how individual patient trajectories produce these counts, we propose an aggregate count explicit-duration hidden Markov model, nicknamed the ACED-HMM, with an interpretable, compact parameterization. We develop an Approximate Bayesian Computation approach that draws samples from the posterior distribution over the model's transition and duration parameters given aggregate counts from a specific location, thus adapting the model to a region or individual hospital site of interest. Samples from this posterior can then be used to produce future forecasts of any counts of interest. Using data from the United States and the United Kingdom, we show our mechanistic approach provides competitive probabilistic forecasts for the future even as the dynamics of the pandemic shift. Furthermore, we show how our model provides insight about recovery probabilities or length of stay distributions, and we suggest its potential to answer challenging what-if questions about the societal value of possible interventions., Comment: To appear in the Proceedings of the Machine Learning for Healthcare (MLHC) conference, 2021. 20 pages, 7 figures and 1 table. 26 additional pages of supplementary material
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- 2021
28. Forecasting COVID-19 Counts At A Single Hospital: A Hierarchical Bayesian Approach
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Lee, Alexandra Hope, Lymperopoulos, Panagiotis, Cohen, Joshua T., Wong, John B., and Hughes, Michael C.
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
We consider the problem of forecasting the daily number of hospitalized COVID-19 patients at a single hospital site, in order to help administrators with logistics and planning. We develop several candidate hierarchical Bayesian models which directly capture the count nature of data via a generalized Poisson likelihood, model time-series dependencies via autoregressive and Gaussian process latent processes, and share statistical strength across related sites. We demonstrate our approach on public datasets for 8 hospitals in Massachusetts, U.S.A. and 10 hospitals in the United Kingdom. Further prospective evaluation compares our approach favorably to baselines currently used by stakeholders at 3 related hospitals to forecast 2-week-ahead demand by rescaling state-level forecasts., Comment: In ICLR 2021 Workshop on Machine Learning for Preventing and Combating Pandemics
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- 2021
29. Identification and Development of Therapeutics for COVID-19
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Rando, Halie M., Wellhausen, Nils, Ghosh, Soumita, Lee, Alexandra J., Dattoli, Anna Ada, Hu, Fengling, Byrd, James Brian, Rafizadeh, Diane N., Lordan, Ronan, Qi, Yanjun, Sun, Yuchen, Brueffer, Christian, Field, Jeffrey M., Guebila, Marouen Ben, Jadavji, Nafisa M., Skelly, Ashwin N., Ramsundar, Bharath, Wang, Jinhui, Goel, Rishi Raj, Park, YoSon, Consortium, the COVID-19 Review, Boca, Simina M., Gitter, Anthony, and Greene, Casey S.
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Quantitative Biology - Quantitative Methods - Abstract
After emerging in China in late 2019, the novel Severe acute respiratory syndrome-like coronavirus 2 (SARS-CoV-2) spread worldwide and as of early 2021, continues to significantly impact most countries. Only a small number of coronaviruses are known to infect humans, and only two are associated with the severe outcomes associated with SARS-CoV-2: Severe acute respiratory syndrome-related coronavirus, a closely related species of SARS-CoV-2 that emerged in 2002, and Middle East respiratory syndrome-related coronavirus, which emerged in 2012. Both of these previous epidemics were controlled fairly rapidly through public health measures, and no vaccines or robust therapeutic interventions were identified. However, previous insights into the immune response to coronaviruses gained during the outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) have proved beneficial to identifying approaches to the treatment and prophylaxis of novel coronavirus disease 2019 (COVID-19). A number of potential therapeutics against SARS-CoV-2 and the resultant COVID-19 illness were rapidly identified, leading to a large number of clinical trials investigating a variety of possible therapeutic approaches being initiated early on in the pandemic. As a result, a small number of therapeutics have already been authorized by regulatory agencies such as the Food and Drug Administration (FDA) in the United States, and many other therapeutics remain under investigation. Here, we describe a range of approaches for the treatment of COVID-19, along with their proposed mechanisms of action and the current status of clinical investigation into each candidate. The status of these investigations will continue to evolve, and this review will be updated as progress is made.
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- 2021
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30. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
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Rando, Halie M., MacLean, Adam L., Lee, Alexandra J., Lordan, Ronan, Ray, Sandipan, Bansal, Vikas, Skelly, Ashwin N., Sell, Elizabeth, Dziak, John J., Shinholster, Lamonica, McGowan, Lucy D'Agostino, Guebila, Marouen Ben, Wellhausen, Nils, Knyazev, Sergey, Boca, Simina M., Capone, Stephen, Qi, Yanjun, Park, YoSon, Sun, Yuchen, Mai, David, Boerckel, Joel D., Brueffer, Christian, Byrd, James Brian, Kamil, Jeremy P., Wang, Jinhui, Velazquez, Ryan, Szeto, Gregory L, Barton, John P., Goel, Rishi Raj, Mangul, Serghei, Lubiana, Tiago, Consortium, COVID-19 Review, Gitter, Anthony, and Greene, Casey S.
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Quantitative Biology - Quantitative Methods - Abstract
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.
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- 2021
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31. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.
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Rando, Halie M, MacLean, Adam L, Lee, Alexandra J, Lordan, Ronan, Ray, Sandipan, Bansal, Vikas, Skelly, Ashwin N, Sell, Elizabeth, Dziak, John J, Shinholster, Lamonica, McGowan, Lucy D'Agostino, Guebila, Marouen Ben, Wellhausen, Nils, Knyazev, Sergey, Boca, Simina M, Capone, Stephen, Qi, Yanjun, Park, YoSon, Sun, Yuchen, Mai, David, Boerckel, Joel D, Brueffer, Christian, Byrd, James Brian, Kamil, Jeremy P, Wang, Jinhui, Velazquez, Ryan, Szeto, Gregory L, Barton, John P, Goel, Rishi Raj, Mangul, Serghei, Lubiana, Tiago, Consortium, Covid-Review, Gitter, Anthony, and Greene, Casey S
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Vaccine Related ,Pneumonia ,Lung ,Infectious Diseases ,Emerging Infectious Diseases ,Prevention ,Pneumonia & Influenza ,Biotechnology ,Biodefense ,2.2 Factors relating to the physical environment ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being ,COVID-19 ,genomics ,review ,viral pathogenesis ,COVID-19 Review Consortium Vikas Bansal ,John P. Barton ,Simina M. Boca ,Joel D. Boerckel ,Christian Brueffer ,James Brian Byrd ,Stephen Capone ,Shikta Das ,Anna Ada Dattoli ,John J. Dziak ,Jeffrey M. Field ,Soumita Ghosh ,Anthony Gitter ,Rishi Raj Goel ,Casey S. Greene ,Marouen Ben Guebila ,Daniel S. Himmelstein ,Fengling Hu ,Nafisa M. Jadavji ,Jeremy P. Kamil ,Sergey Knyazev ,Likhitha Kolla ,Alexandra J. Lee ,Ronan Lordan ,Tiago Lubiana ,Temitayo Lukan ,Adam L. MacLean ,David Mai ,Serghei Mangul ,David Manheim ,Lucy D’Agostino McGowan ,Amruta Naik ,YoSon Park ,Dimitri Perrin ,Yanjun Qi ,Diane N. Rafizadeh ,Bharath Ramsundar ,Halie M. Rando ,Sandipan Ray ,Michael P. Robson ,Vincent Rubinetti ,Elizabeth Sell ,Lamonica Shinholster ,Ashwin N. Skelly ,Yuchen Sun ,Yusha Sun ,Gregory L. Szeto ,Ryan Velazquez ,Jinhui Wang ,Nils Wellhausen - Abstract
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).
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- 2021
32. Association of Urine Biomarkers of Kidney Tubule Injury and Dysfunction With Frailty Index and Cognitive Function in Persons With CKD in SPRINT
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Miller, Lindsay M, Rifkin, Dena, Lee, Alexandra K, Kurella Tamura, Manjula, Pajewski, Nicholas M, Weiner, Daniel E, Al-Rousan, Tala, Shlipak, Michael, and Ix, Joachim H
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Clinical Research ,Clinical Trials and Supportive Activities ,Kidney Disease ,Prevention ,Renal and urogenital ,Good Health and Well Being ,Aged ,Aged ,80 and over ,Biomarkers ,Blood Pressure ,Chemokine CCL2 ,Cognition ,Cross-Sectional Studies ,Female ,Frailty ,Glomerular Filtration Rate ,Hepatitis A Virus Cellular Receptor 1 ,Humans ,Kidney Tubules ,Male ,Middle Aged ,Renal Insufficiency ,Chronic ,cognitive function ,cognitive impairment ,fitness ,frailty ,functional status ,kidney function ,kidney injury ,memory ,renal fibrosis ,tubular dysfunction ,tubule injury ,tubule reabsorptive capacity ,urine biomarkers ,vascular aging ,Clinical Sciences ,Public Health and Health Services ,Urology & Nephrology - Abstract
Rationale & objectiveThe associations of the glomerular markers of kidney disease, estimated glomerular filtration rate (eGFR) and albuminuria, with frailty and cognition are well established. However, the relationship of kidney tubule injury and dysfunction with frailty and cognition is unknown.Study designObservational cross-sectional study.Setting & participants2,253 participants with eGFR
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- 2021
33. Which individual, social, and urban factors in early childhood predict psychopathology in later childhood, adolescence and young adulthood? A systematic review
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Franzoi, Daniele, Bockting, Claudi L., Bennett, Kirsty F., Odom, Annick, Lucassen, Paul J., Pathania, Alisha, Lee, Alexandra, Brouwer, Marlies E., van de Schoot, Rens, Wiers, Reinout W., and Breedvelt, Josefien J.F.
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- 2024
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34. OSIRIS: Oscillating satiety induction and regulation intragastric system
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Jia, Neil Zixun, Packham, Tanner J., Ulloa, Gabriella, Zhang, Ziying, Lee, Alexandra C., Mao, Yuehe, Valdes Martinez, Agustin G., Peng, Grace, Crystal Liang, YongYan, Leclerc, Cecile, McGrath, Olivia B., Maier, Kai, Huang, Laura, Reifschneider, Rostam, Kuosmanen, Johannes, Jenkins, Josh, Pettinari, Andrew, Hayward, Alison M., Fabian, Niora, and Traverso, Giovanni
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- 2024
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35. The Effectiveness of Interactive Visualization Techniques for Time Navigation of Dynamic Graphs on Large Displays
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Lee, Alexandra, Archambault, Daniel, and Nacenta, Miguel A.
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Computer Science - Human-Computer Interaction ,Computer Science - Social and Information Networks - Abstract
Dynamic networks can be challenging to analyze visually, especially if they span a large time range during which new nodes and edges can appear and disappear. Although it is straightforward to provide interfaces for visualization that represent multiple states of the network (i.e., multiple timeslices) either simultaneously (e.g., through small multiples) or interactively (e.g., through interactive animation), these interfaces might not support tasks in which disjoint timeslices need to be compared. Since these tasks are key for understanding the dynamic aspects of the network, understanding which interactive visualizations best support these tasks is important. We present the results of a series of laboratory experiments comparing two traditional approaches (small multiples and interactive animation), with a more recent approach based on interactive timeslicing. The tasks were performed on a large display through a touch interface. Participants completed 24 trials of three tasks with all techniques. The results show that interactive timeslicing brings benefit when comparing distant points in time, but less benefits when analyzing contiguous intervals of time.
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- 2020
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36. Visualisation of long in time dynamic networks on large touch displays
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Lee, Alexandra, Archambault, Daniel, and Tam, Gary
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Any dataset containing information about relationships between entities can be modelled as a network. This network can be static, where the entities/relationships do not change over time, or dynamic, where the entities/relationships change over time. Network data that changes over time, dynamic network data, is a powerful resource when studying many important phenomena, across wide-ranging fields from travel networks to epidemiology. However, it is very difficult to analyse this data, especially if it covers a long period of time (e.g, one month) with respect to its temporal resolution (e.g. seconds). In this thesis, we address the problem of visualising long in time dynamic networks: networks that may not be particularly large in terms of the number of entities or relationships, but are long in terms of the length of time they cover when compared to their temporal resolution. We first introduce Dynamic Network Plaid, a system for the visualisation and analysis of long in time dynamic networks. We design and build for an 84" touch-screen vertically-mounted display as existing work reports positive results for the use of these in a visualisation context, and that they are useful for collaboration. The Plaid integrates multiple views and we prioritise the visualisation of interaction provenance. In this system we also introduce a novel method of time exploration called 'interactive timeslicing'. This allows the selection and comparison of points that are far apart in time, a feature not offered by existing visualisation systems. The Plaid is validated through an expert user evaluation with three public health researchers. To confirm observations of the expert user evaluation, we then carry out a formal laboratory study with a large touch-screen display to verify our novel method of time navigation against existing animation and small multiples approaches. From this study, we find that interactive timeslicing outperforms animation and small multiples for complex tasks requiring a comparison between multiple points that are far apart in time. We also find that small multiples is best suited to comparisons of multiple sequential points in time across a time interval. To generalise the results of this experiment, we later run a second formal laboratory study in the same format as the first, but this time using standard-sized displays with indirect mouse input. The second study reaffirms the results of the first, showing that our novel method of time navigation can facilitate the visual comparison of points that are distant in time in a way that existing approaches, small multiples and animation, cannot. The study demonstrates that our previous results generalise across display size and interaction type (touch vs mouse). In this thesis we introduce novel representations and time interaction techniques to improve the visualisation of long in time dynamic networks, and experimentally show that our novel method of time interaction outperforms other popular methods for some task types.
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- 2021
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37. Air pollution and pregnancy
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Aguilera, Juan, Konvinse, Katherine, Lee, Alexandra, Maecker, Holden, Prunicki, Mary, Mahalingaiah, Shruthi, Sampath, Vanitha, Utz, Paul J., Yang, Emily, and Nadeau, Kari C.
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- 2023
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38. Severe hypoglycemia and falls in older adults with diabetes: The Diabetes & Aging Study
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Moffet, Howard H., Huang, Elbert S., Liu, Jennifer Y., Parker, Melissa M., Lipska, Kasia J., Laiteerapong, Neda, Grant, Richard W., Lee, Alexandra K., and Karter, Andrew J.
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- 2023
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39. FGF23, Frailty, and Falls in SPRINT
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Jovanovich, Anna, Ginsberg, Charles, You, Zhiying, Katz, Ronit, Ambrosius, Walter T, Berlowitz, Dan, Cheung, Alfred K, Cho, Monique, Lee, Alexandra K, Punzi, Henry, Rehman, Shakaib, Roumie, Christianne, Supiano, Mark A, Wright, Clinton B, Shlipak, Michael, Ix, Joachim H, and Chonchol, Michel
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Aging ,Clinical Trials and Supportive Activities ,Kidney Disease ,Hypertension ,Clinical Research ,Prevention ,Accidental Falls ,Aged ,Biomarkers ,Correlation of Data ,Cross-Sectional Studies ,Female ,Fibroblast Growth Factor-23 ,Fibroblast Growth Factors ,Frailty ,Glomerular Filtration Rate ,Humans ,Male ,Renal Insufficiency ,Chronic ,fibroblast growth factor 23 ,falls ,frailty ,chronic kidney disease ,biomarkers ,Medical and Health Sciences ,Geriatrics - Abstract
Background/objectivesChronic kidney disease (CKD) is associated with frailty. Fibroblast growth factor 23 (FGF23) is elevated in CKD and associated with frailty among non-CKD older adults and individuals with human immunodeficiency virus. Whether FGF23 is associated with frailty and falls in CKD is unknown.DesignCross-sectional and longitudinal observational study.SettingSystolic Blood Pressure Intervention Trial (SPRINT), a randomized trial evaluating standard (systolic blood pressure [SBP]
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- 2021
40. Fingerstick Glucose Monitoring in Veterans Affairs Nursing Home Residents with Diabetes Mellitus
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Jeon, Sun Y, Shi, Ying, Lee, Alexandra K, Hunt, Lauren, Lipska, Kasia, Boscardin, John, and Lee, Sei
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Health Services and Systems ,Health Sciences ,Diabetes ,Prevention ,Clinical Research ,Aging ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Metabolic and endocrine ,Aged ,Blood Glucose ,Diabetes Mellitus ,Type 2 ,Drug Monitoring ,Female ,Guideline Adherence ,Homes for the Aged ,Humans ,Hypoglycemia ,Hypoglycemic Agents ,Male ,Nursing Homes ,Practice Guidelines as Topic ,Procedures and Techniques Utilization ,Risk Assessment ,United States ,United States Department of Veterans Affairs ,Unnecessary Procedures ,fingerstick ,diabetes mellitus ,type II ,glucose monitoring ,Veterans Affairs nursing home ,glucose-lowering medication ,diabetes mellitus ,type II ,Medical and Health Sciences ,Geriatrics ,Biomedical and clinical sciences ,Health sciences ,Psychology - Abstract
Background/objectiveGuidelines recommend less intensive glycemic treatment and less frequent glucose monitoring for nursing home (NH) residents. However, little is known about the frequency of fingerstick (FS) glucose monitoring in this population. Our objective was to examine the frequency of FS glucose monitoring in Veterans Affairs (VA) NH residents with diabetes mellitus, type II (T2DM).Design and settingNational retrospective cohort study in 140 VA NHs.ParticipantsNH residents with T2DM and older than 65 years admitted to VA NHs between 2013 and 2015 following discharge from a VA hospital.MeasurementsNH residents were classified into five groups based on their highest hypoglycemia risk glucose-lowering medication (GLM) each day: no GLMs; metformin only; sulfonylureas; long-acting insulin; and any short-acting insulin. Our outcome was a daily count of FS measurements.ResultsAmong 17,474 VA NH residents, mean age was 76 (standard deviation (SD) = 8) years and mean hemoglobin A1c was 7.6% (SD = 1.5%). On day 1 after NH admission, 49% of NH residents were on short-acting insulin, decreasing slightly to 43% at day 90. Overall, NH residents had an average of 1.9 (95% confidence interval (CI) = 1.8-1.9) FS measurements on NH day 1, decreasing to 1.4 (95% CI = 1.3-1.4) by day 90. NH residents on short-acting insulin had the most frequent FS measurements, with 3.0 measurements (95% CI = 2.9-3.0) on day 1, decreasing to 2.6 measurements (95% CI = 2.5-2.7) by day 90. Less frequent FS measurements were seen for NH residents receiving long-acting insulin (2.1 (95% CI = 2.0-2.2) on day 1) and sulfonylureas (1.7 (95% CI = 1.5-1.8) on day 1). Even NH residents on metformin monotherapy had 1.1 (95% CI = 1.1-1.2) measurements on day 1, decreasing to 0.5 (95% CI = 0.4-0.6) measurements on day 90.ConclusionAlthough guidelines recommend less frequent glucose monitoring for NH residents, we found that many VA NH residents receive frequent FS monitoring. Given the uncertain benefits and potential for substantial patient burdens and harms, our results suggest decreasing FS monitoring may be warranted for many low hypoglycemia risk NH residents.
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- 2021
41. Severe Hypoglycemia, Cardiac Structure and Function, and Risk of Cardiovascular Events Among Older Adults With Diabetes.
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Echouffo-Tcheugui, Justin, Daya, Natalie, Lee, Alexandra, Tang, Olive, Ndumele, Chiadi, Windham, B, Shah, Amil, and Selvin, Elizabeth
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Aged ,Cardiovascular Diseases ,Cross-Sectional Studies ,Diabetes Mellitus ,Type 2 ,Female ,Heart Failure ,Humans ,Hypoglycemia ,Incidence ,Male ,Risk Factors - Abstract
OBJECTIVE: To assess the association of severe hypoglycemia measured at baseline with cardiovascular disease (CVD) among community-dwelling older individuals with diabetes, a group particularly susceptible to hypoglycemia. RESEARCH DESIGN AND METHODS: We included older adults with diabetes from the Atherosclerosis Risk in Communities (ARIC) study who attended visit 5 (2011-2013, baseline). Severe hypoglycemia at baseline was defined with use of first position ICD-9 codes from hospitalizations, emergency department visits, and ambulance calls. We examined cross-sectional associations of severe hypoglycemia with echocardiographic indices of cardiac structure-function. We prospectively evaluated the risks of incident or recurrent CVD (coronary heart disease, stroke, or heart failure) and all-cause mortality, from baseline to 31 December 2018, using negative binomial and Cox regression models. RESULTS: Among 2,193 participants (mean [SD] age 76 [5] years, 57% female, 32% Blacks), 79 had a history of severe hypoglycemia at baseline. Severe hypoglycemia was associated with a lower left ventricular (LV) ejection fraction (adjusted β-coefficient -3.66% [95% CI -5.54, -1.78]), higher LV end diastolic volume (14.80 mL [95% CI 8.77, 20.84]), higher E-to-A ratio (0.11 [95% CI 0.03, 0.18]), and higher septal E/e (2.48 [95% CI 1.13, 3.82]). In adjusted models, severe hypoglycemia was associated with incident or recurrent CVD (incidence rate ratio 2.19 (95% CI 1.24, 3.88]) and all-cause mortality (hazard ratio 1.71 [95% CI 1.10, 2.67]) among those without prevalent CVD. CONCLUSIONS: Our findings suggest that a history of severe hypoglycemia is associated with alterations in cardiac function and is an important marker of future cardiovascular risk in older adults.
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- 2021
42. Experimentally Manipulated Low Social Status and Food Insecurity Alter Eating Behavior Among Adolescents: A Randomized Controlled Trial
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Cardel, Michelle I, Pavela, Greg, Janicke, David, Huo, Tianyao, Miller, Darci, Lee, Alexandra M, Gurka, Matthew J, Dhurandhar, Emily, Peters, John C, Caldwell, Ann E, Krause, Eric, Fernandez, Alicia, and Allison, David B
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Public Health ,Biomedical and Clinical Sciences ,Nutrition and Dietetics ,Health Sciences ,Clinical Trials and Supportive Activities ,Nutrition ,Behavioral and Social Science ,Prevention ,Obesity ,Clinical Research ,Metabolic and endocrine ,Oral and gastrointestinal ,Adolescent ,Adult ,Feeding Behavior ,Female ,Food Insecurity ,History ,21st Century ,Humans ,Male ,Psychological Distance ,Young Adult ,Endocrinology & Metabolism - Abstract
ObjectiveThis randomized trial experimentally manipulated social status to assess effects on acute eating behavior and 24-hour energy balance.MethodsParticipants (n = 133 Hispanics; age 15-21 years; 60.2% females) were randomized to low social status ("LOW") or high social status ("HIGH") conditions in a rigged game of Monopoly (Hasbro, Inc.). Acute energy intake in a lunchtime meal was measured by food scales. Twenty-four-hour energy balance was assessed via summation of resting metabolic rate (metabolic cart), physical activity energy expenditure (accelerometer), thermic effect of food, and subtraction of twenty-four-hour energy intake (food diary).ResultsIn the total sample, no significant differences were observed by study condition at lunchtime. LOW females consumed a greater percent of lunchtime daily energy needs (37.5%) relative to HIGH females (34.3%); however, this difference was not statistically significant (P = 0.291). In males, however, LOW consumed significantly less (36.5%) of their daily energy needs relative to HIGH males (45.8%; P = 0.001). For 24-hour energy balance, sex differences were nearly significant (P = 0.057; LOW females: surplus +200 kcal; HIGH males: surplus +445 kcal). Food-insecure individuals consumed a nearly significant greater lunchtime percent daily energy than those with food security (40.7% vs. 36.3%; P = 0.0797).ConclusionsThe data demonstrate differential acute and 24-hour eating behavior responses between Hispanic male and female adolescents in experimentally manipulated conditions of low social status.
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- 2020
43. Improving the American Diabetes Association Framework for individualizing treatment in older adults: evaluating life expectancy.
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Lee, Alexandra K, Steinman, Michael A, and Lee, Sei J
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Humans ,Diabetes Mellitus ,Type 2 ,Blood Glucose ,Life Expectancy ,Prospective Studies ,Comorbidity ,Adolescent ,Aged ,Child ,United States ,ageing ,diabetes mellitus ,epidemiology ,life expectancy ,type 2 ,Clinical Sciences - Abstract
IntroductionFor older adults with type 2 diabetes, the American Diabetes Association (ADA) Framework uses comorbidities and functional status to categorize patients by estimated life expectancy to guide individualization of glycemic treatment. We evaluated whether modifying the ADA Framework by removing three comorbidities and incorporating age could improve life expectancy stratification and better identify patients likely to benefit from intensive treatment.Research design and methodsWe examined 3166 Health and Retirement Study participants aged ≥65 with diabetes from 1998 to 2004, using a prospective cohort design with mortality follow-up through 2016. We classified participants into one of three ADA Framework categories: Healthy, Intermediate Health, and Poor Health. We created modified categories by excluding comorbidities weakly associated with mortality (hypertension, arthritis, and incontinence). Using Gompertz regression, we estimated life expectancy across age strata for both original and modified ADA Framework categories.ResultsThe original ADA Framework classified 34% as Healthy (likely to benefit from intensive treatment), 50% as Intermediate Health, and 16% as Poor Health (unlikely to benefit from intensive treatment). Our comorbidity modification reclassified 20% of participants from Intermediate Health to Healthy. Using the modified ADA Framework, median life expectancy of the Healthy varied greatly by age (aged 65-69: 16.3 years; aged ≥80: 7.6 years), indicating differing likelihood of benefit. Additionally, age ≥80 made extended life expectancy unlikely (median life expectancy for Healthy 7.6 years, Intermediate Health 5.9 years, Poor Health 2.5 years), suggesting adults ≥80 are unlikely to benefit from intensive treatment.ConclusionsModifying the ADA Framework by incorporating age and focusing on comorbidities associated with mortality improved life expectancy stratification, resulting in different treatment recommendations for many older adults.
- Published
- 2020
44. Renters at the Tipping Point of Homeownership : Estimating the Impact of Telework
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Manhertz, Treh and Lee, Alexandra
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- 2022
45. Sympathetic tone dictates the impact of lipolysis on FABP4 secretion
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Prentice, Kacey J., Lee, Alexandra, Cedillo, Paulina, Inouye, Karen E., Ertunc, Meric Erikci, Riveros, Jillian K., Lee, Grace Yankun, and Hotamisligil, Gökhan S.
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- 2023
- Full Text
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46. Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8+ T cell responses post SARS-CoV-2 infection
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Gao, Fei, Mallajosyula, Vamsee, Arunachalam, Prabhu S., van der Ploeg, Kattria, Manohar, Monali, Röltgen, Katharina, Yang, Fan, Wirz, Oliver, Hoh, Ramona, Haraguchi, Emily, Lee, Ji-Yeun, Willis, Richard, Ramachandiran, Vasanthi, Li, Jiefu, Kathuria, Karan Raj, Li, Chunfeng, Lee, Alexandra S., Shah, Mihir M., Sindher, Sayantani B., Gonzalez, Joseph, Altman, John D., Wang, Taia T., Boyd, Scott D., Pulendran, Bali, Jagannathan, Prasanna, Nadeau, Kari C., and Davis, Mark.M.
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- 2023
- Full Text
- View/download PDF
47. Climate change and public health: The effects of global warming on the risk of allergies and autoimmune diseases
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Lee, Alexandra S, Aguilera, Juan, Efobi, Jo Ann, Jung, Youn Soo, Seastedt, Hana, Shah, Mihir M, Yang, Emily, Konvinse, Katherine, Utz, Paul J, Sampath, Vanitha, and Nadeau, Kari C
- Published
- 2023
- Full Text
- View/download PDF
48. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
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Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, and Lavezzo, Enrico
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Human Genome ,Networking and Information Technology R&D (NITRD) ,Genetics ,Generic health relevance ,Animals ,Biofilms ,Candida albicans ,Drosophila melanogaster ,Genome ,Bacterial ,Genome ,Fungal ,Humans ,Locomotion ,Memory ,Long-Term ,Molecular Sequence Annotation ,Pseudomonas aeruginosa ,Protein function prediction ,Long-term memory ,Biofilm ,Critical assessment ,Community challenge ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.
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- 2019
49. Markers of kidney tubule function and risk of cardiovascular disease events and mortality in the SPRINT trial
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Garimella, Pranav S, Lee, Alexandra K, Ambrosius, Walter T, Bhatt, Udayan, Cheung, Alfred K, Chonchol, Michel, Craven, Timothy, Hawfield, Amret T, Jotwani, Vasantha, Killeen, Anthony, Punzi, Henry, Sarnak, Mark J, Wall, Barry M, Ix, Joachim H, and Shlipak, Michael G
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Prevention ,Heart Disease ,Heart Disease - Coronary Heart Disease ,Clinical Research ,Kidney Disease ,Cardiovascular ,Clinical Trials and Supportive Activities ,Aging ,Detection ,screening and diagnosis ,4.1 Discovery and preclinical testing of markers and technologies ,Renal and urogenital ,Good Health and Well Being ,Aged ,Aged ,80 and over ,Biomarkers ,Blood Pressure ,Cardiovascular Diseases ,Female ,Glomerular Filtration Rate ,Humans ,Inflammation ,Kidney Tubules ,Male ,Middle Aged ,Renal Insufficiency ,Chronic ,Risk Factors ,Uromodulin ,Tubular function ,Cardiovascular disease ,Chronic kidney disease ,Alpha-1 microglobulin ,Beta-2 microglobulin ,Cardiorespiratory Medicine and Haematology ,Clinical Sciences ,Cardiovascular System & Hematology - Abstract
AimsBiomarkers of kidney tubule injury, inflammation and fibrosis have been studied extensively and established as risk markers of adverse kidney and cardiovascular disease (CVD) outcomes. However, associations of markers of kidney tubular function with adverse clinical events have not been well studied, especially in persons with chronic kidney disease (CKD).Methods and resultsUsing a sample of 2377 persons with CKD at the baseline Systolic Blood Pressure Intervention Trial (SPRINT) visit, we evaluated the association of three urine tubular function markers, alpha-1 microglobulin (α1m), beta-2 microglobulin (β2m), and uromodulin, with a composite CVD endpoint (myocardial infarction, acute coronary syndrome, stroke, acute decompensated heart failure, or death from cardiovascular causes) and mortality using Cox proportional hazards regression, adjusted for baseline estimated glomerular filtration rate (eGFR), albuminuria, and CVD risk factors. In unadjusted analysis, over a median follow-up of 3.8 years, α1m and β2m had positive associations with composite CVD events and mortality, whereas uromodulin had an inverse association with risk for both outcomes. In multivariable analysis including eGFR and albuminuria, a two-fold higher baseline concentration of α1m was associated with higher risk of CVD [hazard ratio (HR) 1.25; 95% confidence interval (CI): 1.10-1.45] and mortality (HR 1.25; 95% CI: 1.10-1.46), whereas β2m had no association with either outcome. A two-fold higher uromodulin concentration was associated with lower CVD risk (HR 0.79; 95% CI: 0.68-0.90) but not mortality (HR 0.86; 95% CI: 0.73-1.01) after adjusting for similar confounders.ConclusionAmong non-diabetic persons with CKD, biomarkers of tubular function are associated with CVD events and mortality independent of glomerular function and albuminuria.
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- 2019
50. Distinct Dimensions of Kidney Health and Risk of Cardiovascular Disease, Heart Failure, and Mortality
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Lee, Alexandra K, Katz, Ronit, Jotwani, Vasantha, Garimella, Pranav S, Ambrosius, Walter T, Cheung, Alfred K, Gren, Lisa H, Neyra, Javier A, Punzi, Henry, Raphael, Kalani L, Shlipak, Michael G, and Ix, Joachim H
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Biomedical and Clinical Sciences ,Clinical Sciences ,Cardiovascular ,Clinical Research ,Prevention ,Heart Disease ,Kidney Disease ,Renal and urogenital ,Good Health and Well Being ,Aged ,Aged ,80 and over ,Biomarkers ,Blood Pressure ,Cardiovascular Diseases ,Creatinine ,Female ,Glomerular Filtration Rate ,Humans ,Kidney ,Male ,Middle Aged ,Renal Insufficiency ,Chronic ,Risk ,Survival Rate ,albuminuria ,biomarker ,cardiovascular diseases ,epidemiology ,kidney ,Cardiorespiratory Medicine and Haematology ,Public Health and Health Services ,Cardiovascular System & Hematology ,Cardiovascular medicine and haematology ,Clinical sciences - Abstract
Chronic kidney disease is a strong risk factor for cardiovascular disease (CVD), but clinical kidney measures (estimated glomerular filtration rate and albuminuria) do not fully reflect the multiple aspects of kidney tubules influencing cardiovascular health. Applied methods are needed to integrate numerous tubule biomarkers into useful prognostic scores. In SPRINT (Systolic Blood Pressure Intervention Trial) participants with chronic kidney disease at baseline (estimated glomerular filtration ratecr&cys
- Published
- 2019
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