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Health-Related Quality Of Life (Hrqol) In A Population At Risk Of Type 2 Diabetes: A Cross-Sectional Study In Two Latin American Cities, Luis A. Anillo Arrieta, Tania Acosta Vergara, Rafael Tuesca, Sandra Rodríguez Acosta, Karen C. Flórez Lozano, Pablo Aschner, Rafael Gabriel, Sandra De La Rosa, Julieth P. Nieto Castillo, Noël C. Barengo

HWCOM Faculty Publications

PURPOSE: The purpose of this study was to describe the health-related quality of life (HRQoL) characteristics in a population at risk of developing type 2 diabetes in Barranquilla and Bogotá, Colombia. METHODS: A cross-sectional study with 1135 participants older than 30 years-of-age recruited in Bogotá D.C., and Barranquilla by cluster sampling in 2018 to 2019. The Finnish Diabetes Risk Score (FINDRISC) was used to detect participants at risk of developing type 2 diabetes (T2D). HRQoL was assessed using the EQ-5D-3L questionnaire. Unadjusted and adjusted logistic regression models were used to calculate odds ratios (OR) and their corresponding 95% confidence intervals …

Decreased Levels Of Soluble Cd44 In A High-Risk Population Following A Smoking Cessation Program, Drew H. Smith, Shahm Raslan, Isildinha M. Reis, Abdurrahman Al-Awady, Isabella Buitron, Melanie Perez, Huaping Liu, Jerri Halgowich, Claudia Gordon, Monica Webb Hooper, Noël C. Barengo, Elizabeth J. Franzmann

HWCOM Faculty Publications

Tobacco is a risk factor of head and neck cancer (HNC) and smoking cessation alone may reduce HNC risk by 70%. Soluble CD44 (solCD44), a cell surface receptor linked to cell proliferation and migration, and total protein (TP) levels can detect early HNC. This study aims to determine whether salivary solCD44 and TP levels in oral rinses change following a smoking cessation program. 150 smokers provided oral rinse samples at baseline and at a 12-month follow-up after participation in a smoking cessation program. Assays to measure levels of solCD44, TP, and cotinine, a metabolite used as a biomarker of tobacco …

Smoking As A Risk Factor For Surgical Site Complications In Implant-Based Breast Surgery, Isaac Zucker, Antoun Bouz, Grettel Castro, Pura Rodriguez De La Vega, Noel C. Barengo

HWCOM Faculty Publications

Background Smoking is a cause of many postoperative complications, including delayed wound healing, tissue necrosis, and reconstructive flap loss. However, there is a paucity of evidence-based guidelines for smoking cessation in patients undergoing implant-based breast surgery. Objective The objective of this study was to determine if smoking is associated with wound dehiscence or superficial/deep surgical site infection (SSI) in women undergoing implant-based breast surgery. Methods Using theAmerican College of Surgeons National Surgical Quality Improvement Program, data was obtained of U.S. adult females (n=10,077) between the ages of 18 and 70 who underwent insertion of a breast prosthesis from 2014 to …

An Association Between Electronic Nicotine Delivery Systems Use And A History Of Stroke Using The 2016 Behavioral Risk Factor Surveillance System, Ryan A. Bricknell, Christobal Ducaud, Alejandra Figueroa, Logan S. Schwarzman, Pura Rodriguez, Grettel Castro, Juan Carlos Zevallos, Noël C. Barengo

HWCOM Faculty Publications

Electronic nicotine delivery systems (ENDS) are growing in use and many of the health implications with these devices remain unknown. This study aims to assess, using a survey representative of the USA general population, if an association exists between a history of ENDS use and a history of stroke.This cross-sectional study was a secondary data analysis using the 2016 behavioral risk factor surveillance system survey. The main exposure variable of the study was a self-reported history of ENDS use. The main outcome was a self-reported history of stroke. Covariates included sex, race, traditional cigarette use, smokeless tobacco use, chronic kidney …

Carbohydrate-To-Fiber Ratio, A Marker Of Dietary Intake, As An Indicator Of Depressive Symptoms, Sarah S. Makhani, Camron Davies, Kevin A. George, Grettel Castro, Pura Rodriguez De La Vega, Noel C. Barengo

HWCOM Faculty Publications

Objective: The aim of this study is to evaluate the association between a marker of dietary intake, the carbohydrate-to-fiber (CF) ratio, and moderate-to-severe depressive symptoms. Design: Cross-sectional study. Setting: National Health and Nutrition Examination Survey (NHANES) database from 2013-2016. Participants: Individuals 18 years and older were included. Participants with total energy intake outside of three standard deviations of the mean, pregnant or breastfeeding women, and those with missing data were excluded. Measurements: The main independent variable, CF ratio, was generated using corresponding variables in NHANES and divided into quartiles. The main outcome was depressive symptoms using the Patient Health Questionnaire-9. …

The Association Between Social Determinants Of Health And Self-Reported Diabetic Retinopathy: An Exploratory Analysis, Emily L. Silverberg, Trevor W. Sterling, Tyler H. Williams, Grettel Castro, Pura Rodriguez De La Vega, Noël C. Barengo

HWCOM Faculty Publications

One-third of Americans with diabetes will develop diabetic retinopathy (DR), the leading cause of blindness in working-age Americans. Social determinants of health (SDOHs) are conditions in a person's environment that may impact health. The objective of this study was to determine whether there is an association between SDOHs and DR in patients with type II diabetes. This cross-section study used data from the 2018 Behavioral Risk Factor Surveillance System (BRFSS). This study included people with self-reported diabetes in the US in 2018 (n = 60,703). Exposure variables included homeownership, marital status, income, health care coverage, completed level of education, and …

The Associations Between Access To Recreational Facilities And Adherence To The American Heart Association's Physical Activity Guidelines In Us Adults, Larissa Andrade, Ryan Geffin, Mark Maguire, Pura Rodriguez, Grettel Castro, Ahmad Alkhatib, Noel C. Barengo

HWCOM Faculty Publications

Physical activity decreases the risk of long-term health consequences including cardiac diseases. According to the American Health Association (AHA), adults should perform at least 75 min of vigorous physical activity (PA) or 150 min of moderate PA per week to impact long-term health. Results of previous studies are varied and have yet to integrate perceived access to facilities with AHA PA guidelines. We investigated whether access to free or low-cost recreational facilities was associated with meeting the AHA PA guidelines. This cross-sectional study utilized data extracted from the Family Life, Activity, Sun, Health, and Eating (FLASHE) database collected in 2017 …

Global Burden Of Cardiovascular Diseases And Risk Factors, 1990-2019: Update From The Gbd 2019 Study, Gregory A. Roth, George A. Mensah, Catherine O. Johnson, Giovanni Addolorato, Enrico Ammirati, Larry M. Baddour, Noel C. Barengo, Andrea Z. Beaton, Emelia J. Benjamin, Catherine P. Benziger, Aimé Bonny, Michael Brauer, Marianne Brodmann, Thomas J. Cahill, Jonathan Carapetis, Alberico L. Catapano, Sumeet S. Chugh, Leslie T. Cooper, Josef Coresh, Michael Criqui, Nicole Decleene, Kim A. Eagle

HWCOM Faculty Publications

Cardiovascular diseases (CVDs), principally ischemic heart disease (IHD) and stroke, are the leading cause of global mortality and a major contributor to disability. This paper reviews the magnitude of total CVD burden, including 13 underlying causes of cardiovascular death and 9 related risk factors, using estimates from the Global Burden of Disease (GBD) Study 2019. GBD, an ongoing multinational collaboration to provide comparable and consistent estimates of population health over time, used all available population-level data sources on incidence, prevalence, case fatality, mortality, and health risks to produce estimates for 204 countries and territories from 1990 to 2019. Prevalent cases …

A Comparison Between Ams 700 And Coloplast Titan: A Systematic Literature Review, Elias Atri, Vivian Wong, Noel C. Barengo, Alan M. Nieder, Alan S. Polackwich

HWCOM Faculty Publications

There are only two three-piece inflatable penile prostheses (IPP) available to patients in the American market: the AMS (American Medical Systems) 700 series (Boston Scientific, Massachusetts) and the Coloplast Titan® series (Coloplast, Minnesota), and data comparing the two are scant. The aim of our study was to summarize the current scientific evidence comparing the two. A systematic literature review was conducted on PubMed. A 10-year filter was placed to include only studies published after Coloplast launched the Titan Touch® release pump. Eligibility criteria included articles discussing specifically the AMS 700 and Coloplast Titan® models. Further searches for studies on patient/partner …

The Association Between Race And Survival Among Pediatric Patients With Neuroblastoma In The Us Between 1973 And 2015, Farouk S. Farouk, Omar A. Viqar, Zaid Sheikh, Grettel Castro, Noël C. Barengo

HWCOM Faculty Publications

: Conclusive information regarding the influence of race on survival among neuroblastoma patients is limited. Our objective is to investigate the association between race and cause-specific survival in pediatric patients diagnosed with neuroblastoma in the US between 1973 and 2015. : This was a retrospective cohort study using the Surveillance, Epidemiology, and End Result (SEER) database. Patients aged 17 and younger of black, white, or Asian Pacific Islander (API) race diagnosed with neuroblastoma from 1973-2015 were included (n = 2,119). The outcome variable was time from diagnosis to death. Covariates included age, gender, ethnicity, stage, tumor site, and year of …

Dysglycemia Risk Score In Saudi Arabia: A Tool To Identify People At High Future Risk Of Developing Type 2 Diabetes, Suhad Bahijri, Rajaa Al-Raddadi, Ghada Ajabnoor, Hanan Jambi, Jawaher Al Ahmadi, Anwar Borai, Noel C. Barengo, Jaakko Tuomilehto

HWCOM Faculty Publications

AIMS/INTRODUCTION: To develop a non-invasive risk score to identify Saudis having prediabetes or undiagnosed type 2 diabetes. METHODS: Adult Saudis without diabetes were recruited randomly using a stratified two-stage cluster sampling method. Demographic, dietary, lifestyle variables, personal and family medical history were collected using a questionnaire. Blood pressure and anthropometric measurements were taken. Body mass index was calculated. The 1-h oral glucose tolerance test was carried out. Glycated hemoglobin, fasting and 1-h plasma glucose were measured, and obtained values were used to define prediabetes and type 2 diabetes (dysglycemia). Logistic regression models were used for assessing the association between various …

Causal Inference In Microbiomes Using Intervention Calculus, Musfiqur Rahman Sazal, Vitalii Stebliankin, Kalai Mathee, Giri Narasimhan

HWCOM Faculty Publications

Inferring causal effects is critically important in biomedical research as it allows us to move from the typical paradigm of associational studies to causal inference, and can impact treatments and therapeutics. Association patterns can be coincidental and may lead to wrong inferences in complex systems. Microbiomes are highly complex, diverse, and dynamic environments. Microbes are key players in health and diseases. Hence knowledge of genuine causal relationships among the entities in a microbiome, and the impact of internal and external factors on microbial abundance and interactions are essential for understanding disease mechanisms and making treatment recommendations. In this paper, we …

Inferring Directional Relationships In Microbial Communities Using Signed Bayesian Networks, Musfiquer Sazal, Kalai Mathee, Daniel Ruiz-Perez, Trevor Cickovski, Giri Narasimhan

HWCOM Faculty Publications

Background: Microbe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by a Bayesian Network (BN) about a microbial community. Unlike the previously proposed Co-occurrence Networks (CoNs), BNs are based on conditional dependencies and can help in revealing complex associations. Results: In this paper, we propose a way of combining a BN and a CoN to construct a signed Bayesian …

Cellular Stress Responses And Dysfunctional Mitochondrial–Cellular Senescence, And Therapeutics In Chronic Respiratory Diseases, Marko Manaveski, Thivanka Muthumalage, Dinesh Devadoss, Isaac K. Sundar, Qixin Wang, Kameshwar P. Singh, Hoshang Unwalla, Hitendra S. Chand, Irfan Rahman

HWCOM Faculty Publications

The abnormal inflammatory responses due to the lung tissue damage and ineffective repair/resolution in response to the inhaled toxicants result in the pathological changes associated with chronic respiratory diseases. Investigation of such pathophysiological mechanisms provides the opportunity to develop the molecular phenotype-specific diagnostic assays and could help in designing the personalized medicine-based therapeutic approaches against these prevalent diseases. As the central hubs of cell metabolism and energetics, mitochondria integrate cellular responses and interorganellar signaling pathways to maintain cellular and extracellular redox status and the cellular senescence that dictate the lung tissue responses. Specifically, as observed in chronic obstructive pulmonary disease …

Pulmonary Toxicity And The Pathophysiology Of Electronic Cigarette, Or Vaping Product, Use Associated Lung Injury, Hitendra S. Chand

HWCOM Faculty Publications

New emerging tobacco products, especially electronic cigarettes (E-Cig) or electronic nicotine delivery systems (ENDS), have gained a huge popularity, particularly in younger populations. The lack of sufficient evidence-based health effect studies has promoted widespread use/abuse with the assumption that E-Cig or ENDS and/or vaping products are safer and less toxic than conventional tobacco smoking. However, the recent escalation in acute lung injuries and their associated fatalities among ENDS or vaping product users has now brought attention to this silent epidemic via investigation into the constituents of ENDS/vaping products and their toxic effects on pulmonary health. Accordingly, CDC has declared an …

Factors Associated With Low Physical Activity In Two Latin American Populations At Risk Of Developing Type 2 Diabetes: An Exploratory Analysis, Tania Acosta, Rafael Tuesca, Karen Florez, Noël C. Barengo, Luis Anillo, Victor Flórez-García, Jorge Acosta, Liliana Carvajal, Sandra De La Rosa, María Julieta Pachón, Pablo Aschner

HWCOM Faculty Publications

Low level of physical activity is a risk factor for chronic non-communicable diseases. Specifically, people at risk of Type 2 Diabetes (T2D) have shown to benefit from being physically active. The objective of this study was to explore what factors were associated with low physical activity in people at high risk of T2D living in Bogota and Barranquilla, Colombia. Cross-sectional study using baseline data from a quasi-experimental clinical trial (PREDICOL Project). The study included 1,135 participants of Bogota and Barranquilla that presented a high risk of developing T2D according to the Finnish Diabetes Risk Score (>12 points) and who …

Factors Related To Poor Adherence In Latvian Asthma Patients, Dins Smits, Girts Brigis, Jana Pavare, Inga Urtane, Sandis Kovalovs, Noel C. Barengo

HWCOM Faculty Publications

Background: The problem of nonadherence to therapy is a key reason of insufficient asthma control. Evaluating the beliefs about asthma medication, cognitive and emotional perceptions may help to identify patients with poor adherence to treatment in clinical practice which need additional attention in order to increase the likelihood of them taking their asthma medication according to the prescribed treatment protocol. The purpose of this study is to assess whether beliefs about asthma medication, cognitive and emotional factors are related to poor treatment adherence of asthma medication in a sample of asthma patients in Latvia. Methods: Study subjects were asthma patients …

Dynamic Bayesian Networks For Integrating Multi-Omics Time-Series Microbiome Data, Daniel Ruiz-Perez, Jose Lugo-Martinez, Natalia Bourguignon, Betiana Lerner, Ziv Bar-Joseph, Giri Narasimhan

HWCOM Faculty Publications

. A key challenge in the analysis of longitudinal microbiomes data is to go beyond computing their compositional profiles and infer the complex web of interactions between the various microbial taxa, their genes, and the metabolites they consume and produce. To address this challenge, we developed a computational pipeline that first aligns multi-omics data and then uses dynamic Bayesian networks (DBNs) to integrate them into a unified model. We discuss how our approach handles the different sampling and progression rates between individuals, how we reduce the large number of different entities and parameters in the DBNs, and the construction and …

Acetylcholinesterase Inhibitor Pyridostigmine Bromide Attenuates Gut Pathology And Bacterial Dysbiosis In A Murine Model Of Ulcerative Colitis, Sp Singh, Hitendra S. Chand, S. Banerjee, H. Agarwal, V. Raizada, S. Roy, M. Sopori

HWCOM Faculty Publications

Abstract Background Ulcerative colitis (UC) is a Th2 infammatory bowel disease characterized by increased IL-5 and IL-13 expression, eosinophilic/neutrophilic infltration, decreased mucus production, impaired epithelial barrier, and bacterial dysbiosis of the colon. Acetylcholine and nicotine stimulate mucus production and suppress Th2 infammation through nicotinic receptors in lungs but UC is rarely observed in smokers and the mechanism of the protection is unclear. Methods In order to evaluate whether acetylcholine can ameliorate UC-associated pathologies, we employed a mouse model of dextran sodium sulfate (DSS)-induced UC-like conditions, and a group of mice were treated with Pyridostigmine bromide (PB) to increase acetylcholine availability. …

Stimulated Raman Histology For Intraoperative Guidance In The Resection Of A Recurrent Atypical Spheno-Orbital Meningioma: A Case Report And Review Of Literature, Evan Luther, Alejandro Matus, Daniel G. Eichberg, Ashish H. Shah, Michael Ivan

HWCOM Faculty Publications

Meningiomas are the most common intracranial, extra-axial neoplasms and account for a significant proportion of all central nervous system (CNS) tumors. Regardless of the grade, treatment typically involves upfront surgical resection. However, in many instances, especially in meningiomas arising from the skull base, complete removal is often difficult given the close proximity to important anatomic structures. In this report, we discuss the use of stimulated Raman histology as a means to identify tissue boundaries during the resection of an extensive, recurrent, atypical spheno-orbital meningioma. We report a 75-year-old male with a history of a prior left frontotemporal craniotomy for a …

The Association Between Serum Lipids And Risk Of Premature Mortality In Latin America: A Systematic Review Of Population-Based Prospective Cohort Studies, Rodrigo M. Carrillo-Larco, Leonardo Albitres-Flores, Noel C. Barengo, Antonio Bernabe-Ortiz

HWCOM Faculty Publications

Objective

To synthetize the scientific evidence on the association between serum lipids and premature mortality in Latin America (LA).

Methods

Five data bases were searched from inception without language restrictions: Embase, Medline, Global Health, Scopus and LILACS. Population-based studies following random sampling methods were identified. The exposure variable was lipid biomarkers (e.g., total, LDL- or HDL- cholesterol). The outcome was all-cause and cause-specific mortality. The risk of bias was assessed following the Newcastle-Ottawa criteria. Results were summarized qualitatively.

Results

The initial search resulted in 264 abstracts, five (N = 27,903) were included for the synthesis. Three papers reported on …

Quantitative Spatial Upscaling Of Categorical Information: The Multi‐Dimensional Grid‐Point Scaling Algorithm, Daniel Gann

HWCOM Faculty Publications

1. Categorical raster datasets often require upscaling to a lower spatial resolution to make them compatible with the scale of ecological analysis. When aggregating categorical data, two critical issues arise: (a) ignoring compositional information present in the high‐resolution grid cells leads to high and uncontrolled loss of information in the scaled dataset; and (b) restricting classes to those present in the high‐resolution dataset assumes validity of the classification scheme at the lower, aggregated resolution.
2. I introduce a new scaling algorithm that aggregates categorical data while simultaneously controlling for information loss by generating a non‐hierarchical, representative, classification system for the aggregated scale. …

Selective Disruption Of The Blood–Brain Barrier By Zika Virus, Ana Rachel Leda, Luc Bertrand, Ibolya Edit Andras, Nazira El-Hage, Madhavan Nair, Michael Toborek

HWCOM Faculty Publications

The blood–brain barrier (BBB) selectively regulates the cellular exchange of macromolecules between the circulation and the central nervous system (CNS). Here, we hypothesize that Zika virus (ZIKV) infects the brain via a disrupted BBB and altered expression of tight junction (TJ) proteins, which are structural components of the BBB. To assess this hypothesis, in vitro and in vivo studies were performed using three different strains of ZIKV: Honduras (ZIKV-H), Puerto Rico (ZIKV-PR), and Uganda (ZIKV-U). Primary human brain microvascular endothelial cells (BMECs) were productively infected by all studied ZIKV strains at MOI 0.01, and were analyzed by plaque assay, immunofluorescence …

Hemorrhagic Stroke In A Young Adult With Undiagnosed Asymptomatic Dandy–Walker Malformation, Haleem Abdul, Joseph Burns, Andrea Estevez, Carlos Nasr El-Nimer, Brinsley Ekinde, Sherard Lacaille

HWCOM Faculty Publications

No abstract provided.

Signal From The Noise: Model‐Based Interpretation Of Variable Correspondence Between Active And Passive Samplers, Joseph Parkos Iii, Jeffrey L. Kline, Joel C. Trexler

HWCOM Faculty Publications

Combining information from active and passive sampling of mobile animals is challenging because active‐sampling data are affected by limited detection of rare or sparse taxa, while passive‐sampling data reflect both density and movement. We propose that a model‐based analysis allows information to be combined between these methods to interpret variation in the relationship between active estimates of density and passive measurements of catch per unit effort to yield novel information on activity rates (distance/time). We illustrate where discrepancies arise between active and passive methods and demonstrate the model‐based approach with seasonal surveys of fish assemblages in the Florida Everglades, where …

Does Health Insurance Modify The Association Between Race And Cancer-Specific Survival In Patients With Urinary Bladder Malignancy In The U.S.?, Juliana Morales, Aaron Malles, Marrell Kimbell, Pura Rodríguez De La Vega, Grettel Castro, Alan M. Nieder, Noel C. Barengo

HWCOM Faculty Publications

Background: Scientific evidence on the effect of health insurance on racial disparities in urinary bladder cancer patients’ survival is scant. The objective of our study was to determine whether insurance status modifies the association between race and bladder cancer specific survival during 2007–2015. Methods: The 2015 database of the cancer surveillance program of the National Cancer Institute (n = 39,587) was used. The independent variable was race (White, Black and Asian Pacific Islanders (API)), the main outcome was cancer specific survival. Health insurance was divided into uninsured, any Medicaid and insured. An adjusted model with an interaction term for race …

A Model For Point Of Care Testing For Non-Communicable Disease Diagnosis In Resource-Limited Countries, Stuart Malcolm, Joane Cadet, Lindsay Crompton, Vincent Degennaro

HWCOM Faculty Publications

Non-communicable disease diagnosis frequently relies on biochemical measurements but laboratory infrastructure in low-income settings is often insufficient and distances to clinics may be vast. We present a model for point of care (POC) epidemiology as used in our study of chronic disease in the Haiti Health Study, in rural and urban Haiti. Point of care testing (POCT) of creatinine, cholesterol, and hemoglobin A1c as well as physical measurements of weight, height, and waist circumference allowed for diagnosis of diabetes, chronic kidney disease, dyslipidemias, and obesity. Methods and troubleshooting techniques for the data collection of this study are presented. We discuss …

Tgf-Β1 Increases Viral Burden And Promotes Hiv-1 Latency In Primary Differentiated Human Bronchial Epithelial Cells, S. Chinnapaiyan, R. K. Dutta, Madhavan Nair, Hitendra S. Chand, I. Rahman, H. J. Unwalla

HWCOM Faculty Publications

Combination antiretroviral therapy (cART) has increased the life expectancy of HIV patients. However, the incidence of non-AIDS associated lung comorbidities, such as COPD and asthma, and that of opportunistic lung infections have become more common among this population. HIV proteins secreted by the anatomical HIV reservoirs can have both autocrine and paracrine effects contributing to the HIV-associated comorbidities. HIV has been recovered from cell-free bronchoalveolar lavage fluid, alveolar macrophages, and intrapulmonary lymphocytes. We have recently shown that ex-vivo cultured primary bronchial epithelial cells and the bronchial brushings from human subjects express canonical HIV receptors CD4, CCR5 and CXCR4 …

Risk Scores For Type 2 Diabetes Mellitus In Latin America: A Systematic Review Of Population‐Based Studies, R.M. Carrillo, D. J. Aparcana-Granda, J. R. Mejia, Noel C. Barengo, A. Bernabe-Ortiz

HWCOM Faculty Publications

Aim

To summarize the evidence on diabetes risk scores for Latin American populations.

Methods

A systematic review was conducted (CRD42019122306) looking for diagnostic and prognostic models for type 2 diabetes mellitus among randomly selected adults in Latin America. Five databases (LILACS, Scopus, MEDLINE, Embase and Global Health) were searched. type 2 diabetes mellitus was defined using at least one blood biomarker and the reports needed to include information on the development and/or validation of a multivariable regression model. Risk of bias was assessed using the PROBAST guidelines.

Results

Of the 1500 reports identified, 11 were studied in detail and five …

Adapting Flint For Calculating Bacterial Replication Rates In Microbiomes, Vitalii Stebliankin, Camilo Valdes, Kalai Mathee, Giri Narasimhan

HWCOM Faculty Publications

We extend Flint, a Spark-based metagenomic profiling tool, to efficiently measure bacterial growth rates for large data sets. The tool bPTR for bacterial growth rate measurement from metagenomic samples [Brown et al., Nat Biotech, 2016] was adapted and integrated into Flint’s MapReduce framework in order to take advantage of Flint's efficient read alignments and mapping, thus enabling the creation of bacterial abundance profiles that are enhanced with growth-rate information.
To show the viability of our method we analyzed whole metagenome sequence data from a longitudinal study of sampled preterm infants [Gibson et al., Nat Micro, 2016], computing the abundance profile …