Penalized Regression Models to Select Biomarkers of Environmental Enteropathy Associated with Linear Growth Acquisition in a Peruvian Birth Cohort

2019 ◽  
Author(s):  
Josh Colston ◽  
Pablo Peñataro Yori ◽  
Lawrence H. Moulton ◽  
Maribel Paredes Olortegui ◽  
Peter S. Kosek ◽  
...  
Keyword(s):  
Birth Cohort ◽  
Regression Models ◽  
Linear Growth ◽  
Penalized Regression ◽  
Environmental Enteropathy

scholarly journals Penalized regression models to select biomarkers of environmental enteric dysfunction associated with linear growth acquisition in a Peruvian birth cohort

2019 ◽  
Vol 13 (11) ◽  
pp. e0007851
Author(s):  
Josh M. Colston ◽  
Pablo Peñataro Yori ◽  
Lawrence H. Moulton ◽  
Maribel Paredes Olortegui ◽  
Peter S. Kosek ◽  
...  
Keyword(s):  
Birth Cohort ◽  
Regression Models ◽  
Linear Growth ◽  
Penalized Regression ◽  
Environmental Enteric Dysfunction

scholarly journals Diarrheal Pathogens Associated with Growth and Neurodevelopment

2021 ◽  
Author(s):  
Jeffrey R Donowitz ◽  
Jeannie Drew ◽  
Mami Taniuchi ◽  
James A Platts-Mills ◽  
Masud Alam ◽  
...  
Keyword(s):  
Cohort Study ◽  
Socioeconomic Factors ◽  
Birth Cohort ◽  
Linear Growth ◽  
Attributable Fraction ◽  
Birth Cohort Study ◽  
Neurodevelopmental Outcomes ◽  
Typical Epec ◽  
Toddler Development ◽  
Pathogen Burden

Abstract Background Diarrheal pathogens have been associated with linear growth deficits. The effect of diarrheal pathogens on growth is likely due to inflammation which also adversely affects neurodevelopment. We hypothesized that diarrheagenic pathogens would be negatively associated with both growth and neurodevelopment. Methods We conducted a longitudinal birth cohort study of 250 children with diarrheal surveillance and measured pathogen burden in diarrheal samples using quantitative PCR. Pathogen attributable fraction estimates (AFe) of diarrhea over the first two years of life, corrected for socioeconomic variables, were used to predict both growth and scores on the Bayley III Scales of Infant and Toddler Development. Results 180 children were analyzed for growth and 162 for neurodevelopmental outcomes. Rotavirus, Campylobacter, and Shigella were the leading causes of diarrhea in year 1 while Shigella, Campylobacter, and ST-ETEC were the leading causes in year 2. Norovirus was the only pathogen associated with LAZ at 24 months and was positively associated (RC 0.42, CI 0.04, 0.80). Norovirus (RC 2.46, CI 0.05 – 4.87) was also positively associated with cognitive scores while sapovirus (RC -2.64, CI -4.80 – -0.48) and Typical EPEC (RC -4.14, CI -8.02 – -0.27) were inversely associated. No pathogens were associated with language or motor scores. Significant maternal, socioeconomic, and perinatal predictors were identified for both growth and neurodevelopment. Conclusion Maternal, prenatal, and socioeconomic factors were common predictors of growth and neurodevelopment. Only a limited number of diarrheal pathogens were associated with these outcomes.

scholarly journals Survival Analysis by Penalized Regression and Matrix Factorization

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Yeuntyng Lai ◽  
Morihiro Hayashida ◽  
Tatsuya Akutsu
Keyword(s):  
Matrix Factorization ◽  
Regression Models ◽  
Nonnegative Matrix ◽  
B Cell Lymphoma ◽  
Penalized Regression ◽  
Survival Prediction ◽  
Suitable Model ◽  
Gene Expressions ◽  
Combination Methods ◽  
Survival Patterns

Because every disease has its unique survival pattern, it is necessary to find a suitable model to simulate followups. DNA microarray is a useful technique to detect thousands of gene expressions at one time and is usually employed to classify different types of cancer. We propose combination methods of penalized regression models and nonnegative matrix factorization (NMF) for predicting survival. We triedL1- (lasso),L2- (ridge), andL1-L2combined (elastic net) penalized regression for diffuse large B-cell lymphoma (DLBCL) patients' microarray data and found thatL1-L2combined method predicts survival best with the smallest logrankPvalue. Furthermore, 80% of selected genes have been reported to correlate with carcinogenesis or lymphoma. Through NMF we found that DLBCL patients can be divided into 4 groups clearly, and it implies that DLBCL may have 4 subtypes which have a little different survival patterns. Next we excluded some patients who were indicated hard to classify in NMF and executed three penalized regression models again. We found that the performance of survival prediction has been improved with lower logrankPvalues. Therefore, we conclude that after preselection of patients by NMF, penalized regression models can predict DLBCL patients' survival successfully.

Penalized Regression Models

2019 ◽  
pp. 179-206
Author(s):  
Taylor Arnold ◽  
Michael Kane ◽  
Bryan W. Lewis
Keyword(s):  
Regression Models ◽  
Penalized Regression

scholarly journals Delirium symptoms are associated with decline in cognitive function between ages 53 to 69: findings from a British birth cohort study

2017 ◽  
Author(s):  
A Tsui ◽  
D Kuh ◽  
M Richards ◽  
D Davis
Keyword(s):  
Birth Cohort ◽  
Verbal Memory ◽  
Regression Models ◽  
Cognitive Outcomes ◽  
Birth Cohort Study ◽  
Linear Regression Models ◽  
Cognitive Domains ◽  
Time Period ◽  
Search Speed ◽  
Addenbrooke’S Cognitive Examination

AbstractINTRODUCTIONFew population studies have investigated whether longitudinal decline after delirium in mid-to-late life might affect specific cognitive domains.METHODSParticipants from a birth cohort completing assessments of search speed, verbal memory and the Addenbrooke’s Cognitive Examination at age 69 were asked about delirium symptoms between ages 60-69. Linear regression models estimated associations between delirium symptoms and cognitive outcomes.RESULTSPeriod prevalence of delirium between 60 and 69 was 4% (95% CI 3.2%,4.9%). Self-reported symptoms of delirium over the seventh decade were associated with worse scores in the Addenbrooke’s Cognitive Examination (−1.7 points, 95% CI −3.2, −0.1, p=0.04). In association with delirium symptoms, verbal memory scores were initially lower, with subsequent decline in search speed by age 69. These effects were independent of other Alzheimer’s risk factors.DISCUSSIONDelirium symptoms may be common even at relatively younger ages, and their presence may herald cognitive decline, particularly in search speed, over this time period.

scholarly journals Small Intestine Bacterial Overgrowth and Environmental Enteropathy in Bangladeshi Children

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Jeffrey R. Donowitz ◽  
Rashidul Haque ◽  
Beth D. Kirkpatrick ◽  
Masud Alam ◽  
Miao Lu ◽  
...  
Keyword(s):  
Small Intestine ◽  
Systemic Inflammation ◽  
Linear Growth ◽  
Developing World ◽  
Diarrheal Disease ◽  
Intestinal Inflammation ◽  
Bacterial Overgrowth ◽  
Environmental Enteropathy ◽  
Small Intestine Bacterial Overgrowth ◽  
Chronic Intestinal Inflammation

ABSTRACT Recent studies suggest small intestine bacterial overgrowth (SIBO) is common among developing world children. SIBO’s pathogenesis and effect in the developing world are unclear. Our objective was to determine the prevalence of SIBO in Bangladeshi children and its association with malnutrition. Secondary objectives included determination of SIBO’s association with sanitation, diarrheal disease, and environmental enteropathy. We performed a cross-sectional analysis of 90 Bangladeshi 2-year-olds monitored since birth from an impoverished neighborhood. SIBO was diagnosed via glucose hydrogen breath testing, with a cutoff of a 12-ppm increase over baseline used for SIBO positivity. Multivariable logistic regression was performed to investigate SIBO predictors. Differences in concomitant inflammation and permeability between SIBO-positive and -negative children were compared with multiple comparison adjustment. A total of 16.7% (15/90) of the children had SIBO. The strongest predictors of SIBO were decreased length-for-age Z  score since birth (odds ratio [OR], 0.13; 95% confidence interval [CI], 0.03 to 0.60) and an open sewer outside the home (OR, 4.78; 95% CI, 1.06 to 21.62). Recent or frequent diarrheal disease did not predict SIBO. The markers of intestinal inflammation fecal Reg 1β (116.8 versus 65.6 µg/ml; P = 0.02) and fecal calprotectin (1,834.6 versus 766.7 µg/g; P = 0.004) were elevated in SIBO-positive children. Measures of intestinal permeability and systemic inflammation did not differ between the groups. These findings suggest linear growth faltering and poor sanitation are associated with SIBO independently of recent or frequent diarrheal disease. SIBO is associated with intestinal inflammation but not increased permeability or systemic inflammation. IMPORTANCE A total of 165 million children worldwide are considered stunted, which is associated with increased risk of death prior to age 5 years and cognitive disability. Stunting has, in part, been attributed to the presence of environmental enteropathy. Environmental enteropathy is a poorly understood condition leading to chronic intestinal inflammation. It has been postulated that small intestine bacterial overgrowth contributes to the pathogenesis of environmental enteropathy as overgrowth has been associated with intestinal inflammation and micronutrient malabsorption when it develops in other clinical contexts. This study confirms the finding that overgrowth occurs at high rates in the developing world. This is the first study to show that overgrowth is associated with intestinal inflammation and linear growth delay in this setting and is the first to examine why children with no known gastrointestinal dysfunction develop overgrowth from the developing world environment.

scholarly journals A methodologic framework for modeling and assessing biomarkers of environmental enteropathy as predictors of growth in infants: an example from a Peruvian birth cohort

2017 ◽  
Vol 106 (1) ◽  
pp. 245-255 ◽  
Author(s):  
Josh M Colston ◽  
Pablo Peñataro Yori ◽  
Elizabeth Colantuoni ◽  
Lawrence H Moulton ◽  
Ramya Ambikapathi ◽  
...  
Keyword(s):  
Birth Cohort ◽  
Environmental Enteropathy
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