Power of inclusion: Enhancing polygenic prediction with admixed individuals.

Admixed individuals offer unique opportunities for addressing limited transferability in polygenic scores (PGSs), given the substantial trans-ancestry genetic correlation in many complex traits. However, they are rarely considered in PGS training, given the challenges in representing ancestry-matched linkage-disequilibrium reference panels for admixed individuals. Here we present inclusive PGS (iPGS), which captures ancestry-shared genetic effects by finding the exact solution for penalized regression on individual-level data and is thus naturally applicable to admixed individuals. We validate our approach in a simulation study across 33 configurations with varying heritability, polygenicity, and ancestry composition in the training set. When iPGS is applied to n = 237,055 ancestry-diverse individuals in the UK Biobank, it shows the greatest improvements in Africans by 48.9% on average across 60 quantitative traits and up to 50-fold improvements for some traits (neutrophil count, R2 = 0.058) over the baseline model trained on the same number of European individuals. When we allowed iPGS to use n = 284,661 individuals, we observed an average improvement of 60.8% for African, 11.6% for South Asian, 7.3% for non-British White, 4.8% for White British, and 17.8% for the other individuals. We further developed iPGS+refit to jointly model the ancestry-shared and -dependent genetic effects when heterogeneous genetic associations were present. For neutrophil count, for example, iPGS+refit showed the highest predictive performance in the African group (R2 = 0.115), which exceeds the best predictive performance for the White British group (R2 = 0.090 in the iPGS model), even though only 1.49% of individuals used in the iPGS training are of African ancestry. Our results indicate the power of including diverse individuals for developing more equitable PGS models.

m6Aexpress-enet: Predicting the regulatory expression m6A sites by an enet-regularization negative binomial regression model.

As the most abundant mRNA modification, m6A controls and influences many aspects of mRNA metabolism including the mRNA stability and degradation. However, the role of specific m6A sites in regulating gene expression still remains unclear. In additional, the multicollinearity problem caused by the correlation of methylation level of multiple m6A sites in each gene could influence the prediction performance. To address the above challenges, we propose an elastic-net regularized negative binomial regression model (called m6Aexpress-enet) to predict which m6A site could potentially regulate its gene expression. Comprehensive evaluations on simulated datasets demonstrate that m6Aexpress-enet could achieve the top prediction performance. Applying m6Aexpress-enet on real MeRIP-seq data from human lymphoblastoid cell lines, we have uncovered the complex regulatory pattern of predicted m6A sites and their unique enrichment pathway of the constructed co-methylation modules. m6Aexpress-enet proves itself as a powerful tool to enable biologists to discover the mechanism of m6A regulatory gene expression. Furthermore, the source code and the step-by-step implementation of m6Aexpress-enet is freely accessed at https://github.com/tengzhangs/m6Aexpress-enet.

Prediction of individual brain age using movie and resting-state fMRI.

Brain age is a promising biomarker for predicting chronological age based on brain imaging data. Although movie and resting-state functional MRI techniques have attracted much research interest for the investigation of brain function, whether the 2 different imaging paradigms show similarities and differences in terms of their capabilities and properties for predicting brain age remains largely unexplored. Here, we used movie and resting-state functional MRI data from 528 participants aged from 18 to 87 years old in the Cambridge Centre for Ageing and Neuroscience data set for functional network construction and further used elastic net for age prediction model building. The connectivity properties of movie and resting-state functional MRI were evaluated based on the connections supporting predictive model building. We found comparable predictive abilities of movie and resting-state connectivity in estimating brain age of individuals, as evidenced by correlation coefficients of 0.868 and 0.862 between actual and predicted age, respectively. Despite some similarities, notable differences in connectivity properties were observed between the predictive models using movie and resting-state functional MRI data, primarily involving components of the default mode network. Our results highlight that both movie and resting-state functional MRI are effective and promising techniques for predicting brain age. Leveraging its data acquisition advantages, such as improved child and patient compliance resulting in reduced motion artifacts, movie functional MRI is emerging as an important paradigm for studying brain function in pediatric and clinical populations.

expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer.

BACKGROUND: Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventional approaches to HRD prognostication has generally centered on identifying deleterious mutations within the BRCA1/2 genes, along with quantifying the genomic scars, such as Genomic Instability Score (GIS) estimation with scarHRD. However, the scarHRD method has limitations in scenarios involving tumors bereft of corresponding germline data. Although several RNA-seq-based HRD prediction algorithms have been developed, they mainly support cohort-wise classification, thereby yielding HRD status without furnishing an analogous quantitative metric akin to scarHRD. This study introduces the expHRD method, which operates as a novel transcriptome-based framework tailored to n-of-1-style HRD scoring. RESULTS: The prediction model has been established using the elastic net regression method in the Cancer Genome Atlas (TCGA) pan-cancer training set. The bootstrap technique derived the HRD geneset for applying the expHRD calculation. The expHRD demonstrated a notable correlation with scarHRD and superior performance in predicting HRD-high samples. We also performed intra- and extra-cohort evaluations for clinical feasibility in the TCGA-OV and the Genomic Data Commons (GDC) ovarian cancer cohort, respectively. The innovative web service designed for ease of use is poised to extend the realms of HRD prediction across diverse malignancies, with ovarian cancer standing as an emblematic example. CONCLUSIONS: Our novel approach leverages the transcriptome data, enabling the prediction of HRD status with remarkable precision. This innovative method addresses the challenges associated with limited available data, opening new avenues for utilizing transcriptomics to inform clinical decisions.

Prenatal Exposure to Opioids and Neurodevelopmental Disorders in Children: A Bayesian Mediation Analysis.

This study explores natural direct and joint natural indirect effects (JNIE) of prenatal opioid exposure on neurodevelopmental disorders (NDDs) in children mediated through pregnancy complications, major and minor congenital malformations, and adverse neonatal outcomes, using Medicaid claims linked to vital statistics in Rhode Island, United States, 2008-2018. A Bayesian mediation analysis with elastic net shrinkage prior was developed to estimate mean time to NDD diagnosis ratio using posterior mean and 95% credible intervals (CrIs) from Markov chain Monte Carlo algorithms. Simulation studies showed desirable model performance. Of 11,176 eligible pregnancies, 332 had ≥2 dispensations of prescription opioids anytime during pregnancy, including 200 (1.8%) having ≥1 dispensation in the first trimester (T1), 169 (1.5%) in the second (T2), and 153 (1.4%) in the third (T3). A significant JNIE of opioid exposure was observed in each trimester (T1, JNIE = 0.97, 95% CrI: 0.95, 0.99; T2, JNIE = 0.97, 95% CrI: 0.95, 0.99; T3, JNIE = 0.96, 95% CrI: 0.94, 0.99). The proportion of JNIE in each trimester was 17.9% (T1), 22.4% (T2), and 56.3% (T3). In conclusion, adverse pregnancy and birth outcomes jointly mediated the association between prenatal opioid exposure and accelerated time to NDD diagnosis. The proportion of JNIE increased as the timing of opioid exposure approached delivery.

Performance of machine-learning approach for prediction of pre-eclampsia in a middle-income country.

OBJECTIVE: Pre-eclampsia (PE) is a serious complication of pregnancy associated with maternal and fetal morbidity and mortality. As current prediction models have limitations and may not be applicable in resource-limited settings, we aimed to develop a machine-learning (ML) algorithm that offers a potential solution for developing accurate and efficient first-trimester prediction of PE. METHODS: We conducted a prospective cohort study in Mexico City, Mexico to develop a first-trimester prediction model for preterm PE (pPE) using ML. Maternal characteristics and locally derived multiples of the median (MoM) values for mean arterial pressure, uterine artery pulsatility index and serum placental growth factor were used for variable selection. The dataset was split into training, validation and test sets. An elastic-net method was employed for predictor selection, and model performance was evaluated using area under the receiver-operating-characteristics curve (AUC) and detection rates (DR) at 10% false-positive rates (FPR). RESULTS: The final analysis included 3050 pregnant women, of whom 124 (4.07%) developed PE. The ML model showed good performance, with AUCs of 0.897, 0.963 and 0.778 for pPE, early-onset PE (ePE) and any type of PE (all-PE), respectively. The DRs at 10% FPR were 76.5%, 88.2% and 50.1% for pPE, ePE and all-PE, respectively. CONCLUSIONS: Our ML model demonstrated high accuracy in predicting pPE and ePE using first-trimester maternal characteristics and locally derived MoM. The model may provide an efficient and accessible tool for early prediction of PE, facilitating timely intervention and improved maternal and fetal outcome. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Eficiencia de un enfoque de aprendizaje automático para la predicción de la preeclampsia en un país de ingresos medios OBJETIVO: La preeclampsia (PE) es una complicación grave del embarazo asociada a morbilidad y mortalidad materna y del feto. Dado que los modelos de predicción actuales tienen limitaciones y pueden no ser aplicables en situaciones con recursos limitados, se propuso desarrollar un algoritmo de aprendizaje automático (AA) que ofrezca una solución con potencial para desarrollar una predicción precisa y eficiente de la PE en el primer trimestre. MÉTODOS: Se realizó un estudio de cohorte prospectivo en Ciudad de México para desarrollar un modelo de predicción de la PE pretérmino (PEp) en el primer trimestre utilizando AA. Para la selección de variables se utilizaron las características maternas y los múltiplos de la mediana (MdM) obtenidos localmente para la presión arterial media, el índice de pulsatilidad de la arteria uterina y el factor de crecimiento placentario sérico. El conjunto de datos se dividió en subconjuntos de datos de entrenamiento, de validación y de test estadístico. Se empleó un método de red elástica para la selección de predictores, y el rendimiento del modelo se evaluó mediante el área bajo la curva de características operativas del receptor (ABC) y las tasas de detección (TD) con tasas de falsos positivos (TFP) del 10%. RESULTADOS: El análisis final incluyó a 3050 mujeres embarazadas, de las cuales 124 (4,07%) desarrollaron PE. El modelo de AA mostró una buena eficiencia, con un ABC de 0,897, 0,963 y 0,778 para la PEp, la PE de aparición temprana (PEat) y cualquier tipo de PE (todas las PE), respectivamente. Las TD con TFP del 10% fueron del 76,5%, 88,2% y 50,1% para la PEp, PEat y todas las PE, respectivamente. CONCLUSIONES: Nuestro modelo de AA demostró una alta precisión en la predicción de la PEp y la PEat utilizando características maternas del primer trimestre y MdM calculados localmente. El modelo puede proporcionar una herramienta eficiente y accesible para la predicción temprana de la PE, facilitando la intervención oportuna y la mejora de los resultados maternos y del feto.

Face recognition ability can be predicted by microstructural properties of white matter: a study of diffusion tensor imaging (DTI).

There is a great individual difference in people's face recognition ability (FRA). This study aimed to reveal the neural mechanism underlying such individual differences. Elastic-net regression models were constructed to predict FRA based on the white matter (WM) microstructural properties. We found that FRA can be accurately predicted by the WM microstructural properties. For the right inferior longitudinal fasciculus (ILF) and bilateral arcuate fasciculus (AF), FRA was correlated negatively to fractional anisotropy (FA), but positively to radial diffusivity (RD). In contrast, for the corpus callosum forceps minor (CFM), FRA was correlated positively to FA, but negatively to RD. Such various patterns of the WM microstructural properties suggested a positive correlation between FRA and fiber diameter for the right ILF and bilateral AF, but a negative correlation between FRA and diameter of the CFM. These findings reflected that FRA was correlated positively to connectivities of the right ILF and bilateral AF, but negatively to those of the CFM. These findings not only confirmed the significant role of the right ILF in face recognition, but also revealed the involvement of the bilateral AF and CFM in face recognition, particularly implying the important role of hemisphere lateralization modulated by transcallosal connectivity in face recognition.

Associations between exposure to pesticides mixture and semen quality among the non-occupationally exposed males: Four statistical models.

Most epidemiological studies on the associations between pesticides exposure and semen quality have been based on a single pesticide, with inconsistent major results. In contrast, there was limited human evidence on the potential effect of pesticides mixture on semen quality. Our study aimed to investigate the relationship of pesticide profiles with semen quality parameters among 299 non-occupationally exposed males aged 25-50 without any clinical abnormalities. Serum concentrations of 21 pesticides were quantified by gas chromatography-tandem mass spectrometry (GC-MS/MS). Semen quality parameters were abstracted from medical records. Generalized linear regression models (GLMs) and three mixture approaches, including weighted quantile sum regression (WQS), elastic net regression (ENR) and Bayesian kernel machine regression (BKMR), were applied to explore the single and mixed effects of pesticide exposure on semen quality. In GLMs, as the serum levels of Bendiocarb, ß-BHC, Clomazone, Dicrotophos, Dimethenamid, Paclobutrazole, Pentachloroaniline and Pyrimethanil increased, the straight-line velocity (VSL), linearity (LIN) and straightness (STR) decreased. This negative association also occurred between the concentration of ß-BHC, Pentachloroaniline, Pyrimethanil and progressive motility, total motility. In the WQS models, pesticides mixture was negatively associated with total motility and several sperm motility parameters (ß: -3.07∼-1.02 per decile, FDR-P<0.05). After screening the important pesticides derived from the mixture by ENR model, the BKMR models showed that the decreased qualities for VSL, LIN, and STR were also observed when pesticide mixtures were at ≥ 70th percentiles. Clomazone, Dimethenamid, and Pyrimethanil (Posterior inclusion probability, PIP: 0.2850-0.8900) were identified as relatively important contributors. The study provides evidence that exposure to single or mixed pesticide was associated with impaired semen quality.

Gestational exposure to organochlorine compounds and metals and infant birth weight: effect modification by maternal hardships.

BACKGROUND: Gestational exposure to toxic environmental chemicals and maternal social hardships are individually associated with impaired fetal growth, but it is unclear whether the effects of environmental chemical exposure on infant birth weight are modified by maternal hardships. METHODS: We used data from the Maternal-Infant Research on Environmental Chemicals (MIREC) Study, a pan-Canadian cohort of 1982 pregnant females enrolled between 2008 and 2011. We quantified eleven environmental chemical concentrations from two chemical classes - six organochlorine compounds (OCs) and five metals - that were detected in ≥ 70% of blood samples collected during the first trimester. We examined fetal growth using birth weight adjusted for gestational age and assessed nine maternal hardships by questionnaire. Each maternal hardship variable was dichotomized to indicate whether the females experienced the hardship. In our analysis, we used elastic net to select the environmental chemicals, maternal hardships, and 2-way interactions between maternal hardships and environmental chemicals that were most predictive of birth weight. Next, we obtained effect estimates using multiple linear regression, and plotted the relationships by hardship status for visual interpretation. RESULTS: Elastic net selected trans-nonachlor, lead, low educational status, racially minoritized background, and low supplemental folic acid intake. All were inversely associated with birth weight. Elastic net also selected interaction terms. Among those with increasing environmental chemical exposures and reported hardships, we observed stronger negative associations and a few positive associations. For example, every two-fold increase in lead concentrations was more strongly associated with reduced infant birth weight among participants with low educational status (ß = -100 g (g); 95% confidence interval (CI): -215, 16), than those with higher educational status (ß = -34 g; 95% CI: -63, -3). In contrast, every two-fold increase in mercury concentrations was associated with slightly higher birth weight among participants with low educational status (ß = 23 g; 95% CI: -25, 71) compared to those with higher educational status (ß = -9 g; 95% CI: -24, 6). CONCLUSIONS: Our findings suggest that maternal hardships can modify the associations of gestational exposure to some OCs and metals with infant birth weight.

3D Galileo Reference Antenna Pattern for Space Service Volume Applications.

There is an increasing demand for navigation capability for space vehicles. The exploitation of the so-called Space Service Volume (SSV), and hence the extension of the Global Navigation Satellite System (GNSS) from terrestrial to space users, is currently considered a fundamental step. Knowledge of the constellation antenna pattern, including the side lobe signals, is the main input for assessing the expected GNSS signal availability and navigation performance, especially for high orbits. The best way to define and share this information with the final GNSS user is still an open question. This paper proposes a novel methodology for the definition of a high-fidelity and easy-to-use statistical model to represent GNSS constellation antenna patterns. The reconstruction procedure, based on antenna characterization techniques and statistical learning, is presented here through its successful implementation for the "Galileo Reference Antenna Pattern (GRAP)" model, which has been proposed as the reference model for the Galileo programme. The GRAP represents the expected Equivalent Isotropic Radiated Power (EIRP) variation for the Galileo FOC satellites, and it is obtained by processing the measurements retrieved during the characterization campaign performed on the Galileo FOC antennas. The mathematical background of the model is analyzed in depth in order to better assess the GRAP with respect to different objectives such as improved resolution, smoothness and proper representation of the antenna pattern statistical distribution. The analysis confirms the enhanced GRAP properties and envisages the possibility of extending the approach to other GNSSs. The discussion is complemented by a preliminary use case characterization of the Galileo performance in SSV. The accessibility, a novel indicator, is defined in order to represent in a quick and compact manner, the expected Galileo SSV quality for different altitudes and target mission requirements. The SSV characterization is performed to demonstrate how simply and effectively the GRAP model can be inserted into user analysis. The work creates the basis for an improved capability for assessing Galileo-based navigation in SSV according to the current knowledge of the antenna pattern.

Predicting Biochemical and Physiological Parameters: Deep Learning from IgG Glycome Composition.

In immunoglobulin G (IgG), N-glycosylation plays a pivotal role in structure and function. It is often altered in different diseases, suggesting that it could be a promising health biomarker. Studies indicate that IgG glycosylation not only associates with various diseases but also has predictive capabilities. Additionally, changes in IgG glycosylation correlate with physiological and biochemical traits known to reflect overall health state. This study aimed to investigate the power of IgG glycans to predict physiological and biochemical parameters. We developed two models using IgG N-glycan data as an input: a regression model using elastic net and a machine learning model using deep learning. Data were obtained from the Korcula and Vis cohorts. The Korcula cohort data were used to train both models, while the Vis cohort was used exclusively for validation. Our results demonstrated that IgG glycome composition effectively predicts several biochemical and physiological parameters, especially those related to lipid and glucose metabolism and cardiovascular events. Both models performed similarly on the Korcula cohort; however, the deep learning model showed a higher potential for generalization when validated on the Vis cohort. This study reinforces the idea that IgG glycosylation reflects individuals' health state and brings us one step closer to implementing glycan-based diagnostics in personalized medicine. Additionally, it shows that the predictive power of IgG glycans can be used for imputing missing covariate data in deep learning frameworks.

Integrating High-Resolution Mass Spectral Data, Bioassays and Computational Models to Annotate Bioactives in Botanical Extracts: Case Study Analysis of C. asiatica Extract Associates Dicaffeoylquinic Acids with Protection against Amyloid-ß Toxicity.

Rapid screening of botanical extracts for the discovery of bioactive natural products was performed using a fractionation approach in conjunction with flow-injection high-resolution mass spectrometry for obtaining chemical fingerprints of each fraction, enabling the correlation of the relative abundance of molecular features (representing individual phytochemicals) with the read-outs of bioassays. We applied this strategy for discovering and identifying constituents of Centella asiatica (C. asiatica) that protect against Aß cytotoxicity in vitro. C. asiatica has been associated with improving mental health and cognitive function, with potential use in Alzheimer's disease. Human neuroblastoma MC65 cells were exposed to subfractions of an aqueous extract of C. asiatica to evaluate the protective benefit derived from these subfractions against amyloid ß-cytotoxicity. The % viability score of the cells exposed to each subfraction was used in conjunction with the intensity of the molecular features in two computational models, namely Elastic Net and selectivity ratio, to determine the relationship of the peak intensity of molecular features with % viability. Finally, the correlation of mass spectral features with MC65 protection and their abundance in different sub-fractions were visualized using GNPS molecular networking. Both computational methods unequivocally identified dicaffeoylquinic acids as providing strong protection against Aß-toxicity in MC65 cells, in agreement with the protective effects observed for these compounds in previous preclinical model studies.

GBDT_KgluSite: An improved computational prediction model for lysine glutarylation sites based on feature fusion and GBDT classifier.

BACKGROUND: Lysine glutarylation (Kglu) is one of the most important Post-translational modifications (PTMs), which plays significant roles in various cellular functions, including metabolism, mitochondrial processes, and translation. Therefore, accurate identification of the Kglu site is important for elucidating protein molecular function. Due to the time-consuming and expensive limitations of traditional biological experiments, computational-based Kglu site prediction research is gaining more and more attention. RESULTS: In this paper, we proposed GBDT_KgluSite, a novel Kglu site prediction model based on GBDT and appropriate feature combinations, which achieved satisfactory performance. Specifically, seven features including sequence-based features, physicochemical property-based features, structural-based features, and evolutionary-derived features were used to characterize proteins. NearMiss-3 and Elastic Net were applied to address data imbalance and feature redundancy issues, respectively. The experimental results show that GBDT_KgluSite has good robustness and generalization ability, with accuracy and AUC values of 93.73%, and 98.14% on five-fold cross-validation as well as 90.11%, and 96.75% on the independent test dataset, respectively. CONCLUSION: GBDT_KgluSite is an effective computational method for identifying Kglu sites in protein sequences. It has good stability and generalization ability and could be useful for the identification of new Kglu sites in the future. The relevant code and dataset are available at https://github.com/flyinsky6/GBDT_KgluSite .

A machine learning-derived neuroanatomical pattern predicts delayed reward discounting in the Human Connectome Project Young Adult sample.

Delayed reward discounting (DRD) is defined as the extent to which person favors smaller rewards that are immediately available over larger rewards available in the future. Higher levels of DRD have been identified in individuals with a wide range of clinical disorders. Although there have been studies adopting larger samples and using only gray matter volume to characterize the neuroanatomical correlates of DRD, it is still unclear whether previously identified relationships are generalizable (out-of-sample) and how cortical thickness and cortical surface area contribute to DRD. In this study, using the Human Connectome Project Young Adult dataset (N = 1038), a machine learning cross-validated elastic net regression approach was used to characterize the neuroanatomical pattern of structural magnetic resonance imaging variables associated with DRD. The results revealed a multi-region neuroanatomical pattern predicted DRD and this was robust in a held-out test set (morphometry-only R2 = 3.34%, morphometry + demographics R2  = 6.96%). The neuroanatomical pattern included regions implicated in the default mode network, executive control network, and salience network. The relationship of these regions with DRD was further supported by univariate linear mixed effects modeling results, in which many of the regions identified as part of this pattern showed significant univariate associations with DRD. Taken together, these findings provide evidence that a machine learning-derived neuroanatomical pattern encompassing various theoretically relevant brain networks produces robustly predicts DRD in a large sample of healthy young adults.

Transcriptomes of the tumor-adjacent normal tissues are more informative than tumors in predicting recurrence in colorectal cancer patients.

BACKGROUND: Previous investigations of transcriptomic signatures of cancer patient survival and post-therapy relapse have focused on tumor tissue. In contrast, here we show that in colorectal cancer (CRC) transcriptomes derived from normal tissues adjacent to tumors (NATs) are better predictors of relapse. RESULTS: Using the transcriptomes of paired tumor and NAT specimens from 80 Korean CRC patients retrospectively determined to be in recurrence or nonrecurrence states, we found that, when comparing recurrent with nonrecurrent samples, NATs exhibit a greater number of differentially expressed genes (DEGs) than tumors. Training two prognostic elastic net-based machine learning models-NAT-based and tumor-based in our Samsung Medical Center (SMC) cohort, we found that NAT-based model performed better in predicting the survival when the model was applied to the tumor-derived transcriptomes of an independent cohort of 450 COAD patients in TCGA. Furthermore, compositions of tumor-infiltrating immune cells in NATs were found to have better prognostic capability than in tumors. We also confirmed through Cox regression analysis that in both SMC-CRC as well as in TCGA-COAD cohorts, a greater proportion of genes exhibited significant hazard ratio when NAT-derived transcriptome was used compared to when tumor-derived transcriptome was used. CONCLUSIONS: Taken together, our results strongly suggest that NAT-derived transcriptomes and immune cell composition of CRC are better predictors of patient survival and tumor recurrence than the primary tumor.

Methods for estimating insulin resistance from untargeted metabolomics data.

CONTEXT: Insulin resistance is associated with multiple complex diseases; however, precise measures of insulin resistance are invasive, expensive, and time-consuming. OBJECTIVE: Develop estimation models for measures of insulin resistance, including insulin sensitivity index (SI) and homeostatic model assessment of insulin resistance (HOMA-IR) from metabolomics data. DESIGN: Insulin Resistance Atherosclerosis Family Study (IRASFS). SETTING: Community based. PARTICIPANTS: Mexican Americans (MA) and African Americans (AA). MAIN OUTCOME: Estimation models for measures of insulin resistance, i.e. SI and HOMA-IR. RESULTS: Least Absolute Shrinkage and Selection Operator (LASSO) and Elastic Net regression were used to build insulin resistance estimation models from 1274 metabolites combined with clinical data, e.g. age, sex, body mass index (BMI). Metabolite data were transformed using three approaches, i.e. inverse normal transformation, standardization, and Box Cox transformation. The analysis was performed in one MA recruitment site (San Luis Valley, Colorado (SLV); N = 450) and tested in another MA recruitment site (San Antonio, Texas (SA); N = 473). In addition, the two MA recruitment sites were combined and estimation models tested in the AA recruitment sample (Los Angeles, California; N = 495). Estimated and empiric SI were correlated in the SA (r2 = 0.77) and AA (r2 = 0.74) testing datasets. Further, estimated and empiric SI were consistently associated with BMI, low-density lipoprotein cholesterol (LDL), and triglycerides. We applied similar approaches to estimate HOMA-IR with similar results. CONCLUSIONS: We have developed a method for estimating insulin resistance with metabolomics data that has the potential for application to a wide range of biomedical studies and conditions.

Reader reaction to "Outcome-adaptive lasso: Variable selection for causal inference" by Shortreed and Ertefaie (2017).

Shortreed and Ertefaie introduced a clever propensity score variable selection approach for estimating average causal effects, namely, the outcome adaptive lasso (OAL). OAL aims to select desirable covariates, confounders, and predictors of outcome, to build an unbiased and statistically efficient propensity score estimator. Due to its design, a potential limitation of OAL is how it handles the collinearity problem, which is often encountered in high-dimensional data. As seen in Shortreed and Ertefaie, OAL's performance degraded with increased correlation between covariates. In this note, we propose the generalized OAL (GOAL) that combines the strengths of the adaptively weighted L1 penalty and the elastic net to better handle the selection of correlated covariates. Two different versions of GOAL, which differ in their procedure (algorithm), are proposed. We compared OAL and GOAL in simulation scenarios that mimic those examined by Shortreed and Ertefaie. Although all approaches performed equivalently with independent covariates, we found that both GOAL versions were more performant than OAL in low and high dimensions with correlated covariates.

Variable selection for discrete survival model with frailty in presence of left truncation and right censoring: Studying association of environmental toxicants on time-to-pregnancy.

Understanding the association between mixtures of environmental toxicants and time-to-pregnancy (TTP) is an important scientific question as sufficient evidence has emerged about the impact of individual toxicants on reproductive health and that individuals are exposed to a whole host of toxicants rather than an individual toxicant. Assessing mixtures of chemical effects on TTP poses significant statistical challenges, namely (i) TTP being a discrete survival outcome, typically subject to left truncation and right censoring, (ii) chemical exposures being strongly correlated, (iii) appropriate transformation to account for some lipid-binding chemicals, (iv) non-linear effects of some chemicals, and (v) high percentage of concentration below the limit of detection (LOD) for some chemicals. We propose a discrete frailty modeling framework (named Discnet) that allows selection of correlated covariates while appropriately addressing the methodological issues mentioned above. Discnet is shown to have better and stable false negative and false positive rates compared to alternative methods in various simulation settings. We did a detailed analysis of the pre-conception endocrine disrupting chemicals and TTP from the LIFE study and found that older females, female exposure to cotinine (smoking), DDT conferred a delay in getting pregnant, which was consistent across various approaches to account for LOD as well as non-linear associations.

A hybrid of regularization method and generalized path analysis: modeling single-vehicle run-off-road crashes in a cross-sectional study.

BACKGROUND: Determining risk factors of single-vehicle run-off-road (SV-ROR) crashes, as a significant number of all the single-vehicle crashes and all the fatalities, may provide infrastructure for quicker and more effective safety measures to explore the influencing and moderating variables in SV-ROR. Therefore, this paper emphasizes utilizing a hybrid of regularization method and generalized path analysis for studying SV-ROR crashes to identify variables influencing their happening and severity. METHODS: This cross-sectional study investigated 724 highway SV-ROR crashes from 2015 to 2016. To drive the key variables influencing SV-ROR crashes Ridge, Least Absolute Shrinkage and Selection Operator (Lasso), and Elastic net regularization methods were implemented. The goodness of fit of utilized methods in a testing sample was assessed using the deviance and deviance ratio. A hybrid of Lasso regression (LR) and generalized path analysis (gPath) was used to detect the cause and mediators of SV-ROR crashes. RESULTS: Findings indicated that the final modified model fitted the data accurately with [Formula: see text]= 16.09, P < .001, [Formula: see text]/ degrees of freedom = 5.36 > 5, CFI = .94 > .9, TLI = .71 < .9, RMSEA = 1.00 > .08 (90% CI = (.06 to .15)). Also, the presence of passenger (odds ratio (OR) = 2.31, 95% CI = (1.73 to 3.06)), collision type (OR = 1.21, 95% CI = (1.07 to 1.37)), driver misconduct (OR = 1.54, 95% CI = (1.32 to 1.79)) and vehicle age (OR = 2.08, 95% CI = (1.77 to 2.46)) were significant cause of fatality outcome. The proposed causal model identified collision type and driver misconduct as mediators. CONCLUSIONS: The proposed HLR-gPath model can be considered a useful theoretical structure to describe how the presence of passenger, collision type, driver misconduct, and vehicle age can both predict and mediate fatality among SV-ROR crashes. While notable progress has been made in implementing road safety measures, it is essential to emphasize that operative preventative measures still remain the most effective approach for reducing the burden of crashes, considering the critical components identified in this study.

Development of a novel machine learning-based weighted modeling approach to incorporate Salmonella enterica heterogeneity on a genetic scale in a dose-response modeling framework.

Estimating microbial dose-response is an important aspect of a food safety risk assessment. In recent years, there has been considerable interest to advance these models with potential incorporation of gene expression data. The aim of this study was to develop a novel machine learning model that considers the weights of expression of Salmonella genes that could be associated with illness, given exposure, in hosts. Here, an elastic net-based weighted Poisson regression method was proposed to identify Salmonella enterica genes that could be significantly associated with the illness response, irrespective of serovar. The best-fit elastic net model was obtained by 10-fold cross-validation. The best-fit elastic net model identified 33 gene expression-dose interaction terms that added to the predictability of the model. Of these, nine genes associated with Salmonella metabolism and virulence were found to be significant by the best-fit Poisson regression model (p < 0.05). This method could improve or redefine dose-response relationships for illness from relative proportions of significant genes from a microbial genetic dataset, which would help in refining endpoint and risk estimations.