scholarly journals Multikernel linear mixed model with adaptive lasso for complex phenotype prediction

2020 ◽  
Vol 39 (9) ◽  
pp. 1311-1327
Author(s):  
Yalu Wen ◽  
Qing Lu
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Adaptive Lasso ◽  
Complex Phenotype ◽  
Phenotype Prediction

scholarly journals Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data

2019 ◽  
Vol 36 (6) ◽  
pp. 1785-1794
Author(s):  
Jun Li ◽  
Qing Lu ◽  
Yalu Wen
Keyword(s):  
Risk Prediction ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
R Package ◽  
Kernel Functions ◽  
Adaptive Lasso ◽  
Supplementary Information ◽  
High Dimensional ◽  
Omics Data ◽  
Modeling Framework

Abstract Motivation The use of human genome discoveries and other established factors to build an accurate risk prediction model is an essential step toward precision medicine. While multi-layer high-dimensional omics data provide unprecedented data resources for prediction studies, their corresponding analytical methods are much less developed. Results We present a multi-kernel penalized linear mixed model with adaptive lasso (MKpLMM), a predictive modeling framework that extends the standard linear mixed models widely used in genomic risk prediction, for multi-omics data analysis. MKpLMM can capture not only the predictive effects from each layer of omics data but also their interactions via using multiple kernel functions. It adopts a data-driven approach to select predictive regions as well as predictive layers of omics data, and achieves robust selection performance. Through extensive simulation studies, the analyses of PET-imaging outcomes from the Alzheimer’s Disease Neuroimaging Initiative study, and the analyses of 64 drug responses, we demonstrate that MKpLMM consistently outperforms competing methods in phenotype prediction. Availability and implementation The R-package is available at https://github.com/YaluWen/OmicPred. Supplementary information Supplementary data are available at Bioinformatics online.

Analyzing discontinuities in longitudinal count data: A multilevel generalized linear mixed model.

2020 ◽  
Author(s):  
James L. Peugh ◽  
Sarah J. Beal ◽  
Meghan E. McGrady ◽  
Michael D. Toland ◽  
Constance Mara
Keyword(s):  
Count Data ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Longitudinal Count Data

Predicting bycatch hotspots based on suitable habitat derived from fishery-independent data

2020 ◽  
Vol 641 ◽  
pp. 159-175
Author(s):  
J Runnebaum ◽  
KR Tanaka ◽  
L Guan ◽  
J Cao ◽  
L O’Brien ◽  
...  
Keyword(s):  
Habitat Suitability ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Homarus Americanus ◽  
Management Tool ◽  
American Lobster ◽  
Suitable Habitat ◽  
Climate Conditions ◽  
Suitability Index

Bycatch remains a global problem in managing sustainable fisheries. A critical aspect of management is understanding the timing and spatial extent of bycatch. Fisheries management often relies on observed bycatch data, which are not always available due to a lack of reporting or observer coverage. Alternatively, analyzing the overlap in suitable habitat for the target and non-target species can provide a spatial management tool to understand where bycatch interactions are likely to occur. Potential bycatch hotspots based on suitable habitat were predicted for cusk Brosme brosme incidentally caught in the Gulf of Maine American lobster Homarus americanus fishery. Data from multiple fisheries-independent surveys were combined in a delta-generalized linear mixed model to generate spatially explicit density estimates for use in an independent habitat suitability index. The habitat suitability indices for American lobster and cusk were then compared to predict potential bycatch hotspot locations. Suitable habitat for American lobster has increased between 1980 and 2013 while suitable habitat for cusk decreased throughout most of the Gulf of Maine, except for Georges Basin and the Great South Channel. The proportion of overlap in suitable habitat varied interannually but decreased slightly in the spring and remained relatively stable in the fall over the time series. As Gulf of Maine temperatures continue to increase, the interactions between American lobster and cusk are predicted to decline as cusk habitat continues to constrict. This framework can contribute to fisheries managers’ understanding of changes in habitat overlap as climate conditions continue to change and alter where bycatch interactions could occur.

Long-term seizure outcomes after pediatric temporal lobectomy: does brain MRI lesion matter?

2019 ◽  
Vol 24 (2) ◽  
pp. 200-208
Author(s):  
Ravindra Arya ◽  
Francesco T. Mangano ◽  
Paul S. Horn ◽  
Sabrina K. Kaul ◽  
Serena K. Kaul ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Hippocampal Sclerosis ◽  
Brain Mri ◽  
Temporal Lobectomy ◽  
Seizure Freedom ◽  
Seizure Onset

OBJECTIVEThere is emerging data that adults with temporal lobe epilepsy (TLE) without a discrete lesion on brain MRI have surgical outcomes comparable to those with hippocampal sclerosis (HS). However, pediatric TLE is different from its adult counterpart. In this study, the authors investigated if the presence of a potentially epileptogenic lesion on presurgical brain MRI influences the long-term seizure outcomes after pediatric temporal lobectomy.METHODSChildren who underwent temporal lobectomy between 2007 and 2015 and had at least 1 year of seizure outcomes data were identified. These were classified into lesional and MRI-negative groups based on whether an epilepsy-protocol brain MRI showed a lesion sufficiently specific to guide surgical decisions. These patients were also categorized into pure TLE and temporal plus epilepsies based on the neurophysiological localization of the seizure-onset zone. Seizure outcomes at each follow-up visit were incorporated into a repeated-measures generalized linear mixed model (GLMM) with MRI status as a grouping variable. Clinical variables were incorporated into GLMM as covariates.RESULTSOne hundred nine patients (44 females) were included, aged 5 to 21 years, and were classified as lesional (73%), MRI negative (27%), pure TLE (56%), and temporal plus (44%). After a mean follow-up of 3.2 years (range 1.2–8.8 years), 66% of the patients were seizure free for ≥ 1 year at last follow-up. GLMM analysis revealed that lesional patients were more likely to be seizure free over the long term compared to MRI-negative patients for the overall cohort (OR 2.58, p < 0.0001) and for temporal plus epilepsies (OR 1.85, p = 0.0052). The effect of MRI lesion was not significant for pure TLE (OR 2.64, p = 0.0635). Concordance of ictal electroencephalography (OR 3.46, p < 0.0001), magnetoencephalography (OR 4.26, p < 0.0001), and later age of seizure onset (OR 1.05, p = 0.0091) were associated with a higher likelihood of seizure freedom. The most common histological findings included cortical dysplasia types 1B and 2A, HS (40% with dual pathology), and tuberous sclerosis.CONCLUSIONSA lesion on presurgical brain MRI is an important determinant of long-term seizure freedom after pediatric temporal lobectomy. Pediatric TLE is heterogeneous regarding etiologies and organization of seizure-onset zones with many patients qualifying for temporal plus nosology. The presence of an MRI lesion determined seizure outcomes in patients with temporal plus epilepsies. However, pure TLE had comparable surgical seizure outcomes for lesional and MRI-negative groups.

scholarly journals Reducing Aggression by Developing Emotional and Inhibitory Control

2021 ◽  
Vol 18 (10) ◽  
pp. 5263
Author(s):  
Miriam Romero-López ◽  
María Carmen Pichardo ◽  
Ana Justicia-Arráez ◽  
Judit Bembibre-Serrano
Keyword(s):  
Psychosocial Development ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Emotional Control ◽  
Control Group ◽  
Post Intervention ◽  
Mixed Model Analysis ◽  
Intervention Measures ◽  
Experimental Group

The objective of this study is to measure the effectiveness of a program on improving inhibitory and emotional control among children. In addition, it is assessed whether the improvement of these skills has an effect on the reduction of aggressive behavior in pre-school children. The participants were 100 children, 50 belonging to the control group and 50 to the experimental group, aged between 5 and 6 years. Pre-intervention and post-intervention measures of inhibitory and emotional control (BRIEF-P) and aggression (BASC) were taken. A Generalized Linear Mixed Model analysis (GLMM) was performed and found that children in the experimental group scored higher on inhibitory and emotional control compared to their peers in the control group. In addition, these improvements have an effect on the decrease in aggressiveness. In conclusion, preventive research should have among its priorities the design of such program given their implications for psychosocial development.

scholarly journals Socioeconomic Conditions and Landowners’ Perception Affect the Intention to Restore Polylepis Forests in the Central Andes of Peru

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 118
Author(s):  
Lunel Joseph ◽  
Raúl Marino Yaranga Cano ◽  
Marco Arizapana-Almonacid ◽  
Marcela Venelli Pyles ◽  
Flávia Freire de Siqueira ◽  
...  
Keyword(s):  
Rural Communities ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Negative Impact ◽  
Positive Impact ◽  
Central Andes ◽  
Socioeconomic Conditions ◽  
Native Flora ◽  
The Family ◽  
Andes Region

Research Highlights: Families more dependent on crops as the main source of income of properties have a greater intention of restoring Polylepis forest areas. However, this intention reduces with the increase of family dependence on subsistence products supplied by Polylepis forests. Properties where the chances of restoration of Polylepis forests are greater are those where the educational and technical level is better. Objectives: We aimed to comprehend which socioeconomic factors of rural properties and families’ perception were determinant for the intention to restore Polylepis forests in the Central Andes region of Peru. Material and Methods: We collected data through visits and the application of questionnaires. We selected 13 rural communities in the Tulumayo River Basin. We randomly sampled 10 to 20 families in each community, depending on its size, totaling 200 families. We used generalized linear mixed model (GLMM) to test which variables affect the intention to restore the forest. Results: When crops are the main source of income in the property, the families have more intention to restore Polylepis areas, on the other hand, when Polylepis forests are an important source of products for the family subsistence, the intention to restore forests reduces, indicating that higher technological status has a positive impact on restoration. The perception that Polylepis forests are important for the existence of water sources had a positive impact on the families’ intention to restore the areas. However, the perception that Polylepis forests are important for native flora persistence had a negative impact on the intention to restore their areas. Conclusions: Our results showed that investment in improving the productivity of the properties and in the education of their landowners should increase the success of eventual programs for restoration of Polylepis forests.

A comparison of the Remote Food Photography Method and the Automated Self-Administered 24-hour Dietary Assessment Tool for measuring full day dietary intake among school-aged children

2021 ◽  
pp. 1-26
Author(s):  
Traci A. Bekelman ◽  
Corby K. Martin ◽  
Susan L. Johnson ◽  
Deborah H. Glueck ◽  
Katherine A. Sauder ◽  
...  
Keyword(s):  
Dietary Intake ◽  
Energy Intake ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Assessment Tool ◽  
Dietary Assessment ◽  
Ease Of Use ◽  
Self Report ◽  
Food Photography ◽  
Photography Method

Abstract The limitations of self-report measures of dietary intake are well known. Novel, technology-based measures of dietary intake may provide a more accurate, less burdensome alternative to existing tools. The first objective of this study was to compare participant burden for two technology-based measures of dietary intake among school-age children: the Automated-Self Administered 24-hour Dietary Assessment Tool-2018 (ASA24-2018) and the Remote Food Photography Method (RFPM). The second objective was to compare reported energy intake for each method to the Estimated Energy Requirement for each child, as a benchmark for actual intake. Forty parent-child dyads participated in 2, 3-day dietary assessments: a parent proxy-reported version of the ASA24 and the RFPM. A parent survey was subsequently administered to compare satisfaction, ease of use and burden with each method. A linear mixed model examined differences in total daily energy intake (TDEI) between assessments, and between each assessment method and the EER. Reported energy intake was 379 kcal higher with the ASA24 than the RFPM (p=0.0002). Reported energy intake with the ASA24 was 231 kcal higher than the EER (p = 0.008). Reported energy intake with the RFPM did not differ significantly from the EER (difference in predicted means = −148 kcal, p = 0.09). Median satisfaction and ease of use scores were 5 out of 6 for both methods. A higher proportion of parents reported that the ASA24 was more time consuming than the RFPM (74.4% vs. 25.6%, p = 0.002). Utilization of both methods is warranted given their high satisfaction among parents.

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