A generalized, multi-stage adjusted, latent class linear mixed model for testing genetic association

2018 ◽  
Vol 48 (8) ◽  
pp. 2301-2312 ◽  
Author(s):  
Özge Karadağ ◽  
Serpil Aktaş
Keyword(s):  
Genetic Association ◽  
Latent Class ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Multi Stage

Bias in common catch-curve methods applied to age frequency data from fish surveys

2019 ◽  
Vol 76 (7) ◽  
pp. 2090-2101
Author(s):  
Gary A Nelson
Keyword(s):  
Linear Regression ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Standard Errors ◽  
Cluster Sampling ◽  
Probability Models ◽  
Generalized Poisson ◽  
Random Intercept ◽  
Multi Stage ◽  
Wide Range

Abstract Catch curve analysis is often used in data-limited fisheries stock assessments to estimate total instantaneous mortality (Z). There are now six catch-curve methods available in the literature: the Chapman–Robson, linear regression, weighted linear regression, Heincke, generalized Poisson linear, and random-intercept Poisson linear mixed model. An assumption shared among the underyling probability models of these estimators is that fish collected for ageing are sampled from the population by simple random sampling. This type of sampling is nearly impossible in fisheries research because populations are sampled in surveys that use gears that capture individuals in clusters and often fish for ageing are selected from multi-stage sampling. In this study, I explored the effects of multi-stage cluster sampling on the bias of the estimates of Z and their associated standard errors. I found that the generalized Poisson linear model and the Chapman–Robson estimators were the least biased, whereas the random-intercept Poisson linear mixed model was the most biased under a wide range of simulation scenarios that included different levels of recruitment variation, intra-cluster correlation, sample sizes, and methods used to generate age frequencies. Standard errors of all estimators were under-estimated in almost all cases and should not be used in statistical comparisons.

Genetic Association Analysis of Lipid Profiles Using Linear Mixed Model

2006 ◽  
Vol 36 (3) ◽  
pp. 229
Author(s):  
Kijun Song ◽  
Chan Mi Park ◽  
Kil Seob Lim ◽  
Yang Soo Jang ◽  
Dong Kee Kim
Keyword(s):  
Genetic Association ◽  
Association Analysis ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Lipid Profiles ◽  
Genetic Association Analysis

scholarly journals Modeling individual disability evolution in multiple sclerosis patients based on longitudinal multimodal imaging and clinical data

2019 ◽  
Author(s):  
Ceren Tozlu ◽  
Dominique Sappey-Marinier ◽  
Gabriel Kocevar ◽  
François Cotton ◽  
Sandra Vukusic ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Multimodal Imaging ◽  
Latent Class ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Posterior Probabilities ◽  
Disease Evolution ◽  
Clinical Model ◽  
Combined Models ◽  
Individual Disease

ABSTRACTBackgroundThe individual disease evolution of multiple sclerosis (MS) is very different from one patient to another. Therefore, the prediction of long-term disability evolution is difficult based on only clinical information. Magnetic resonance imaging (MRI) provides a very efficient tool to distinguish between healthy and abnormal brain tissue, monitor disease evolution, and help decision-making for personalized treatment of MS patients.ObjectiveWe aim to develop a patient-specific model to predict individual disease evolution in MS, using demographic, clinical, and imaging data that were collected at study onset.MethodsThe study included 75 patients tracked over 5 years. The latent class linear mixed model was used to consider individual and unobserved subgroup variability. First, the clinical model was established with demographic and clinical variables to predict clinical disease evolution. Second, the imaging model was built using the multimodal imaging variables. Third, the imaging variables were added one by one, two by two, and all three together to investigate their contribution to the clinical model. The clinical disability is measured with the Expanded Disability Status Scale (EDSS). The performances of the clinical, imaging, and the combined models were compared mainly using the Bayesian Information Criterion (BIC). The mean of the posterior probabilities was also given as the secondary performance evaluation criterion.ResultsThe clinical model gave higher BIC value than imaging and any combined models. The means of the posterior probabilities given by the three models were over 0.94. The clinical model clustered the patients into two latent classes: stable evolution class (n=6, 88%) and severe evolution class (n=9, 12%).ConclusionThe latent class linear mixed model may provide a well-fitted prediction for the disability evolution in MS patients, thus giving further information for personalized treatment decisions after thorough validation with a larger and independent dataset.

The progression of an acceptable pulmonary stenosis immediately after total correction of tetralogy of Fallot

2020 ◽  
Vol 30 (6) ◽  
pp. 774-778
Author(s):  
Yi-Seul Kim ◽  
Jinyoung Song ◽  
June Huh ◽  
I-Seok Kang ◽  
Ji-Hyuk Yang ◽  
...  
Keyword(s):  
Tetralogy Of Fallot ◽  
Latent Class ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Pulmonary Valve ◽  
Pulmonary Stenosis ◽  
Total Correction ◽  
Related Factors ◽  
Main Site ◽  
Z Value

AbstractBackground:A certain degree of pulmonary stenosis after total correction of tetralogy of Fallot has been considered acceptable. But the long-term outcomes are not well understood. We observed the natural course of immediate pulmonary stenosis and investigated related factors for progression.Methods:Fifty-two patients with acceptable pulmonary stenosis immediately after operation were enrolled. Acceptable pulmonary stenosis was defined as peak pressure gradient between 15 and 45 mmHg by Doppler echocardiography. Latent class linear mixed model was used to differentiate patients with progressed pulmonary stenosis, and the factors related to progression were analysed.Results:Pulmonary stenosis progressed in 14 patients (27%). Between the progression group and no progression group, there were no significant differences in operative age, sex, and the use of the transannular patch technique. However, immediate gradient was higher in the progression group (32.1 mmHg versus 25.7 mmHg, p = 0.009), and the cut-off value was 26.8 mmHg (sensitivity = 65.3%, specificity = 65.8%). Main stenosis at the sub-valve was observed more frequently in the progression group (85.7% versus 52.6%, p = 0.027). Despite no difference in the preoperative pulmonary valve z value, the last follow-up pulmonary valve z value was significantly lower in the progression group (−1.15 versus 0.35, p = 0.002).Conclusions:Pulmonary stenosis immediately after tetralogy of Fallot total correction might progress in patients with immediate pulmonary stenosis higher than ≥26.8 mmHg and the main site was sub-valve area.

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.

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