Determining the dependence of marine pile driving sound levels on strike energy, pile penetration, and propagation effects using a linear mixed model based on damped cylindrical spreading

2019 ◽  
Vol 146 (1) ◽  
pp. 109-121 ◽  
Author(s):  
S. Bruce Martin ◽  
David R. Barclay
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Pile Driving ◽  
Energy Pile ◽  
Model Based ◽  
Pile Penetration ◽  
Sound Levels ◽  
Propagation Effects

scholarly journals The Design of Early-Stage Plant Breeding Trials Using Genetic Relatedness

2020 ◽  
Vol 25 (4) ◽  
pp. 553-578 ◽  
Author(s):  
Brian R. Cullis ◽  
Alison B. Smith ◽  
Nicole A. Cocks ◽  
David G. Butler
Keyword(s):  
Plant Breeding ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Genetic Relatedness ◽  
Early Stage ◽  
Genetic Effects ◽  
Breeding Programs ◽  
Model Based ◽  
Selection Decisions ◽  
Design Generation

Abstract The use of appropriate statistical methods has a key role in improving the accuracy of selection decisions in a plant breeding program. This is particularly important in the early stages of testing in which selections are based on data from a limited number of field trials that include large numbers of breeding lines with minimal replication. The method of analysis currently recommended for early-stage trials in Australia involves a linear mixed model that includes genetic relatedness via ancestral information: non-genetic effects that reflect the experimental design and a residual model that accommodates spatial dependence. Such analyses have been widely accepted as they have been found to produce accurate predictions of both additive and total genetic effects, the latter providing the basis for selection decisions. In this paper, we present the results of a case study of 34 early-stage trials to demonstrate this type of analysis and to reinforce the importance of including information on genetic relatedness. In addition to the application of a superior method of analysis, it is also critical to ensure the use of sound experimental designs. Recently, model-based designs have become popular in Australian plant breeding programs. Within this paradigm, the design search would ideally be based on a linear mixed model that matches, as closely as possible, the model used for analysis. Therefore, in this paper, we propose the use of models for design generation that include information on genetic relatedness and also include non-genetic and residual models based on the analysis of historic data for individual breeding programs. At present, the most commonly used design generation model omits genetic relatedness information and uses non-genetic and residual models that are supplied as default models in the associated software packages. The major reasons for this are that preexisting software is unacceptably slow for designs incorporating genetic relatedness and the accuracy gains resulting from the use of genetic relatedness have not been quantified. Both of these issues are addressed in the current paper. An updating scheme for calculating the optimality criterion in the design search is presented and is shown to afford prodigious computational savings. An in silico study that compares three types of design function across a range of ancillary treatments shows the gains in accuracy for the prediction of total genetic effects (and thence selection) achieved from model-based designs using genetic relatedness and program specific non-genetic and residual models. Supplementary materials accompanying this paper appear online.

Development of a Third Trimester Contingent Prognostic Prediction Scheme for Suspected Early-Onset Pre-Eclampsia

2021 ◽  
pp. 1-9
Author(s):  
Enric Sabrià ◽  
Paula Lafuente-Ganuza ◽  
Paloma Lequerica-Fernández ◽  
Ana Isabel Escudero ◽  
Eduardo Martínez-Morillo ◽  
...  
Keyword(s):  
Early Onset ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
False Positive Rate ◽  
Area Under The Curve ◽  
Prediction Tool ◽  
Model Based ◽  
Prognostic Prediction ◽  
Short Term Prediction ◽  
Plgf Ratio

<b><i>Introduction:</i></b> Short-term prediction of pre-eclampsia (PE) using soluble FMS-like tyrosine kinase-1 (sFlt-1)/ placental growth factor (PlGF) ratio has high false-positive rate. Therefore, we developed a prognostic prediction tool that predicts early-onset PE leading to delivery within 1 week on pregnancies with an sFlt-1/PlGF ratio above 38 and compared it with an analogous model based on sFlt-1/PlGF ratio and with the 655 sFlt-1/PlGF ratio cutoff. <b><i>Methods:</i></b> Cohort study of 363 singleton pregnancies with clinical suspicion of PE before 34 weeks of gestation, allowing repeated assessments (522). 213 samples with an sFlt-1/PlGF ratio above 38 were assessed to construct and identify the best-fit linear mixed model. N-terminal pro-B-type natriuretic peptide (NT-proBNP), sFlt-1 MoM, PlGF MoM, and sFlt-1/PlGF ratio combined with gestational age (GA) were assessed. <b><i>Results:</i></b> None of the pregnancies with an sFlt-1/PlGF ratio of 38 or below developed early-onset PE (309 samples from 240 pregnancies). Conversely, 47 women of 213 assessments (22.1%) with an sFlt-1/PlGF ratio above 38 developed the assessed outcome. The selected model included sFlt-1 MoM, NT-proBNP, and GA. Differences in area under the curve were observed between the selected model and the GA + sFlt-1/PlGF model (<i>p</i> = 0.04). At an sFlt-1/PlGF ratio cutoff of 655, detection rate was 31.9% (15/47), while the selected model detection was 55.3% (26/47) (<i>p</i> = 0.008). <b><i>Discussion:</i></b> Considering repeated assessments, the sFlt-1/PlGF ratio of 38 or below adequately ruled out early-onset PE, leading to delivery within 1 week. However, when sFlt-1/PlGF ratio is above 38, the prediction tool derived from linear mixed model based on GA, NT-proBNP, and sFlt-1 MoM, provided a better prognosis prediction than the sFlt-1/PlGF ratio.

On the analysis of cubic smoothing spline-based stem curve prediction for forest harvesters

2006 ◽  
Vol 36 (11) ◽  
pp. 2909-2919 ◽  
Author(s):  
Laura Koskela ◽  
Tapio Nummi ◽  
Simone Wenzel ◽  
Veli-Pekka Kivinen
Keyword(s):  
Variable Exponent ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Prediction Method ◽  
Smoothing Spline ◽  
Model Based ◽  
Cutting Pattern ◽  
Taper Equation

In the cut-to-length (CTL) harvesting system the felling, delimbing, and bucking processes take place at the harvesting site. The optimal cutting points along the stem can be determined if the whole stem curve is known. In practice, however, it is not economically feasible to measure the whole stem first before crosscutting, and hence the first cutting decisions are usually made when only a short part of the stem is known. Predictions are used to determine the cutting pattern to compensate for the unknown part of the stem. In this paper our interest focuses on stem curve prediction in a harvesting situation and we study a modified version of a cubic smoothing spline-based prediction method devised by Nummi and Mottonen (T. Nummi and J. Mottonen. 2004. J. Appl. Stat. 31: 105–114). The method's performance was assessed in five different final felling stands of spruce and pine, collected by harvesters in southern Finland. The results for the spline approach are very promising and show the superiority of the method over the linear mixed-model-based approach of Liski and Nummi (E. Liski and T. Nummi. 1995. Scand. J. Stat. 22: 255–269) and also over the approach based on the variable-exponent taper equation of Kozak (A. Kozak. 1988. Can. J. For. Res. 18: 1363–1368).

scholarly journals Genetic Studies: The Linear Mixed Models in Genome-wide Association Studies

2013 ◽  
Vol 7 (1) ◽  
pp. 27-33 ◽  
Author(s):  
Gengxin Li ◽  
Hongjiang Zhu
Keyword(s):  
Population Structure ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Model Based ◽  
Genome Wide ◽  
A Genome ◽  
Sample Structure

With the availability of high-density genomic data containing millions of single nucleotide polymorphisms and tens or hundreds of thousands of individuals, genetic association study is likely to identify the variants contributing to complex traits in a genome-wide scale. However, genome-wide association studies are confounded by some spurious associations due to not properly interpreting sample structure (containing population structure, family structure and cryptic relatedness). The absence of complete genealogy of population in the genome-wide association studies model greatly motivates the development of new methods to correct the inflation of false positive. In this process, linear mixed model based approaches with the advantage of capturing multilevel relatedness have gained large ground. We summarize current literatures dealing with sample structure, and our review focuses on the following four areas: (i) The approaches handling population structure in genome-wide association studies; (ii) The linear mixed model based approaches in genome-wide association studies; (iii) The performance of linear mixed model based approaches in genome-wide association studies and (iv) The unsolved issues and future work of linear mixed model based approaches.

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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