scholarly journals Efficient Multiple-Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed Model

Genetics ◽  
2015 ◽  
Vol 200 (1) ◽  
pp. 59-68 ◽  
Author(s):  
N. A. Furlotte ◽  
E. Eskin
2017 ◽  
Vol 23 (1) ◽  
pp. 200-220 ◽  
Author(s):  
Hans Stadthagen-González ◽  
M Carmen Parafita Couto ◽  
C Alejandro Párraga ◽  
Markus F Damian

Objectives: Spanish and English contrast in adjective–noun word order: for example, brown dress (English) vs. vestido marrón (‘dress brown’, Spanish). According to the Matrix Language model ( MLF) word order in code-switched sentences must be compatible with the word order of the matrix language, but working within the minimalist program (MP), Cantone and MacSwan arrived at the descriptive generalization that the position of the noun phrase relative to the adjective is determined by the adjective’s language. Our aim is to evaluate the predictions derived from these two models regarding adjective–noun order in Spanish–English code-switched sentences. Methodology: We contrasted the predictions from both models regarding the acceptability of code-switched sentences with different adjective–noun orders that were compatible with the MP, the MLF, both, or none. Acceptability was assessed in Experiment 1 with a 5-point Likert and in Experiment 2 with a 2-Alternative Forced Choice (2AFC) task. Data and analysis: Data from both experiments were subjected to linear mixed model analyses. Results from the 2AFC task were also analyzed using Thurstone’s law of comparative judgment. Conclusions: We found an additive effect in which both the language of the verb and the language of the adjective determine word order. Originality: Both experiments examine adjective–noun word order in English–Spanish code-switched sentences. Experiment 2 represents a novel application of Thurstone’s law of comparative judgements to the study of linguistic acceptability which yielded clearer results than Likert scales. We found convincing evidence that neither the MLF nor the MP can fully account for the acceptability of adjective–noun switches. Implications: We suggest that advances in our understanding of grammaticality in code-switching will be achieved by combining the insights of the two frameworks instead of considering them in isolation, or by espousing a probabilistic model of code-switching.


2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 29-30
Author(s):  
Yao Chang ◽  
Yachun Wang

Abstract The objectives of this study were to estimate genetic parameters for temperament via three approaches and to examine associations of temperament with other economically important traits in Chinese Holstein. Records for temperament score (TS) on 6,586 lactating cows from 2015 to 2017 were obtained. Temperament assessed during rectal temperature measurements was recorded on a 3-point scale (1 = quiet; 2 = average; 3 = nervous). TS was treated as a ternary trait or a binary trait in different scenarios. The genetic parameters were estimated by: 1) a linear model using AI-REML; 2) a Generalized Linear Mixed Model (GLMM); or 3) a Bayesian threshold model via Gibbs sampling. Each record was partitioned into the fixed effects of herd-scorer and parity, an additive genetic effect and a residual effect. Then approximate genetic correlation between TS with production traits [milk yield (MY), fat and protein percentage (FP and PP)], fertility traits [age at first service (AFS), age at first calving (AFC), stillbirth (SB)], overall type, health traits [somatic cell score (SCS), udder diseases (UD) claw and leg diseases (CLD) metabolic disorders (MD)] and productive life (PL) were estimated. Estimates of heritability and accuracy of EBV for TS were listed in Table 1. Low to moderate genetic correlation between TS and above-mentioned traits were found. There was a favorable genetic correlation between TS and FP (-0.35), PP (-0.42), AFC (0.31), UD (0.58) and PL (-0.24); however, undesirable genetic correlation existed between TS and the other traits (-0.43~0.27). Current results suggested that a Bayesian threshold model can be the most recommended algorithm for analyzing temperament since it brought a relatively higher heritability and consequently EBV with higher accuracy, and selection for calmer individuals will translate into increased fat and protein yields, a lower age at first calving, better resistance to udder diseases and a longer functional longevity.


Author(s):  
Yongge Tian

Reverse order laws for generalized inverses of matrix products is a classic object of study in the theory of generalized inverses. One of the well-known reverse order laws for a matrix product $AB$ is $(AB)^{(i,\ldots,j)} = B^{(s_2,\ldots,t_2)}A^{(s_1,\ldots,t_1)}$, where $(\cdot)^{(i,\ldots,j)}$ denotes an $\{i,\ldots, j\}$-generalized inverse of matrix. Because $\{i,\ldots, j\}$-generalized inverse of a singular matrix is unique, the relationships between both sides of the reverse order law can be divided into four situations for consideration. This paper provides a thorough coverage of the reverse order laws for $\{i,\ldots, j\}$-generalized inverses of $AB$, from the development of background and preliminary tools to the collection of miscellaneous formulas and facts on the reverse order laws in one place with cogent introduction and references for further study. We begin with the introduction of a linear mixed model $y = AB\beta + A\gamma + \epsilon$ and the presentation of two least-squares methodologies to estimate the fixed parameter vector $\beta$ in the model, and the description of connections between the two types of least-squares estimators and the reverse order laws for generalized inverses of $AB$. We then prepare some valued matrix analysis tools, including a general theory on linear or nonlinear matrix identities, a group of expansion formulas for calculating ranks of block matrices, two groups of explicit formulas for calculating the maximum and minimum ranks of $B^{(s_2,\ldots,t_2)}A^{(s_1,\ldots,t_1)}$, as well as necessary and sufficient conditions for $B^{(s_2,\ldots,t_2)}A^{(s_1,\ldots,t_1)}$ to be invariant with respect to the choice of $B^{(s_2,\ldots,t_2)}A^{(s_1,\ldots,t_1)}$. We then present a unified approach to the 512 matrix set inclusion problems associated with the above reverse order laws for the eight commonly-used types of generalized inverses of $A$, $B$, and $AB$ through use of the definitions of generalized inverses, the block matrix method (BMM), the matrix rank method (MRM), the matrix equation method (MEM), and various algebraic calculations of matrices.


2020 ◽  
Author(s):  
James L. Peugh ◽  
Sarah J. Beal ◽  
Meghan E. McGrady ◽  
Michael D. Toland ◽  
Constance Mara

2020 ◽  
Vol 641 ◽  
pp. 159-175
Author(s):  
J Runnebaum ◽  
KR Tanaka ◽  
L Guan ◽  
J Cao ◽  
L O’Brien ◽  
...  

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.


2019 ◽  
Vol 24 (2) ◽  
pp. 200-208
Author(s):  
Ravindra Arya ◽  
Francesco T. Mangano ◽  
Paul S. Horn ◽  
Sabrina K. Kaul ◽  
Serena K. Kaul ◽  
...  

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.


Author(s):  
Miriam Romero-López ◽  
María Carmen Pichardo ◽  
Ana Justicia-Arráez ◽  
Judit Bembibre-Serrano

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.


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 ◽  
...  

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.


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