Univariate analysis revealed that longer procedure time was associated with infection (p=0.0008), seroma (p=0.002), necrosis/dehiscence (p=0.01), and reoperation (p=0.002). These associations persisted following multivariate analyses. There was a trend toward history of bariatric surgery being associated with minor reoperation (p=0.054). No significant increase in the incidence of major reoperation was found in association with overweight or obese patient habitus, history of bariatric surgery, or prolonged procedure time. BMI was not found to be an individual risk factor for morbidity in this patient population.
In abdominal body contouring surgery, length of surgery longer six hours is associated with higher incidence of seroma and infectious complications, as well as higher rates of minor reoperation.
In abdominal body contouring surgery, length of surgery longer six hours is associated with higher incidence of seroma and infectious complications, as well as higher rates of minor reoperation.
Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signaling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tiile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signaling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signaling.
The method was developed with the R statistical software and is made available through the R package "irg" hosted on the GitHub repository https//github.com/SMAC-Group/irg where also a running example vignette can be found (https//smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete Arabidopsis thaliana data can be found at https//www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500.
Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.
Investigating the relationships between two sets of variables helps to understand their interactions and can be done with canonical correlation analysis (CCA). However, the correlation between the two sets can sometimes depend on a third set of covariates, often subject-related ones such as age, gender, or other clinical measures. In this case, applying CCA to the whole population is not optimal and methods to estimate conditional CCA, given the covariates, can be useful.
We propose a new method called Random Forest with Canonical Correlation Analysis (RFCCA) to estimate the conditional canonical correlations between two sets of variables given subject-related covariates. The individual trees in the forest are built with a splitting rule specifically designed to partition the data to maximize the canonical correlation heterogeneity between child nodes. We also propose a significance test to detect the global effect of the covariates on the relationship between two sets of variables. The performance of the proposed method and the global significance test is evaluated through simulation studies that show it provides accurate canonical correlation estimations and well-controlled Type-1 error. https://www.selleckchem.com/products/guanosine-5-monophosphate-disodium-salt.html We also show an application of the proposed method with EEG data.
RFCCA is implemented in a freely available R package on CRAN (https//CRAN.R-project.org/package=RFCCA).
Supplementary material are available at Bioinformatics online.
Supplementary material are available at Bioinformatics online.
Batch effects heavily impact results in omics studies, causing bias and false positive results, but software to control them preemptively is lacking. Sample randomization prior to measurement is vital for minimizing these effects, but current approaches are often ad hoc, poorly documented, and ill-equipped to handle multiple batches and outcomes.
We developed Omixer-a Bioconductor package implementing multivariate and reproducible sample randomization for omics studies. It proactively counters correlations between technical factors and biological variables of interest by optimizing sample distribution across batches.
Omixer is available from Bioconductor at http//bioconductor.org/packages/release/bioc/html/Omixer.html.
Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.A class of epigenetic inheritance patterns known as genomic imprinting allows alleles to influence the phenotype in a parent-of-origin-specific manner. Various pedigree-based parent-of-origin analyses of quantitative traits have attempted to determine the share of genetic variance that is attributable to imprinted loci. In general, these methods require four random gametic effects per pedigree member to account for all possible types of imprinting in a mixed model. As a result, the system of equations may become excessively large to solve using all available data. If only the offspring have records, which is frequently the case for complex pedigrees, only two averaged gametic effects (transmitting abilities) per parent are required (reduced model). However, the parents may have records in some cases. Therefore, in this study, we explain how employing single gametic effects solely for informative individuals (i.e., phenotyped individuals), and only average gametic effects otherwise, significantly reduces the complexity compared with classical gametic models.
Univariate analysis revealed that longer procedure time was associated with infection (p=0.0008), seroma (p=0.002), necrosis/dehiscence (p=0.01), and reoperation (p=0.002). These associations persisted following multivariate analyses. There was a trend toward history of bariatric surgery being associated with minor reoperation (p=0.054). No significant increase in the incidence of major reoperation was found in association with overweight or obese patient habitus, history of bariatric surgery, or prolonged procedure time. BMI was not found to be an individual risk factor for morbidity in this patient population.
In abdominal body contouring surgery, length of surgery longer six hours is associated with higher incidence of seroma and infectious complications, as well as higher rates of minor reoperation.
In abdominal body contouring surgery, length of surgery longer six hours is associated with higher incidence of seroma and infectious complications, as well as higher rates of minor reoperation.
Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signaling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tiile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signaling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signaling.
The method was developed with the R statistical software and is made available through the R package "irg" hosted on the GitHub repository https//github.com/SMAC-Group/irg where also a running example vignette can be found (https//smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete Arabidopsis thaliana data can be found at https//www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500.
Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.
Investigating the relationships between two sets of variables helps to understand their interactions and can be done with canonical correlation analysis (CCA). However, the correlation between the two sets can sometimes depend on a third set of covariates, often subject-related ones such as age, gender, or other clinical measures. In this case, applying CCA to the whole population is not optimal and methods to estimate conditional CCA, given the covariates, can be useful.
We propose a new method called Random Forest with Canonical Correlation Analysis (RFCCA) to estimate the conditional canonical correlations between two sets of variables given subject-related covariates. The individual trees in the forest are built with a splitting rule specifically designed to partition the data to maximize the canonical correlation heterogeneity between child nodes. We also propose a significance test to detect the global effect of the covariates on the relationship between two sets of variables. The performance of the proposed method and the global significance test is evaluated through simulation studies that show it provides accurate canonical correlation estimations and well-controlled Type-1 error. https://www.selleckchem.com/products/guanosine-5-monophosphate-disodium-salt.html We also show an application of the proposed method with EEG data.
RFCCA is implemented in a freely available R package on CRAN (https//CRAN.R-project.org/package=RFCCA).
Supplementary material are available at Bioinformatics online.
Supplementary material are available at Bioinformatics online.
Batch effects heavily impact results in omics studies, causing bias and false positive results, but software to control them preemptively is lacking. Sample randomization prior to measurement is vital for minimizing these effects, but current approaches are often ad hoc, poorly documented, and ill-equipped to handle multiple batches and outcomes.
We developed Omixer-a Bioconductor package implementing multivariate and reproducible sample randomization for omics studies. It proactively counters correlations between technical factors and biological variables of interest by optimizing sample distribution across batches.
Omixer is available from Bioconductor at http//bioconductor.org/packages/release/bioc/html/Omixer.html.
Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.A class of epigenetic inheritance patterns known as genomic imprinting allows alleles to influence the phenotype in a parent-of-origin-specific manner. Various pedigree-based parent-of-origin analyses of quantitative traits have attempted to determine the share of genetic variance that is attributable to imprinted loci. In general, these methods require four random gametic effects per pedigree member to account for all possible types of imprinting in a mixed model. As a result, the system of equations may become excessively large to solve using all available data. If only the offspring have records, which is frequently the case for complex pedigrees, only two averaged gametic effects (transmitting abilities) per parent are required (reduced model). However, the parents may have records in some cases. Therefore, in this study, we explain how employing single gametic effects solely for informative individuals (i.e., phenotyped individuals), and only average gametic effects otherwise, significantly reduces the complexity compared with classical gametic models.
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