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result(s) for
"Concordances"
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Knot Floer homology obstructs ribbon concordance
We prove that the map on knot Floer homology induced by a ribbon concordance is injective. As a consequence, we prove that the Seifert genus is monotonic under ribbon concordance. Generalizing theorems of Gabai and Scharlemann, we also prove that the Seifert genus is super-additive under band connected sums of arbitrarily many knots. Our results give evidence for a conjecture of Gordon that ribbon concordance is a partial order on the set of knots.
Journal Article
New Methods to Calculate Concordance Factors for Phylogenomic Datasets
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of “decisive” gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).
Journal Article
Common pitfalls in statistical analysis: Measures of agreement
Agreement between measurements refers to the degree of concordance between two (or more) sets of measurements. Statistical methods to test agreement are used to assess inter-rater variability or to decide whether one technique for measuring a variable can substitute another. In this article, we look at statistical measures of agreement for different types of data and discuss the differences between these and those for assessing correlation.
Journal Article
Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations
A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor‐binding events. In concert with RNA‐sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short‐duration treatments with specific perturbations. Here, we used tandem, bulk ATAC‐seq, and RNA‐seq measurements from MCF‐7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF‐β. We found two classes of genes whose expression showed a significant change: those that showed some changes in the accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had lower baseline accessibility prior to exposure to signal. Focusing the analysis specifically on peaks with motifs for transcription factors associated with retinoic acid and TGF‐β signaling did not reduce the lack of correspondence. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than driving altered transcriptional status. Together, these results show many gene expression changes can happen independently of changes in the accessibility of local chromatin in the context of a single‐factor perturbation.
Synopsis
Systematic analysis of tandem, bulk ATAC‐seq and RNA‐seq measurements from cells exposed to single‐factor perturbations shows two groups of genes: those with concordance between accessibility and expression changes and those without.
MCF‐7 cells exposed to retinoic acid or TGF‐β have genes that show high expression changes without changes in local chromatin.
By comparison, data from hematopoietic differentiation show much more concordance between chromatin accessibility changes and gene expression changes.
Genes in the single‐factor perturbation data set that demonstrated more concordance had peaks that were less accessible at baseline prior to retinoic acid or TGF‐β exposure.
Graphical Abstract
Systematic analysis of tandem, bulk ATAC‐seq, and RNA‐seq measurements from cells exposed to single‐factor perturbations shows two groups of genes: those with concordance between accessibility and expression changes and those without.
Journal Article
Changing behaviour: Increasing the effectiveness of workplace interventions in creating pro-environmental behaviour change
There is a great deal of research outlining interventions to increase pro-environmental behaviour, many of which are aimed at employees. However, to date the results for these have not lived up to their initial promise. Instead of offering another intervention, we propose a model which identifies psychological conditions under which these interventions are most likely to succeed. Through the integration of previously separate literatures from experimental social psychology, organisational psychology, organisational behaviour and environmental psychology, we suggest that the degree to which the intervention-related goal is efficacious and attractive, self-concordant, in conflict with other goals, and perceived to be completed will affect the level and type of behaviour change. Our model aims to provide actionable knowledge that extends our understanding of the effectiveness of workplace interventions designed to increase green organisational behaviour.
Journal Article
A novel evolutionary-concordance lifestyle score is inversely associated with all-cause, all-cancer, and all-cardiovascular disease mortality risk
Purpose
Evolutionary discordance may contribute to the high burden of chronic disease-related mortality in modern industrialized nations. We aimed to investigate the associations of a 7-component, equal-weight, evolutionary-concordance lifestyle (ECL) score with all-cause and cause-specific mortality.
Methods
Baseline data were collected in 2003–2007 from 17,465 United States participants in the prospective REasons for Geographic and Racial Differences in Stroke (REGARDS) study. The ECL score’s components were: a previously reported evolutionary-concordance diet score, alcohol intake, physical activity, sedentary behavior, waist circumference, smoking history, and social network size. Diet was assessed using a Block 98 food frequency questionnaire and anthropometrics by trained personnel; other information was self-reported. Higher scores indicated higher evolutionary concordance. We used multivariable Cox proportional hazards regression models to estimate ECL score–mortality associations.
Results
Over a median follow-up of 10.3 years, 3771 deaths occurred (1177 from cardiovascular disease [CVD], 1002 from cancer). The multivariable-adjusted hazard ratios (HR) (95% confidence intervals [CI]) for those in the highest relative to the lowest ECL score quintiles for all-cause, all-CVD, and all-cancer mortality were, respectively, 0.45 (0.40, 0.50), 0.47 (0.39, 0.58), and 0.42 (0.34, 0.52) (all
P
trend < 0.01). Removing smoking and diet from the ECL score attenuated the estimated ECL score–all-cause mortality association the most, yielding fifth quintile HRs (95% CIs) of 0.56 (0.50, 0.62) and 0.50 (0.46, 0.55), respectively.
Conclusions
Our findings suggest that a more evolutionary-concordant lifestyle may be inversely associated with all-cause, all-CVD, and all-cancer mortality. Smoking and diet appeared to have the greatest impact on the ECL–mortality associations.
Journal Article