BearUCE_with_PartitionsRob

Nexus file of 996,381 nucleotides of concatenated Ultra Conserved Elements sequences from polar, brown, and black bears and other carnivora

a and b. Gene co-expression network subset including all genes which are or are correlated with a transcription factor (N = 1,673).

<p>Genes (or nodes) are connected by an edge only when a significant partial correlation with a TF was found. Fig 5a displays nodes colored by tissue of highest relative expression for each gene: pituitary (light blue), skeletal muscle (red), liver (light green), visceral adipose (yellow), and duodenum (orange). The key transcription factor for each cluster is labeled. Fig 5b highlights differentially expressed genes (dark blue) and genes harboring GWAS SNP for RFI (red) or both (purple), with all other nodes colored grey.</p

Phenotypic differences between sire groups (low RFI sire–high RFI sire) compared with expected progeny difference based on bull breeding values.

<p>Differences between sire progeny groups for growth, intake, feed efficiency, feeding behavior, methane production, and carcass traits are provided, including trait, trait mean, mean difference between sire groups, P-value for that difference (P<0.05 bolded), and expected progeny difference based on sire breeding values where available.</p

Composition of the total mixed ration (TMR) used in the growing and finishing periods.

<p>Finishing diet possessed a higher proportion of grain and higher energy content (Mcal/kg).</p

Pathway analysis of differentially expressed genes between low and high RFI sire groups by tissue, for pituitary (P), skeletal muscle (M), liver (L), adipose (A), and duodenum (D).

<p>Top biofunctions by |Z-score| from IPA are provided, expressed as low relative to high RFI sire progeny group differences; all are significant (P<0.05). Functions associated with the immune system or fat deposition are grouped together, all other significant functions at the bottom.</p

Gene co-expression network diagram including differentially expressed genes between sire groups, tissue specific genes, transcription factors regulating growth and feed efficiency, and genes harboring GWAS SNP for RFI.

<p>Genes (or nodes) are connected by an edge when a significant partial correlation was determined by PCIT. Colors represent the tissue of highest relative expression for each gene: pituitary (light blue), skeletal muscle (red), liver (light green), visceral adipose (yellow), and duodenum (orange).</p

Venn diagram of DE, TS, TF, and SNP genes.

<p>Venn diagram of DE, TS, TF, and SNP genes.</p

The top 10 enriched GO terms for the muscle specific gene clusters.

<p>Clusters are centered by the transcription factors <i>MYOD1TTF1</i>-<i>ZSCAN21</i> and <i>ZFX-IRX3</i>-<i>ZNF35</i>. The latter set of clusters had a higher proportion of SNP genes, suggesting conserved function in regulating RFI in beef cattle populations.</p

Distribution of significant partial correlations per gene in the co-expression network.

<p>This figure shows the number of significant partial correlations (or edges in the gene co-expression network) with other genes, ranging up to 280 per gene node. For each bin, genes are grouped by the tissue of highest relative expression, including pituitary (light blue), skeletal muscle (red), liver (light green), visceral adipose (yellow), and duodenum (orange), to give an approximation of the distribution within tissue. The pituitary, liver and duodenum are most highly represented among the genes with the highest number of edges.</p

The Capabilities Approach and Gendered Education: An Examination of South African Complexities

This article examines Amartya Sen's writings on the capabilities approach and education. Sen sometimes suggests a loose association between education and schooling. Elsewhere he concludes that one can read off the outputs of schooling as an indication of capabilities and an enhancement of freedom. While the capability approach provides a valuable way beyond human capital theorizing about education, Sen's writing fails to take account of the complex settings in which schooling takes place. Sometimes schooling does not entail an enhancement of capabilities and substantive freedom. South African policy responses to the HIV/AIDS epidemic highlight how using the capability approach to evaluation without paying attention to conditions of gender and race inequality yield only half the picture. © 2003, SAGE Publications. All rights reserved