Identification of the expressome by machine learning on omics data.

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes

Investigation into the Role of Platelet Derived Growth Factor (PDGF) in Type I Collagen Glomerulopathy

Progressive accumulation of collagen and extracellular matrix (ECM) proteins within renal glomeruli have implications for or result in renal fibrosis and glomerulosclerosis, with both events culminating in renal failure. To model this accumulation the Col1a2-deficient mouse model was used. The Col1a2-deficientmouse model is characterized by a mutation in the a2(I) chain, preventing incorporation into the type I collagen molecule. As a result, an α1(I) collagen chain incorporates into the collagen triple helix forming homotrimeric type I collagen, as opposed to heterotrimeric type I collagen. This change is due to the secondary wound healing response in response to ECM accumulation, fibrosis, or damage. Transforming growth factor-beta (TGF-β) has been studied within this model and demonstrated it was not the initiating molecule in collagen deposition. This study looks at Tumor Necrosis Factor-Alpha (TNF-a) and Platelet Derived Growth Factor (PDGF) as potential mediators of this hypothesized secondary wound healing response. TNF-ais an inflammatory cytokine produced following tissue damage, released by mesangial cells, and has been shown to induce epithelial-to-mesenchymal transition (EMT). Recently, PDGF receptors and ligand upregulation has been shown in other mouse models of renal fibrosis. However, TNF-ashowed no differential staining upon Picrosirius Red (PSR) between experimental and control groups. PDGFR-ββ and PDGF-BB displayed differential labeling in Col1a2-deficient in comparison to age matched wild type animals. The results for PDGF-DD mice were less conclusive when comparing the Col1a2-deficient mice to that of their wild type counterparts

Reexamining the Impact of Employee Relocation Assistance on Housing Prices

In this paper, we reexamine the issue of whether corporate relocation assistance programs for transferred employees significantly affect sale prices of single-family homes. We estimate a hedonic price equation that includes physical housing characteristics, location factors, occupancy status, and type of seller for a sample of 2,441 transactions. Seller types include (a) transferred employees who were given direct relocation assistance, (b) transferred employees who were not given direct relocation assistance, and (c) sellers who were not facing an employment transfer. After controlling for vacancy and tenant occupancy, we find that houses sold by transferred employees who receive direct relocation assistance exhibit no significant price differential, but that houses sold by transferred employees who do not receive direct relocation assistance sell at a discount of approximately 3%.

Complexified sigma model and duality

We show that the equations of motion associated with a complexified sigma-model action do not admit manifest dual SO(n,n) symmetry. In the process we discover new type of numbers which we called `complexoids' in order to emphasize their close relation with both complex numbers and matroids. It turns out that the complexoids allow to consider the analogue of the complexified sigma-model action but with (1+1)-worldsheet metric, instead of Euclidean-worldsheet metric. Our observations can be useful for further developments of complexified quantum mechanics.Comment: 15 pages, Latex, improved versio

Property Tax Lids and the Effect on Kansas

Cross sectional time series data in a partial adjustment model examine local government behavior under an aggregate property tax levy limit and under Truth in Taxation in Kansas. Results indicate that the aggregate levy limit would have continued to restrict property tax revenue and spending had it not been replaced.Public Economics,

Trust Building Tools for Talking with Youth During Times of Conflict

This presentation will provide tools and strategies for turning crisis into opportunity. The skills of Life Space Crisis Intervention provide helping adults faced with the extreme behavior of youth during times of crisis strategies which build trust and connections in meaningful and healing ways; turning crisis into opportunity for at risk youth to develop social responsibility and grow emotionall

Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes