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Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance(More)
WTF ("Who to Follow") is Twitter's user recommendation service, which is responsible for creating millions of connections daily between users based on shared interests, common connections, and other related factors. This paper provides an architectural overview and shares lessons we learned in building and running the service over the past few years.(More)
In plants, systemic acquired resistance (SAR) is established as a result of NPR1-regulated expression of pathogenesis-related (PR) genes. Using gene expression profiling in Arabidopsis, we found that in addition to controlling the expression of PR genes, NPR1 also directly controls the expression of the protein secretory pathway genes. Up-regulation of(More)
The phytohormone auxin regulates almost every aspect of plant development. At the molecular level, auxin induces gene expression through direct physical interaction with the TIR1-like F box proteins, which in turn remove the Aux/IAA family of transcriptional repressors [1-4]. A growing body of evidence indicates that many plant pathogens can either produce(More)
Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. To date, few plant CCCH proteins have been studied functionally. In this study, a comprehensive computational analysis identified 68 and(More)
Accumulation of lipids in nonadipose tissues can lead to cell dysfunction and cell death, a phenomenon known as lipotoxicity. However, the signaling pathways and mechanisms linking lipid accumulation to cell death are poorly understood. The present study examined the hypothesis that saturated fatty acids disrupt endoplasmic reticulum (ER) homeostasis and(More)
MOTIVATION According to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and(More)
We introduce a SAT based automatic abstraction refinement framework for model checking systems with several thousand state variables in the cone of influence of the specification. The abstract model is constructed by designating a large number of state variables as invisible. In contrast to previous work where invisible variables were treated as free inputs(More)
Nonalcoholic fatty liver disease is a relatively new hepatic sequela of obesity and type 2 diabetes. The pathogenesis of liver injury and disease progression in nonalcoholic fatty liver disease, however, is poorly understood. The present study examined the hypothesis that the composition of fatty acids in the steatotic liver promotes liver injury. Using(More)
Several recent reports have suggested that microRNAs (miRNAs) might play critical roles in acute myocardial infarction (AMI). However, the miRNA expression signature in the early phase of AMI has not been identified. In this study, the miRNA expression signature was investigated in rat hearts 6 h after AMI. Compared with the expression signature in the(More)