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Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic responses. Although substantial effort has been made to define the genomic constitution of cancer cell line panels, the transcriptome remains understudied. Here we describe RNA sequencing and single-nucleotide polymorphism (SNP) array(More)
Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of the major factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different(More)
Ionic liquids (ILs) have recently been demonstrated to be highly effective solvents for the dissolution of cellulose and lignocellulosic biomass. To date, there is no definitive rationale for selecting ionic liquids that are capable of dissolving these biopolymers. In this work, an all-atom force field for the IL 1-ethyl-3-methylimidazolium acetate(More)
The effect of distant mutations on the catalytic reaction of dihydrofolate reductase (DHFR) is reexamined by empirical valence bond simulations. The simulations reproduce for the first time the changes in the observed rate constants (without the use of adjustable parameters for this purpose) and show that the changes in activation barriers are strongly(More)
Gastric cancer is the second leading cause of worldwide cancer mortality, yet the underlying genomic alterations remain poorly understood. Here we perform exome and transcriptome sequencing and SNP array assays to characterize 51 primary gastric tumours and 32 cell lines. Meta-analysis of exome data and previously published data sets reveals 24(More)
BACKGROUND The use of Ionic liquids (ILs) as biomass solvents is considered to be an attractive alternative for the pretreatment of lignocellulosic biomass. Acid catalysts have been used previously to hydrolyze polysaccharides into fermentable sugars during IL pretreatment. This could potentially provide a means of liberating fermentable sugars from biomass(More)
Cel9A from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius belongs to the subfamily E1 of family 9 glycoside hydrolases, many members of which have an N-terminal Ig-like domain followed by the catalytic domain. The Ig-like domain is not directly involved in either carbohydrate binding or biocatalysis; however, deletion of the Ig-domain(More)
Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and(More)
The convergence of parallel tempering Monte Carlo simulations of the 38-atom Lennard-Jones cluster starting from the Oh global minimum and from the C(5v) second-lowest-energy minimum is investigated. It is found that achieving convergence is appreciably more difficult, particularly at temperatures in the vicinity of the Oh --> C(5v) transformation when(More)