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The analysis of tandem mass (MS/MS) data to identify and quantify proteins is hampered by the heterogeneity of file formats at the raw spectral data, peptide identification, and protein identification levels. Different mass spectrometers output their raw spectral data in a variety of proprietary formats, and alternative methods that assign peptides to MS/MS(More)
There is an increasing interest in the quantitative proteomic measurement of the protein contents of substantially similar biological samples, e.g. for the analysis of cellular response to perturbations over time or for the discovery of protein biomarkers from clinical samples. Technical limitations of current proteomic platforms such as limited(More)
Active learning is a promising way for sentiment classification to reduce the annotation cost. In this paper, we focus on the imbalanced class distribution scenario for sentiment classification, wherein the number of positive samples is quite different from that of negative samples. This scenario posits new challenges to active learning. To address these(More)
We describe an algorithm for the automated statistical analysis of protein abundance ratios (ASAPRatio) of proteins contained in two samples. Proteins are labeled with distinct stable-isotope tags and fragmented, and the tagged peptide fragments are separated by liquid chromatography (LC) and analyzed by electrospray ionization (ESI) tandem mass(More)
The RIG-I-like receptors (RLRs), RIG-I and MDA5, recognize single-stranded RNA with 5' triphosphates and double-stranded RNA (dsRNA) to initiate innate antiviral immune responses. LGP2, a homolog of RIG-I and MDA5 that lacks signaling capability, regulates the signaling of the RLRs. To establish the structural basis of dsRNA recognition by the RLRs, we have(More)
Microbial consortia isolated from aged oil-contaminated soil were used to degrade 16 polycyclic aromatic hydrocarbons (15.72 mgkg(-1)) in soil and slurry phases. The three microbial consortia (bacteria, fungi and bacteria-fungi complex) could degrade polycyclic aromatic hydrocarbons (PAHs), and the highest PAH removals were found in soil and slurry(More)
Thirty-nine fungal metabolites 1-39, including two new alkaloids, 12β-hydroxy-13α-methoxyverruculogen TR-2 (6) and 3-hydroxyfumiquinazoline A (16), were isolated from the fermentation broth of Aspergillus fumigatus LN-4, an endophytic fungus isolated from the stem bark of Melia azedarach. Their structures were elucidated on the basis of detailed(More)
For ultrathin gate oxide, soft breakdown (SBD) has been extensively studied but not fully integrated into circuit reliability simulation. Using a 6T SRAM cell as a generic circuit example, the time-dependent SBD was incorporated into circuit degradation analysis based on the exponential defect current growth model [1]. SRAM cell stability degradation due to(More)
Quantitative proteome profiling using stable isotope protein tagging and automated tandem mass spectrometry (MS/MS) is an emerging technology with great potential for the functional analysis of biological systems and for the detection of clinical diagnostic or prognostic marker proteins. Owing to the enormous complexity of proteomes, their comprehensive(More)
PURPOSE Recent studies have reported high frequencies of somatic mutations in the phosphoinositide-3-kinase catalytic-alpha (PIK3CA) gene in various human solid tumors. More than 75% of those somatic mutations are clustered in the helical (exon 9) and kinase domains (exon 20). The three hot-spot mutations, E542K, E545K, and H1047R, have been proven to(More)