Neutral lipids fulfill multiple specialized roles in cellular function. These roles include energy storage and utilization, the synthesis of complex lipids in cellular membranes, lipid second messengers for cellular signaling, and the modulation of membrane molecular dynamics. We have developed a novel mass spectrometric technology, now termed shotgun lipidomics, that can identify the types and...

We consider the problem of shotgun identification patterns on groups, which extends previous work DNA sequences and labeled graphs. A a group $G$ is specified by two finite subsets $C \subset G$ $K alphabet $\mathcal{A}$. In such problems, there ``global" pattern $w \in \mathcal{A}^{CK}$, one would like to be able identify this (up translation) based only observation ``local" $K$-shaped subpatt...

In this supplement, we analyze the system-level bottlenecks of Shotgun’s scalability on multicore. Currently, we are able to get maximum of about 3− 4× speedup on 8 cores. To analyze multicore performance, we run a series of tests which try to isolate effects of various factors. Our analysis indicates that Shotgun is held back by memory access, but we give suggestions for future improvements to...

background patients, who survived from shotgun injuries, often have some retained lead pellets in their bodies. several cases of lead toxicity have been reported regarding these patients. objectives this study seeks to compare the serum lead level in patients who have retained lead pellets in their bodies with the control group. patients and methods in this case-control study, we gathered the s...

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more import...

Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inve...

Finishing is rate limiting for genome projects, and improvements in the efficiency of complete genome-sequence compilation will require improved protocols for gap closure. Here we report a novel approach for extending shotgun contigs and closing gaps that we termed PCR-assisted contig extension (PACE). PACE depends on the capture of rare mismatched interactions that occur between arbitrary prim...

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polym...