SUMMARY The increasing throughput and sharing of proteomics mass spectrometry data have now yielded over one-third of a million public mass spectrometry runs. However, these discoveries are not continuously aggregated in an open and error-controlled manner, which limits their utility. To facilitate the reusability of these data, we built the MassIVE Knowledge Base (MassIVE-KB), a community-wide, continuously updating knowledge base that aggregates proteomics mass spectrometry discoveries into an open reusable format with full provenance information for community scrutiny. Reusing >31 TB of public human data stored in a mass spectrometry interactive virtual environment (MassIVE), the MassIVE-KB contains >2.1 million precursors from 19,610 proteins (48% larger than before; 97% of the total) and doubles proteome coverage to 6 million amino acids (54% of the proteome) with strict library-scale false discovery controls, thereby providing evidence for 430 proteins for which sufficient protein-level evidence was previously missing. Furthermore, MassIVE-KB can inform experimental design, helps identify and quantify new data, and provides tools for community construction of specialized spectral libraries.

A small silicon mode (de)multiplexer with cascaded asymmetrical directional couplers is demonstrated experimentally. As an example, a four channel mode (de)multiplexer is designed and realized for TM polarization. The fabricated mode (de)multiplexer has a low excess loss (<1 dB) as well as low crosstalk (≤23 dB) over a broad wavelength range (~20 nm). More channels can be achieved with two sets of orthogonal-polarization modes (e.g., 2N=8) multiplexed when desired.

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Polyamines are essential for cell migration during early mucosal restitution after wounding in the gastrointestinal tract. Activity of voltage-gated K(+) channels (Kv) controls membrane potential (E(m)) that regulates cytoplasmic free Ca(2+) concentration ([Ca(2+)](cyt)) by governing the driving force for Ca(2+) influx. This study determined whether polyamines are required for the stimulation of cell migration by altering K(+) channel gene expression, E(m), and [Ca(2+)](cyt) in intestinal epithelial cells (IEC-6). The specific inhibitor of polyamine synthesis, alpha-difluoromethylornithine (DFMO, 5 mM), depleted cellular polyamines (putrescine, spermidine, and spermine), selectively inhibited Kv1.1 channel (a delayed-rectifier Kv channel) expression, and resulted in membrane depolarization. Because IEC-6 cells did not express voltage-gated Ca(2+) channels, the depolarized E(m) in DFMO-treated cells decreased [Ca(2+)](cyt) as a result of reduced driving force for Ca(2+) influx through capacitative Ca(2+) entry. Migration was reduced by 80% in the polyamine-deficient cells. Exogenous spermidine not only reversed the effects of DFMO on Kv1.1 channel expression, E(m), and [Ca(2+)](cyt) but also restored cell migration to normal. Removal of extracellular Ca(2+) or blockade of Kv channels (by 4-aminopyridine, 1-5 mM) significantly inhibited normal cell migration and prevented the restoration of cell migration by exogenous spermidine in polyamine-deficient cells. These results suggest that polyamine-dependent intestinal epithelial cell migration may be due partially to an increase of Kv1.1 channel expression. The subsequent membrane hyperpolarization raises [Ca(2+)](cyt) by increasing the driving force (the electrochemical gradient) for Ca(2+) influx and thus stimulates cell migration.

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