Notes on mineralogical genera

For the identification of peptides with tandem mass spectrometry (MS/MS), many software tools rely on the comparison between an experimental spectrum and a theoretically predicted spectrum. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the peptide identification performance and is an important problem for mass spectrometry based proteomics. In this study a new approach, called MS-Simulator, is presented for predicting the <i>y</i>-ion intensities in the spectrum of a given peptide. The new approach focuses on the accurate prediction of the relative intensity ratio between every two adjacent <i>y</i>-ions. The theoretical spectrum can then be derived from these ratios. The prediction of a ratio is a closed-form equation that involves up to five consecutive amino acids nearby the two <i>y</i>-ions and the two peptide termini. Compared with another existing spectrum prediction tool MassAnalyzer, the new approach not only simplifies the computation, but also improves the prediction accuracy

MS-Simulator: Predicting <i>Y</i>‑Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

For the identification of peptides with tandem mass spectrometry (MS/MS), many software tools rely on the comparison between an experimental spectrum and a theoretically predicted spectrum. Consequently, the accurate prediction of the theoretical spectrum from a peptide sequence can potentially improve the peptide identification performance and is an important problem for mass spectrometry based proteomics. In this study a new approach, called MS-Simulator, is presented for predicting the <i>y</i>-ion intensities in the spectrum of a given peptide. The new approach focuses on the accurate prediction of the relative intensity ratio between every two adjacent <i>y</i>-ions. The theoretical spectrum can then be derived from these ratios. The prediction of a ratio is a closed-form equation that involves up to five consecutive amino acids nearby the two <i>y</i>-ions and the two peptide termini. Compared with another existing spectrum prediction tool MassAnalyzer, the new approach not only simplifies the computation, but also improves the prediction accuracy

Histopathological examinations following burn wound infection with <i>P. aeruginosa</i>.

<p>The histopathological analyses included (A) skin within the burn wound, (B) lung, (C) liver, (D) kidney.</p

The levels of serum cytokines following burn-wound infection with <i>P. aeruginosa</i>.

<p>The data from 7(control) treatment are shown. The analyzed cytokines included (A) IL-1β, (B) IL-6, (C) TNF-α, (D) IL-4, and (E) IL-10. (A–C) The cytokine levels were generally elevated in the mice treated with WTD, reaching peak levels at 3 d post-infection. In contrast, the cytokine levels were not significantly elevated in the NPWT group. (D, E) For IL-4 and Il-10, significant deviations from baseline were not detected in either treatment group.</p

The burn wound bacteria levels following infection with bioluminescent <i>P. aeruginosa</i>.

<p>Comparisons are shown between NPWT and WTD (i.e., control) groups of mice during 7 d of treatment.</p

Survival rate analysis.

<p>NPWT resulted in a significantly higher survival rate than was observed in the scald plus infection group (<i>p</i><0.01). A significant difference in survival was not detected between the groups treated with NPWT or WTD (<i>p</i>>0.05).</p

Experimental design and survival time of the transplanted grafts.

#<p>At POD 30, 2 recipients in groups 5 and 6 were killed for myeloid chimerism evaluation.</p>*<p>At POD 100, the other 6 recipients in group 5 were killed for evaluation of myeloid chimerism and determination of underlying mechanisms.</p

Dynamic changes in peripheral and myeloid chimerism.

<p>(a) Time kinetics of chimerism in groups 5 and 6. At POD 7, they showed almost the same chimerism level (<i>P</i>>0.05). At POD 21, the level of chimerism in group 6 was mildly decreased, but it increased sharply in group 5 (<i>P</i><0.05). At POD 42, chimerism in group 5 returned to a total level 8.7%±0.6% but it decreased to background level in group 6 (<i>P</i><0.05). In addition, donor-origin CD45RA+ B cells in group 5 prevailed beginning at POD 21 and maintained thereafter. (b) Myeloid chimerism was detectable at 6.3±0.5% at POD 100 in group 5 and it never appeared in group 6 when allografts were rejected (n = 6, <i>P</i><0.05).</p

Dynamic changes of peripheral chimerism.

<p>Flow cytometry analysis for the presence of donor-specific CD4+/CD8+ T lymphocytes and CD45RA+ B lymphocytes at POD 7, POD 21, and POD 42 of one representative intact allogeneic hind limb recipient with CsA treatment. Levels of donor-specific chimerism were 3.3% in CD4/RT1ⁿ cells, 1.2% in CD8/RT1ⁿ cells, and 1.6% in CD45RA/RT1ⁿ cells at POD 7. They rose to the highest level for donor-origin CD4/RT1ⁿ 13.2%, CD8/RT1ⁿ 2.9%, and CD45RA/RT1ⁿ 2.1% at POD 21, remained at 3.6% CD4/RT1ⁿ, 2.0% CD8/RT1ⁿ, and 3.0% CD45RA/RT1ⁿ. The background levels observed in isograft controls were assessed at 0.3%, 0.2%, and 0.3%, respectively.</p

Flow cytometry analysis for myeloid chimerism and immunocytofluorescence staining for the presence of donor-origin cells in recipients' innate femurs.

<p>(a)The proportion of donor-origin cells observed from 2 representative recipients at POD 30 were at 5.7% and 5.5%, respectively, with the background level assessed at 0.1%. (b, c) The presence of RT1n cells in the contralateral femurs of recipients in group 5 and their absence in other groups was confirmed by immunocytofluorescence (×20).</p