Supplemental Material - Prediction Performance of Feature Selectors and Classifiers on Highly Dimensional Transcriptomic Data for Prediction of Weight Loss in Filipino Americans at Risk for Type 2 Diabetes

Supplemental Material for Prediction Performance of Feature Selectors and Classifiers on Highly Dimensional Transcriptomic Data for Prediction of Weight Loss in Filipino Americans at Risk for Type 2 Diabetes by Lisa Chang, Yoshimi Fukuoka, Bradley E. Aouizerat, Li Zhang, and Elena Flowers in Biological Research for Nursing</p

Histological evaluation of the ear after trans-TM peptide phage application, compared to WT phage negative control and saline control.

<p><b>A.</b> Hematoxylin and eosin (H&E) stained sections illustrate the external auditory canal (EAC), TM and ME, 24 hrs after application of 10¹⁰ TM-3 phage or controls to the external surface of the TM. <b>B-E.</b> The ME and ME mucosa (<b>B</b>); the organ of Corti (C); the ME, RWM and cochlear basal turn (<b>D</b>) and the cochlea (<b>E</b>), 24 hrs after application of 10¹⁰ TM-3 phage directly into the ME.</p

3-D structural analysis of the five trans-TM peptides.

Structures were predicted using Pep-Fold 3.0. N = amino-terminus; C = carboxy terminus. Selected amino acids indicated by position relative to N.</p

Impact of trans-TM peptide phage on hearing.

<p>ABR thresholds measured in dB SPL (Sound Pressure Level relative to .0002 dynes/cm²) were recorded pre-operatively and daily for four days following 10¹⁰ phage particle injection into the ME bulla. Responses were obtained for 8, 16, and 32 kHz pure-tone stimuli. Results indicate that thresholds were elevated up to 20 dB on postoperative days 1 and 2, recovered to within +/- 5 dB of baseline by day 3. Results for four TM-transiting phage, WT phage and saline were similar, indicating that the temporary change in threshold is due to fluid, and that no damage to hearing occurred as a result of TM-transiting phage application. Data are means + SEM (n = 8).</p

Composition analysis of trans-TM peptides.

The peptides of five trans-TM phage exhibiting a range of TM transit efficiencies were evaluated. PEPCALC analysis of amino acid characteristics and hydrophility/hydrophobicity (A) and isoelectric properties (B).</p

Kinetics of peptide-mediated trans-TM transport.

<p>ME recovery kinetics of five TM-transiting peptide phage, compared to WT phage particles, following incubation of 10¹⁰ phage on the exterior surface of the TM for 1, 2 or 4 hrs. <b>A</b> = log scale, <b>B</b> = linear scale. All TM-transiting peptide phage were recovered at levels much higher than were WT phage not bearing a peptide. Phage bearing TM-3 peptide were recovered at much higher titers (more than 10⁵ higher at 4 hrs) than WT phage, and significantly more than any other TM-transiting phage. TM-3 phage also exhibited exponential increases in ME recovery over time consistent with an active transport mechanism. Error bars = SEM (n = 6 animals).</p

Comparison of trans-TM peptide entry into the IE versus the ME.

<p>Compared to ME recovery of TM-3 after 4-hr application of 10⁹ phage to the TM (white bar, taken from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172158#pone.0172158.g001" target="_blank">Fig 1</a>), recovery of TM-transiting phage from perilymph, 4 hrs after instillation of 10⁹ phage onto the area of the RWM (black bars) is absent or very low. Phage recovery from the IE improved somewhat at 24 hrs, but was not greater for TM-transiting phage than for WT Phage not bearing a peptide. Thus, any movement of phage into the IE does not appear to be peptide-mediated. Error bars = SD (n = 4).</p

Comparison of peptide phage transport to systemic antibiotic delivery in the ME.

<p><b>A.</b> Proportion of systemically delivered antibiotics that were observed in the ME of patients at 1, 2 or 3 hrs after systemic administration by Silverstein et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172158#pone.0172158.ref043" target="_blank">43</a>] (penicillin, 500,000 units; black bars) or Nicolau et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172158#pone.0172158.ref044" target="_blank">44</a>] (cefprozil, 15 mg/kg; white bars). <b>B.</b> Proportion of TM-3 peptide phage, applied to the TM, that was recovered from the ME 1, 2 or 4 hrs later, and TM-3 peptide, applied to the TM, recovered from the ME 1 hr later. Error bars = SEM (n = 4).</p

Additional file 3 of Parkinson’s disease-related Leucine-rich repeat kinase 2 modulates nuclear morphology and genomic stability in striatal projection neurons during aging

Additional file 3: Figure S1. No alteration of nuclear size in midbrain dopaminergic neurons and hippocampal neurons of 12-month-old Lrrk2−/− mice. a-c Co-staining of Lamin B and TH in SNc and VTA neurons of 12-month-old Lrrk2+/+ and Lrrk2−/− mice (a). Scale bar, 20 μm. The areas of soma and nuclei in SNc neurons were measured from five 12-month-old Lrrk2+/+ and Lrrk2−/− mice (b). N = 5 mice per genotype, about 30 neurons counted per animal. Conditional logistic regression test, no statistically significant difference was identified. The areas of soma and nuclei in VTA neurons were measured from five 12-month-old Lrrk2+/+ and Lrrk2−/− mice (c). N = 5 mice per genotype, about 30 neurons counted per animal. Conditional logistic regression test, no statistically significant difference was identified. d-f Co-staining of Lamin B and MAP2 in hippocampal dentate gyrus (DG) neurons of 12-month-old Lrrk2+/+ and Lrrk2−/− mice (d). Scale bar, 20 μm. The area of nuclei in DG neurons was measured from three 12-month-old Lrrk2+/+ and Lrrk2−/− mice e). N = 3 mice per genotype, about 50 neurons counted per animal. Conditional logistic regression test, no statistically significant difference was identified. The circularity of nuclei in DG neurons was measured from three 12-month-old Lrrk2+/+ and Lrrk2−/− mice (f). N = 3 mice per genotype, about 50 neurons counted per animal. Conditional logistic regression test, no statistically significant difference was identified

Additional file 5 of Parkinson’s disease-related Leucine-rich repeat kinase 2 modulates nuclear morphology and genomic stability in striatal projection neurons during aging

Additional file 5: Figure S3. No alteration of nuclear and soma size of the Lrrk2−/− SPNs after 2 weeks in culture. a Co-staining of βIII-tubulin and DAPI of the cultured SPNs. Scale bar, 20 μm. b Unpaired t-test, n = 50 neurons per genotype