Real-time polymerase chain reaction analysis of mRNA expression in anterior lens capsules

Total RNA was extracted from the anterior lens capsule of XFG/senile cataracts. Real-time PCR analysis was performed with expression assay probes. The amount of relative expression was normalized to that of 18Sr RNA. (N.S.: Not statistically significant, p=0.529; Mann–Whitney’s U-test).<p><b>Copyright information:</b></p><p>Taken from " genetic polymorphisms are associated with exfoliation glaucoma in the Japanese population"</p><p></p><p>Molecular Vision 2008;14():1037-1040.</p><p>Published online 05 Jun 2008</p><p>PMCID:PMC2426718.</p><p></p

Study design.

<p>(A) We first performed the “Present GWAS” for POAG and identified the 9p21.3 locus. This result was confirmed by the combined analysis with the “Previous GWAS”. (B) We then subdivided the POAG subjects into two subtypes, POAG/HPG and POAG/NPG, and each group was analyzed by combining the two data sets in order to investigate the differences of statistical significance in the 9p21.3 locus.</p

Association results of genome-wide significant SNPs in the Present GWAS.

a<p>Risk allele frequency in POAG/controls.</p>b<p><i>P</i> value of combined 2 GWAS results by Mantel-Haenszel test.</p>c<p><i>P</i> value of Cochran's Q heterogeneity test between Previous and Present GWAS.</p

Data_Sheet_1_Potential marker subset of blood-circulating cytokines on hematopoietic progenitor-to-Th1 pathway in COVID-19.pdf

In this study, we analyzed a relatively large subset of proteins, including 109 kinds of blood-circulating cytokines, and precisely described a cytokine storm in the expression level and the range of fluctuations during hospitalization for COVID-19. Of the proteins analyzed in COVID-19, approximately 70% were detected with Bonferroni-corrected significant differences in comparison with disease severity, clinical outcome, long-term hospitalization, and disease progression and recovery. Specifically, IP-10, sTNF-R1, sTNF-R2, sCD30, sCD163, HGF, SCYB16, IL-16, MIG, SDF-1, and fractalkine were found to be major components of the COVID-19 cytokine storm. Moreover, the 11 cytokines (i.e., SDF-1, SCYB16, sCD30, IL-11, IL-18, IL-8, IFN-γ, TNF-α, sTNF-R2, M-CSF, and I-309) were associated with the infection, mortality, disease progression and recovery, and long-term hospitalization. Increased expression of these cytokines could be explained in sequential pathways from hematopoietic progenitor cell differentiation to Th1-derived hyperinflammation in COVID-19, which might also develop a novel strategy for COVID-19 therapy with recombinant interleukins and anti-chemokine drugs.</p

Heat map of the SVM analysis to differentiate each time point after PHx.

<p>The lower left half of the figure provides the results of cross-validation analyses to estimate the success rate of the SVM model in separating user-defined groups of spectra. The accuracy is denoted by color: 100–90% (red); 89–80% (pink); 79–70% (purple), and < 69% (blue). The upper right half of the figure describes the <i>m/z</i> of the top 2 peaks that most efficiently discriminated each time point with statistical significance. The detailed data used for the analysis were provided as pseudogel and stack view of the spectra in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167647#pone.0167647.s001" target="_blank">S1 Fig</a>, and the statistical data were as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167647#pone.0167647.s004" target="_blank">S2 Table</a>. The identified albumin peaks are shown in blue (2558: 25–45^*1; 2743: 26–48; 2883: 25–48^*2; 3000: 25–49^*3; 3028: 25–49^*4, 3042: 25–50, 8926: 25–103), and the hemoglobin subunit α is shown in red (3163: 1–32; 3538: 110–141; 3627: 1–36; 3852: 107–141). *1: Ala->Pro: 4, *2: Ala->Pro: 20, *3: Gly -> Ser: 22, *4: Q -> deamidated: 18, SVM, support vector machine; <i>m/z</i>, mass to charge ratio.</p

AUC determined by ROC curve analysis for each peak used to compare 0 min <i>vs</i>. 24 h (acute phase), and 24 h <i>vs</i>.120 h (recovery phase).

<p>AUC determined by ROC curve analysis for each peak used to compare 0 min <i>vs</i>. 24 h (acute phase), and 24 h <i>vs</i>.120 h (recovery phase).</p

Representation of the principal components generated from the data set of a first cohort.

<p>(A) 0 min (red) <i>vs</i>. 24 h (green), (B) 24 h (red) <i>vs</i>. 48 h (green), (C) 48 h (red) <i>vs</i>. 72 h (green), (D) 72 h (red) <i>vs</i>. 96 h (green), (E) 96 h (red) <i>vs</i>. 120 h (green)*, (F) 120 h (red)* <i>vs</i>. 168 h (green). For each plasma sample, 4 measurements were automatically performed. The detailed data used for the analysis were provided as pseudogel and stack view of the spectra in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167647#pone.0167647.s001" target="_blank">S1 Fig</a>. *Three pigs were analyzed, except at 120 h, at which time point data were missing for 1 pig. PC, principal component.</p

Box-and-whisker plots of the representative markers for discriminating the phases after PHx.

<p>The discriminatory peaks were classified into 3 groups according to the patterns of change; peptides (A) down-regulated at recovery phase; (B) up-regulated at recovery phase; (C) down-regulated at acute phase. Pre (red), 0 min (light green), 24 h (blue), 48 h (yellow), 120 h (purple), 168 h (black). The top and bottom end marks of the plot indicated the maximum and minimum peak area/intensity within a given class. The box indicated the 25%-quartile (bottom) and the 75%-quartile (top) and the horizontal intersection denotes the median. The statistical data were detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167647#pone.0167647.s005" target="_blank">S3 Table</a>. The plot was drawn on a unique scale independent of the peak intensity scale. The identified peaks were as follows; 3000: ALB, 25–49^*1; 3028: ALB, 25–49^*2, 3042: ALB, 25–50, 8926: ALB, 25–103, 3627: HBA, 1–36. *1: Gly -> Ser: 22, *2: Q -> deamidated: 18. <i>m/z</i>, mass to charge ratio; ALB, albumin; HBA, hemoglobin subunit α.</p

Profiling of human plasma native peptides after PHx (n = 4).

<p>The upper right part of the figure described the results of cross-validation analyses to estimate the success rate of the SVM model in separating user-defined groups of spectra. The accuracy is denoted by color: 100–90% (red); 89–80% (pink). The 2-dimensional distribution plot analysis revealed the top 2 representative peaks, which discriminated the peptidomic patterns at 0 min (red), 24 (light green), 48 (blue), and 168 h (yellow) (<i>x</i> axis: 2378 <i>m/z</i>, P-value: <0.000001, <i>y</i> axis: 9080 <i>m/z</i>, P-value: <0.00001). LC-MALDI-TOF/TOF MS analyses identified the peak at 2378 <i>m/z</i> as a fragment derived from complement C4b (position:1429–1449). PHx, partial hepatectomy; SVM, support vector machine; <i>m/z</i>, mass to charge ratio, LC-MALDI-TOF/TOF MS, liquid chromatography-matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry.</p

Swine Plasma peptides after PHx detected by magnetic bead-based LC-MALDI-TOF/TOF MS analyses.

<p>Swine Plasma peptides after PHx detected by magnetic bead-based LC-MALDI-TOF/TOF MS analyses.</p