An Unorthodox Introduction to QCD

These are lecture notes presented at the 2017 CTEQ Summer School at the University of Pittsburgh and the 2018 CTEQ Summer School at the University of Puerto Rico, Mayaguez. The title is a reference to hep-th/0309149 and introduces perturbative QCD and its application to jet substructure from a bottom-up perspective based on the approximation of QCD as a weakly-coupled, conformal field theory. Using this approach, a simple derivation of the Sudakov form factor with soft gluon emission modeled as a Poisson process is presented. Topics of the identification and discrimination of quark- versus gluon-initiated jets and jet grooming are also discussed.Comment: 16 pages, 18 figures. Comments welcome!, v2: updated to include both lectures from the 2018 CTEQ schoo

Figure 4

<p>A. Quantitative real-time PCR of CK5 expression in lung transplant patients correlated with time post-transplant. This box plot shows the increase in CK5 mRNA expression (decrease in ΔCt for CK5) with time post transplant. The X-axis represents set time points post transplant (0 = time of transplant; 1 = 1day post-transplant (PT); 2 = 1week PT; 3 = 1month PT; 4 = 3months PT; 5 = 6months PT). B. Percentage decrease in FEV1 in lung transplant patients correlated with time post-transplant. Box plot of FEV1 on the Y-axis with 0.0 being 100% FEV1 compared to time post transplant on the X-axis (0 = time of transplant; 1 = 1day PT; 2 = 1week PT; 3 = 1month PT; 4 = 3months PT; 5 = 6months PT). C. Quantitative real-time PCR of CK5 expression in lung transplant patients correlated with percentage decrease in FEV1 post-transplant. There is a moderate negative correlation between average FEV1 and average ΔCt values of −0.39. However, this does not reach statistical significance with a p-value = 0.085.</p

Lung transplant patient demographics.

<p>COPD = chronic obstructive pulmonary disease; IPF = idiopathic pulmonary fibrosis; PHTN = pulmonary hypertension; ILD = interstitial lung disease; PCH = Pulmonary capillary hemangiomatosis.</p

Optimization of the Assay for Primers and Probes.

<p>The Quantitative Real Time PCR assay was first performed with varying concentrations of primer and then probe to determine the optimal concentration of primers and probe for the assay. The concentration at which, for both primers and probe, the ΔCt and ΔRn did not change with increasing concentrations was selected. Thus primer concentrations of 600 nM and probe concentration of 250 nM were chosen.</p

Figure 2

<p>A. Quantitative real-time PCR of CK5 plotted against age of normal human subjects. A scatter plot of data shows no significant difference between the log of the age and CK5 mRNA expression levels in all 38 normal human subjects examined (p = 0.273). B. Quantitative real-time PCR expression of CK5 does not differ with gender. A box plot demonstrates the similarity in CK5 levels in male and female normal human subjects (p = 0.84).</p

Quantitative real-time PCR of CK5 expression in normal human subjects compared to lung transplant patients and heart transplant patients.

<p>A box plot demonstrates the differences between CK5 values in normal human subjects compared to lung transplant patients (p = 3.1×10⁻¹³). A further comparison is made between CK5 mRNA expression in the circulation of heart transplant patients (n = 6) and lung transplant patients (p = 0.004).</p

Figure 1

<p>A. PCR for CK5 mRNA from the circulation of healthy volunteers and lung transplant patients. The top panel shows the expected 439 bp fragment for CK5 using cDNA as template in healthy volunteers (Lanes 1–4) and CK5 mRNA expression from a representative group of patients post lung transplantation (Lanes 5–9). CK5 mRNA expression was not found in PCR Lanes 5, 8 and 9 and neither was CK5 mRNA expression detectible by quantitative real-time PCR in these samples. Lane 10 represents the positive control, which consists of a bacterial artificial chromosome (BAC) containing 170 kb of genomic sequence surrounding the CK5 locus as template, which is why the band is a larger size. Lane 11 is the negative control without cDNA template. The bottom panel shows PCR amplification of GAPDH from the same templates. B. Standard curve of real-time PCR amplification of CK5 and GAPDH. The log quantity of RNA is plotted against the mean threshold cycle (Ct), measured in triplicate. Slope and intercept are represented in the equations of the regression lines, along with the regression coefficient.</p

Plots of the log Cox Relative Hazard ratio for BOS against percent T regulatory lymphocyte subsets.

<p>The log of the Cox Relative Hazard (y-axis) decreases, i.e., less likely to develop BOS, as the percent of Treg, Treg subset or CCL21 protein level (x-axis) increases. The steeper the curve, as indicated by the blue line, the more protective the association with each Treg subset. The most significant effect is seen with the CCR7⁺ Treg subset. Confidence intervals are given by the gray bands. (top left) A plot for total BALF Treg, which demonstrates a non-significant protective effect. (top right) A plot of percent CCR4⁺ Treg, which demonstrates no significant protective effect. (bottom left) A plot of percent CCR7⁺ Treg, which demonstrates a significant protective effect. (botom right) A plot of BALF CCL21 protein level (pg) as determined by ELISA, which demonstrates a significant protective effect.</p

Density plots of chemokine receptor expression by Treg.

<p>Representative density plots of CCR4 and CCR7 expression by BALF Treg. The parent populations for determination of chemokine receptor positivity were singlet, live, CD3⁺CD4⁺CD25^hiFoxp3⁺ lymphocytes as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011354#pone-0011354-g001" target="_blank">Figure 1</a>. (left) Demonstrates the generally high level of CCR4 expression by Treg. The CCR4 gate was determined such that <0.1% of the cells were positive in the CCR4 FMO tube (see text for detail). (right) Demonstrates the variability of CCR7 expression by Treg. The CCR7 gate was determined such that <0.3% of the cells were positive in the CCR7 FMO tube.</p

Flow chart description of the number of samples and outcomes from each group.

<p>Forty-seven lung transplant recipients were in the study. Thirteen went on to develop BOS. Seventy BALF samples were collected and ten had insufficient cells to allow detection of Treg, thus 60 samples were used for total Treg analysis. Of the 60 samples, 27 were dropped from analysis for the Treg subsets due to inadequate number of Treg as explained in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011354#s2" target="_blank">Methods</a>.</p