Universal scaling of strange particle pTp_{\rm T} spectra in pp collisions

As a complementary study to that performed on the transverse momentum ($p_{\rm T}$) spectra of charged pions, kaons and protons in proton-proton (pp) collisions at LHC energies 0.9, 2.76 and 7 TeV, we present a scaling behaviour in the $p_{\rm T}$ spectra of strange particles ($K_{S}^{0}$, $\rm \Lambda$, $\rm \Xi$ and $\phi$) at these three energies. This scaling behaviour is exhibited when the spectra are expressed in a suitable scaling variable $z=p_{\rm T}/K$, where the scaling parameter $K$ is determined by the quality factor method and increases with the center of mass energy ($\sqrt{s}$). The rates at which $K$ increases with $\mathrm{ln}\sqrt{s}$ for these strange particles are found to be identical within errors. In the framework of the colour string percolation model, we argue that these strange particles are produced through the decay of clusters that are formed by the colour strings overlapping. We observe that the strange mesons and baryons are produced from clusters with different size distributions, while the strange mesons (baryons) $K_{S}^{0}$ and $\phi$ ($\rm \Lambda$ and $\rm \Xi$) originate from clusters with the same size distributions. The cluster's size distributions for strange mesons are more dispersed than those for strange baryons. The scaling behaviour of the $p_{\rm T}$ spectra for these strange particles can be explained by the colour string percolation model in a quantitative way.Comment: 8 pages, 10 figures, accepted by EPJ

knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable

Abstract Background Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). Results We addressed this problem by using knnAUC (k-nearest neighbors AUC test, the R package is available at https://sourceforge.net/projects/knnauc/ ). In the knnAUC software framework, we first resampled a dataset to get the training and testing dataset according to the sample ratio (from 0 to 1), and then constructed a k-nearest neighbors algorithm classifier to get the yhat estimator (the probability of y = 1) of testy (the true label of testing dataset). Finally, we calculated the AUC (area under the curve of receiver operating characteristic) estimator and tested whether the AUC estimator is greater than 0.5. To evaluate the advantages of knnAUC compared to seven other popular methods, we performed extensive simulations to explore the relationships between eight different methods and compared the false positive rates and statistical power using both simulated and real datasets (Chronic hepatitis B datasets and kidney cancer RNA-seq datasets). Conclusions We concluded that knnAUC is an efficient R package to test non-linear dependence between one continuous variable and one binary dependent variable especially in computational biology area.https://deepblue.lib.umich.edu/bitstream/2027.42/146514/1/12859_2018_Article_2427.pd

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

The Impact of Bodily States on Divergent Thinking: Evidence for a Control-Depletion Account

Given previous evidence that bodily states can impact basic cognitive processes, we asked whether such impact can also be demonstrated for creative cognition. In particular, we had participants perform a design improvement task and a consequences imagination task while standing up, walking in a predetermined pattern, or walking freely. Results show better divergent-thinking performance with unconstrained than with constrained walking, and better performance for walking than for standing. A second experiment assessed performance in an alternative uses task and a figural combination task while participants were lying, sitting, or standing. Results showed better performance when standing up than when lying or sitting. Taken altogether, these observations provide evidence for an approach in terms of cognitive-control depletion: the more a bodily activity exhausts control resources, the better divergent thinking can unfold, presumably because reduced top-down control brings more ideas into play

Hepatic autophagy fluctuates during the development of non-alcoholic fatty liver disease

Introduction and objectives: Autophagy has emerged as a critical regulatory pathway in non-alcoholic fatty liver disease (NAFLD). However, the variability of hepatic autophagy during NAFLD development remains controversial. This study aimed to elucidate the dynamics of hepatic autophagy and its underlying mechanism during NAFLD development both in vivo and in vitro. Materials and methods: Autophagy markers were evaluated in the livers of mice fed a high fat diet or a methionine-choline-deficient diet and in HepG2 cells treated with palmitic acid (PA) by western blotting. Intrahepatic and intracellular triacylglycerol levels were assessed using biochemical quantification and lipid staining. Autophagic flux was monitored using an LC3 turnover assay and tandem mRFP-GFP-LC3 fluorescence analysis. Results: Hepatic autophagy was enhanced in early stages but blocked at later stages of NAFLD development both in vivo and in vitro. Analysis of autophagic flux revealed that both autophagic synthesis and degradation were initially activated and progressively inhibited afterwards. The activation of mammalian target of rapamycin complex 1 (mTORC1), a central regulator of autophagy, was found to be negatively correlated with autophagic synthesis; moreover, pharmacological inhibition of mTORC1 by rapamycin alleviated hepatic steatosis through recovery of autophagic flux in hepatocytes with prolonged PA treatment. Conclusions: Hepatic autophagy fluctuates during the development of NAFLD in which mTORC1 signalling plays a critical regulatory role, suggesting a therapeutic potential of autophagy modulation by targeting the mTORC1 signalling pathway in NAFLD

Optimization of High Hydrostatic Pressure Treatments on Soybean Protein Isolate to Improve Its Functionality and Evaluation of Its Application in Yogurt

This work aimed to improve the functional properties of soybean protein isolate (SPI) by high hydrostatic pressure (HHP) and develop SPI incorporated yogurt. Response surface methodology (RSM) was used to optimize the HHP treatment parameters, including pressure, holding time, and the ratio of SPI/water. Water holding capacity, emulsifying activity index, solubility, and hardness of SPI gels were evaluated as response variables. The optimized HPP treatment conditions were 281 MPa of pressure, 18.92 min of holding time, and 1:8.33 of SPI/water ratio. Water and oil holding capacity, emulsifying activity, and stability of SPI at different pH were improved. Additionally, relative lipoxygenase (LOX) activity of HHP treated SPI (HHP-SPI) was decreased 67.55 ± 5.73%, but sulphydryl group content of HHP-SPI was increased 12.77%, respectively. When incorporating 8% of SPI and HHP-SPI into yogurt, the water holding capacity and rheological properties of yogurt were improved in comparison with yogurt made of milk powders. Moreover, HHP-SPI incorporated yogurt appeared better color and flavor