Potential anti-inflammatory and anti-cancer properties of farnesol

© 2018 by the authors. Farnesol, an acyclic sesquiterpene alcohol, is predominantly found in essential oils of various plants in nature. It has been reported to exhibit anti-cancer and anti-inflammatory effects, and also alleviate allergic asthma, gliosis, and edema. In numerous tumor cell lines, farnesol can modulate various tumorigenic proteins and/or modulates diverse signal transduction cascades. It can also induce apoptosis and downregulate cell proliferation, angiogenesis, and cell survival. To exert its anti-inflammatory/anti-oncogenic effects, farnesol can modulate Ras protein and nuclear factor kappa-light-chain-enhancer of activated B cells activation to downregulate the expression of various inflammatory mediators such as cyclooxygenase-2, inducible nitric oxide synthase, tumor necrosis factor alpha, and interleukin-6. In this review, we describe the potential mechanisms of action underlying the therapeutic effects of farnesol against cancers and inflammatory disorders. Furthermore, these findings support the clinical development of farnesol as a potential pharmacological agent in clinical studies

Structure and function in flow networks

Peer reviewedPublisher PD

Thermal Emission from Warm Dust in the Most Distant Quasars

We report new continuum observations of fourteen z~6 quasars at 250 GHz and fourteen quasars at 1.4 GHz. We summarize all recent millimeter and radio observations of the sample of the thirty-three quasars known with 5.71<=z<=6.43, and present a study of the rest frame far-infrared (FIR) properties of this sample. These quasars were observed with the Max Plank Millimeter Bolometer Array (MAMBO) at 250 GHz with mJy sensitivity, and 30% of them were detected. We also recover the average 250 GHz flux density of the MAMBO undetected sources at 4 sigma, by stacking the on-source measurements. The derived mean radio-to-UV spectral energy distributions (SEDs) of the full sample and the 250 GHz non-detections show no significant difference from that of lower-redshift optical quasars. Obvious FIR excesses are seen in the individual SEDs of the strong 250 GHz detections, with FIR-to-radio emission ratios consistent with that of typical star forming galaxies. Most 250 GHz-detected sources follow the L_{FIR}--L_{bol} relationship derived from a sample of local IR luminous quasars (L_{IR}>10^{12}L_{\odot}), while the average L_{FIR}/L_{bol} ratio of the non-detections is consistent with that of the optically-selected PG quasars. The MAMBO detections also tend to have weaker Ly\alpha emission than the non-detected sources. We discuss possible FIR dust heating sources, and critically assess the possibility of active star formation in the host galaxies of the z~6 quasars. The average star formation rate of the MAMBO non-detections is likely to be less than a few hundred M_{\odot} yr^{-1}, but in the strong detections, the host galaxy star formation is probably at a rate of \gtrsim10^{3} M_{\odot} yr^{-1}, which dominates the FIR dust heating.Comment: 32 pages with 6 figures; ApJ, in press; Added references; Corrected typo

Heat Capacity of Protein Folding

We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal dipoles that are ordered around the unfolded surfaces, where the influence of these surfaces, covered with an ``ice-like'' shell of water, is represented by an effective field that directs the water dipoles. An intermolecular pair interaction between water molecules is also introduced. The heat capacity of the model exhibits the common feature of small globular proteins, two peaks corresponding to cold and warm unfolding, respectively. By introducing vibrational modes, we obtain quantitatively good accordance with experiments.Comment: 14 pages, LaTex, 4 figure

A Novel Bioluminescent Protease Assay Using Engineered Firefly Luciferase

Proteases play important roles in a variety of disease processes. Understanding their biological functions underpins the efforts of drug discovery. We have developed a bioluminescent protease assay using a circularly permuted form of firefly luciferase, wherein the native enzyme termini were joined by a peptide containing a protease site of interest. Protease cleavage of these mutant luciferases greatly activates the enzyme, typically over 100 fold. The mutant luciferase substrates are easily generated by molecular cloning and cell-free translation reactions and thus the protease substrates do not need to be chemically synthesized or purchased. The assay has broad applicability using a variety of proteases and their cognate sites and can sensitively detect protease activity. In this report we further demonstrate its utility for the evaluation of protease recognition sequence specificity and subsequent establishment of an optimized assay for the identification and characterization of protease inhibitors using high throughput screening

Selection of tuning parameters in bridge regression models via Bayesian information criterion

We consider the bridge linear regression modeling, which can produce a sparse or non-sparse model. A crucial point in the model building process is the selection of adjusted parameters including a regularization parameter and a tuning parameter in bridge regression models. The choice of the adjusted parameters can be viewed as a model selection and evaluation problem. We propose a model selection criterion for evaluating bridge regression models in terms of Bayesian approach. This selection criterion enables us to select the adjusted parameters objectively. We investigate the effectiveness of our proposed modeling strategy through some numerical examples.Comment: 20 pages, 5 figure

Fast matrix computations for pair-wise and column-wise commute times and Katz scores

We first explore methods for approximating the commute time and Katz score between a pair of nodes. These methods are based on the approach of matrices, moments, and quadrature developed in the numerical linear algebra community. They rely on the Lanczos process and provide upper and lower bounds on an estimate of the pair-wise scores. We also explore methods to approximate the commute times and Katz scores from a node to all other nodes in the graph. Here, our approach for the commute times is based on a variation of the conjugate gradient algorithm, and it provides an estimate of all the diagonals of the inverse of a matrix. Our technique for the Katz scores is based on exploiting an empirical localization property of the Katz matrix. We adopt algorithms used for personalized PageRank computing to these Katz scores and theoretically show that this approach is convergent. We evaluate these methods on 17 real world graphs ranging in size from 1000 to 1,000,000 nodes. Our results show that our pair-wise commute time method and column-wise Katz algorithm both have attractive theoretical properties and empirical performance.Comment: 35 pages, journal version of http://dx.doi.org/10.1007/978-3-642-18009-5_13 which has been submitted for publication. Please see http://www.cs.purdue.edu/homes/dgleich/publications/2011/codes/fast-katz/ for supplemental code

Probing the Intrinsic Shape and Alignment of Dark Matter Haloes using SDSS Galaxy Groups

We study the three-dimensional and projected shapes of galaxy groups in the Sloan Digital Sky Survey Data Release 4, and examine the alignment between the orientation of the central galaxy and the spatial distribution of satellite galaxies. The projected ellipticity of a group is measured using the moments of the discrete distribution of its member galaxies. We infer the three-dimensional and projected axis ratios of their dark matter haloes by comparing the measured ellipticity distributions with those obtained from Monte Carlo simulations of projected, triaxial dark matter haloes with different axis ratios. We find that the halo shape has a strong dependence on the halo mass. While the haloes of low-mass groups are nearly spherical, those of massive groups tend to be prolate. For groups containing at least four members, the statistical distribution of their measured ellipticities does not have a strong dependence on the colors of their central galaxies. Our analysis further shows that the average three-dimensional axis ratio for haloes with $12<{\rm log}[M/(h^{-1}M_{\odot})]\leq15$ is about $1:0.46:0.46$, resulting in a projected axis ratio of $\sim 0.77$. Our results for the alignment between the orientation of the central galaxy of a group and the distribution of their satellite galaxies are in broad agreement with those obtained by Yang et al. The distribution of satellite galaxies preferentially aligns with the major axis of the central galaxy, with a clear dependence on both halo mass and galaxy colors. (abridged)Comment: 13 pages, 10 figures and 2 tables. Accepted for publication in MNRA