Metallopanstimulin as a marker for head and neck cancer

BACKGROUND: Metallopanstimulin (MPS-1) is a ribosomal protein that is found in elevated amounts in the sera of patients with head and neck squamous cell carcinoma (HNSCC). We used a test, denoted MPS-H, which detects MPS-1 and MPS-1-like proteins, to determine the relationship between MPS-H serum levels and clinical status of patients with, or at risk for, HNSCC. PATIENTS AND METHODS: A total of 125 patients were prospectively enrolled from a university head and neck oncology clinic. Participants included only newly diagnosed HNSCC patients. Two control groups, including 25 non-smokers and 64 smokers, were studied for comparison. A total of 821 serum samples collected over a twenty-four month period were analyzed by the MPS-H radioimmunoassay. RESULTS: HNSCC, non-smokers, and smokers had average MPS-H values of 41.5 ng/mL, 10.2 ng/mL, and 12.8 ng/mL, respectively (p = 0.0001). CONCLUSION: We conclude that MPS-1 and MPS-1-like proteins are elevated in patients with HNSCC, and that MPS-H appears to be a promising marker of presence of disease and response to treatment in HNSCC patients

Stochastic Processes Crossing from Ballistic to Fractional Diffusion with Memory: Exact Results

We address the now classical problem of a diffusion process that crosses over from a ballistic behavior at short times to a fractional diffusion (sub- or super-diffusion) at longer times. Using the standard non-Markovian diffusion equation we demonstrate how to choose the memory kernel to exactly respect the two different asymptotics of the diffusion process. Having done so we solve for the probability distribution function (pdf) as a continuous function which evolves inside a ballistically expanding domain. This general solution agrees for long times with the pdf obtained within the continuous random walk approach but it is much superior to this solution at shorter times where the effect of the ballistic regime is crucial

Two-Frequency Jahn-Teller Systems in Circuit QED

We investigate the simulation of Jahn-Teller models with two non-degenerate vibrational modes using a circuit QED architecture. Typical Jahn-Teller systems are anisotropic and require at least a two-frequency description. The proposed simulator consists of two superconducting lumped-element resonators interacting with a common flux qubit in the ultrastrong coupling regime. We translate the circuit QED model of the system to a two-frequency Jahn-Teller Hamiltonian and calculate its energy eigenvalues and the emission spectrum of the cavities. It is shown that the system can be systematically tuned to an effective single mode Hamiltonian from the two-mode model by varying the coupling strength between the resonators. The flexibility in manipulating the parameters of the circuit QED simulator permits isolating the effective single frequency and pure two-frequency effects in the spectral response of Jahn-Teller systems.Comment: 8 pages, 4 figures, figures revise

Symbolic Reachability Analysis of B through ProB and LTSmin

We present a symbolic reachability analysis approach for B that can provide a significant speedup over traditional explicit state model checking. The symbolic analysis is implemented by linking ProB to LTSmin, a high-performance language independent model checker. The link is achieved via LTSmin's PINS interface, allowing ProB to benefit from LTSmin's analysis algorithms, while only writing a few hundred lines of glue-code, along with a bridge between ProB and C using ZeroMQ. ProB supports model checking of several formal specification languages such as B, Event-B, Z and TLA. Our experiments are based on a wide variety of B-Method and Event-B models to demonstrate the efficiency of the new link. Among the tested categories are state space generation and deadlock detection; but action detection and invariant checking are also feasible in principle. In many cases we observe speedups of several orders of magnitude. We also compare the results with other approaches for improving model checking, such as partial order reduction or symmetry reduction. We thus provide a new scalable, symbolic analysis algorithm for the B-Method and Event-B, along with a platform to integrate other model checking improvements via LTSmin in the future

Immunological basis of differences in disease resistance in the chicken

Genetic resistance to diseases is a multigenic trait governed mainly by the immune system and its interactions with many physiologic and environmental factors. In the adaptive immunity, T cell and B cell responses, the specific recognition of antigens and interactions between antigen presenting cells, T cells and B cells are crucial. It occurs through a network of mediator proteins such as the molecules of the major histocompatibility complex (MHC), T cell receptors, immunoglobulins and secreted proteins such as the cytokines and antibodies. The diversity of these proteins that mainly is due to an intrinsic polymorphism of the genes causes phenotypic variation in disease resistance. The well-known linkage of MHC polymorphism and Marek's disease resistance difference represents a classic model revealing immunological factors in resistance differences and diversity of mediator molecules. The molecular bases in any resistance variation to infectious pathogens are vaguely understood. This paper presents a review of the major immune mediators involved in resistance and susceptibility to infectious diseases and their functional mechanisms in the chicken. The genetic interaction of disease resistance with production traits and the environment is mentioned

Biaxial nematic phases in fluids of hard board-like particles

We use density-functional theory, of the fundamental-measure type, to study the relative stability of the biaxial nematic phase, with respect to non-uniform phases such as smectic and columnar, in fluids made of hard board-like particles with sizes $\sigma_1>\sigma_2>\sigma_3$. A restricted-orientation (Zwanzig) approximation is adopted. Varying the ratio $\kappa_1=\sigma_1/\sigma_2$ while keeping $\kappa_2=\sigma_2/\sigma_3$, we predict phase diagrams for various values of $\kappa_2$ which include all the uniform phases: isotropic, uniaxial rod- and plate-like nematics, and biaxial nematic. In addition, spinodal instabilities of the uniform phases with respect to fluctuations of the smectic, columnar and plastic-solid type, are obtained. In agreement with recent experiments, we find that the biaxial nematic phase begins to be stable for $\kappa_2\simeq 2.5$. Also, as predicted by previous theories and simulations on biaxial hard particles, we obtain a region of biaxility centred on $\kappa_1\approx\kappa_2$ which widens as $\kappa_2$ increases. For \kappa_2\agt 5 the region $\kappa_2\approx\kappa_1$ of the packing-fraction vs. $\kappa_1$ phase diagrams exhibits interesting topologies which change qualitatively with $\kappa_2$. We have found that an increasing biaxial shape anisotropy favours the formation of the biaxial nematic phase. Our study is the first to apply FMT theory to biaxial particles and, therefore, it goes beyond the second-order virial approximation. Our prediction that the phase diagram must be asymmetric is a genuine result of the present approach, which is not accounted for by previous studies based on second-order theories.Comment: Preprint format. 18 pages, 5 figure

Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes

Introduction: In recent years, there has been an exponential increase in the number of studies aiming to understand the biology of exosomes, as well as other extracellular vesicles. However, classification of membrane vesicles and the appropriate protocols for their isolation are still under intense discussion and investigation. When isolating vesicles, it is crucial to use systems that are able to separate them, to avoid cross-contamination. Method: EVs released from three different kinds of cell lines: HMC-1, TF-1 and BV-2 were isolated using two centrifugation-based protocols. In protocol 1, apoptotic bodies were collected at 2,000×g, followed by filtering the supernatant through 0.8 µm pores and pelleting of microvesicles at 12,200×g. In protocol 2, apoptotic bodies and microvesicles were collected together at 16,500×g, followed by filtering of the supernatant through 0.2 µm pores and pelleting of exosomes at 120,000×g. Extracellular vesicles were analyzed by transmission electron microscopy, flow cytometry and the RNA profiles were investigated using a Bioanalyzer®. Results: RNA profiles showed that ribosomal RNA was primary detectable in apoptotic bodies and smaller RNAs without prominent ribosomal RNA peaks in exosomes. In contrast, microvesicles contained little or no RNA except for microvesicles collected from TF-1 cell cultures. The different vesicle pellets showed highly different distribution of size, shape and electron density with typical apoptotic body, microvesicle and exosome characteristics when analyzed by transmission electron microscopy. Flow cytometry revealed the presence of CD63 and CD81 in all vesicles investigated, as well as CD9 except in the TF-1-derived vesicles, as these cells do not express CD9. Conclusions: Our results demonstrate that centrifugation-based protocols are simple and fast systems to distinguish subpopulations of extracellular vesicles. Different vesicles show different RNA profiles and morphological characteristics, but they are indistinguishable using CD63-coated beads for flow cytometry analysis

Whole genome sequencing-based mapping and candidate identification of mutations from fixed zebrafish tissue

As forward genetic screens in zebrafish become more common, the number of mutants that cannot be identified by gross morphology or through transgenic approaches, such as many nervous system defects, has also increased. Screening for these difficult-to-visualize phenotypes demands techniques such as whole-mount in situ hybridization (WISH) or antibody staining, which require tissue fixation. To date, fixed tissue has not been amenable for generating libraries for whole genome sequencing (WGS). Here, we describe a method for using genomic DNA from fixed tissue and a bioinformatics suite for WGS-based mapping of zebrafish mutants. We tested our protocol using two known zebrafish mutant alleles, gpr126st49 and egr2bfh227, both of which cause myelin defects. As further proof of concept we mapped a novel mutation, stl64, identified in a zebrafish WISH screen for myelination defects. We linked stl64 to chromosome 1 and identified a candidate nonsense mutation in the F-box and WD repeat domain containing 7 (fbxw7) gene. Importantly, stl64 mutants phenocopy previously described fbxw7vu56 mutants, and knockdown of fbxw7 in wild-type animals produced similar defects, demonstrating that stl64 disrupts fbxw7. Together, these data show that our mapping protocol can map and identify causative lesions in mutant screens that require tissue fixation for phenotypic analysis