Nonlinear energy transfers and phase diagrams for geostrophically balanced rotating-stratified flows

Equilibrium statistical mechanics tools have been developed to obtain indications about the natural tendencies of nonlinear energy transfers in two-dimensional and quasi-two-dimensional flows like rotating and stratified flows in geostrophic balance. In this article we consider a simple model of such flows with a nontrivial vertical structure, namely, two-layer quasigeostrophic flows, which remain amenable to analytical study. We obtain the statistical equilibria of the system in the case of a linear vorticity-stream function relation, build the corresponding phase diagram, and discuss the most probable outcome of nonlinear energy transfers, both on the horizontal and on the vertical, in the presence of stratification and rotation.

Towards a more precise neurophysiological assessment of cognitive functions in patients with disorders of consciousness

PURPOSE

To analyze the principles that guide inference of covert cognitive functions and consciousness in patients with extremely severe brain damage on the basis of neurophysiological test results.

METHODS

(1) A quantitative analysis of a range of possible inferences based on neurophysiological findings in low- and non-responsive patients; (2) a logical analysis of the various possible orders of application of neurophysiological tests in such patients.

RESULTS

Surprisingly, improvement of neurophysiological test qualities contributes to the improvement of diagnostic results less than some other factors, such as the structure of the patient population, the quality of the previous clinical diagnosis, and the variability of the methods used.

CONCLUSIONS

A sequential decision procedure is suggested. Different test paradigms should be combined most effectively to arrive at a reliable evaluation of cognitive functions in this patient population.

Restricted partition functions and inverse energy cascades in parity symmetry breaking flows

When the symmetries of homogenous isotropic turbulent flows are broken, different sets of modes with different physical roles emerge. In particular, choosing a forcing which puts more weight on one or the other of these sets may result in different statistics for the energy transfers. We use the general method of computing a partition function restricted to a portion of phase space to study analytically these different statistics. We illustrate this method in the case of parity symmetry breaking, measured by helicity. It is shown that when helicity is sign-definite at all scales, an inverse cascade is expected for the energy. When sign-definiteness is lost, even for a small set of modes, this cascade disappears and there is a sharp phase transition to the standard helical equipartition spectra.

Stereotactic Body Radiotherapy: Volumetric Modulated Arc Therapy versus 3D Non-Coplanar Conformal Radiotherapy for the Treatment of Early Stage Lung Cancer

Stereotactic body radiotherapy (SBRT) is a treatment option for patients with early stage lung cancer. Treatment duration can be >30 minutes per fraction with non-coplanar 3D-conformal radiotherapy (3D-CRT). Whilst this is generally well tolerated, faster delivery techniques are desirable. Volumetric modulated arc therapy (VMAT) allows for fast delivery of radiation treatment. The purpose of this planning study was to compare SBRT with 3D-CRT and VMAT, with VMAT plans generated using both single arc and 3 non-coplanar partial arcs. Ten patients who previously underwent SBRT (48 Gy in 4 fractions) with 3D-CRT were selected. VMAT plans were generated to treat the PTV while limiting doses to organs at risk. Cumulative dose volume histogram (DVH) parameters were compared between the 3 techniques using the Wilcoxon matched pairs test. Treatment delivery time was also assessed. Both VMAT techniques covered target volumes more conformally than 3D-CRT with a mean V48/VPTV of 1.21 for 3D-CRT, 1.03 for 3 arc plans and 1.01 for single arc plans (ρ = 0.005). Dose constraints to organs at risk were met using all three techniques. Mean lung doses were 2.93 Gy for 3D-CRT, 2.87 Gy for single arc and 2.73 Gy for the 3 arc technique (3-arc vs. 3D-CRT: ρ = 0.009). Lung V20 for 3D-CRT, 1 arc and 3 arcs were 3.24%, 2.89% and 2.73%, respectively (3-arc vs. 3D-CRT: ρ = 0.028). Mean time to deliver a single fraction was 13 minutes for 3D-CRT, 9.2 minutes for 3 arcs and 5.5 minutes for 1 arc. VMAT resulted in improved conformality compared to 3D-CRT. The 3 arc technique appears to have the lowest dose to lung although the magnitude is unlikely to be clinically significant. The main advantage of VMAT over 3D-CRT is faster treatment delivery time. Shortened treatment times are anticipated to improve tolerability of this treatment and reduce the chance of error due to intra-fraction motion.

Psychophysiological correlates of coping and quality of life in patients with ALS

OBJECTIVE

Self-regulation models of coping suggest that patients with chronic diseases reporting low quality of life (QoL), an indicator of failed coping efforts, should show facilitated access to disease related words. Here we investigated whether a reduced N400 amplitude within an incongruent, i.e. unpredictable disease-related context would be a correlate of this facilitated access.

METHODS

ERPs were recorded in N=18 patients with amyotrophic lateral sclerosis (ALS) and N=20 age-matched healthy controls during reading of sentences, ending either with congruent or incongruent words. Incongruent and congruent words were disease related or disease unrelated. Mean N400 amplitudes were analyzed with mixed models.

RESULTS

Generally, incongruent words elicited a more negative N400 amplitude than congruent words in all groups and conditions, i.e. an N400 effect. In patients with high QoL this N400 effect did not differ between disease related and unrelated words. In patients with low QoL, however, the N400 effect was significantly smaller for disease related than for disease unrelated words. In healthy controls N400 amplitudes showed no such interaction between congruence, disease relatedness and QoL. Results remained stable when controlling for disease severity, duration and depression.

CONCLUSION

The N400 indicates increased accessibility to disease related information in ALS patients with low QoL. The increased access may imply a constantly activated disease related context which is linked to low QoL.

SIGNIFICANCE

N400 modulation by disease related information may serve as a psychophysiological correlate of coping and the patient's QoL.

Automated image analysis of in vitro angiogenesis assay

Angiogenesis is the biological process of generating new capillary blood vessels. It is a fundamental component of a number of normal (reproduction and wound healing) and pathological processes (diabetic retinopathy, rheumatoid arthritis, tumor growth, and metastasis). In vitro angiogenesis assays provide a platform for evaluating the effects of pro- or antiangiogenic compounds. One of the most informative assays is the endothelial cells capillary tube formation assay performed on a biological matrix. This assay is based on quantification of the stimulatory and inhibitory effects of various agents, which is estimated through the measurement of the pseudo-tubules network length. This standard measurement is usually carried out manually by trained operators but requires time, attention, and dedication to achieve a reasonable degree of accuracy. Moreover, the screening is operator dependent. In this article, we propose an automated procedure to evaluate the pseudo-tubule network lengths. We propose a series of image analysis procedures developed using a freely available image analysis software library. More than 800 images from 12 experiments were analyzed automatically and manually, and their results were compared to improve and validate the proposed image analysis procedure. The resulting image analysis software is currently running on a dedicated server, with comparable accuracy to manual measurements. Using this new automated procedure, we are able to treat 540 images, or three complete assays per hour.

Inhibition of tumor angiogenesis and growth by a small-molecule multi-FGF receptor blocker with allosteric properties

Receptor tyrosine kinases (RTK) are targets for anticancer drug development. To date, only RTK inhibitors that block orthosteric binding of ligands and substrates have been developed. Here, we report the pharmacologic characterization of the chemical SSR128129E (SSR), which inhibits fibroblast growth factor receptor (FGFR) signaling by binding to the extracellular FGFR domain without affecting orthosteric FGF binding. SSR exhibits allosteric properties, including probe dependence, signaling bias, and ceiling effects. Inhibition by SSR is highly conserved throughout the animal kingdom. Oral delivery of SSR inhibits arthritis and tumors that are relatively refractory to anti-vascular endothelial growth factor receptor-2 antibodies. Thus, orally-active extracellularly acting small-molecule modulators of RTKs with allosteric properties can be developed and may offer opportunities to improve anticancer treatment.

Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling

The fibroblast growth factor (FGF)/fibroblast growth factor receptor (FGFR) signaling network plays an important role in cell growth, survival, differentiation, and angiogenesis. Deregulation of FGFR signaling can lead to cancer development. Here, we report an FGFR inhibitor, SSR128129E (SSR), that binds to the extracellular part of the receptor. SSR does not compete with FGF for binding to FGFR but inhibits FGF-induced signaling linked to FGFR internalization in an allosteric manner, as shown by crystallography studies, nuclear magnetic resonance, Fourier transform infrared spectroscopy, molecular dynamics simulations, free energy calculations, structure-activity relationship analysis, and FGFR mutagenesis. Overall, SSR is a small molecule allosteric inhibitor of FGF/FGFR signaling, acting via binding to the extracellular part of the FGFR.

Phase transitions and marginal ensemble equivalence for freely evolving flows on a rotating sphere

The large-scale circulation of planetary atmospheres such as that of the Earth is traditionally thought of in a dynamical framework. Here we apply the statistical mechanics theory of turbulent flows to a simplified model of the global atmosphere, the quasigeostrophic model, leading to nontrivial equilibria. Depending on a few global parameters, the structure of the flow may be either a solid-body rotation (zonal flow) or a dipole. A second-order phase transition occurs between these two phases, with associated spontaneous symmetry breaking in the dipole phase. This model allows us to go beyond the general theory of marginal ensemble equivalence through the notion of Goldstone modes.

Increased resting metabolic rate in girls with Rett syndrome compared to girls with developmental disabilities

The aim of this study was to determine the body composition and resting metabolic rate (RMR) of girls with Rett syndrome (RS) (n=15) and to compare them with an equally handicapped group of girls with developmental disabilities (DD) (n=13). Body composition was measured by bioelectrical impedance analysis and RMR  -  the amount of energy expended while at rest  -  by indirect calorimetry. Weight, height, body mass index (BMI), BMI percentiles and food intake were all measured and calculated by standardized procedures. Feeding time, ambulatory status and ability to self-feed were also assessed. Due to the sampling, there were no significant differences in age, height, weight, BMI, BMI percentiles and ambulatory status. Significant differences between groups were found for lower percentage lean body mass (LBM) (64.2±14.6 vs. 84.4±24.6) and higher absolute and relative fat mass (FM) in RS. RMR values adjusted for LBM were significantly higher in the group of girls with RS (approximately 160 kcal/day), indicating that higher energy expenditure is a component of increased risk of severely low body weight.

Influence of heparin mimetics on assembly of the FGF.FGFR4 signaling complex

Fibroblast growth factor (FGF) signaling regulates mammalian development and metabolism, and its dysregulation is implicated in many inherited and acquired diseases, including cancer. Heparan sulfate glycosaminoglycans (HSGAGs) are essential for FGF signaling as they promote FGF.FGF receptor (FGFR) binding and dimerization. Using novel organic synthesis protocols to prepare homogeneously sulfated heparin mimetics (HM), including hexasaccharide (HM(6)), octasaccharide (HM(8)), and decasaccharide (HM(10)), we tested the ability of these HM to support FGF1 and FGF2 signaling through FGFR4. Biological assays show that both HM(8) and HM(10) are significantly more potent than HM(6) in promoting FGF2-mediated FGFR4 signaling. In contrast, all three HM have comparable activity in promoting FGF1.FGFR4 signaling. To understand the molecular basis for these differential activities in FGF1/2.FGFR4 signaling, we used NMR spectroscopy, isothermal titration calorimetry, and size-exclusion chromatography to characterize binding interactions of FGF1/2 with the isolated Ig-domain 2 (D2) of FGFR4 in the presence of HM, and binary interactions of FGFs and D2 with HM. Our data confirm the existence of both a secondary FGF1.FGFR4 interaction site and a direct FGFR4.FGFR4 interaction site thus supporting the formation of the symmetric mode of FGF.FGFR dimerization in solution. Moreover, our results show that the observed higher activity of HM(8) relative to HM(6) in stimulating FGF2.FGFR4 signaling correlates with the higher affinity of HM(8) to bind and dimerize FGF2. Notably FGF2.HM(8) exhibits pronounced positive binding cooperativity. Based on our findings we propose a refined symmetric FGF.FGFR dimerization model, which incorporates the differential ability of HM to dimerize FGFs.

Abstract 1396: FGFR1-induced radioresistance of Panc02 pancreatic tumor cells is decreased by SSR128129 treatment in vitro and in vivo

We have previously established the important role of FGF-2 pathways in tumor cell radioresistance. Although radiotherapy is commonly used in the treatment of pancreatic carcinomas which are known to express FGF and FRGFR, the role of FGFR pathways in radioresistance of pancreatic tumor has not yet been studied. We established a new syngenic mouse model of orthotopic pancreatic xenograft of Panc02 cells transfected with hFGFR1-receptor (Panc02-FGFR1). Whereas the in vitro radioresistance of the parental cell line (Panc02) was not affected by the addition of the specific FGF-receptor antagonist SSR128129, Panc02-FGFR1 radioresistance was significantly decreased by treating cells with SSR128129 (1 µM) 4 hours before irradiation (mean inactivation dose [MID] was 6.1±0.2 Gy in control PancO2-FGFR1 versus 4.2±0.2 Gy in SSR128129 treated cells, P<0.001). Orthotopic injection of Panc02-FGFR1 cells in syngeneic C57B6 mice led to rapid growth of pancreatic tumors. While SSR128129 (30 mg/kg/d) was ineffective on the tumor growth, this compound significantly decreased microvessel density in Panc02-FGFR1 tumors (104.7±14.6 vs 136.6±10.3 vessels/field, P<0.001). Local irradiation (2×2.5 Gy) of tumor-bearing animals previously treated for 1 week with SSR128129, led to a strong decrease of tumor size (40% decrease, P<0.05) one week after radiotherapy, whereas the tumor size of untreated animals was not affected by irradiation. The effect of SSR128129 on microvessel density was not affected by radiotherapy. Together, these data show that inhibiting FGFR pathways leads to a major radiosensitization of pancreatic tumors in vitro and in vivo.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1396.

Suppression of cytokine expression by roflumilast and dexamethasone in a model of chronic asthma

BACKGROUND

In a mouse model of mild chronic asthma, both inflammation and remodelling can be suppressed by dexamethasone (a glucocorticoid) and roflumilast (a selective phosphodiesterase-4 inhibitor).

OBJECTIVE

To better understand the underlying molecular mechanisms, we investigated the effects of treatment on airway expression of inflammation-related cytokines, as well as on epithelial expression of growth factors.

METHODS

BALB/c mice systemically sensitized to ovalbumin were challenged with aerosolized antigen for 6 weeks and treated with roflumilast or dexamethasone during the final 2 weeks. Expression of mRNA, for a variety of cytokines and growth factors, was assessed in selectively dissected proximal airways or in airway epithelium obtained by laser capture microdissection.

RESULTS

In the airway wall of vehicle-treated challenged animals, there was significantly elevated expression of mRNA for a variety of pro-inflammatory and T helper type 2 cytokines, as well as for IFN-gamma. All these cytokines were suppressed by dexamethasone. Treatment with roflumilast reduced expression of IL-17A, TNF-alpha, granulocyte-macrophage colony-stimulating factor and IL-6, but did not inhibit other cytokines. Both drugs suppressed the enhanced expression of mRNA for growth factors such as TGF-beta1 and FGF-2 in airway epithelium.

CONCLUSIONS

Whereas dexamethasone non-specifically inhibits numerous mediators involved in inflammation and the immune response, roflumilast selectively inhibits a subset of pro-inflammatory cytokines and growth factors. These mediators and/or the cells that produce them may have critical roles in the pathogenesis of the lesions of chronic asthma.

Transgenic sequences are frequently lost in Phytophthora parasitica transformants without reversion of the transgene-induced silenced state

Little data exist on the mechanism and stability of transformation in Phytophthora parasitica, a major oomycete parasite of plants. Here, we studied the stability of drug-resistant protoplast transformants by analyzing single-zoospore derivatives. We show that the transgenic sequences are not stably integrated into the chromosomes, resulting in the loss of drug resistance in single-zoospore derivatives. However, in strains where the P. parasitica gene encoding the CBEL elicitor was silenced by transformation with sense or antisense constructs, silencing is not reversed when the transgenic sequences are lost. This suggests that instability of P. parasitica transformants is not an obstacle for loss-of-function studies in this organism.