Reduction of amplitude equations by the renormalization group approach

This article elucidates and analyzes the fundamental underlying structure of the renormalization group (RG) approach as it applies to the solution of any differential equation involving multiple scales. The amplitude equation derived through the elimination of secular terms arising from a naive perturbation expansion of the solution to these equations by the RG approach is reduced to an algebraic equation which is expressed in terms of the Thiele semi-invariants or cumulants of the eliminant sequence { Zi } i=1 . Its use is illustrated through the solution of both linear and nonlinear perturbation problems and certain results from the literature are recovered as special cases. The fundamental structure that emerges from the application of the RG approach is not the amplitude equation but the aforementioned algebraic equation. © 2008 The American Physical Society.

Swelling induced finite strain flexure in a rectangular block of an isotropic elastic material

The deformation of a rectangular block into an annular wedge is studied with respect to the state of swelling interior to the block. Nonuniform swelling fields are shown to generate these flexure deformations in the absence of resultant forces and bending moments. Analytical expressions for the deformation fields demonstrate these effects for both incompressible and compressible generalizations of conventional hyperelastic materials. Existing results in the absence of a swelling agent are recovered as special cases.

On helical shear of a compressible elastic circular cylindrical tube

In this paper we examine the combined azimuthal and axial shear of a compressible isotropic elastic circular cylindrical tube of finite extent, otherwise referred to as helical shear (which is an isochoric deformation). The equilibrium equations are formulated in terms of the principal stretches, and explicit necessary and sufficient conditions on the strain-energy function for the material to support this deformation are obtained and compared with those obtained previously for this problem. Several classes of strain-energy functions are derived and in some general cases complete solutions of the equilibrium equations are obtained. Existing results are recovered as special cases and some new results for the strain-energy functions derived are determined and discussed.

On extension and torsion of a compressible elastic circular cylinder

In this paper we examine the combined extension and torsion of a compressible isotropic elastic cylinder of finite extent. The equilibrium equations are formulated in terms of the principal stretches and then applied to the special case of pure torsion superimposed on a uniform extension (an isochoric deformation). Explicit necessary and sufficient conditions on the strain-energy function for the material to support this deformation with vanishing traction on the lateral surfaces of the cylinder are obtained. Some strain-energy functions satisfying these conditions are considered, existing results are recovered as special cases and new results are obtained. We also point out how the strain-energy functions generated from the considered isochoric deformation considered (of a compressible material) can be used to generate energy functions and corresponding solutions for the incompressible theory.

CFD simulations of flow and heat transfer through the porous interface of a metal foam heat exchanger

This paper offers numerical modelling of a waste heat recovery system. A thin layer of metal foam is attached to a cold plate to absorb heat from hot gases leaving the system. The heat transferred from the exhaust gas is then transferred to a cold liquid flowing in a secondary loop. Two different foam PPI (Pores Per Inch) values are examined over a range of fluid velocities. Numerical results are then compared to both experimental data and theoretical results available in the literature. Challenges in getting the simulation results to match those of the experiments are addressed and discussed in detail. In particular, interface boundary conditions specified between a porous layer and a fluid layer are investigated. While physically one expects much lower fluid velocity in the pores compared to that of free flow, capturing this sharp gradient at the interface can add to the difficulties of numerical simulation. The existing models in the literature are modified by considering the pressure gradient inside and outside the foam. Comparisons against the numerical modelling are presented. Finally, based on experimentally-validated numerical results, thermo-hydraulic performance of foam heat exchangers as waste heat recovery units is discussed with the main goal of reducing the excess pressure drop and maximising the amount of heat that can be recovered from the hot gas stream.

Towards a phylogeny of the Tenebrionoidea (Coleoptera)

The phylogenetic relationships of the beetle superfamily Tenebrionoidea are investigated using the most comprehensive genetic data set compiled to date. With ∼34,000 described species in approximately 1250 genera and 28 families, Tenebrionoidea represent one of the most diverse and species-rich superfamilies of beetles. The interfamilial relationships of the Tenebrionoidea are poorly known; previous morphological and molecular phylogenies recovered few well-supported and often conflicting relationships between families. Here we present a molecular phylogeny of Tenebrionoidea based on genes commonly used to resolve family and superfamily-level phylogenies of beetles (18S, 28S, 16S, 12S, tRNA Val and COI). The alignment spanned over 6.5 KB of DNA sequence and over 300 tenebrionoid genera from 24 of the 28 families were sampled. Maximum Likelihood and Bayesian analysis could not resolve deeper level divergences within the superfamily and very few relationships between families were supported. Increasing gene coverage in the alignment by removing taxa with missing data did not improve clade support but when rogue taxa were removed increased resolution was recovered. Investigation of signal strength suggested conflicting phylogenetic signal was present in the standard genes used for beetle phylogenetics, even when rogue taxa were removed. Our study of Tenebrionoidea highlights that even with relatively comprehensive taxon sampling within a lineage, this standard set of genes is unable to resolve relationships within this superfamily.

Suppression of mRNAs encoding tegument tetraspanins from schistosoma mansoni results in impaired tegument turnover

Schistosomes express a family of integral membrane proteins, called tetraspanins (TSPs), in the outer surface membranes of the tegument. Two of these tetraspanins, Sm-TSP-1 and Sm-TSP-2, confer protection as vaccines in mice, and individuals who are naturally resistant to S. mansoni infection mount a strong IgG response to Sm-TSP-2. To determine their functions in the tegument of S. mansoni we used RNA interference to silence expression of Sm-tsp-1 and Sm-tsp-2 mRNAs. Soaking of parasites in Sm-tsp dsRNAs resulted in 61% (p = 0.009) and 74% (p = 0.009) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in adult worms, and 67%–75% (p = 0.011) and 69%–89% (p = 0.004) reductions in Sm-tsp-1 and Sm-tsp-2 transcription levels, respectively, in schistosomula compared to worms treated with irrelevant control (luciferase) dsRNA. Ultrastructural morphology of adult worms treated in vitro with Sm-tsp-2 dsRNA displayed a distinctly vacuolated and thinner tegument compared with controls. Schistosomula exposed in vitro to Sm-tsp-2 dsRNA had a significantly thinner and more vacuolated tegument, and morphology consistent with a failure of tegumentary invaginations to close. Injection of mice with schistosomula that had been electroporated with Sm-tsp-1 and Sm-tsp-2 dsRNAs resulted in 61% (p = 0.005) and 83% (p = 0.002) reductions in the numbers of parasites recovered from the mesenteries four weeks later when compared to dsRNA-treated controls. These results imply that tetraspanins play important structural roles impacting tegument development, maturation or stability.

Artemisinin induced dormancy in Plasmodium falciparum : duration, recovery rates and implications in treatment failure

Background Despite the remarkable activity of artemisinin and its derivatives, monotherapy with these agents has been associated with high rates of recrudescence. The temporary arrest of the growth of ring-stage parasites (dormancy) after exposure to artemisinin drugs provides a plausible explanation for this phenomenon. Methods Ring-stage parasites of several Plasmodium falciparum lines were exposed to different doses of dihydroartemisinin (DHA) alone or in combination with mefloquine. For each regime, the proportion of recovering parasites was determined daily for 20 days. Results Parasite development was abruptly arrested after a single exposure to DHA, with some parasites being dormant for up to 20 days. Approximately 50% of dormant parasites recovered to resume growth within the first 9 days. The overall proportion of parasites recovering was dose dependent, with recovery rates ranging from 0.044% to 1.313%. Repeated treatment with DHA or with DHA in combination with mefloquine led to a delay in recovery and an ∼10-fold reduction in total recovery. Strains with different genetic backgrounds appeared to vary in their capacity to recover. Conclusions These results imply that artemisinin-induced arrest of growth occurs readily in laboratory-treated parasites and may be a key factor in P. falciparum malaria treatment failure.

Human amnion epithelial cell transplantation abrogates lung fibrosis and augments repair

Rationale: Chronic lung disease characterized by loss of lung tissue,inflammation, and fibrosis represents a major global health burden. Cellular therapies that could restore pneumocytes and reduce inflammation and fibrosis would be a major advance in management. Objectives: To determine whether human amnion epithelial cells (hAECs), isolated from term placenta and having stem cell–like and antiinflammatory properties, could adopt an alveolar epithelial phenotype and repair a murine model of bleomycin-induced lung injury. Methods: Primary hAECs were cultured in small airway growth medium to determine whether the cells could adopt an alveolar epithelial phenotype. Undifferentiated primary hAECs were also injected parenterally into SCID mice after bleomycin-induced lung injury and analyzed for production of surfactant protein (SP)-A, SP-B, SP-C, and SP-D. Mouse lungs were also analyzed for inflammation and collagen deposition. Measurements and Main Results: hAECs grown in small airway growth medium developed an alveolar epithelial phenotype with lamellar body formation, production of SPs A–D, and SP-D secretion. Although hAECs injected into mice lacked SPs, hAECs recovered from mouse lungs 2 weeks posttransplantation produced SPs. hAECs remained engrafted over the 4-week test period. hAEC administration reduced inflammation in association with decreased monocyte chemoattractant protein-1, tumor necrosis factor-a, IL-1 and -6, and profibrotic transforming growth factor-b in mouse lungs. In addition,lung collagen content was significantly reduced by hAEC treatment as a possible consequence of increased degradation by matrix metalloproteinase-2 and down-regulation of the tissue inhibitors f matrix metalloproteinase-1 and 2. Conclusions: hAECs offer promise as a cellular therapy for alveolar restitution and to reduce lung inflammation and fibrosis.

The MyD88+ phenotype is an adverse prognostic factor in epithelial ovarian cancer

The prognosis of epithelial ovarian cancer is poor in part due to the high frequency of chemoresistance. Recent evidence points to the Toll-like receptor-4 (TLR4), and particularly its adaptor protein MyD88, as one potential mediator of this resistance. This study aims to provide further evidence that MyD88 positive cancer cells are clinically significant, stem-like and reproducibly detectable for the purposes of prognostic stratification. Expression of TLR4 and MyD88 was assessed immunohistochemically in 198 paraffin-embedded ovarian tissues and in an embryonal carcinoma model of cancer stemness. In parallel, expression of TLR4 and MyD88 mRNA and regulatory microRNAs (miR-21 and miR-146a) was assessed, as well as in a series of chemosensitive and resistant cancer cells lines. Functional analysis of the pathway was assessed in chemoresistant SKOV-3 ovarian cancer cells. TLR4 and MyD88 expression can be reproducibly assessed via immunohistochemistry using a semi-quantitative scoring system. TLR4 expression was present in all ovarian epithelium (normal and neoplastic), whereas MyD88 was restricted to neoplastic cells, independent of tumour grade and associated with reduced progression-free and overall survival, in an immunohistological specific subset of serous carcinomas, p<0.05. MiR-21 and miR-146a expression was significantly increased in MyD88 negative cancers (p<0.05), indicating their participation in regulation. Significant alterations in MyD88 mRNA expression were observed between chemosensitive and chemoresistant cells and tissue. Knockdown of TLR4 in SKOV-3 ovarian cells recovered chemosensitivity. Knockdown of MyD88 alone did not. MyD88 expression was down-regulated in differentiated embryonal carcinoma (NTera2) cells, supporting the MyD88+ cancer stem cell hypothesis. Our findings demonstrate that expression of MyD88 is associated with significantly reduced patient survival and altered microRNA levels and suggest an intact/functioning TLR4/MyD88 pathway is required for acquisition of the chemoresistant phenotype. Ex vivo manipulation of ovarian cancer stem cell (CSC) differentiation can decrease MyD88 expression, providing a potentially valuable CSC model for ovarian cancer.

Competitive interactions of anti-carcinogens with serum albumin: A spectroscopic study of bendamustine and dexamethasone with the aid of chemometrics

Interactions between the anti-carcinogens, bendamustine (BDM) and dexamethasone (DXM), with bovine serum albumin (BSA) were investigated with the use of fluorescence and UV–vis spectroscopies under pseudo-physiological conditions (Tris–HCl buffer, pH 7.4). The static mechanism was responsible for the fluorescence quenching during the interactions; the binding formation constant of the BSA–BDM complex and the binding number were 5.14 × 105 L mol−1 and 1.0, respectively. Spectroscopic studies for the formation of BDM–BSA complex were interpreted with the use of multivariate curve resolution – alternating least squares (MCR–ALS), which supported the complex formation. The BSA samples treated with site markers (warfarin – site I and ibuprofen – site II) were reacted separately with BDM and DXM; while both anti-carcinogens bound to site I, the binding constants suggested that DXM formed a more stable complex. Relative concentration profiles and the fluorescence spectra associated with BDM, DXM and BSA, were recovered simultaneously from the full fluorescence excitation–emission data with the use of the parallel factor analysis (PARAFAC) method. The results confirmed that on addition of DXM to the BDM–BSA complex, the BDM was replaced and the DXM–BSA complex formed; free BDM was released. This finding may have consequences for the transport of these drugs during any anti-cancer treatment.

Single step purification of plasmid DNA using peptide ligand affinity chromatography

Single step affinity chromatography was employed for the purification of plasmid DNA (pDNA), thus eliminating several steps compared with current commercial purification methods for pDNA. Significant reduction in pDNA production time and cost was obtained. This chromatographic operation employed a peptide-monolith construct to isolate pDNA from Escherichia coli (E. coli) impurities present in a clarified lysate feedstock. Mild conditions were applied to avoid any degradation of pDNA. The effect of some important parameters on pDNA yield was also evaluated with the aim of optimising the affinity purification of pDNA. The results demonstrate that 81% of pDNA was recovered and contaminating gDNA, RNA and protein were removed below detectable levels. © 2008 Elsevier B.V. All rights reserved.

Affinity purification of plasmid DNA directly from crude bacterial cell lysates

We have shown previously that a sequence-specific DNA-binding protein based on the Lac repressor protein can isolate pre-purified DNA efficiently from simple buffer solution but our attempts to purify plasmids directly from crude starting materials were disappointing with unpractically low DNA yields. We have optimized tbe procedure and present a simple affinity methodology whereby plasmid DNA is purified directly by mixing two crude cell lysates, one cell lysate containing the plasmid and the other the protein affinity ligand, without the need for treatment by RNaseA. After IMAC chromatography, high purity supercoiled DNA is recovered in good yields of 100-150 μg plasmid per 200 mL shake flask culture. Moreover, the resulting DNA is free from linear or open-circular plasmid DNA, genomic DNA, RNA, and protein, to the limits of our detection. Furthermore, we show that lyophilized affinity ligand can be stored at room temperature and re-hydrated for use when required.

Hydrotherapy as a recovery strategy after exercise: A pragmatic controlled trial

Background Our aim was to evaluate the recovery effects of hydrotherapy after aerobic exercise in cardiovascular, performance and perceived fatigue. Methods A pragmatic controlled repeated measures; single-blind trial was conducted. Thirty-four recreational sportspeople visited a Sport-Centre and were assigned to a Hydrotherapy group (experimental) or rest in a bed (control) after completing a spinning session. Main outcomes measures including blood pressure, heart rate, handgrip strength, vertical jump, self-perceived fatigue, and body temperature were assessed at baseline, immediately post-exercise and post-recovery. The hypothesis of interest was the session*time interaction. Results The analysis revealed significant session*time interactions for diastolic blood pressure (P=0.031), heart rate (P=0.041), self perceived fatigue (P=0.046), and body temperature (P=0.001); but not for vertical jump (P=0.437), handgrip (P=0.845) or systolic blood pressure (P=0.266). Post-hoc analysis revealed that hydrotherapy resulted in recovered heart rate and diastolic blood pressure similar to baseline values after the spinning session. Further, hydrotherapy resulted in decreased self-perceived fatigue after the spinning session. Conclusions Our results support that hydrotherapy is an adequate strategy to facilitate cardiovascular recovers and perceived fatigue, but not strength, after spinning exercise. Trial registration ClinicalTrials.gov Identifier: NCT01765387 Keywords: Hydrotherapy; Heart rate; Fatigue; Strength; Blood pressure; Body temperature

Practical attack on NLM-MAC scheme

The NLM stream cipher designed by Hoon Jae Lee, Sang Min Sung, Hyeong Rag Kim is a strengthened version of the LM summation generator that combines linear and non-linear feedback shift registers. In recent works, the NLM cipher has been used for message authentication in lightweight communication over wireless sensor networks and for RFID authentication protocols. The work analyses the security of the NLM stream cipher and the NLM-MAC scheme that is built on the top of the NLM cipher. We first show that the NLM cipher suffers from two major weaknesses that lead to key recovery and forgery attacks. We prove the internal state of the NLM cipher can be recovered with time complexity about nlog7×2, where the total length of internal state is 2⋅n+22⋅n+2 bits. The attack needs about n2n2 key-stream bits. We also show adversary is able to forge any MAC tag very efficiently by having only one pair (MAC tag, ciphertext). The proposed attacks are practical and break the scheme with a negligible error probability.