Approximating the set of local minima in partial RNA folding landscapes

MOTIVATION

We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

RESULTS

The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n(2)Dνlnν), where n is the sequence length, ν is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

Monte Carlo modeling of Co HDR brachytherapy source in water and in different solid water phantom materials

The reference medium for brachytherapy dose measurements is water. Accuracy of dose measurements of brachytherapy sources is critically dependent on precise measurement of the source–detector distance. A solid phantom can be precisely machined and hence source–detector distances can be accurately determined. In the present study, four different solid phantom materials such as polymethylmethacrylate (PMMA), polystyrene, Solid Water, and RW1 are modeled using the Monte Carlo methods to investigate the influence of phantom material on dose rate distributions of the new model of BEBIG ⁶⁰Co brachytherapy source. The calculated dose rate constant is 1.086 ± 0.06% cGy h⁻¹ U⁻¹ for water, PMMA, polystyrene, Solid Water, and RW1. The investigation suggests that the phantom materials RW1 and Solid Water represent water-equivalent up to 20 cm from the source. PMMA and polystyrene are water-equivalent up to 10 cm and 15 cm from the source, respectively, as the differences in the dose data obtained in these phantom materials are not significantly different from the corresponding data obtained in liquid water phantom. At a radial distance of 20 cm from the source, polystyrene overestimates the dose by 3% and PMMA underestimates it by about 8% when compared to the corresponding data obtained in water phantom.

Antibacterial Activity of Barringtonia acutangula against Selected Urinary Tract Pathogens

Barringtonia acutangula (L.) Gaertn belonging to family Barringtoniaceae was investigated to evaluate In vitro antibacterial activity of aqueous, ethanolic, petroleum ether and chloroform extracts against Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus faecalis and Escherichia coli the major urinary tract infection causing pathogens were tested by disc diffusion assay method and the minimum inhibitory concentration was evaluated. Ethanol (95%) extract exhibited broader spectrum of inhibition followed by chloroform, petroleum ether and aqueous extracts against the urinary tract pathogens under test. An attempt has been made to compare the activity of extracts with standard antibiotics against selected urinary tract infection causing pathogens.

Visibility of dichalcogenide nanolayers

Dichalcogenides with the common formula MX(2) are layered materials with electrical properties that range from semiconducting to superconducting. Here, we describe optimal imaging conditions for the optical detection of ultrathin, two-dimensional dichalcogenide nanocrystals containing single, double and triple layers of MoS(2), WSe(2) and NbSe(2). A simple optical model is used to calculate the contrast for nanolayers deposited on wafers with varying thicknesses of SiO(2). The model is extended for imaging using the green channel of a video camera. Using AFM and optical imaging we confirm that single layers of MoS(2) and WSe(2) can be detected on 90 and 270 nm SiO(2) using optical means. By measuring contrast under broadband green illumination we are also able to distinguish between nanostructures containing single, double and triple layers of MoS(2) and WSe(2.) We observe and discuss discrepancies in the case of NbSe(2).

EGSnrc-based Monte Carlo dosimetry of CSA1 and CSA2 137Cs brachytherapy source models

PURPOSE

AAPM TG-56 recommends the use of a specific dosimetric dataset for each brachytherapy source model. In this study, a full dosimetric dataset for indigenously developed 137Cs source models, namely, the CSA1 and CSA2, in accordance with the AAPM TG-43U1 formalism is presented. The study includes calculation of dose-to-kerma ratio D/K in water around these sources including stainless steel encapsulated 137Cs sources such as RTR, 3M, and selectron/LDR 137Cs.

METHODS

The Monte Carlo-based EGSnrcMP code system is employed for modeling the sources in vacuum and in water. Calculations of air-kerma strength, S(K) for the investigated sources and collision kerma in water along the transverse axis of the RTR source are based on the FLURZnrc code. Simulations of water-kerma and dose in water for the CSA1, CSA2, RTR, 3M, and selectron/ LDR 137Cs sources are carried out using the DOSRZnrc code. In DOSRZnrc calculations, water-kerma and dose are scored in a cylindrical water phantom having dimensions of 80 cm diameter x 80 cm height.

RESULTS

The calculated dose-rate constants for the CSA1 and CSA2 sources are 0.945(1) and 1.023(1) cGy/(h U), respectively. The calculated value of S(K) per unit source activity, S(K)/A for the CSA1 and CSA2 sources is 7.393(7) x 10(-8) cGy cm2/(h Bq). The EGSnrcMP-based collision kerma rates for the RTR source along the transverse axis (0.25-10 cm) agree with the corresponding GEANT4-based published values within 0.5%. Anisotropy profiles of the CSA1 and CSA2 sources are significantly different from those of other sources. For the selectron/LDR single pellet 137Cs spherical source (modeled as a cylindrical pellet with dimensions similar to the seed selectron), the values of D/K at 1 and 1.25 mm from the capsule are 1.023(1) and 1.029(1), respectively. The value of D/K at 1 mm from the CSA1, CSA2, RTR, and 3M 137Cs source capsules (all sources have an external radius of 1.5 mm) is 1.017(1) and this ratio is applicable to axial positions z = 0 to z = -L/2. This is in contrast to a published GEANT4-based Monte Carlo dosimetric study on RTR and 3M 137Cs sources wherein the authors have assumed that collision kerma is approximately equal to absorbed dose at 1 mm from the source capsules. Collision kerma is approximately equal to absorbed dose for distances > or = 2 mm from source capsules as opposed to > or = 1 mm reported in published studies. A detailed electron transport is necessary up to 2 mm from source capsules.

CONCLUSIONS

The Monte Carlo-calculated dose-rate data for the CSA1 and CSA2 sources can be used as input data for treatment planning or to verify the calculations by radiotherapy treatment planning system.

Self-assembly of magnetic Ni nanoparticles into 1D arrays with antiferromagnetic order

In this paper, we report on the magnetic properties of isolated nanoparticles and interacting nanochains formed by the self-assembly of Ni nanoparticles. The magnetic properties were studied using superconducting quantum interference device (SQUID) magnetometry and magnetic force microscopy (MFM). We demonstrate that single-domain Ni nanoparticles spontaneously form one-dimensional (1D) chains under the influence of an external magnetic field. Furthermore, such magnetic field-driven self-assembly in conjunction with surface templating produces regular arrays of 1D nanochains with antiferromagnetic intra-chain order. The antiferromagnetic order, which is in striking contrast to what is found for non-interacting nanoparticle assemblies within the chains, can be evidenced from MFM and SQUID measurements.

Plasmin enhances cell surface tissue factor activity in mesothelial and endothelial cells

BACKGROUND

Mesothelial cells that line the thoracic cavity play an important role in maintaining the local balance between procoagulant and fibrinolytic activity, a role akin to the endothelial cells in blood vessels. The mechanism(s) responsible for increased tissue factor (TF) expression in mesothelial cells in response to injury are at present unclear.

OBJECTIVE

To investigate whether plasmin or thrombin, two major proteases that may be generated on the pleural surface upon injury, induce TF expression in human pleural mesothelial cells (HMC) and elucidate the underlying mechanism(s).

METHODS

Confluent monolayers of HMC and human umbilical vein endothelial cells (HUVEC) were exposed to plasmin or thrombin for varying time periods and TF expression was analyzed by measuring its activity in a factor Xa generation assay, TF antigen levels by immunoblot analysis and TF mRNA by Northern blot analysis.

RESULTS

Both plasmin and thrombin treatments increased cell surface TF activity in HMC by 3- to 4-fold. In contrast to thrombin, plasmin-induced TF activity is not dependent on the de novo synthesis of TF. In HUVEC, plasmin had a minimal effect on unperturbed HUVEC whereas it markedly increased TF activity of activated HUVEC. Plasmin treatment neither affected anionic phospholipid levels at the cell surface nor released protein disulfide isomerase, an oxidoreductase protein that was newly described to play a role in TF activation. Plasmin cleaved cell-associated TFPI.

CONCLUSION

Thrombin up-regulates TF activity in HMC through the transcriptional activation of TF whereas plasmin increases TF activity by inactivating the cell-associated TFPI by a limited proteolysis.

Evidence of short-range screening in shock-compressed aluminum plasma

We have investigated the angular variation in elastic x-ray scattering from a dense, laser-shock-compressed aluminum foil. A comparison of the experiment with simulations using an embedded atom potential in a molecular dynamics simulation shows a significantly better agreement than simulations based on an unscreened one-component plasma model. These data illustrate, experimentally, the importance of screening for the dense plasma static structure factor.

Optimization of magneto-optical Kerr setup: analyzing experimental assemblies using Jones matrix formalism

We present a comparative study on an experimental and theoretical optimization of magneto-optical Kerr setups based on photoelastic modulation and phase sensitive detector methodology. The first and second harmonics, I omega,2 omega, of the reflected light intensity are measured for a CoO/Co magnetic reference film. The magnetic field dependence of the optical off-diagonal Fresnel reflection coefficients rps and rsp follows the sample magnetization. Different Kerr setups provide various dependencies of I omega,2 omega on the reflection coefficients and, hence, on the Kerr ellipticity epsilon K and rotation theta K. Jones matrix formalism has been used to analyze the impact of a systematic variation of relative analyzer and polarizer orientations with respect to each other and with respect to the retardation axis of the modulator involved in longitudinal Kerr setups for incoming s-polarized light. We find one particular setup which maximizes I(omega) as well as I2 omega and maximizes the signal-to-noise ratio. Inefficient setups are characterized by I omega,2 omega intensities involving large nonmagnetic contributions of rp and rs.

Compton scatter profiles for warm dense matter

In this paper, we discuss the possibility of using x-ray Compton scattering as a probe of the outer electronic structure of ions immersed in warm dense matter. It is proposed that the x-ray free-electron lasers currently under construction will provide an ideal tool for this, with the main pulse being used to create a uniform well-defined sample and the third harmonic providing a clean monochromatic probe. We model the plasma photon scatter spectrum by combining self-consistent finite-temperature electronic structure calculations with molecular dynamics simulations of the ion-ion structure factor. In particular, we present bound-free Compton profiles that are more accurate that those obtained using form factor or impulse approximations.

Optimization of physical and nutritional parameters for hyaluronidase production by <i> Streptococcus mitis</i>

The effect of some physical and nutritional parameters were studied for the optimum production of extracellular enzyme hyaluronidase employing Streptococcus mitis MTCC*2695 by submerged fermentation. The effects of initial pH, incubation temperature and time, inoculum level and age of inoculum were studied. The maximum enzymatic activity was obtained with an initial pH 5.8, incubation temperature 37°, incubation time for 48 h and inoculum level 6% with inoculum age 24 h. The effect of different carbon and nitrogen sources and antibiotics were studied. The results indicated that sucrose and ammonium chloride showed the highest enzymatic activity among various carbon and nitrogen sources. Antibiotic clarithromycin showed strong inhibitory effect on hyaluronidase production.

Characterization of a Novel Polymeric Scaffold for Potential Application in Tendon/Ligament Tissue Engineering

Unlike braided fabrics, knitted scaffolds have been proven to favor deposition of collagenous connective tissue matrix, which is crucial for tendon/ligament reconstruction. But cell seeding of such scaffolds often requires a gel system, which is unstable in a dynamic situation, especially in the knee joint. This study developed a novel, biodegradable nano-microfibrous polymer scaffold by electrospinning PLGA nanofibers onto a knitted PLGA scaffold in order to provide a large biomimetic surface for cell attachment. Porcine bone marrow stromal cells were seeded onto either the novel scaffolds by pipetting a cell suspension (Group I) or the knitted PLGA scaffolds by immobilizing in fibrin gel (Group II). Cell attachment at 36 hours, cell proliferation and extracellular matrix synthesis at 1 week, and mechanical properties over 2 weeks were investigated. Cell attachment was comparable and cell proliferation was faster in Group I. Moreover, cellular function was more actively exhibited in Group I, as evident by the higher expression of collagen I, decorin, and biglycan genes. Thus, this novel scaffold, facilitating cell seeding and promoting cell proliferation, function, and differentiation, could be applied with promise in tissue engineering of tendon/ligament.

Neonatal aortic arch thrombosis masquerading as coarctation of the aorta

We report two neonates with thrombosis of the aortic arch and isthmus diagnosed by echocardiography. Neonatal transient protein C deficiency was present in one patient and the other patient had severe perinatal asphyxia. Both patients presented with markedly reduced left ventricular function and severe aortic obstruction. In one infant, the thrombus was successfully removed surgically, and the second infant died due to serious complications of perinatal asphyxia.

Coding DNA sequences: statistical distributions

The base distributions in coding DNA sequences (CDS) are investigated. We explore the scaling properties of the 4-dimensional directed random walk and compare them with that for the DNA sequences. Inference from these observation are, however, contradicted by alternate analysis using factorial moments. To resolve this conflict we look directly at the nucleotide base distributions. In all the cases the base distributions change from gaussian to non-gaussian as the scale size is increased. The CDS, therefore, have nucleotide distributions different from the random.

Graft copolymerization of acrylonitrile and ethyl methacrylate comonomers on cellulose using ceric ions

The graft copolymerization of acrylonitrile and ethyl methacrylate from their binary mixtures onto cellulose has been carried out in the presence of Ce(IV) ions in acidic media at 30 +/- 0.1 degrees C. The graft copolymerization has shown an increasing trend on increasing the feed molarity of the comonomers and on increasing the reaction time. The analysis of grafted cellulose prepared with different feed compositions (f(AN)) has clearly indicated the existence of the synergistic effect of ethyl methacrylate on acrylonitrile which normally shows poor affinity for grafting on cellulose while used individually. The elemental analysis and IR data were used to determine the composition of grafted copolymers and reactivity ratios (r(1), r(2)) of the monomers using the Mayo and Lewis method. The reactivity ratios for acrylontrile and ethyl methacrylate have been found to be 0.68 and 1.15, respectively, which supported the alternate arrangement of the monomer blocks of individual monomers in the grafted chains. The rate of grafting has shown a square dependence on the concentration of the comonomers within the studied range of feed molarity from 0.5 to 2.5 mol dm(-3). The grafting data were used to calculate the number of grafted chains (N(g)), frequency of grafting (G(F)) per molecule of the cellulose and efficiency of grafting (G(E)). The variation in these parameters as a function of feed molarity, feed composition, and ceric ion concentration has been determined. The rate of ceric ion disappearance as a function of feed molarity and reaction time has provided strong support to consider the participation of ceric ions in the formation of free radicals at the backbone of the cellulose. On the basis of the experimental observations, reaction steps for grafting of monomers on cellulose have been proposed.

Cytokeratin 19 immunoreactivity in the diagnosis of papillary thyroid carcinoma: a note of caution

To evaluate the expression of cytokeratin (CK) 19, we stained sections obtained from formalin-fixed, paraffin tissue blocks of 35 thyroid tumors (follicular adenoma [FA], 20; papillary thyroid carcinoma [PTC], 10 follicular variant [FV] and 5 usual type) and scored the extent of staining as follows: 1+ (<5% positively stained cells), 2+ (5%-25% positively stained cells), 3+ (25%-75% positively stained cells), and 4+ (>75% positively stained cells). All 15 PTCs (including 10 FV-PTCs) were CK19 positive: 14 were 4+ and 1 (FV-PTC) was 2+. All 20 FAs also were CK19 positive: 15 were 1+, 1 was 2+, 4 were 3+, and none was 4+. In the FAs that were scored 1+, reactivity usually was confined to follicular cells lining cystically dilated atrophic follicles that lacked the typical nuclear features of PTC. The remaining FAs showed more diffuse reactivity, which was, however, less intense than that observed in the PTCs. Thus, immunoreactivity for CK19 is not specific for PTC, although we acknowledge that the extent and intensity of staining are considerably greater in this tumor than in FA. There were no significant differences in staining for CK19 between nonneoplastic follicles adjacent to PTCs and those adjacent to FAs.

Improvement in enzyme productivities from mold cultivations using the liquid-phase oxygen supply strategy

Cultivations of Aspergillus niger cells in which oxygen was provided through the liquid-phase oxygen supply strategy (which involves the need-based decomposition of H2O2 pulses to yield the necessary oxygen) were studied. Concentrations of H2O2 in the range of 1 to 5 mM were found to be suitable for use in cultivations. The growth rate constant of 0.17 h(-1) obtained in the H2O2-based cultivation, was comparable to that obtained in the cultivation with aeration; however, the maximum cell concentration in the H2O2-based cultivation was 124% of that obtained in cultivation with aeration. Maximum concentrations of catalase, protease and glucose oxidase obtained in the H2O2-based cultivation, were 240%, 172%, and 124% respectively, of those obtained in the cultivation with aeration. Further, the specific enzyme levels (units per gram cell) of catalase and protease obtained in the H2O2-based cultivation were 172% and 156% of those obtained in the cultivation with aeration, whereas, the specific glucose oxidase levels were comparable. In addition, the oxygen profiles inside the pellets ofA. niger during both the modes of oxygen supply were described using mathematical models. Studies to elucidate the mechanism of oxygen availability showed that the decomposition of the H2O2 supplied in the extracellular space occurred intracellularly, as well as extracellularly, to yield oxygen. Also, the proton motive force (PMF) was found to be involved in the process of oxygen availability from H2O2 to A. niger cells.

Metastatic prostatic adenocarcinoma within a primary solid papillary carcinoma of the male breast

We report the case of a 78-year-old man who developed a breast mass 12 months after hormonal therapy for palliation of prostatic adenocarcinoma. On histologic and immunohistochemical examination, the breast tumor revealed a unique collision tumor composed of metastatic prostatic adenocarcinoma and solid papillary breast carcinoma.

Tumor necrosis factor genetic polymorphisms correlate with infections after renal transplantation

BACKGROUND

Nonimmunosuppressed individuals possessing a NcoI restriction enzyme site in the tumor necrosis factor (TNF) gene locus produce less TNF-alpha in vitro and in vivo than do individuals lacking this site. We have previously shown that this NcoI+/low TNF-alpha genotype is independently associated with increased rates of infection for liver transplant recipients.

METHODS

In this study, we performed polymerase chain reaction amplification and restriction fragment length polymorphism analysis of the TNF locus from 45 renal transplant recipients to determine whether the presence of the NcoI site is associated with the frequency of rejection, infection, time to rejection or infection, and patient or graft survival.

RESULTS

Twenty-six recipients were typed with the NcoI+/low TNF-alpha genotype, whereas 19 recipients had the NcoI-/high TNF-alpha genotype. Age, sex, donor type, secondary immunosuppression, use of anti-lymphocyte preparations, graft ischemia time, and year of transplant were evenly distributed in the two groups. There was no difference between the genotype groups in the rate of, or time to, rejection. In contrast, significantly more patients with the NcoI+/low TNF-alpha site developed infections (46% vs. 10% P=0.01). In bivari able models, each controlling for donor type, ischemia time, recipient age, use of antilymphocyte agents, and secondary immunosuppression, the NcoI+/low TNF-alpha genotype was still independently associated with increased numbers of infections (relative risk, 5.38; confidence interval, 1.20-23.8). Conclusion. We conclude that in individuals genetically predetermined to be low TNF-alpha producers, the additional inhibition of TNF-alpha production by routine immunosuppression may be excessive, rendering these individuals less able to respond to infectious stimuli. These patients may benefit from lower doses or withdrawal of corticosteroids, which are known inhibitors of TNF-alpha transcription.

Somatic embryogenesis and plantlet regeneration from cell suspension cultures of palmarosa grass (Cymbopogon martinii)

A cell suspension culture was established from nodal callus ofCymbopogon martinii (Roxb.) Wats in a liquid medium containing Murashige and Skoog (1962) basal salts, vitamins, 100 mg 1^-1 myo-inositol and 20 g l^-1 of sucrose (MS) that was supplemented with 13.6 μM 2,4-dichlorophenoxyacetic acid and 1.15 μM kinetin. An initial inoculum density of 2 x 10⁴ cells ml^-1exhibited optimum cell growth. Calli were obtained 12-15 days after the suspension was plated onto semisolid medium of a similar composition. When calli were transferred to semisolid regeneration medium containing MS + 6.7 μM N ⁶-benzyl-adenine + 1.15 μM kinetin, somatic embryogenesis and plantlet regeneration occurred after 10-25 days. There was no significant decrease in the regeneration potential of the calli even when the cultures were initiated from 47-week-old cell suspensions. Chromosome counts of cells in suspensions, calli and somatic embryos derived from cultures of different ages revealed the presence of diploids, tetraploids and octaploids. However, the 33 regenerated plants tested were all diploid, indicating that only diploid cells were capable of regeneration in vitro.

Rapid propagation of lemongrass (Cymbopogon flexuosus (Nees) Wats.) through somatic embryogenesis in vitro

Somatic embryos induced from callus cultures of lemongrass [Cymbopogon flexuosus (Nees) Wats.] on Murashige and Skoog medium supplemented with 5 mg/l of 2,4-D, 0.1 mg/l of NAA and 0.5 mg/l of Kn developed into plantlets when plated on a medium supplemented with 3 mg/l of BA, 1 mg/l of GA3 and 0.1 mg/l of NAA. The regeneration potential of callus was retained for more than 2 years on the nutrient medium supplemented with comparatively lower levels of growth regulators (2,4-D at 2 mg/l, NAA at 0.1 mg/l and Kn at 0.25 mg/l). Approximately 30-35 plantlets were produced after two months of culture per 100 mg of callus inoculated. Regenerants were transplanted into soil and transferred to the field for assessment of various morphological and biochemical characteristics. The results of 1 year of field trials showed that plants derived from somatic embryoids were more uniform in all the characteristics examined when compared with the field performance of plants raised through slips by standard propagation procedures. Thus, a procedure has been developed for high frequency long term plant production of lemongrass through in vitro methods.