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PubMed2006

Optimization of slitlike carbon nanopores for storage of hythane fuel at ambient temperatures.

Carbons with slitlike pores can serve as effective host materials for storage of hythane fuel, a bridge between the petrol combustion and hydrogen fuel cells. We have used grand canonical Monte Carlo simulation for the modeling of the hydrogen and methane mixture storage at 293 K and pressure of methane and hydrogen mixture up to 2 MPa. We have found that these pores serve as efficient vessels for the storage of hythane fuel near ambient temperatures and low pressures. We find that, for carbons having optimized slitlike pores of size H congruent with 7 A (pore width that can accommodate one adsorbed methane layer), and bulk hydrogen mole fraction >or=0.9, the volumetric stored energy exceeds the 2010 target of 5.4 MJ dm(-3) established by the U.S. FreedomCAR Partnership. At the same condition, the content of hydrogen in slitlike carbon pores is approximately = 7% by energy. Thus, we have obtained the composition corresponding to hythane fuel in carbon nanospaces with greatly enhanced volumetric energy in comparison to the traditional compression method. We proposed the simple system with added extra container filled with pure free/adsorbed methane for adjusting the composition of the desorbed mixture as needed during delivery. Our simulation results indicate that light slit pore carbon nanomaterials with optimized parameters are suitable filling vessels for storage of hythane fuel. The proposed simple system consisting of main vessel with physisorbed hythane fuel, and an extra container filled with pure free/adsorbed methane will be particularly suitable for combustion of hythane fuel in buses and passenger cars near ambient temperatures and low pressures.

Journal Article↗

PubMedDate not supplied

Using proteomics to mine genome sequences.

We present a method for mining unannotated or annotated genome sequences with proteomic data to identify open reading frames. The region of a genome coding for a protein sequence is identified by using information from the analysis of proteins and peptides with MALDI-TOF mass spectrometry. The raw genome sequence or any unassembled contigs of an organism are theoretically cleaved into a number of equal sized but overlapping fragments, and these are then translated in all six frames into a series of virtual proteins. Each virtual protein is then subjected to a theoretical enzymatic digestion. Standard proteomic sample preparation methods are used to separate, array, and digest the proteins of interest to peptides. The masses of the resulting peptides are measured using mass spectrometry and compared to the theoretical peptide masses of the virtual proteins. The region of the genome responsible for coding for a particular protein can then be identified when there are a large number of hits between peptides from the protein and peptides from the virtual protein. The method makes no assumptions about the location of a protein in a particular gene sequence or the positions or types of start and stop codons. To illustrate this approach, all 773 proteins of Pseudomonas aeruginosa contained in SWISS-PROT were used to theoretically test the method and optimize parameters. Increasing the size of the virtual proteins results in an overall improvement in the ability to detect the coding region, at the cost of decreasing the sensitivity of the method for smaller proteins. Increasing the minimum number of matching peptides, lowering the mass error tolerance, or increasing the signal-to-noise ratio of the simulated mass spectrum, improves the ability to detect coding regions. The method is further demonstrated on experimental data from Mycobacterium tuberculosis and is also shown to work with eukaryotic organisms (e.g., Homo sapiens).

Amino Acid Sequence↗

PubMed2001

Receptor-mediated transfer of DNA--galactosylated poly-L-lysine complexes into mammalian cells in vitro and in vivo.

With the goal of developing non-viral techniques for exogenous gene delivery into mammalian cells, we have studied receptor-mediated gene transfer using complexes of plasmid DNA and galactosylated poly-L-lysine, poly(L-Lys)Gal. To evaluate the optimal parameters for efficient gene transfer into human hepatoma HepG2 cells by the DNA-poly(L-Lys)Gal complexes, the bacterial reporter genes lacZ and cat were used. Examination of the reporter gene expression level showed that the efficiency of DNA delivery into the cells depends on the structure of DNA--poly(L-Lys)Gal complexes formed at various ionic strength values. The efficiency of DNA transfer into the cells also depends on DNA/poly(L-Lys)Gal molar ratio in the complexes. Plasmid vector carrying human apolipoprotein A-I (apoA-I) gene was injected as its complex with poly(L-Lys)Gal into rat tail vein. Some level of ApoA-I was detected in the serum of the injected rats. Also, the human apoA-I-containing plasmid was found to be captured specifically by the rat liver cells and transported into the cell nuclei, where it can persist as an episome-like structure for at least a week. After repeated injections of DNA--poly(L-Lys)Gal complexes, the level of human ApoA-I in rat serum increases, probably, due to accumulation of functional human apoA-I gene in the liver cell nuclei. The data seem to be useful for the development of non-viral approaches to gene therapy of cardiovascular diseases.

3T3 Cells↗

PubMed2000

Anaerobic biodegradation of sugar beet pulp.

Sugar beet pulp is a by-product of sugar production and consists mainly of cellulose, hemicellulose and pectin. Its composition is suitable for biological degradation. A possible alternative for the utilization of this material (besides cattle feeding) can be anaerobic methanogenic degradation. It has an additional advantage--biogas production. Beet pulp was treated by a two-step anaerobic process. The first step consisted of hydrolysis and acidification. The second step was methanogenesis. In this paper, observation of the process of anaerobic degradation and determination of optimal parameters is discussed. A laboratory-scale model for sugar beet pulp anaerobic biodegradation was operated. Results of model performance have shown very good pulp digestion characteristics. In addition, high efficiency removal of organic matter was achieved. Methane yield was over 0.360 m3 kg(-1) dried pulp and excess sludge production was 0.094 g per gram COD added.

Anaerobiosis↗

PubMed2000

16S rDNA-based characterization of BTX-catabolizing microbial associations isolated from a South African sandy soil.

In the presence of different selection pressures, particularly pH and electron donor concentration, indigenous microbial associations which catabolize selected petroleum hydrocarbon components (benzene, toluene and o-, m- and p-xylene (BTX)) were enriched and isolated from a petroleum hydrocarbon-contaminated KwaZulu-Natal sandy soil. Electron microscopy revealed that, numerically, rods constituted the majority of the populations responsible for BTX catabolism. Molecular techniques (polymerase chain reaction (PCR) and 16S rDNA fingerprinting by denaturing-gradient gel electrophoresis (DGGE)) were employed to explore the diversities and analyze the structures of the isolated microbial associations. Pearson product-moment correlation indicated that the different, but chemically similar, petroleum hydrocarbon molecules, effected the isolation of different associations. However, some similar numerically-dominant bands characterized the associations. A 30% similarity was evident between the m- and o-xylene-catabolizing associations regardless of the molecule concentration and the enrichment pH. PCR-DGGE was also used to complement conventional culture-based microbiological procedures for environmental parameter optimization. Band pattern differences indicated profile variations of the isolated associations which possibly accounted for the growth rate changes recorded in response to pH and temperature perturbations.

Benzene↗

PubMed1991

Optimization of spray-dried and -congealed lipid micropellets and characterization of their surface morphology by scanning electron microscopy.

Lipid micropellets prepared from glycerides and phospholipids may be a physiological drug carrier system for improving the intestinal absorption of lipophilic drugs. They can be prepared by spray-drying and spray-congealing processes. In this study, formulation and optimization parameters of spray-dried and -congealed lipid pellets in the micro- and nanometer size were investigated. The rapid evaporation of solvents from the droplets, which in turn causes a rapid solidification, influenced the crystalline structures of spray-dried glycerides. Moreover, solvents, the chain length, and the type of lipids and drugs used in the formulations of spray-dried micropellets affected the surface morphology of the micropellets. In contrast to the variations of the surface structure of spray-dried micropellets, formulated spray-congealed micropellets possessed smooth surface properties. The surface morphology and microstructure of both types of micropellets were characterized by SEM.

Chemistry, Pharmaceutical↗

PubMed2003

High efficiency production of germ-line transgenic Japanese medaka (Oryzias latipes) by electroporation with direct current-shifted radio frequency pulses.

Although there have been several studies showing the production of transgenic fish through electroporation techniques, success rates have been low and few studies show germ-line integration and expression. When electroporation has been successful, the device used is no longer commercially available. The goal of this experiment was to find an alternative efficient method of generating transgenic Japanese medaka (Oryzias latipes) using a commercially available electroporation device. The Gene Pulser II and RF module (Bio-Rad Laboratories, USA), along with two reporter gene constructs, were used. In contrast to other electroporation devices, which are based on a single pulse with exponential decay or square wave technology, the Gene Pulser II incorporates a direct current (DC)-shifted radio frequency (RF) signal. With this technique, over 1000 embryos can be electroporated in less than 30 min. The plasmid pCMV-SPORT-beta-gal (Invitrogen, USA) was used in the supercoiled form to optimize parameters for gene transfer into single-celled embryos, and resulted in up to 100% somatic gene transfer. Similar conditions were used to generate fish transgenic for both the pCMV-EGFP plasmid (Clontech, USA) and a cytomegalovirus (CMV) driven phytase-EGFP construct. The conditions used were a voltage of 25 V, a percent modulation of 100%, a radio frequency of 35 kHz, a burst duration of 10 ms, 3 bursts, and a burst interval of 1.0 s. Seventy percent of the embryos electroporated with the pCMV-EGFP construct survived to sexual maturity, and of those, 85% were capable of passing the transgene on to their offspring. Transgenic second generation back-crossed (BC2) fry were subjected to Southern blot analysis, which confirmed germ-line integration, and observation for green fluorescence protein, which confirmed protein expression. DC-shifted RF pulses are effective and efficient in the production of transgenic medaka, and germ-line integration and expression can be achieved without linearization of the transgene vector.

Animals↗

PubMed2003

Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G.

Because the overall tumbling provides a major contribution to protein spectral densities measured in solution, the choice of a proper model for this motion is critical for accurate analysis of protein dynamics. Here we study the overall and backbone dynamics of the B3 domain of protein G using (15)N relaxation measurements and show that the picture of local motions is markedly dependent on the model of overall tumbling. The main difference is in the interpretation of the elevated R(2) values in the alpha-helix: the isotropic model results in conformational exchange throughout the entire helix, whereas no exchange is predicted by anisotropic models that place the longitudinal axis of diffusion tensor almost parallel to the helix axis. Due to small size (fast tumbling) of the protein, the T(1) values have low sensitivity to NH bond orientation. The diffusion tensor derived from orientation dependence of R(2)/R(1) is anisotropic (D(par)/D(perp)=1.4), with a small rhombic component. In order to distinguish the correct picture of motion, we apply model-independent methods that are sensitive to conformational exchange and do not require knowledge of protein structure or assumptions about its dynamics. A comparison of the CSA/dipolar cross-correlation rate constants with (15)N relaxation rates and the estimation of R(ex) terms from relaxation data at 9.4 and 14.1 T indicate no conformational exchange in the helix, in support of the anisotropic models. The experimentally derived diffusion tensor is in excellent agreement with theoretical predictions from hydrodynamic calculations; a detailed comparison with various hydrodynamic models revealed optimal parameters for hydrodynamic calculations.

Anisotropy↗

PubMed2004

Vesical pacing in patients with overactive bladder: technique and results.

OBJECTIVES: A recent study has demonstrated that the electric activity of the overactive bladder (OAB) is 'dysrhythmic'. The cause was attributed to a disordered vesical pacemaker which discharges these waves. In a subsequent study, the dysrhythmic waves have been 'normalized' by vesical pacing and the optimal parameters which are required to achieve normalization have been defined. We investigated the hypothesis that vesical pacing of the OAB might improve not only the vesical electric activity but also the symptoms. METHODS: Vesical pacing was used in 9 patients (age 39.2 +/- 10.3; 5 women, 4 men) with OAB. Under anesthesia, the pacemaker was implanted in an inguinal subcutaneous pocket and connected to 2 pacing electrodes implanted into the vesical vault. The normalization of the waves was tested by 2 recording electrodes which were temporarily applied to the vesical wall and removed post-testing. The pacemaker was then programmed for home pacing to be activated at given times. RESULTS: Vesical pacing effected normalization of the dysrhythmic electric waves with disappearance of the OAB symptoms in 7 patients and failed in 2. Vesical pacing was abandoned in 3/7 patients after a few months following the spontaneous disappearance of the symptoms. CONCLUSIONS: Vesical pacing has normalized the dysrhythmic electric activity and suppressed the symptoms of the OAB in 77.7% of patients. The pacemaker was removed in 5 patients: 2 failures and 3 after spontaneous waves normalization. No complications were encountered. Vesical pacing is suggested as a treatment for OAB when commonly used therapeutic modalities have failed.

Adult↗

PubMed2004

Decreasing effect sizes for effectiveness studies- implications for the transport of evidence-based treatments: comment on curtis, ronan, and borduin (2004).

The most important finding from the N. M. Curtis, K. R. Ronan, and C. M. Borduin (2004) meta-analysis for the broader field is likely the difference in effect sizes between multisys- multisystemic therapy efficacy versus effectiveness studies. This difference has important implications for research on the transport of evidence-based treatments to community practice settings. For example, factors rarely considered in efficacy research (e.g., funding structures, organizational climate, program maturity, site characteristics) are emerging as important determinants of treatment fidelity and, in turn, clinical outcomes for practice in real-world settings. Current research is clearly demonstrating that evidence-based practices can be successfully transported, but much remains to be learned regarding the optimal parameters of such transport.

Adolescent↗

PubMed2001

A cellular mechanism of reward-related learning.

Positive reinforcement helps to control the acquisition of learned behaviours. Here we report a cellular mechanism in the brain that may underlie the behavioural effects of positive reinforcement. We used intracranial self-stimulation (ICSS) as a model of reinforcement learning, in which each rat learns to press a lever that applies reinforcing electrical stimulation to its own substantia nigra. The outputs from neurons of the substantia nigra terminate on neurons in the striatum in close proximity to inputs from the cerebral cortex on the same striatal neurons. We measured the effect of substantia nigra stimulation on these inputs from the cortex to striatal neurons and also on how quickly the rats learned to press the lever. We found that stimulation of the substantia nigra (with the optimal parameters for lever-pressing behaviour) induced potentiation of synapses between the cortex and the striatum, which required activation of dopamine receptors. The degree of potentiation within ten minutes of the ICSS trains was correlated with the time taken by the rats to learn ICSS behaviour. We propose that stimulation of the substantia nigra when the lever is pressed induces a similar potentiation of cortical inputs to the striatum, positively reinforcing the learning of the behaviour by the rats.

Animals↗

PubMed2001

Multiphoton-evoked color change of DsRed as an optical highlighter for cellular and subcellular labeling.

DsRed, a recently cloned red fluorescent protein, has attracted great interest as an expression tracer and fusion partner for multicolor imaging. We report that three-photon excitation (lambda <760 nm) rapidly changes the fluorescence of DsRed from red to green when viewed subsequently by conventional (one-photon) epifluorescence. Mechanistically, three-photon excitation (lambda <760 nm) selectively bleaches the mature, red-emitting form of DsRed, thereby enhancing emission from the immature green form through reduction of fluorescence resonance energy transfer (FRET). The "greening" effect occurs in live mammalian cells at the cellular and subcellular levels, and the resultant color change persists for >30 h without affecting cell viability. This technique allows individual cells, organelles, and fusion proteins to be optically marked and has potential utility for studying cell lineage, organelle dynamics, and protein trafficking, as well as for selective retrieval of cells from a population. We describe optimal parameters to induce the color change of DsRed, and demonstrate applications that show the potential of this optical highlighter.

3T3 Cells↗

PubMed2001

Natural signal statistics and sensory gain control.

We describe a form of nonlinear decomposition that is well-suited for efficient encoding of natural signals. Signals are initially decomposed using a bank of linear filters. Each filter response is then rectified and divided by a weighted sum of rectified responses of neighboring filters. We show that this decomposition, with parameters optimized for the statistics of a generic ensemble of natural images or sounds, provides a good characterization of the nonlinear response properties of typical neurons in primary visual cortex or auditory nerve, respectively. These results suggest that nonlinear response properties of sensory neurons are not an accident of biological implementation, but have an important functional role.

Acoustic Stimulation↗

PubMed1981

Successful immunotherapy with micrococcus, BCG or related polysaccharides on L1210 leukaemia after BCNU chemotherapy.

The experiments aimed at evaluating the optimal parameters in the chemo-immunotherapeutic treatment of the L1210 lymphoid leukaemia grafted to [female BALB/c (H2d) X male DBA/2 (H2d)]F1 hybrid mice, hereafter referred to as CDF1 mice. In vitro irradiation of leukaemic ascites cells by X- or gamma-rays and subsequent inoculation in mice showed that optimum immunogenicity is radiation dose-dependent. Grafting mice with 10(7) leukaemic ascites cells irradiated at optimum dose (80 GyX- or gamma-rays) delays mortality of the animals when challenged later with untreated L1210 cells, but is unable to cure mice. By contrast, specific immunoprophylaxis induced by Micrococcus, complement-triggering polysaccharides or BCG and irradiated leukaemic cells was able to protect mice against grafts of 10(4) L1210 cells. The i.p. route was notably superior to the i.v. route. When mice bearing advanced L1210 tumour were treated by chemotherapy (12 mg/kg of BCNU) on Day 6.5 after grafting 10(4) L1210 cells and subsequently treated by immunotherapy, a very high percentage (up to 90%) of mice with 10(8) leukaemic cells could be cured by repeated 1mg injections of bacterium or polysaccharide, and challenge with irradiated leukaemic cells was unnecessary. Because of the high cure rate obtained, the very regular response pattern and the non-pathogenicity, the bacterium Micrococcus lysodeikticus would seem a promising new candidate for chemo-immunotherapeutic antitumour strategies.

Animals↗

PubMed1988

Direct comparison of single-scan autoradiographic with multiple-scan least-squares fitting approaches to PET CMRO2 estimation.

The time course of local cerebral radioactivity concentration after bolus inhalation of oxygen gas labeled with O-15 was measured in a rapid dynamic sequence of positron tomographic images. Four normal subjects were studied at rest. In each study, 15 multiple-slice image sets were acquired over a 3-min period in a Scanditronix model 384 tomograph. The radioactivity concentration in arterial blood was measured at 1-s intervals by means of a pump-fed flow-through detector. Pump effluent was directed to discrete samples that were separated into plasma and cell fractions to estimate the accumulation of labeled, recirculating water arising from systemic metabolism. Stereotactically matched scans of local cerebral blood flow and volume were acquired in the same imaging session, and the derived values were used as fixed parameters in the model fits of the time courses of pixel radioactivity in the oxygen study. Rapid nonlinear least-squares parameter optimization was used to estimate simultaneously the local CMRO2 and the brain/blood relative distribution volume for water in each image pixel. The same scan data were combined into effective single frames of various starting times and durations for analysis using the single-scan ("autoradiographic") approach to CMRO2 estimation, which requires a presumed value for relative distribution volume. Oxygen use values derived using this approach were observed to be strongly dependent on the relative distribution volume value chosen, particularly for long study durations. However, for each gray matter region of interest studied, a uniform value for the relative distribution volume existed such that the estimated CMRO2 values were independent of the starting time and duration of the single scan used, and were furthermore the same as that yielded by the multiple-scan least-squares fitting of the total time course in the same region. We conclude that the properties of the single-scan and multiple-scan approaches are very similar at the same total study duration, provided that the value selected for the water relative distribution volume brings the measured and computed tissue time courses into correspondence.

Autoradiography↗

PubMed2026

Improved spike-in normalization clarifies the relationship between active histone modifications and transcription.

Spike-in normalization enables quantitative analysis of chromatin immunoprecipitation sequencing (ChIP-seq) signal. Here we introduce a robust dual spike-in normalization approach for ChIP-seq (ChIP-wrangler), optimize parameters and verify its accuracy in quantifying changes in ChIP-seq signal and detecting technical artifacts. We use ChIP-wrangler to revisit recent claims that active histone marks depend on transcription. We show that acute depletion of RNA polymerase II (RNAPII) has a modest impact on H3K27ac levels, with only 6% of peaks significantly changing after RNAPII depletion, indicating that histone acetylation maintenance is not entirely dependent on ongoing transcription. Promoters and enhancers are differentially affected, with 82% of decreasing acetylation peaks located at promoter-distal elements with enhancer-related motifs. ChIP-wrangler provides increased rigor and 'guardrails' for successful spike-in normalization and, as applied here, refines the understanding of crosstalk between RNAPII activity and transcription-associated histone marks.

Histones↗

PubMed2002

Factors affecting the yield and properties of bacterial cellulose.

Acetobacter xylinum E(25) has been applied in our studies in order to find optimal culture conditions for effective bacterial cellulose (BC) production. The strain displays significantly higher stability in BC production under stationary culture conditions. In contrast, intensive agitation and aeration appear to drastically reduce cellulose synthesis since such conditions induced formation of spontaneous cellulose nonproducing mutants (Cel-), which dominated in the culture. Mutation frequency strictly depends on the medium composition in agitated cultures. Enrichment of the standard SH and Yamanaka media with 1% ethanol significantly enhanced BC production in stationary cultures. Horizontal fermentors equipped with rotating discs or rollers were successfully applied in order to improve culture conditions. Relatively slow rotation velocity (4 rpm) and large surface area enabling effective cell attachment are optimal parameters for cellulose production. Physical properties of BC samples synthesized either in stationary cultures or in a horizontal fermentor revealed that cellulose from stationary cultures demonstrated a much higher value of Young's modulus, but a much lower value of water-holding capacity.

Acetobacter↗

PubMed2000

Digitisation and display of intra-oral films.

AIM: To determine the optimal parameters for the digitisation and display of intra-oral radiographs. MATERIALS AND METHODS: Six intra-oral radiographs (EP size 2 dental film, Eastman Kodak Co., Rochester, NY, USA) were digitised using an Arcus II image scanner (Agfa-Gevaert N. V., Mortsel, Belgium). Each film was digitised at 8 bits, with and without a film mask, using three scanner resolutions (200, 400 and 600 p.p.i.), resulting in six versions of each radiograph. Seven experienced observers were asked to evaluate the quality of the resulting images as they were displayed on a Nokia 445Xi monitor (Nokia Display Products, Helsinki, Finland). Monitor settings were varied by changing the colour palette and screen resolution. RESULTS: Digital images of masked films had a statistically significant (t-test with alpha 2 tail < or = 0.05) higher quality than those scanned without a mask. The best image quality was obtained at a resolution of 400 p.p.i. Display options were optimum with 256 colours and a screen size of 1152 x 864 pixels. CONCLUSIONS: Better results were obtained when intra-oral radiographs were digitised with a mask at a resolution of 200 or 400 p.p.i. and displayed using 256 colours and the largest screen size possible. Further studies are needed to extend these results to other makes and models of scanner and monitor.

Algorithms↗