Contour integral method for obtaining the self-energy matrices of electrodes in electron transport calculations

We propose an efficient computational method for evaluating the self-energy matrices of electrodes to study ballistic electron transport properties in nanoscale systems. To reduce the high computational cost incurred in large systems, a contour integral eigensolver based on the Sakurai-Sugiura method combined with the shifted biconjugate gradient method is developed to solve exponential-type eigenvalue problem for complex wave vectors. A remarkable feature of the proposed algorithm is that the numerical procedure is very similar to that of conventional band structure calculations. We implement the developed method in the framework of the real-space higher-order finite difference scheme with nonlocal pseudopotentials. Numerical tests for a wide variety of materials validate the robustness, accuracy, and efficiency of the proposed method. As an illustration of the method, we present the electron transport property of the free-standing silicene with the line defect originating from the reversed buckled phases.Comment: 36 pages, 13 figures, 2 table

Factors influencing response to treatment of pulmonary tuberculosis.

We analyzed 150 patients with pulmonary tuberculosis from 1990 to 1996 (i) to evaluate the frequency of drug resistance, (ii) to elucidate factors influencing the response to chemotherapy, and (iii) to attempt to improve the therapeutic approach. Multidrug-resistant tuberculosis strains were not found. By univariate analysis, there were 8 factors associated with an increased sputum conversion time: male gender, prior treatment, complications, progressive chest radiographic findings, a high Ziehl-Neelsen stain score, lymphocytopenia, a high erythrocyte sedimentation rate (ESR), and hypoproteinemia. Complications, prior treatment, a high Ziehl-Neelsen stain score, and a high ESR were independent predictive factors in a Cox proportional hazard model. Recursive partitioning and amalgamation (RPA) defined 3 subgroups that responded to treatment. In order to reduce the time to sputum conversion, poor responders according to the RPA should be treated with a 4-drug regimen containing pyrazinamide.</p

Indocyanine green-laden poly(ethylene glycol)-block-polylactide (PEG-b-PLA) nanocapsules incorporating reverse micelles: Effects of PEG-b-PLA composition on the nanocapsule diameter and encapsulation efficiency

Reverse micelles are thermodynamically stable systems, with a capacity to encapsulate hydrophilic molecules in their nanosized core, which is smaller than the core generally obtained with water-in-oil-emulsion droplets. Herein, we present a simple technique for the preparation of poly(ethylene glycol)-block-polylactide (PEG-b-PLA) nanocapsules encapsulating a hydrophilic photosensitizer (indocyanine green, ICG), which exploits reverse micelle formation and subsequent emulsion-solvent diffusion. We establish the effect of the PEG-b-PLA composition and the co-surfactant volume on the diameter and water content of the reverse micelles. We demonstrate that the composition of PEG-b-PLA affects also the diameter and encapsulation efficiency of the resulting nanocapsules. We show that the ICG-laden nanocapsules fabricated under the most optimal conditions have a diameter of approximately 100 nm and an ICG encapsulation efficiency of 58%. We believe that the method proposed here is a promising step towards the preparation of hydrophilic drug-laden polymer nanocapsules with a small diameter and therefore suitable for use in drug delivery applications based on enhanced permeability and retention (EPR) effect-driven passive targeting

Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays

<p>Abstract</p> <p>Background</p> <p>High-density oligonucleotide arrays are widely used for analysis of genome-wide expression and genetic variation. Affymetrix GeneChips – common high-density oligonucleotide arrays – contain perfect match (PM) and mismatch (MM) probes generated by changing a single nucleotide of the PMs, to estimate cross-hybridization. However, a fraction of MM probes exhibit larger signal intensities than PMs, when the difference in the amount of target specific hybridization between PM and MM probes is smaller than the variance in the amount of cross-hybridization. Thus, pairs of PM and MM probes with greater specificity for single nucleotide mismatches are desirable for accurate analysis.</p> <p>Results</p> <p>To investigate the specificity for single nucleotide mismatches, we designed a custom array with probes of different length (14- to 25-mer) tethered to the surface of the array and all possible single nucleotide mismatches, and hybridized artificially synthesized 25-mer oligodeoxyribonucleotides as targets in bulk solution to avoid the effects of cross-hybridization. The results indicated the finite availability of target molecules as the probe length increases. Due to this effect, the sequence specificity of the longer probes decreases, and this was also confirmed even under the usual background conditions for transcriptome analysis.</p> <p>Conclusion</p> <p>Our study suggests that the optimal probe length for specificity is 19–21-mer. This conclusion will assist in improvement of microarray design for both transcriptome analysis and mutation screening.</p

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX), Illumina Genome Analyzer (GA), and Applied Biosystems SOLiD system (SOLiD). A common genomic DNA sample obtained from Escherichia coli strain DH1 was applied to these sequencers. The obtained sequence reads were aligned to the complete genome sequence of E. coli DH1, to evaluate the accuracy and sequence bias of these sequence methods. We found that the fraction of “junk” data, which could not be aligned to the reference genome, was largest in the data set of SOLiD, in which about half of reads could not be aligned. Among data sets after alignment to the reference, sequence accuracy was poorest in GA data sets, suggesting relatively low fidelity of the elongation reaction in the GA method. Furthermore, by aligning the sequence reads to the E. coli strain W3110, we screened sequence differences between two E. coli strains using data sets of three different next-generation platforms. The results revealed that the detected sequence differences were similar among these three methods, while the sequence coverage required for the detection was significantly small in the FLX data set. These results provided valuable information on the quality of short sequence reads and the performance of SNP detection in three next-generation sequencing platforms

Proteomic analysis of fatty liver induced by starvation of medaka fish larvae

When medaka fish (Oryzias latipes) larvae are grown in the absence of exogenous nutrition, the liver becomes dark and positive to Oil Red O staining from 7 days post-hatch (dph). We determined the mechanism of this starvation-induced development of fatty liver by proteomic analysis using livers obtained from larvae grown in the presence or absence of 2% glucose at 5 dph. Results showed that changes in the expression levels of enzymes involved in glycolysis or the tricarboxylic acid cycle were modest, whereas the expression levels of enzymes involved in amino acid catabolism or β-oxidation of fatty acids were significantly elevated, suggesting that they become major energy sources under starvation conditions. Expression levels of enzymes for the uptake and β-oxidation of fatty acids as well as synthesis of triacylglycerol were elevated, whereas those for the synthesis of cholesterol as well as export of cholesterol and triacylglycerol were decreased under starvation conditions, which explains the accumulation of triacylglycerol in the liver. Our results provide the basis for future research to understand how gene malfunction(s) affects the development of fatty liver, which can lead to nonalcoholic steatohepatitis and then to liver cirrhosis.Key words: amino acid catabolism, β-oxidation, triacylglycerol, cholesterol, export

A Quantitative Immunochromatography Assay of Whole Blood Samples for Antigen-specific IgE—A New Method for Point of Care Testing for Allergens—

ABSTRACTBackgroundThe development of an inexpensive point-of-care testing system for antigen-specific IgE is greatly needed. We, therefore, tried to develop a quantitative enzyme immunochromatography assay system for antigen-specific IgE in fresh whole blood.MethodsWhole blood sample was mixed with a reagent containing detergent to lyse red blood cells, and the mixture was applied to an immunochromatography strip. The lysate was observed to migrate in the strip and was washed away by the substrate buffer. When the sample contained the specific IgE, the antigen-specific IgE line was clearly observed on the strip macroscopically.ResultsResults were obtained 20 minutes after the application of hemolysed blood sample to immunochromatography, and these results showed positive correlation with those obtained by the AlaSTAT system, which is one of the popular assay kits for specific IgE. The results were not affected significantly by the hematocrit value of the blood sample, by the kind of anticoagulant in the blood collection tube, or by the concentration of the total IgE, provided it was lower than 20000IU/ml.ConclusionsThese results indicate that our system is applicable for point-of-care testing for antigen-specific IgE