Adversarial Example Generation using Evolutionary Multi-objective Optimization

This paper proposes Evolutionary Multi-objective Optimization (EMO)-based Adversarial Example (AE) design method that performs under black-box setting. Previous gradient-based methods produce AEs by changing all pixels of a target image, while previous EC-based method changes small number of pixels to produce AEs. Thanks to EMO's property of population based-search, the proposed method produces various types of AEs involving ones locating between AEs generated by the previous two approaches, which helps to know the characteristics of a target model or to know unknown attack patterns. Experimental results showed the potential of the proposed method, e.g., it can generate robust AEs and, with the aid of DCT-based perturbation pattern generation, AEs for high resolution images

Graph Spatio-Spectral Total Variation Model for Hyperspectral Image Denoising

The spatio-spectral total variation (SSTV) model has been widely used as an effective regularization of hyperspectral images (HSI) for various applications such as mixed noise removal. However, since SSTV computes local spatial differences uniformly, it is difficult to remove noise while preserving complex spatial structures with fine edges and textures, especially in situations of high noise intensity. To solve this problem, we propose a new TV-type regularization called Graph-SSTV (GSSTV), which generates a graph explicitly reflecting the spatial structure of the target HSI from noisy HSIs and incorporates a weighted spatial difference operator designed based on this graph. Furthermore, we formulate the mixed noise removal problem as a convex optimization problem involving GSSTV and develop an efficient algorithm based on the primal-dual splitting method to solve this problem. Finally, we demonstrate the effectiveness of GSSTV compared with existing HSI regularization models through experiments on mixed noise removal. The source code will be available at https://www.mdi.c.titech.ac.jp/publications/gsstv.Comment: Accepted to IEEE Geoscience and Remote Sensing Letters. The code is available at https://www.mdi.c.titech.ac.jp/publications/gsst

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

Dynamic nuclear polarization and Knight shift measurements in a breakdown regime of integer quantum Hall effect

Nuclear spins are polarized electrically in a breakdown regime of an odd-integer quantum Hall effect (QHE). Electron excitation to the upper Landau subband with the opposite spin polarity flips nuclear spins through the hyperfine interaction. The polarized nuclear spins reduce the spin-splitting energy and accelerate the QHE breakdown. The Knight shift of the nuclear spins is also measured by tuning electron density during the irradiation of radio-frequency magnetic fields.Comment: 3 pages, 2 figures, EP2DS-1

Phenotypic convergence in bacterial adaptive evolution to ethanol stress

Stability of ethanol tolerance. Strain F at the end point (2,500 h) and at 576 h was cultivated for 200 generations absent ethanol stress. After the cultivation, ethanol tolerance was evaluated by measuring specific growth rates in 5 % ethanol stress (red bars). The growth rates under ethanol stress were similar to those before the non-stress cultivation (blue bars) and were significantly higher than that of the parent strain. (PDF 976 kb

Induction of Apoptosis of Rat Neonatal Cardiomyocytes by Chemical Ischemia and Reoxygenation: The Role of Phosphatidylserine

Ischemia/reperfusion injury plays a crucial role in the induction of the cell death of myocytes. The precise mechanism of the cell death, however, has not been elucidated enough. This study examined the cell death of rat neonatal myocytes induced by chemical ischemia and reoxygenation with an in vitro model, in terms of apoptosis, and the role of phosphatidylserine, which is recognized with annexin V. Chemical ischemia and reoxygenation were conducted on the cultured myocytes obtained from 1- or 2-day-old Wistar rats. The cells were divided into 4 groups exposed to chemical ischemia for 9 h (Group A), 18 h (Group B) and 24 h (Group C) and one group not exposed to chemical ischemia (Control Group). DNA ladder formation on agarose gel electrophoresis was noted in Groups B and C followed by reoxygenation, but not in Group A, as well as all 4 groups without reoxygenation. There were cells positive to terminal deoxynucleotidyl transferase-mediated dUDP-biotin nick end labeling in all 3 groups except for the Control Group; after reoxygenation, the number of cells became larger in Groups B and C than in Group A. Flow cytometry revealed that annexin V-positive cells were 1.15 ± 0.82% in the Control Group, 4.07 ± 3.8% in Group A without reoxygenation and 15.5 ± 6.3% in Group A after 30-min reoxygenation, respectively; the value was significantly higher in the latter than the former two (P < 0.01). Although 18-h and 24-h ischemia increased the annexin V-positive cells, reoxygenation did not alter the number of cells in Groups B and C. These results indicate that i) chemical ischemia followed by reoxygenation variably induces apoptosis of rat myocytes, ii) long-term ischemia causes phosphatidylserine translocation on the cell surface membrane, regardless of reoxygenation and iii) mild ischemia necessitates reoxygenation to translocate phosphatidylserine, which might play a crucial role in the initiation of apoptosis of the myocytes

Effect of substrate and thickness on the photoconductivity of nanoparticle titanium dioxide thin film vacuum ultraviolet photoconductive detector

Vacuum ultraviolet radiation (VUV, from 100 nm to 200 nm wavelength) is indispensable in many applications, but its detection is still challenging. We report the development of a VUV photoconductive detector, based on titanium dioxide (TiO2 ) nanoparticle thin films. The effect of crystallinity, optical quality, and crystallite size due to film thickness (80 nm, 500 nm, 1000 nm) and type of substrate (silicon Si, quartz SiO2, soda lime glass SLG) was investigated to explore ways of enhancing the photoconductivity of the detector. The TiO2 film deposited on SiO2 substrate with a film thickness of 80 nm exhibited the best photoconductivity, with a photocurrent of 5.35 milli-Amperes and a photosensitivity of 99.99% for a bias voltage of 70 V. The wavelength response of the detector can be adjusted by changing the thickness of the film as the cut-off shifts to a longer wavelength, as the film becomes thicker. The response time of the TiO2 detector is about 5.8 µs and is comparable to the 5.4 µs response time of a diamond UV sensor. The development of the TiO2 nanoparticle thin film detector is expected to contribute to the enhancement of the use of VUV radiation in an increasing number of important technological and scientific applications.Cadatal-Raduban M., Kato T., Horiuchi Y., et al. Effect of substrate and thickness on the photoconductivity of nanoparticle titanium dioxide thin film vacuum ultraviolet photoconductive detector. Nanomaterials 12, 10 (2022); https://doi.org/10.3390/nano12010010