Numerical investigation of quasi-coplanar plasmonic waveguide-based photonic components.
Using 3-dimensional numerical simulations, we investigated the characteristics and performance of essential photonic components based on the recently proposed quasi-coplanar waveguide (QCPW) including bends, couplers, and splitters. The results confirmed the QCPW's potential in high density photonic integration. We also explored the application of various RF-originated concepts and techniques to QCPW-based photonic components to enhance and enrich their functionalities.

title: Sucrose-based fabrication of 3D-networked, cylindrical microfluidic channels for rapid prototyping of lab-on-a-chip and vaso-mimetic devices.
abstract: We present a new fabrication scheme for 3D-networked, cylindrical microfluidic (MF) channels based on shaping, bonding, and assembly of sucrose fibers. It is a simple, cleanroom-free, and environment-friendly method, ideal for rapid prototyping of lab-on-a-chip devices. Despite its simplicity, it can realize complex 3D MF channel architectures such as cylindrical tapers, internal loops, end-to-side junctions, tapered junctions, and stenosis. The last two will be of special use for realizing vaso-mimetic MF structures. It also enables molding with polymers incompatible with high-temperature processing.

title: Elastomeric microwire-based optical gas flowmeter with stretching-enabled tunability in measurement range.
abstract: We report the utilization of transparent poly(dimethylsiloxane) (PDMS) microwires as the transducer for optical gas flowmetry. The elasticity of the PDMS microwire was exploited not only to miniaturize and simplify the flowmeter but also to widen and tune the measurement range through mechanical stretching. Using a 9 mm long microwire, we achieved 2.8~9.8 dB/SLM sensitivity. A 500 μm stretching of the microwire also shifted the measurement range from 1 to 4 SLM. The experimental results agreed well with predictions based on the fluid dynamic/optical model.

title: Bioconjugated superstructures of CdTe nanowires and nanoparticles: multistep cascade Förster resonance energy transfer and energy channeling.
abstract: Nanoparticle/nanowire assemblies with a degree of radial organization were prepared around luminescent semiconducting CdTe nanowires using bioconjugation with streptavidin and D-biotin linkers. Red-emitting nanowires (6.62 +/- 1.55 nm diameter, 512 +/- 119 nm length) and green-emitting nanoparticles (3.2 +/- 0.7 nm diameter) were surface-modified with biotin, while orange-emitting nanoparticles (4.1 +/- 1.2 nm diameter) were decorated with streptavidin. CdTe nanocrystals produced two fuzzy layers around the nanowires in which the diameter of CdTe nanoparticles decreased with the distance from the nanowire axis. Förster resonance energy transfer (FRET) from the outside layer of nanoparticles to the central nanowire was observed for nanowires conjugated with 4.1 nm CdTe. Addition of 3.2 nm CdTe resulted in a red-orange-green optical progression with band gaps of CdTe decreasing toward the axis of the superstructure. In this case, 4-fold luminescence enhancement of the nanowire luminescence was observed and was attributed to multistep FRET. This observation indicated the accumulation of photogenerated excitons in the cascade terminal. A simple model of multiconjugated superstructure with cascade energy transfer is developed and used to describe and understand the experimental data. The experimental data and theoretical model suggest the possibility of utilization of the prepared superstructures with radial symmetry in several classes of optoelectronic devices including nanomaterials for energy collection. They can also be a convenient model object for the investigation of methods of energy funneling in nanoscale assemblies.

title: Bioconjugated Ag nanoparticles and CdTe nanowires: metamaterials with field-enhanced light absorption.
abstract: The hybrid assembly of inorganic and metallic nanomaterials by means of chemical and biological bonding to yield manifold optical and electromagnetic properties has received widespread attention. Currently available highly monodispersed nanomaterials such as semiconductors and noble metals that can be conjugated by ligand–receptor, antigen– antibody reactions, polymer tethering, and DNA hybridization are used as building blocks for 2D or 3D superstructures in which new collective properties of these artificial assemblies have been obtained. They represent a large class of newmaterials (i.e., metamaterials) in which the properties are determined not only by classical atomic composition, but also by nanoscale organization of structural components. Recently, metamaterials based on metallic composites have received special attention as these are expected to display negative values for permittivity and refractive index. This property should lead to a multitude of unique optical effects. Many of these effects are related to surface plasmons on Au or Ag nanoparticles (NPs), which generate exceptionally high localized electromagnetic fields, and have been exploited in surface-enhanced Raman spectroscopy and some optoelectronic devices. 22] Metamaterials from semiconductors and their combinations with metals can also produce optical effects that are useful for development of advanced sensing and imaging technologies. Recently, we

title: High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements
abstract: Approximately 80 long interspersed element (LINE-1 or L1) copies are able to retrotranspose actively in the human genome, and these are termed retrotransposition-competent L1s. The 5′ untranslated region (UTR) of the human-specific L1 contains an internal promoter and several transcription factor binding sites. To better understand the effect of the L1 5′ UTR on the evolution of human-specific L1s, we examined this population of elements, focusing on the sequence diversity and accumulated substitutions within their 5′ UTRs. Using network analysis, we estimated the age of each L1 component (the 5′ UTR, ORF1, ORF2, and 3′ UTR). Through the comparison of the L1 components based on their estimated ages, we found that the 5′ UTR of human-specific L1s accumulates mutations at a faster rate than the other components. To further investigate the L1 5′ UTR, we examined the substitution frequency per nucleotide position among them. The results showed that the L1 5′ UTRs shared relatively conserved transcription factor binding sites, despite their high sequence diversity. Thus, we suggest that the high level of sequence diversity in the 5′ UTRs could be one of the factors controlling the number of retrotransposition-competent L1s in the human genome during the evolutionary battle between L1s and their host genomes.

title: Synthesis and evaluation of aza-peptidyl inhibitors of the lysosomal asparaginyl endopeptidase, legumain.
abstract: Legumain or asparaginly endopeptidase (AEP) is a lysosomal cysteine protease with a high level of specificity for cleavage of protein substrates after an asparagine residue. It is also capable of cleaving after aspartic acids sites when in the acidic environment of the lysosome. Legumain expression and activity is linked to a number of pathological conditions including cancer, atherosclerosis and inflammation, yet its biological role in these pathologies is not well-understood. Highly potent and selective inhibitors of legumain would not only be valuable for studying the functional roles of legumain in these conditions, but may have therapeutic potential as well. We describe here the design, synthesis and in vitro evaluation of selective legumain inhibitors based on the aza-asparaginyl scaffold. We synthesized a library of aza-peptidyl inhibitors with various non-natural amino acids and different electrophilic warheads, and characterized the kinetic properties of inactivation of legumain. We also synthesized fluorescently labeled inhibitors to investigate cell permeability and selectivity of the compounds. The inhibitors have second order rate constants of up to 5 × 10(4)M(-1)s(-1) and IC(50) values as low as 4 nM against recombinant mouse legumain. In addition, the inhibitors are highly selective toward legumain and have little or no cross-reactivity with cathepsins. Overall, we have identified several valuable new inhibitors of legumain that can be used to study legumain function in multiple disease models.

title: Spectrum measurement of fast optical signal of neural activity in brain tissue and its theoretical origin
abstract: Functional brain imaging technologies have enabled recent advances in understanding human brain function. In particular, a noninvasive and fast optical technique will become one of the most promising tools for future studies. As a fundamental ex vivo study for the development of such a technique, this paper demonstrates the spectral measurement of fast optical changes associated with neural activity in bulk brain tissue. For this purpose, a high-speed confocal near-infrared spectrometer was built and used. The results verified that observed transient optical responses (tORs) are associated with neural activity by showing that the following: tORs were concurrent and correlated with local field potentials (LFPs); tORs disappeared following tetrodotoxin application; and tORs were reproducibly observed across preparations. In addition, the amplitude of tORs was statistically significantly larger in longer wavelengths (approximately 1200 nm). The time course of tORs, however, is quite different from that of LFPs. Since this difference implies that tORs may originate not directly from the electric potential variation but from other neurophysiological events accompanying excitation, this paper tested the hypothesis that tORs are attributed to transient cellular volume changes (tCVCs). With no previous dynamic equation to elucidate such different temporal dynamics of the optical responses, a novel mathematical neuron model to describe tCVCs was developed. This neuron model, along with finite-difference time-domain simulations, showed that tCVCs and tORs were similar in the temporal dynamics, order of magnitude, response direction, and detectability in the bulk tissue; thus supporting the hypothesis.