Cautionary observations on preparing and interpreting brain images using molecular biology-based staining techniques

Though molecular biology-based visualization techniques such as antibody staining, in situ hybridization, and induction of reporter gene expression have become routine procedures for analyzing the structures of the brain, precautions to prevent misinterpretation have not always been taken when preparing and interpreting images. For example, sigmoidal development of the chemical processes in staining might exaggerate the specificity of a label. Or, adjustment of exposure for bright fluorescent signals might result in overlooking weak signals. Furthermore, documentation of a staining pattern is affected easily by recognized organized features in the image while other parts interpreted as "disorganized" may be ignored or discounted. Also, a higher intensity of a label per cell can often be confused with a higher percentage of labeled cells among a population. The quality, and hence interpretability, of the three-dimensional reconstruction with confocal microscopy can be affected by the attenuation of fluorescence during the scan, the refraction between the immersion and mounting media, and the choice of the reconstruction algorithm. Additionally, visualization of neurons with the induced expression of reporter genes can suffer because of the low specificity and low ubiquity of the expression drivers. The morphology and even the number of labeled cells can differ considerably depending on the reporters and antibodies used for detection. These aspects might affect the reliability of the experiments that involves induced expression of effector genes to perturb cellular functions. Examples of these potential pitfalls are discussed here using staining of Drosophila brain.     

MolSpace: a computer desktop tool for visualization of massive molecular data

The authors have developed a software tool, MolSpace, to visualize massive molecular datasets. MolSpace can project a set of massive multivariate data onto a visual space (two- or three-dimensional space) by means of principal component analysis. MolSpace allows users not only to draw a scatter diagram of the data but also to display their two- or three-dimensional molecular structures as the objects in that space. With a probe (a molecular object) the user can navigate vast data spaces, thus facilitating understanding of the data structure. In addition, partial space searching is also available that is based on similarity searching techniques. It is possible to interrogate a three-dimensional structure of a chemical compound that corresponds to each object on the space in real time. The detail of the system is discussed with an illustrative example.     

ε-Entropy and Fractal Dimension of a State for a Gaussian Measure

Kolmogorov introduced the concept of -entropy to analyze information in classical continuous systems. The fractal dimension of a geometric set was introduced by Mandelbrot as a new criterion to analyze the geometric complexity of the set. The -entropy and the fractal dimension of a state in a general quantum system were introduced by one of the present authors (MO) in order to characterize chaotic properties of general states.In this paper, we show that -entropy of a state includes Kolmogorov's -entropy, and that the fractal dimension of a state describes fractal structure of Gaussian measures.     

22–29 GHz Ultra-Wideband CMOS Pulse Generator for Short-Range Radar Applications

The pseudo-millimeter-wave ultra-wideband (UWB) is attractive for applications in short-range automotive radar systems using 22 to 29 GHz in order to realize road safety and intelligent transportation. Although the CMOS is suitable for short- range radar since processing units can be implemented in the same chip as the UWB front-end building block, it is difficult to operate CMOS pulse generators at such a high frequency. To realize the pseudo-millimeter-wave band using CMOS, we have proposed a new pulse generator consisting of a series of delay cells and edge combiners with waveform shaping for short-range radar. As a result of measurement using 90-nm CMOS technology, 1 Gb/s/bit pulses with 71 mV peak-to-peak, 39.2 ps monopulse width and 552 ps envelope width are successfully generated with a power consumption of 1.4 mW at a supply voltage of 0.91 V. This result can be the basis for developing the key technology for one-chip short-range radar sensors.     

Metamorphic Heterostructure InP/GaAsSb/InP HBTs on GaAs Substrates by MOCVD

Good-quality metamorphic InP buffer layers have been successfully grown on GaAs substrates by metal-organic chemical vapor deposition. Characterization by atomic force microscope, transmission electron microscopy, high-resolution X-ray diffraction, and Hall measurements indicated that the layers are of high crystalline quality, good mobility, and excellent surface morphology. On this buffer, we demonstrated the first metamorphic InP/GaAsSb/InP double heterojunction bipolar transistors (DHBTs) with good material quality and device performance. Metamorphic DHBTs showed direct-current and radio-frequency characteristics that are comparable to those grown on lattice-matched InP substrates.     

BAAQ: an infrastructure for application integration and knowledge discovery in bioinformatics.

The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory, in which they share public databases, computational tools as well as their analysis workflows. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments, standards and high-level services. Here, we present a system, which we named Bioinformatics: Ask Any Questions (BAAQ), to automate this development procedure as much as possible. BAAQ allows scientists to store and manage remote biological data and programs, to build analysis workflows that integrate these resources seamlessly, and to discover knowledge from available resources. This paper addresses two issues in building grid applications in bioinformatics: how to smoothly compose an analysis workflow using heterogeneous resources and how to efficiently discover and re-use available resources in the grid community. Correspondingly an intelligent grid programming environment and an active solution recommendation service are proposed. Finally, we present a case study applying BAAQ to a bioinformatics problem.     

Twisted bit-line architectures for multi-megabit DRAMs

As the memory cell array of DRAM has been scaled down, inter-bit-line coupling noise has emerged as a serious problem. The signal loss due to this noise is estimated at about 40% of the signal amplitude in a polycide-bit-line 16-Mb DRAM with a technologically attainable scaling scheme. Twisted bit-line architectures to reduce or eliminate the noise are proposed and demonstrated by the soft-error rate improvement of a 1-Mb DRAM. The effective critical charge is improved by 35%, which is attributed not only to the improvement of the signal amplitude but also to the elimination of large coupling noise during the sensing operation. The impact of these twisted bit-line architectures from a scaling viewpoint is also examined, and they are shown to be promising candidates for overcoming the scaling problems of DRAMs     

Current reliability issues and future technologies for systems on silicon – processes, circuits, chip architecture, and design

The progress of silicon technology is opening the era of “systems on silicon” in which a large-scale memory, a CPU, and other logic macros will be integrated on a single chip. These kinds of chips, called system LSIs, have an especially promising future in mobile and multimedia applications but face inherent technical problems related to the reliability of ultrathin oxide film, conflict in the processing of different components, increased gate and subthreshold leakage currents, memory bottlenecks, and design complexity. This paper reviews the system LSIs and then introduces related technologies in processing, circuits, chip architecture, and design. It also discusses the influence of the system LSIs on business strategies.     

Characterisation of volatile sulphur-containing compounds generated in crushed leaves of Chinese chive (Allium tuberosum Rottler)

To characterise the composition of sulphur-containing constituents in Chinese chive (Allium tuberosum Rottler), GC–MS and HPLC analyses were carried out, using 12 varieties of Chinese origin, 4 varieties of Japanese origin and 6 commercially available cultivars. Five disulphides (dimethyl, allyl methyl, methyl 1-(E)-propenyl, diallyl, and allyl 1-(E)-propenyl), two trisulphides (dimethyl and allyl methyl), and two vinyldithiins (3-vinyl-[4H]-1,2- and 2-vinyl-[4H]-1,3-) were identified on the basis of their mass spectral and GC-retention data. Among the detected sulphur compounds, sulphides with a methyl group predominated over those with an allyl group. This was supported by the HPLC estimations, suggesting that all cultivars examined had much greater amounts of methiin than alliin. Also, two novel compounds were tentatively identified as [3H,4H]-1,2-dithiin and [2H,4H]-1,3-dithiin on the basis of their mass spectral features, GC-retention data, and some experimental results on their formation in reaction mixtures with different proportions of methiin and alliin. Their formation mechanism was proposed.     

An outcome of nuclear safety research in JAERI: case study for LOCA

An outcome of nuclear safety research (NSR) done by JAERI (Japan Atomic Energy Research Institute) was case studied by the bibliometric method. (1) For LOCA (loss-of-coolant accident) a domestic share of JAERI in monoclinic research paper was 63% at the past (20) 1978–1982 but was decreased to 40% at the present 1998–2002. For co-authored papers a domestic share between JAERI and PS (public sectors) was zero at past (20) but increased to 4% at the present. Research cooperation is active between Tokyo University and JAERI or between JAERI and Nagoya University. (2) It is revealed that LOCA outputs born by NSR-JAERI reflected partly to those of the Safety Licensing Guidelines, however, a share of NSR-JAERI could not determined due to the lack of necessary information in the Guideline.