Hewlett-Packard (Japan)

SUMMARY: KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. AVAILABILITY AND IMPLEMENTATION: KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We have identified piezoelectric fields in strained GaInN/GaN quantum well p-i-n structures using the quantum-confined Stark effect. The photoluminescence peak of the quantum wells showed a blueshift with increasing applied reverse voltages. This blueshift is due to the cancellation of the piezoelectric field by the reverse bias field. We determined that the piezoelectric field points from the growth surface to the substrate and its magnitude is 1.2 MV/cm for Ga0.84In0.16N/GaN quantum wells on sapphire substrate. In addition, from the direction of the field, the growth orientation of our nitride epilayers can be determined to be (0001), corresponding to the Ga face.

We describe a sheath flow capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) method in the negative mode using a platinum electrospray ionization (ESI) spray needle, which allows the comprehensive analysis of anionic metabolites. The material of the spray needle had significant effect on the measurement of anions. A stainless steel spray needle was oxidized and corroded at the anodic electrode due to electrolysis. The precipitation of iron oxides (rust) plugged the capillary outlet, resulting in shortened capillary lifetime. Many anionic metabolites also formed complexes with the iron oxides or migrating nickel ion, which was also generated by electrolysis and moved toward the cathode (the capillary inlet). The metal-anion complex formation significantly reduced detection sensitivity of the anionic compounds. The use of a platinum ESI needle prevented both oxidation of the metals and needle corrosion. Sensitivity using the platinum needle increased from several- to 63-fold, with the largest improvements for anions exhibiting high metal chelating properties such as carboxylic acids, nucleotides, and coenzyme A compounds. The detection limits for most anions were between 0.03 and 0.87 micromol/L (0.8 and 24 fmol) at a signal-to-noise ratio of 3. This method is quantitative, sensitive, and robust, and its utility was demonstrated by the analysis of the metabolites in the central metabolic pathways extracted from mouse liver.

The formation of pits in GaInN quantum wells (QWs) has been studied by atomic force microscopy and transmission electron microscopy. It is found that the pits have a hexahedron cone morphology with six sidewalls on 〈11̄01〉 planes and dislocations connected to their vertexes. The dislocations may induce the formation of pits during the growth of GaInN QWs.

Nanometer size polarized domains were written in a PbZr1−xTixO3 (PZT) thin film using an atomic force microscope (AFM) and the relationship between the polarized domain and the grain of the film was investigated. The polarized domain was formed by applying a pulse voltage to the ferroelectric PZT thin film through a conductive AFM tip. The polarized domain structure was observed by imaging the piezoelectric-induced surface vibration by an AFM with an ac voltage applied between the tip and the bottom electrode of a sample. The polarized domains with a diameter of 50 nm were written within a single grain.

Abstract Summary KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. Availability KofamKOALA, KofamScan, and KOfam are freely available from https://www.genome.jp/tools/kofamkoala/ Contact ogata@kuicr.kyoto-u.ac.jp

Portable devices demand low power consumption to prolong battery life. Gating the clock is one strategy for saving power. The authors' technique identifies self-loops in an FSM and uses the function described by the self-loops to gate the clock. Applying these techniques to standard benchmarks achieved an average 25% less power dissipation at a cost of only 5% more area.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Techniques for modeling an object through observation are very important in object recognition and virtual reality. A wide variety of techniques have been developed for modeling objects with opaque surfaces, whereas less attention has been paid to objects with transparent surfaces. A transparent surface has only surface reflection; it has little body reflection. We present a new method for obtaining surface orientations of transparent surfaces through analysis of the degree of polarization in surface reflection and emission in visible and far-infrared wavelengths, respectively. This parameter, the polarization degree of reflected light at the visible wavelengths, is used for determining the surface orientation at a surface point. The polarization degree at visible wavelengths provides two possible solutions, and the proposed method uses the polarization degree at far-infrared wavelengths to resolve this ambiguity.

In this paper, the failsafe performance of front-and-rear-wheel-independent-drive-type electric vehicles (FRID EVs) is clarified from a practical viewpoint through vehicle dynamics analysis under various road conditions and experiments on a running test course. Dynamic analyses at the time of failure were performed under severe road conditions by comparing the vehicle trajectories of FRID EVs with those of conventional EVs, i.e., two- and four-wheel motor drive-type EVs. The analyzed results show that after failure, FRID EVs continue to run safely and stably; all of the conventional EVs deviate from the travel lane in less than 2 s, which is not sufficient time for an ordinary driver to steer the vehicle to safety after being notified about vehicle failure. Using a prototype FRID EV with practical specifications, failsafe performance at the time of failure was evaluated on test courses, including roads having an ultra-low friction coefficient (μ). The experimental results showed that even if failure occurred while cornering and when running on low- μ roads, the FRID EV continued to run stably. These results proved that FRID EVs could ensure safety at the time of failure under practical running conditions.

Ultrafine powder of single‐phase manoclinic ZrO 2 was prepared by hydrothermal treatments of amorphous hydrated zirconia with 8 wt% KF solution under 100 MPa at 200° to 500°C for 24 h. The process yielded well‐crystallized particles 16 nm and 22 nm in size at 200° and 500°C, respectively .

Reuse is not just a technical issue. Hewlett-Packard studied why people sometimes resist reuse and which organizational models appear to encourage reuse more than others. The study found that successful reuse programs must be integrated within the culture of a company's existing organizational structure. One crucial organizational factor is the relationship between producers and consumers of reuse components and services. What are these relationships and how well do they work? To answer this question, I conducted an empirical study of 10 engineering sites at Hewlett-Packard engaged in systematic reuse. From this reuse experience, I identified four models of producer-consumer relationships; evaluated the models in terms of their organizational structures, advantages, and disadvantages; and identified goals for management to enable a successful implementation. The four models are: lone producer, nested producer, pool producer and team producer. Two or more models may occur within a given reuse program. Recommendations to management are based on both current successful practices and interviewees' suggestions. I also include some tentative guidelines on which environments are best suited to each model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

This paper describes a digital beamforming (DBF) multibeam antenna that incorporates a compact digital signal processor (DSP) engine, and the results of using it in a beamforming experiment receiving a satellite signal in a land-mobile environment. A considerable reduction in the scale of the DSP engine has been achieved by using field programmable gate arrays (FPGAs). To capture a satellite signal arriving from an unknown direction, a two-dimensional (2-D) spatial FFT signal processing provides orthogonal multibeam patterns on the broad side of a planar array antenna. The experimental results demonstrated the features of coarse acquisition and tracking of a signal arrival by selecting the strongest of the beams without assistance from direction finding sensors or microwave phase shifters. The DBF multibeam antenna will provide high-quality communications and increase traffic capacity if it is applied to high-gain mobile antennas or multispot-beam base station antennas in cellular or satellite mobile communications.

Abstract Ferroelectric thin films as the recording media of scanning probe microscope-based storage devices were investigated using an atomic force microscope(AFM) technique. Polarization domains were formed in the PbZrxTi1-xO3(PZT) thin films epitaxialy grown on the epitaxial SrRuO3(SRO) thin films on SrTiO3 substrate by applying a pulse voltage between the conductive tip of AFM and SRO as a bottom electrode. The polarized domains were observed by detecting the inverse-piezoelectricity-induced surface vibration of the PZT thin film caused by applying an ac modulation voltage to the conductive tip. The recording density of polarized domains, domain switching speed and preliminary retention characteristics of polarized domains were studied. The polarized domains as small as 30 nm are formed in the PZT thin film with the thickness of 45 nm. The small domains can be formed by applying a 100 ns pulse of 10 V to the conductive tip. As for the retention characteristics of polarized domains with a size of 90–110 nm, the temperature dependence of d⊘main retention time was found to be in accordance with the Arrhenius model. Extrapolation of the Arrhenius plot leads to an estimation that the time for 50% of polarized domains to become smaller than half initial size at 50 °C is 34 years for 90–110 nm polarized domains in the 45 nm PZT thin film.

A 10-nm-thick PbZr0.25Ti0.75O3 thin film is epitaxially grown on a SrRuO3/BaTiO3/ZrO2/Si heterostructure substrate by reactive evaporation. Structural and electrical properties of the film are investigated. It is concluded that the film is ferroelectric and retains a native uniform upward polarization. Artificial downward polarization domains, whose average diameter is 24 nm, can be formed in the film.

MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In a scenario where each peer of an ad-hoc wireless local area network (WLAN) receives one of many available video streams from a wireless wide area network (WWAN), we propose a network-coding-based cooperative repair framework for the ad-hoc peer group to improve broadcast video quality during channel losses. Specifically, we first impose network coding structures globally, and then select the appropriate video streams and network coding types within the structures locally, so that repair can be optimized for broadcast video in a rate-distortion manner. Innovative probability—the likelihood that a repair packet is useful in data recovery to a receiving peer—is analyzed in this setting for accurate optimization of the network codes. Our simulation results show that by using our framework, video quality can be improved by up to 19.71 dB over un-repaired video stream and by up to 5.39 dB over video stream using traditional unstructured network coding. </para>

We investigate coding tools for interactive multiview streaming (IMVS), where clients interactively request desired views for successive video frames, and in response the server sends the appropriate pre-compressed video data to the clients. Solution based on using only I-frames to support view switching would incur high transmission cost, while for that based on using only P-frames to encode every possible traversal, although it can minimize transmission cost, prohibitive server's storage may be required. Therefore, efficient solutions for IMVS need to consider the trade-off between transmission and storage cost. In this paper, we study the potential use of distributed source coding (DSC) in IMVS. Specifically, we propose two DSC constructions that could achieve good transmission-storage trade-offs. Central to these constructions is a method that can efficiently encode the least significant bits (LSB) of a frame to be decoded, leading to competitive storage and transmission requirements. Experiment results demonstrate these constructions compare favorably to existing tools, and could be valuable for interactive multiview streaming.

A universal calibration method for four-terminal-pair (4TP) admittance standards, developed for frequencies up to around 10 MHz, is presented. The method is applicable to calibration of conversion adapters that convert a system from a 4TP to either a three-terminal system or a one-port system. Implementation of the method requires only a set of driving-point-impedance measurements, using proven one-port technology, and calculations of 4TP transfer admittance and output impedances using an impedance matrix. >

Cooperative Peer-to-Peer Repair (CPR) has been proposed to recover from packet losses incurred during 3G broadcast. CPR leverages the increasing presence of multi-homed mobile devices having both 3G cellular and IEEE 802.11 wireless interfaces. Mobile devices can, therefore, draw upon IEEE 802.11 peering links to cooperatively achieve out-of-band repair of 3G broadcasting losses. This paper considers the problem of employing Network Coding (NC) to exploit the broadcast nature of the wireless medium towards enhancing the efficiency of CPR. We show that the minimum latency scheduling problem for NC based CPR (NC-CPR) is NP-Hard. We present heuristics for NC-CPR that assume a priori topology and packet loss information. Insights gained from our heuristics are leveraged to propose NC-DCPR, a fully distributed protocol for NC-CPR. We conduct extensive simulation experiments under realistic network conditions. Our results show that employing network coding significantly improves the efficiency of CPR.

A GaN based laser diode with Fabry-Perot resonator mirrors fabricated by focused ion beam etching was demonstrated for the first time. It shows lasing by pulsed current injection at room temperature. The threshold current and the lasing wavelength are 0.75 A and around 410 nm, respectively.