bluuebunny/crossref_metadata_2025 huggingface dataset:
Multilevel coding for low‐density parity‐check codes
Authors: Matsumoto Wataru , Xu Weigang , Imai Hideki
Published: April 2007

In recent years attention has turned to LDPC codes, which show performance approaching communication path capacity. In the past, application of LDPC codes has mainly been BPSK‐based proposals. In this paper, we propose a new design method for multilevel coding that uses LDPC codes as element codes. First, we focus on the possibility of freedom of design for LDPC codes in regards to any desired encoding rate, optimize a degree profile using Gaussian Approximation, and use the actual BER characteristics shown in LDPC codes of finite length formed by this degree file to find the differential SNRnorm up to the Shannon limit of SNR values at the time of some specific BER. With the SNRnorm for the encoding rate at several points, we calculate an SNRnorm approximation formula for a continuous, wide‐range encoding rate, and use this approximation formula to propose a method for designing multivalue coded modulation based on multilevel coding. In addition, we demonstrate the results of a simulation of this proposed method using irregular EG‐LDPC codes, and demonstrate that this method is effective for restricting deterioration of performance in actual usage. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(8): 57–68, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20173 Copyright © 2004 Wiley Periodicals, Inc.Copyright © 2007 Wiley Periodicals, Inc.
Fair bandwidth allocation method for broadband packet network
Authors: Yoshida Yukihiro , Kasahara Yasunobu , Maeda Yoichi
Published: April 2007

As broadband Internet access channels such as ADSL and FTTH become more widely used, network compression by power users becomes a problem. In order to deal with this problem, bandwidth control that assigns bandwidth among users in a fair manner is needed. In this paper, we studied the DRR method, which is known to allow fair bandwidth allocation and to be highly realizable. A new method that resolves the problem of realizability at high speeds in the range of gigabits and tens of gigabits typical of the DRR method is proposed. By this method, it is possible to realize fair allocation of bandwidth even if the channel speed is increased to several gigabits or several tens of gigabits. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(8): 50–56, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20266 Copyright © 2004 Wiley Periodicals, Inc.Copyright © 2007 Wiley Periodicals, Inc.
Optical burst switched ring network with upstream prioritized switching and distributed fairness control
Authors: Arakawa Yutaka , Yamanaka Naoaki , Sasase Iwao
Published: April 2007

With a view to constructing a metropolitan network that can flexibly handle highly bursty traffic, an optical burst switched ring network with upstream prioritized switching and distributed fairness control is proposed. In optical burst switching, high burst drop rates at intermediate nodes constitute a problem. In the proposed system, burst signal dropping at the relay nodes is eliminated by means of upstream prioritized switching. At the same time, by using distributed fairness control, the problem of upstream prioritized switching‐related unfairness, in which positional priority provides higher priority to more distant transmission nodes, is resolved. Further, by modifying the reservation of downstream nodes by using the trailer packet after disconnection of the transmission, unnecessary bandwidth is eliminated and the throughput is improved. By computer simulation, the throughput and the fairness with regard to the throughput are evaluated. It is shown that the proposed architecture exhibits excellent characteristics even in cases of hot‐spot traffic, in which concentrated traffic occurs at a particular destination. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(8): 30–39, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20338 Copyright © 2004 Wiley Periodicals, Inc.Copyright © 2007 Wiley Periodicals, Inc.
Rheometry experiment for a wire antenna aboard spacecraft at low frequencies
Authors: Imachi Tomohiko , Yagitani Satoshi , Higashi Ryoichi , Nagano Isamu
Published: April 2007

For satellite observation of the electric fields of waves, a dipole antenna using a wire (wire antenna) is often used. An antenna with probes on both ends (probe antenna) is used for observation of the static electric field. For calibration of these antennas, the effective length of the antenna is a problem. In general, in AC wave observation, the effective length of the wire antenna is half the total length L and hence L/2. It has been verified that this is correct at frequencies of several hundred hertz or higher. However, in the GEOTAIL antenna, the same antenna is co‐used for wave observation and the static field observation. Calibration is performed with an effective length of L/2 for wave observation with an effective length of L for static electric field measurement. Reliable data are obtained in both cases. This paper reports a rheometry experiment in which the output voltage of a small antenna is measured in water for the wire antenna, obtaining the frequency dependence of the effective length in the low‐frequency region. It is found that the frequency dependence of the effective length depends on the antenna configuration. When a wire antenna with only its side surfaces insulation coated is placed in a conductive medium such as water or plasma, it is found that the effective length approaches L at low frequencies and L/2 at higher frequencies. This result is theoretically analyzed by means of an equivalent circuit and it is found that the phenomenon depends on the balance among surrounding medium, the insulation coating of the wire, and the input impedance of the receiver. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(9): 45–53, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20353
Investigation of radiated field analysis model for moment method from microstrip line on PCB
Authors: Koyama Hiroaki , Kawabata Masato , Ishida Yasuhiro , Kuwabara Nobuo
Published: April 2007

The method of moments and the FDTD method have been widely used for the analysis of radiated electromagnetic fields. In comparison with the FDTD method, the method of moments calculates the electromagnetic field by a light computational load and analyzes the far field accurately. A wire grid model of the printed circuit board placed on the upper plane of the imitated equipment has been reported and it can calculate the electromagnetic field below 1 GHz. However, the wire grid model using the calculation above 1 GHz has not been reported. This paper proposes the analytical model that can analyze the radiated electromagnetic fields with horizontal polarization at frequencies above 1 GHz. Since the contribution of the current on a microstrip line (MSL) is significant in the case of horizontal polarization, the proposed method attempts to simulate the current distribution by inserting impedances and admittances into the wire grid model of MSL. As a result of the studies, it is found that an analysis is possible with an accuracy within ±5 dB of the measured results in the frequency range of 1 to 3 GHz when the current distribution, calculated by the FDTD method, is simulated by inserting inductance and capacitance into the wire grid model. It is also found that the result of calculation by the model is similar to that by the FDTD method, which requires a computation time about 4 times longer. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(8): 20–29, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20354 Copyright © 2004 Wiley Periodicals, Inc.Copyright © 2007 Wiley Periodicals, Inc.
New antenna weighting method for adaptable beamwidth with zero sidelobe constraints
Authors: Suzuki Junichiro , Masuda Yasuharu , Shinonaga Mitsuyoshi , Nishimoto Shinkichi
Published: April 2007

For sidelobe suppression design of antennas, weighting with window functions has been traditionally used. The antenna gain is degraded if a low sidelobe level is sought, so that expansion of the antenna beamwidth is inevitable. Also, there have been discussions of using the convergent calculation in the derivation of a window function that realizes desired characteristics such as sidelobe‐free conditions, but it has not been clear whether the theoretically maximum antenna gain is realized. This paper presents a method of analytical derivation of a weight vector satisfying the maximum achievable antenna gain while the desired beamwidth is obtained under the null sidelobe constraint for the sidelobe region output. In addition, we demonstrate the effectiveness of the method by simulation examples. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(9): 35–44, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20370
Experimental verification of measurement principle in standing wave radar capable of measuring distances down to zero meters
Authors: Okubo Yoshihiro , Uebo Tetsuji
Published: April 2007

In general, it is difficult to measure short distances by radar, which has a minimum detection distance of several meters. The standing wave radar proposed by the present authors has a minimum detection distance of about 2 m when the frequency bandwidth is 76 MHz. A solution to reduce the minimum detection distance is to increase the frequency bandwidth. This is not realistic due to limits imposed by radio regulations. The authors have proposed a method with measurable distances down to 0 m without enlarging the bandwidth and have presented the configuration and the measurement principle. The measurement principle has been verified by numerical simulation. In the present paper, the measurement principle is experimentally verified by using an actual standing wave radar and the realizability of a standing wave radar with measurement capability down to 0 m is confirmed. It is shown that the distance to the target at locations closer than the minimum detection distance of 2 m (0.14, 0.3, 0.5, and 1 m) can be measured with an error of several centimeters for a frequency bandwidth of 76 MHz at 24 GHz. For distances less than 0.14 m, the target could not be placed closer than 0.14 m due to positional interference of the target and the antenna in the present experimental environment so that physical confirmation was not possible. However, at the confirmed distance, the range spectrum predicted from the theory is obtained. Hence, it is considered possible to make measurements without special restrictions. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(9): 25– 34, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20375
Determination of satellite orbital elements by means of on‐board GPS receiver and its verification
Authors: Okamoto Yoshiwo , Hayashi Tomonao , Yokoyama Koji , Hosokawa Shigeru , Masumoto Yoshinari
Published: April 2007

We optimized orbital elements to minimize the squared deviation of the satellite position intermittently measured by an on‐board GPS receiver from the satellite position measured from orbital elements using the SGP orbit model, and then reentered the results into the SGP orbital model to attempt an interpolation calculation of the satellite position and velocity at any given point in time. As a result of applying this system to data from a GPS receiver on board the Whale Ecology Observation Satellite (WEOS), we found that by using positions measured at several minute intervals over a period of about 2 hours, we could calculate the position of WEOS with an error of about 50 m at any given instant within the time frame, among other conclusions. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(8): 10–19, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20378
A method of decreasing cross‐polarization in dual‐polarized patch antennas
Authors: Nishimoto Kengo , Fukasawa Toru , Ohtsuka Masataka , Makino Shigeru , Sunahara Yonehiko
Published: April 2007

In this paper, we propose a method for decreasing cross‐polarization in the tilt plane by optimizing the dielectric substrates of dual‐polarized patch antennas. At the same time, we clarify the limit values for the cross‐polarization level. First, we use a cavity model of the patch antenna to find cross‐polarization dielectric characteristics in the tilt plane. We learn from this that the direction of cross‐polarization increase or decrease in relation to the dielectric is reversed during horizontal polarized excitation and vertical polarized excitation. Therefore, if the cross‐polarization level during horizontal polarized excitation and vertical polarized excitation is the same dielectric, the lowest cross‐polarization level can be obtained in conditions where both horizontal polarization and vertical polarization are decreasing cross‐polarization. Next, we investigate the case where parasitic elements are mounted on the patch antenna, and use the FDTD method and test to show that our method is valid. In addition, if the patch is positioned perpendicularly to the horizontal plane, we show that the optimum dielectric remains virtually unchanged in the tilt plane up to about 15°from the horizontal plane. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 90(8): 1–9, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.20393 Copyright © 2004 Wiley Periodicals, Inc.Copyright © 2007 Wiley Periodicals, Inc.
Improvement in reliability of InP‐based HEMTs by suppressing impact ionization
Authors: Hara Naoki , Okamoto Naoya , Imanishi Kenji , Takahashi Tsuyoshi , Makiyama Kozo
Published: April 2007

The reliability of InP‐based high‐electron‐mobility transistors (HEMTs) which hold promise as ultrafast transistors for handling the expansion of the communication capacity was investigated, and was shown to be successfully improved by an InP‐based HEMT structure capable of suppressing impact ionization. The structures used are a lattice‐matched composite channel InGaAs/InAlGaAs structure and a double‐doped structure. In the composite channel structure, impact ionization is suppressed because electrons move from InGaAs to InAlGaAs under a high voltage. In the double‐doped structure, the electric field concentration is relaxed and impact ionization is suppressed because the built‐in electric field is small, and the electrons are widely distributed in the channel layer. The results of an aging test at a drain voltage of 2 V and an ambient temperature of 175°C confirmed an improved reliability in both structures. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 90(5): 33– 38, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20321
Leakage losses of quasi‐phase‐matched second‐harmonic‐generation devices with air gap
Authors: Ishikawa Yoshiki , Saitoh Kunimasa , Fujisawa Takeshi , Koshiba Masanori
Published: April 2007

This paper theoretically evaluates the leakage loss characteristics of a quasi‐phase‐matched second‐harmonic generation device using a ridge‐type MgO:LiNbO3/LiNbO3 waveguide with a gap proposed as an efficient low‐loss wave conversion device. The full‐vectorial finite element method for an analysis of the anisotropic waveguide is used. The effects of the distance from the MgO:LiNbO3 surface to the gap and the width and depth of the gap on the leakage loss are studied in detail. Also, it is found that there are cases where the leakage loss of the polarization related to wavelength conversion does not become less than a certain level even if the depth of the gap is made sufficiently deep. Its mechanism is found and a provision for further reduction of such a leakage loss is described. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 90(5): 11–18, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20328
Monohydrocalcite and Its Relationship to Hydrated Amorphous Calcium Carbonate in Biominerals (Eur. J. Inorg. Chem. 14/2007)
Authors: Neumann Markus , Epple Matthias
Published: April 2007

The cover picture shows an apple snail (Pomacea bridgesi) and scanning electron micrographs of five different forms of calcium carbonate that were prepared in vitro (vaterite, calcite, monohydrocalcite, amorphous calcium carbonate, and aragonite). Details are discussed in the article by M. Neumann and M. Epple on p. 1953 ff.
Electrophoretic affinity measurements on microchip. Determination of binding affinities between diketopiperazine receptors and peptide ligands
Authors: Stettler Alexandra R. , Krattiger Philipp , Wennemers Helma , Schwarz Maria A.
Published: April 2007

ACE on a microchip (MC‐ACE) is introduced as a fast and reliable method to determine binding affinities. It is based on monitoring the change in the ionic mobility of a receptor upon binding to a ligand, or vice versa. The method is complementary to other standard methods for binding affinity determinations, like isothermal titration calorimetry (ITC), NMR, UV‐Vis spectroscopy, etc. and allows for affinity studies of weak to strong binding interactions. The method is attractive since it principally allows for the analysis of the binding affinity of multiple receptors to a given ligand and requires comparatively small quantities of the binding partners (particularly in comparison to affinity measurements on capillary). We demonstrate the applicability of MC‐ACE for the determination of the binding affinities between acid‐rich diketopiperazine receptors and basic tripeptides in aqueous solution.
Determination of sertraline and N‐desmethylsertraline in human plasma by CE with LIF detection
Authors: Musenga Alessandro , Kenndler Ernst , Mercolini Laura , Amore Mario , Fanali Salvatore , Raggi Maria Augusta
Published: April 2007

A method has been developed for the analysis of the antidepressant drug sertraline together with its main metabolite N‐desmethylsertraline (DMS) in human plasma. It is based on CE with LIF detection (λ = 488 nm). A SPE procedure is employed for biological sample pretreatment, followed by a derivatization step with FITC; reboxetine was the internal standard. The effect of CD, acetone and N‐methyl‐D‐glucamine (GLC) as constituents of the BGE for analyte separation was investigated. The final BGE consisted of 20 mM carbonate buffer, pH 9.0, with 2.5 mM heptakis(2,6‐di‐O‐methyl)‐β‐CD, 50 mM GLC and 20% v/v acetone. With 30 kV applied voltage, the electrophoretic run is completed in 7.5 min. Linearity was observed in the plasma concentration range from 3.0 to 500 ng/mL for sertraline and 4.0 to 500 ng/mL for DMS. Extraction yield was >97.1%, precision – expressed as RSD% – was <3.7, accuracy (recovery) was >95.6%. Due to its sensitivity and selectivity, the method was suited for the analysis of plasma samples from patients undergoing therapy with sertraline.
The dynamic network subserving the three phases of cognitive procedural learning
Authors: Hubert Valérie , Beaunieux Hélène , Chételat Gaël , Platel Hervé , Landeau Brigitte , Danion Jean‐Marie , Viader Fausto , Desgranges Béatrice , Francis Eustache
Published: April 2007

Cognitive procedural learning is characterized by three phases (cognitive, associative, and autonomous), each involving distinct processes. We performed a behavioral study and a positron emission tomography (PET) activation study using the Tower of Toronto task. The aim of the behavioral study was to determine cognitive predictors for the length of each of the three learning phases, in order to preselect subjects for the PET study. The objective of the second study was to describe the cerebral substrates subtending these three phases. Contrasted with a reference (motor) task, the cognitive phase activated the prefrontal cortex, cerebellum, and parietal regions, all of which became less active as learning progressed. The associative phase was characterized by the activation of the occipital regions, right thalamus, and caudate nucleus. During the autonomous phase, new regions were involved, including the left thalamus and an anterior part of the cerebellum. These results, by employing a direct comparison between phases, provide the first evidence of the involvement and the time course of activation of different regions in each learning phase, in accordance with current models of cognitive procedural learning. The involvement of a frontoparietal network suggests the use of strategies in problem solving during the cognitive phase. The involvement of the occipital regions during the associative and autonomous phase suggests the intervention of mental imagery. Lastly, the activation of the cerebellum during the autonomous phase is consistent with the fact that performance in this phase is determined by psychomotor abilities. Hum Brain Mapp, 2007. © 2007 Wiley‐Liss, Inc.
Biphasic hemodynamic responses influence deactivation and may mask activation in block‐design fMRI paradigms
Authors: Meltzer Jed A. , Negishi Michiro , Constable R. Todd
Published: April 2007

A previous block‐design fMRI study revealed deactivation in the hippocampus in the transverse patterning task, specifically designed, on the basis of lesion literature, to engage hippocampal information processing. In the current study, a mixed block/event‐related design was used to determine the temporal nature of the signal change leading to the seemingly paradoxical deactivation. All positive activations in the hippocampal‐dependent condition, relative to a closely matched control task, were seen to result from positive BOLD transients in the typical 4–7 s poststimulus time range. However, most deactivations, including in the hippocampus and in other “default mode” regions commonly deactivated in cognitive tasks, were attributable to enhanced negative transient signals in a later time range, 10–12 s. This late hemodynamic transient was most pronounced in medial prefrontal cortex. In some regions, the hippocampal‐dependent condition enhanced both the early positive and late negative transients to approximately the same degree, resulting in no significant signal change when block analysis is used, despite very different event‐related responses. These results imply that delayed negative transients can play a role in determining the presence and sign of brain activation in block‐design studies, in which case an event‐related analysis can be more sensitive than a block analysis, even if the different conditions occur within blocks. In this case, default mode deactivations are timelocked to stimulus presentation as much as positive activations are, but in a later time range, suggesting a specific role of negative transient signals in task performance. Hum Brain Mapp, 2008. © 2007 Wiley‐Liss, Inc.
Study on heat transfer characteristics of reservoir embedded loop heat pipe (1st report, Influence of evaporator orientation against gravity and charged liquid weight on heat transfer characteristics)
Authors: Ishikawa Hiroaki , Ogushi Tetsuro , Nomura Takehide , Iwakami Takeshi , Noda Hiroyuki , Yabe Takahiro
Published: April 2007

High‐powered satellites need larger heat rejection areas. A deployable radiator is one of the key technologies for a high‐powered satellite bus. A Reservoir Embedded Loop Heat Pipe (RELHP) is a two‐phase heat transfer device that constitutes a deployable radiator. RELHP has an evaporator core which is used as a liquid reservoir to enhance operational reliability. This paper presents the heat transport characteristics of a RELHP under changing evaporator orientation against gravity and charged ammonia weight by experiment and calculation. Liquid slug position in the reservoir has a great influence on heat transport characteristics, caused by changing heat transfer coefficients between returned liquid into the evaporator and vapor in the reservoir. © 2007 Wiley Periodicals, Inc. Heat Trans Asian Res, 36(3): 143– 157, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20150
Fluid flow and heat transfer of opposing mixed convection adjacent to upward‐facing, inclined heated plates
Authors: Misumi Toshiyuki , Shigemaru Syogo , Kitamura Kenzo , Kamiya Kazunori
Published: April 2007

Opposing mixed convective flows of air induced over uniformly heated, upward‐facing, inclined plates were investigated experimentally. The experiments covered the ranges of the Reynolds and modified Rayleigh numbers, ReL=7.2×102 to 1×104 and RaL*=5×106 to 8×108, and the inclination angles from θ=15 to 75° from horizontal. The flow fields over plates were visualized with smoke. The results showed that a separation of forced boundary layer flow occurs first at the trailing edge, and then the separation point shifts toward upstream with increasing the wall heat flux, and finally, reaches to the leading edge of the plates. It was also found that the separations at the trailing and leading edges are correlated well with the non‐dimensional parameter as (Grθ*/ReL2.5)=0.35 and 1.0, respectively. The local heat transfer coefficients of the inclined plates were also measured and the results showed that the above separation retards the heat transfer significantly from that of the forced convection. It was also revealed that the heat transfer by forced, natural, and combined convections can be classified with the above parameter as (Grθ*/ReL2.5)<0.2,(Grθ*)/ReL2.5)>3, and 0.2<(Grθ*/ReL2.5)<3, respectively. © 2007 Wiley Periodicals, Inc. Heat Trans Asian Res, 36(3): 127– 142, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20151
Synergistic antitumor effects of celecoxib with 5‐fluorouracil depend on IFN‐γ
Authors: Irie Takanobu , Tsujii Masahiko , Tsuji Shingo , Yoshio Toshiyuki , Ishii Shuji , Shinzaki Shinichiro , Egawa Satoshi , Kakiuchi Yoshimi , Nishida Tsutomu , Yasumaru Masakazu , Iijima Hideki , Murata Hiroaki , Takehara Tetsuo , Kawano Sunao , Hayashi Norio
Published: April 2007

Cyclooxygenase‐2 (COX‐2) inhibitors are effective chemopreventive agents against colorectal cancers. For treatment of advanced cancers, combination of COX‐2 inhibitors and chemotherapy has been attempted, but the results are still controversial. In the present study, the effects of the COX‐2 inhibitor celecoxib on the anticancer potential of chemotherapy, and its mechanisms of action were investigated in point of the angiogenesis, using an advanced cancer model in mice. BALB/c mice were inoculated with colon 26 cells. After the allograft grew up to 5 mm in diameter, the animals received celecoxib, 5FU, or a combination of 5FU and celecoxib (5FU/celecoxib). After 21‐days of the treatment, 5FU/celecoxib significantly inhibited the tumor growth and the tumor vessel density compared with the other groups. Celecoxib, 5FU or 5FU/celecoxib significantly suppressed the VEGF content in tumor tissues. 5FU/celecoxib also enhanced IFN‐γ levels in tumor tissue, which could be involved in the potent antitumor effects of 5FU/celecoxib. This hypothesis was proven, because in IFN‐γ knockout (IFN‐γ−/−) mice, the inhibitory effects of 5FU/celecoxib on angiogenesis and tumor growth were significantly impaired compared with that in wild type mice. These results suggest that celecoxib enhances the antitumor effect of 5FU against an advanced colon cancer model by suppressing angiogenesis. In addition to VEGF, IFN‐γ has pivotal roles in tumor suppression induced by celecoxib. © 2007 Wiley‐Liss, Inc.
Gene expression profiling in melanoma identifies novel downstream effectors of p14ARF
Authors: Packer Leisl M. , Pavey Sandra J. , Boyle Glen M. , Stark Mitchell S. , Ayub Ana L. , Rizos Helen , Hayward Nicholas K.
Published: April 2007

p14ARF is inactivated by deletions/mutations in many cancer types and can suppress cell growth by both p53‐dependent and p53‐independent mechanisms. To identify novel downstream effectors of p14ARF, we used gene expression profiling as a primary screening tool to select candidates for follow up validation studies using in vitro cell‐based assays. Gene expression profiles of a panel of 35 melanoma cell lines with either wild‐type (n = 12) or mutant (n = 23) p14ARF were compared to identify genes associated with inactivation of p14ARF. Analysis of the microarray data identified 1,316 probe sets that were significantly (p < 0.01) differentially expressed between the p14ARF wild‐type and mutant cell lines. Pathway analysis of these genes showed an overrepresentation of many receptor‐mediated signal transduction pathways, e.g. TGFβ, EGF, HGF, PDGF, MAPK, Wnt and integrin pathways. A number of components of these pathways, including FLRT3, RUNX2, MIG‐6 and SMURF2 were confirmed as downstream targets of p14ARF using p14ARF‐inducible cell lines and RNAi. We propose that regulation of these genes may contribute to melanoma development when p14ARF function is lost. © 2007 Wiley‐Liss, Inc.
Risk factors for prostate cancer incidence and progression in the health professionals follow‐up study
Authors: Giovannucci Edward , Liu Yan , Platz Elizabeth A. , Stampfer Meir J. , Willett Walter C.
Published: April 2007

Risk factors for prostate cancer could differ for various sub‐groups, such as for “aggressive” and “non‐aggressive” cancers or by grade or stage. Determinants of mortality could differ from those for incidence. Using data from the Health Professionals Follow‐Up Study, we re‐examined 10 factors (cigarette smoking history, physical activity, BMI, family history of prostate cancer, race, height, total energy consumption, and intakes of calcium, tomato sauce and α‐linolenic acid) using multivariable Cox regression in relation to multiple subcategories for prostate cancer risk. These were factors that we previously found to be predictors of prostate cancer incidence or advanced prostate cancer in this cohort, and that have some support in the literature. In this analysis, only 4 factors had a clear statistically significant association with overall incident prostate cancer: African–American race, positive family history, higher tomato sauce intake (inversely) and α‐linolenic acid intake. In contrast, for fatal prostate cancer, recent smoking history, taller height, higher BMI, family history, and high intakes of total energy, calcium and α‐linolenic acid were associated with a statistically significant increased risk. Higher vigorous physical activity level was associated with lower risk. In relation to these risk factors, advanced stage at diagnosis was a good surrogate for fatal prostate cancer, but high‐grade (Gleason ≥ 7 or Gleason ≥ 8) was not. Only for high calcium intake was there a close correspondence for associations among high‐grade cancer, advanced and fatal prostate cancer. Tomato sauce (inversely) and α‐linolenic acid (positively) intakes were strong predictors of advanced cancer among those with low‐grade cancers at diagnosis. Although the proportion of advanced stage cancers was much lower after PSA screening began, risk factors for advanced stage prostate cancers were similar in the pre‐PSA and PSA era. The complexity of the clinical and pathologic manifestations of prostate cancer must be considered in the design and interpretation of studies. © 2007 Wiley‐Liss, Inc.
Nano finite element modeling of the mechanical behavior of biocomposites using multi‐scale (virtual internal bond) material models
Authors: Thiagarajan Ganesh , Deshmukh Kavita , Wang Yong , Misra A. , Katz J. Lawrence , Spencer Paulette
Published: April 2007

It is evident that biocomposites, specifically mineralized Type‐I collagen fibrils, have strong mechanical properties, such as a desirable combination of elastic modulus, fracture toughness, and fracture strength. The mineral Hydroxyapatite [Hap] by itself is stiffer, and it is not clear whether a collagen fiber by itself has a lower breaking strength than the mineralized fiber. Hence, the objective of this paper is to develop, outline, apply, and demonstrate issues involving a new nano explicit finite element based framework, by which the mechanical behavior of mineralized collagen fibrils and their constituents can be studied. A multi‐scale virtual internal bond model is used to model the material behavior and failure of such biocomposites. In this research two models have been studied. The first model attempts to illustrate the hypothesis that materials are less sensitive to flaws at nanoscale and the second model studies the mechanical behavior of a nano sized dahlite mineral crystal commonly found in collagen fibril. Two important implementation characteristics have been introduced and illustrated, namely that scaled properties can be used at the micro and nano length scales along with scaled dimensions and secondly the loading time can be appropriately scaled without the loading becoming a dynamic loading. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Biodegradable fibrous scaffolds composed of gelatin coated poly(ϵ‐caprolactone) prepared by coaxial electrospinning
Authors: Zhao Pengcheng , Jiang Hongliang , Pan Hui , Zhu Kangjie , Chen Weiliam
Published: April 2007

A facile coaxial electrospinning technique was devised to prepare biodegradable core‐shell fibrous scaffolds with poly(ϵ‐caprolactone) (PCL) comprising the core structure and gelatin forming the coating of the fibers. The effect of the feed rate of the inner dope on the electrospinning process and fiber morphology was investigated. The results indicated that core‐shell fibers with narrow size distribution and smooth surface morphology could be obtained when the feed rate was below 8 mL/h. An increase of the feed rate resulted in analogous increase in the diameters of both the inner PCL fiber core and the entire core‐shell fibers. XPS analyses revealed that the surface of the core‐shell fibers was tainted with a small amount of PCL. The outer gelatin layer in the core‐shell fibers was crosslinked with glutaraldehyde. By optimizing the glutaraldehyde/gelatin feed ratio, crosslinked scaffolds with high porosity were obtained. The mechanic strength of the hydrated, crosslinked core‐shell fibrous scaffolds was significantly enhanced because of the presence of hydrophobic PCL in the core region of the fibers. Results of cell culture studies suggested that the crosslinked, core‐shell fibrous scaffold were nontoxic and capable of supporting fibroblast adhesion and proliferation. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
In vitro biocompatibility of degradable biopolymers in cell line cultures from various ocular tissues: Direct contact studies
Authors: Huhtala A. , Pohjonen T. , Salminen L. , Salminen A. , Kaarniranta K. , Uusitalo H.
Published: April 2007

Synthetic biodegradable polymers have many potential therapeutic applications. In ophthalmology, biodegradable polymers have been used as viscoelastic agents and surgical implants. Other potential applications include controlled release of drugs and growth factors, gene therapy, and tissue engineering. In the present study, in vitro biocompatibility of three biodegradable polymers, 50:50 PDLGA, 85:15 PDLGA, and Inion GTR™ membrane was evaluated in comparison to tissue culture polystyrene by investigating cell proliferation and potential acute toxicity by the WST‐1 cytotoxicity/cell proliferation test, the ATP test, and the lactate dehydrogenase (LDH) test. Evaluations were conducted with cell line cultures from various ocular tissues, human corneal epithelial cells (HCE), rabbit stromal fibroblasts (SIRC), bovine corneal endothelial cells (BCE), human conjunctival epithelial cells (IOBA‐NHC), and human retinal pigment epithelial cells (ARPE‐19) by direct contact studies by plating the cells on the polymer film specimens in 96‐wells. The proliferation results show that cell lines from various ocular tissues attached and grew on PDLGA 50:50, PDLGA 85:15, and Inion GTR™ membrane. Cytotoxicity experiments with the LDH and ATP tests showed no or extremely slight toxic adverse effects. These polymers have potential to be used as scaffolds in cell transplantation devices or as surgical implants. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices
Authors: González‐Díaz Humberto , Pérez‐castillo Yunierkis , Podda Gianni , Uriarte Eugenio
Published: April 2007

In principle, there are different protein structural parameters that can be used in computational chemistry studies to classify protein mutants according to thermal stability including: sequence, connectivity, and 3D descriptors. Connectivity parameters (called topological indices, TIs) are simpler than 3D parameters being then less computationally expensive. However, TIs ignore important aspects of protein structure and hence are expected to be inaccurate. In any case, a comparison of 3D and TIs has not been reported with respect to the power of discrimination of proteins according to stability. In this study, we compare both classes of indices in this sense by the first time. The best model found, based on 3D spectral moments correctly classified 507 out of 525 (96.6%) proteins while TIs model correctly classified 404 out of 525 (77.0%) proteins. We have shown that, in fact, 3D descriptor models gave more accurate results than TIs but interestingly, TIs give acceptable results in a timely way in spite of their simplicity. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
NLOPredict: Visualization and data analysis software for nonlinear optics
Authors: Moad Andrew J. , Moad Charles W. , Perry John M. , Wampler Ronald D. , Goeken G. Scott , Begue Nathan J. , Shen Tian , Heiland Randy , Simpson Garth J.
Published: April 2007

A data analysis and visualization program was developed to assist in the interpretation of second‐order nonlinear optical (NLO) processes, including vibrational sum‐frequency generation and electronically resonant second harmonic generation. A novel diagrammatic approach allows concise visual representations of the resonant NLO molecular response. By mapping the predicted NLO response as a function of molecular orientation, molecular modeling results can be combined with experimental measurements for orientational analysis. A method is developed and implemented to predict the nonlinear optical properties of the amide backbones in complete proteins with known structures. NLOPredict is available for most computer operating systems from http://sda.iu.edu/nlopredict/. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Chiral discrimination via nuclear magnetic shielding polarisabilities from NMR spectroscopy: Theoretical study of (Ra)‐1,3‐dimethylallene, (2R)‐2‐methyloxirane, and (2R)‐N‐methyloxaziridine
Authors: Zanasi R. , Pelloni S. , Lazzeretti P.
Published: April 2007

Three medium‐size optically active molecules have been studied to make a guess at candidates suitable for chiral discrimination in an isotropic medium via nuclear magnetic resonance spectroscopy. The criterion for experimental detection is given by the magnitude of the isotropic part of nuclear magnetic shielding polarisability tensors, related to a pseudoscalar of opposite sign for the two enantiomers. The pseudoscalar shielding polarisability at the 17O nucleus in N‐methyloxaziridine, calculated at the Hartree‐Fock level, is ≈7.8 ×10−17 mV−1. To obtain an experimentally observable magnetic field induced at the 17O nucleus in N‐methyloxaziridine, electric fields as large as ≈107–108 Vm−1 should be applied to the probe. The molecular electric dipole moment induced by precession of the magnetic dipole of the 17O nucleus in a magnetic field of 10 T is, in absolute value, ≈8.8 × 10−42 Cm. The estimated rf‐voltage at a resonance circuit is ≈10 nV. Smaller values have been estimated for N, C, and H nuclei in 1,3‐dimethylallene and 2‐methyloxirane. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
A computational investigation on the sequential rearrangement mechanism of 2‐allyl‐2,4,5‐hexatrienaldehyde involving [1,5]‐hydrogen migration and 8π‐electrocyclization
Authors: Zhu Yuanqiang , Guo Yong , Zhang Lidong , Xie Daiqian
Published: April 2007

The sequential rearrangement reaction mechanism of the 2‐allyl‐2,4,5‐hexatrienaldehyde has been studied at the unrestricted Becke three‐parameter hybrid functional combined with Lee–Yang–Parr correlation functional (UB3LYP)/6‐31G**, Complete Active Space Self‐Consistent Field (CAS (8,8))/6‐31G**, Configuration Interaction with Single and Double Excitations (CISD)//UB3LYP/6‐31G** and the second‐order perturbation theory based on the CASSCF reference wave function (CASPT2)//CAS(8,8)/6‐31G** levels. Two pathways have been found to be involved for this reaction. The first pathway includes four processes of the rotation of the C3C4 single bond, the stepwise [2 + 2] cycloaddition, the [1,5]‐hydrogen migration, and the ring opening isomerization, while the second pathway undergoes only two processes of the [1,5]‐hydrogen migration and the 8π‐electrocyclization. The calculation results indicate that the second pathway is favorable, in good agreement with the recent experimental observation. The whole reaction is stepwise and strong exothermic. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Algorithm to evaluate rate constants for polyatomic chemical reactions. II. Applications
Authors: González Javier , Giménez Xavier , Bofill Josep Maria
Published: April 2007

A new implementation of the classical reaction path–Liouville algorithm, as developed by the authors in the preceding paper, is tested with several chemical reactions. It results in a simple algorithm, which may be used straightforwardly for the calculation of rate constants, as well as to extract dynamical information of the reactive process. Results for the rate constant have been compared to transition state calculations, confirming that it provides a new lower bound than traditional transition state estimates. In addition, the time‐dependence of the kinetic energy stored in vibrational modes has been studied, as a means of characterizing the importance of each normal mode inside the reaction mechanism. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Peptide reagent design based on physical and chemical properties of amino acid residues
Authors: Du Qi‐Shi , Huang Ri‐Bo , Wei Yu‐Tuo , Wang Cheng‐Hua , Chou Kuo‐Chen
Published: April 2007

It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so‐called AABPD (amino acid based‐peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three‐dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three‐dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C‐like proteinase and the affinity prediction for epitope‐peptides with Class I MHC molecules are studied by using the peptide reagent design strategy. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Genetic algorithm for the determination of binodal curves in ternary systems polymer–liquid(1)–liquid(2) and polymer(1)–polymer(2)–solvent
Authors: Milani G. , Milani F.
Published: April 2007

A simple genetic algorithm for the numerical evaluation of binodal curves in ternary systems polymer–liquid (1)–liquid (2) and polymer (1)–polymer (2)–solvent is presented. The technique exploits a specifically developed restarting technique based on a combined elitist and zooming strategy on the last population at each iteration. The objective function (fitness) is represented by the weighted sum of the squared differences of chemical potentials of the two phases of each component, obtained evaluating first derivatives of Gibbs free energy of the mixture with respect to the number of moles of the components. The method proposed (a) is numerically stable since it does not require the evaluation of first derivatives of the objective function and (b) can be applied in a wide range of cases changing the equation of state. Several comparisons with simplified iterative procedures presented in the past in the technical literature both for mixtures of two polymers with identical characteristics in a solvent and for mixtures of solvent–nonsolvent–polymer with solvent–polymer interaction parameter equal to zero are reported. Finally, a comparison between present results and the “alternating tangent approach” is reported for two technically meaningful binary systems, when a simplified PC‐SAFT equation of state is adopted. The comparisons show that reliable results can be obtained by means of the algorithm proposed and suggest that the procedure presented can be used for practical purposes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Prostacyclin inhibits endothelial cell XIAP ubiquitination and degradation
Authors: Liou Jun‐Yang , Matijevic‐Aleksic Nena , Lee Sang , Wu Kenneth K.
Published: April 2007

To understand the role of prostacyclin (PGI2) in protecting endothelial cells from apoptosis, we evaluated the effects of carbaprostacyclin (cPGI2) on H2O2‐induced human umbilical vein endothelial cell (HUVEC) apoptosis. cPGI2 suppressed H2O2‐induced annexin V‐positive cells in a concentration‐ and time‐dependent manner. Pre‐treatment of HUVEC with 50 µM cPGI2 for 4 h produced the maximal anti‐apoptotic effect. Authentic PGI2 generated by adenoviral transfer of PGI2 synthetic genes exerted a similar protective effect. cPGI2 inhibited Smac/DIABLO release from mitochondria, caspase 3 activation, focal adhesion protein degradation, and cell detachment. cPGI2 selectively protected X‐linked inhibitor of apoptosis protein (X‐linked IAP, XIAP) from H2O2‐induced ubiquitination, and preserved XIAP protein levels. PD‐98059 but not H‐89 abrogated the protective action of cPGI2. cPGI2 increased ERK phosphorylation which was blocked by PD‐98059. HUVEC stably transfected with dominant negative Ras abrogated XIAP preservation by cPGI2 while constitutive active Ras increased ERK phosphorylation and protected XIAP from degradation. Our results demonstrate for the first time that PGI2 inhibits XIAP ubiquitination and degradation via the Ras/MEK‐1/ERK signaling pathway. Preservation of XIAP proteins represents a key mechanism by which PGI2 protects endothelial cells from oxidant‐induced apoptosis. J. Cell. Physiol. 212:840–848, 2007. © 2007 Wiley‐Liss, Inc.