bluuebunny/crossref_metadata_2025 huggingface dataset:
A method of SCR improvement with a two‐dimensional weighted moving average filter
Authors: Kouya Satoshi , Miwa Susumu
Published: March 2003

There have been different methods to suppress radar clutter depending on its amplitude distribution. This paper describes a two‐dimensional weighted moving average filter and a two‐dimensional moving filter for clutter having a k‐distribution, both with weighted samples of a reflected signal from an illuminated surface. A genetic algorithm is used for the weighting, since its optimum value is obtained in a relatively short time. To simulate various field conditions, two kinds of data were used: data of reflected waves from objects in the green belt of an airport, and composite data of reflected waves from objects in clear weather (no clutter) and reflected waves from a field on a rainy day. The two‐dimensional weighted moving average improves the signal‐to‐clutter ratio significantly: by 0.5 to 2.3 dB compared with a two‐dimensional moving average without weighting; and by 0.9 to 3.7 dB compared with no averaging treatment. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(8): 58–67, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.1172
A transmission mode detector for OFDM systems
Authors: Nogami Hiroshi , Tsuruga Sadao , Morinaga Norihiko
Published: March 2003

Digital terrestrial TV broadcasting systems employing orthogonal frequency division multiplexing (OFDM), such as DVB‐T in Europe, accept more than one transmission mode in terms of the carrier spacing (or the effective symbol duration) and the guard interval. When the transmission mode is not uniquely fixed and previously unknown, a receiver set has to detect the transmission mode so as to demodulate the OFDM signal properly.

In this paper, we propose a detection scheme for the transmission mode, where the transmission mode can be detected for a relatively short observation time with no demodulation of the OFDM signal. The proposed technique uses the wide sense cyclostationarity of the OFDM signal, that is, the averaged product (correlation) of the OFDM signal and itself delayed by the time of the effective symbol duration is a periodical signal with a period of the transmission symbol duration. Then the proposed technique detects the transmission mode by discrimination of the period through what we will call the spectrum emphasis filters, which basically consist of IIR filters.

Computer simulation has been conducted to evaluate the detection performance of the proposed technique for the OFDM system which accepts eight transmission modes (1/4, 1/8, 1/16, and 1/32 guard intervals for both the 2k‐FFT and 8k‐FFT systems). The results show that the detection error rate of 1 × 10−2 or less is attained around the carrier‐to‐noise power ratio of 3 dB in the additive white Gaussian noise channel with the observation time being only four times the maximum transmission symbol duration among the eight modes. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 86(8): 79–94, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.1174
Subset threshold autoregression
Authors: So Mike K. P. , Chen Cathy W. S.
Published: March 2003

We develop in this paper an efficient way to select the best subset threshold autoregressive model. The proposed method uses a stochastic search idea. Differing from most conventional approaches, our method does not require us to fix the delay or the threshold parameters in advance. By adopting the Markov chain Monte Carlo techniques, we can identify the best subset model from a very large of number of possible models, and at the same time estimate the unknown parameters. A simulation experiment shows that the method is very effective. In its application to the US unemployment rate, the stochastic search method successfully selects lag one as the time delay and five best models from more than 4000 choices. Copyright © 2003 John Wiley & Sons, Ltd.
Strategic bias, herding behaviour and economic forecasts
Authors: Pons‐Novell Jordi
Published: March 2003

Professional forecasters can have other objectives as well as minimizing expected squared forecast errors. This paper studies whether the people or companies which make forecasts behave strategically with the aim of maximizing aspects such as publicity, salary or their prestige, or more generally to minimize some loss function; or whether, on the contrary, they make forecasts which resemble consensus forecasts (herding behaviour). This study also analyses whether, as forecasters gain more reputation and experience, they make more radical forecasts, that is, they deviate further from the consensus. For this the Livingston Survey is used, a panel of experts who make forecasts on the future evolution of the United States economy. Copyright © 2003 John Wiley & Sons, Ltd.
5‐AZA‐2′‐deoxycytidine (5‐AZA‐CdR): a demethylating agent affecting development and reproductive capacity
Authors: Cisneros F. Javier , Branch Stacy
Published: March 2003

The objective was to evaluate the effects of 5‐AZA‐2′‐deoxycytidine (5‐AZA‐CdR) on postnatal development and reproductive capacity. Pregnant mice were administered 1 mg kg−1 5‐AZA‐CdR at gestation day 10. The body weights of F1 control and treated (in uterine‐exposed) pups were recorded. To evaluate the reproductive capacity, 5‐AZA‐CdR F1 males and females were mated with control mice. The presence of plugs and the number of pregnancies were recorded. The 5‐AZA‐CdR F1 male mice were killed. Total body, testes and epididymis weights were recorded. Spermatid head counting, histological analyses and serum testosterone levels were performed. Body weights of 5‐AZA‐CdR F1 mice were statistically lower than controls (P < 0.01), with the females more strongly affected (P < 0.05). Male mating capacity appeared to be more adversely affected. Mating of 5‐AZA‐CdR F1 males with control females resulted in a lower pregnancy rate compared with control mating groups (P < 0.01). Gross testicular and epididymis weights were lower in 5‐AZA‐CdR F1 mice (P < 0.01). However, testicular and epididymis weights in these mice were higher than controls when correlated to body weight (P < 0.01). In 5‐AZA‐CdR F1 male mice, all measured reproductive parameters, including total number of spermatid heads per testis, are signiﬁcantly lower (P < 0.01) than the controls except for the number of spermatid heads per milligram of testis. Published in 2003 by John Wiley & Sons, Ltd.
Effects of ethylene glycol on the synthesis of ampicillin using immobilized penicillin G acylase
Authors: Wei Dong‐Zhi , Yang Liu
Published: March 2003

The effects of organic cosolvents on the synthesis of ampicillin from phenylglycine methyl ester (PGME) and 6‐amino penicillanic acid (6‐APA) using immobilized Bacillus megaterium penicillin G acylase have been examined. Several cosolvents were tested for their influence on the enzyme in terms of enzyme stability and hydrophobicity. Among the cosolvents tested, ethylene glycol was found to increase the yield of ampicillin by 39–50%. The effects of ethylene glycol on the pKa of PGME, the hydrolysis of ampicillin and PGME, and synthetase/amidase and esterase/amidase ratios were also studied. Experimental data indicated that ethylene glycol inhibited more the hydrolysis of the ampicillin than the hydrolysis of the PGME and the synthetase/amidase ratio varied from 0.2 to 0.88 when the concentration (v/v) of the cosolvent increased from 0 to 40%. The enhancement of the synthesis yield was mainly caused by the reduction in the hydrolysis of acyl donor (PGME) and product (ampicillin) in the water–cosolvent system.

© 2003 Society of Chemical Industry
Biodegradability of slaughterhouse wastewater with high blood content under anaerobic and aerobic conditions
Authors: Pozo Rodrigo del , Taş Didem Okutman , Dulkadiroğlu Hakan , Orhon Derin , Diez Victorino
Published: March 2003

In this work, the biodegradability of wastewater from a slaughterhouse located in Keşan, Turkey, was studied under aerobic and anaerobic conditions. A very high total COD content of 7230 mg dm−3 was found, due to an inefficient blood recovery system. Low BOD5/COD ratio, high organic nitrogen and soluble COD contents, were in accordance with a high blood content. A respirometry test for COD fractionation showed a very low readily biodegradable fraction (SS) of 2%, a rapidly hydrolysable fraction (SH) of 51%, a slowly hydrolysable fraction (XS) of 33% and an inert fraction of 6%. Kinetic analysis revealed that hydrolysis rates were much slower than these of domestic sewage. The results underlined the need for an anaerobic stage prior to aerobic treatment. Tests with an anaerobic batch reactor indicated efficient COD degradation, up to around 80% removal. Further anaerobic degradation of the remaining COD was much slower and resulted in the build up of inert COD compounds generated as part of the metabolic activities in the anaerobic reactor. Accordingly, it is suggested that an appropriate combination of anaerobic and aerobic reactors would have to limit anaerobic degradation to around 80% of the tCOD and an effluent concentration above 1000 mg dm−3, for the optimum operation of the following aerobic stage.

© 2003 Society of Chemical Industry
Valorisation of waste fractions from autohydrolysis of selected lignocellulosic materials
Authors: Garrote G , Cruz J M , Domínguez H , Parajó J C
Published: March 2003

Non‐isothermal processing of lignocellulosic materials in aqueous media (autohydrolysis reaction) under mild conditions leads to solutions containing valuable chemicals (oligosaccharides, sugars and acetic acid) and other, undesired, compounds (belonging to the extractive and acid‐soluble lignin fractions) which have to be removed in further purification treatments. Liquors obtained by non‐isothermal autohydrolysis of Eucalyptus globulus wood and corncobs under a variety of operational conditions were extracted with ethyl acetate in order to remove non‐saccharide components, and the suitability of the fraction dissolved in the organic phase was assayed for possible utilisation as an antioxidant. The yield and antioxidant activity of ethyl acetate extracts (measured by the α,α‐diphenyl‐β‐picrylhydrazyl (DPPH) radical scavenging capacity) showed a strong dependence on the autohydrolysis conditions. The antioxidant activity of extracts obtained under selected operational conditions compared well with synthetic antioxidants.

© 2003 Society of Chemical Industry
Thiol‐mediated degradation of DNA adsorbed on a colloidal gold surface
Authors: Mittal Shalu , Bushman Frederic , Orgel Leslie E
Published: March 2003

When [32P]‐labeled DNA is adsorbed on colloidal gold from a 130 mmol dm−3 solution of KH2PO4, it can subsequently be eluted with cold DNA without undergoing detectable degradation. Similarly, DNA can be incubated in solution in the presence or absence of colloidal gold with high concentrations of β‐mercaptoethanol or hexane‐1‐thiol without significant degradation. However, when adsorbed DNA is eluted from gold with solutions of one of the thiols, it is recovered as a mixture of mononucleotides and short oligomers. The extent of degradation increases with increasing concentration of the thiol and with increasing elution temperature. Our results emphasize that in designing protocols involving DNA adsorbed on gold surfaces, it is important to avoid allowing the DNA to come into contact with even moderate concentrations of thiols.

© 2003 Society of Chemical Industry
Kinetics of lipase‐catalysed interesterification of triolein and caprylic acid to produce structured lipids
Authors: Camacho Paez B , Robles Medina A , Camacho Rubio F , Esteban Cerdán L , Molina Grima E
Published: March 2003

The influence of the molar ratio caprylic acid/triolein, enzyme concentration and water content on the kinetics of the interesterification reaction of triolein (TO) and caprylic acid (CA) were studied. The enzyme used was the 1,3‐specific Rhizomucor miehei lipase. Data modelling was based on a simple scheme in which the acid was only incorporated in positions 1 and 3 of the glyceride backbone. In addition, it was assumed that positions 1 and 3 of the triglycerides were equivalent and that the events at position 1 did not depend on the nature of the fatty acid in position 3 and vice versa. Monoglycerides and diglycerides were not detected during the experiments. This was attributed to the low water content of the immobilised enzyme particles. The value of the equilibrium constant, K, for the exchange of caprylic and oleic acids was 2.7, which indicated that the incorporation of caprylic acid into triglycerides was favoured compared with the incorporation of oleic acid. Simple first order kinetics could describe the interesterification reaction. Using this model and the calculated equilibrium constant, the apparent kinetic constants were calculated. The model fitted all the experimental data except for the CA/TO molar ratios larger than 6. Moreover, the interesterification reaction rate had a maximum value at CA/TO molar ratios of 4–6 mol mol−1.

Copyright © 2003 Society of Chemical Industry
Highly suppressible expression of single‐chain interleukin‐12 by doxycycline following adenoviral infection with a single‐vector Tet‐regulatory system
Authors: Block Andreas , Puls Florian , Müller Jürgen , Milasinovic Dragan , Igelmann Dana , Schäfer Peter , Kupfermann Nikolai , Schmoldt Achim , Ameis Detlev , Greten Heiner
Published: March 2003

Background

Adenoviral vectors have been shown to efficiently transfer DNA into a wide variety of eukaryotic cells in vitro and in vivo. However, the therapeutic benefit of this approach is limited by severe side effects as a result of uncontrolled transgene expression.

Methods

A bi‐directional promoter that controls the desired transgene as well as a tetracycline‐suppressible transactivator (tTA) was cloned into the E1‐region of E1‐deleted recombinant adenoviral vectors. Autoregulation within this construct was obtained by tTA expression under control of the operator, to which tTA binds in the absence of tetracycline. Consequently, binding of tetracycline to tTA results in downregulation of tTA as well as the co‐expressed transgene in the infected cell.

Results

We were able to suppress luciferase‐reporter gene expression by up to 16 000‐fold in the presence of doxycycline (dox, 2 µg/ml). Under control of this tetracycline‐regulated system, single‐chain interleukin‐12 (scIL12) was expressed. Adenovirally mediated expression of this potentially lethal cytokine with strong activation of antitumoral immune response was downregulated by up to 6000‐fold in the presence of dox. Subsequently, this downregulation also resulted in a highly significant reduction of interferon‐γ secretion by stimulated splenocytes. These mainly contribute to the toxicity of this immunotherapeutic approach.

Conclusions

With expression levels exceeding those of the cytomegalovirus (CMV) promoter in almost all cell lines tested, these new vectors will also contribute to the safety of adenoviral approaches by controlled expression without compromising on maximum expression levels. Copyright © 2002 John Wiley & Sons, Ltd.
Genotyping single nucleotide polymorphisms by mass spectrometry
Authors: Tost Jörg , Gut Ivo G.
Published: March 2003

I.
Introduction
389

A. A Brief History of DNA Analysis by Mass Spectrometry
389

B. What Exactly Are SNPs
390

C. Why Use MALDI for DNA Analysis?
391

II.
Methods for Allele‐Discrimination
391

A. Hybridization
391

B. Oligonucleotide Ligation
394

C. Cleavage
394

D. Primer Extension
395

   1. Purification Procedures and Sample Preparation
395

   2. The PinPoint Assay
396

   3. The PROBE Assay
398

   4. The VSET Assay
398

   5. The GenoLINK and GenoSNIP Assay
400

   6. The GOOD Assay
400

E. High‐Throughput SNP Genotyping by Mass Spectrometry
401

F. Other Applications
403

   1. Quantitation
403

   2. Haplotyping
404

   3. Epigenotyping
404

   4. Analysis of Larger DNA Segments/Complete PCR Products
405

III.
Strategies for the Discovery of Unknown Mutations
406

A. Sequencing by Mass Spectrometry
406

B. Transcription into RNA
407

C. Base‐Specific Fragmentation of Amplified DNA
408

IV.
ESI for DNA Analysis
409

A. Whole PCR Products
409

B. Liquid Chromatography‐ESI
409

C. Cleavage
410

D. The Survivor Assay
410

 V.
Use of Other Kinds of Mass Spectrometers for DNA Analysis
410

VI.
Conclusions
411

Acknowledgments
411

Abbreviations
411

References
412

In the last decade, the demand for high‐throughput DNA analysis methods has dramatically increased, mainly due to the advent of the human genome sequencing project that is now nearing completion. Even though mass spectrometry did not contribute to that project, it is clear that it will have an important role in the post‐genome sequencing era, in genomics and proteomics. In genomics, mainly matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry will contribute to large‐scale single nucleotide polymorphism (SNP) genotyping projects. Here, the development and history of DNA analysis by mass spectrometry is reviewed and put into the context with the requirements of genomics. All major contributions to the field and their status and limitations are described in detail. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:388–418, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.1009
p53 is a regulator of the metastasis suppressor gene Nm23‐H1
Authors: Chen Shen‐Liang , Wu Yi‐Shin , Shieh Hsin‐Ying , Yen Chun‐Che , Shen Jiann‐Jong , Lin Kwang‐Huei
Published: March 2003

p53, a tumor suppressor gene involved in the G1 cell cycle checkpoint, is also the most frequently mutated gene in human cancer. In addition, p53 modifies the ability of tumor cells to metastasize. The metastasis‐associated gene Nm23‐H1, which encodes an 18‐kDa nucleoside diphosphate kinase, was previously identified in cells with low metastatic potential. Although p53 and Nm23‐H1 proteins play an important part in regulating the progression of cancer, any functional relationship between these two proteins is currently unknown. Here we report an association between p53 levels and expression of the Nm23‐H1 gene. Our data indicate that wild‐type (wt) p53 upregulated the expression of Nm23‐H1 at protein and mRNA levels in MCF‐7 and J7B cells. This capacity of wt p53 to regulate expression of Nm23‐H1 was not only dependent on the endogenous but also the exogenous origin of p53, and could not be reproduced with mutant p53. Subsequently, the invasive ability of MCF‐7 and J7B cells was suppressed upon induction of the Nm23‐H1 protein by p53. In contrast, increased levels of p53 downregulated the expression of Nm23‐H1 at the protein and mRNA levels in RKO and H1299 cells and, as a consequence, increased the invasive ability of both cell types. Thus, our results implicated the differential regulation of Nm23‐H1 by p53 in different cell types as an important component in the molecular mechanisms of tumor metastasis. © 2003 Wiley‐Liss, Inc.
Skin tumor–promoting potential and systemic effects of pentachlorophenol and its major metabolite tetrachlorohydroquinone in CD‐1 Mice
Authors: Chang Wen‐Ching , Jeng Jiiang‐Huei , Shieh Chi‐Chang , Tsai Yi‐Chang , Ho Yuan‐Soon , Guo How‐Ran , Liu Hsin‐I , Lee Ching‐Chang , Ho Sheng‐Yow , Wang Ying‐Jan
Published: March 2003

The mouse skin carcinogenesis model provides a conceptual framework to study the carcinogenesis process. It has been used extensively to assess whether a chemical or physical agent carries a carcinogenic hazard to humans and to define the mechanism involved with the carcinogenic effects. We conducted a study to evaluate whether the tumor‐promoting activity of pentachlorophenol (PCP) is mainly from its major metabolite tetrachlorohydroquinone (TCHQ). We applied the mouse skin model to CD‐1 mice and the results showed that PCP and TCHQ are much weaker promoters than 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA) in mouse skin during a 25‐wk experiment. Both PCP and TCHQ could induce mice skin epidermal hyperplasia and proliferating cell nuclear antigen (PCNA) labeling index in the epidermis. However, TCHQ caused a more significant induction of epidermal hyperplasia and PCNA positive cells than PCP. Topical application of PCP, but not TCHQ, induced significant organ enlargement and lymphoma in mice, whereas short‐term treatment of TCHQ increased tumor necrosis factor‐α (TNF‐α) gene expression in mouse skin. We did not observe a significant association between the carcinogenic process and serum TNF‐α or interleukin‐1β (IL‐1β) levels in mice. © 2003 Wiley‐Liss, Inc.
Alsterpaullone, a novel cyclin‐dependent kinase inhibitor, induces apoptosis by activation of caspase‐9 due to perturbation in mitochondrial membrane potential
Authors: Lahusen Tyler , De Siervi Adriana , Kunick Conrad , Senderowicz Adrian M.
Published: March 2003

The majority of human neoplasms have aberrations in the retinoblastoma pathway due to hyperactivation of cyclin‐dependent kinases (CDK). Based on this observation, novel small molecules, such as flavopiridol and UCN‐01, are being developed and are currently being tested in the clinic. Efforts to develop CDK modulators led us to the discovery of a novel class of CDK inhibitors, the paullones [Cancer Res 1999;59:2566]. Initial studies demonstrated that paullones inhibit CDKs in vitro, thereby blocking cell‐cycle progression. However, the exact mechanism for the antiproliferative effects of paullones was never explored. In this report, we demonstrate for the first time that the most potent paullone, alsterpaullone (Alp), induced apoptosis and promoted loss in clonogenicity in the Jurkat cell line. Alp caused early activation of both caspase‐8 and ‐9, leading to cleavage of caspase‐3 and poly(ADP‐ribose) polymerase (PARP). Moreover, apoptosis by Alp was not associated with loss in anti‐apoptotic proteins such as XIAP or BCL‐XL. Pre‐incubation with cell‐permeable inhibitors z‐Asp(OMe)‐Glu(OMe)‐Val‐Asp(Ome)‐fluoromethylketone and benzyloxycarbonyl‐Val‐Ala‐Asp (OMe)‐fluoromethylketone (ZVAD) blocked Alp‐induced apoptosis. Moreover, the general caspase inhibitor ZVAD blocked the cleavage and activation of most caspases tested except caspase‐9. Studies of mitochondrial membrane potential also demonstrated that Alp is able to disrupt mitochondrial potential in the presence of ZVAD, suggesting that the activation of caspase‐9 by Alp follows mitochondrial perturbation. Pre‐incubation of Jurkat cells with ZVAD did not prevent the depletion of cyclin D3, loss of CDK, or cell‐cycle arrest by Alp. In summary, these experiments suggest that Alp activates caspase‐9 via mitochondrial perturbation. Active caspase‐9 cleaves and activates caspase‐8 and caspase‐3, leading to apoptosis. In the presence of the general caspase inhibitor ZVAD, the cell‐cycle effects of Alp are unaltered while apoptosis is blocked, suggesting that the CDK effects of Alp are not sufficient for Alp‐induced apoptosis. Additional studies with paullones are warranted to further characterize their preclinical effects and to explore their potential use in the clinical setting. Published 2003 Wiley‐Liss, Inc.
High‐speed countercurrent chromatography as a valuable tool to isolate C‐glycosylflavones from Cecropia lyratiloba Miquel.
Authors: Oliveira R. R. , Moraes M. C. C. , Castilho R. O. , Valente A. P. , Carauta J. P. P. , Lopes D. , Kaplan M. A. C.
Published: March 2003

A new apigeninglycoside, apigenin 6‐C‐galactosyl‐6″‐O‐β‐galactopyranoside (1), isoorientin, and a mixture of orientin and isovitexin were isolated from leaves of Cecropia lyratiloba by high‐speed countercurrent chromatography using a solvent system containing ethyl acetate, butanol, methanol and water. The structural elucidation of 1 was based on NMR spectroscopy. Copyright © 2003 John Wiley & Sons, Ltd.
Investigation of the reaction of magnesium with p‐Nitro‐o‐carboxylazochromotropic acid and the determination of magnesium in plants and in water
Authors: Gao Hong‐Wen , Yang Jia‐Xiang , Zhou Zhong‐Ze , Zhao Jian‐Fu
Published: March 2003

The formation of a novel complex between magnesium and p‐nitro‐o‐carboxylazochromotropic acid (NCBAC) has been observed which is sensitive and selective at pH 10.4 in the presence of ethylenediamine and fluoride. The constants of formation of this complex have been determined by a spectral correction technique, and the complexation reaction has been applied to the spectrophotometric determination of trace magnesium in plants and in water with satisfactory results. Copyright © 2003 John Wiley & Sons, Ltd.
Complexation of tetrapropoxycalix[4]arene with uracil and adenine derivatives in water‐containing solution
Authors: Kalchenko Olga , Poznański Jarek , Marcinowicz Agnieszka , Cherenok Sergey , Solovyov Andrew , Zielenkiewicz Wojciech , Kalchenko Vitaly
Published: March 2003

The host–guest complexation of tetrapropoxycalix[4]arene with uracil, 5‐amino‐, 5‐methyl‐, 5‐ethyl‐, 5‐chloro‐, 5‐nitro‐, 6‐methyl‐, 1,3‐dimethyl‐, 6‐amino‐1‐methyl‐ and 6‐amino‐1,3‐dimethyluracil, adenine and 9‐methyladenine in methanol–acetonitrile–tetrahydrofuran–water (15:10:5:70, v/v) solution was investigated by reversed‐phase high‐performance liquid chromatography. The association constants of the 1:1 host–guest complexes of the guests with the calixarene host within the range 3250–54300 M
−1 were determined from the capacity factor of the guest and concentration of the calixarene host in the mobile phase. Molecular dynamic (MD) simulation of the host–guest interaction was performed. Basing on the MD trajectories atomic partition to the net molecular solvent‐exposed surface was analyzed for the separated guest and host molecules and for the complex. Copyright © 2003 John Wiley & Sons, Ltd.
An analysis of bifurcated H‐bonds: crystal and molecular structures of O,O‐diphenyl 1‐(3‐phenylthioureido)­pentanephosphonate and O,O‐diphenyl 1‐(3‐phenylthioureido)butanephosphonate
Authors: Chęcińska Lilianna , Grabowski Sławomir J. , Małecka Magdalena
Published: March 2003

In the crystal structures of O,O‐diphenyl 1‐(3‐phenylthioureido)pentanephosphonate (1) and O,O‐diphenyl 1‐(3‐phenylthioureido)butanephosphonate (2) analysed here, bifurcated H‐bonds within R21(6) motifs are formed. It seems that such interactions play a crucial role in the crystal architecture. This is supported by ab initio MP2/6–311 ++ G** calculations on simple, modelled complexes of urea, thiourea and their derivatives with water, where the oxygen atom of water molecule is the bifurcated proton‐accepting centre. The calculations show that single H‐bonds within bifurcated systems are of medium strength (2.7–3.6 kcal mol−1). The topological parameters obtained from the Bader theory are applied for the analysis of these bifurcated H‐bonds. Copyright © 2003 John Wiley & Sons, Ltd.
Neural networks as data mining tools in drug design
Authors: Gasteiger Johann , Teckentrup Andreas , Terfloth Lothar , Spycher Simon
Published: March 2003

Neural networks are powerful data mining tools with a wide range of applications in drug design. This paper largely concentrates on self‐organizing neural networks that can be used for investigating datasets both by unsupervised and by supervised learning. The representation of chemical structures is the key to success in establishing useful relationships. Applications are shown for exploring different structure representations, for establishing quantitative structure–activity relationships and for handling compounds having multicategory activities. The applications comprise the separation of compounds according to different biological activities, the location of biologically active compounds in large chemical spaces, the analysis of high‐throughput screening data and the classification of compounds according to mode of toxic action. Copyright © 2003 John Wiley & Sons, Ltd.
Synthesis and UV/Vis spectroscopic properties of new [2‐(N,N‐dialkylamino)‐1,3‐dithiolium‐4‐yl]phenolates
Authors: Birsa Mihail Lucian , Ganju Dumitru
Published: March 2003

In weak alkaline aqueous medium, 4‐(hydroxyphenyl)‐2‐(N,N‐dialkylamino)‐1,3‐dithiolium salts led to the corresponding dipolar betaines. These compounds were described as zwitterionic phenolates with an intramolecular charge‐transfer UV/Vis absorption and represent useful precursors for the preparation of the first 1,3‐dithiolium chlorides. Copyright © 2003 John Wiley & Sons, Ltd.
Effect of carbonyls on the reactivity of polyenes in autoxidation
Authors: Krasnokutskaya I. S. , Leontieva S. V. , Finkelshtein E. I. , Khodonov A. A. , Shvets V. I.
Published: March 2003

Autoxidation of the biologically active polyenes β‐carotene, canthaxanthin, retinyl acetate, methyl retinoate, retinal and 3,7,11,11‐tetramethyl‐10,15‐dioxo‐2,4,6,8‐hexadecatetraenal (diketoretinal) in solid amorphous films was investigated. The course of the process was followed by electronic and IR spectroscopy. The overall activation energies were obtained. It was shown that insertion in the polyene molecule of a carbonyl group conjugated with polyene chain results in a drastic decrease in the reactivity towards molecular oxygen. The results are discussed and explained on the basis of radical stabilization energy, ES(R·), as a driving force of the autoxidation process. Semi‐empirical AM1 calculations of ΔHf of some retinyl polyenes and polyenyl radicals were carried out and the C—H bond strengths and ES(R·) values of corresponding polyenyl radicals were evaluated. It was shown that the incorporation of a carbonyl group in the polyene results in a decrease in the overall autoxidation rate due to the decrease in both the initiation and propagation rates. Copyright © 2003 John Wiley & Sons, Ltd.
Competing nature of intramolecular [4 + 2] and [3 + 2] cycloaddition reactions: a theoretical study
Authors: Ananikov Valentine P.
Published: March 2003

Comparative study of the intramolecular alkyne triple bond addition reaction to the conjugated ­C≡C—CHX moiety (X = CH2,O,S,NH) revealed that two different pathways are possible in the system, namely [4 + 2] and [3 + 2] cycloaddition reactions. The energetically preferred pathway for enynes (X = CH2) involves [4 + 2] cycloaddition leading to benzene derivatives, whereas heteroatom‐substituted substrates undergo [3 + 2] cycloaddition resulting in an five‐membered aromatic ring in the final product. This paper reports a detailed mechanistic study based on full potential energy surface calculations at the MP2 and B3LYP theory levels, with MP4(SDTQ) energy evaluation. The effect of solvent was included within the PCM approach. Copyright © 2003 John Wiley & Sons, Ltd.
Three power‐aware routing algorithms for sensor networks
Authors: Aslam Javed , Li Qun , Rus Daniela
Published: March 2003

This paper discusses online power‐aware routing in large wireless ad hoc networks (especially sensor networks) for applications in which the message sequence is not known. We seek to optimize the lifetime of the network. We show that online power‐aware routing does not have a constant competitive ratio to the off‐line optimal algorithm. We develop an approximation algorithm calledmax–minzPminthat has a good empirical competitive ratio. To ensure scalability, we introduce a second online algorithm for power‐aware routing. This hierarchical algorithm is called zone‐based routing. Our experiments show that its performance is quite good. Finally, we describe a distributed version of this algorithm that does not depend on any centralization. Copyright © 2003 John Wiley & Sons, Ltd.
Media access using dynamic bandwidth system to improve satellite network uplink performance
Authors: Foudriat Edwin C. , Maly Kurt J. , Olariu Stephan , Todorova Petia
Published: March 2003

The paper describes a media access system for satellite network uplinks. The media access protocol is designed to support a range of low‐level protocols using a dual‐framing system, that is, there is a synchronous traffic subframe in which registered station requests are assigned fixed blocks or slots and an asynchronous traffic subframe for unregistered station random access on a contention basis. Slots for the registered stations are assigned through request to the satellite; the remaining frame time is assigned to unregistered stations. Capacity waste through contention resulting in collisions is minimized. The system uses dynamic bandwidth (bit rate) allocation for each channel, that is, the base frequency and bandwidth are changed for each channel at frame boundaries. The total bandwidth for the sum of all uplink channels is fixed. Channels that have low load based upon their request in a prior uplink frame are assigned lower bandwidth, while those with higher loading are provided larger bandwidth. By sharing bandwidth over channels at frame boundaries, overall network efficiency and fairness are significantly enhanced. Bandwidth allocation is decided in the satellite. It allocates sufficient bandwidth for all synchronous traffic and then commits the remaining bandwidth to asynchronous traffic. Here, the allocation for asynchronous traffic provides each channel with sufficient slots so that equal probability of success for stations sharing the channel can be expected. The combination of traffic assignment and bandwidth allocation provides significant improvement in overall network efficiency and fairness for all traffic types. The hardware implementation of media access for variable bandwidth sharing between channels use the concepts of Digital Software Radio. Copyright © 2003 John Wiley & Sons, Ltd.
Spectroimmunochemistry Using Colloidal Gold Bioconjugates
Authors: Kamnev Alexander A. , Dykman Lev A. , Tarantilis Petros A. , Polissiou Moschos G.
Published: March 2003

Using surface-enhanced infrared absorption (SEIRA) spectroscopy of dry films of colloidal gold (CG) bioconjugates with protein A, it is shown that certain characteristic bands of the protein (e.g., amide I, amide II and some other vibration modes) are essentially affected by the metal surface. Thus, the method may be used for controlling the quality of such bioconjugates. Moreover, it is demonstrated that the biospecific reaction of protein A attached to CG particles with human immunoglobulin G (IgG) results in further essential changes in SEIRA spectra, providing a means for an easy and rapid IR spectroscopic detection of biospecific immunochemical interactions (i.e., spectroimmunochemistry). The results obtained can form a basis for developing test systems for detecting various biospecific interactions.
An Ecologically Differentiated, Multifactor Model of Adolescent Network Orientation
Authors: Barone Charles , Iscoe Ellen , Trickett Edison J. , Schmid Kathy D.
Published: March 2003

The paper presents a test of an ecologically differentiated model of social network orientation for adolescents that distinguished between different social network reference groups (family, peers, and nonfamily adults). The model was tested in two consecutive studies. Study 1 describes initial model development (N = 120). Study 2 presents a confirmatory factor analysis with a second sample (N = 430) to replicate the factor structure developed in Study 1. Results supported a three‐factor model of network orientation that differentiated between network reference groups. Analyses of concurrent and predictive validity indicated that orientation to network reference groups was differentially related to the perceived quality and frequency of support from members of respective social network groups. Group differences (gender, race) regarding network orientation to different network reference groups were consistent with studies of other social network processes. Implications for the study of the network orientation and the study of social networks more generally are discussed.
Biochemical and genetic characterization of a novel enzyme of pentitol metabolism: d-arabitol-phosphate dehydrogenase
Authors: POVELAINEN Mira , ENEYSKAYA Elena V. , KULMINSKAYA Anna A. , IVANEN Dina R. , KALKKINEN Nisse , NEUSTROEV Kirill N. , MIASNIKOV Andrei N.
Published: March 2003

An enzyme with a specificity that has not been described previously, d-arabitol-phosphate dehydrogenase (APDH), has been purified from cell lysate of Enterococcus avium. SDS/PAGE indicated that the enzyme had a molecular mass of 41±2kDa, whereas a molecular mass of 160±5kDa was observed under non-denaturing conditions, implying that the APDH may exist as a tetramer with identical subunits. Purified APDH was found to have a narrow substrate specificity, converting only d-arabitol 1-phosphate and d-arabitol 5-phosphate into xylulose 5-phosphate and ribulose 5-phosphate, respectively, in the oxidative reaction. Both NAD+ and NADP+ were accepted as cofactors. Based on the partial protein sequences, the APDH gene was cloned. Homology comparisons place APDH within the medium-range dehydrogenase family. Unlike most members of this family, APDH requires Mn2+ but no Zn2+ for enzymic activity. The DNA sequence surrounding the gene suggests that it belongs to an operon that also contains several components of phosphotransferase system. Both biochemical evidence and protein sequence homology comparisons indicate that similar enzymes are widespread among the Gram-positive bacteria. Their apparent biological role is to participate in arabitol catabolism via the ‘arabitol phosphate route’, similar to the ribitol and xylitol catabolic routes described previously.
Mutations of penicillin acylase residue B71 extend substrate specificity by decreasing steric constraints for substrate binding
Authors: MORILLAS Manuel , McVEY Colin E. , BRANNIGAN James A. , LADURNER Andreas G. , FORNEY Larry J. , VIRDEN Richard
Published: March 2003

Two mutant forms of penicillin acylase from Escherichia coli strains, selected using directed evolution for the ability to use glutaryl-l-leucine for growth [Forney, Wong and Ferber (1989) Appl. Environ. Microbiol. 55, 2550—2555], are changed within one codon, replacing the B-chain residue PheB71 with either Cys or Leu. Increases of up to a factor of ten in kcat/Km values for substrates possessing a phenylacetyl leaving group are consistent with a decrease in Ks. Values of kcat/Km for glutaryl-l-leucine are increased at least 100-fold. A decrease in kcat/Km for the CysB71 mutant with increased pH is consistent with binding of the uncharged glutaryl group. The mutant proteins are more resistant to urea denaturation monitored by protein fluorescence, to inactivation in the presence of substrate either in the presence of urea or at high pH, and to heat inactivation. The crystal structure of the LeuB71 mutant protein, solved to 2Å resolution, shows a flip of the side chain of PheB256 into the periphery of the catalytic centre, associated with loss of the π-stacking interactions between PheB256 and PheB71. Molecular modelling demonstrates that glutaryl-l-leucine may bind with the uncharged glutaryl group in the S1 subsite of either the wild-type or the LeuB71 mutant but with greater potential freedom of rotation of the substrate leucine moiety in the complex with the mutant protein. This implies a smaller decrease in the conformational entropy of the substrate on binding to the mutant proteins and consequently greater catalytic activity.
Chronic activation of extracellular-signal-regulated protein kinases by phenylephrine is required to elicit a hypertrophic response in cardiac myocytes
Authors: BARRON Anthony J. , FINN Stephen G. , FULLER Stephen J.
Published: March 2003

Extracellular-signal-regulated protein kinases (ERKs) are activated rapidly and transiently in response to phenylephrine (PE) and endothelin-1 (ET-1) in cardiac myocytes, but whether this is linked to the subsequent development of the hypertrophic phenotype remains equivocal. To investigate this, we examined the dependence of the hypertrophic response on the length of exposure to PE in neonatal myocyte cultures. In addition to the initial transient activation of ERKs (maximum at 5—10min), PE (10μM) induced a second, more prolonged peak of activity several hours later. The activity of a transfected atrial natriuretic factor—luciferase reporter gene was increased 10- to 24-fold by PE. This response was inhibited by the α1-antagonist prazosin (100nM) and by U0126 (10μM) and PD184352 (1μM), inhibitors of ERK activation, irrespective of whether these were added before or up to 24h after the addition of PE. Prazosin had no effect on ET-1 (50nM)-stimulated atrial natriuretic factor—luciferase activity. Protein synthesis was enhanced by 35±6% by PE, and this was blocked by prazosin added 1h after the addition of PE, but decreased only by half when added 8h after PE. Similarly, PE (48h) increased myocyte area by 49% and this was prevented by prazosin added 1h after PE, but decreased only by half when added at 24h. These results demonstrate that prolonged exposure to PE is required to elicit alterations in gene expression, protein synthesis and cell size, characteristic of hypertrophied myocytes, and they confirm that the initial peak of ERK activity is insufficient to trigger hypertrophic responses.
pKa measurements from nuclear magnetic resonance of tyrosine-150 in class C beta-lactamase
Authors: KATO-TOMA Yoko , IWASHITA Takashi , MASUDA Katsuyoshi , OYAMA Yoshiaki , ISHIGURO Masaji
Published: March 2003

13C-NMR spectroscopy was used to estimate the pKa values for the Tyr150 (Y150) residue in wild-type and mutant class C β-lactamases. The tyrosine residues of the wild-type and mutant lactamases were replaced with 13C-labelled l-tyrosine ([phenol-4-13C]tyrosine) in order to observe the tyrosine residues selectively. Spectra of the wild-type and K67C mutant (Lys67→Cys) enzyme were compared with the Y150C mutant lactamase spectra to identify the signal originating from Tyr150. Titration experiments showed that the chemical shift of the Tyr150 resonance in the wild-type enzyme is almost invariant in a range of 0.1p.p.m. up to pH11 and showed that the pKa of this residue is well above 11 in the substrate-free form. According to solvent accessibility calculations on X-ray-derived structures, the phenolic oxygen of Tyr150, which is near the amino groups of Lys315 and Lys67, appears to have low solvent accessibility. These results suggest that, in the native enzyme, Tyr150 in class C β-lactamase of Citrobacter freundii GN346 is protonated and that when Tyr150 loses a proton, a proton from Lys67 would replace it. Consequently, Tyr150 would be protonated during the entire titration.
Converging signals synergistically activate the LAMC2 promoter and lead to accumulation of the laminin gamma2 chain in human colon carcinoma cells
Authors: OLSEN J⊘rgen , KIRKEBY Lene T. , BRORSSON Marianne M. , DABELSTEEN Sally , TROELSEN Jesper T. , BORDOY Randi , FENGER Kirsten , LARSSON Lars-Inge , SIMON-ASSMANN Patricia
Published: March 2003

The trimeric extracellular matrix molecule laminin-5 and its constituent chains (α3, β3, γ2) are normally not detectable intracellularly in intestinal epithelial cells but the laminin γ2 chain can be detected in cancer cells at the invasive front of a subset of colon carcinomas. These cells are subjected to cytokines such as transforming growth factor β1 (TGF-β1) and hepatocyte growth factor (HGF), produced by the tumour cells or by the surrounding stromal cells. The purpose of the present work was to investigate whether TGF-β1 and HGF, known to stimulate the LAMC2 gene encoding the laminin γ2 chain, might synergize to activate the LAMC2 promoter, and to identify the promoter elements involved. We find evidence for synergy between TGF-β and HGF with respect to laminin γ2 chain expression and promoter activation and demonstrate that this requires the 5′ activator protein-1 (AP-1) element of the promoter and an additional upstream element which is also responsive to co-expression of the Smad3 protein from the TGF-β signalling pathway. The transcripts encoding the other laminin-5 chains are not synergistically activated by HGF and TGF-β. Thus the synergistic activation of the LAMC2 gene is mediated via different cis-elements and results in an overproduction of the laminin γ2 chain relative to the other laminin-5 constituent chains. This difference may explain why laminin γ2 chains accumulate in the cells at the invasive front of colon carcinomas.
Identification and cloning of two isoforms of human high-temperature requirement factor A3 (HtrA3), characterization of its genomic structure and comparison of its tissue distribution with HtrA1 and HtrA2
Authors: NIE Gui-Ying , HAMPTON Anne , LI Ying , FINDLAY Jock K. , SALAMONSEN Lois A.
Published: March 2003

In the present study, we identified an additional member of the human high-temperature requirement factor A (HtrA) protein family, called pregnancy-related serine protease or HtrA3, which was most highly expressed in the heart and placenta. We cloned the full-length sequences of two forms (long and short) of human HtrA3 mRNA, located the gene on chromosome 4p16.1, determined its genomic structure and revealed how the two mRNA variants are produced through alternative splicing. The alternative splicing was also verified by Northern blotting. Four distinct domains were found for the long form HtrA3 protein: (i) an insulin/insulin-like growth factor binding domain, (ii) a Kazal-type S protease-inhibitor domain, (iii) a trypsin protease domain and (iv) a PDZ domain. The short form is identical to the long form except it lacks the PDZ domain. Comparison of all members of human HtrA proteins, including their isoforms, suggests that both isoforms of HtrA3 represent active serine proteases, that they may have different substrate specificities and that HtrA3 may have similar functions to HtrA1. All three HtrA family members showed very different mRNA-expression patterns in 76 human tissues, indicating a specific function for each. Interestingly, both HtrA1 and HtrA3 are highly expressed in the placenta. Identification of the tissue-specific function of each HtrA family member is clearly of importance.
A newly established in vitro culture using transgenic Drosophila reveals functional coupling between the phospholipase A2-generated fatty acid cascade and lipopolysaccharide-dependent activation of the immune deficiency (imd) pathway in insect immunity
Authors: YAJIMA Masashi , TAKADA Masatoshi , TAKAHASHI Nahoko , KIKUCHI Haruhisa , NATORI Shunji , OSHIMA Yoshiteru , KURATA Shoichiro
Published: March 2003

Innate immunity is the first line of defence against infectious micro-organisms, and the basic mechanisms of pathogen recognition and response activation are evolutionarily conserved. In mammals, the innate immune response in combination with antigen-specific recognition is required for the activation of adaptive immunity. Therefore, innate immunity is a pharmaceutical target for the development of immune regulators. Here, for the purpose of pharmaceutical screening, we established an in vitro culture based on the innate immune response of Drosophila. The in vitro system is capable of measuring lipopolysaccharide (LPS)-dependent activation of the immune deficiency (imd) pathway, which is similar to the tumour necrosis factor signalling pathway in mammals. Screening revealed that well-known inhibitors of phospholipase A2 (PLA2), dexamethasone (Dex) and p-bromophenacyl bromide (BPB) inhibit LPS-dependent activation of the imd pathway. The inhibitory effects of Dex and BPB were suppressed by the addition of an excess of three (arachidonic acid, eicosapentaenoic acid and γ-linolenic acid) of the fatty acids so far tested. Arachidonic acid, however, did not activate the imd pathway when used as the sole agonist. These findings indicate that PLA2 participates in LPS-dependent activation of the imd pathway via the generation of arachidonic acid and other mediators, but requires additional signalling from LPS stimulation. Moreover, PLA2 was activated in response to bacterial infection in Sarcophaga. These results suggest a functional link between the PLA2-generated fatty acid cascade and the LPS-stimulated imd pathway in insect immunity.