bluuebunny/crossref_metadata_2025 huggingface dataset:
Absolute determination of film thickness from photoemission: Application to atomically uniform films of Pb on Si
Authors: Upton M. H. , Miller T. , Chiang T.-C.
Published: August 2004

We report on a method to unequivocally determine the thickness of a film in terms of atomic layers, as demonstrated by a study of Pb growth on Si(111). Deposition at low temperatures on a pretreated Si substrate results in atomically uniform Pb films. These films exhibit large monolayer-by-monolayer variations in electronic structure as observed by angle-resolved photoemission. Intense and sharp peaks derived from quantum-well states are observed for odd film thicknesses N=5, 7, and 9 monolayers, but not for the adjacent even film thicknesses N=4, 6, 8, and 10 monolayers. The dramatic differences facilitate an accurate calibration of the amount of Pb deposited.
Strain field fluctuation effects on lattice thermal conductivity of ZrNiSn-based thermoelectric compounds
Authors: Yang J. , Meisner G. P. , Chen L.
Published: August 2004

We present a model calculation of the lattice thermal conductivity of ZrNiSn-based half-Heusler thermoelectric compounds for temperatures where phonon scattering is dominated by Umklapp and point defect scattering. The difference in mass between impurity and host atoms dominates point defect scattering for alloying Hf on the Zr sublattice, whereas differences in size and interatomic coupling forces between impurity and host atoms dominate point defect scattering for alloying Pd on the Ni sublattice. Because Pt is heavier and larger than Pd, we predict that Pt will further reduce lattice thermal conductivity when alloyed on the Ni sublattice of these half-Heusler compounds.
Influences of oligomer length on carrier-transport properties of oligofluorenes
Authors: Wu Chung-Chih , Liu Tsung-Li , Lin Yu-Ting , Hung Wen-Yi , Ke Tung-Huei , Wong Ken-Tsung , Chao Teng-Chih
Published: August 2004

In this letter, carrier-transport properties of a homologous series of oligofluorenes with C9 diaryl substitution have been examined. These substituted oligofluorenes possess stable amorphous states, ambipolar carrier-transport properties, and processability to thin films for a range of oligomer lengths, rendering feasible investigating dependence of carrier transport on oligomer length in disordered systems. It is found that carrier mobilities of these oligofluorenes show a clear decreasing trend with the oligomer length. Such findings are in contrast with previous observations for crystalline oligomers and impose certain implications in carrier transport of conjugated polymers and oligomers.
Dynamic measurement of electrical conductivity of carbon nanotubes during mechanical deformation by nanoprobe manipulation in transmission electron microscopy
Authors: Kuzumaki Toru , Mitsuda Yoshitaka
Published: August 2004

The effect of mechanical deformation on the electrical characteristics of individual multiwall carbon nanotubes (MWCNTs) was investigated by a nanoprobe manipulation technique in a transmission electron microscope (TEM). The electrical conductivity was measured during the deformation of the MWCNT in TEM. The electrical conductivity of the MWCNTs was sensitive to structural variation. The electromechanical characteristics were reversible within the elastic limit. However, when lattice defects were formed due to deformation, the electrical conductivity was not restored to the original state, even when the applied stress was released.
Synthesis, Characterization, and Near-Infrared Photoluminescence of Novel Neodymium(III) Complexes
Authors: He Hongshan , Wong Wai-Kwok , Guo Jianping , Li King-Fai , Wong Wai-Yeung , Lo Wing-Kit , Cheah Kok-Wai
Published: August 2004

A series of monoporphyrinate neodymium(iii) complexes stabilized by the anionic tripodal ligand hydridotris(pyrazol-1-yl)borate were prepared and characterized. These complexes were characterized by elemental analysis and spectroscopy. The structure of resulting complex was determined by single-crystal X-ray diffraction. The complex crystallized in the monoclinic space group P21/c, with a 13.7347(11), b 27.156(2), c 15.5397(13) Å, β 114.1490(10)°, and V 5288.8(7) Å3. The neodymium(iii) ion is coordinated by four nitrogen atoms from the porphyrinate dianion and three nitrogen atoms from the anionic tripodal ligand. Photoluminescence studies showed that the porphyrinate dianion absorbed light and transferred energy to the Nd3+ centre, a process which then allowed the metal ion to emit efficiently at 885, 900, and 1071 nm. The effects of the substituent and the solvent on emission efficiency were also investigated.
Modifying the Regioselectivity of Glycosynthase Reactions Through Changes in the Acceptor
Authors: Stick Robert V. , Stubbs Keith A. , Watts Andrew G.
Published: August 2004

Successful glycosynthase-mediated reactions have been performed on 6-O-benzyl-, 6-O-(4-nitrobenzyl)-, and 6-O-benzoyl-d-glucopyranose to give 1,2-β- and 1,3-β-d-glycosylated products; 4-O-benzyl-d-xylopyranose gave only a 1,2-β-glycosylated product. A rationale is presented for these rather unusual results.
Lipase-Catalyzed 1,6-Acylation of D-Mannitol
Authors: Duggan Peter J. , Humphrey David G. , McCarl Victoria
Published: August 2004

The selective synthesis of 1,6-diacyl d-mannitols from 2,2,2-trifluoroethyl esters using transesterification, catalyzed by lipases, has been investigated, and the results have been compared with those obtained from a typical acid chloride procedure and a phenylboronic acid-assisted approach. Three commercially available lipases and five 2,2,2-trifluoroethyl esters were examined. In most cases, the yields obtained from the lipase reactions were superior to those produced from either of the other two methods.
Organosilicon Compounds with Blue Photoluminescence Properties
Authors: Zheng Guorong , Li Wei , Wang Zixing , Lu Ping
Published: August 2004

A series of π-conjugated compounds and related Si compounds with blue photoluminescent properties have been prepared. Structures of products were confirmed by NMR spectra and mass spectrometry. Photoluminescent properties are discussed. Based on luminescent properties, these Si compounds might find utility as emitters in organic light-emitting diode displays.
Differences in carcass grading schemes used in the USA, Japan and Australia
Authors: Strong J.
Published: August 2004

Over the past 30 years there has been increasing pressure for the establishment of a beef, quality grading system in Australia. During this time, many and varied options have been proposed and comparisons have often been made with the United States Department of Agriculture (USDA) and the Japanese Meat Grading Association (JMGA) systems. Australia has now developed a grading system that is driven by the consumer — Meat Standards Australia (MSA). Although some years (70+) behind the USDA, the Australian model has been scientifically proven to identify product that can achieve a guaranteed level of satisfaction to the consumer. While this paper evaluates the 3 systems and their specific operations, both the USDA and JMGA systems are compared with the potential performance of the MSA system applied on a cut by grade by cooking method basis.
Bayesian analysis of botanical epidemics using stochastic compartmental models
Authors: Gibson G. J. , Kleczkowski A. , Gilligan C. A.
Published: August 2004

A stochastic model for an epidemic, incorporating susceptible, latent, and infectious states, is developed. The model represents primary and secondary infection rates and a time-varying host susceptibility with applications to a wide range of epidemiological systems. A Markov chain Monte Carlo algorithm is presented that allows the model to be fitted to experimental observations within a Bayesian framework. The approach allows the uncertainty in unobserved aspects of the process to be represented in the parameter posterior densities. The methods are applied to experimental observations of damping-off of radish (Raphanus sativus) caused by the fungal pathogenRhizoctonia solani, in the presence and absence of the antagonistic fungusTrichoderma viride, a biological control agent that has previously been shown to affect the rate of primary infection by using a maximum-likelihood estimate for a simpler model with no allowance for a latent period. Using the Bayesian analysis, we are able to estimate the latent period from population data, even when there is uncertainty in discriminating infectious from latently infected individuals in data collection. We also show that the inference thatT. viridecan control primary, but not secondary, infection is robust to inclusion of the latent period in the model, although the absolute values of the parameters change. Some refinements and potential difficulties with the Bayesian approach in this context, when prior information on parameters is lacking, are discussed along with broader applications of the methods to a wide range of epidemiological systems.
Ecological theory suggests that antimicrobial cycling will not reduce antimicrobial resistance in hospitals
Authors: Bergstrom Carl T. , Lo Monique , Lipsitch Marc
Published: August 2004

Hospital-acquired infections caused by antibiotic-resistant bacteria pose a grave and growing threat to public health. Antimicrobial cycling, in which two or more antibiotic classes are alternated on a time scale of months to years, seems to be a leading candidate in the search for treatment strategies that can slow the evolution and spread of antibiotic resistance in hospitals. We develop a mathematical model of antimicrobial cycling in a hospital setting and use this model to explore the efficacy of cycling programs. We find that cycling is unlikely to reduce either the evolution or the spread of antibiotic resistance. Alternative drug-use strategies such as mixing, in which each treated patient receives one of several drug classes used simultaneously in the hospital, are predicted to be more effective. A simple ecological explanation underlies these results. Heterogeneous antibiotic use slows the spread of resistance. However, at the scale relevant to bacterial populations, mixing imposes greater heterogeneity than does cycling. As a consequence, cycling is unlikely to be effective and may even hinder resistance control. These results may explain the limited success reported thus far from clinical trials of antimicrobial cycling.
A tagging-via-substrate technology for detection and proteomics of farnesylated proteins
Authors: Kho Yoonjung , Kim Sung Chan , Jiang Chen , Barma Deb , Kwon Sung Won , Cheng Jinke , Jaunbergs Janis , Weinbaum Carolyn , Tamanoi Fuyuhiko , Falck John , Zhao Yingming
Published: August 2004

A recently developed proteomics strategy, designated tagging-via-substrate (TAS) approach, is described for the detection and proteomic analysis of farnesylated proteins. TAS technology involves metabolic incorporation of a synthetic azido-farnesyl analog and chemoselective derivatization of azido-farnesyl-modified proteins by an elegant version of Staudinger reaction, pioneered by the Bertozzi group, using a biotinylated phosphine capture reagent. The resulting protein conjugates can be specifically detected and/or affinity-purified by streptavidin-linked horseradish peroxidase or agarose beads, respectively. Thus, the technology enables global profiling of farnesylated proteins by enriching farnesylated proteins and reducing the complexity of farnesylation subproteome. Azido-farnesylated proteins maintain the properties of protein farnesylation, including promoting membrane association, Ras-dependent mitogen-activated protein kinase kinase activation, and inhibition of lovastatin-induced apoptosis. A proteomic analysis of farnesylated proteins by TAS technology revealed 18 farnesylated proteins, including those with potentially novel farnesylation motifs, suggesting that future use of this method is likely to yield novel insight into protein farnesylation. TAS technology can be extended to other posttranslational modifications, such as geranylgeranylation and myristoylation, thus providing powerful tools for detection, quantification, and proteomic analysis of posttranslationally modified proteins.
Creating ribosomes with an all-RNA 30S subunit P site
Authors: Hoang Lee , Fredrick Kurt , Noller Harry F.
Published: August 2004

Ribosome crystal structures have revealed that two small subunit proteins, S9 and S13, have C-terminal tails, which, together with several features of 16S rRNA, contact the anticodon stem-loop of P-site tRNA. To test the functional importance of these protein tails, we created genomic deletions of the C-terminal regions of S9 and S13. All of the tail deletions, including double mutants containing deletions in both S9 and S13, were viable, showing that
Escherichia coli
cells can synthesize all of their proteins by using ribosomes that contain 30S P sites composed only of RNA. However, these mutants have slower growth rates, indicating that the tails may play a supporting functional role in translation.
In vitro
analysis shows that 30S subunits purified from the S13 deletion mutants have a generally decreased affinity for tRNA, whereas deletion of the S9 tail selectively affects the binding of tRNAs whose anticodon stem sequences are most divergent from that of initiator tRNA.
Social Exclusion and Opportunity Structures in European Cities and Neighbourhoods
Authors: Murie Alan , Musterd Sako
Published: August 2004

The increased research and policy interest in social exclusion has included a focus on the concentration of disadvantage within cities. The role of neighbourhoods in the dynamics of social exclusion is consequently receiving greater attention. This paper reports the results of a major European research programme designed to explore the neighbourhood dimension of social exclusion. The results raise important issues related to the differential opportunities associated with neighbourhoods and the conceptualisation of neighbourhood effects as well as issues for policy. Understanding the role of neighbourhood in social exclusion involves attention to different levels of analysis and different fault lines and to the resources that are produced within neighbourhoods.
Privatising Cape Town: From Apartheid to Neo-liberalism in the Mother City
Authors: McDonald David A. , Smith Laïla
Published: August 2004

One of the most remarkable features of the post -apartheid political landscape in South Africa is the increasingly hegemonic nature of neo-liberal thought and practice. This ideological dominance is most noticeable at the national level but has trickled down to urban policy-making as well. This paper documents the new urban neo-liberalism in the city of Cape Town. Based on extensive interviews, policy analysis and a critique of the track record of local government since 1996, the paper provides the first comprehensive overview of the character and extent of neo-liberalism in a large South African city. The empirical data are coupled with an analysis of the structural and ideological pressures from the national and international levels that have given rise to this policy focus, and an assessment of the room for alternative policy manoeuvre at the local level. We argue that there is considerable potential for policy autonomy in Cape Town, but that non-neo-liberal policy alternatives have been largely ignored, abandoned or intentionally shut out by the majority of senior decision-makers in the city, making for a self-reinforcing loop of neo-liberal discourse and practice at different levels of government in South Africa and with international funding bodies and advisors.
Participation Determinants in Armenia's Housing Purchase Certificate Programme
Authors: Struyk Raymond J. , Petkova Dessislava
Published: August 2004

A housing purchase certificate (HPC) is a voucher for the purchase of a dwelling unit, either for the full price (up to a programme-determined maximum) or a grant for a partial payment (i.e. a downpayment subsidy). Using a special sample survey of programme participants, this paper examines why some participants have been successful and others not in using the certificates for the full price of a unit distributed under the HPC programme providing assistance to victims of Armenia's 1988 earthquake. Findings indicate that participants with the following attributes are more likely to succeed in finding a unit (and using the certificate): living in more difficult housing conditions at the time they receive the certificate, having more economic resources, considering more units in their housing search, relying on information about available dwellings from friends and family members rather than relying on information in the mass media and searching in markets where the supply of units on offer is relatively great. These findings form the basis for considering ways to increase success rates.
Valuing Air Pollution Mortality in China's Cities
Authors: Brajer Victor , Mead Robert W.
Published: August 2004

Although China has made tremendous economic progress in recent years, air pollution continues to exact significant health and economic costs. Using pollution data from 38 Chinese cities and China-based epidemiological functions, this paper estimates some of the economic benefits of reducing urban air pollution. It calculates the averted mortality which would result from the clean-up of particulates, sulphur dioxide and nitrogen dioxide—a pollutant not included in most previous China studies. The paper expands on earlier studies by examining the impact of seasonal variations in pollution levels. Finally, the monetary valuation of pollution-related averted mortality is developed using a China-based valuation study and, for a number of cities, the valuation is compared with city-level GDP.
Historic Preservation and Neighbourhood Change
Authors: Coulson N. Edward , Leichenko Robin M.
Published: August 2004

Historical designation has become an important tool in efforts to revitalise central-city neighbourhoods. Yet designation has also come under scrutiny because of its presumed association with gentrification and displacement of lower-income residents. Using Fort Worth, Texas, as a case study, the paper asks whether historical designation is associated with demographic change in neighbourhoods. It is found that historically designated areas started out with slightly worse neighbourhood indicators than those without designation—a finding that is consistent with the idea that preservation efforts are targeted to areas in 'need' of revitalisation. However, we find no evidence that preservation efforts altered the demographic composition of neighbourhoods. This finding runs counter to the notion that historic preservation is a precursor to gentrification.
Senegalese émigrés: new information & communication technologies
Authors: Tall Serigne Mansour
Published: August 2004

Emigration from Senegal increased rapidly between 1980 and 1990, and its economic and social implications grew in significance. These migratory flows diversified in terms of their departure points and destinations, making complex the challenge of preserving relationships with families at home. As Senegalese emigrated to countries with fewer links to Senegal, the need to find ways of maintaining long-distance relationships became more urgent.

How do the émigrés appropriate New Information and Communications Technologies (NICT)? How do the new technologies provide for financial transfers without the physical movement of funds? What role do the émigrés play in the penetration of new technologies in certain disadvantaged sectors? What are the economic and social implications of this advance of NICTs? Tall shows that the types of use made of the new technologies follow from a complex process of appropriation that can make a highly personal tool such as the cellular telephone into a collective instrument to bring a village out of its isolation and connect it with the world.

Tall concludes that the emergence of the new technologies and their appropriation by émigrés creates new social configurations both in the new home and in the community of origin, and contributes to the emergence of new spatial understandings.
Engineering civil society: ICT in Tanzania
Authors: Mercer Claire
Published: August 2004

The international development community has recently focussed attention on the potential role Information and Communication Technologies (ICTs; email and Internet) can play in promoting democratic development. The ‘Zapatista effect’ has prompted claims that access to ICTs will strengthen civil society by giving voice to the poor and marginalised, widening popular participation, and encouraging information-sharing and alliance-building. Drawing on research carried out in Dar es Salaam and Arusha, two of Tanzania's ‘most connected’ cities, this paper critically analyses such claims in the light of the experiences of non-governmental organisations' (NGOs) use of ICTs. In the first instance, only a minority of well-resourced, urban and/or international NGOs have access to ICT facilities. Moreover, NGOs are not using ICTs in the ways imagined by donors, who ignore the social, cultural and political contexts within which they would wish to embed technological professionalism. Access to ICTs has to some extent facilitated networking among Tanzania's elite NGOs whose advocacy and lobbying activities have had some impact upon national policies. Overall, however, while donors may enjoy limited success in engineering an elite civil society, the paper concludes that the recent ‘ICT fetishism’ of international donors is likely to result in a case of misplaced optimism.
Election observation in Nigeria & Madagascar: diplomatic vs. technocratic bias
Authors: Kohnert Dirk
Published: August 2004

International election observation has become a valuable means of supporting African democratic polity. Notably, EU observer missions adopting a professional approach are meant to shield against political pressures from partisan stakeholder interests. However, this growing professionalism did not necessarily lead to less biased observation results. Available evidence suggests that in crucial cases, the origin and orientation of the bias changed from ‘diplomatic’ to ‘technocratic’. The latter can be as least as damaging to the declared aims of election observation as the former. Two outstanding examples, the observation of transitional elections in Nigeria and Madagascar, will serve to illustrate this hypothesis and its consequences for the necessary reorientation of election observation methodology.
Discourse, ‘Development’ & the ‘Digital Divide’: ICT & the World Bank
Authors: Thompson Mark
Published: August 2004

Information and communication technology(ies) (ICT) is tipped to play an increasingly enabling role in the inclusion and exclusion of groups from participation in the discourse of ‘development’, with material consequences. In affecting how ‘development’ is framed, discussed and practised, the conception and use of such technologies itself thus becomes an important field of discourse for the analysis of power relations in the ‘developmental’ field. This paper shows how a recent ICT-related initiative by the World Bank Group can be seen as an attempt to replicate its position of strength within the predominant, technocratic discourse of development, to the exclusion of alternative views of technology, and even of ‘development’ itself. Using a method of critical discourse analysis, the paper then examines a recent speech on ICT by the Bank’s president, which provides a detailed example of the way in which existing, macro-level power structures are replicated at the micro-level of discursive practice.
Involvement of fractalkine and macrophage inflammatory protein‐1 alpha in moderate‐severe depression
Authors: Merendino Rosaria Alba , Di Pasquale Giuseppe , De Luca Filippo , Di Pasquale Laura , Ferlazzo Edoardo , Martino Gabriella , Palumbo Maura Carmela , Morabito Fortunato , Gangemi Sebastiano
Published: August 2004

MODERATE‐severe depression (MSD) is linked to overexpression of proinflammatory cytokines and chemokines. Fractalkine (FKN) and macrophage inflammatory protein‐1 alpha (MIP‐1α) are, respectively, members of CX3C and C‐C chemokines, and both are involved in recruiting and activating mononuclear phagocytes in the central nervous system. We analysed the presence of FKN and MIP‐1α in sera of untreated MSD patients and healthy donors. High FKN levels were observed in all MSD patients as compared with values only detectable in 26% of healthy donors. MIP‐1α was measurable in 20% of patients, while no healthy donors showed detectable chemokine levels. In conclusion, we describe a previously unknown involvement of FKN in the pathogenesis of MSD, suggesting that FKN may represent a target for a specific immune therapy of this disease.
The effects of peritoneal dialysis and hemodialysis on serum tumor necrosis factor‐alpha, interleukin‐6, interleukin‐10 and C‐reactive‐protein levels
Authors: Borazan Ali , Ustün Hasan , Ustundag Yucel , Aydemir Selim , Bayraktaroglu Taner , Sert Mehmet , Yilmaz Ahmet
Published: August 2004

BACKGROUND: Markers of an acute phase reaction, such as C‐reactive protein (CRP) or tumor necrosis factor‐alpha (TNF‐α) and interleukin (IL)‐6, are predictive for cardiovascular morbidity and mortality in normal subjects and in chronic renal failure patients. In this study, we aimed to investigate serum TNF‐α, IL‐6, IL‐10 and CRP levels in continuous ambulatory peritoneal dialysis (CAPD) and hemodialysis (HD) patients.

Materials and methods: Serum levels of TNF‐α, IL‐6, IL‐10 and CRP levels were measured in 30 patients who were just diagnosed with end‐stage renal failure and treated, with 16 CAPD (nine female, seven male) and 14 HD (eight female, six male) patients, before CAPD or HD treatment and after 3 months from the beginning of CAPD or HD in patients with no clinical signs of infection. The control groups were 20 healthy persons of similar age and sex. Serum levels of TNF‐α, IL‐6, IL‐10 and CRP were measured by enzyme‐linked immunosorbent assay in stable CAPD and HD patients and in healthy persons.

Results: The mean serum levels of TNF‐α, IL‐6, IL‐10 and CRP showed no significant differences between the CAPD and HD patients for the beginning values and the third month of treatment. However, serum TNF‐α, IL‐6, IL‐10 and CRP levels were higher than the control group in the CAPD and HD patients regarding the beginning values and the third month of treatment (p < 0.001).

Conclusions: CAPD and HD of the renal replacement therapy have no effects on serum CRP and cytokines.
Inflammatory bowel disease: the role of inflammatory cytokine gene polymorphisms
Authors: Balding Joanna , Livingstone Wendy J. , Conroy Judith , Mynett-Johnson Lesley , Weir Donald G. , Mahmud Nasir , Smith Owen P.
Published: August 2004

THE mechanisms responsible for development of inflammatory bowel disease (IBD) have not been fully elucidated, although the main cause of disease pathology is attributed to up‐regulated inflammatory processes. The aim of this study was to investigate frequencies of polymorphisms in genes encoding pro‐inflammatory and anti‐inflammatory markers in IBD patients and controls. We determined genotypes of patients with IBD (n = 172) and healthy controls (n = 389) for polymorphisms in genes encoding various cytokines (interleukin (IL)‐1β, IL‐6, tumour necrosis factor (TNF), IL‐10, IL‐1 receptor antagonist). Association of these genotypes to disease incidence and pathophysiology was investigated. No strong association was found with occurrence of IBD. Variation was observed between the ulcerative colitis study group and the control population for the TNF‐α‐308 polymorphism (p = 0.0135). There was also variation in the frequency of IL‐6‐174 and TNF‐α‐308 genotypes in the ulcerative colitis group compared with the Crohn′s disease group (p = 0.01). We concluded that polymorphisms in inflammatory genes are associated with variations in IBD phenotype and disease susceptibility. Whether the polymorphisms are directly involved in regulating cytokine production, and consequently pathophysiology of IBD, or serve merely as markers in linkage disequilibrium with susceptibility genes remains unclear.
Involvement of prostaglandins in inflammation induced by latex of Calotropis procera
Authors: Kumar Vijay L. , Shivkar Yatin M.
Published: August 2004

INTRODUCTION: The aerial parts of the plant Calotropis procera produce milky white latex that causes inflammation of the skin and mucous membranes. Prostaglandins are one of the mediators released in an inflammatory response following induction of cyclooxygenase (COX). In the present study, we have evaluated the role of prostaglandins in inflammatory response elicited by the latex of C. procera.

Methods: Aqueous extract of dried latex of C. procera was injected into the 6‐day air‐pouch in the rat. The inflammatory response was evaluated by studying the air‐pouch fluid for its volume, protein and prostaglandin (PG) E2 concentrations, and leucocyte counts. The granulation tissue from the pouch was quantified and studied for COX‐2 expression by reverse transcriptase‐polymerase chain reaction. The inhibitory effect of celecoxib and dexamethasone was evaluated on the aforementioned parameters.

Results: Dried latex produced an inflammatory response that was maximum at 6 h. It was associated with the accumulation of protein‐rich fluid, leucocytes and PGE2 production. It also resulted in granulation of the pouch cavity that was a maximum on day 3. COX‐2 expression could be detected in the granulation tissue on day 1 and it increased progressively up to day 5. The anti‐inflammatory drugs celecoxib and dexamethasone significantly attenuated the inflammatory response and inhibited COX‐2 expression in granulation tissue.

Conclusions: Latex of C. procera induces an inflammatory response characterized by an early exudative phase accompanied by PGE2 production and a late proliferative phase associated with COX‐2 induction. Both the phases were effectively inhibited by COX‐2 inhibitors.
The first encounter with Norwegian psychomotor physiotherapy: patients' experiences, a basis for knowledge
Authors: Ekerholt Kirsten , Bergland Astrid
Published: August 2004

Aims: The intention of this study was to elucidate patients' experiences of the examination of the body given in Norwegian Psychomotor Physiotherapy. Methods: A qualitative approach was used, based on interviews with nine women and one man aged between 41 and 65 years. The data were analysed with the aid of grounded theory, using the first two steps: open and axial coding. Results: Three categories were identified from the patients' experiences. The first category "The Situation before Treatment'', emerged from the subcategories "Prejudice concerning the prefix `psycho''', "Difficulties in recognizing the body's information'', and "The body is ambiguous''. The second category, "Establishing the Relationship'', emerged from the subcategories "Getting to know the therapist as an empathic person'' and "Discovering professional skills''. The third category, "Examination is Interaction'', emerged from the subcategories "Dialogues - room for reflection'', "Undress, the feeling of disclosure'', and "Personal boundaries - good to be seen''. These three categories emphasize the importance of cooperation between the physiotherapist and the patient in exploring the social and emotional context in order to understand the meaning of the body's symptoms. There must be no doubt about the skill and competence of the therapists, including their insight, personal responsibility, engagement, attentiveness, and awareness. Conclusions: Our material reflects the great impact the body examination had on the informants. Examination requires mutual interpretation. The patients' knowledge represents a significant potential for understanding of their own situation.
Chfr acts with the p38 stress kinases to block entry to mitosis in mammalian cells
Authors: Matsusaka Takahiro , Pines Jonathon
Published: August 2004

Entry into mitosis in vertebrate cells is guarded by a checkpoint that can be activated by a variety of insults, including chromosomal damage and disrupting microtubules (Rieder, C.L., and R.W. Cole. 1998. J. Cell Biol. 142:1013–1022; Rieder, C.L., and R.W. Cole. 2000. Curr. Biol. 10:1067–1070). This checkpoint acts at the end of interphase to delay cells from entering mitosis, causing cells in prophase to decondense their chromosomes and return to G2 phase. Here, we show that in response to microtubule poisons this “antephase” checkpoint is primarily mediated by the p38 stress kinases and requires the Chfr protein that is absent or inactive in several transformed cell lines (Scolnick, D.M., and T.D. Halazonetis. 2000. Nature. 406:430–435) and lung tumors (Mizuno, K., H. Osada, H. Konishi, Y. Tatematsu, Y. Yatabe, T. Mitsudomi, Y. Fujii, and T. Takahashi. 2002. Oncogene. 21:2328–2333). Furthermore, in contrast to previous reports, we find that the checkpoint requires ubiquitylation but not proteasome activity, which is in agreement with the recent demonstration that Chfr conjugates ubiquitin through lysine 63 and not lysine 48 (Bothos, J., M.K. Summers, M. Venere, D.M. Scolnick, and T.D. Halazonetis. 2003. Oncogene. 22:7101–7107).
Topoisomerase II and histone deacetylase inhibitors delay the G2/M transition by triggering the p38 MAPK checkpoint pathway
Authors: Mikhailov Alexei , Shinohara Mio , Rieder Conly L.
Published: August 2004

When early prophase PtK1 or Indian muntjac cells are exposed to topoisomerase II (topo II) inhibitors that induce little if any DNA damage, they are delayed from entering mitosis. We show that this delay is overridden by inhibiting the p38, but not the ATM, kinase. Treating early prophase cells with hyperosmotic medium or a histone deacetylase inhibitor similarly delays entry into mitosis, and this delay can also be prevented by inhibiting p38. Together, these results reveal that agents or stresses that induce global changes in chromatin topology during G2 delay entry into mitosis, independent of the ATM-mediated DNA damage checkpoint, by activating the p38 MAPK checkpoint. The presence of this pathway obviates the necessity of postulating the existence of multiple “chromatin modification” checkpoints during G2. Lastly, cells that enter mitosis in the presence of topo II inhibitors form metaphase spindles that are delayed in entering anaphase via the spindle assembly, and not the p38, checkpoint.
Masking of Phosphatidylserine Inhibits Apoptotic Cell Engulfment and Induces Autoantibody Production in Mice
Authors: Asano Kenichi , Miwa Miyu , Miwa Keiko , Hanayama Rikinari , Nagase Hiroko , Nagata Shigekazu , Tanaka Masato
Published: August 2004

Apoptotic cells are rapidly phagocytosed by professional phagocytes, such as macrophages and dendritic cells. This process prevents the release of potentially noxious or immunogenic intracellular materials from dying cells, and is thought to play a critical role for the maintenance of normal functions in surrounding tissues. Milk fat globule-EGF-factor 8 (MFG-E8), secreted by activated macrophages and immature dendritic cells, links apoptotic cells and phagocytes, and promotes phagocytosis of apoptotic cells. Here, we report that an MFG-E8 mutant, designated as D89E, carrying a point mutation in an RGD motif, inhibited not only the phagocytosis of apoptotic cells by a wide variety of phagocytes, but also inhibited the enhanced production of IL-10 by thioglycollate-elicited peritoneal macrophages phagocytosing apoptotic cells. When intravenously injected into mice, the D89E protein induced the production of autoantibodies including antiphospholipids antibodies and antinuclear antibodies. The production of autoantibodies was enhanced by the coinjection of syngeneic apoptotic thymocytes. After the induction of autoantibody production by D89E, the treated mice showed a long-term elevation of the titer for autoantibodies, and developed IgG deposition in the glomeruli. These results indicated that the impairment of apoptotic cell phagocytosis led to autoantibody production.
CCR7 Signals Are Essential for Cortex–Medulla Migration of Developing Thymocytes
Authors: Ueno Tomoo , Saito Fumi , Gray Daniel H.D. , Kuse Sachiyo , Hieshima Kunio , Nakano Hideki , Kakiuchi Terutaka , Lipp Martin , Boyd Richard L. , Takahama Yousuke
Published: August 2004

Upon TCR-mediated positive selection, developing thymocytes relocate within the thymus from the cortex to the medulla for further differentiation and selection. However, it is unknown how this cortex–medulla migration of thymocytes is controlled and how it controls T cell development. Here we show that in mice deficient for CCR7 or its ligands mature single-positive thymocytes are arrested in the cortex and do not accumulate in the medulla. These mutant mice are defective in forming the medullary region of the thymus. Thymic export of T cells in these mice is compromised during the neonatal period but not in adulthood. Thymocytes in these mice show no defects in maturation, survival, and negative selection to ubiquitous antigens. TCR engagement of immature cortical thymocytes elevates the cell surface expression of CCR7. These results indicate that CCR7 signals are essential for the migration of positively selected thymocytes from the cortex to the medulla. CCR7-dependent cortex–medulla migration of thymocytes plays a crucial role in medulla formation and neonatal T cell export but is not essential for maturation, survival, negative selection, and adult export of thymocytes.
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
Authors: Zou Min , Conzen Suzanne D.
Published: August 2004

Motivation: Signaling pathways are dynamic events that take place over a given period of time. In order to identify these pathways, expression data over time are required. Dynamic Bayesian network (DBN) is an important approach for predicting the gene regulatory networks from time course expression data. However, two fundamental problems greatly reduce the effectiveness of current DBN methods. The first problem is the relatively low accuracy of prediction, and the second is the excessive computational time.

Results: In this paper, we present a DBN-based approach with increased accuracy and reduced computational time compared with existing DBN methods. Unlike previous methods, our approach limits potential regulators to those genes with either earlier or simultaneous expression changes (up- or down-regulation) in relation to their target genes. This allows us to limit the number of potential regulators and consequently reduce the search space. Furthermore, we use the time difference between the initial change in the expression of a given regulator gene and its potential target gene to estimate the transcriptional time lag between these two genes. This method of time lag estimation increases the accuracy of predicting gene regulatory networks. Our approach is evaluated using time-series expression data measured during the yeast cell cycle. The results demonstrate that this approach can predict regulatory networks with significantly improved accuracy and reduced computational time compared with existing DBN approaches.

Availability: The programs described in this paper can be obtained from the corresponding author upon request.

Contact:  sconzen@medicine.bsd.uchicago.edu
BioLingua: a programmable knowledge environment for biologists
Authors: Massar J. P. , Travers Michael , Elhai Jeff , Shrager Jeff
Published: August 2004

Summary: BioLingua is an interactive, web-based programming environment that enables biologists to analyze biological systems by combining knowledge and data through direct end-user programming. BioLingua embeds a mature symbolic programming language in a frame-based knowledge environment, integrating genomic and pathway knowledge about a class of similar organisms. The BioLingua language provides interfaces to numerous state-of-the-art bioinformatic tools, making these available as an integrated package through the novel use of web-based programmability and an integrated Wiki-based community code and data store. The pilot instantiation of BioLingua, which has been developed in collaboration with several cyanobacteriologists, integrates knowledge about a subset of cyanobacteria with the Gene Ontology, KEGG and BioCyc knowledge bases. We introduce the BioLingua concept, architecture and language, and give several examples of its use in complex analyses.

Availability: Extensive documentation is available online at http://nostoc.stanford.edu/Docs/index.html

Contact:  JShrager@Stanford.edu
Protein structure alignment by deterministic annealing
Authors: Chen Luonan , Zhou Tianshou , Tang Yun
Published: August 2004

Motivation: Protein structure alignment is one of the most important computational problems in molecular biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and so on. From the viewpoint of computational complexity, a pairwise structure alignment is also a NP-hard problem, in contrast to the polynomial time algorithm for a pairwise sequence alignment.

Results: We propose a method for solving the structure alignment problem in an accurate manner at the amino acid level, based on a mean field annealing technique. We define the structure alignment as a mixed integer-programming (MIP) problem. By avoiding complicated combinatorial computation and exploiting the special structure of the continuous partial problem, we transform the MIP into a reduced non-linear continuous optimization problem (NCOP) with a much simpler form. To optimize the reduced NCOP, a mean field annealing procedure is adopted with a modified Potts model, whose solution is generally identical to that of the MIP. There is no ‘soft constraint’ in our mean field model and all constraints are automatically satisfied throughout the annealing process, thereby not only making the optimization more efficient but also eliminating many unnecessary parameters that depend on problems and usually require careful tuning. A number of benchmark examples are tested by the proposed method with comparisons to several existing approaches.

Contact:  chen@elec.osaka-sandai.ac.jp
SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data
Authors: Tebbutt Scott J. , Opushnyev Igor V. , Tripp Ben W. , Kassamali Ayaz M. , Alexander Wendy L. , Andersen Marilyn I.
Published: August 2004

Summary: SNP Chart is a Java application for the visualization and interpretation of microarray genotyping data primarily derived from arrayed primer extension-based chemistries. Spot intensity output files from microarray analysis tools are imported into SNP Chart, together with a multi-channel TIFF image of the original array experiment and a list of the actual single nucleotide polymorphisms (SNPs) being tested. Data from different and/or replicate probes that interrogate the same SNP, but that are scattered across the array grid, can be reassembled into a single chart format, specific for the SNP. This allows a quick and very effective ‘visualization’/‘quality control’ of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype.

Availability:  http://www.snpchart.ca

Contact:  stebbutt@mrl.ubc.ca

Supplementary information: A comprehensive manual describing SNP Chart is available at the above website, together with sample data files.
Convectively unstable wave packets in spatially developing open flows and media with algebraically decaying tails
Authors: Brevdo Leonid
Published: August 2004

In this paper we extend our recently developed theory of global and absolute instabilities of spatially developing open flows and media with algebraically decaying tails to treating propagating unstable wave packets in such flows. No restriction is imposed on the rate of variability of the spatially developing state in the finite domain. In the case when the limit state in infinity, i.e. the associated uniform state, is stable, but the inhomogeneous flow is absolutely unstable, a relatively simple complete description of the characteristics of the instability in a moving frame of reference is obtained in terms of the characteristics of the absolute instability and of the dispersion–relation function of the associated uniform state. When the associated uniform state is stable and the inhomogeneous flow is absolutely stable the inhomogeneous flow is convectively stable. Hence, any unstable inhomogeneous flow having a stable associated uniform state is absolutely unstable.
Saccharothrix algeriensis sp. nov., isolated from Saharan soil
Authors: Zitouni A. , Lamari L. , Boudjella H. , Badji B. , Sabaou N. , Gaouar A. , Mathieu F. , Lebrihi A. , Labeda D. P.
Published: August 2004

The taxonomic position of a soil isolate, strain SA 233T, recovered from Saharan soil from Algeria was established using a polyphasic approach. This isolate has been previously reported to produce three novel dithiolopyrrolone antibiotics, and preliminary chemotaxonomic and morphological characteristics suggested that it was representative of a member of the genus Saccharothrix. Phylogenetic analysis of the strain from 16S rDNA sequences, along with a detailed analysis of morphological, chemotaxonomic and physiological characteristics, indicates that it belongs to the genus Saccharothrix and represents a novel species that is readily distinguished from all recognized Saccharothrix species. The name Saccharothrix algeriensis sp. nov. is proposed for the isolate, with type strain SA 233T (=NRRL B-24137T=DSM 44581T).
Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides×nigra DN34)
Authors: Van Aken Benoit , Peres Caroline M. , Doty Sharon Lafferty , Yoon Jong Moon , Schnoor Jerald L.
Published: August 2004

A pink-pigmented, aerobic, facultatively methylotrophic bacterium, strain BJ001T, was isolated from internal poplar tissues (Populus deltoides×nigraDN34) and identified as a member of the genusMethylobacterium. Phylogenetic analyses showed that strain BJ001Tis related toMethylobacterium thiocyanatum,Methylobacterium extorquens,Methylobacterium zatmaniiandMethylobacterium rhodesianum. However, strain BJ001Tdiffered from these species in its carbon-source utilization pattern, particularly its use of methane as the sole source of carbon and energy, an ability that is shared with only one other member of the genus,Methylobacterium organophilum. In addition, strain BJ001Tis the only member of the genusMethylobacteriumto be described as an endophyte of poplar trees. On the basis of its physiological, genotypic and ecological properties, the isolate is proposed as a member of a novel species of the genusMethylobacterium,Methylobacterium populisp. nov. (type strain, BJ001T=ATCC BAA-705T=NCIMB 13946T).