bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of biocorrosion of low alloy steel by sulfate‐reducing Desulfotomaculum sp. isolated from crude oil field
Authors: Çetin D. , Bilgiç S. , Dönmez S. , Dönmez G.
Published: November 2007

In this study corrosion behavior of low alloy steel, in the presence of anaerobic sulfate‐reducing Desulfotomaculum sp. which was isolated from an oil production well, was investigated. In order to determine corrosion rates and mechanisms, mass loss measurements and electrochemical polarization studies were performed without and with bacteria in the culture medium. Scanning electron microscopic observations and energy dispersive X‐ray spectra (EDS) analysis were made on steel coupons.

The effect of iron concentration on corrosion behavior was determined by Tafel extrapolation method. In a sterile culture medium, as the FeSO4 · 7H2O concentration increased, corrosion potential (Ecor) values shifted towards more anodic potentials and corrosion current density (Icor) values increased considerably. After inoculation of sulfate‐reducing bacteria (SRB), Ecor shifted towards cathodic values. Icor values increased with increasing incubation time for 10 and 100 mg/L concentrations of FeSO4 · 7H2O.

Results have shown that the corrosion activity changed due to several factors such as bacterial metabolites, ferrous sulfide, hydrogen sulfide, iron phosphide, and cathodic depolarization effect.
Characterization of rust phases formed on low carbon steel exposed to natural marine environment of Chennai harbour – South India
Authors: Ramana K. V. S. , Kaliappan S. , Ramanathan N. , Kavitha V.
Published: November 2007

The corrosion behaviour of low carbon steel exposed to marine atmospheric, splash and immersion zones has been systematically studied by exposing steel specimens for a period of 12 months at the boat basin corrosion station of Chennai harbour, Chennai, Tamil Nadu, South India. The literature on similar work has been thoroughly reviewed which led to the initiation of this study for the first time at this harbour. The corrosion product (rust) on the specimens at 1, 2, 3 and 12 months was obtained and characterized by Fourier transform infrared spectroscopy (FT‐IR) and X‐ray diffraction (XRD) analysis. Acaganeite was the rust phase identified in the splash zone as revealed by the FT‐IR and XRD analysis. The other dominant phases were lepidocrocite, goethite and ferroxyhite. Small amounts of magnetite were also found to be present. The transformation of phases was observed in this investigation and discussed. A remarkable difference in the FT‐IR and XRD patterns of the corrosion products at the splash and immersion zones were noticed and the corresponding phases formed were reported in this paper. The rate of corrosion in all the three zones was compared.
When and how to start insulin therapy in type 2 diabetes
Authors: Kilvert Anne
Published: November 2007

Most patients with type 2 diabetes will eventually require insulin due to the progressive decline in beta‐cell function. Dr Kilvert describes when to introduce insulin in type 2 diabetes and how the regimen needs to be tailored to the individual patient. Copyright © 2007 Wiley Interface Ltd
Current management of vaginal discharge in general practice
Authors: Nandy Utpal , Malu Manoj
Published: November 2007

Our Drug review of vaginitis considers the diagnosis and recommended management of bacterial vaginosis, vulvovaginal candidosis and trichomoniasis, followed by a review of prescription data, sources of further information and the Datafile. Copyright © 2007 Wiley Interface Ltd
Emollients: effective use and pump dispenser waste
Authors: Chaplin Steve
Published: November 2007

Emollient therapy is the mainstay of treatment of dry skin conditions like eczema; however, it is under‐prescribed and underused by patients. In this article Steve Chaplin reviews the effective use of emollients and highlights a recent study looking at potential savings that can be made through reduced wastage. Copyright © 2007 Wiley Interface Ltd
Molecular motion study of [N(CH3)4]2Zn1–xCux Cl4 (x = 0, 0.01, 0.1, 1) mixed crystals by 1H NMR relaxation
Authors: Lim Ae Ran , Lim Kye‐Young
Published: November 2007

The temperature dependences of the 1H relaxation times in mixed crystals of formula [N(CH3)4]2Zn1–x Cux Cl4 (x = 0, 0.01, 0.1, and 1) were investigated. The phase transition temperatures and lattice constants of the mixed crystals were insensitive to the Cu impurity concentration. However, for relaxation above 290 K, deviations in the spin–lattice relaxation time, T1, and the spin–spin relaxation time, T2, on increasing x with respect to T1 and T2 observed for x = 0 were obtained. The experimentally observed 1/T1 above 290 K equals 1/T1r from reorientation motion plus 1/T1p due to paramagnetic Cu. From this result, the paramagnetic contribution to the proton relaxation rate is proportional to the abundance of paramagnetic impurities. From the results obtained it is concluded that the molecular motion is dependent on the concentration of the Cu impurity at high temperatures. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Knowledge work, design science and problem structuring methodologies
Authors: Keys Paul
Published: November 2007

It has been argued in a previous paper in this journal that taking a knowledge work perspective enables key aspects of the processes underpinning OR analysis to be better understood. This paper furthers this discussion by exploring knowledge‐related aspects of a particular type of OR, the use of problem structuring methodologies (PSMs). The notion of a design science for the use of PSMs provides a coherent and useful means of organizing this discussion and the content of such a science is presented in order to support the analysis. It is shown that this approach generates useful insights into the nature of some critical practical issues for the continuing development of PSMs and suggestions for how they may be addressed. Copyright © 2007 John Wiley & Sons, Ltd.
From economic to sustainable development: unfolding the concept of law
Authors: Jensen Hanne Birgitte
Published: November 2007

The paper presents an analysis of the interrelationship of law, policy and knowledge under conditions of globalization. The paper's basic premise is that the emergence of the sustainable development policy has been driven by an expanding awareness of the world as a singular and interdependent entity. The principal argument is that the policy of sustainable development is part of a wider epistemic shift, which means that the global community at large understands the world differently today than 50–60 years ago when the United Nations and the Bretton Woods‐inspired institutions were established. The theory of change underlying these policies represents, therefore, a shift from the model of economic development, which builds on the idea of separation and functional specialization, to a model of sustainable development, which builds on interdependence and integration. It is suggested that the sustainable development policy provides us with a key to develop a common theoretical framework for explaining the implications of the epistemic shift, but, giving effect to the shift will require research and co‐operation between a wide range of disciplines. It is further suggested that expanding the concept of law provides a necessary condition for making the epistemic shift operational as a new paradigm in a global governance context. In conclusion, the paper proposes that the theoretical insight from policymaking provides the resources to answer the post‐modern crisis of truth, which in essence is a crisis of reality, self and language. And further, that sustainable development has the potential for enabling a change equivalent to that of the Copernican revolution, which concerned man's place in the cosmos, while sustainable development concerns man's place in the biosphere. Effectuating the change will, however, require a fundamental willingness of the global scholarly community to engage with—and not merely describe, prescribe, and measure—reality and the human condition. Copyright © 2007 John Wiley & Sons, Ltd.
Multi‐stage sampling for population estimation
Authors: Kuno Eizi
Published: November 2007

Multi‐stage sampling is a convenient technique suited to the desnity estimation of biological populations living in habitats with complicated structures. This paper describes a general method of its application to population estimation in which the preliminary information on the spatial distribution pattern of the population under study can be incorporated as the parameters of the mean crowding‐mean relationship. The formulae that are necessary to perform sequential or double sampling plans for its efficient application are derived. The procedure of application of the method is explained with a numerical example.
Ovipositional response of Venturia canescens (Grav.) (Hymenoptera: Ichneumonidae) to various host and parasite densities
Authors: Stinner R. E.
Published: November 2007

Ovipositional response in Venturia canescens (Grav.) parasitizing Anagasta kühniella (Zeller) is analyzed for all combinations of five parasite densities (2, 5, 10, 25, and 50), four host densities (25, 50, 100, and 200), and three floor area universe sizes (76 cm2, 160 cm2, and 345 cm2). Over this range, no mutual interference (as measured by decreasing parasite fecundity) was observed, althoughNicholson'sarea of discovery decreased significantly with parasite density increase as a result of a non‐Poisson distribution of parasite eggs; use of this parameter is therefore not a suitable means of determining if mutual interference is present.

Other parameters studied, and for which significant correlations were obtained, include mean parasite eggs per host, percentage parasitization, percentage of parasite eggs wasted, and negative binomial k approximations.
Analysis of the aggregation behavior in the larvae of Harmonia axyridisPallas (Coleoptera: Coccinellidae) to prey colony
Authors: Kawai Akira
Published: November 2007

The searching and handling behaviors of Harmonia axyridis larvae to the colony of Rhopalosiphum padi were experimentally examined and the processes of their aggregation to the prey colony was analyzed.

All the instar larvae searched for the prey at random and they have no preference to the prey colony, but except the 1st instar they tend to aggregate to the plants with prey colonies. The 1st instar larvae tend to stay on the plants they once located. The 2nd to 4th instar larvae often emigrate from the plants without prey colony but seldom emigrate from the plants with prey colonies, and consequently, they aggregate to the plants with prey colonies. The expense of time to eat prey (in the 2nd and 3rd instars) and the change of searching behavior for the prey after feeding (in the 3rd and 4th instars) are responsible for the larval concentration to prey colony as a trapping effect for predators to prey colony.
The effect of the rate of successful dispersal of a Phytoseiid mite, Phytoseiulus persimilisAthias‐Henriot (Acarina: Phytoseiidae) on the persistence in the interactive system between the predator and its prey
Authors: Takafuji Akio
Published: November 2007

Dispersal behaviour was studied on a predacious phytoseiid mite, Phytoseiulus persimilisAthias‐Henriot in response to the density of its prey, Tetranychus kanzawaiKishida. And the effect of the change in the rate of successful dispersal of the predators among patches was tested on the persistence of the predator‐prey system. The results of the study are summarized as follows:

With a severe decline in prey density available per individual predator, the predators exhibited a marked behavioural change and dispersed to other areas.

When two neighboring host plants did not touch with each other and the dispersal of the predators was possible only through a 20cm plywood “bridge” which connected the two plants, the rate of successful dispersal of the predators was only 20 to 25%, whereas it was 95% when the plants touched with each other.

In the system where 32 host plants touched with each other, the predators succeeded in immigrating into all the plants by the 16th day, and they completely eliminated all the prey by the 33rd day.

In another system, the 32 plants were equally divided into eight “patches” which were connected with each other with two of the bridges and the predators could move between them only through the bridges as mentioned above. In such a system the predators and their prey coexisted about three times longer than in the other one.

It is suggested that for a longer continued coexistence of the predators and prey, it would be necessary to introduce more physical barrier against the dispersal of the predators and to provide more chances for the prey to disperse.
Generation carryover of a fraction of population members as an animal adaptation to unstable environmental conditions
Authors: Takahashi Fumiki
Published: November 2007

A heterogeneous life cycle of individuals in a population was examined on its adaptive significance to an unstable environmental condition. The trend of population growth was simulated by a simple mathematical model in which a part of population in a certain generation was carried over to the next generation without participating in the reproduction.

With the increase of the rate of carryover of individuals to the next generation the population fluctuation tended to be stabilized. A minute fraction of population is carried over, the effect is very large to prevent the population decline at a sequence of adverse environmental conditions. The population level increased greatly depending upon the extent of environmental change as far as the rate of carryover took an intermediate value. The optimum proportion of members to be carried over to the next generation was determined by the extent of environmental change and its frequency of occurrence.
Analysis of spatial association between two species based on the interspecies mean crowding
Authors: Iwao Syun'iti
Published: November 2007

Summary and Conclusion

The measurement of spatial association between two species is considered on the basis of interspecies mean crowding. Two indices of overlapping, γ and Cμ, are derived as geometric and weighted arithmetic means of the same component ratios related to inter‐ and intraspecies mean crowdings. Both indices behave in a similar way, ranging from 1 when the distributions of two species are completely overlapped to 0 when they are completely exclusive with each other. The former is essentially identical with indices proposed byKuno (1968) andPianka (1973), and the latter is a modified form ofMorisita's (1959)Cδ index. Indices to measure the degree of spatial correlation between species, ω and Rμ, are then derived for both kinds of overlapping indices, which vary from 1 in complete overlapping, through 0 in independent occurrence, to −1 in complete exclusion.

Various kinds of interspecies association are analyzed using these indices and an extended form of the regression graph which provides a convenient way of indicating the spatial interrelation between two species as well as distribution patterns of respective species.

The method presented in this paper may also be applicable to compare temporal distribution patterns between species, similarity between communities, etc. For such a wider application which includes continuous as well as discrete distributions, the interpretation of intra‐ and interspecies mean crowdings is not necessarily appropriate, and hence the concept of mean concentration with the symbols and for intraspecies relation and and for interspecies relation is suggested.
The influence of pheromones produced by freely growing laboratory populations on the reproductive maturation of prairie deermice following prenatal and postnatal exposure
Authors: Kipps Patricia L. , Terman C. Richard
Published: November 2007

Significantly more females reared on bedding soiled by different populations reproduced by 100 days of age than those reared on bedding soiled by the same populations (P<.1) or on clean bedding (P<.025) whereas the latter two groups did not differ significantly. Significantly greater percentages of females reproduced in both treatments maintained on soiled bedding than was true in the populations from which the bedding came. There were no significant differences between treatments in the weights of the reproductive organs (testes, seminal vesicles, ovaries, uteri) or in the numbers of corpora lutea or mature follicles in the ovaries of nulliparous females. The data suggest that if there were reproductively inhibiting pheromones influencing the population animals, they were altered or dissipated immediately after removal of the bedding from the population enclosures or that they were nonfunctional in the absence of the population animals. These data further suggest that the reproductive inhibition of population young is due to the presence of the populaton animals and that sociobiological factors within the populations act to prevent the reproductively stimulating influence of materials which may be present.
Characterization of Lipases and Esterases from Metagenomes for Lipid Modification
Authors: Bertram Mark , Hildebrandt Petra , Weiner David P. , Patel Jesal S. , Bartnek Flash , Hitchman Timothy S. , Bornscheuer Uwe T.
Published: November 2007

Three hundred and fifty novel lipases and esterases discovered from environmental DNA samples were characterized for their fatty acid profile using GC‐analysis. Enzymes were selected for further study based on activity and fatty acid chain length specificity. Additional characterization was based on enzyme activity towards tributyrin and 4‐methylumbelliferyl butyrate, and enzyme heat stability. Several lipases were identified, which show high specificity towards short‐chain fatty acids similar to pregastric lipases from kid and calf and a lipase from Mucor javanicus. Additionally, the metagenome‐derived enzymes were thermostable. Selected metagenomic lipases were immobilized on Celite and used for the synthesis of structured triglycerides.
ARCHAEOLOGY OF THE SELF: MICHAEL FINNISSY'S ‘FOLKLORE’
Authors: Beirens Maarten
Published: November 2007

The compositional output of Michael Finnissy includes several major cycles for piano solo, which stand out by reason of their dimensions and their scope. English Country-Tunes (1977/1982–85), Verdi Transcriptions (1972–92/1988–95/2002-), Gershwin Arrangements (1975–88) and Folklore (1993–94) are all long, technically demanding and full of expressive potential. Yet they have been outdone by Finnissy's most recent piano cycle: The History of Photography in Sound (1995–2001), a phenomenal endeavour, lasting over five and a half hours and employing every conceivable means of articulating musical expression and intellectual significance. Speaking of the scope of these works, however, does not merely entail their unusual length – although the extended duration, in comparison to what is considered customary for a solo piano piece, is indeed one of their prominent features. What is more significant here is their scope in terms of the wide array of ideas, concepts and statements that make up the musical text. In that respect, Folklore (like the other pieces mentioned here) is an unrelenting statement, reflecting upon or formulating a critique of many issues that are crucial to late-20th-century human existence. This article tries to demonstrate how all these layers of significance can indeed form the subject of a piece that is supposed to be ‘abstract’ (because textless, instrumental) music.
COMPOSER IN INTERVIEW: AARON COPLAND
Authors: Dickinson Peter
Published: November 2007

Aaron Copland gave many interviews during his lifetime but the present conversation only came to light recently. On 19 and 20 October 1976 Aaron Copland visited the University of Keele. The evening of the 19th was devoted to a concert including his music in the Walter Moberly Hall, after which he answered questions in front of a large audience. The next morning he spoke informally to music students. Copland has discussed some of these issues before but each time he gives them a different slant which makes his responses worth preserving.
SCHOENBERG'S PIANO SONATA
Authors: Bailey Kathryn
Published: November 2007

Arnold Schoenberg, of course, did not write a piano sonata. At any rate, none of his works for piano bears this title. As I have suggested elsewhere, however, sonata form was much in his thoughts as he wrote the piano pieces of opus 23, and one of his last two pieces for solo piano, written five years later, is a sonata movement which should stand as a model of the integration of twelve-note technique and classical form. When Pierre Boulez, in 1952, famously condemned Schoenberg for using the old forms instead of inventing new ones that were derived entirely from serialism, he might have taken just a moment to consider the ways in which the old form is articulated in opus 33a and been ever so slightly more charitable, for in this sonata movement, as in certain pieces of op. 23, themes and sections are defined and distinguished from each other in ways that have meaning only in relation to the twelve-note technique: though the form is an old one, the several parts are defined by reference to possibilities offered by the new method.
PERENNIAL QUESTIONS
Authors: Graubart Michael
Published: November 2007

What are twelve-note rows really for?

‘…I don't need to use serialism to…achieve a unity between the motifs’ says David Matthews in his interview with Mark Doran (Tempo, Vol. 57, No. 223, January 2003, p.11); and most composers would say the same. After all, the motifs and themes of the first movement of Schubert's Third Symphony are so integrated that even the accompanimental cliché of repeated quaver chords turns out to be motivic and the whole of the ‘Unfinished’ is based dialectically on the tonic and dominant versions of a single three-note motif and their sublation. And in his Ninth symphony, Beethoven manages to base not only themes but key-successions, too, on a basic group of four notes and finally even creates that shattering dissonance at the start of the finale out of a simultaneous sounding of its notes. Or is that already proto-serialism?
London, Barbican: ‘Etudes and Elegies’. Recent Turnage world premières (and CD releases)
Authors: Conway Paul
Published: November 2007

This year's BBC weekend at the Barbican dedicated to a single composer was given over to Mark-Anthony Turnage. Even Turnage himself expressed doubts initially about whether his music was diverse enough to withstand such exposure. His worries were unfounded, as the chance to explore his recent output, in particular, revealed a composer who is constantly growing in stature and breaking out in new and fruitful directions.
Deal Summer Music Festival: David Matthews UK and World Premières
Authors: Doran Mark
Published: November 2007

Nestling on the Kent coast between Ramsgate and Dover, the historic town of Deal is the distinctly pleasant home of a Summer Music Festival which in its 21 seasons has come to incorporate a fair amount of important contemporary music alongside more traditional offerings. This year's programme featured a welcome performance of the Seventh Piano Sonata (1956) by Harold Truscott (1914–92), marking the tenth anniversary of the death of this composer (resident in Deal from 1954); the world première of the choral work Town and Country (2002) by the Festival's new President, Kent-born Sir Richard Rodney Bennett (b.1936); and two compositions (and one arrangement) by David Matthews (b.1943), part-time Deal resident and the Festival's Artistic Director since 1989.
York University: Roger Marsh's ‘Pierrot Lunaire’
Authors: Jessen Edward
Published: November 2007

There is something of the poisoned chalice about setting the Belgian poet Albert Giraud's Pierrot Lunaire, Rondels Bergamasques – if nothing more than by association to the all-too-famous Schoenberg Sprechgesang melodrama. As interpreters of Giraud's work (and often as compositional interlopers), we are conditioned to assume that we ought not to bathe in the same water as Schoenberg. And yet the Yorkshire-based composer Roger Marsh has succeeded in (re)making Pierrot as a living resource with a tremendous staged production of Giraud's complete and enigmatic torrent of fantasy.
London, Barbican: Knussen's Symphony in One Movement
Authors: Service Tom
Published: November 2007

Oliver Knussen's Symphony in One Movement is his latest symphony. It is also his earliest – originally composed as the Concerto for Orchestra in 1969, and premièred by the 17-year old Knussen and the London Symphony Orchestra, with André Previn playing the flamboyant piano part. 33 years later, the piece has finally reached its definitive form, and Knussen conducted the BBC Symphony Orchestra in its world première as part of an all-Knussen programme in celebration of his 50th birthday, at the Barbican Hall on 1 November.
Birmingham, Symphony Hall and Manchester, RNCM: Muldowney's Piano Concerto No. 2 and ‘Serenade’
Authors: Conway Paul
Published: November 2007

The world première of Dominic Muldowney's Second Piano Concerto on 7 November came as part of a concert marking the 80th birthday of the BBC. The work was fashioned for Angela Hewitt, who was accompanied by the BBC Symphony Orchestra under Leonard Slatkin. Hewitt's core repertoire of Bach, Ravel and Messiaen was reflected in the style of Muldowney's new piece, which married Classical with neo-Classical idioms yet at the same time sounded thoroughly post-modern in its cheerful eclecticism, witty sidesteps and theatrical leaps of imagination.
London, Purcell Room: Inscape – the UK and Eire Composition Platform
Authors: Rickards Guy
Published: November 2007

The final round of the second ‘Inscape’ competition, brainchild of violinist Adam Summerhayes, took place in the Purcell Room on 27 November 2002. The award structure is three-fold: a jury prize, deliberated over several months from the preliminary entry phase through to the final award; a critics' prize, decided on the night by a panel of four critics who had had access to the seven finalist pieces a week or so beforehand; and an audience prize, made up of an exit poll after the seven finalists had each been played.
Variability for morphological traits and high molecular weight glutenin subunits in Spanish spelt lines
Authors: Alvarez J. B. , Caballero L. , Martín L. M.
Published: November 2007

Spelt (TriticumspeltaL.) is hulled wheat which was widely cultivated in Spain until the first half of the 20th century and is still cultivated in Asturias (northern Spain). Much of the variability of this species has been preserved, but little evaluation has been carried out. We describe the characterization of some of these spelt lines for several quantitative traits, including plant height and awnedness.
Is atherosclerosis a mitochondrial disorder?
Authors: Finsterer
Published: November 2007

There is increasing evidence that damage to the vascular environment from oxidative stress plays a major role in the pathogenesis of atherosclerosis in addition to classical risk factors, such as age, arterial hypertension, diabetes, dyslipidemia, smoking, vascular wall inflammation, or genetic predisposition. Oxidative stress results from the endogenous or exogenous generation of reactive oxidative or nitrogen species, generated by the respiratory chain or enzymatic sources. Oxidative stress results in lipid peroxidation, damage of mitochondrial components including mitochondrial DNA, mitochondrial dysfunction, damage of endothelial cells, vascular smooth muscle cells, and erythrocytes, and lastly apoptosis via either the receptor-mediated pathway or the mitochondria-mediated pathway and activation of the caspase cascade. Though re-balancing of the redox homeostasis by various agents is clinically hardly effective, various trials with experimental agents are promising in this respect. Overall, atherosclerosis appears to be the endpoint of various different pathogenetic mechanisms, of which oxidative stress and disturbed mitochondrial metabolism and function are key factors.
Periodic whole body acceleration: A novel therapy for cardiovascular disease
Authors: Kohler  , Amann-Vesti  , Clarenbach  , Brack  , Noll  , Russi  , Bloch
Published: November 2007

Background: Periodic whole body acceleration in the spinal axis (pGz) applied by a motion platform is a novel treatment modality that induced endothelial nitric oxide release into the circulation of animals, healthy subjects and patients with inflammatory diseases during single treatment sessions in previous studies. We hypothesized that patients with advanced arteriosclerotic diseases who are not candidates for a surgical intervention would clinically benefit from repeated pGz treatments over several weeks through improvement of endothelial function. Patients and methods: 11 patients, 5 men (37 to 71y) with stable ischemic heart disease, LVEF < 35%, NYHA stage > II, and 6 patients (51 to 83y, 1 woman) with intermittent leg claudication, Fontaine stage II, were enrolled after optimization of pharmacological therapy. PGz was applied for 40 min, 5 days/week during 5 weeks. Quality of life (SF-36 questionnaire), exercise performance, and endothelial function were assessed at baseline, during the treatment period, and 4 weeks after discontinuation of pGz. Results: PGz was well tolerated. In heart failure paitents, pGz therapy improved quality of life, increased 6 min walking distance by a mean ± SE of 105 ± 24 m, and improved postischemic skin hyperemia (p < .05 in all instances). In 4 of 6 patients with intermittent claudication, quality of life, treadmill walking distance and post-ischemic skin hyperemia improved with pGz therapy (p < .05). Four weeks after discontinuation of pGz, most therapeutic effects had vanished in both patient groups. Conclusions: In patients with severe heart failure and with leg claudication who remain symptomatic despite maximal medical therapy and who were not candidates for surgery, periodic acceleration applied over several weeks improved quality of life and exercise capacity. The clinical benefits appear to be mediated through improved endothelial function.
Designing Semantic Substrates for Visual Network Exploration
Authors: Aris Aleks , Shneiderman Ben
Published: November 2007

A semantic substrate is a spatial template for a network, where nodes are grouped into regions and laid out within each region according to one or more node attributes. This paper shows how users can be given control in designing their own substrates and how this ability leads to a different approach to network data exploration. Users can create a semantic substrate, enter their data, get feedback from domain experts, edit the semantic substrate, and iteratively continue this procedure until the domain experts are satisfied with the insights they have gained. We illustrate this process in two case studies with domain experts working with legal precedents and food webs. Guidelines for designing substrates are provided, including how to locate, size, and align regions in a substrate, which attributes to choose for grouping nodes into regions, how to select placement methods and which attributes to set as parameters of the selected placement method. Throughout the paper, examples are illustrated with NVSS 2.0, the network visualization tool developed to explore the semantic substrate idea.
Rapid magnetosome formation shown by real-time x-ray magnetic circular dichroism
Authors: Staniland Sarah , Ward Bruce , Harrison Andrew , van der Laan Gerrit , Telling Neil
Published: November 2007

Magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. Although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process, and no real-time studies of such processes have yet been performed. Thus, suggested formation mechanisms still need substantiating with data. Here we report the examination of the magnetosome material throughout the formation process in a real-timein vivostudy ofMagnetospirillum gryphiswaldense, strain MSR-1. Transmission EM and x-ray absorption spectroscopy studies reveal that full-sized magnetosomes are seen 15 min after formation is initiated. These immature magnetosomes contain a surface layer of the nonmagnetic iron oxide-phase hematite. Mature magnetite is found after another 15 min, concurrent with a dramatic increase in magnetization. This rapid formation result is contrary to previously reported studies and discounts the previously proposed slow, multistep formation mechanisms. Thus, we conclude that the biomineralization of magnetite occurs rapidly in magnetotactic bacteria on a similar time scale to high-temperature chemical precipitation reactions, and we suggest that this finding is caused by a biological catalysis of the process.
The 1.3-Å resolution structure of
Nitrosomonas europaea
Rh50 and mechanistic implications for NH
3
transport by Rhesus family proteins
Authors: Lupo Domenico , Li Xiao-Dan , Durand Anne , Tomizaki Takashi , Cherif-Zahar Baya , Matassi Giorgio , Merrick Mike , Winkler Fritz K.
Published: November 2007

The Rhesus (Rh) proteins are a family of integral membrane proteins found throughout the animal kingdom that also occur in a number of lower eukaryotes. The significance of Rh proteins derives from their presence in the human red blood cell membrane, where they constitute the second most important group of antigens used in transfusion medicine after the ABO group. Rh proteins are related to the ammonium transport (Amt) protein family and there is considerable evidence that, like Amt proteins, they function as ammonia channels. We have now solved the structure of a rare bacterial homologue (from
Nitrosomonas europaea
) of human Rh50 proteins at a resolution of 1.3 Å. The protein is a trimer, and analysis of its subunit interface strongly argues that all Rh proteins are likely to be homotrimers and that the human erythrocyte proteins RhAG and RhCE/D are unlikely to form heterooligomers as previously proposed. When compared with structures of bacterial Amt proteins, NeRh50 shows several distinctive features of the substrate conduction pathway that support the concept that Rh proteins have much lower ammonium affinities than Amt proteins and might potentially function bidirectionally.
Growth and age structure of sea urchins (Heliocidaris erythrogramma) in complex barrens and native macroalgal beds in eastern Tasmania
Authors: Pederson Hugh G. , Johnson Craig R.
Published: November 2007

Pederson, H. G., and Johnson, C. R. 2008. Growth and age structure of sea urchins (Heliocidaris erythrogramma) in complex barrens and native macroalgal beds in eastern Tasmania. – ICES Journal of Marine Science, 65: 1–11. The formation of small-scale barrens of sea urchins on the east coast of Tasmania allows for direct comparison of the growth rates and age structures of sea urchin populations in barrens and habitats dominated by native macroalgae. However, such barrens are atypical of any previously described in temperate regions worldwide mainly because of the establishment and seasonal colonization by the introduced macroalga Undaria pinnatifida. Growth models were fitted to sea urchin (Heliocidaris erythrogramma) data, based on tag-recapture information from two distinct community types, a native macroalgal bed and a sea urchin barren colonized by U. pinnatifida. Despite the distinct contrast in habitats, size-at-age relationships and age frequency distributions were not significantly different between the two populations. However, the relationship between jaw length and test diameters was significantly different between populations, sea urchins in barrens possessing larger jaws relative to conspecifics of similar test diameter in native macroalgal habitats. It is proposed that the growth of sea urchins on barrens is not adversely affected by the loss of native macroalgae in the presence of U. pinnatifida. However, sea urchins display a level of resource limitation in barrens because of differences in the relationships of sea urchin morphometrics.
Pelvic abscess caused by Arcanobacterium haemolyticum mimicking a soft tissue tumour
Authors: van Loo I. H. M. , van den Wildenberg W. J. , van Huijstee P. J. , Roukema J. A. , Apperloo A. J. , Peeters M. F.
Published: November 2007

Arcanobacterium haemolyticum has usually been isolated in cases of pharyngitis and wound infections. Rarely it has been reported to cause deep tissue infections. Here, a case of a 71-year-old-male, who developed a pelvic abscess due to A. haemolyticum that initially was thought to be a malignant tumour, is described.
Characterization of skin microbiota in patients with atopic dermatitis and in normal subjects using 16S rRNA gene-based comprehensive analysis
Authors: Dekio Itaru , Sakamoto Mitsuo , Hayashi Hidenori , Amagai Masayuki , Suematsu Makoto , Benno Yoshimi
Published: November 2007

A previous study using bacterial 16S rRNA gene-based clone libraries revealed that the microbiota in healthy human skin included uncultured micro-organisms, although the micro-organisms in skin exposed to disease conditions remain to be examined. To compare the profiles of skin microbiota in 13 patients with atopic dermatitis (AD) and 10 healthy controls, terminal RFLP analysis of bacterial 16S rRNA genes was applied to 23 swab-scrubbed samples from facial skin. This culture-independent analysis successfully revealed the complex bacterial members of the microbiota as peak patterns following capillary electrophoresis of terminal restriction fragments (T-RFs). Each T-RF peak reflected a micro-organism, and the micro-organism to which each peak was assigned could be identified by computer simulation of T-RF length using the nucleotide sequence data of bacterial species residing in the skin. Among 18 species detected in the study,Stenotrophomonas maltophiliawas detected significantly more commonly in AD patients (5/13 for AD patients vs 0/10 for controls), whilstDietzia mariswas detected significantly more commonly in normal controls (8/10 for controls vs 2/13 for AD patients). Moreover,Streptococcusspecies, which are considered to be uncommon in uninfected skin, were detected in seven patients and eight normal controls. Although further studies should be undertaken to investigate the roles of these micro-organisms in AD, the microbiota were presumed to include hitherto uninvestigated bacterial species in the major population of patients with AD and of healthy controls.
Imbalance in the composition of the duodenal microbiota of children with coeliac disease
Authors: Nadal Inmaculada , Donant Esther , Ribes-Koninckx Carmen , Calabuig Miguel , Sanz Yolanda
Published: November 2007

Coeliac disease (CD) is the most common immune-mediated enteropathy characterized by chronic inflammation of the small intestinal mucosa. The ingestion of gluten is responsible for the symptoms of CD, but other environmental factors are also thought to play a role in this disorder. In this study, the composition of the duodenal microbiota of coeliac children with active disease, symptom-free CD patients on a gluten-free diet and control children was determined. Bacteriological analyses of duodenal biopsy specimens were carried out by fluorescentin situhybridization coupled with flow cytometry. The proportions of total bacteria and Gram-negative bacteria were significantly higher in CD patients with active disease than in symptom-free CD patients and controls.BacteroidesandEscherichia coligroups were significantly more abundant in CD patients with active disease than in controls, whilst these bacterial deviations were normalized in symptom-free CD patients. The ratio ofLactobacillus–BifidobacteriumtoBacteroides–E. coliwas significantly reduced in coeliac patients with either active or inactive disease compared with controls. The differences inAtopobium,Eubacterium rectale–Clostridium coccoides,Clostridium histolyticum,Clostridium lituseburense, sulphate-reducing bacteria andFaecalibacterium prausnitziipopulations among the three groups of children were less relevant. Overall, the higher incidence of Gram-negative and potentially pro-inflammatory bacteria in the duodenal microbiota of coeliac children was linked to the symptomatic presentation of the disease and could favour the pathological process of the disorder.
Experimental infection of dairy calves with Ehrlichia chaffeensis
Authors: delos Santos Jose R. C. , Boughan Kirsten , Bremer William G. , Rizzo Brian , Schaefer John J. , Rikihisa Yasuko , Needham Glen R. , Capitini L. A. , Anderson David E. , Oglesbee Michael , Ewing S. A. , Stich Roger W.
Published: November 2007

Human monocytic ehrlichiosis (HME) is a zoonotic emerging tick-borne disease with clinical signs that range from mild symptoms to multiple organ failure and death.Ehrlichia chaffeensis, the aetiologic agent of HME, is reported to infect a divergent range of mammals. Although cattle are common hosts of the primary vector of this pathogen, the susceptibility of this host toE. chaffeensishas not been reported to date. This study was undertaken to determine if cattle could provide a useful infection model ofE. chaffeensis. Dairy calves were injected with DH82 cells infected with the Arkansas, St Vincent or 91HE17 strain ofE. chaffeensis, and monitored for signs of clinical ehrlichiosis and for infection of peripheral blood and ticks by PCR assay. Splenectomized and spleen-intact calves were injected with cryopreserved stabilates ofE. chaffeensis-infected DH82 cells for the first experiment. Mild clinical signs were occasionally observed among these calves, and only two blood samples were PCR-positive, while several ticks fed on each calf tested PCR-positive. The second experiment involved injection of normal calves with active cultures of the sameE. chaffeensisstrains. Interestingly, three of six calves inoculated with active cultures became recumbent and died or had to be euthanized. All of the surviving calves in this experiment tested PCR-positive on multiple dates, but fewer ticks fed on these calves were PCR-positive. These results suggest that a bovine disease model could facilitate the understanding of factors that affect the severity of HME.
Misidentification of Bordetella bronchiseptica as Bordetella pertussis using a newly described real-time PCR targeting the pertactin gene
Authors: Register Karen B. , Nicholson Tracy L.
Published: November 2007

Recently, a real-time PCR (RT-PCR) assay based on sequence from the gene for pertactin was proposed for identification of Bordetella pertussis. Here, it is reported that the B. pertussis pertactin gene sequence for the region that encompasses the RT-PCR probe and primers is nearly identical to that of many Bordetella bronchiseptica strains of human and avian origin. Additionally, it is demonstrated that such strains are erroneously identified as B. pertussis using the RT-PCR assay. These data suggest that the use of the assay without confirmatory testing may result in erroneous identification of a significant proportion of human isolates of B. bronchiseptica as B. pertussis.
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
Authors: Schwartz Schraga , Silva João , Burstein David , Pupko Tal , Eyras Eduardo , Ast Gil
Published: November 2007

Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5′ splice site (5′ss), the branch site (BS), and the polypyrimdine tract/3′splice site (PPT-3′ss). To study the evolution of these splicing signals, we have conducted a systematic comparative analysis of these signals in over 1.2 million introns from 22 eukaryotes. Our analyses suggest that all these signals have dramatically evolved: The PPT is weak among most fungi, intermediate in plants and protozoans, and strongest in metazoans. Within metazoans it shows a gradual strengthening from Caenorhabditis elegans to human. The 5′ss and the BS were found to be degenerate among most organisms, but highly conserved among some fungi. A maximum parsimony-based algorithm for reconstructing ancestral position-specific scoring matrices suggested that the ancestral 5′ss and BS were degenerate, as in metazoans. To shed light on the evolutionary variation in splicing signals, we have analyzed the evolutionary changes in the factors that bind these signals. Our analysis reveals coevolution of splicing signals and their corresponding splicing factors: The strength of the PPT is correlated to changes in key residues in its corresponding splicing factor U2AF2; limited correlation was found between changes in the 5′ss and U1 snRNA that binds it; but not between the BS and U2 snRNA. Thus, although the basic ability of eukaryotes to splice introns has remained conserved throughout evolution, the splicing signals and their corresponding splicing factors have considerably evolved, uniquely shaping the splicing mechanisms of different organisms.
Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution
Authors: Du Xiangjun , Wang Zhuo , Wu Aiping , Song Lin , Cao Yang , Hang Haiying , Jiang Taijiao
Published: November 2007

The recent availability of full genomic sequence data for a large number of human influenza A (H3N2) virus isolates over many years provides us an opportunity to analyze human influenza virus evolution by considering all gene segments simultaneously. However, such analysis requires development of new computational models that can capture the complex evolutionary features over the entire genome. By analyzing nucleotide co-occurrence over the entire genome of human H3N2 viruses, we have developed a network model to describe H3N2 virus evolutionary patterns and dynamics. The network model effectively captures the evolutionary antigenic features of H3N2 virus at the whole-genome level and accurately describes the complex evolutionary patterns between individual gene segments. Our analyses show that the co-occurring nucleotide modules apparently underpin the dynamics of human H3N2 evolution and that amino acid substitutions corresponding to nucleotide co-changes cluster preferentially in known antigenic regions of the viral HA. Therefore, our study demonstrates that nucleotide co-occurrence networks represent a powerful method for tracking influenza A virus evolution and that cooperative genomic interaction is a major force underlying influenza virus evolution.
Gene expression profiling by massively parallel sequencing
Authors: Torres Tatiana Teixeira , Metta Muralidhar , Ottenwälder Birgit , Schlötterer Christian
Published: November 2007

Massively parallel sequencing holds great promise for expression profiling, as it combines the high throughput of SAGE with the accuracy of EST sequencing. Nevertheless, until now only very limited information had been available on the suitability of the current technology to meet the requirements. Here, we evaluate the potential of 454 sequencing technology for expression profiling using Drosophila melanogaster. We show that short (< ∼80 bp) and long (> ∼300–400 bp) cDNA fragments are under-represented in 454 sequence reads. Nevertheless, sequencing of 3′ cDNA fragments generated by nebulization could be used to overcome the length bias of the 454 sequencing technology. Gene expression measurements generated by restriction analysis and nebulization for fragments within the 80- to 300-bp range showed correlations similar to those reported for replicated microarray experiments (0.83–0.91); 97% of the cDNA fragments could be unambiguously mapped to the genomic DNA, demonstrating the advantage of longer sequence reads. Our analyses suggest that the 454 technology has a large potential for expression profiling, and the high mapping accuracy indicates that it should be possible to compare expression profiles across species.