bluuebunny/crossref_metadata_2025 huggingface dataset:
An observation on Korn’s inequality for nonconforming finite element methods
Authors: Mardal Kent-Andre , Winther Ragnar
Published: November 2005

By utilizing a simple observation on traces of rigid motions we are able to strengthen a result of Brenner (2004) on Korn’s inequality for nonconforming finite element methods. The approach here is tightly connected to the theory developed in Brenner’s work. Our motivation for the analysis was the desire to show that a robust Darcy–Stokes element satisfies Korn’s inequality, and to achieve this the stronger result seems necessary.
Gröbner bases and generalized Padé approximation
Authors: Farr Jeffrey , Gao Shuhong
Published: November 2005

It is shown how to find general multivariate Padé approximation using the Gröbner basis technique. This method is more flexible than previous approaches, and several examples are given to illustrate this advantage. When the number of variables is small compared to the degree of approximation, the Gröbner basis technique is more efficient than the linear algebra methods in the literature.
Hierarchical decomposition of domains with fractures
Authors: Gebauer Susanna , Kornhuber Ralf , Yserentant Harry
Published: November 2005

We consider the efficient and robust numerical solution of elliptic problems with jumping coefficients occurring on a network of thin fractures. We present an iterative solution concept based on a hierarchical separation of the fractures and the surrounding rock matrix. Upper estimates for the convergence rates are independent of the width of the fractures and of the jumps of the coefficients. Inexact solution of the local subproblems is also considered. The theoretical results are illustrated by numerical experiments.
Full-Length Dimeric MCAK Is a More Efficient Microtubule Depolymerase than Minimal Domain Monomeric MCAK
Authors: Hertzer Kathleen M. , Ems-McClung Stephanie C. , Kline-Smith Susan L. , Lipkin Thomas G. , Gilbert Susan P. , Walczak Claire E.
Published: November 2005

MCAK belongs to the Kinesin-13 family, whose members depolymerize microtubules rather than translocate along them. We defined the minimal functional unit of MCAK as the catalytic domain plus the class specific neck (MD-MCAK), which is consistent with previous reports. We used steady-state ATPase kinetics, microtubule depolymerization assays, and microtubule·MCAK cosedimentation assays to compare the activity of full-length MCAK, which is a dimer, with MD-MCAK, which is a monomer. Full-length MCAK exhibits higher ATPase activity, more efficient microtubule end binding, and reduced affinity for the tubulin heterodimer. Our studies suggest that MCAK dimerization is important for its catalytic cycle by promoting MCAK binding to microtubule ends, enhancing the ability of MCAK to recycle for multiple rounds of microtubule depolymerization, and preventing MCAK from being sequestered by tubulin heterodimers.
Classification of microarray data with factor mixture models
Authors: Martella Francesca
Published: November 2005

Motivation: The classification of few tissue samples on a very large number of genes represents a non-standard problem in statistics but a usual one in microarray expression data analysis. In fact, the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. We consider high-density oligonucleotide microarray data, where the expression level is associated to an ‘absolute call’, which represents a qualitative indication of whether or not a transcript is detected within a sample. The ‘absolute call’ is generally not taken in consideration in analyses.

Results: In contrast to frequently used cluster analysis methods to analyze gene expression data, we consider a problem of classification of tissues and of the variables selection. We adopted methodologies formulated by Ghahramani and Hinton and Rocci and Vichi for simultaneous dimensional reduction of genes and classification of tissues; trying to identify genes (denominated ‘markers’) that are able to distinguish between two known different classes of tissue samples. In this respect, we propose a generalization of the approach proposed by McLachlan et al. by advising to estimate the distribution of log LR statistic for testing one versus two component hypothesis in the mixture model for each gene considered individually, using a parametric bootstrap approach. We compare conditional (on ‘absolute call’) and unconditional analyses performed on dataset described in Golub et al. We show that the proposed techniques improve the results of classification of tissue samples with respect to known results on the same benchmark dataset.

Availability: The software of Ghahramani and Hinton is written in Matlab and available in ‘Mixture of Factor Analyzers’ on while the software of Rocci and Vichi is available upon request from the authors.

Contact:  francesca.martella@uniroma1.it
Equivalent binding sites reveal convergently evolved interaction motifs
Authors: Henschel Andreas , Kim Wan Kyu , Schroeder Michael
Published: November 2005

Motivation: Much research has been devoted to the characterization of interaction interfaces found in complexes with known structure. In this context, the interactions of non-homologous domains at equivalent binding sites are of particular interest, as they can reveal convergently evolved interface motifs. Such motifs are an important source of information to formulate rules for interaction specificity and to design ligands based on the common features shared among diverse partners.

Results: We develop a novel method to identify non-homologous structural domains which bind at equivalent sites when interacting with a common partner. We systematically apply this method to all pairs of interactions with known structure and derive a comprehensive database for these interactions. Of all non-homologous domains, which bind with a common interaction partner, 4.2% use the same interface of the common interaction partner (excluding immunoglobulins and proteases). This rises to 16% if immunoglobulin and proteases are included. We demonstrate two applications of our database: first, the systematic screening for viral protein interfaces, which can mimic native interfaces and thus interfere; and second, structural motifs in enzymes and its inhibitors. We highlight several cases of virus protein mimicry: viral M3 protein interferes with a chemokine dimer interface. The virus has evolved the motif SVSPLP, which mimics the native SSDTTP motif. A second example is the regulatory factor Nef in HIV which can mimic a kinase when interacting with SH3. Among others the virus has evolved the kinase’s PxxP motif. Further, we elucidate motif resemblances in Baculovirus p35 and HIV capsid proteins. Finally, chymotrypsin is subject to scrutiny wrt. its structural similarity to subtilisin and wrt. its inhibitor’s similar recognition sites.

Contact:  ah@biotec.tu-dresden.de

Supplementary informaton: A database is online at
2SNP: scalable phasing based on 2-SNP haplotypes
Authors: Brinza Dumitru , Zelikovsky Alexander
Published: November 2005

Summary: 2SNP software package implements a new very fast scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs. This software can be used for comparatively accurate phasing of large number of long genome sequences, e.g. obtained from DNA arrays. As an input 2SNP takes genotype matrix and outputs the corresponding haplotype matrix. On datasets across 79 regions from HapMap 2SNP is several orders of magnitude faster than GERBIL and PHASE while matching them in quality measured by the number of correctly phased genotypes, single-site and switching errors. For example, 2SNP requires 41 s on Pentium 4 2 Ghz processor to phase 30 genotypes with 1381 SNPs (ENm010.7p15:2 data from HapMap) versus GERBIL and PHASE requiring more than a week and admitting no less errors than 2SNP.

Availability: 2SNP software package is publicly available at

Contact:  alexz@cs.gsu.edu
The South Kensington Music Schools and the Development of the British Conservatoire in the Late Nineteenth Century
Authors: Wright David
Published: November 2005

In 1876, the National Training School for Music was established by the Society of Arts as a model of advanced music education after the pattern of leading European conservatoires. But, despite having Arthur Sullivan as Principal, the School failed amidst the rumblings of an academic scandal that dogged George Grove's attempt to establish the new Royal College of Music. The article sets this failure against the successful start of the Royal College and explains how conservatoires, after being in all practical senses virtually an irrelevance to professional concert life, managed to reinvent themselves as vital incubators of British musical talent.
A Hungarian Patriot in American Exile: Béla Bartók and Émigré Politics
Authors: Dreisziger Nándor F.
Published: November 2005

Béla Bartók was an intensely private man who avoided politics throughout most of his life. At the same time he was so passionately devoted to his Hungarian nation that, even during the difficult years of his American exile, he felt compelled to become involved in pro-Hungarian activities. At one point he accepted the leadership of an organization that had started out as a political lobby and a base for a possible Hungarian government-in-exile.
Non-slipping adhesive contact of an elastic cylinder on stretched substrates
Authors: Chen Shaohua , Gao Huajian
Published: November 2005

The plane strain problem of an elastic cylinder in adhesive contact with a stretched substrate is studied via a generalized JKR model taking into account the transmission of both tangential and normal tractions across the contact interface. The width of the contact region is determined from the Griffith energy balance near the contact edge. In the absence of external loading, the tangential traction is found to have a negligible effect on the contact size. As an external stress is applied to stretch the substrate, the contact solution exhibits three distinct regimes characterized by two threshold strains: (i) the size of the contact region is hardly affected by the applied loading when the substrate strain is below the first threshold level; (ii) the contact size decreases quickly with stretch as the substrate strain increases to between the two threshold levels; (iii) the contact size approaches zero when the substrate strain exceeds the second threshold level. Interestingly, these results share a number of common features with the experimentally observed cell reorientation on a cyclically stretched substrate. An approximate solution is presented in an
appendix
to represent the numerical results in closed form.
Travelling waves for delayed reaction–diffusion equations with global response
Authors: Faria Teresa , Huang Wenzhang , Wu Jianhong
Published: November 2005

We develop a new approach to obtain the existence of travelling wave solutions for reaction–diffusion equations with delayed non-local response. The approach is based on an abstract formulation of the wave profile as a solution of an operational equation in a certain Banach space, coupled with an index formula of the associated Fredholm operator and some careful estimation of the nonlinear perturbation. The general result relates the existence of travelling wave solutions to the existence of heteroclinic connecting orbits of a corresponding functional differential equation, and this result is illustrated by an application to a model describing the population growth when the species has two age classes and the diffusion of the individual during the maturation process leads to an interesting non-local and delayed response for the matured population.
Expansion formulae in wave structure interaction problems
Authors: Manam S.R , Bhattacharjee J , Sahoo T
Published: November 2005

A large class of problems in the field of fluid–structure interaction involves higher-order boundary conditions for the governing partial differential equation and the eigenfunctions associated with these problems are not orthogonal in the usual sense. In the present study, mode-coupling relations are derived by utilizing the Fourier integral theorem for the solutions of the Laplace equation with higher-order derivatives in the boundary conditions in both the cases of a semi-infinite strip and a semi-infinite domain in two dimensions. The expansion for the velocity potential is derived in terms of the corresponding eigenfunctions of the boundary-value problem. Utilizing such an expansion of the velocity potential, the symmetric wave source potentials or the so-called Green's function for the boundary-value problem of the flexural gravity wave maker is derived. Alternatively, utilizing the integral form of the wave source potential, the expansion formulae for the velocity potentials are recovered, which justifies the completeness of the eigenfunctions involved. As an application of the wave maker problem, oblique water wave scattering caused by cracks in a floating ice-sheet is analysed in the case of infinite depth.
Association of the C677T methylenetetrahydrofolate reductase mutation with congenital heart diseases
Authors: Lee Chien‐Nan , Su Yi‐Ning , Cheng Wen‐Fang , Lin Ming‐Tai , Wang Jou‐Kou , Wu Mei‐Hwan , Hsieh Fon‐Jou
Published: November 2005

Background.  To investigate whether the cytosine‐to‐thymine mutation at base 677 of the gene for methylenetetrahydrofolate reductase (MTHFR) is associated with congenital heart diseases (CHD), using high throughput heteroduplex analysis based upon the powerful technique of denaturing high‐performance liquid chromatography.

Methods.  We investigated the MTHFR genotype of a cytosine‐to‐thymine mutation at base 677 for 213 patients of CHDs as confirmed by cardiac catheterization and also for 195 healthy controls.

Results.  The overall genotype frequencies of the MTHFR C677T polymorphism were not significantly different between the CHD patients and the healthy control (P = 0.345). Furthermore, taking various subgroups of CHD patients into consideration, we noted a significantly increased proportion of homozygous TT genotypes for patients suffering from valvular pulmonary stenosis (PS) or pulmonary atresia with an intact ventricular septum (PA + IVS) (p = 0.0005). For patients revealing heterotaxy syndrome, a conotruncal anomaly including tetralogy of Fallot, an interruption of the aortic arch, persistent truncus arteriosus, and aortopulmonary window, no statistically significant difference existed.

Conclusions.  The discrepancy in the distribution of MTHFR genotypes amongst various subtypes of CHD reflects some heterogeneity in the developmental mechanism of CHD. The increased percentage of homozygous TT genotypes might contribute to the pathogenesis of valvular PS and PA + IVS.
Increased granulocyte chemotactic protein‐2 concentrations in peritoneal fluid of women with endometriosis
Authors: Suzumori Nobuhiro , Zhao Xaio Xi , Suzumori Kaoru
Published: November 2005

Background.  To evaluate the release of granulocyte chemotactic protein‐2 (GCP‐2) into peritoneal fluid in women with endometriosis, we measured its concentration with reference to the disease stage and the phase of the menstrual cycle.

Methods.  Surgery was scheduled in the proliferative or secretory phase of the menstrual cycle for 64 women with endometriosis (n = 38) or cystadenomas (n = 26). GCP‐2 concentrations in the peritoneal fluid were measured using an enzyme‐linked immunosorbent assay.

Result.  Our findings indicated elevated concentrations of GCP‐2 in peritoneal fluid from women with endometriosis during the proliferative phase, which were positively correlated with the stage of endometriosis.

Conclusion.  Inflammation associated with endometriosis may be involved in the pathogenesis of the disease through increasing levels of peritoneal fluid GCP‐2.
Maternal underweight and the risk of spontaneous abortion
Authors: Helgstrand Stine , Andersen Anne‐Marie Nybo
Published: November 2005

Background.  To evaluate the risk of spontaneous abortion in relation to maternal pre‐pregnant underweight.

Methods.  The study was designed as a cohort study within the framework of the Danish National Birth Cohort (DNBC). The participants were a total of 23 821 women recruited consecutively to the DNBC from October 1, 1997 to March 31, 1999 and interviewed subsequently. The pregnant women were recruited in first half of pregnancy and interviewed about pre‐pregnant body size, obstetric history, exposures in pregnancy, and socio‐demographic factors. Pregnancies were followed‐up regarding spontaneous abortion. Relative risk of spontaneous abortion was calculated as Hazard Ratios using Cox regression with delayed entry.

Results.  The outcome measure was spontaneous abortion. The hazard ratio for spontaneous abortion in women with a pre‐pregnant body mass index (BMI) below 18.5 was 1.24 (95% confidence limits 0.95–1.63) compared to women with pre‐pregnant BMI 18.5–24.9. Women with a BMI of 25 or more had a smaller increase in risk of spontaneous abortion. Adjustment for maternal age, parity, previous miscarriages, and lifestyle factors did not affect the estimates substantially, neither did exclusion of women with metabolic or eating disorders.

Conclusion.  These results indicate that pre‐pregnant underweight may affect the risk of spontaneous abortion negatively.
A study of oligosaccharide variants of alpha‐fetoproteins produced by normal fetuses and fetuses with trisomy 21
Authors: Yamamoto Ritsu , Ohkouchi Toshihiro , Tabata Kouichi , Ebina Yasuhiko , Watari Hidemichi , Kudo Masataka , Shimizu Kayoko , Satomura Shinji , Minakami Hisanori , Sakuragi Noriaki
Published: November 2005

Background.  The mechanisms of the increase in the percentage of alpha‐fetoproteins (AFPs) that strongly binds to Lens culinaris agglutinin (AFP‐L3) in pregnancies with a trisomy 21 fetus have not been analyzed. To investigate the oligosaccharide variants of AFP produced by normal fetuses and fetuses with trisomy 21, the lectin reactivity of AFP was analyzed.

Methods.  Fetal liver tissue, amniotic fluid, and maternal serum were obtained from five normal pregnancies and five pregnancies with a trisomy 21 fetus. The percentages of AFP reactive to lectins were determined by lectin‐affinity electrophoresis coupled with antibody‐affinity blotting.

Results.  The percentages of AFP‐L3 in the fetal liver and the maternal serum were 23.9 and 27.0%, respectively, in normal pregnancies, and 28.7 and 38.5%, respectively, in pregnancies with a trisomy 21 fetus. There was no statistically significant difference between the percentage in the fetal liver and the percentage in the maternal serum in normal pregnancies; however, a significant difference (P < 0.01) was found in pregnancies with a trisomy 21 fetus. In regard to the percentage of AFP‐L3 in the fetal liver, there was no significant difference; however, a significant difference (P < 0.05) was found in the maternal serum between normal pregnancies and pregnancies with a trisomy 21 fetus.

Conclusions.  The transference of the AFP‐L3 fraction might be relatively high in the placentas of women carrying a trisomy 21 fetus, and this could be the one of the reasons for the increase in the percentage of AFP‐L3 in the maternal serum in pregnancies with a trisomy 21 fetus.
O3 2  Cumulative delivery rate from a single oocyte harvest
Authors: Hydén‐Granskog C , Unkila‐Kallio L , Ahola U , Halttunen M , Tiitinen A.
Published: November 2005

Background.  There is an urgent need to evaluate the cumulative delivery rate (DR) from a single oocyte harvest after both fresh and frozen embryo transfers (ET). Elective single embryo transfer (eSET) in combination with embryo cryopreservation has reduced the multiple delivery rate (MDR) compared with transfer of two embryos (DET), but the effect of frozen embryo transfers (FET) on cumulative DR and multiple DR has not been evaluated. In cases of imminent risk of ovarian hyperstimulation syndrome (OHSS) fresh ET is not performed and all embryos are cryopreserved. However, little is known about the DR after later frozen ETs from these OHSS cycles.

The aim was to find out the total reproductive potential from a single oocyte harvest i.e. DR after fresh transfer and one or several frozen embryo transfers performed after an unsuccesful fresh transfer.

The FET cycles performed during 1.3.1998–30.6.2004 were as follows: in the eSET group 907 FETs, in eDET 516 FETs and in no ET 161 FETs. In FET cycles one or two embryos were transferred in the eSET group. The mean number of embryos transferred in FET cycles was 1.5/1.6/1.5 respectively.

Methods.  All OPU‐cycles with ET and/or cryopreservation during 1998–2003.

Type of transfer
SET
eSET*
DET
eSET + cryo
eDET + cryo
No ET + cryo

Number
260
10
197
791
608
66

Mean age
33.6
36.2
34.5
32.3
34.1
31.9

mean n of cryo
0
0
0
6.4
3.4
12.4

embryos (range)

(1–31)
(1–24)
(1–39)

no cryopreservation due to poor quality of the other embryo

Findings.

Type of transfer
SET
eSET*
DET
eSET + cryo
eDET + cryo
No ET + cryo

DR in fresh cycles
15.4%
20.0%
23.5%
29.0%
30.9%
0

MDR
2.5%
0
10.9%
1.3%
26.6%
0

DR in FET cycles
0
0
0
24.9%
18.8%
24.2%

Cumulative DR
15.4%
20%
23.5%
52.6%
42.8%
54.5%

Cumulative MDR
2.5%
0
10.9%
6.7%
25.0%
16.7%

no cryopreservation due to poor quality of the other embryo

Interpretation.  Delivery rate in OPU cycles without cryopreservation was lower than in cycles with cryopreservation. In OPU cycles with cryopreservation the DR was not effected by the number of embryos transferred, but more twins were seen in cycles with eDET than with eSET (26.6% compared to 1.3%). The cumulative DR in the group with eSET in the fresh cycle exceeded that with eDET (52.6% vs 42.8%). In the eSET group only 6.7% of the deliveries were multiples compared to 25% in the group with eDET. Elective SET and cryopreservation is an effective tool not only to achieve a good cumulative delivery rate, but also to reduce multiple births. The possibility to cryopreserve all embryos in case of risk for OHSS is associated with good DR from frozen cycles, since at least one delivery has been achieved in 54.5% of these cycles.
Relative strengths of trait‐mediated and density‐mediated indirect effects of a predator vary with resource levels in a freshwater food chain
Authors: Wojdak Jeremy M. , Luttbeg Barney
Published: November 2005

Predators can affect the density and traits (e.g. morphology, behavior) of their prey, and either change may influence how prey interact with their resources. Thus, predators can interact indirectly with resource species (i.e. two trophic levels below) through two separate mechanisms. The relative strengths of these two kinds of indirect effects have rarely been compared directly, and how their relative importance varies across environmental gradients is virtually unknown. We investigated the relative strength of trait‐ and density‐mediated indirect effects of the predatory insect Belostoma flumineum on algal communities through predation on the pond snail, Physa gyrina, across a gradient of basal resource abundance. Because prey balance the benefits of foraging against the increased risk of predation while foraging, the availability of the prey's resource should influence the strength of anti‐predator behavioral responses and hence the strength of trait‐mediated indirect interactions. Belostoma presence had positive indirect effects on resources as expected and total predator effects were constant across the basal resource gradient. At low initial resource levels, trait‐mediated indirect effects on algal biomass exceeded density‐mediated indirect effects, while at high initial resources the reverse was true. Snails showed similar habitat use across the resource gradient suggesting that the anti‐predator response was most likely a depression of activity levels.
Should I stay or should I go? Patch departure decisions by herbivores at multiple scales
Authors: Searle Kate R. , Thompson Hobbs N. , Shipley Lisa A.
Published: November 2005

The question of how much time a foraging herbivore should spend in a patch of food poses a central challenge in classical foraging theory. However, there remains uncertainty about the relevance of the patch paradigm to foraging decisions by large herbivores. This paper examines evidence for successfully predicting and quantifying patch departure decisions for large mammalian herbivores foraging across several spatial and temporal scales. Departure decisions at fine scales are influenced by tradeoffs between maximizing intake rate and food quality. Classical models for departure decisions at larger spatial scales, particularly the marginal value theorem, appear inadequate. We advocate exploring alternative models for predictions of residence time at the patch scale.
Decoupling of pelagic and littoral food webs in oligotrophic Canadian Shield lakes
Authors: Bertolo Andrea , Carignan Richard , Magnan Pierre , Pinel‐Alloul Bernadette , Planas Dolors , Garcia Edenise
Published: November 2005

The importance of top‐down effects of piscivorous fish on phytoplankton in natural oligotrophic lakes is still debated. In this study, we analyzed patterns in phytoplankton and zooplankton abundance in 37 oligotrophic Canadian Shield lakes in relation to variations in both piscivorous fish predation and resources (total phosphorus; TP). Zooplankton community structure (but not total biomass) was partially affected by the variation in fish predation while the phytoplankton community structure and total biomass showed no response. Carbon isotope analyses revealed that the lack of top‐down effects is due to the uncoupling of the littoral and the pelagic food webs. We found that the fish community depends mostly on benthic resources, suggesting that only low planktivory occurred in our study lakes. Due to the absence of specialized zooplanktivorous fish, zooplankton is poorly exploited in these lakes and thus able to control phytoplankton by grazing. A comparison of our data with published studies on the TP–chlorophyll a relationships in both natural and manipulated systems shows that the phytoplankton biomass per unit of TP is relatively low in Canadian Shield lakes.
Liquidity and Twin Crises
Authors: Song Shin Hyun
Published: November 2005

This paper proposes a simple analytical framework for understanding ‘twin crises’– i.e. crises where a currency crisis and banking crisis occur simultaneously and reinforce each other. The distinguishing feature of such crises is the spill‐over effects across financial institutions through collateral constraints, declines in market values of assets, currency mismatches on the balance sheet and the endogenous amplification of financial distress through asset sales. We explore the role of liquidity and the role of monetary policy in such crises. In particular, a central question is whether raising interest rates in the face of a twin crisis is the appropriate policy response. Raising interest rates has two countervailing effects. Holding the domestic currency becomes more attractive (other things being equal), but the value of the domestic banking system falls due to the fall in asset prices. When assets are marked to market, there is a potential for endogenously generated financial distress that leads to a collapse of asset prices, as well as the exchange rate. It is thus possible that raising interest rates can have the perverse effect of exacerbating both the currency crisis and the banking crisis.
Competition and Profitability in European Banking: Why Are British Banks So Profitable?
Authors: Llewellyn David T.
Published: November 2005

Substantial differences remain between the profitability of banks in different European countries. This article considers the relationship between competition and profitability in European banking focussing on the experience of the UK where two issues are considered: why British banks have been earning excess returns for more than a decade and why British banks seem to be more profitable than their Continental counterparts. A paradigm is offered to explain this. A distinction is made between shareholder value (SHV) and stakeholder value (STV) banks whose business objectives are often different. Significant differences exist between European countries in the balance of SHV and STV banks. The UK is almost unique in Europe in having almost exclusively SHV‐based banks. Pressures will intensify for all European banks to adopt SHV strategies, which will imply substantial changes in bank strategies and business operations.
Equilibrium Determinacy under Monetary and Fiscal Policies in an Overlapping Generations Model
Authors: Piergallini Alessandro
Published: November 2005

This paper studies the issue of equilibrium determinacy under monetary and fiscal policy feedback rules in an optimizing general equilibrium model with overlapping generations and flexible prices. It is shown that equilibria may be determinate also when monetary and fiscal policies are both ‘passive’. In particular, under passive monetary rules, equilibrium uniqueness is more likely to be verified when fiscal policies are less committed to public debt stabilization.
Determinants of Corporate Governance in the Italian Financial Market
Authors: Barucci Emilio , Falini Jury
Published: November 2005

We evaluate the determinants of corporate governance of companies listed at the Italian Stock Exchange. We consider ownership structure, balance sheet data, company performance and some qualitative features as determinants. We evaluate the convergence of Italian companies’ governance towards a system with effective governance mechanisms. Our analysis shows definitely that companies with a large shareholder and/or minority blockholders controlling a large stake and companies belonging to a pyramidal group or controlled by a shareholders’ coalition are characterized by a poor governance/shareholders’ protection standard. Institutional investors play a positive role.
Social enrichment by virtual characters – differential benefits
Authors: Gulz A.
Published: November 2005

AbstractIt is frequently held forth, within the area of virtual pedagogical characters, that such characters are beneficial for learning as they strengthen the social dimension of electronic learning environments. This article presents more details on this proposal together with a survey of corresponding empirical evidence. In addition, materials from a recently conducted empirical study are presented. Ninety school children, 12–15‐year‐old, were asked (i) to grade the idea of virtual characters in electronic learning environments and (ii) to chose between a strictly task‐oriented, socially ‘shallow’ and a more socially oriented pedagogical character. The participants were also asked to articulate the reasons behind their answers, and to share their thoughts and opinions on the issues. The results of the study, as well as of several of the studies reviewed, indicate that responses and attitudes towards social aspects of virtual pedagogical characters are highly divergent. In particular, the notion that social dimensions of virtual characters increase learners' motivation and engagement may be less generally applicable in a student population than is sometimes hypothesized. An ensuing design guideline suggests interface solutions with an emphasis on flexibility regarding social orientation and communicative style in virtual characters.
Reconfigurability: creating new courses from existing learning objects will always be difficult!
Authors: Tompsett C.
Published: November 2005

Abstract
The suggestion that new courses can be constructed from existing learning objects appears technically self‐evident but remains unproven. Despite increasing evidence that learning objects can provide a suitable structure for constructing courses most evidence is based on creating learning objects, either through restructuring existing materials or as a set of newly created learning objects. There is little evidence for building a new course from existing learning objects where any significant number of these have been developed for a different course elsewhere. Authors who adopt a constructivist model of knowledge might view this lack of evidence as confirmation of the inherent difficulty of integrating resources created within different communities. Those following a scientific model of knowledge would view this as a temporary problem that will be resolved when a sufficient volume of materials exists in repositories. This paper argues that reconfiguration of learning objects to create new courses is significantly more complex than is currently recognized, even within a scientific framework of knowledge. By implication, far more research is needed to understand reconfiguration and re‐integration than initial ‘creation’.
Asymmetric synthesis of chiral 4‐substituted 5,5‐diethyl oxazolidin‐2‐ones as potential effective chiral auxiliaries
Authors: Li J.‐F. , Yang R. , Nie L. , Huang R. , Lin J.
Published: November 2005

Abstract:  Four new chiral 4‐substituted 5,5‐diethyl oxazolidin‐2‐ones (5a–5d) as potential effective chiral auxiliaries were synthesized from readily available amino acids via asymmetric etherification, Boc protection, Grignard reaction and cyclization reactions in four steps with overall yields of 50–60%.
Improved solid‐phase synthesis of α,α‐dialkylated amino acid‐rich peptides with antimicrobial activity*
Authors: Haynes S.R. , Hagins S.D. , Juban M.M. , Elzer P.H. , Hammer R.P.
Published: November 2005

Abstract:  A homologous series of nonapeptides and their acetylated versions were successfully prepared using solid‐phase synthetic techniques. Each nonapeptide was rich in α,α‐dialkylated amino acids [one 4‐aminopiperidine‐4‐carboxylic acid (Api) and six α‐aminoisobutyric acid (Aib) residues] and also included lysines or lysine analogs (two residues). The incorporation of the protected dipeptide 9‐fluorenylmethyloxycarbonyl (Fmoc)‐Aib‐Aib‐OH improved the purity and overall yields of these de novo designed peptides. The helix preference of each nonapeptide was investigated in six different solvent environments, and each peptide's antimicrobial activity and cytotoxicity were studied. The 310‐helical, amphipathic design of these peptides was born out most prominently in the N‐terminally acetylated peptides. Most of the peptides exhibited modest activity against Escherichia coli and no activity against Staphylococcus aureus. The nonacetylated peptides (concentrations ≤100 μm) and the acetylated peptides (concentrations ≤200 μm) did not exhibit any significant cytotoxicity with normal (nonactivated) murine macrophages.
Bacterial diversity of metagenomic and PCR libraries from the Delaware River
Authors: Cottrell Matthew T. , Waidner Lisa A. , Yu Liying , Kirchman David L.
Published: November 2005

To determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make‐up of a large insert metagenomic library constructed with bacterial DNA from the Delaware River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community structure determined by fluorescence in situ hybridization (FISH). The composition of the libraries and community structure determined by FISH differed for the major bacterial groups in the river, which included Actinobacteria, beta‐proteobacteria and Cytophaga‐like bacteria. Beta‐proteobacteria were underrepresented in the metagenomic library compared with the PCR library and FISH, while Cytophaga‐like bacteria were more abundant in the metagenomic library than in the PCR library and in the actual community according to FISH. The Delaware River libraries contained bacteria belonging to several widespread freshwater clusters, including clusters of Polynucleobacter necessarius, Rhodoferax sp. Bal47 and LD28 beta‐proteobacteria, the ACK‐m1 and STA2‐30 clusters of Actinobacteria, and the PRD01a001B Cytophaga‐like bacteria cluster. Coverage of bacteria with > 97% sequence identity was 65% and 50% for the metagenomic and PCR libraries respectively. Rarefaction analysis of replicate PCR libraries and of a library constructed with re‐conditioned amplicons indicated that heteroduplex formation did not substantially impact the composition of the PCR library. This study suggests that although it may miss some bacterial groups, the metagenomic approach can sample other groups (e.g. Cytophaga‐like bacteria) that are potentially underrepresented by other culture‐independent approaches.
Fishing for biodiversity: novel methanopterin‐linked C1 transfer genes deduced from the Sargasso Sea metagenome
Authors: Kalyuzhnaya Marina G. , Nercessian Olivier , Lapidus Alla , Chistoserdova Ludmila
Published: November 2005

The recently generated database of microbial genes from an oligotrophic environment populated by a calculated 1800 major phylotypes (the Sargasso Sea metagenome – SSM) presents a great source for expanding local databases of genes indicative of a specific function. In this article we analyse the SSM for the presence of methanopterin‐linked C1 transfer genes that are signature for methylotrophy. We conclude that more than 10 phylotypes possessing genes of interest are present in this environment. The sequences representative of these major phylotypes do not appear to belong to any known microbial group capable of methanopterin‐linked C1 transfer. Instead, these sequences separate from all known sequences on phylogenetic trees, pointing toward their affiliation with novel microbial phyla. These data imply a broader distribution of methanopterin‐linked functions in the microbial world than has been previously known.
Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics
Authors: Yutin Natalya , Béjà Oded
Published: November 2005

Photosynthetic core complexes of anoxygenic bacteria consist of reaction centres (RCs) surrounded by light‐harvesting complexes (LHC). The structural proteins of the RC–LHC1 complex are encoded by the puf‐operon. We find diverse operon organizations of puf‐operons that reflect structural differences of the core complex in marine aerobic anoxygenic photosynthetic bacteria (AAnP). By analysis of environmental DNA records coming from AAnP bacteria we find several unknown proteins downstream to the pufM, which were assigned as novel PufX proteins. As all known pufX genes belong to Rhodobacter strains which carry out anaerobic photosynthesis, this may be the first observation of a PufX‐containing RCs in aerobic anoxygenic photosynthetic bacteria. Phylogenetic analyses of PufM proteins from cultured as well as from uncultured bacteria show that PufM from operons containing putative novel pufX genes are grouped with Rhodobacter and not with Roseobacter strains.
Insights into the genomes of archaea mediating the anaerobic oxidation of methane
Authors: Meyerdierks Anke , Kube Michael , Lombardot Thierry , Knittel Katrin , Bauer Margarete , Glöckner Frank Oliver , Reinhardt Richard , Amann Rudolf
Published: November 2005

The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate‐reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large‐insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME‐1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME‐2a, ANME‐2c and ANME‐3 group. Genome walking for ANME‐1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME‐2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10‐methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl‐CoA synthase enzyme complex.
A wide host‐range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase
Authors: Wexler Margaret , Bond Philip L. , Richardson David J. , Johnston Andrew W. B.
Published: November 2005

Using DNA obtained from the metagenome of an anaerobic digestor in a waste water treatment plant, we constructed a gene library cloned in the wide host‐range cosmid pLAFR3. One cosmid enabled Rhizobium leguminosarum to grow on ethanol as sole carbon and energy source, this being due to the presence of a gene, termed adhEMeta. The AdhEMeta protein most closely resembles the AdhE alcohol dehydrogenase of Clostridium acetobutylicum, where it catalyses the formation of ethanol and butanol in a two‐step reductive process. However, cloned adhEMeta did not confer ethanol utilization ability to Escherichia coli or to Pseudomonas aeruginosa, even though it was transcribed in both these hosts. Further, cell‐free extracts of E. coli and R. leguminosarum containing cloned adhEMeta had butanol and ethanol dehydrogenase activities when assayed in vitro. In contrast to the well‐studied AdhE proteins of C. acetobutylicum and E. coli, the enzyme specified by adhEMeta is not inactivated by oxygen and it enables alcohol to be catabolized. Cloned adhEMeta did, however, confer one phenotype to E. coli. AdhE– mutants of E. coli fail to ferment glucose and introduction of adhEMeta restored the growth of such mutants when grown under fermentative conditions. These observations show that the use of wide host‐range vectors enhances the efficacy with which metagenomic libraries can be screened for genes that confer novel functions.
Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments
Authors: Nunoura Takuro , Hirayama Hisako , Takami Hideto , Oida Hanako , Nishi Shinro , Shimamura Shigeru , Suzuki Yohey , Inagaki Fumio , Takai Ken , Nealson Kenneth H. , Horikoshi Koki
Published: November 2005

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic‐type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing‐endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non‐thermophilic uncultivated Crenarchaeota.
Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities
Authors: Janssen Dick B. , Dinkla Inez J. T. , Poelarends Gerrit J. , Terpstra Peter
Published: November 2005

Bacterial dehalogenases catalyse the cleavage of carbon‐halogen bonds, which is a key step in aerobic mineralization pathways of many halogenated compounds that occur as environmental pollutants. There is a broad range of dehalogenases, which can be classified in different protein superfamilies and have fundamentally different catalytic mechanisms. Identical dehalogenases have repeatedly been detected in organisms that were isolated at different geographical locations, indicating that only a restricted number of sequences are used for a certain dehalogenation reaction in organohalogen‐utilizing organisms. At the same time, massive random sequencing of environmental DNA, and microbial genome sequencing projects have shown that there is a large diversity of dehalogenase sequences that is not employed by known catabolic pathways. The corresponding proteins may have novel functions and selectivities that could be valuable for biotransformations in the future. Apparently, traditional enrichment and metagenome approaches explore different segments of sequence space. This is also observed with alkane hydroxylases, a category of proteins that can be detected on basis of conserved sequence motifs and for which a large number of sequences has been found in isolated bacterial cultures and genomic databases. It is likely that ongoing genetic adaptation, with the recruitment of silent sequences into functional catabolic routes and evolution of substrate range by mutations in structural genes, will further enhance the catabolic potential of bacteria toward synthetic organohalogens and ultimately contribute to cleansing the environment of these toxic and recalcitrant chemicals.
Research on Higher Education in Europe
Authors: TEICHLER ULRICH
Published: November 2005

Research on higher education grew in European countries from scattered individual activities towards a certain degree of visibility in the 1970s, largely as consequence of growing public problem awareness. In the 1980s, it experienced a set‐back due to declining public interest in higher education as a key issue of societal policies. From the late 1980s onwards, research in this domain again drew attention and support in the wake of debates about the knowledge society, new modes of steering and management and the increasing internationalisation of higher education. However, growth and consolidation of this research were accompanied by a more rapid growth of policy‐geared information collection and dissemination in the framework of evaluation, consultancy, expert commissions and the daily work of the growing number of higher education professionals. Research on higher education often does not have a solid institutional base and it both benefits and suffers from the fact that it is a theme‐base area of research, drawing from different disciplines, and that the borderline is fuzzy between researchers and other experts on higher education. But a growth and quality improvement of research on higher education can be observed in recent years — certainly to some extent due to growing cooperation of researchers across Europe and to increasing cooperation in comparative projects. In the future, the first steps undertaken to establish study programmes for higher education experts could turn out be beneficial not only for the dissemination of research findings, but also for the quality of young researchers in this domain.
Unrealistic Expectations? Zambia's Mineworkers from Independence to the One‐Party State, 1964–1972
Authors: LARMER MILES
Published: November 2005

Abstract  Political scientists have neglected the extent of opposition and resistance to the policies of African states amongst civil society organisations in the immediate post‐colonial period. Unionised Zambian mineworkers expected Independence to bring about a transformation in their work and living conditions, a demand that brought them into conflict with the new Zambian Government and its dependency on mine revenue. Government attempts to control the behaviour of mineworkers through legislation and the union bureaucracy proved unsuccessful, and popular grassroots challenges to the union leadership, and the Government itself, were only ended by state suppression, and the establishment of a one‐party state.