bluuebunny/crossref_metadata_2025 huggingface dataset:
A city under Siege: Banditry & modes of accumulation in Nairobi, 1991-2004
Authors: Katumanga Musambayi
Published: December 2005

This is a study of the impact of political and economic liberalisation on modes of socio-economic engagement and accumulation in Kenya's capital city, Nairobi, subsequent to the introduction of multiparty ‘democracy’ in 1992.1 On the one hand economic liberalisation led to a diminished state-provisioning capacity and unwillingness to protect public interests. On the other hand, political conditionalities opened up political space but also spawned anomic tendencies within the regime and among social groups and individuals, with struggles in defence of economic position against each other at one level, and against the state and local councils at another. This account focuses on the political economy underlying the resultant urban banditry in Nairobi. It seeks to demonstrate how a besieged regime facilitates the criminalisation of urban existence in a bid to ensure its survival.

The argument here is that beleaguered regimes survive through a twin strategy. They privatise public violence and appropriate private violence. The net effect is the perversion of social order and the emergence of bandit economies. Regime longevity may derive not only from lack of an alternative leadership and organising ideology, but also from the threat to perceived benefits accruing from such informal economies. The ruling elite responds to the possibility of losing power by using neo-patrimonial structures to selectively allocate public spaces to their cronies, thereby subverting social order and undermining democratisation, security and social harmony; this in turn spawns urban banditry. Urban banditry here denotes the unregulated deployment of instruments of coercion by ruling elite and various elements within the citizenry in bids to facilitate acquisition of economic benefits and political leverage.
John Garang's legacy to the peace process, the SPLM/A & the south
Authors: Young John
Published: December 2005

The death of Dr. John Garang, First Vice President of Sudan, President of Southern Sudan, and Chairman of the Sudan People's Liberation Movement/ Army (SPLM/A) in a helicopter crash on 30 July, and the riots that followed, produced doubts about the viability of the 9 January 2005 Comprehensive Peace Agreement (CPA) and the prospects of peace processes underway elsewhere in the country. On the surface, this is not surprising because Garang had been the leader of the SPLM/A since its founding in 1983 and for many in Sudan and abroad he virtually personified the struggle of the south. Garang was also the unchallenged focal point during the various peace processes, in particular during the final phase of the Inter-Governmental Authority on Development (IGAD) negotiations which were largely reduced to then First Vice President Ali Osman Taha and himself. And more than anyone else on either side of the table, Garang was the biggest beneficiary of the peace process which granted him a virtual hegemonic position in the south and the holding of a strong vice presidency nationally.
New Barbarians at the Gate: Losing the liberal peace in Africa
Authors: Willett Susan
Published: December 2005

Within contemporary liberal peace discourse, poverty and underdevelopment are being constructed as ‘new threats’ that feed conflict and terrorism. This perception has encouraged a growing convergence between the security and development policies of the major donors. However, in Africa, where the need to simultaneously tackle conflict and underdevelopment is most pressing, the global institutions have failed to acknowledge that the neo-liberal policies that they pursue have been instrumental in structuring the domestic political and economic tensions that have contributed to violent conflict. Moreover, the current preoccupation with the war on terror has encouraged the co-option of development resources for security functions resulting in the incremental securitisation of development policies. Regardless of its expanding base and the process of mission creep, the liberal peace complex has failed to secure sustainable peace in Africa. Into the vacuum created by failure, the ‘new barbarian’ agenda that underpins the ‘war on terror’ has surreptitiously moved, expanding its reach and its wake of pillage and destruction.
The impacts of road runoff on periphyton in a small upland stream during summer
Authors: Boisson Jean-Claude , Boisson Claire , Perrodin Yves
Published: December 2005

Motorway runoff transports mineral and organic materials to aquatic ecosystems which may provoke changes in the latter's chemical, physical and biological characteristics. We measured the water quality of a road runoff discharge and its effect on the periphyton communities in a small upland stream. The study was carried out during a summer low flow period (June to September 1998). We did not record notable, or lasting, effects of road runoff on physical and chemical parameters. Similarly, road runoff discharges did not change the mass (biomass, chlorophyll a) or the functioning (net primary production, respiration) of periphyton. The development of this community was most sensitive to rainfall and river flow conditions. The absence of impact possibly results from the fact that our monitoring was not carried out at times of more extreme road runoff. In fact, traffic and pollution, brought to the stream, were quite low and discharge dilutions were generally high during the study period. Thus this study should be continued to determine effects when discharges have potentially a high impact on the receiving water quality.
Chitobiase activity as an indicator of aquatic ecosystem health
Authors: Hanson Mark L. , Lagadic Laurent
Published: December 2005

The sampling of benthic arthropods is one of several common approaches to monitor and assess ecosystem health in both lotic and lentic systems. This type of environmental effects monitoring has a number of drawbacks that support the development of new methodologies to improve our ability to detect and mitigate effects in the field. We propose an enzymatic technique to assess the status of arthropod communities and ecosystem health rapidly and efficiently. The method is based on measuring the activity of free chitobiase, an arthropod moulting enzyme, in natural waters. The rationale behind using chitobiase activity and how it could be applied to general field monitoring and assessment situations are discussed. An example of results obtained from field level monitoring using this assay is presented from the Oir River catchment and one of its tributaries, the La Roche, in Lower Normandy, France. Chitobiase activity was detected and quantified with low variability in the Oir and La Roche with the enzyme's activity statistically related (p < 0.0001, r2 = 0.77) to standard water quality physico-chemical parameters using multiple linear regression. A decrease in chitobiase activity was noted downstream of a sewage treatment plant releasing effluent into the Oir. This is the first time chitobiase activity has been measured in a freshwater ecosystem as an indicator of ecosystem health. However, extensive validation is required before chitobiase activity can be used in an environmental monitoring context.
Abundance, morphological diversity, and spatial distribution of autotrophic picoplankton in Lake Hovsgol (Mongolia)
Authors: Belykh O. I. , Sorokovikova E. G. , Tikhonova I. V. , Fedotov A. F.
Published: December 2005

Hovsgol is the largest deep lake in Central Asia located in the south-west of the Baikal Rift zone. Until now there has been only one study on the autotrophic picoplankton in Lake Hovsgol. The present work summarizes results of picoplankton studies obtained with light, epifluorescence and scanning electron microscopy. Microscopic analysis showed the presence of picoplankton cyanobacteria and algae in Lake Hovsgol. Autotrophic picoplankton of the lake is characterized by morphotype diversity of Synechococcus species, Synechocystis-like aggregates, and picocyanobacteria cells of small sizes. Picocyanobacteria are dominated by Synechococcus species with single, rarely double, coccoid cells. There is also a picoplankton form of the diatom Cyclotella ocellata reaches 4–13 percent of the total species abundance. Three picocyanobacterial cultures belonging to the genus Synechococcus and exhibiting distinct morphological and ultrastructural characteristics were isolated from the plankton samples.

Chlorophyll a content in the pelagic zone of Lake Hovsgol in August was 0.182–0.374 μ g l− 1. In February, the abundance of picoplankton cyanobacteria in the surface layer, which make up the basic autotrophic picoplankton mass, was 2.78 × 105 cells ml−1, in March 1.36 × 105 cells ml−1, and in July 6.06 × 104 cells ml−1. In August, picocyanobacteria abundance fell to 3.42 × 104 cells ml−1 in the 0 to 10 m layer and 7.52 × 104 cells ml−1 in the 0 to 50 m layer. Quantitative variations in autotrophic picoplankton development throughout the lake are negligible. The greatest abundance of picocyanobacteria is recorded in the hypolimnion, 25–50 m deep.
Gammarus aequicauda(Crustacea: Amphipoda): A potential test species in marine sediment toxicity assessment
Authors: Prato Ermelinda , Biandolino Francesca
Published: December 2005

In this study, the amphipod Gammarus aequicauda was evaluated as a test organism for use in sediment toxicity bioassays. Sensitivity to noncontaminant variables, to the reference toxicants and to some contaminated field sediments was analysed. Amphipods were tolerant to various salinity and temperature combinations during a ten-day assay. The organisms tested with different type of diet showed highest survival on the natural diet.

The organism density effect on survival and growth of Gammarus aequicauda during a 28-day assay was examined. The results indicated that the density did not affect survival and production, but the effect of density was significant on the average weight.

No effect on survival was observed on three sediment types during the 10-day exposure. Sensitivity to contaminants was assessed using cadmium chloride and copper chloride as reference toxicants in a 96 h water-only test. Methods were developed for conducting a short-term toxicity test with cadmium chloride-spiked sediment using this species. Water-only testing revealed high sensitivity of amphipods to reference toxicants. Experiments conducted with organisms of four different size classes demonstrated no significant differences in sensitivity.
An overview of the impact of non-indigenous species on the food web integrity of North American Great Lakes: Lake Erie example
Authors: Munawar M. , Munawar I.F. , Mandrak N.E. , Fitzpatrick M. , Dermott R. , Leach J.
Published: December 2005

For the past several decades, the North American Great Lakes have suffered from eutrophication. The deteriorating state of the Great Lakes alarmed both the governments of Canada and the United States resulting in the Great Lakes Water Quality Agreement, which has brought about substantial improvements in water quality. While phosphorus abatement resulted in a significant decrease in nutrients, the sudden invasions of exotic species posed a serious threat to Great Lakes food webs. The zebra mussel (Dreissena polymorpha) and the quagga mussel (D. bugensis), followed by other exotic species, infested Lakes Erie and Ontario causing a drastic reduction in phytoplankton biomass and increasing water clarity. In Lake Erie, post-Dreissena declines in phytoplankton size structure and changes in community composition were observed in this study, along with significant declines in primary productivity in the west basin. At the other end of the food web, exotic species such as alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax) and white perch (Morone americana) have become important to the Lake Erie commercial fishery, while other native fish species have declined. This paper presents an historical perspective and a general overview of the impact of nonindigenous species in the North American Great Lakes from the base of the food web to the fisheries. Lake Erie has been chosen as a case study to provide a detailed treatment. The expansion and growth of nonindigenous species has been responsible for significant modifications to the structural and functional characteristics of the food webs and fisheries of the Great Lakes. Our experience demonstrates the significance of the impact of exotics and the need to manage this serious problem on a global basis so that the integrity of food webs and fisheries throughout the world can be protected.

This paper is dedicated to Dr. Jack Vallentyne for his contributions to Great Lakes research, especially for the implementation of the ‘ecosystem approach’. These contributions were in evidence in revisions to the Great Lakes Water Quality Agreement and more currently in the management of exotic species.
Assessing the ecological integrity after nutrient inputs in streams: The relevance of the observation scale
Authors: Sabater Sergi , Acuña Vicenç , Giorgi Adonis , Guasch Helena , Guerra Elena , Muñoz Isabel , Romaní Anna M.
Published: December 2005

Two different streams receiving high nutrient content were compared in relation to evidence provided by structural (biomass) and functional (community metabolism) descriptors. The first (Gaià) was an unshaded agricultural stream, where high net community metabolism and chlorophyll concentration were only modified by flood episodes which caused the sloughing of the benthic community. The second stream (Fuirosos) was forested and nutrients were added for 44 days. In this case, bacteria and macroinvertebrates were also observed and were compared to a control upstream stretch with low nutrient content. Even though there was an increase of chlorophyll because of the nutrient addition, the macroinvertebrate community density as a whole was not affected. Moreover, metabolism (net community metabolism and respiration) did not experience significant changes. An unexpected effect of nutrient addition was detected using a finer scale of observation: during a colonization experiment, chlorophyll and bacterial density became uniform for the different substrata analyzed (sand, cobbles) after 44 days. These structural changes implied a loss of structural heterogeneity which may be associated with significant modifications of stream functioning (such as the nutrient retention) for these systems in the longer term.
The Signature of the Shapovalov Form on Irreducible Verma Modules
Authors: Yee Wai
Published: December 2005

A Verma module may admit an invariant Hermitian form, which is unique up to a real scalar when it exists. Suitably normalized, it is known as the Shapovalov form. The collection of highest weights decomposes under the affine Weyl group action into alcoves. The signature of the Shapovalov form for an irreducible Verma module depends only on the alcove in which the highest weight lies. We develop a formula for this signature, depending on the combinatorial structure of the affine Weyl group. Classifying the irreducible unitary representations of a real reductive group is equivalent to the algebraic problem of classifying the Harish-Chandra modules admitting a positive definite invariant Hermitian form. Finding a formula for the signature of the Shapovalov form is a related problem which may be a necessary first step in such a classification.
Depletion of Phosphatidylcholine in Yeast Induces Shortening and Increased Saturation of the Lipid Acyl Chains: Evidence for Regulation of Intrinsic Membrane Curvature in a Eukaryote
Authors: Boumann Henry A. , Gubbens Jacob , Koorengevel Martijn C. , Oh Chan-Seok , Martin Charles E. , Heck Albert J.R. , Patton-Vogt Jana , Henry Susan A. , de Kruijff Ben , de Kroon Anton I.P.M.
Published: December 2005

To study the consequences of depleting the major membrane phospholipid phosphatidylcholine (PC), exponentially growing cells of a yeast cho2opi3 double deletion mutant were transferred from medium containing choline to choline-free medium. Cell growth did not cease until the PC level had dropped below 2% of total phospholipids after four to five generations. Increasing contents of phosphatidylethanolamine (PE) and phosphatidylinositol made up for the loss of PC. During PC depletion, the remaining PC was subject to acyl chain remodeling with monounsaturated species replacing diunsaturated species, as shown by mass spectrometry. The remodeling of PC did not require turnover by the SPO14-encoded phospholipase D. The changes in the PC species profile were found to reflect an overall shift in the cellular acyl chain composition that exhibited a 40% increase in the ratio of C16 over C18 acyl chains, and a 10% increase in the degree of saturation. The shift was stronger in the phospholipid than in the neutral lipid fraction and strongest in the species profile of PE. The shortening and increased saturation of the PE acyl chains were shown to decrease the nonbilayer propensity of PE. The results point to a regulatory mechanism in yeast that maintains intrinsic membrane curvature in an optimal range.
Syntaxins 3 and 4 Are Concentrated in Separate Clusters on the Plasma Membrane before the Establishment of Cell Polarity
Authors: Low Seng Hui , Vasanji Amit , Nanduri Jayasri , He Min , Sharma Nikunj , Koo Michelle , Drazba Judith , Weimbs Thomas
Published: December 2005

Syntaxins 3 and 4 localize to the apical and basolateral plasma membrane, respectively, of epithelial cells where they mediate vesicle fusion. Here, we report that before establishment of cell polarity, syntaxins 3 and 4 are confined to mutually exclusive, submicron-sized clusters. Syntaxin clusters are remarkably uniform in size, independent of expression levels, and are distinct from caveolae and clathrin-coated pits. SNAP-23 partially colocalizes with both syntaxin 3 and 4 clusters. Deletion of the apical targeting signal of syntaxin 3 does not prevent sorting into clusters away from syntaxin 4. Syntaxin 3 and 4 cluster formation depends on different mechanisms because the integrity of syntaxin 3 clusters depends on intact microtubules, whereas syntaxin 4 clusters depend on intact actin filaments. Cholesterol depletion causes dispersion of syntaxin 3 but not syntaxin 4 clusters. In migrating cells, syntaxin clusters polarize to the leading edge, suggesting a role in polarized exocytosis. These results suggest that exocytosis occurs at small fusion sites exhibiting high local concentrations of SNARE proteins that may be required for efficient membrane fusion. The establishment of separate clusters for each syntaxin suggests that the plasma membrane is inherently polarized on an ultrastructural level even before the establishment of true cell polarity.
Multiple feedback loop design in the tryptophan regulatory network of
Escherichia coli
suggests a paradigm for robust regulation of processes in series
Authors: Bhartiya Sharad , Chaudhary Nikhil , Venkatesh K.V , Doyle Francis J
Published: December 2005

Biological networks have evolved through adaptation in uncertain environments. Of the different possible design paradigms, some may offer functional advantages over others. These designs can be quantified by the structure of the network resulting from molecular interactions and the parameter values. One may, therefore, like to identify the design motif present in the evolved network that makes it preferable over other alternatives. In this work, we focus on the regulatory networks characterized by serially arranged processes, which are regulated by multiple feedback loops. Specifically, we consider the tryptophan system present in
Escherichia coli
, which may be conceptualized as three processes in series, namely transcription, translation and tryptophan synthesis. The multiple feedback loop motif results from three distinct negative feedback loops, namely genetic repression, mRNA attenuation and enzyme inhibition. A framework is introduced to identify the key design components of this network responsible for its physiological performance. We demonstrate that the multiple feedback loop motif, as seen in the tryptophan system, enables robust performance to variations in system parameters while maintaining a rapid response to achieve homeostasis. Superior performance, if arising from a design principle, is intrinsic and, therefore, inherent to any similarly designed system, either natural or engineered. An experimental engineering implementation of the multiple feedback loop design on a two-tank system supports the generality of the robust attributes offered by the design.
Laminar premixed flame extinction limits. II Combined effects of stretch and radiative loss in the single flame unburnt-to-burnt and the twin-flame unburnt-to-unburnt opposed flow configurations
Authors: Dixon-Lewis Graham
Published: December 2005

Numerical methods have been used to examine the effects of (a) stretch alone, and (b) a combination of stretch and radiative loss, on the properties and extinction limits of methane–air flames near the lean flammability limit. Two axisymmetric opposed flow configurations were examined: (i) a single flame, unburnt-to-burnt (UTB) system in which fresh reactant is opposed by a stream of its own combustion products at the unburnt temperature, and (ii) a symmetric unburnt-to-unburnt (UTU) configuration where twin flames are supported back to back, one on each side of the stagnation plane. The maximum temperatures achieved in the UTB system are always away from the stagnation plane. For a fixed sufficiently sub-adiabatic product stream temperature, increasing flame stretch or gaseous radiative emissivity, or a combination of both, will augment downstream conductive heat loss, leading to a reduction in
T
max
and eventually to an abrupt extinction if the loss rate is sufficiently large. The UTU system is more complex, and offers the additional possibility of purely stretch-induced extinctions where the flames are forced together back-to-back so that radiative loss is restricted to upstream of the maximum temperature. Extinction in these cases occurs by straightforward truncation of the hot sides of the reaction zones. At sufficiently low stretch, near and at the standard flammability limit, radiative loss makes a major contribution to the overall extinction mechanism in both configurations.

The detailed effects of flame stretch on extinction behaviour depend on the diffusion characteristics within the near-limit mixtures, in particular the Lewis number, Le, of the deficient component. The effect of high stretch is always to attenuate the composition range of flammability. However, for Le<1 this range is extended at low to moderate stretch, particularly in the UTU situations where downstream radiative loss is not present at extinction. Lewis number effects for a global methane–air chemistry, and with assumed Le≥1, are discussed in the light of numerical results previously presented by Ju
et al
. (

Ju
et al
. 1998

Combust. Flame
113
, 603–614).
Elastic–plastic contact of a rough surface with Weierstrass profile
Authors: Gao Yan-Fei , Bower A.F
Published: December 2005

We analyse contact between a rigid cylindrical indenter and an elastic–perfectly plastic solid with a fractal surface roughness, which is idealized as a Weierstrass profile. A hierarchical scheme is used to calculate quantities such as the number of contact spots; their size; the true contact pressure acting on the contact spots, and the total true area of contact. In addition, we calculate critical conditions that will initiate plastic flow in the asperities, and determine the extent of this plastic flow as a function of the applied loading, the material properties of the deforming solid, and the surface roughness. An important conclusion of our study is that a perfectly fractal description of surface roughness appears to lead to unphysical predictions of the true contact size and number of contact spots, for both elastic and elastic–plastic solids. Possible approaches to resolving these difficulties are discussed.
Selection for protection in an ant–plant mutualism: host sanctions, host modularity, and the principal–agent game
Authors: Edwards David P , Hassall Mark , Sutherland William J , Yu Douglas W
Published: December 2005

Retaliation against cheaters can prevent the breakdown of cooperation. Here we ask whether the ant–plantCordia nodosais able to apply retaliatory sanctions against its ant symbiontAllomerus octoarticulatus, which patrols new shoots to prevent herbivory. We test the hypothesis that the modular design ofC. nodosaphysiologically ties the growth of housing (stem swellings known as domatia) to the successful development of the attached leaves. We experimentally simulated herbivory by cutting leaves from patrolled shoots and found that the domatia on such ‘cheated’ shoots suffered higher mortality and lower growth than did controls, evidence for a host sanction. On the other hand, patrolling is costly to the ant, and experiment shows that non-patrollers run a low risk of being sanctioned because most leaves (and the attached domatia) escape heavy herbivory even when patrollers are absent. This suggests that cheaters might enjoy a higher fitness than do mutualists, despite sanctions, but we find that patrolling provides a net fecundity benefit when the colony and plant exceed a minimum size, which requires sustained ant investment in patrolling. These results map directly onto the principal–agent (P–A) game from economics, which we suggest can be used as a framework for studying stability in mutualisms, where high sampling costs and cheating do not allow market effects to select for mutual benefits.
The human brain is a detector of chemosensorily transmitted HLA-class I-similarity in same- and opposite-sex relations
Authors: Pause Bettina M , Krauel Kerstin , Schrader Claudia , Sojka Bernfried , Westphal Eckhard , Müller-Ruchholtz Wolfgang , Ferstl Roman
Published: December 2005

Studies on subjective body odour ratings suggest that humans exhibit preferences for human leucocyte antigen (HLA)-dissimilar persons. However, with regard to the extreme polymorphism of the HLA gene loci, the behavioural impact of the proposed HLA-related attracting signals seems to be minimal. Furthermore, the role of HLA-related chemosignals in same- and opposite-sex relations in humans has not been specified so far. Here, we investigate subjective preferences and brain evoked responses to body odours in males and females as a function of HLA similarity between odour donor and smeller. We show that pre-attentive processing of body odours of HLA-similar donors is faster and that late evaluative processing of these chemosignals activates more neuronal resources than the processing of body odours of HLA-dissimilar donors. In same-sex smelling conditions, HLA-associated brain responses show a different local distribution in male (frontal) and female subjects (parietal). The electrophysiological results are supported by significant correlations between the odour ratings and the amplitudes of the brain potentials. We conclude that odours of HLA-similar persons function as important social warning signals in inter- and intrasexual human relations. Such HLA-related chemosignals may contribute to female and male mate choice as well as to male competitive behaviour.
Conflict between datasets and phylogeny of centipedes: an analysis based on seven genes and morphology
Authors: Giribet Gonzalo , Edgecombe Gregory D
Published: December 2005

Although the phylogeny of centipedes has found ample agreement based on morphology, recent analyses incorporating molecular data show major conflict at resolving the deepest nodes in the centipede tree. While some genes support the classical (morphological) hypothesis, others suggest an alternative tree in which the relictual order Craterostigmomorpha, restricted to Tasmania and New Zealand, is resolved as the sister group to all other centipedes. We combined all available data including seven genes (totalling more than 8 kb of genetic information) and 153 morphological characters for 24 centipedes, and conducted a sensitivity analysis to evaluate where the conflict resides. Our data showed that the classical hypothesis is obtained primarily when nuclear ribosomal genes exert dominance in the character data matrix (at high gap costs), while the alternative tree is obtained when protein-encoding genes account for most of the cladogram length (at low gap costs). In this particular case, the addition of genetic data does not produce a more stable hypothesis for deep centipede relationships than when analysing certain genes independently, but the overall conflict in the data can be clearly detected via a sensitivity analysis, and support and stability of shallow nodes increase as data are added.
Conventional and novel processing methods for cellular ceramics
Authors: Colombo Paolo
Published: December 2005

Cellular ceramics are a class of highly porous materials that covers a wide range of structures, such as foams, honeycombs, interconnected rods, interconnected fibres, interconnected hollow spheres. Recently, there has been a surge of activity in this field, because these innovative materials have started to be used as components in special and advanced engineering applications. These include filtering liquids and particles in gas streams, porous burners, biomedical devices, lightweight load-bearing structures, etc. Improvements in conventional processing methods and the development of innovative fabrication approaches are required because of the increasing specific demands on properties and morphology (cell size, size distribution and interconnection) for these materials, which strictly depend on the application considered. This paper will cover the main fabrication methods for cellular ceramics, focusing primarily on foams, offering some insight into novel fabrication processes and recent developments.
Supercritical carbon dioxide: putting the fizz into biomaterials
Authors: Barry John J.A , Silva Marta M.C.G , Popov Vladimir K , Shakesheff Kevin M , Howdle Steven M
Published: December 2005

This paper describes recent progress made in the use of high pressure or supercritical fluids to process polymers into three-dimensional tissue engineering scaffolds. Three current examples are highlighted: foaming of acrylates for use in cartilage tissue engineering; plasticization and encapsulation of bioactive species into biodegradable polyesters for bone tissue engineering; and a novel laser sintering process used to fabricate three-dimensional biodegradable polyester structures from particles prepared via a supercritical route.
Designing porous scaffolds for tissue engineering
Authors: Bonfield William
Published: December 2005

Biomaterials are either modified natural or synthetic materials, with an appropriate response in the host tissue, which find application in a wide spectrum of implants and prostheses used in reconstructive medicine. The subsequent integration and longevity of the implanted device depends on the effectiveness of the associated biological repair. Hence, there has been considerable interest in the development of novel, second generation, biomaterials, which are favourably bioactive in terms of promoting the desired cellular response
in vivo
. Such biomaterials in a porous form can also act as cellular scaffolds and allow
in vitro
, as well as
in vivo
incorporation of the appropriate tissue cells, with potential control of the sequence of cell attachment, proliferation and the production of extra-cellular matrix. Such generic tissue engineering depends critically on the porous architecture of the biomaterial scaffold so as to allow both the cellular ingress and vascularization required to create a living tissue. The particular requirements of tissue-engineering scaffolds with respect to macro- and micro-porosity, as well as chemistry, are reviewed.
Insights on biology and evolution from microbial genome sequencing
Authors: Fraser-Liggett Claire M.
Published: December 2005

No field of research has embraced and applied genomic technology more than the field of microbiology. Comparative analysis of nearly 300 microbial species has demonstrated that the microbial genome is a dynamic entity shaped by multiple forces. Microbial genomics has provided a foundation for a broad range of applications, from understanding basic biological processes, host-pathogen interactions, and protein-protein interactions, to discovering DNA variations that can be used in genotyping or forensic analyses, the design of novel antimicrobial compounds and vaccines, and the engineering of microbes for industrial applications. Most recently, metagenomics approaches are allowing us to begin to probe complex microbial communities for the first time, and they hold great promise in helping to unravel the relationships between microbial species.
Genomics in C. elegans: So many genes, such a little worm: Table 1.
Authors: Hillier LaDeana W. , Coulson Alan , Murray John I. , Bao Zhirong , Sulston John E. , Waterston Robert H.
Published: December 2005

The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data sets and analyses, including a curated set of 19,735 protein-coding genes—with >90% directly supported by experimental evidence—and >1300 noncoding RNA genes. High-throughput efforts are under way to complete the gene sets, along with studies to characterize gene expression, function, and regulation on a genome-wide scale. The success of the worm project has had a profound effect on genome sequencing and on genomics more broadly. We now have a solid platform on which to build toward the lofty goal of a true molecular understanding of worm biology with all its implications including those for human health.
The canine genome
Authors: Ostrander Elaine A. , Wayne Robert K.
Published: December 2005

The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.
Impact of genomics on research in the rat
Authors: Lazar Jozef , Moreno Carol , Jacob Howard J. , Kwitek Anne E.
Published: December 2005

The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to be combined with the years of physiological knowledge accumulated in numerous rat models, which is the subject of this perspective. Based on the successes to date and the research projects under way to further enhance the infrastructure of the rat, we also project where research in the rat will be in the near future. The impact of the rat genome project has just started, but it is an exciting time with tremendous progress.
Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors
Authors: Thomas Rachael , Scott Allyson , Langford Cordelia F. , Fosmire Susan P. , Jubala Cristan M. , Lorentzen Travis D. , Hitte Christophe , Karlsson Elinor K. , Kirkness Ewen , Ostrander Elaine A. , Galibert Francis , Lindblad-Toh Kerstin , Modiano Jaime F. , Breen Matthew
Published: December 2005

Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many human and dog diseases extend to a range of cancers. Human tumors frequently display recurrent chromosome aberrations, many of which are hallmarks of particular tumor subtypes. Using a range of molecular cytogenetic techniques we have generated evidence indicating that this is also true of canine tumors. Detailed knowledge of these genomic abnormalities has the potential to aid diagnosis, prognosis, and the selection of appropriate therapy in both species. We recently improved the efficiency and resolution of canine cancer cytogenetics studies by developing a small-scale genomic microarray comprising a panel of canine BAC clones representing subgenomic regions of particular interest. We have now extended these studies to generate a comprehensive canine comparative genomic hybridization (CGH) array that comprises 1158 canine BAC clones ordered throughout the genome with an average interval of 2 Mb. Most of the clones (84.3%) have been assigned to a precise cytogenetic location by fluorescence in situ hybridization (FISH), and 98.5% are also directly anchored within the current canine genome assembly, permitting direct translation from cytogenetic aberration to DNA sequence. We are now using this resource routinely for high-throughput array CGH and single-locus probe analysis of a range of canine cancers. Here we provide examples of the varied applications of this resource to tumor cytogenetics, in combination with other molecular cytogenetic techniques.
Genomics of the future: Identification of quantitative trait loci in the mouse
Authors: Flaherty Lorraine , Herron Bruce , Symula Derek
Published: December 2005

Positional cloning of quantitative trait loci in rodents is a common approach to identify genes involved in complex phenotypes, including genes important to human disease. However, cloning the causative genes has proved to be more difficult than determining their positions. New tools such as genomic sequence, clone libraries, and new genomic-based methods offer new approaches to identify these genes. Here we review how these new tools and approaches will improve our ability to discover the genes important in complex traits.
Genome annotation past, present, and future: How to define an ORF at each locus
Authors: Brent Michael R.
Published: December 2005

Driven by competition, automation, and technology, the genomics community has far exceeded its ambition to sequence the human genome by 2005. By analyzing mammalian genomes, we have shed light on the history of our DNA sequence, determined that alternatively spliced RNAs and retroposed pseudogenes are incredibly abundant, and glimpsed the apparently huge number of non-coding RNAs that play significant roles in gene regulation. Ultimately, genome science is likely to provide comprehensive catalogs of these elements. However, the methods we have been using for most of the last 10 years will not yield even one complete open reading frame (ORF) for every gene—the first plateau on the long climb toward a comprehensive catalog. These strategies—sequencing randomly selected cDNA clones, aligning protein sequences identified in other organisms, sequencing more genomes, and manual curation—will have to be supplemented by large-scale amplification and sequencing of specific predicted mRNAs. The steady improvements in gene prediction that have occurred over the last 10 years have increased the efficacy of this approach and decreased its cost. In this Perspective, I review the state of gene prediction roughly 10 years ago, summarize the progress that has been made since, argue that the primary ORF identification methods we have relied on so far are inadequate, and recommend a path toward completing the Catalog of Protein Coding Genes, Version 1.0.
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion
Authors: Barbosa-Morais Nuno L. , Carmo-Fonseca Maria , Aparício Samuel
Published: December 2005

Although more than 200 human spliceosomal and splicing-associated proteins are known, the evolution of the splicing machinery has not been studied extensively. The recent near-complete sequencing and annotation of distant vertebrate and chordate genomes provides the opportunity for an exhaustive comparative analysis of splicing factors across eukaryotes. We describe here our semiautomated computational pipeline to identify and annotate splicing factors in representative species of eukaryotes. We focused on protein families whose role in splicing is confirmed by experimental evidence. We visually inspected 1894 proteins and manually curated 224 of them. Our analysis shows a general conservation of the core spliceosomal proteins across the eukaryotic lineage, contrasting with selective expansions of protein families known to play a role in the regulation of splicing, most notably of SR proteins in metazoans and of heterogeneous nuclear ribonucleoproteins (hnRNP) in vertebrates. We also observed vertebrate-specific expansion of the CLK and SRPK kinases (which phosphorylate SR proteins), and the CUG-BP/CELF family of splicing regulators. Furthermore, we report several intronless genes amongst splicing proteins in mammals, suggesting that retrotransposition contributed to the complexity of the mammalian splicing apparatus.
Strategy and leadership
Authors: Gray Harry
Published: December 2005

Purpose

The long‐time preoccupation with leadership as the key concept in organisational change ought to be replaced by a more general view that it is the quality of strategic thinking that leads to appropriate change within organisations.

Design/methodology/approach

As an example of how strategic thinking works, the current demographic changes in longevity are explored and opportunities for drawing on the experience of older people in business are suggested.

Findings

Strategic thinking depends on a collective view of organisational membership and takes for granted that leadership is a collective function not an individual one.

Originality/value

Explores a neglected area of strategic concern – namely demographic change and its implications for organizations.
Tools to manage continuing change
Authors: Harpham Alan
Published: December 2005

Purpose

The purpose of this paper is to inform readers about new ways of coping with change in organizations.

Design/methodology/approach

The paper examines the environment in which today's organizations operate and gives advice about up‐to date training methods.

Findings

Program and project management can help the organization embrace change.

Practical implications

The implications of this paper are that organizations can change effectively if they have the right training and or help from outside consultants.

Originality/value

This paper looks at a new diploma and methods for enlisting the services of consultants who can help the organization through transitional periods.
Usefulness of a delayed test for the diagnosis of Helicobacter pylori infection in bleeding peptic ulcer
Authors: GÜELL M. , ARTIGAU E. , ESTEVE V. , SÁNCHEZ‐DELGADO J. , JUNQUERA F. , CALVET X.
Published: December 2005

Aim

To evaluate (i) the diagnostic usefulness of a delayed test in initially negative patients; and (ii) the reliability of the rapid urease test, histology or a combination of the two to diagnose Helicobacter pylori during emergency endoscopy in a large clinical practice series.

Patients and methods

Records of patients with ulcer bleeding from 1995 to 2000 were reviewed. Patients with initially negative tests were retested 4–8 weeks after the bleeding episode. Sensitivity of urease, histology or a combination of the two to detect H. pylori at initial endoscopy and the efficacy of delayed Urea Breath Test in detecting missed infection was determined.

Results

The study included 429 patients. A delayed second test detected H. pylori infection in 57 out of 72 (79%) of initially negative patients. The sensitivity for detecting H. pylori was 76%, 78% and 86% for urease, histology and their combination, respectively. The prevalence of H. pylori was 95% in duodenal and 88% in gastric ulcer. In addition, only one test was performed in 17 of the 32 patients who were considered negative.

Conclusion

Not even the combination of a negative urease and histology in the initial endoscopy is able to rule out infection in bleeding ulcer patients. A delayed test should be performed to rule out Helicobacter pylori infection completely.
Clinical utility of telomerase for the diagnosis of malignant well‐differentiated endocrine tumours
Authors: Vezzosi Delphine , Bouisson Michèle , Escourrou Ghislaine , Laurell Henrik , Selves Jannick , Seguin Philippe , Pradayrol Lucien , Caron Philippe , Buscail Louis
Published: December 2005

Objective  The distinction between benign and malignant well‐differentiated endocrine tumours is hard to achieve. The aim of the present study was to determine whether detection of telomerase or quantification of human telomerase reverse transcriptase protein subunit (hTERT) differ between benign and malignant endocrine tumours.

Patients and methods  This retrospective study investigated 31 well‐differentiated primary endocrine tumours. Based on clinical and histopathological criteria, tumours were categorized with the most recent WHO classification as ‘benign’ (n = 14), ‘uncertain’ (n = 5) or ‘malignant’ (n = 12) with (n = 7) or without (n = 5) metastasis after a mean follow‐up of 40·4 ± 25·8 months (4–122 months). All these tumours were assayed for telomerase activity and hTERT mRNA expression [real‐time quantitative reverse transcriptase–polymerase chain reaction (RT‐PCR)].

Results  Telomerase activity was detected in 7 malignant and metastatic tumours, in 1 malignant tumour without metastases, in 1 uncertain tumour and in 1 benign tumour. hTERT mRNA levels were significantly higher in malignant endocrine tumours with or without metastases (P = 0·001) when compared to benign tumours. The negative predictive value of hTERT mRNA quantification for the diagnosis of malignancy was 88·9%, whereas the positive predictive value was 68·7%.

Conclusion  The presence of telomerase activity within the primary endocrine tumour might indicate a malignant tumour and might suggest the need for an attentive search for concomitant metastases. Quantification of hTERT mRNA could be used in clinical practice to exclude malignancy in most endocrine tumours.
Consequences of climatic change for water temperature and brown trout populations in Alpine rivers and streams
Authors: HARI RENATA E. , LIVINGSTONE DAVID M. , SIBER ROSI , BURKHARDT‐HOLM PATRICIA , GÜTTINGER HERBERT
Published: December 2005

Twenty‐five years of extensive water temperature data show regionally coherent warming to have occurred in Alpine rivers and streams at all altitudes, reflecting changes in regional air temperature. Much of this warming occurred abruptly in 1987/1988. For brown trout populations, the warming resulted in an upward shift in thermal habitat that was accelerated by an increase in the incidence of temperature‐dependent Proliferative Kidney Disease at the habitat's lower boundary. Because physical barriers restrict longitudinal migration in mountain regions, an upward habitat shift in effect implies habitat reduction, suggesting the likelihood of an overall population decrease. Extensive brown trout catch data documenting an altitudinally dependent decline indicate that such a climate‐related population decrease has in fact occurred. Our analysis employs a quantitatively defined reference optimum temperature range for brown trout, based on the sinusoidal regression of seasonally varying field data.