bluuebunny/crossref_metadata_2025 huggingface dataset:
Exhaustive whole-genome tandem repeats search
Authors: Krishnan Arun , Tang Francis
Published: May 2004

Motivation: Approximate tandem repeats (ATR) occur frequently in the genomes of organisms, and are a source of polymorphisms observed in individuals, and thus are of interest to those studying genetic disorders. Though extensive work has been done in order to identify ATRs, there are inherent limitations with the current approaches in terms of the number of pattern sizes that can be searched or the size of the input length.

Results: This paper describes (1) a new algorithm which exhaustively finds all variable-length ATRs in a genomic sequence and (2) a precise description of, and an algorithm to significantly reduce, redundancy in the output. Our ATR definition is parameterized by a mismatch ratio p which allows for more mismatches in longer tandem repeats (and fewer in shorter). Furthermore, our algorithm is embarrassingly parallel and thus can attain near-linear speed-up on Beowulf clusters. We present results of our algorithm applied to sequences of widely differing lengths (from genes to chromosomes).

Availability: Source and binaries are available on request.

Supplementary information:  http://web.bii.a-star.edu.sg/~francis/Research/Exhaustive/
Mining gene expression data for positive and negative co-regulated gene clusters
Authors: Ji Liping , Tan Kian-Lee
Published: May 2004

Motivation: Analysis of gene expression data can provide insights into the positive and negative co-regulation of genes. However, existing methods such as association rule mining are computationally expensive and the quality and quantities of the rules are sensitive to the support and confidence values. In this paper, we introduce the concept of positive and negative co-regulated gene cluster (PNCGC) that more accurately reflects the co-regulation of genes, and propose an efficient algorithm to extract PNCGCs.

Results: We experimented with the Yeast dataset and compared our resulting PNCGCs with the association rules generated by the Apriori mining algorithm. Our results show that our PNCGCs identify some missing co-regulations of association rules, and our algorithm greatly reduces the large number of rules involving uncorrelated genes generated by the Apriori scheme.

Availability: The software is available upon request.

Supplementary information: Supplementary tables and figures for this paper can be found at http://www.comp.nus.edu.sg/~jiliping/p1.html
Thermodynamics of enzyme-catalyzed reactions—a database for quantitative biochemistry
Authors: Goldberg Robert N. , Tewari Yadu B. , Bhat Talapady N.
Published: May 2004

Summary: The Thermodynamics of Enzyme-catalyzed Reactions Database (TECRDB) is a comprehensive collection of thermodynamic data on enzyme-catalyzed reactions. The data, which consist of apparent equilibrium constants and calorimetrically determined molar enthalpies of reaction, are the primary experimental results obtained from thermodynamic studies of biochemical reactions. The results from 1000 published papers containing data on 400 different enzyme-catalyzed reactions constitute the essential information in the database. The information is managed using Oracle and is available on the Web.

Availability:  http://xpdb.nist.gov/enzyme_thermodynamics/
Computational definition of sequence motifs governing constitutive exon splicing
Authors: Zhang Xiang H-F. , Chasin Lawrence A.
Published: May 2004

We have searched for sequence motifs that contribute to the recognition of human pre-mRNA splice sites by comparing the frequency of 8-mers in internal noncoding exons versus unspliced pseudo exons and 5′ untranslated regions (5′ untranslated regions [UTRs]) of transcripts of intronless genes. This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA.
Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic ArchaeonHalobacterium NRC-1
Authors: Baliga Nitin S. , Bjork Sarah J. , Bonneau Richard , Pan Min , Iloanusi Chika , Kottemann Molly C.H. , Hood Leroy , DiRuggiero Jocelyne
Published: May 2004

We report a remarkably high UV-radiation resistance in the extremely halophilic archaeonHalobacterium NRC-1withstanding up to 110 J/m2with no loss of viability. Gene knockout analysis in two putative photolyase-like genes (phr1andphr2) implicated onlyphr2in photoreactivation. The UV-response was further characterized by analyzing simultaneously, along with gene function and protein interactions inferred through comparative genomics approaches, mRNA changes for all 2400 genes during light and dark repair. In addition to photoreactivation, three other putative repair mechanisms were identified including d(CTAG) methylation-directed mismatch repair, four oxidative damage repair enzymes, and two proteases for eliminating damaged proteins. Moreover, a UV-induced down-regulation of many important metabolic functions was observed during light repair and seems to be a phenomenon shared by all three domains of life. The systems analysis has facilitated the assignment of putative functions to 26 of 33 key proteins in the UV response through sequence-based methods and/or similarities of their predicted three-dimensional structures to known structures in the PDB. Finally, the systems analysis has raised, through the integration of experimentally determined and computationally inferred data, many experimentally testable hypotheses that describe the metabolic and regulatory networks ofHalobacterium NRC-1.
Visualizing Sequence Similarity of Protein Families
Authors: Veeramachaneni Vamsi , Makałowski Wojciech
Published: May 2004

Classification of proteins into families is one of the main goals of functional analysis. Proteins are usually assigned to a family on the basis of the presence of family-specific patterns, domains, or structural elements. Whereas proteins belonging to the same family are generally similar to each other, the extent of similarity varies widely across families. Some families are characterized by short, well-defined motifs, whereas others contain longer, less-specific motifs. We present a simple method for visualizing such differences. We applied our method to the Arabidopsis thaliana families listed at The Arabidopsis Information Resource (TAIR) Web site and for 76% of the nontrivial families (families with more than one member), our method identifies simple similarity measures that are necessary and sufficient to cluster members of the family together. Our visualization method can be used as part of an annotation pipeline to identify potentially incorrectly defined families. We also describe how our method can be extended to identify novel families and to assign unclassified proteins into known families.
Predicting Protein Complex Membership Using Probabilistic Network Reliability
Authors: Asthana Saurabh , King Oliver D. , Gibbons Francis D. , Roth Frederick P.
Published: May 2004

Evidence for specific protein–protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are frequent among large-scale studies, and that error frequency depends on the large-scale method used. Despite knowledge of the error-prone nature of interaction evidence, edges (connections) in this network are typically viewed as either present or absent. However, use of a probabilistic network that considers quantity and quality of supporting evidence should improve inference derived from protein networks. Here we demonstrate inference of membership in a partially known protein complex by using a probabilistic network model and an algorithm previously used to evaluate reliability in communication networks.
Awareness of quality assurance procedures in digital preservation
Authors: Williamson Andrew
Published: May 2004

Awareness and implementation of appropriate quality assurance procedures at each stage in the process of digital preservation is vital for achieving the goals of long‐term access and integrity of electronic information, and maximising the return on the high levels of investment being made in digital preservation. This paper outlines the four stages of quality assurance within the digitisation process suggested in the UK by the JISC QA Focus, and identifies issues to be considered at each stage.
The changing face of India. Part I: bridging the digital divide
Authors: Nikam Khaiser , Ganesh A.C. , Tamizhchelvan M.
Published: May 2004

“India lives in villages” said the Father of the Nation, Mahatma Gandhi. With 1,000 million people and 180 million households, India is one of the biggest growing economies in the world. With the advent of the Information, Communication and Technology (ICT) revolution, India and its villages are slowly but steadily getting connected to the cities of the nation and the world beyond. Owing to the late Rajiv Gandhi, India is now a powerful knowledge economy, and though India may have been slow to start, it certainly has caught up with the West and is ahead in important respects. The Government, the corporate sector, NGOs and educational institutions have supported rural development by encouraging digital libraries, e‐business, e‐learning and e‐governance. The aim of this paper is to touch upon and highlight some of the areas where, by using ICT, the masses have been reached in this way. A follow‐up paper will outline collections of significant cultural material which, once national IT strategies are fully achieved, could form part of a digitally preserved national heritage collection.
An academic library partnership in the Indian Ocean region
Authors: Gross Julia , Riyaz Aminath
Published: May 2004

The emergence of a global marketplace in education offers valuable partnership opportunities. Libraries in small developing countries often do not have a critical mass of library professionals to share knowledge and to provide advice and collegial support. This case study describes a World Bank funded “Link Institution Arrangement”, which established a library partnership between an academic library in Western Australia and one in the Republic of Maldives. The authors describe the state of libraries and the emerging library profession in the Maldives. They also reveal ways in which the partners explored development issues facing an isolated academic library, shared knowledge in developing print and digital collections and planning collection development. The authors affirm the value of building enduring professional partnerships and conclude with recommendations for building print and digital collections, which may have implications for other small academic libraries.
Modern apprenticeships: hitting the target?
Authors: Spielhofer Thomas , Sims David
Published: May 2004

This article presents the results of a qualitative study that examined the views and experiences of 12 large city employers of modern apprenticeships (MAs). Given the government's target that by 2004 at least 28 per cent of young people should enter an apprenticeship before the age of 22, it is imperative that large employers are fully involved in taking on young people as apprentices. However, this study found that many such employers are either not aware of these qualifications or do not see them as relevant to their businesses. The paper concludes by providing suggestions, based on the findings of this study, for different ways of raising the status of MAs and getting more large employers to take up the award.
Finding the niche? Competition and collaboration for sixth form colleges
Authors: Briggs Ann R.J.
Published: May 2004

This paper reports on aspects of a Nuffield‐funded study carried out in 2001‐2002 into the impact of government policy upon sixth form colleges. Case study research was carried out at five colleges, following regional and national surveys of sixth form colleges, general further education colleges and schools. This paper examines the environment for competition and collaboration within which the colleges work. It defines and discusses examples of positive and negative competition, and offers evidence of collaboration, largely to support curriculum development and provision. The implications of working within a market‐driven environment are examined.
The value of tourism degrees: a Luton‐based case study
Authors: Petrova Petia , Mason Peter
Published: May 2004

Travel and tourism graduates are facing challenges in securing jobs within the travel and tourism industry, as their degrees have low recognition among travel and tourism employers. Yet there are growing numbers of tourism courses provided by universities, and these are increasingly popular among students. This paper attempts an informed discussion of the relevance of travel and tourism degrees, comparing students' career expectations and aspirations with industry needs and perceptions of travel and tourism degrees and graduates. Students' perceptions were investigated, using a questionnaire survey, while the employers' perceptions and needs were explored through semi‐structured interviews. The results indicate a desire and optimism amongst current travel and tourism undergraduate students towards securing a job in the tourism industry, while the industry is not convinced, or at best unaware, of the benefits of tourism degrees and employing tourism graduates.
Strategy‐managerial characteristics alignment and performance
Authors: Kathuria Ravi , Porth Stephen J.
Published: May 2004

Prior research of the influence of “upper echelon” managers has confirmed the importance of matching the characteristics of senior executives with the requirements of their organizations’ strategies. Firms that achieved higher levels of strategy‐manager alignment at both the corporate and business unit levels were found to have correspondingly higher levels of organizational performance. This study extends prior research of the strategy‐managerial characteristics relationship to the functional level of the organization. Specifically, based on a sample of 196 managers from 98 companies, this study investigates whether manufacturing units pursuing dissimilar strategies are led by manufacturing managers with dissimilar attributes, and whether the strategy‐manager alignment is related to the performance of the manufacturing unit. Results provide evidence to support these hypothesized relationships.
Supply chain implications of modularization
Authors: Doran Desmond
Published: May 2004

This paper explores the development of modular supply within the automotive sector with particular emphasis on the impact that modularization is likely to have on the value‐adding processes of key component suppliers. In addition, a reclassification of the term “first‐tier” supplier is proposed with a view to exploring the attributes necessary for such suppliers to succeed within the emerging modular environment.
Technology in Education: TechEd 2004 Conference
Authors: Gelfand Julia , Riggs Colby
Published: May 2004

Reports on some of the sessions held at the ninth annual Technology in Education International Conference and Exposition held in March 2004, the theme of which was “Leading and learning in the digital age”. Sessions outlined include one on a new national distance education master’s degree program, an examination of successful connections between industry and education, and advances in technology which allow us to see how the brain processes information during the learning process.
The impact of service failures on customer loyalty
Authors: Mattila Anna S.
Published: May 2004

This purpose of this study was to investigate the negative impact of service failures on customer loyalty. More specifically, we examined the moderating role of affective commitment on post‐failure attitudes and loyalty intentions under two service failure conditions: a successful and poor service recovery. Our findings indicate that emotionally‐bonded customers might feel “betrayed” when a service failure occurs, thus resulting in sharp decrease in post‐recovery attitudes. Conversely, this negativity effect was limited to poor service recovery among consumers with low affective commitment. Customers with lower levels of emotional bonding with the service provider were more “forgiving” when the service recovery was effectively handled. Poor service recovery led to more ambivalent post‐failure attitudes irrespective of the degree of affective commitment between the customer and the service provider. Finally, the results suggest that affective commitment might reduce the spill‐over effects of service failures to future loyalty behaviors. The implications for retention management strategies are briefly discussed.
Consumer responses to compensation, speed of recovery and apology after a service failure
Authors: Wirtz Jochen , Mattila Anna S.
Published: May 2004

This experimental study examined how the three dimensions of fairness (distributive, procedural and interactional) influence consumers' attributional processes, their post‐recovery satisfaction and behavioral responses (repatronage intent and negative word‐of‐mouth) in a service failure context that does not involve monetary costs to the consumer. Our results indicate that recovery outcomes (e.g. compensation), procedures (e.g. speed of recovery) and interactional treatment (e.g. apology) have a joint effect on post‐recovery satisfaction. Specifically, our findings suggest that compensation may not enhance satisfaction when the recovery process is well‐executed (an immediate response combined with an apology). Similarly, compensation failed to lessen dissatisfaction with a poor recovery process (a delayed response without apology). It thus seems that compensation is a poor substitute for a good recovery process. However, offering compensation was effective in increasing satisfaction in mixed‐bag recovery situations (delayed recovery with an apology, or immediate recovery without apology). Furthermore, we found that service recovery satisfaction acted as a full mediator between service recovery attributes (compensation, recovery speed and apology) and behavioral intentions (repurchase intent and negative WOM). Finally, our findings suggest that consumer attributions for stability and controllability for the failure vary across recovery efforts. Managerial implications for these findings are discussed.
Participative customers as partial employees and service provider workload
Authors: Hsieh An‐Tien , Yen Chang‐Hua , Chin Ko‐Chien
Published: May 2004

For service providers, whether customers can act the role of partial employees when participating in the service production and delivery process is a subject that has been receiving conflicting explanations and has not been analysed empirically. The purpose of this study is to examine the relationship between customer participation and service providers' perceived workload. Empirical results of survey data collected from 293 customer‐contact employees at 64 restaurants in Taiwan indicate that customer participation is positively related to service providers' perceived workload, which implies that it is inappropriate to decrease the number of service employees based on service designs that include customer participation. Implications of these findings for managing customer participation, as well as future research directions, are subsequently discussed.
Auditing and mapping key skills within university curricula
Authors: Tariq Vicki N. , Scott Eileen M. , Clive Cochrane A. , Lee Maria , Ryles Linda
Published: May 2004

Universities are encouraged to embed key skills in their undergraduate curricula, yet there is often little support on how to identify skills development and progression. This paper describes a tool that facilitates colleagues in auditing key skills and career/employability skills within individual modules and mapping these skills across degree pathways. The instrument presented supports a systematic approach to collect information on skills development. It enables tutors to highlight those skills students have the opportunity to develop or practise within a module, and to record for each skill whether explicit learner support is provided, whether the skill is assessed, and the desired standard of proficiency. The latter is identified from descriptors defined for three standards. Data collected for all modules within a degree pathway may subsequently be summarised (mapped). The tool provides valuable summary data for institutional quality assurance purposes and facilitates reflection on how to enhance students' learning experiences.
A constructivist model for evaluating postgraduate supervision: a case study
Authors: Zuber‐Skerritt Ortrun , Roche Val
Published: May 2004

This paper presents a new constructivist model of knowledge development in a case study that illustrates how a group of postgraduate students defined and evaluated effective postgraduate supervision. This new model is based on “personal construct theory” and “repertory grid technology” which is combined with interviews and group discussion. It is argued that this approach leads to a more meaningful interpretation of results and facilitates formative evaluation and professional development of supervisors. In this case study we discuss details of our evaluation method and its benefits and limitations. We explain how this approach enables both supervisors and students to participate actively in research and development activities, to develop their own constructs or theories of effective supervision, and to communicate their suggestions for improvement. Further applications of this constructivist model to postgraduate supervision practice and to research in higher education are suggested.
From brand image research to teaching assessment: using a projective technique borrowed from marketing research to aid an understanding of teaching effectiveness
Authors: Boddy Clive Roland
Published: May 2004

This paper describes how a simple qualitative market research technique using a projective device called a bubble drawing can be used as a useful feedback device to gain an understanding of students' views of the teaching effectiveness of a market research lecture. Comparisons are made with feedback gained from teaching observations and insights drawn from this. Some areas for further research are suggested.
Reception study: the labor world as a communication mediator
Authors: Fígaro Paulino Roseli A.
Published: May 2004

This research project is a major metallurgy company worker reception study. Based on a survey of the interviewees' socioeconomic segmentation in levels B, C, D, E, and on the results of their media consumption habits, a list of questions was elaborated for in‐depth interviews to be made. It was concluded that the work world is the main mediation in the means of communication reception. Television is the preferred medium and its reception occurs through the different discourses that circulate in the work world, most especially through those promoted by the labor union press and through interpersonal relations between colleagues and union representatives, allowing the worker to establish a critical view on such messages.
Breaking symmetry: a clinical overview of left‐right patterning
Authors: Maclean K , Dunwoodie SL
Published: May 2004

It is increasingly recognized that mutations in genes and pathways critical for left‐right (L‐R) patterning are involved in common isolated congenital malformations such as congenital heart disease, biliary tract anomalies, renal polycystic disease, and malrotation of the intestine, indicating that disorders of L‐R development are far more common than a 1 in 10,000 incidence of heterotaxia might suggest. Understanding L‐R patterning disorders requires knowledge of molecular biology, embryology, pediatrics, and internal medicine and is relevant to day‐to‐day clinical genetics practice. We have reviewed data from mammalian (human and mouse) L‐R patterning disorders to provide a clinically oriented perspective that might afford the clinician or researcher additional insights into this diagnostically challenging area.
Changes in species richness with stocking density of marine bivalves
Authors: BEADMAN H. A. , KAISER M. J. , GALANIDI M. , SHUCKSMITH R. , WILLOWS R. I.
Published: May 2004

Monocultures of mussels might alter the infaunal benthic community of adjacent and interstitial sediments through provision of a complex habitat, input of organically rich material and larval removal through filter feeding. At a site of commercial seabed mussel cultivation, we aimed to determine the effect of mussels on the infaunal community of an intertidal mudflat at different spatial scales and under different stocking strategies.

Mussels were laid at four different densities (2, 3, 5 and 7·5 kg m−2) on 400‐m2 plots in a 4 × 4 Latin square. Benthic samples were collected within and 10–100 m distant from the cultivation area c. 7 months prior to and 18 months after seeding the plots with blue mussels. Benthic community characteristics were related to initial seeding density and to the actual surface area of mussels associated with each set of samples collected within replicate plots.

The presence of mussels significantly changed the occurrence of some species of the infaunal community within the cultivated area. The infaunal communities supported fewer individuals and species than control treatments at all but the lowest mussel cover.

Species richness and the abundance of individuals per unit area also declined with increased area of mussel cover. The abundance of cirratulids and amphipods declined strongly with increasing mussel surface area.

Although the species composition and abundance of individual invertebrate species were altered by the presence of mussels, the distribution of individuals among species remained relatively unchanged.

Synthesis and applications. Overall, mussel beds changed the infaunal community, but the effects were localized (0–10 m) and not detectable at larger scales (10–100 m). Changes in benthic community composition could be reduced (but not eliminated) by lowering the stocking density of mussels to either 2 or 3 kg m−2. Given the small edge effects associated with cultivated mussel beds, the use of larger mussel beds would be preferable to many smaller mussel beds.
Linking contaminant profiles to the diet and breeding location of American dippers using stable isotopes
Authors: MORRISSEY CHRISTY A. , BENDELL‐YOUNG LEAH I. , ELLIOTT JOHN E.
Published: May 2004

Individual variation in contaminant levels is a common occurrence in many toxicology studies, but the exact cause is often unclear. We investigated the influence of diet and breeding location on individual bird contaminant profiles using a colour‐marked population of American dippers Cinclus mexicanus. The population comprised two distinct groups within a single river system: resident dippers breeding on the main river and altitudinal migrants breeding on tributaries.

Residue analysis revealed that total organochlorines (OC), polychlorinated biphenyls (PCB) and mercury (Hg) were all significantly higher in eggs from river residents compared with tributary migrants. This trend was also apparent for the three most prevalent organochlorine compounds: p,p′‐dichlorodiphenyl‐dichloroethylene (DDE), hexachlorobenzene and trans‐nonachlor.

We hypothesized that the observed differences in contaminant concentrations were partially related to the proportion of salmon fry Oncorhynchus spp. in the diet relative to aquatic invertebrates. Stable isotope analyses using δ13C and δ15N were conducted on blood and feathers of dippers in addition to aquatic invertebrates and salmon fry prey. Linear mixing models using the 15N isotope in the dippers’ diet and blood revealed considerable variability in the proportion of fish consumed (0–71%). Resident dippers on the main river ate significantly higher proportions of fish (42%) than tributary migrants (22%) (P = 0·01).

The difference in diet between migratory groups explained some of the observed variation in egg contaminant profiles, as total OC (P = 0·002) in dipper eggs was positively correlated with blood δ15N values, indicating fish may be the primary source of contamination.

Synthesis and applications. We conclude that dipper eggs represent local conditions at the breeding site, making them useful tools for biomonitoring aquatic contaminants in watersheds. However, given the distinct difference in contaminant profiles between resident and migrant dippers and the link with diet, the results emphasize the importance of understanding individual species’ ecology for assessing toxicological effects at the population level.
Managing threatened species: the ecological toolbox, evolutionary theory and declining‐population paradigm
Authors: NORRIS KEN
Published: May 2004

The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining‐population paradigm identified by Caughley.

There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour‐based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application.

These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviour‐based models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions.

Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past.

Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population‐level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level.

Synthesis and applications.It is argued that evolutionary theory underpins Caughley's declining‐population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision‐making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.
Using satellite telemetry and aerial counts to estimate space use by grey seals around the British Isles
Authors: MATTHIOPOULOS JASON , MCCONNELL BERNIE , DUCK CALLAN , FEDAK MIKE
Published: May 2004

In the UK, resolving conflicts between the conservation of grey seals, the management of fish stocks and marine exploitation requires knowledge of the seals’ use of space. We present a map of grey seal usage around the British Isles based on satellite telemetry data from adult animals and haul‐out survey data.

Our approach combined modelling and interpolation. To model the seals’ association with particular coastal sites (the haul‐outs), we divided the population into subpopulations associated with 24 haul‐out groups. Haul‐out‐specific maps of accessibility were used to supervise usage estimation from satellite telemetry. The mean and variance of seal numbers at each haul‐out group were obtained from haul‐out counts. The aggregate map of usage for the entire population was produced by adding together the haul‐out‐specific usage maps, weighted by mean number of animals using that haul‐out.

Seal usage was primarily concentrated (i) off the northern coasts of the British Isles, (ii) closer to the coast than might be expected purely on the basis of accessibility from the haul‐outs and (iii) in a limited number of marine hot‐spots.

Although our results currently represent the best estimate of how grey seals use the marine environment around Britain, they are neither definitive nor equally precise for all haul‐outs. Further data collection should focus in the south‐west of the British isles and aerial counts should be repeated for all haul‐outs.

Synthesis and applications. This work provides environmental managers with current estimates of grey seal usage and describes a methodology for maximizing data efficiency. Our results could guide government departments in licensing marine exploitation by the oil industry, in estimating grey seal predation pressure on vulnerable or economically important prey and in delineating marine special areas of conservation (SAC). Our finding that grey seal usage is characterized by a limited number of hot‐spots means that the species is particularly suited to localized conservation efforts.
Reduced numbers of generalist arthropod predators after crop management
Authors: THORBEK P. , BILDE T.
Published: May 2004

Generalist arthropod predators act as natural enemies of insect pests in agro‐ecosystems. Crop management activities may cause a reduction in arthropod densities, either directly through mortality and emigration, or indirectly through habitat disruption. Our aim was to quantify direct mortality caused by mechanical crop treatments. For some treatments, we also quantified emigration and other indirect effects, such as population declines caused by the impact of habitat deterioration on reproduction and survival.

Direct mortality was determined by measuring predator densities simultaneously in control and treatment plots using closed emergence traps immediately following a mechanical treatment. Treatments consisted of the following crop management activities: ploughing, non‐inversion tillage, superficial soil loosening, mechanical weed control and grass cutting. Predator densities were measured a second time 5–26 days after treatment to quantify emigration and indirect effects.

All treatments had a negative influence on one or more arthropod taxa. Direct mortality caused a 25–60% reduction in arthropod densities. Overall, spiders were more vulnerable to mechanical crop treatment than carabid and staphylinid beetles. Intensive soil cultivation, such as ploughing and soil loosening, did not kill more arthropods than weed harrowing and grass cutting.

We estimated the cumulative effects of mortality, emigration and indirect effects 3 weeks following treatment. The cumulative effect was greater than direct arthropod mortality, suggesting delayed effects of habitat disruption.

Grass cutting caused spiders and staphylinid beetles to move out of the crop, except in one case when the grass was left to dry, suggesting an important role of organic material or structural elements for arthropod persistence. Our results also suggest that arthropod predators aggregate in undisturbed or less disrupted habitats.

Synthesis and applications. Mechanical operations in arable crops and grass cutting cause mortality and emigration of generalist arthropod predators, especially spiders. Effects can be species‐specific and are likely to be affected by the timing of management. In grassland, cutting and removal have greater adverse impacts than leaving cuttings that contribute to habitat structure. Adjacent, less‐disturbed refuge areas are colonized by predators following husbandry events, demonstrating significant spatial dynamics among farmland arthropods. The negative effects of crop husbandry operations might be mitigated by the provision of refuge areas within and adjacent to fields and by maintaining crop and landscape diversity.
Has Danish agriculture maintained farmland bird populations?
Authors: FOX A. D.
Published: May 2004

Rapid agricultural change in western Europe has occurred in the last three decades, at cost to farmland biodiversity, particularly birds. This study reviewed agricultural change in Denmark from 1983 to 2001, to compare patterns of intensification and farmland bird abundance with the UK.

Changes in 26 agricultural variables summarized using principal components analysis (PCA) showed consistent changes throughout the period that were similar to the UK. Pig and sheep production, and the extent of winter cereals, rape and fodder maize, all increased. The area used to grow fodder beet and spring barley, the applications of agrochemicals and the numbers of cattle reared all declined. The greatest change in land area in Denmark was the switch from spring‐ to autumn‐sown cereals in the 1980s, almost a decade later than in the UK.

PCA described changes in annual indices of bird abundance based on Danish point count surveys from 1983 to 2001, which were most marked during 1983–90, after which ordination values varied little despite continued agricultural change. Of 27 bird species associated with farmland habitat in Denmark, five declined, 10 showed stable trends and 12 increased, compared with 15, eight and four, respectively, among the same species in the UK.

Agricultural yields have been sustained or enhanced during the survey period, while most farmland bird species declining in the UK have remained stable or increased in Denmark. Of the five declining Danish species, only lapwing Vanellus vanellus and yellowhammer Emberiza citrinella are associated with predominantly farmland habitat. The timing of the declines suggests that the switch to autumn sowing in Denmark has had little effect on any species.

In contrast to the UK, pesticide and inorganic fertilizer use has declined and organic farming has expanded in Denmark since 1983, coinciding with the period of stability/increase in farmland bird abundance. It is not possible to establish any causality from this analysis.

The ability of species showing marked declines in Europe to maintain their number and distribution in the Danish landscape in the face of agricultural intensification gives some optimism for safeguarding farmland birds and biodiversity in the future. However, we need to understand the reasons behind contrasting population trends in Denmark and the UK.

Synthesis and applications. Marked differences between national patterns of agriculture and the contrasting nature of historical intensification offer the opportunity to contrast the effects of major changes in land‐use practice on European farmland biodiversity. Appropriate comparative and individual studies of the effects of changes in specific agricultural management at greater spatial (i.e. supranational) scales are necessary in order to underpin the successful development of future European agricultural policies that will sustain and enhance agricultural yields whilst maintaining farmland biodiversity.
Redescription of the Chengjiang arthropod Squamacula clypeata Hou and Bergström, from the Lower Cambrian, south‐west China
Authors: Zhang Xingliang , Han Jian , Zhang Zhifei , Liu Huqin , Shu Degan
Published: May 2004

The anatomy of the arthropod Squamacula clypeata Hou and Bergström, 1997 from the Lower Cambrian Chengjiang Lagersta¨tte is redescribed based on four newly excavated specimens. The new material was collected from localities recently discovered in the Kunming area, Yunnan Province, south‐west China, and preserves remarkable details of the ventral morphology, revealed by preparation. Squamacula clypeata is dorsoventrally flattened and rounded in outline. The cephalon was covered by a wide, short shield, with a large doublure and a pair of uniramous antennae on the ventral side. The thorax consists of nine somites, each protected by a tergite and carrying at least one pair of biramous limbs. The pygidium is covered with a small rounded tergum. The endopod is segmented, equipped with short spines on the inner margin of the coxa and a claw‐like structure distally, and the exopod flap‐like, fringed with setae. The limbs in the pygidium are like those in the thorax in shape. Squamacula was most probably a nektobenthic predator. The spinose endopod could walk, grasp and grind. The large flap‐like exopod was adapted for swimming and respiration. Its affinities lie with the Arachnomorpha, but the relationships with other known taxa remain ambiguous.
Biota, palaeoenvironments and biostratigraphy of continental Oligocene deposits of the South German Molasse Basin (Penzberg Syncline)
Authors: Reichenbacher Bettina , Uhlig Undine , Kowalke Thorsten , Bassler Barbara , Matzke‐Karasz Renate , Schenk Bettina
Published: May 2004

Six charophyte, 13 mollusc, four ostracod and nine fish otolith taxa are taxonomically described, and one fruit, one seed and two foraminiferal taxa are briefly noted from the Lower Cyrena Beds and the Lower Coloured Molasse of the Sindelsdorf section near Penzberg (approximately 50 km south of Munich). Our palaeoecological and lithological data from the Lower Cyrena Beds suggest a delta plain with lagoons, estuaries, slowly flowing rivers, lakes and swamps. Faunal and floral elements of the Lower Coloured Molasse indicate lacustrine environments. The gastropod Tympanotonos and the tropical to subtropical fish fauna (Eleotridae, Ambassidae and Cyprinodontidae) suggest a warm, at least subtropical climate. Furthermore, Tympanotonos suggests comparisons with Recent molluscan faunas of the mangrove swamps of the West African coast, and thus hints at mangrove vegetation bordering the coasts of the Upper Bavarian Molasse Sea. A biostratigraphical classification for the Oligocene Molasse deposits of the Penzberg Syncline is established for the first time based on otoliths and charophytes. The Lower Cyrena Beds are attributed to the newly defined otolith zone OT‐O1/2 and probably correspond to the oldest part of the Chara microcera Zone. The lowermost part of the Lower Coloured Molasse can be correlated both with otolith zone OT‐O2 and the Chara microcera Zone. The Sindelsdorf section lies within the Rupelian–Chattian transition zone and thus the chronostratigraphic age is approximately 29–28 Ma.
A new galesaurid (Therapsida: Cynodontia) from the Lower Triassic of South Africa
Authors: Sidor Christian A. , Smith Roger M. H.
Published: May 2004

A new galesaurid cynodont, Progalesaurus lootsbergensis gen. et sp. nov., is described on the basis of a well‐preserved skull, lower jaw, right scapula and left atlantal neural arch. Autapomorphies of Progalesaurus include postcanine teeth bearing numerous mesial and distal accessory cusps that flank a recurved main cusp, a post‐temporal fenestra bordered by the squamosal ventrally and a large external naris. Progalesaurus is similar to Galesaurus in possessing a poorly defined masseteric fossa on the dentary, a strongly recurved main cusp of the postcanine dentition, an incomplete secondary palate and a similar basisphenoid‐parasphenoid morphology. A cladistic analysis of ten early cynodont genera resolves a monophyletic Galesauridae encompassing Cynosaurus, Progalesaurus and Galesaurus, although support for this clade is weak. Procynosuchus and Dvinia are placed at the base of Cynodontia whereas Thrinaxodon and Platycraniellus are positioned higher, but outside of Eucynodontia. The holotype and only known specimen of Progalesaurus was collected during systematic prospecting of Permo/Triassic boundary strata at New Lootsberg Pass, Graaff‐Reinet District, South Africa. The discovery of Progalesaurus increases the number of valid Early Triassic cynodonts to four and sheds light on the tempo of early cynodont diversification after the end‐Permian mass extinction.
Late Ordovician and early Silurian Proetida (Trilobita) from north‐western and central Europe
Authors: Owens R. M.
Published: May 2004

Species belonging to genera of three families of the Proetida (Proetidae, Rorringtoniidae and Toernquistiidae) are described from the upper Ashgill of southern Sweden, and the same or related species noted from the adjacent parts of northern and central Europe. Proetidae are represented by Paraproetus brevifrons (Angelin), Ogmocnemis irregularis Kielan, Ogmocnemis jaanussoni sp. nov. and Parvigena putealis sp. nov.; it is argued that all belong to the Cornuproetinae, not Tropidocoryphinae where they were previously classified. Ogmocnemis is resurrected for some Upper Ordovician species included previously in Decoroproetus. The rorringtoniid genera Rorringtonia and Madygenia are recognised for the first time in southern Sweden, and it is argued that these are probably closely related, and both are included in the same family; both are recorded for the first time from Silurian (Llandovery) strata. Zetaproetus is claimed to be a junior subjective synonym of Rorringtonia. Solariproetus, first described from north‐west China, is assigned to the Toernquistiidae as a late, derived member, and S. prosthemesos sp. nov. is described from late Rawtheyan strata in the Holy Cross Mountains, Skåne and the English Lake District. Comments are given on the stratigraphical and palaeogeographical distribution of these taxa.
Coccolith biomineralisation studied with atomic force microscopy
Authors: Henriksen K. , Young J. R. , Bown P. R. , Stipp S. L. S.
Published: May 2004

Biomineralisation can only be understood as an interplay between organic and mineral phases. With this objective, we conducted an investigation of coccoliths using atomic force microscopy (AFM), an ultra‐high resolution technique that requires no surface coating and can be used in air or under solution at ambient conditions of temperature and pressure. The detailed morphology, crystal structure, organic scales and organic coating of the coccolith species Coccolithus pelagicus, Helicosphaera carteri and Oolithotus fragilis were investigated. The fine structure of coccoliths is very complex, with the calcite either being smooth, dominated by steps or tuberculate; organic cover can be either granular or fibrous. Behaviour of coccolith surfaces during dissolution is influenced both by mineral and organic material and different surface types show variable resistance to dissolution. The organic coating protects element faces against etching. Through atomic resolution AFM, it is possible to establish the crystallographic structure of the distal shields of C. pelagicus and O. fragilis. Though elements of both species are dominated by stable crystal faces, there are important differences between them, with the external edge of elements being parallel to a cleavage direction in C. pelagicus but parallel to the atomic rows in O. fragilis. Thus, there is evidence that the biomineralisation of each species, and also of select areas of coccoliths of the same species, is markedly different.