Data storage optimization strategy in distributed column-oriented database by considering spatial adjacency

Scan operation will involve many fragments and cause many extra invalid partitioning query operations in distributed column-oriented database which affects query efficiency seriously, especially for spatial data. To solve this question, this paper refers to partitioning strategy in distributed column-oriented database and advocates a spatial data storage optimization strategy named ‘SPPS’. This strategy makes adjacent spatial objects stored in the same data fragment with considering spatial adjacency, and reserves the spatial information of each fragment. Thus spatial query operation can locate the relevant fragment on basis of spatial information of fragment, and extra invalid partitioning scan operations would be lighted. Then the storage and query efficiency would be improved. To verify the validity of ‘SPPS’ optimization strategy, this paper carries on relevant experiments based on HBase and records spatial query efficiency with and without ‘SPPS’ respectively. The experiments results indicate that ‘SPPS’ strategy can optimize the storage and query efficiency in distributed column-oriented databases.     

Integrative taxonomy,or iterative taxonomy?

The recently introduced term ‘integrative taxonomy’ refers to taxonomy that integrates all available data sources to frame species limits. We survey current taxonomic methods available to delimit species that integrate a variety of data, including molecular and morphological characters. A literature review of empirical studies using the term ‘integrative taxonomy’ assessed the kinds of data being used to frame species limits, and methods of integration. Almost all studies are qualitative and comparative – we are a long way from a repeatable, quantitative method of truly ‘integrative taxonomy’. The usual methods for integrating data in phylogenetic and population genetic paradigms are not appropriate for integrative taxonomy, either because of the diverse range of data used or because of the special challenges that arise when working at the species/population boundary. We identify two challenges that, if met, will facilitate the development of a more complete toolkit and a more robust research programme in integrative taxonomy using species tree approaches. We propose the term ‘iterative taxonomy’ for current practice that treats species boundaries as hypotheses to be tested with new evidence. A search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses. We identify two recent empirical examples that use the process of iterative taxonomy.     

Weismann Versus Morgan Revisited: Clashing Interpretations on Animal Regeneration

This paper has three principal aims: first, through a detailed analysis of the hypotheses and assumptions underlying Weismann’s and Morgan’s disagreement on the nature of animal regeneration, it seeks to readdress the imbalance in coverage of their discussion, providing, at the same time, a fascinating case-study for those interested in general issues related to controversies in science. Second, contrary to Morgan’s beliefs according to which Weismann employed a speculative and unempirical method of scientific investigation, the article shows that Weismann performed experiments, made observations and proposed ‘undogmatic’ theories open to refutation. Third, through the reconstruction of Weismann’s and Morgan’s disagreement, this study illustrates how biology, during the very late nineteenth and early twentieth centuries, was undergoing important changes. I argue that this controversy clearly and convincingly demonstrates how some important epistemic assumptions became increasingly problematic for some members of the younger generations of biologists. At the end of my discussion I will also argue that Weismann and Morgan both had strong well-grounded arguments supporting their conclusions; for this reason I suggest a few factors (“taken-for-granted” beliefs or assumptions) that could explain why their disagreement was doomed to remain unresolved. In particular, I will analyze their diverse explicative interests, their different theoretical concerns and their distinct use of the available evidence.     

‘It's true,I'm English… I'm not lying’: essentialized and precarious English identities

This article explores relationships between Englishness and racialization in order to consider the potential for English identities that are progressive in anti-essentialist or multicultural terms. The article draws on data from interviews in which people from a South London area talk about Englishness. I will examine how English identities are understood by participants who are white and participants who are not white. While white participants experience Englishness as a taken-for-granted identity, for participants who are not white English identities are a more calculated, precarious performance. I will then examine discussions of ‘who can be English’. While most participants argue that ‘anyone can be English’ in principle, this is not necessarily the case in practice. It will be suggested that talk of Englishness is particularly constrained by relationships between Englishness, whiteness and ancestry, but that for those who experience Englishness as precarious there are signs that this is not necessarily the case.     

Journeying Between Desire and Anthropology: A Story in Suspense

Anthropology is a discipline based on the motif of the journey and ‘the myth of the eternal return’. This is the journey out to the ‘other’in order to return to constitute ‘self, and this movement is a movement of desire. The desire is for wholeness, for self‐presence, for a unified self. It is a desire for origins. And this desire is evident in anthropological practices as it is in myths and fairytales—all tell stories that speak of the desire for a separate, an original, self. Yet ‘the myth of the eternal return’reveals that the enactment of the story is itself originating. The origin is not a thing to be hunted down and appropriated—it is no thing. Like the archetypes which flow through stories, it is alive in the telling. The story I tell in this paper is about my own desires. It speaks of the desire to undergo the rite of passage of anthropology, and of how this journey was interrupted by the anthropologist who always journeys before me. And yet. it is through the inextricable relations with the writings of the “other‘ anthropologist that alluring moments of different desiring are fleetingly revealed. In the end. my relations with anthropology tell of a paradox: of the desire for a transcendental journey in order to constitute self and the seductive desire for immersion—to lose self, the story remains in suspense.     

Experimentalist Meets Theoretician: A Tale of Two Scientific Cultures

This is the story of how a small team of experimentalists and theoreticians collaborated to develop a theoretical model for vesicle formation during endocytosis. In telling our story, we hope to distil some general conclusions about the purpose and value of theoretical models and how best to navigate collaborations between experimentalists and theoreticians. We encountered challenges in building and publishing our model, but through our experiences we gained insight into how such collaborations can be profitably conducted. We also developed opinions about how theoretical models should be evaluated by peer reviewers and editors. During the evolution of our theoretical model, we educated each other, organized our thoughts and our data, developed a conceptual framework for understanding the mechanochemistry of endocytosis, and generated testable hypotheses that stimulated new experiments.     

The IDIP framework for assessing protein function and its application to the prion protein

The quest to determine the function of a protein can represent a profound challenge. Although this task is the mandate of countless research groups, a general framework for how it can be approached is conspicuously lacking. Moreover, even expectations for when the function of a protein can be considered to be ‘known’ are not well defined. In this review, we begin by introducing concepts pertinent to the challenge of protein function assignments. We then propose a framework for inferring a protein's function from four data categories: ‘inheritance’, ‘distribution’, ‘interactions’ and ‘phenotypes’ (IDIP). We document that the functions of proteins emerge at the intersection of inferences drawn from these data categories and emphasise the benefit of considering them in an evolutionary context. We then apply this approach to the cellular prion protein (PrP^C), well known for its central role in prion diseases, whose function continues to be considered elusive by many investigators. We document that available data converge on the conclusion that the function of the prion protein is to control a critical post-translational modification of the neural cell adhesion molecule in the context of epithelial-to-mesenchymal transition and related plasticity programmes. Finally, we argue that this proposed function of PrP^C has already passed the test of time and is concordant with the IDIP framework in a way that other functions considered for this protein fail to achieve. We anticipate that the IDIP framework and the concepts analysed herein will aid the investigation of other proteins whose primary functional assignments have thus far been intractable.     

THINK Back: KNowledge-based Interpretation of High Throughput data

Results of high throughput experiments can be challenging to interpret. Current approaches have relied on bulk processing the set of expression levels, in conjunction with easily obtained external evidence, such as co-occurrence. While such techniques can be used to reason probabilistically, they are not designed to shed light on what any individual gene, or a network of genes acting together, may be doing. Our belief is that today we have the information extraction ability and the computational power to perform more sophisticated analyses that consider the individual situation of each gene. The use of such techniques should lead to qualitatively superior results. The specific aim of this project is to develop computational techniques to generate a small number of biologically meaningful hypotheses based on observed results from high throughput microarray experiments, gene sequences, and next-generation sequences. Through the use of relevant known biomedical knowledge, as represented in published literature and public databases, we can generate meaningful hypotheses that will aide biologists to interpret their experimental data. We are currently developing novel approaches that exploit the rich information encapsulated in biological pathway graphs. Our methods perform a thorough and rigorous analysis of biological pathways, using complex factors such as the topology of the pathway graph and the frequency in which genes appear on different pathways, to provide more meaningful hypotheses to describe the biological phenomena captured by high throughput experiments, when compared to other existing methods that only consider partial information captured by biological pathways.     

Data mining for protein–protein interactions in invertebrate model organisms

Well-annotated genome databases are available for many invertebrate species, notably the fruitfly, Drosophila melanogaster, and the nematode, Caenorhabditis elegans. An adequate interpretation of this information at the biological level requires the exploration of the interactions between the gene products. Knowledge of protein interactions and the components of cell signalling pathways in the fly and worm are particularly valuable as hypotheses can be rapidly tested using the powerful genetic toolkits available. Invertebrates offer additional experimental advantages when attempting to characterise protein–protein interactions (PPIs). Their relatively small genome size compared to mammals helps to reduce missed interactions due to redundancy, and their function can be addressed using forward (mutants) and reverse (RNA interference) genetics. However, the researcher looking for evidence of PPIs for a protein of interest is faced with the challenge of extracting interaction data from sources that are highly varied, such as the results of microarray experiments in the unstructured text of research papers. This challenge is greatly reduced by a range of public databases of curated information, as well as publicly available, enhanced search engines, which can provide either direct experimental evidence for a PPI, or valuable clues for generating new hypotheses.     

What Is a Story?

This paper attempts to discover the criteria by which a listener accepts or rejects an item of oral narrative as being a story. The hypotheses are: (1) such criteria relate to structure rather than content, although the listener does not consciously distinguish structure from content; (2) the structure must have a certain minimal and maximal degree of complexity and be of a certain kind; (3) the criteria will hold cross-culturally. Information gathered from ethnographies and folklore literature is inadequate to confirm the hypotheses, but it does not contradict them. An experiment to test hypotheses (1) and (2) produced a certain degree of negative confirmation: listeners rejected as a story any narrative item which did not conform to the structural criteria regarded as minimal by myself; however, they also rejected items which I regarded as well structured but which were bizarre or nonsensical in content. The confusion of structure and content tended to confirm hypothesis (1).     

WWW and the aerobiologist: operating instructions

For several years now, the World Wide Web (WWW) has left the realm of information technology and represents a fundamental everyday working tool for a wide variety of disciplines. Aerobiology, though a newcomer in this virtual space, is proceeding at a fast pace towards the creation of an easily accessible and effective information network. The web gives access to text, imagery, movie and sound with relatively low-cost and user-friendly interfaces conceived as graphical magazines. A practical way to start navigating and looking for information is to operate a ‘search engine’ which is a large database containing addresses on a wide spectrum of subjects. As an alternative, a few selected sites exist that can initialize your search by providing a thematic list of addresses. After leaving the entry ‘port’ you are directed from site to site and eventually end up with a lot more information than you initially thought. Excerpts: information on public and private institutions, access to databases and image catalogs, bibliographical information, overview of monitoring networks, directions on national and international research programs, news (calendar of meetings, courses, etc.). Information is provided for the non-expert user who asks himself the key questions: ‘Where do I start to browse the net?’ or ‘Can I become a provider of information on the net and, if so, is it terribly difficult?’ The idea is that everybody can in principle become a ‘surfer’ or a ‘provider’ dedicating a reasonable amount of time and effort to the task. What one ends up with is an easy-to-use and powerful tool that is already helping the whole aerobiological community to pursue its goals and reach out for necessary interdisciplinary approaches to unsolved scientific issues. The server AEROBIOLOGY INTERNATIONAL (http://www.fisbat.bo.cnr.it/AERO/) is presented as an example on how to proceed with the creation of a new server and its management.     

The Path to Enlightenment： Making Sense of Genomic and Proteomic Information

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.     

Is New Zealand vegetation really ‘problematic’? Dansereau's puzzles revisited

Over four decades ago, Pierre Dansereau, the noted North American ecologist, proposed six features of New Zealand vegetation as being problematic or unusual in a global context. We examine his propositions in the light of current ecological knowledge to determine whether or not these can still be considered unusual characteristics of New Zealand vegetation. (1) ‘Climatic change is still progressing’ resulting in disequilibrium between species' distributions and the present climate. New data and methods of analysis now available have removed the impression that Dansereau gained of imprecise zonation, unclear vegetation/climate relations and missing vegetation types. Communities cited as having regeneration failure can now be seen as even‐aged stands that developed after major disturbance, although there are other, also non‐climatic, explanations. However, the cause of the Westland ‘Nothofagus gap’ has become more, rather than less, controversial. (2) ‘Continuity of community composition defies classification’ and ‘Very few New Zealand associations have faithful species' are correct observations, but perhaps equally true of vegetation elsewhere. Dansereau's assertion of low species richness in New Zealand is not supported by the comparative data available. (3) ‘Lack of intolerant [i.e. mid‐seral] trees …’ is not evident with newer information. The order of species in succession, seen as unclear by Dansereau, has been determined by a range of approaches, largely confirming each other. (4) ‘Discrepancies of form and function …’ in divaricate shrubs and widespread heteroblasty are still controversial, with many more explanations. Several abiotic explanations have failed to stand up to investigation. Explanations in terms of herbivory have been well supported, although the extinction of the large avian herbivores makes certainty impossible. (5) ‘Incidence of hybridization …’ remains problematic. We do not know whether the incidence is unusually high, as Dansereau alleged, but the limited comparative data available suggest not. (6) The ‘overwhelming … competing power of exotics' is strongly context dependent. They are prominent in many non‐forest habitats. It seems that they are drivers of the vegetation change in some habitats, yet passengers after disturbance in others. Invasions can be slow, and may still be very incomplete in some ecosystem types. Whether exotics will eventually take over in most communities, or whether the native species will ‘laugh them to scorn’ as Cockayne suggested, only time will tell. In conclusion, some aspects of New Zealand's vegetation seem less unusual with increased knowledge, but others remain ‘problems’.     

To speciate,or not to speciate? Resource heterogeneity,the subjectivity of similarity,and the macroevolutionary consequences of niche‐width shifts in plant‐feeding insects

Coevolutionary studies on plants and plant‐feeding insects have significantly improved our understanding of the role of niche shifts in the generation of new species. Evolving plant lineages essentially constitute moving islands and archipelagoes in resource space, and host shifts by insects are usually preceded by colonizations of novel resources. Critical to hypotheses concerning ecological speciation is what happens immediately before and after colonization attempts: if an available plant is too similar to the current host(s), it simply will be incorporated into the existing diet, but if it is too different, it will not be colonized in the first place. It thus seems that the probability of speciation is maximized when alternative hosts are at an ‘intermediate’ distance in resource space. In this review, I wish to highlight the possibility that resource similarity and, thus, the definition of ‘intermediate’, are subjective concepts that depend on the herbivore lineage's tolerance to dietary variation. This subjectivity of similarity means that changes in tolerance can either decrease or increase speciation probabilities depending on the distribution of plants in resource space: insect lineages with narrow tolerances are likely to speciate by ‘island‐hopping’ on young, species‐rich plant groups, whereas more generalized lineages could speciate by shifting among resource archipelagoes formed by higher plant taxa. Repeated and convergent origins of traits known to broaden or to restrict host‐plant use in multiple different insect groups provide opportunities for studying how tolerance and resource heterogeneity may interact to determine speciation rates.     

Do experiments exploring plant diversity–ecosystem functioning relationships inform how biodiversity loss impacts natural ecosystems?

An enormous recent research effort focused on how plant biodiversity (notably species richness) influences ecosystem functioning, usually through experiments in which diversity is varied through random draws of species from a species pool. Such experiments are increasingly used to predict how species losses influence ecosystem functioning in ‘real’ ecosystems. However, this assumes that comparisons of experimental communities with low vs high species richness are analogous to comparisons of natural communities from which species either have or have not been lost. I explore the validity of this assumption, and highlight difficulties in using such experiments to draw conclusions about the ecosystem consequences of biodiversity loss in natural systems. Notably, these experiments do not mimic what happens in real ecosystems either when local extinctions occur or when species losses are offset by gains of new species. Despite limitations, this single experimental approach for studying how biodiversity loss affects ecosystems has often been advocated and implemented at the expense of other approaches; this limits understanding of how natural ecosystems respond to biodiversity loss. I conclude that a broader spectrum of approaches, and more explicit consideration of how species losses and gains operate in concert to influence ecosystems, will help progress this field.     

A bioinformatics approach to investigating developmental pathways in the kidney and other tissues.

Over the past few years, large amounts of data linking gene-expression (GE) patterns and other genetic data with the development of the mouse kidney have been published, and the next task will be to integrate these data with the molecular networks responsible for the emergence of the kidney phenotype. This paper discusses how a start to this task can be made by using the kidney database and its associated search tools, and shows how the data generated by such an approach can be used as a guide to future experimentation. Many of the events taking place as the kidney develops do, of course, also take place in other tissues and organisms and it will soon be possible to incorporate relevant information from these systems into analyses of kidney data as well as the new information from microarray technology. The key to success here will be the ability to access over the internet data from the textual and graphical databases for the mouse and other organisms now being established. In order to do this, informatic tools will be needed that will allow a user working with one database to query another. This paper also considers both the types of tools that will be necessary and the databases on which they will operate.     

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network

New ‘omics’ technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information that accompanies data-intense technologies. NuGO, the European Nutrigenomics Organization, the major collaborating network in molecular nutritional sciences, is supporting the application of modern information technologies in this area. We have developed and implemented a concept for data management and computing infrastructure that supports collaboration between nutrigenomics researchers. The system fills the gap between “private” storing with occasional file sharing by email and the use of centralized databases. It provides flexible tools to share data, also during experiments, while preserving ownership. The NuGO Information Network is a decentral, distributed system for data exchange based on standard web technology. Secure access to data, maintained by the individual researcher, is enabled by web services based on the the BioMoby framework. A central directory provides information about available web services. The flexibility of the infrastructure allows a wide variety of services for data processing and integration by combining several web services, including public services. Therefore, this integrated information system is suited for other research collaborations.     

The jazz of cladistics*

In this metaphorical ‘composition’, I comment on nine ‘dissonant chords’ related to the drowning out of cladistic performance: (1) DNA-based phylogenetic hypotheses supported only by bootstrap values and without molecular synapomorphies; (2) the use of molecular data to the exclusion of morphological data, with the classification of clades diagnosed by morphological plesiomorphies plus bootstrap values; (3) neglect of the results of the congruence test and how they are interpreted; (4) the combination of character optimization using both model-based and parsimony methods, and its consequences; (5) the need to effectively integrate ontogeny and phylogeny; (6) the estimation of the ages of clades based on molecular-clock analyses; (7) the belief that new methods, theories, and hypotheses are more reliable than old ones, with the idea that model-based analyses achieve better results than parsimony analyses; (8) the false assumption of the irrelevance of classification; and (9) clashes amongst cladists themselves, who endorse distinct methods, philosophies, and theories. Finally, I present 10 ‘refrains’ in order to intensify the cladistic performance.     

LCI data and data quality

Life cycle inventory (LCI) is becoming an established environmental management tool that quantifies all resource usage and waste generation associated with providing specific goods or services to society. LCIs are increasingly used by industry as well as policy makers to provide a holistic ‘macro’ overview of the environmental profile of a good or service. This information, effectively combined with relevant information obtained from other environmental management tools, is very useful in guiding strategic environmental decision making. LCIs are very data intensive. There is a risk that they imply a level of accuracy that does not exist. This is especially true today, because the availability of accurate LCI data is limited. Also, it is not easy for LCI users, decision-makers and other interested parties to differentiate between ‘good quality’ and ‘poor quality’ LCI data. Several data quality requirements for ‘good’ LCI data can be defined only in relation to the specific study in which they are used. In this paper we show how and why the use of a common LCI database for some of the more commonly used LCI data, together with increased documentation and harmonisation of the data quality features of all LCI data, is key to the further development of LCI as a useful and pragmatic environmental management tool. Initiatives already underway to make this happen are also described.