New Kinds Of Data Research Articles

Quaternary beetle research: the state of the art

Quaternary beetle research has progressed in a variety of ways during the last decade. New kinds of data are being extracted from the fossil specimens themselves, such as ancient DNA and stable isotopes. The ancient DNA studies hold the promise of proving new insights on the stability of beetle genotypes. The study of stable isotopes of H and O from fossil beetle chitin holds the promise of providing an independent proxy for the reconstruction of temperature and precipitation. The discipline is also expanding into previously unstudied regions, such as Australia, New Zealand, and northern Asia. Along with the new study regions, new schools of thought are also forming in the discipline, challenging old research paradigms. This is a necessary step forward for the discipline, as it grows and develops in the 21st Century.

The politics of punishing

This article asks why some American states are more likely to rely on imprisonment in response to crime than others. Employing comparative historical methodology it brings new kinds of data to address contested questions in the field. In three case studies, it examines archival material, including citizens' letters to political leaders, transcripts from townhall meetings, internal government reports, public testimony; and it uses extensive secondary sources, including statistical data and political histories to tease out complex causal processes of crime control policy formation and its impact on imprisonment patterns. Analyzing evidence both temporarily and spatially, the article introduces a new account of American imprisonment variation based on the democratic process itself.

VALENTINE, J. W. 2004. On the Origin of Phyla. xxiv+614 pp. Chicago, London: University of Chicago Press. Price US $55.00, £38.50 (hard covers). ISBN 0 226 84548 6

In his magum opus , Darwin famously evaded saying anything too explicit about the origin of species. Rather, the argument emerged as a consilience of trenchant observation, strategic apology and inspired mistake. A century and a half on, the mystery of mysteries may have inflated to the origin of phyla, but the approach remains very much the same. The only real issue is dealing with the avalanche of accumulating new data – and new kinds of data. On the Origin of phyla does a superb job of data management and, at one level, serves simply as a review of where we have got to, circa 2003, in addressing the question of early animal evolution. All the pertinent literature is …

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities

The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

Integrating Genomic and Proteomic Data: The Integr8 Project

Summary Integr8 (http://www.ebi.ac.uk/integr8/) has been developed to provide an integration layer for the exploitation of genomic and proteomic data. High-quality databases from major bioinformatics centres in Europe are included, and some core data and the relationships of biological entities to each other and to entries in other databases are stored. Thus, a framework exists that allows for new kinds of data to be integrated, and an entity-centric view of complete genomes and proteomes is offered. Integr8 is an automatically populated database, providing different entry points to the data, depending on the user’s entity of interest. The Proteome Analysis database for statistical analysis and the Genome Reviews for annotated genome information are the main developments within the Integr8 project. With the BioMart application, an interactive querying tool for performing customisable proteome analysis and data mining is offered. Future developments will especially focus on the Genome Reviews, including mapping not yet annotated protein sequences onto their corresponding genomes, generating new predictions for non-coding RNA genes, and generally extending the scope to lower metazoan organisms.

A new approach to phase retrieval of a wave front

The main thrust of this project was to develop a process including data-gathering and processing techniques that would consistently and without fail discover the phase distribution of a wave front. In the course of the work, new thoughts on data gathering evolved to the point where a novel type of intensity picture bearing little or no resemblance to the wave front or its phase distribution was required for mathematical processing to achieve the phase distribution. For convenience these information images have been dubbed phasorgrams. Phasorgrams are recorded in the diffractive plane or in the image plane of an application device. Additional data, while helpful, are not required, thus eliminating the need for data from two Fourier conjugate planes as in the well-known method of Gerchberg and Saxton. The mathematical processing of these data is carried out by an iterative algorithm which also is new. This algorithm, given good data, has not failed to achieve the phase distribution. Contemporary devices have not been designed to measure the new kinds of data required for the process. Therefore, several novel devices are suggested. The new process could have major implications for the phase problem of X-ray crystallography.

Climat urbain et qualité de l'air : approches géographiques et collaborations pluridisciplinaires (Urban climate and air pollution : geographical approaches and pluridisciplinary collaborations)

Abstract. - Urban climate and air pollution in big cities provide a new field of research for geographers interested in climate studies. In order to efficiently contribute to research works with strong social implications, they have to collect fine-scale meteorological data and adapt their traditional knowledge in meteorological data processing for new kinds of data. Mapping the urban climate or air pollution requires specific methods of spatial interpolation, using statistical relationships between atmospheric parameters and urban descriptors ; in the near future, models of physical and chemical processes in the urban atmosphere will probably become the most useful tool in that purpose.

Are listed threatened plant species actually at risk?

Despite the fact that the most changes in lists of threatened species reflect changes in knowledge rather than changes in conservation status, the lists continue to provide social and legal mandates for conservation; they are used to report on the state of the environment and to guide the allocation of scarce resources. There is a substantial under-representation of non-vascular species in threatened plant lists, reflected in an absence of documented extinctions among fungi and algae. Turnover in the composition of extinct flora lists in Australia suggests that the lists of threatened species may not be sufficiently reliable to form the basis for reporting on the state of the environment. They are of limited use in distinguishing between levels of threat and may not be a reliable guide for the allocation of scarce conservation resources among plant species. Systems for listing threatened species create a feedback loop, responsive to the subjective preferences of scientists, largely unresponsive to underlying true threats, self-perpetuating and accentuating bias with each iteration. Other tools, including formal decision approaches and the acquisition of new kinds of data, are needed to fill the roles.

Corrigendum to: TURNER REVIEW No. 5: Are listed threatened plant species actually at risk?

Despite the fact that the most changes in lists of threatened species reflect changes in knowledge rather than changes in conservation status, the lists continue to provide social and legal mandates for conservation; they are used to report on the state of the environment and to guide the allocation of scarce resources. There is a substantial under-representation of non-vascular species in threatened plant lists, reflected in an absence of documented extinctions among fungi and algae. Turnover in the composition of extinct flora lists in Australia suggests that the lists of threatened species may not be sufficiently reliable to form the basis for reporting on the state of the environment. They are of limited use in distinguishing between levels of threat and may not be a reliable guide for the allocation of scarce conservation resources among plant species. Systems for listing threatened species create a feedback loop, responsive to the subjective preferences of scientists, largely unresponsive to underlying true threats, self-perpetuating and accentuating bias with each iteration. Other tools, including formal decision approaches and the acquisition of new kinds of data, are needed to fill the roles.

New kinds of data, new options for HIV prevention among women: a public health challenge.

This theoretical article applies and extends the theory of gender and power developed by Robert Connell to define the exposures and risk factors that put women at increased vulnerability to HIV. Gina M.Wingood and Ralph J. DiClemente in “Application of the Theory of Gender and Power to Examine HIV-Related Exposures Risk Factors and Effective Interventions for Women” propose a new and innovative theoretical framework for understanding the risk factors for HIV among women. They provide fairly detailed recommendations for HIV interventions to address the three major structures that characterize the gendered relationships between men and women: the sexual division of labor the sexual division of power and the structure of cathexis. Public health researchers and practitioners are in need of new models for addressing this issue. The predominant theoretical models prevalent in HIV/STD behavior change (i.e. health belief model theory of reasoned action social cognitive theory transtheoretical stages of change model AIDS risk reduction model) even those that have informed community interventions have been justly criticized as being individualistic in their conceptualization. Although several include sociocultural and interpersonal elements such as perceived norms concerning behaviors their applications often ignore the social and cultural context of women’s (and men’s) sexual behaviors. They assume that the individual has total control over behavior and do not address the diverse contextual factors related to gender (e.g. power differentials gender roles) that likely influence behaviors that put women at risk for HIV. Thus the elaboration of the theory of gender and power to better understand the determinants of risk factors for HIV among women is an important and timely addition to our thinking about this public health issue. (excerpt)

Application of the Theory of Gender and Power to Examine HIV-Related Exposures, Risk Factors, and Effective Interventions for Women

Developed by Robert Connell, the theory of gender and power is a social structural theory based on existing philosophical writings of sexual inequality and gender and power imbalance. According to the theory of gender and power, there are three major social structures that characterize the gendered relationships between men and women: the sexual division of labor, the sexual division of power, and the structure of cathexis. The aim of this article is to apply an extended version of the theory of gender and power to examine the exposures, social/behavioral risk factors, and biological properties that increase women's vulnerability for acquiring HIV. Subsequently, the authors review several public health level HIV interventions aimed at reducing women's HIV risk. Employing the theory of gender and power among women marshals new kinds of data, asks new and broader questions with regard to women and their risk of HIV, and, most important, creates new options for prevention.

The complete nucleotide sequence of the mitochondrial DNA of the agnathan Lampetra fluviatilis: bearings on the phylogeny of cyclostomes.

There are two competing theories about the interrelationships of craniates: the cyclostome theory assumes that lampreys and hagfishes are a clade, the cyclostomes, whose sister group is the jawed vertebrates (gnathostomes); the vertebrate theory assumes that lampreys and gnathostomes are a clade, the vertebrates, whose sister group is hagfishes. The vertebrate theory is best supported by a number of unique anatomical and physiological characters. Molecular sequence data from 18S and 28S rRNA genes rather support the cyclostome theory, but mtDNA sequence of Myxine glutinosa rather supports the vertebrate theory. Additional molecular data are thus needed to elucidate this three-taxon problem. We determined the complete nucleotide sequence of the mtDNA of the lamprey Lampetra fluviatilis. The mtDNA of L. fluviatilis possesses the same genomic organization as Petromyzon marinus, which validates this gene order as a synapomorphy of lampreys. The mtDNA sequence of L. fluviatilis was used in combination with relevant mtDNA sequences for an approach to the hagfish/lamprey relationships using the maximum-parsimony, neighbor-joining, and maximum-likelihood methods. Although trees compatible with our present knowledge of the phylogeny of craniates can be reconstructed by using the three methods, the data collected do not support the vertebrate or the cyclostome hypothesis. The present data set does not allow the resolution of this three-taxon problem, and new kinds of data, such as nuclear DNA sequences, need to be collected.

The Emergence of Pottery: Technology and Innovation in Ancient Societies ed. by William K. Barnett and John W. Hoopes

TECHNOLOGY AND CULTURE Book Reviews 315 Valley, killing four hundred people. In response, California tight­ ened controls over all dam building by private companies. East­ wood’s structures were all intact, but after he died of a heart attack in 1924, no powerful voice remained to defend his legacy. Jackson surveys the others who carried on, but arch dams faded away by the end of the 1930s, not least because big-budget New Deal builders favored the monumental aesthetics of gravity dams. There was more than one possible “second nature.” In the decade that Jackson devoted to this work he appears to have examined every relevant archive and all of Eastwood’s dams. This solid, instructive, innovative, and well-constructed book de­ serves a wide readership. David E. Nye Dr. Nye, professor of American history at Odense University, received the 1993 Dexter Prize for Electrifying America. His most recent books are Consuming Power: A Social History ofAmerican Energies (Cambridge, Mass.: MIT Press, 1997) and Narratives and Spaces: Technology and the Construction ofAmerican Culture (New York: Columbia University Press, 1997). The Emergence ofPottery: Technology and Innovation in Ancient Societies. Edited by William K. Barnett and John W. Hoopes. Washington, D.C.: Smithsonian Institution Press, 1996. Pp. xviii+285; illustra­ tions, maps, figures, tables, notes, index. $55.00 (cloth); $29.95 (paper). After decades of neglect, material culture and technology have risen recently to the forefront of sociocultural inquiry and interpre­ tation theory. Scholars have begun to explore in greater depth and in a wider interdisciplinary context the interdependence between material culture and society, matter and mind, and between technol­ ogy and human evolutionary processes. This volume of essays on the earliest appearance and development of pottery throughout the world provides a thought-provoking addition to the growing litera­ ture on the relationships between society and technology in varied historical and sociocultural contexts. Archaeologists today can reconstruct much more of the past than they could just a few years ago. Sophisticated new techniques of chemical, physical, and biological analysis in combination with re­ cent developments in archaeological methods and sociocultural in­ terpretation theory make available new kinds of data and new in­ sights into the nature of prehistoric societies. Pottery today is analyzed not only with reference to vessel shape and size or surface decoration to establish chronologies, typologies, and uncontextual­ ized sériations grounded primarily in visual analysis. With the aid of such methods as thermoluminescence dating and neutron-activa­ 316 Book Reviews TECHNOLOGY AND CULTURE tion analysis for trace-element analyses of clays, archaeologists may locate the vessels’ geographical sources and map their distribution to determine trade links and other forms of exchange and social interaction. Residues adhering to vessels or shards, too, are now ana­ lyzed along with shape and decoration to recover information on not only subsistence and quality of nutrition in early populations but also vessel function—i.e., whether it was used for storage, cook­ ing, ritual, or social display. Given the availability of these new data, the authors of these essays can ask and answer new questions about ceramic technology and the relationship of pottery to society and to sociocultural change over time. Seeking to address the “social factors” behind earliest pottery production and use, the editors state that their primary aim is “to deconstruct commonly held assumptions about prehistoric ce­ ramics” (p. 1). Collectively, the essays in this volume make a power­ ful statement on the importance of the individual case in historic time and space and the likely futility of seeking universal laws in human and social behavior. The book clearly drives home, for exam­ ple, the fact that the emergence of pottery can no longer be associ­ ated solely with the appearance of agriculture. Nor is it necessarily part ofa package that includes settled village life or social complexity or any other trait previously linked with the so-called Neolithic life­ style. Instead, pottery was developed and first used by seasonally mo­ bile populations of the late Upper Palaeolithic era, among hunters and gatherers of wild foods, and most likely among those reliant upon fish and shellfish food resources. The earliest pottery so far excavated in both Old and New World contexts...

IN-PACT: A Pragmatic Approach Leading to a Smooth Transition or a New Architecture for Distribution Control Centers

Abstract SIT-R is a project of EDF-GDF-Services for the renewal of their Distribution Centers. Two approaches: either EDF buys an off the shelf system from a major Vendor of Ems-Scada Systems or EDF remains technically in charge. At the moment the first option is in experimentation at Paris, Lyon and Versailles. For the second option, IN-PACT proposed in 1994 a step by step approach. This project has been divided into two phases. The first phase consists in preserving the actual EMS-Scada System (SIT3), by carrying over the SIT3 on a new hardware platform, through Object-Oriented Techniques. This phase has consisted in elaborating an object designed configurator, and by transcoding the Real Time system in C++ language. The second phase is to provide an architecture based on new interoperability features provided by a software bus like Corba. Through this new architecture, IN-PACT will connect new functionalities provided inside EDF or furnished by Vendors. The architecture and the concepts defined will guarantee reduction in the cost of specification, maintenance, and ameliorate the perennity of the overall system. In order to experiment the IN-PACT solution, a real site has been provided at the Distribution Center Gard-Cevennes located in the city of Nimes, in the south of France. The results: At the end of 1996, the new configurator is validated and operational at Nimes, the Real Time System will be fully operational in February 1997. In parallel, the architecture vision and concepts have been validated and defined. They have led to a specification of the future Human Machine Interface (HMI) and an International bid was made in December 1996. In 1997, the architectural concepts will be fully integrated by connecting the new HMI. The connection of internal functions will also begin. The configurator will be upgraded in order to be able to manage different kinds of network image representation, and last but not least, new kinds of data will be processed in order to increase the responsiveness of EDF to the internal and external market, opportunities and constraints.

Algorithms for computing and integrating physical maps using unique probes.

Current physical mapping projects based on STS-probes involve additional clues such as the fact that some probes are anchored to a known map and that others come from the ends of clones. Because of the disparate combinatorial contributions of these varied data items, it is difficult to design a "tailored" algorithm that incorporates them all. Moreover, it is inevitable that new experiments will provide new kinds of data, making obsolete any such algorithm. We show how to convert the physical mapping problem into a 0/1 linear programming (LP) problem. We further show how one can incorporate additional clues as additional constraints in the LP formulation. We give a simple relaxation of the 0/1 LP problem, which solves problems of the same scale as previously reported tailored algorithms, to equal or greater optimization levels. We also present a theorem proving that when the data is 100% accurate, then the relaxed and integer solutions coincide. The LP algorithm suffices to solve problems on the order of 80-100 probes--the typical size of the 2- or 3-connected contigs of Arratia et al. (1991). We give a heuristic algorithm which attempts to order and link the set of LP-solved contigs. Unlike previous work, this algorithm only links and orders contigs when the join is 90% or more likely to be correct. It is our view that there is no value in computing an optimal solution with respect to some criteria over very noisy data as this optimal solution rarely corresponds to the true solution. The paper involves extensive empirical trials over real and simulated data.

Analysis of the total 12C( alpha, gamma )16O cross section based on available angular distributions and other primary data.

Because a knowledge of the 12C/16O ratio is crucial to the understanding of the later evolution of massive stars, new R- and K-matrix fits have been completed using the available angular distribution data from radiative α capture and elastic α scattering on 12C. Estimates of the total 12C(α,γ)16O rate at stellar energies are reported. In contrast with previous work, the analyses generally involve R- and K-matrix fits directly to the primary data, i.e., the energy- and angle-dependent differential yields, with all relevant partial waves fitted simultaneously (referred to here as surface fits). It is shown that, while the E1 part of the reaction is well constrained by a recent experiment on the β-delayed α-particle decay of 16N, only upper limits can be placed on the E2 ground state cross section factor which we take conservatively as SE2(300)<140 keV b. Simulations were then carried out to explore what kind of new data could lead to better restrictions on SE2(300). We find that improved elastic scattering data may be the best short-term candidate for such restrictions while significantly improving S(300) with new radiative capture data may require a longer-term effort. Theoretical models and estimates from α-transfer reactions for the E2 part of 12C(α,γ)16O are then discussed for comparison with the R- and K-matrix fits of the present work.

Using Patient Focus Groups for New Patient Services

This article is intended to illustrate the usefulness of patient input in the strategic planning process and to demonstrate in particular the use of focus groups in concept development, concept testing, and program evaluation. Three areas of patient services were designed partly on the basis of patient input. "Service Teams with Appropriate Resources" (STARs) were conceived as basic organizational units to deliver interdisciplinary care to meet the needs of specific groups of patients. A patient services "menu" was envisioned to allow the patient or caregiver to decide which service would most appropriately and efficiently meet patient needs. The "Service Expectation Program" was formulated to ease entry into the hospital by providing information on what patients should expect from the hospital experience. Focus groups were used again to test and refine the concepts developed during the interactive planning stage. General themes included the need for improved communication, the desire to be treated with respect and dignity (personhood), the need for coordination across the continuum of care, and the desire for more personal choice and control. Sources of patient feedback used in the ongoing evaluation process included a patient satisfaction survey and a telephone survey. Additional focus groups and telephone surveys are planned. The focus group discussions with patients introduced useful data into the quality improvement and interactive planning process. Findings were disseminated to all levels of hospital management and program staff through newsletters, reports, and in-service training sessions. Data were useful in interactive planning, program concept testing, and the development and implementation of new services.

A Postencounter View of Comets

Ground-based and space observations of Comet Halley during its 1986 perihelion passage are reviewed, with an emphasis on their implications for theoretical models. Consideration is given to the shape, surface morphology, and composition of the comet nucleus; the shape, dynamics, and composition of the dust tail; neutral and ionic gas species in the head and plasma tail; and the comet/solar-wind interaction. Extensive diagrams, graphs, and sample images are provided, and the potential value of the new kinds of data to be obtained with the NASA Comet-Rendezvous/Asteroid-Flyby spacecraft is discussed.

The Use of Biological Markers in Risk Assessment

The use of biologic markers (such as DNA adducts) as more proximate measures of effective dose has many potential advantages for risk assessment. We can hope for: Better modeling of dose-response relationships, by avoiding the attribution of high dose pharmacokinetic nonlinearities to the fundamental multiple mutation process of carcinogenesis. Better interspecies projection of doses and risks. Improved evaluation of past doses in epidemiologic studies. Insights into the magnitude and significance of human interindividual variability. Possibly some identification of previously unrecognized genetic hazards. In the very long run, the quantification of rates of post-initiation stages in tumor development by comparative measurements of the prevalence of adducts, premalignant foci/clones and tumors as a function of age in different tissues. Realizing these advantages will require statistically oriented professionals in risk assessment to gain familiarity with more complex, simulation-type modeling approaches with multiple points of comparison between theory and experiment--rather than the straightforward curve-fitting that has built the field to this point. It will also require some precautions to avoid mistakes and misuse of these new kinds of data and related theory.

A program for semi-automatic sequential resonance assignments in protein 1H nuclear magnetic resonance spectra

A new approach to the sequential resonance assignment of protein 1H NMR spectra based on a computer program is presented. Two main underlying concepts were used in the design of this program. First, it considers at any time all possible assignments that are consistent with the currently available data. If new information is added then assignments that have become inconsistent are eliminated. Second, the process of the assignment is split into formal steps that follow strictly from the available data and steps that involve the interpretation of ambiguous NMR data. The first kind of step is safe in the sense that it never leads to false assignments provided that the input does not contain any error; these steps are executed automatically by the program when the input files are read and whenever new data have been entered interactively. The second kind of step is left to the user: An interactive dialog provides detailed information on the current situation of the assignment and indicates what kind of new data would be most promising for further assignment. The user then provides new data to the program and restarts the automatic part which will attempt to draw logical conclusions from the joint use of the new data and the earlier available information and will eliminate assignments that have become inconsistent. Results of test problems using simulated NMR data for proteins consisting of up to 99 residues as well as the application of the program to obtain the complete assignment of α-bungarotoxin, a 74-residue snake neurotoxin, are reported.