bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon isotope exchange during polymetamorphism in the Panamint Mountains, California, USA
Authors: BERGFELD D. , NABELEK P. I. , LABOTKA T. C. 
Published: November 2003

Carbon isotope fractionations between calcite and graphite in the Panamint Mountains, California, USA, demonstrate the importance of mass balance on carbon isotope values in metamorphosed carbon‐bearing minerals while recording the thermal conditions during peak regional metamorphism. Interbedded graphitic marbles and graphitic calcareous schists in the Kingston Peak Formation define distinct populations on a δ13C(gr)–δ13C(cc) diagram. The δ13C values of both graphite and calcite in the marbles are higher than the values of the respective minerals in the schists. δ13C values in both rock types were controlled by the relative proportions of the carbon‐bearing minerals: calcite, the dominant carbon reservoir in the marble, largely controlled the δ13C values in this lithology, whereas the δ13C values in the schists were largely controlled by the dominant graphite. This is in contrast to graphite‐poor calcsilicate systems where carbon isotope shifts in carbonate minerals are controlled by decarbonation reactions.The marbles record a peak temperature of 531±30 °C of a Jurassic low‐pressure regional metamorphic event above the tremolite isograd. In the schists there is a much wider range of recorded temperatures. However, there is a mode of temperatures at c. 435 °C, which approximately corresponds to the temperatures of the principal decarbonation metamorphic reactions in the schists, suggesting that the carbon exchange was set by loss of calcite and armouring of graphite by newly formed silicate minerals. The armouring may explain the relatively large spread of apparent temperatures. Although the modal temperature also corresponds to the approximate temperature of the Cretaceous retrograde event, retrograde exchange is thought less likely due to very slow exchange rates involving well‐crystallized graphite, armouring of graphite by silicates during the earlier event, and because of other barriers to retrograde carbon exchange. Thus, only the calcite–graphite carbon isotope fractionations recorded by the marbles demonstrate the high‐temperature conditions of the low‐pressure Jurassic metamorphic event that was associated with the emplacement of granitic plutons to the west of the Panamint Mountains.
Codon adaptation index as a measure of dominating codon bias
Authors: Carbone A. , Zinovyev A. , Képès F. 
Published: November 2003

Abstract
We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a ‘universal’ measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading–lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster.
Availability: http://www.ihes.fr/~materials.
Applying signal theory to the analysis of biomolecules
Authors: Kauer Gerhard , Blöcker Helmut 
Published: November 2003

Abstract
Motivation: The accumulation of sequence-related and other biological data for basic research and application purposes invites disaster. It appears very likely that neither traditional thinking nor current technologies (including their foreseeable evolutionary developments) will be able to cope with this ever intensifying situation.
Results: We present the detailed theoretical background for applying signal theory, as known from speech recognition and image analysis, to the analysis of biomolecules. The general scheme is as follows: biochemical and biophysical properties of biomolecules are used to model an n-dimensional signal which represents the entire information-bearing biomolecule. Such signals are used to search for biological principles, analogies or similarities between biomolecules. In a series of simple experiments (bacterial DNA, generation of real signals using melting enthalpies, detection filtering by convolution of signals) we have shown that the novel system for comparative analysis of the properties of information-bearing biomolecules works as in theory.
Supplementary information: http://genome.gbf.de/wavepaper
Development of an integrated laboratory information management system for the maize mapping project
Authors: Sanchez-Villeda H. , Schroeder S. , Polacco M. , McMullen M. , Havermann S. , Davis G. , Vroh-Bi I. , Cone K. , Sharopova N. , Yim Y. , Schultz L. , Duru N. , Musket T. , Houchins K. , Fang Z. , Gardiner J. , Coe E. 
Published: November 2003

Abstract
Motivation: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons.
Results: The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available.
Availability: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.
A novel strategy for microarray quality control using Bayesian networks
Authors: Hautaniemi Sampsa , Edgren Henrik , Vesanen Petri , Wolf Maija , Järvinen Anna-Kaarina , Yli-Harja Olli , Astola Jaakko , Kallioniemi Olli , Monni Outi 
Published: November 2003

Abstract
Motivation: High-throughput microarray technologies enable measurements of the expression levels of thousands of genes in parallel. However, microarray printing, hybridization and washing may create substantial variability in the quality of the data. As erroneous measurements may have a drastic impact on the results by disturbing the normalization schemes and by introducing expression patterns that lead to incorrect conclusions, it is crucial to discard low quality observations in the early phases of a microarray experiment. A typical microarray experiment consists of tens of thousands of spots on a microarray, making manual extraction of poor quality spots impossible. Thus, there is a need for a reliable and general microarray spot quality control strategy.
Results: We suggest a novel strategy for spot quality control by using Bayesian networks, which contain many appealing properties in the spot quality control context. We illustrate how a non-linear least squares based Gaussian fitting procedure can be used in order to extract features for a spot on a microarray. The features we used in this study are: spot intensity, size of the spot, roundness of the spot, alignment error, background intensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment.
Supplementary information: http://sigwww.cs.tut.fi/TICSP/SpotQuality/
Extraction of protein interaction information from unstructured text using a context-free grammar
Authors: Temkin Joshua M. , Gilder Mark R. 
Published: November 2003

Abstract
Motivation: As research into disease pathology and cellular function continues to generate vast amounts of data pertaining to protein, gene and small molecule (PGSM) interactions, there exists a critical need to capture these results in structured formats allowing for computational analysis. Although many efforts have been made to create databases that store this information in computer readable form, populating these sources largely requires a manual process of interpreting and extracting interaction relationships from the biological research literature. Being able to efficiently and accurately automate the extraction of interactions from unstructured text, would greatly improve the content of these databases and provide a method for managing the continued growth of new literature being published.
Results: In this paper, we describe a system for extracting PGSM interactions from unstructured text. By utilizing a lexical analyzer and context free grammar (CFG), we demonstrate that efficient parsers can be constructed for extracting these relationships from natural language with high rates of recall and precision. Our results show that this technique achieved a recall rate of 83.5% and a precision rate of 93.1% for recognizing PGSM names and a recall rate of 63.9% and a precision rate of 70.2% for extracting interactions between these entities. In contrast to other published techniques, the use of a CFG significantly reduces the complexities of natural language processing by focusing on domain specific structure as opposed to analyzing the semantics of a given language. Additionally, our approach provides a level of abstraction for adding new rules for extracting other types of biological relationships beyond PGSM relationships.
Availability: The program and corpus are available by request from the authors.
Protein structural class identification directly from NMR spectra using averaged chemical shifts
Authors: Mielke S.P. , Krishnan V.V. 
Published: November 2003

Abstract
Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of proteins. Comprehensive experimental methods, on the other hand, are limited to nuclear magnetic resonance (NMR) and X-ray crystallography. The full characterization of individual structures, using either of these techniques, is extremely time intensive. The demands of high throughput proteomics necessitate the development of new, faster experimental methods for providing structural information. As a first step toward such a method, we explore the possibility of determining the structural classes of proteins directly from their NMR spectra, prior to resonance assignment, using averaged chemical shifts. This is achieved by correlating NMR-based information with empirical structure-based information available in widely used electronic databases. The results are analyzed statistically for their significance. The robustness of the method as a structure predictor is probed by applying it to a set of proteins of unknown structure. Our results show that this NMR-based method can be used as a low-resolution tool for protein structural class identification.
RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events
Authors: Farahi Kamyar , Whitman William B. , Kraemer Eileen T. 
Published: November 2003

Abstract
Summary: RED-T is a Java application for phylogenetic analysis based on a unique method, RED, that utilizes the ratios of evolutionary distances Ed to distinguish between alternative evolutionary histories. RED-T allows the user to examine if any given experimental gene shares the same evolutionary history as the designated control gene(s). Moreover, the tool detects any differences in evolutionary history and allows the user to examine comparisons of Ed for a likely explanation. Lateral gene transfer, which may have a significant influence in organismal evolution is one mechanism that could explain the findings of these RED-T analyses.
Availability: The application is available online at http://www.arches.uga.edu/~whitman/RED.
iMap: a database-driven utility to integrate and access the genetic and physical maps of maize
Authors: Fang Z. , Cone K. , Sanchez-Villeda H. , Polacco M. , McMullen M. , Schroeder S. , Gardiner J. , Davis G. , Havermann S. , Yim Y. , Bi I. Vroh , Coe E. 
Published: November 2003

Abstract
Motivation: Because of the unique biological features, a bioinformatic platform for the integrated genetic and physical map of maize is required for storing, integrating, accessing and visualizing the underlying data.
Results: The goal of the Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs. The database also contains integrated information produced by applying a set of anchoring rules to assign BAC contigs to specific locations on the genetic map. The iMap Viewer and iMap Search functions are combined in the user interface to allow viewing and retrieving many types of genetic and physical map data. The iMap Viewer features side-by-side chromosome-based displays of the genetic map and associated BAC contigs. For each genetic locus, information about marker type or contig can be viewed via pop-up windows that feature links to external data resources. Searches can be conducted for genetic locus, probe or sequence accession number; search results include relevant map positions, anchored BAC contigs and links to the graphical display of relevant chromosomes. iMap can be accessed at http://www.maizemap.org
Availability: The iMap utility package is available for non-commercial use upon request from the authors.
Personality Development: An Introduction Toward Process Approaches to Long‐Term Stability and Change in Persons
Authors: Graziano William G. 
Published: November 2003

AbstractThis special issue is concerned with the systematic transformation of persons and personalities as they move through their lives. The focus is on developmental processes early in the life course that influence both long‐term stability and change. Contributors represent diverse topics and viewpoints, but offer new data on classical issues of personality, including trait structure, self‐regulation and internalization, self‐evaluation, and self‐efficacy. In addition, the issue includes empirical contributions on newer approaches to bullying, developmental processes in psychopathology, the influence of racial and ethnic discrimination on subsequent adjustment, and cultural influences on personality development. The issue also includes a special contribution addressing methodological and statistical advances in dealing with prospective longitudinal data assessing personality over time.
Personality Structure as Derived From Parental Ratings of Free Descriptions of Children: The Inventory of Child Individual Differences
Authors: Halverson Charles F. , Havill Valerie L. , Deal James , Baker Spencer R. , Victor James B. , Pavlopoulos Vassilis , Besevegis Elias , Wen Liu 
Published: November 2003

AbstractBased on over 50,000 parental descriptors of children gathered in eight different countries, we used a combination of focus group sorting of descriptors in each country and factor analyses of instruments developed in four of the countries (United States, China, Greece, and the Netherlands) to describe children ages 3 to 12 years to select items for an instrument that would work well across countries to access personality. Through many factor analyses of indigenous items in each country, a core set of 141 items was used in three of the countries, with over 3000 parents responding to our instruments in China, Greece, and the United States. Much cross‐comparative research analysis has resulted in 15 robust midlevel scales that describe the structures of parental descriptors that are common to the three countries. The data on the English (U.S.) sample are presented in detail. Links to temperament and behavior problems are presented and discussed.
Aesthetics and the Problem of Evil
Authors: Nussbaum Charles 
Published: November 2003

Abstract:Much of Western speculative metaphysics has subscribed to what has been called “explanatory rationalism,” which holds that there is a reason for everything that is and for the way everything is. Theodicies, or metaphysical attempts to solve the problem of evil, have relied on a special application of this principle of explanatory rationalism, namely, the principle of plenitude, which holds that the evil in the world is a necessary ingredient in the world's overall perfection or degree of reality. This essay argues that the principle of plenitude is aesthetically motivated, and that only in art and perhaps in revealed religion can the demands of explanatory rationalism be satisfied.
What do we Want from a Theory of Happiness?
Authors: Haybron Daniel M. 
Published: November 2003

Abstract:I defend a methodology for theorizing about happiness. I reject three methods: conceptual analysis; scientific naturalism; and the “pure normative adequacy” approach, where the best conception of happiness is the one that best fills a role in moral theory. The concept of happiness is a folk notion employed by laypersons who have various practical interests in the matter, and theories of happiness should respect this fact. I identify four such interests in broad terms and then argue for a set of desiderata that theories of happiness ought to satisfy. The theory of happiness falls within the province of ethics. It should, however, be viewed as autonomous and not merely secondary to moral theory.
Anecdote And History
Authors: Gossman Lionel 
Published: November 2003

AbstractAlthough the term “anecdote” entered the modern European languages fairly recently and remains to this day ill‐defined, the short, freestanding accounts of particular events, true or invented, that are usually referred to as anecdotes have been around from time immemorial. They have also always stood in a close relation to the longer, more elaborate narratives of history, sometimes in a supportive role, as examples and illustrations, sometimes in a challenging role, as the repressed of history —“la petite histoire.” Historians' relation to them, in turn, varied from appreciative to dismissive in accordance with their own objectives in writing history. It appears that highly structured anecdotes of the kind that are remembered and find their way into anecdote collections depend on and tend to confirm established views of history, the world, and human nature. In contrast, loosely structured anecdotes akin to the modern fait divers have usually worked to undermine established views and stimulate new ones, either by presenting material known to few and excluded from officially authorized histories, or by reporting “odd” occurrences for which the established views of history, the world, and human nature do not easily account.
Actualism and the Fascist Historic Imaginary
Authors: Fogu Claudio 
Published: November 2003

AbstractThis essay argues that, just like liberalism and communism, fascist ideology was based on a specific philosophy of history articulated by Giovanni Gentile in the aftermath of World War I. Gentile's actualist notion that history “belongs to the present” articulated an immanent vision of the relationship between historical agency, representation, and consciousness against all transcendental conceptions of history. I define this vision as historic (as opposed to “historical”) because it translated the popular notion of historic eventfulness into the idea of the reciprocal immanence of the historical and the historiographical act. I further show that the actualist philosophy of history was historically resonant with the Italian experience of the Great War and was culturally modernist. I insist, however, that the actualist catastrophe of the histori(ographi)cal act was also genealogically connected to the Latin‐Catholic rhetorical signification of “presence” that had sustained the development of Italian visual culture for centuries. Accordingly, I argue that the fascist translation of actualism into a historic imaginary was at the root of Italian fascism's appeal to both masses and intellectuals. Fascism presented itself as a historic agent that not only “made history,” but also made it present to mass consciousness. In fact, I conclude by suggesting that the fascist success in institutionalizing a proper mode of historic representation in the 1920s, and a full‐blown historic culture in the 1930s, may have also constituted a fundamental laboratory for the formation of posthistoric(al) imaginaries.
The Netherlands National Model: a Review of Seven Years of Application
Authors: Gunn Hugh 
Published: November 2003

Disaggregate modelling is now firmly established as a powerful and practical alternative to the traditional four‐stage models originally developed in the sixties. The disaggregate methodology was originally pioneered in the United States, but much important development has taken place in Europe in the 1980s. The basis of the modelling and the scope of the models both broadened and developed. A substantial advance was made by establishing a link between the models and classical theories of micro‐economics, allowing the development of ‘behavioural’ models consistent with rational decision‐making. The competitive, or sometimes complementary, roles of other modes of travel have been recognised and brought into the modelling framework.In recent years, forecasts of travel demand have been generated in studies in a number of countries in Northern Europe. These studies have encountered a common problem, which is that the assumptions and capabilities of the standard methodology have not been appropriate to address the problems of planning facilities in the early twenty‐first century. Amongst the principal difficulties are:1. the population base is expected to change radically in terms of its age distribution — this the legacy of the Second World War, increased life expectancy and the aftermath of altered behaviour concerning family formation, linked to an increased participation of women in the work force;2. the work force itself is expected to be radically different, also due to increased female participation;3. there is an increasing pressure to suppress travel by private car, by any means politically feasible, in the anticipation of growing damage to the environment;4. in consequence to the previous remark, there is the emergence of new types of travel (in particular, organised car‐pooling) and new types of regulation of movement (‘demand management’ measures to control car commuters, and road‐pricing policies to reduce peak‐hour demand).Increasingly, the modellers are asked to look at very different futures to the present day, and the models themselves are required to perform a role very much more demanding than the mere extrapolation of present day trends.This paper reviews the performance of one particular disaggregate demand model system. the Netherlands National Model, used over a period of seven years to address the problem of producing forecasts appropriate to these new circumstances. The emphasis is on the results of the work, and the lessons that have been learned in the application of the system. Some discussion is given around the extension planned to the system in coming years.