bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ontologies of engineering knowledge: general structure and the case of Software Engineering
Authors: Sicilia Miguel-Angel , García-Barriocanal Elena , Sánchez-Alonso Salvador , Rodríguez-García Daniel 
Published: September 2009

AbstractEngineering knowledge is a specific kind of knowledge that is oriented to the production of particular classes of artifacts, is typically related to disciplined design methods, and takes place in tool-intensive contexts. As a consequence, representing engineering knowledge requires the elaboration of complex models that combine functional and structural representations of the resulting artifacts with process and methodological knowledge. The different categories used in the engineering domain vary in their status and in the way they should be manipulated when building applications that support engineering processes. These categories include artifacts, activities, methods and models. This paper surveys existing models of engineering knowledge and discusses an upper ontology that abstracts the categories that crosscut different engineering domains. Such an upper model can be reused for particular engineering disciplines. The process of creating such elaborations is reported on the particular case study of Software Engineering as a concrete application example.
No evidence of transmission of H5N1 highly pathogenic avian influenza to humans after unprotected contact with infected wild swans
Authors: WALLENSTEN A. , SALTER M. , BENNETT S. , BROWN I. , HOSCHLER K. , OLIVER I. 
Published: September 2009

SUMMARYHighly pathogenic avian influenza (HPAI) subtype H5N1 remains a public health threat as long as it circulates in wild and domestic birds. Information on the transmissibility of H5N1 HPAI from wild birds is needed for evidence-based public health advice. We investigated if transmission of H5N1 HPAI had taken place in people that had unprotected contact with infected wild mute swans during an incident at the Abbotsbury Swannery in Dorset, England. Thirteen people who had been exposed to infected swans were contacted and actively followed up for symptoms. Serology was taken after 30 days. We did not find evidence of transmission of H5N1 HPAI to humans during the incident. The incident provided a rare opportunity to study the transmissibility of the virus from wild birds to humans.
A new multiplex PCR for differential identification ofShigella flexneriandShigella sonneiand detection ofShigellavirulence determinants
Authors: FARFÁN M. J. , GARAY T. A. , PRADO C. A. , FILLIOL I. , ULLOA M. T. , TORO C. S. 
Published: September 2009

SUMMARYMost of the multiplex PCR (mPCR) used to identifyShigellado not discriminate betweenShigellaspecies or serotypes. We designed a mPCR to differentiate betweenS. flexneriandS. sonneistrains based on the detection of markers associated with theshepathogenicity island described inShigella. In addition, specific primers were included to detect theShigellavirulence determinants ShET-1 and ShET-2 enterotoxin genes. The analysis of 304Shigellastrains from Chile and 79Shigellastrains from other geographic locations indicated that the mPCR described here detected allShigellaspecies and specifically differentiatedS. flexneriandS. sonnei. The technique was sensitive, reproducible, specific and simple to perform, providing a new tool with the potential to be employed for epidemiological and diagnostic purposes.
NifHgene diversity and expression in a microbial mat community on the McMurdo Ice Shelf, Antarctica
Authors: Jungblut Anne D. , Neilan Brett A. 
Published: September 2009

AbstractN2-fixation is an important mechanism in microbial mats of the McMurdo Ice Shelf as nitrogen sources are limited. Here we applied molecular analyses of the N2-fixing diversity in cyanobacterial dominated microbial mats in a meltwater pond, known as Orange Pond, on the McMurdo Ice Shelf. Phylogenetic analyses ofnifHgenes andnifHgene transcripts were performed in association with acetylene reduction assay measurements. Eighteen phylotypes with the highest similarities to cyanobacteria, firmicutes, beta-, gamma- and deltaproteobacteria, spirochaetes and verrumicrobia were identified. All cyanobacterialnifHphylotypes grouped solely in the genusNostocspp. Clone-library analysis ofnifHgene transcripts only identified sequences with a highest match toNostocspp. and acetylene reduction activity was identified in the presence of light and absence of 3-(3,4-dichlorophenyl)-1,1-dimethyl urea. These molecular results indicate that a variety of bacterial phyla possess the ability to fix nitrogen. However, under the tested conditions the only organisms actively transcribingnifHgenes wereNostocspp. This underlines the importance ofNostocfor the nitrogen budget on the McMurdo Ice Shelf.
A precise and rapid mapping protocol for correlative light and electron microscopy of small invertebrate organisms
Authors: Kolotuev Irina , Schwab Yannick , Labouesse Michel 
Published: September 2009

Background information. CLEM (correlative live cell and electron microscopy) seeks to bridge the data acquired with different imaging strategies, typically between light microscopy and electron microscopy. It has been successfully applied in cell cultures, although its use in multicellular systems is hampered by difficulties in locating the ROI (region of interest).Results. We developed a CLEM technique that enables easy processing of small model animals and is adequate both for morphology and immunoelectron‐microscopic specimen preparations. While this method has been initially developed for Caenorhabditis elegans samples, we found that it works equally well for Drosophila samples. It enables handling and observation of single animals of any complex genotype in real time, fixation by high‐pressure freezing and flat embedding. Our major improvement has been the development of a precise mapping system that considerably simplifies and speeds up the retrospective location of the ROI within 1 μm distance. This method can be successfully used when correlative microscopy is required, as well as to facilitate the treatment of non‐correlative TEM procedures. Our improvements open the possibility to treat statistically significant numbers of animals processed by electron microscopy and considerably simplifies electron‐microscopic protocols, making them more accessible to a wider range of researchers.Conclusions. We believe that this technique will contribute to correlative studies in multicellular models and will facilitate the time‐demanding procedure of specimen preparation for any kind of TEM.
PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins
Authors: Oliva Romina , Thornton Janet M. , Pellegrini-Calace Marialuisa 
Published: September 2009

Abstract
Summary: The increasing number of available atomic 3D structures of transmembrane channel proteins represents a valuable resource for better understanding their structure–function relationships and to eventually predict their selectivity. Herein, we present PoreLogo, an automatic tool for analysing, visualizing and comparing the amino acid composition of transmembrane channels and its conservation across the corresponding protein family.
Availability: PoreLogo is accessible as a public web server at http://www.ebi.ac.uk/thornton-srv/software/PoreLogo/.
Contacts: marial@ebi.ac.uk; romina.oliva@uniparthenope.it.
Introduction: The Study of Religion and Emotion
Authors: Corrigan John 
Published: September 2009

Abstract
This book is about religion and emotion. It explores the emotional component in religion within the framework of a certain tradition, focusing on emotion in new religious movements. There are essays on Judaism, Christianity, Hinduism, Japanese religions, Buddhism, and Islam. The book remarks on ways that emotion has been overlooked in the study of religious traditions, and how a focus on the emotional can lead to fresh understandings about how persons create, through religion, relationships with nature, deities, and each other. It also includes essays that address the emotion component in various areas of religious life, including ritual, gender, sexuality, music, and material culture. The book shows that emotional life is profoundly shaped by religion, and that religion, in turn, directs and reinforces the construction of emotional ideologies having to do with a wide array of behaviors. In addition, it addresses specific emotions such as ecstasy, love, terror, hate, melancholy, and hope.
Realism
Authors: Harrison Bernard 
Published: September 2009

Abstract
This article considers the relation between literature and philosophy during the period of realism. It explains that the notion of realism, in its development as a term of literary criticism, is in origin a genre concept and that discussions of realism in nineteenth- and twentieth-century literary criticism and polemic rapidly acquire a moral, political, and philosophical dimensions. It suggests that all questions of literary form and technique fall to the will of the writer to determine. However, the article states, it does not follow that literature is a free field for play in the sense of frivolity because the connection between literature and reality does not run by way of the truth or falsity of statements, but by way of deeper linkages, internal to language, between the meanings of words and the practices that constitute human worlds and form the outlook and personalities of their inhabitants.
The Epistemology and Metaphysics of Socrates
Authors: Matthews Gareth B. 
Published: September 2009

AbstractEpistemology and metaphysics as described by Socrates is the crux of this article. Socrates here is all set to assess the wisdom of the candidates. He goes about arguing as to who is wiser and the various aspects of wisdom. He also elaborates on wisdom as a virtue. The article further harps on the idea of what counts as knowledge and also highlights the differences between Socratic Ignorance and Complete Ignorance.
TheTimaeuson the Principles of Cosmology
Authors: Johansen Thomas K. 
Published: September 2009

AbstractUnderstanding of principles forms the basis of mastering Greek Philosophy. This article focuses on the idea of Principled Knowledge. Plato, too, seems to hold that grasping a body of knowledge requires a grasp of its principles. One example is the Republic where Socrates explains the image of the line. He has divided the line into two sections, the intelligible and the perceptible. The Timaeus, like the Republic, emphasizes the need for us to grasp the proper principle of our disciplines of study. The major principles enlisted in the Timaeus are as follows: Being is that which is graspable by intelligence with an account (logos); becoming is that which is graspable by opinion (doxa) with unreasoning (alogos) perception. Everything that comes into being has a cause (aition). When a craftsman uses an eternal model, his product is necessarily fine (kalon); if he uses a generated one, the product is not fine. The article further elaborates upon the standards of the cosmological argument and the most proper principle of coming into being which Socrates argues is the prelude.
The Sciences and Epistemology
Authors: Goldman Alvin I. 
Published: September 2009

Abstract
This article finds that epistemology cannot be subsumed under or identified with a science. Epistemology and the sciences should remain distinct yet cooperative. This article presents several examples that illustrate the relevance of science to epistemology. For example, classical epistemology was heavily concerned with the sources of knowledge, where “sources” refers to the kinds of psychological faculties responsible for knowledge. Drawing from work in psychology, this article proposes that science can shed light on epistemic achievements by contributing to the understanding of the nature and extent of human cognitive endowments. It suggests, in addition, that psychology can also contribute to understanding of the sources of knowledge. Finally, it argues that some specific projects in epistemology can receive important contributions from psychology, economics, and sociology.
Theories of Justification
Authors: Fumerton Richard 
Published: September 2009

Abstract
The task of explaining and evaluating theories of justification is daunting. There are not only a host of different theories of justification, there are also radical differences among epistemologists concerning how they understand what it is to offer such a theory. This article offers an overview of several prominent positions on the nature of justification. It begins by isolating epistemic justification from nonepistemic justification. It also distinguishes between “having justification for a belief” and “having a justified belief,” arguing that the former is conceptually more fundamental. It then addresses the possibility that justification is a normative matter, suggesting that this possibility has little to offer a concept of epistemic justification. It also critically examines more specific attempts to capture the structure and content of epistemic justification. These include traditional foundationalism and variants thereof, externalist versions of foundationalism; contextualism; coherentism; and “mixed” theories which combine aspects of coherentism and foundationalism.
Mind and Knowledge
Authors: Heil John 
Published: September 2009

Abstract
This article notes that the knowledge of the world depends on the nature as knowers. Many people, philosophers included, assume realism about the world toward which one's beliefs are directed: that is, that the world is as it is independently of how one might take it to be. It is unclear how one could convincingly establish, in a noncircular manner, that the world is as one thinks it is. This suggests skepticism, and, according to this article, realism and skepticism go hand in hand. This article discusses the implications of such a view, particularly as they concern knowledge people seemingly have of their own states of mind. It considers the view that to calibrate oneself as knower one should proceed from resources “immediately available to the mind” to conclusions about the external world. It examines two other possibilities: an externalist view of mental content and an internalist approach to content.
Molecules, Systems, and Behavior: Another View of Memory Consolidation
Authors: Bechtel William 
Published: September 2009

Abstract
This article examines the behavioural aspects and the molecular and cellular processes in the brain associated with memory consolidation. It suggests that ruthless reduction and mechanistic reduction are both reductionist in that they recognize the importance of seeking knowledge of brain processes at different levels of organization to understand cognitive function. They are also united in standing opposed to the attempts to divorce psychology and cognitive science from being constrained by our rapidly growing knowledge of brain processes and they both agree that information about molecular and cellular processes is also of potentially great relevance to understanding memory consolidation.
Enactivism's Vision: Neurocognitive Basis or Neurocognitively Baseless?
Authors: Wallis Charles , Wright Wayne 
Published: September 2009

Abstract
This article aims to clarify the central commitment and the claimed advantages of enactivism, a theoretical approach for understanding the mind. The analysis reveals that there is no compelling reason to embrace either the enactivists' aim of completely revolutionizing vision science or their understanding of the character of that new vision science. There are also numerous serious empirical and conceptual problems for even the more modest enactivism. This article discusses enactivist responses to empirical evidence cited as posing difficulties for enactivism and considers areas of neuroscience deemed highly relevant but that remain unconsidered by enactivism.
The Emerging Theory of Motivation
Authors: Landreth Anthony 
Published: September 2009

Abstract
This article attempts to elate aspects of our commonsense understanding of motivation to an emerging, mechanistic account of motivation in neuroscience. It identifies various points in the neural process where motivational control will have an opportunity to play a role. It suggests that these points of influence occur in the early stages of planning a course of action by sequencing a set of subgoals, at the stage of action selection when the type of instrumental action to be performed is chosen and at the stage of online action correction when adjustments are made in the midst of performance. The article argues that it is possible to advance the understanding of motivational states by modeling them on reinforcement learning principles.
The Case for Animal Emotions: Modeling Neuropsychiatric Disorders
Authors: Sufka Kenneth , Weldon Morgan , Allen Colin 
Published: September 2009

Abstract
This article focuses on the modeling of neuropsychiatric disorders in the case of animal emotions. It examines critically the evidence that philosophers have used to justify the claim that some nonhuman animals experience emotions similar to those of humans, such as pain and suffering. It provides an alternative strategy to making similar claims in a manner that avoids the possible confusion present in the existing pain literature. It also discusses evidence of animal emotions from human pain and suffering and describes the chick anxiety-depression continuum model.
Neuro‐Eudaimonics or Buddhists Lead Neuroscientists to the Seat of Happiness
Authors: Flanagan Owen 
Published: September 2009

Abstract
This article examines the neurobiological aspects of eudaimonics, the naturalistic inquiry into the constituents, and the causes of happiness. It comments on the evidence for the claim that there is a connection between Buddhism and happiness. It suggests that a promising program of eudaimonics would require an accurate description of the multiplicity of theory and tradition-specific conceptions that offer true happiness.
Logicism Reconsidered
Authors: Rayo Agustín 
Published: September 2009

AbstractThis article is divided into four sections. The first two identify different logicist theses, and show that their truth-values can be established given minimal assumptions. The third section sets forth a notion of “content-recarving” as a possible constraint on logicist theses. The fourth section—which is largely independent from the rest of the article—is a discussion of “neologicism.”
Mathematics—Application and Applicability
Authors: Steiner Mark 
Published: September 2009

Abstract
To an unappreciated degree, the history of Western philosophy is the history of attempts to understand why mathematics is applicable to Nature, despite apparently good reasons to believe that it should not be. A cursory look at the great books of philosophy bears this out. Plato's Republic invokes the theory of “participation” to explain why, for instance, geometry is applicable to ballistics and the practice of war, despite the Theory of Forms, which places mathematical entities in a different (higher) realm of being than that of empirical Nature. This argument is part of Plato's general claim that theoretical learning, in the end, is more useful than “practical” pursuits. John Stuart Mill's account of the applicability of mathematics to nature is unique: it is the only one of the major Western philosophies which denies the major premise upon which all other accounts are based. Mill simply asserts that mathematics itself is empirical, so there is no problem to begin with.
Higher‐order Logic
Authors: Shapiro Stewart 
Published: September 2009

AbstractThe philosophical literature contains numerous claims on behalf of and numerous claims against higher-order logic. Virtually all of the issues apply to second-order logic (vis-à-vis first-order logic), so this article focuses on that. It develops the syntax of second-order languages and present typical deductive systems and model-theoretic semantics for them. This will help to explain the role of higher-order logic in the philosophy of mathematics. It is assumed that the reader has at least a passing familiarity with the theory and metatheory of first-order logic.
Religious Language
Authors: Alston William P. 
Published: September 2009

Abstract
Many philosophers and theologians have protested against the concentration of philosophers on religious statements to the neglect of other religious uses of language. Their complaint can be briefly summed up as follows. The heart of religion is found in talk to God in prayer, worship, and liturgy. Talk about God is a secondary phenomenon that gets its religious significance by its dependence on the former. The valid concerns of philosophers with statements about God can be pursued while recognizing their connections with the rest of religion. Instead of speaking of predicates of religious statements, one could speak of religious concepts. Because predicates express concepts, problems about the meaning of the former are translatable into problems about the content of the latter.
Science and Religion in the New Religions
Authors: Rothstein Mikael 
Published: September 2009

Abstract
This article demonstrates how religion is propagated through a scientistic strategy or discourse, and how religion, not science, is in control. Scientistic religious groups, however, are not “paradoxical”—what they have accomplished is simply an expanded usage of a traditional religious strategy. Traditional religions are able to interpret any event, place, individual, object, or subject according to religious standards. Within the fabric of any given religion, everything in the world can be understood and measured along specific mythological or ritual paths. Scientistic religions have simply added the phenomenon of science to this capacity. By embracing science, which is basically a secular discourse, a number of new religions have overcome one of the paradoxes of the modern world, that is, the parallel existence of two mutually incongruous epistemological systems—science and religion.
Millennialism
Authors: Landes Richard 
Published: September 2009

AbstractLiterally, millennialism refers to the belief, expressed in the book of Revelation, that Christ will establish a one-thousand-year reign of the saints on earth before the Last Judgment. More broadly defined, millennialists expect a time of super-natural peace and abundance here on earth. This article surveys millenarian movements and outlines a typology for classifying such groups. The author sets his analysis of contemporary movements in the context of a broader analysis of historically prior movements and movements that have arisen in the so-called third world in response to the intrusion of colonial powers. The article concludes with a suggested agenda for future research.
The Mythic Dimensions of New Religious Movements
Authors: Tumminia Diana G. , Kirkpatrick R. George 
Published: September 2009

Abstract
This article argues that, despite the significant body of theoretical work that has been carried out by anthropologists and others, the mythological dimension of new religions has been largely ignored. Using Unarius Society, feminist witchcraft, and the Movement of Spiritual Inner Awareness as examples, it suggests that new religious movement myths are not fixed, but, rather, change in response to the ongoing process of reality construction taking place within such movements.
Women in New Religious Movements
Authors: Palmer Susan J. 
Published: September 2009

Abstract
Observers have often noted that new religious movements (NRMs) sometimes experiment with gender roles. The position of women in certain new religions has also been a focus of concern for critics. This article develops a typology of NRM sexual identity and points out that the actual arrangements within different new religions are often quite complex. To illustrate this complexity, it examines women's roles in the Osho Rajneesh group and in the Raelian movement.