bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond Digital Naturalism
Authors: Fontana Walter , Wagner Günter , Buss Leo W.
Published: April 2010

The success of Artificial Life (ALife) depends on whether it will help solve the conceptual problems of biology. Biology may be viewed as the science of the transformation of organizations. Yet biology lacks a theory of organization. We use this as an example of the challenge that ALife must meet.
Computer Viruses as Artificial Life
Authors: Spafford Eugene H.
Published: April 2010

There has been considerable interest in computer viruses since they first appeared in 1981, and especially in the past few years as they have reached epidemic numbers in many personal computer environments. Viruses have been written about as a security problem, as a social problem, and as a possible means of performing useful tasks in a distributed computing environment. However, only recently have some scientists begun to ask if computer viruses are not a form of artificial life—a self-replicating organism. Simply because computer viruses do not exist as organic molecules may not be sufficient reason to dismiss the classification of this form of “vandalware” as a form of life. This paper begins with a description of how computer viruses operate and their history, and of the various ways computer viruses are structured. It then examines how viruses meet properties associated with life as defined by some researchers in the area of artificial life and self-organizing systems. The paper concludes with some comments directed toward the definition of artificially “alive” systems and experimentation.
Why Do We Need Artificial Life?
Authors: Bonabeau Eric W. , Theraulaz G.
Published: April 2010

In this paper, we ask the question of whether we need artificial life (AL) at all. We find a lot of convincing arguments in favor of AL, but we also point out some dangers AL is exposed to. This careful epistemological review reveals the potential richness of AL without being either too reductionist or too holistic. We give some examples showing how this can be done in practice, and conclude that almost everybody needs AL.
On Modeling Life
Authors: Adami Chris
Published: April 2010

We present a theoretical as well as experimental investigation of a population of self-replicating segments of code subject to random mutation and survival of the fittest. Under the assumption that such a system constitutes a minimal system with characteristics of life, we obtain a number of statements on the evolution of complexity and the trade-off between entropy and information.
Selection for Wandering Behavior in a Small Robot
Authors: Miglino Orazio , Nafasi Kourosh , Taylor Charles E.
Published: April 2010

We have evolved artificial neural networks to control the wandering behavior of small robots. The task and environment were very simple—to touch as many squares in a grid as possible during a fixed period of time. A number of the simulated robots were embodied in a small Lego™ robot, controlled by a Motorola™ 6811 processor; and their performance was compared to the simulations. We observed that: (a) evolution was an effective means to program the robot's behavior; (b) progress was characterized by sharply stepped periods of improvement, separated by periods of stasis that corresponded to levels of behavioral/computational complexity; and (c) the simulated and realized robots behaved quite similarly, the realized robots in some cases outperforming the simulated ones. Introducing random noise to the simulations improved the fit somewhat (from r = 0.73 to 0.79). Hybrid simulated/embodied selection regimes for evolutionary robots are discussed.
Preadaptation in Populations of Neural Networks Evolving in a Changing Environment
Authors: Lund Henrik Hautop , Parisi Domenico
Published: April 2010

Populations of simple artificial organisms modeled as neural networks evolve a preference for one particular food type in an environment that contains more than one food type if the quantity of energy extracted from each food type is allowed to coevolve with the behavioral preference (evolvable fitness formula). If, after the emergence of the food preference, the preferred food gradually disappears from the environment at the evolutionary time scale, the evolved specialist strategy is maintained until the preferred food type has completely disappeared. Then a new specialist strategy suddenly emerges with a preference for another food type present in the environment. The appearance of the new strategy takes very few generations, in fact much fewer than in a population starting from zero (random initial population) in the same environment. This, together with the fact that the population with an evolutionary past is more efficient than the population starting from zero, suggests that the former population is preadapted to the changed environment. An analysis of the activation values of the hidden units indicates that the new food preference can be an “exaptation,” that is, a new adaptation based on a structure that has previously emerged for adaptively neutral reasons.
Coevolutionary Computation
Authors: Paredis Jan
Published: April 2010

This article proposes a general framework for the use of coevolution to boost the performance of genetic search. It combines coevolution with yet another biologically inspired technique, called lifetime fitness evaluation (LTFE).

Two unrelated problems—neural net learning and constraint satisfaction—are used to illustrate the approach. Both problems use predator-prey interactions to boost the search. In contrast with traditional “single population” genetic algorithms (GAs), two populations constantly interact and coevolve.

However, the same algorithm can also be used with different types of coevolutionary interactions. As an example, the symbiotic coevolution of solutions and genetic representations is shown to provide an elegant solution to the problem of finding a suitable genetic representation.

The approach presented here greatly profits from the partial and continuous nature of LTFE. Noise tolerance is one advantage. Even more important, LTFE is ideally suited to deal with coupled fitness landscapes typical for coevolution.
Artificial Evolution
Authors: Ennenga George R. vB.
Published: April 2010

Most of us know about specific biotechnologies but may be less aware of the underlying process. This essay analyzes that process and speculates on its meaning. It introduces the term artificial evolution, here defined as the controlled micromanipulation of genetic information from one generation to the next, where the first variational step is engineered and the second selection step is insured by humankind. This is qualitatively different from natural evolution. The characteristics of this artificial mode of evolution are immediacy, as opposed to Darwin's law of gradualism, transclass descent, unlike Darwin's common descent, identity, as opposed to variety, and an artificial rate of mutational change, as opposed to a natural one. It constitutes evolution out of evolution, and redoubles our ethical responsibility for the future.
Abstract Genetic Representation of Dynamical Neural Networks Using Kauffman Networks
Authors: East Ian Robert , Rowe Jon
Published: April 2010

Abstract (developmental) genetic representations are schemes where each genotype encodes a program for the construction of a phenotype. A new method for contriving abstract genetic representations is presented, based upon Kauffman's ideas regarding biological development [13-16]. Phenogenesis is controlled by genotype via cell replication and differentiation. Comparison is made with the earlier published methods of Gruau [9] and Kitano [18]. It is argued that greater expressive power is obtained using Kauffman networks. The new method was tested in the artificial evolution of morphology and finally successfully applied to the synthesis of structure in dynamical neural networks.
Evolutionary Stagnation Due to Pattern-Pattern Interactions in a Coevolutionary Predator-Prey Model
Authors: Savill Nicholas J. , Hogeweg Paulien
Published: April 2010

We consider a spatially stmctured model of a coevolutionary predator-prey system with interactions in a one-dimensional phenotype space. We show that in phenotype space predators and prey organize themselves into distinct clusters of phenotypes called quasi-species. The prey quasi-species also cluster in patches in real space. As the prey quasi-species evolve away from the predator quasi-species (in phenotype space) the prey patch size reduces and the single predator quasi-species is inhibited from evolving toward either of the two prey species. We show that it is the interaction between the phenotype space patterns (quasi-species) and the real space patterns (patches) that inhibit the predators from evolving.
The Ecology of Echo
Authors: Hraber Peter T. , Jones Terry , Forrest Stephanie
Published: April 2010

Echo is a generic ecosystem model in which evolving agents are situated in a resource-limited environment. The Echo model is described, and the behavior of Echo is evaluated on two well-studied measures of ecological diversity: relative species abundance and the species-area scaling relation. In simulation experiments, these measures are used to compare the behavior of Echo with that of a neutral model, in which selection on agent genotypes is random. These simulations show that the evolutionary component of Echo makes a significant contribution to its behavior and that Echo shows good qualitative agreement with naturally occurring species abundance distributions and species-area scaling relations.
An Ecology of Text: Using Text Retrieval to Study Alife on the Net
Authors: Best Michael L.
Published: April 2010

I introduce a new alife model, an ecology based on a corpus of text, and apply it to the analysis of posts to USENET News. In this corporal ecology posts are organisms, the newsgroups of NetNews define an environment, and human posters situated in their wider context make up a scarce resource. I apply latent semantic indexing (LSI), a text retrieval method based on principal component analysis, to distill from the corpus those replicating units of text. LSI arrives at suitable replicators because it discovers word co-occurrences that segregate and recombine with appreciable frequency. I argue that natural selection is necessarily in operation because sufficient conditions for its occurrence are met: replication, mutagenicity, and trait/fitness covariance. I describe a set of experiments performed on a static corpus of over 10,000 posts. In these experiments I study average population fitness, a fundamental element of population ecology. My study of fitness arrives at the tinhappy discovery that a flame-war, centered around an overly prolific poster, is the king of the jungle.
EUZONE: Simulating the Evolution of Aquatic Ecosystems
Authors: Downing Keith
Published: April 2010

In the spirit of contemporary artificial life research, EUZONE provides a virtual laboratory for the emergence of complex ecosystems from simple primitives. However, whereas most alife systems abstract away many real-world environmental constraints, EUZONE employs detailed physical and chemical models in combination with evolutionary algorithms to support the emergence of carbon-based aquatic ecosystems. With an emphasis on planktonlike organisms, this research focuses upon the self-organization and evolution of (a) lower levels of aquatic food webs, (b) Gaian interactions between primitive organisms and their physical environments, and (c) species interactions governed by varying life-history strategies.
Determinants of Multiple Semantic Priming: A Meta-analysis and Spike Frequency Adaptive Model of a Cortical Network
Authors: Lavigne Frédéric , Dumercy Laurent , Darmon Nelly
Published: April 2010

Recall and language comprehension while processing sequences of words involves multiple semantic priming between several related and/or unrelated words. Accounting for multiple and interacting priming effects in terms of underlying neuronal structure and dynamics is a challenge for current models of semantic priming. Further elaboration of current models requires a quantifiable and reliable account of the simplest case of multiple priming resulting from two primes on a target. The meta-analytic approach offers a better understanding of the experimental data from studies on multiple priming regarding the additivity pattern of priming. The meta-analysis points to the effects of prime–target stimuli onset asynchronies on the pattern of underadditivity, overadditivity, or strict additivity of converging activation from multiple primes. The modeling approach is then constrained by results of the meta-analysis. We propose a model of a cortical network embedding spike frequency adaptation, which allows frequency and time-dependent modulation of neural activity. Model results give a comprehensive understanding of the meta-analysis results in terms of dynamics of neuron populations. They also give predictions regarding how stimuli intensities, association strength, and spike frequency adaptation influence multiple priming effects.
Encoding Social Interactions: The Neural Correlates of True and False Memories
Authors: Straube Benjamin , Green Antonia , Chatterjee Anjan , Kircher Tilo
Published: April 2010

In social situations, we encounter information transferred in firsthand (egocentric) and secondhand (allocentric) communication contexts. However, the mechanism by which an individual distinguishes whether a past interaction occurred in an egocentric versus allocentric situation is poorly understood. This study examined the neural bases for encoding memories of social interactions through experimentally manipulating the communication context. During fMRI data acquisition, participants watched video clips of an actor speaking and gesturing directly toward them (egocentric context) or toward an unseen third person (allocentric context). After scanning, a recognition task gauged participants' ability to recognize the sentences they had just seen and to recall the context in which the sentences had been spoken. We found no differences between the recognition of sentences spoken in egocentric and allocentric contexts. However, when asked about the communication context (“Had the actor directly spoken to you?”), participants tended to believe falsely that the actor had directly spoken to them during allocentric conditions. Greater activity in the hippocampus was related to correct context memory, whereas the ventral ACC was activated for subsequent inaccurate context memory. For the interaction between encoding context and context memory, we observed increased activation for egocentric remembered items in the bilateral and medial frontal cortex, the BG, and the left parietal and temporal lobe. Our data indicate that memories of social interactions are biased to be remembered egocentrically. Self-referential encoding processes reflected in increased frontal activation and decreased hippocampal activation might be the basis of correct item but false context memory of social interactions.
The Literate Brain: The Relationship between Spelling and Reading
Authors: Rapp Brenda , Lipka Kate
Published: April 2010

We report the results of an fMRI investigation of the neural bases of written language comprehension (reading) and production (spelling). Both tasks were examined in the same individuals, allowing greater precision in establishing the relationship between the neural underpinnings of these two cognitive functions. Also examined was the relationship between written language substrates and those involved in face and object (house) processing. The results reveal that reading and spelling share specific left hemisphere substrates in the mid-fusiform gyrus and in the inferior frontal gyrus/junction. Furthermore, the results indicate that the left mid-fusiform substrates are specifically involved in lexical orthographic processing. We also find that written language and face processing exhibit largely complementary activation patterns in both the fusiform and the inferior frontal/junction areas, with left and right lateralization, respectively. In sum, these results provide perhaps the strongest evidence to date of components that are shared by written language comprehension (reading) and production (spelling), and they further our understanding of the role of literacy within the larger repertoire of cognitive operations and their neural substrates.
Right Hemisphere Dominance in Visual Statistical Learning
Authors: Roser Matthew E. , Fiser József , Aslin Richard N. , Gazzaniga Michael S.
Published: April 2010

Several studies report a right hemisphere advantage for visuospatial integration and a left hemisphere advantage for inferring conceptual knowledge from patterns of covariation. The present study examined hemispheric asymmetry in the implicit learning of new visual feature combinations. A split-brain patient and normal control participants viewed multishape scenes presented in either the right or the left visual fields. Unbeknownst to the participants, the scenes were composed from a random combination of fixed pairs of shapes. Subsequent testing found that control participants could discriminate fixed-pair shapes from randomly combined shapes when presented in either visual field. The split-brain patient performed at chance except when both the practice and the test displays were presented in the left visual field (right hemisphere). These results suggest that the statistical learning of new visual features is dominated by visuospatial processing in the right hemisphere and provide a prediction about how fMRI activation patterns might change during unsupervised statistical learning.
Sharing Cases: The Observationes in Early Modern Medicine
Authors: Pomata Gianna
Published: May 2010

This paper examines the rise of an epistemic genre, the Observationes, a new form of medical writing that emerged in Renaissance humanistic medicine. The Observationes (collections of case-histories) originated in the second half of the sixteenth century, grew rapidly over the course of the seventeenth, and had become a primary form of medical writing by the eighteenth century. The genre developed initially as a form of self-advertisement by court and town physicians, who stressed success in practice, over and above academic learning, as a core element of their professional identity. This unprecedented emphasis on practice as a source of knowledge remained a key feature of the Observationes in its subsequent development. As the genre evolved, the original emphasis on therapeutic success gave way to a new focus on the descriptive knowledge of disease through detailed observation. The authorial identity projected by the writers of Observationes was increasingly that of the learned and experienced observer, bent on comparing notes and sharing his cases with the fellow members of the res publica medica. This paper charts the development of the genre, examining how its growth contributed to the new epistemological value of observation in the age of the Scientific Revolution.
The Sikh Foundations of Ayurveda
Authors: Aggarwal Neil Krishan
Published: May 2010

This paper explores how Sikh scriptures establish a unique claim to Ayurvedic knowledge. After considering Ayurvedic creation myths in the classical Sanskrit canon, passages from Sikh liturgical texts are presented to show how Ayurveda is refashioned to meet the exigencies of Sikh theology. The Sikh texts are then analysed through their relationship with general Puranic literatures and the historical context of Hindu-Sikh relations. Finally, the Indian government’s current propagation of Ayurveda is scrutinised to demonstrate its affiliation with one particular religion to the possible exclusion of others. The Sikh example provides a glimpse into local cultures of Ayurveda before the professionalisation and standardisation of Ayurvedic practice in India’s post-independence period and may serve as a model for understanding other traditions.
Yang Chongrui and the First National Midwifery School: Childbirth Reform in Early Twentieth-Century China
Authors: Johnson Tina Phillips
Published: May 2010

This paper examines the First National Midwifery School (FNMS) and its connexions with the Rockefeller Foundation and the Nationalist government. During the Nationalist era (1927‐37), western medical personnel and Chinese intellectuals attempted to modernise China by reforming childbirth as part of a new public health system. As most of the biomedical personnel in China were trained in the United States, it may be expected that midwifery reform would have followed the same path as in the West, with physicians displacing midwives. On the contrary, in China we see a blending of Chinese cultural and social needs with western public health methods to create a system that has survived in China to this day. The FNMS acted as a liaison between East and West, between private philanthropic organisations and the government. The most significant player in this field, Dr Yang Chongrui, played a vital role in professionalizing the new occupation of the modern Chinese midwife. Yang’s vision to train midwives to reduce the high maternal and infant mortality rates was one of the most important public health efforts in China during this time. In the process, women were targeted both as actors in China’s nation-building strategies and as reproducers of China’s citizenry.
Socio-Economic Dimensions of Tibetan Medicine in the Tibet Autonomous Region, China
Authors: Hofer Theresia
Published: May 2010

This article investigates some of the socio-economic dimensions of contemporary Tibetan medical practices in the rural areas of the Tibet Autonomous Region (TAR), China. The article is divided into two parts. Part One, printed in the last issue of the journal, deals with traditional medical practitioners and their medical practices within the governmental health care system in the TAR. It sheds light on the workings and the effects that the commodification of the official health care system have had on its Tibetan medical practitioners, most of whom now work as hybrid practitioners and incorporate Chinesestyle biomedicine into their practice. I argue that several historical, social and political factors have brought about unequal access and availability of Tibetan medicine as compared to Chinese style biomedical care in the rural areas. Special attention is given to the role of the reintroduction of the Cooperative Medical Services (CMS) scheme in the sidelining of Tibetan medical practices in the rural areas. Part Two describes the work of private Tibetan medical practitioners and explores some of the social dynamics and ethical dilemmas that have arisen for them due to the commodification of the official system and the reintroduction of the CMS. Both parts focus on the situation in the Tsang or Shigatse region of the western and central TAR, hence enabling there to be useful comparisons with medical practices in the capital Lhasa, where most of the anthropological literature has focused on so far. Both contributions are based on extensive anthropological fieldwork in Lhasa and the Tsang region of Tibet.
Have careers become boundaryless?
Authors: Rodrigues Ricardo A , Guest David
Published: May 2010

The idea the boundaryless career has recently permeated the careers literature. However, critics have claimed that the concept is fuzzy and difficult to operationalize. Moreover, one of the core assumptions, namely the collapse of traditional organizational careers allied to increasing mobility across organizational boundaries, has rarely been seriously analysed in the careers literature. This article aims to take forward the analysis of the boundaryless career concept in two ways. First, we discuss its conceptual and operational problems. We argue that the current debate, focused on the permeability of organizational boundaries, fails fully to address the complexity of contemporary careers. Second, we integrate contributions from labour economics on job stability to argue that the assumption of the collapse of the traditional career model is not supported by the evidence. In our conclusions, we draw on boundary theory to outline the potential of a different approach to the conceptualization of career boundaries.
An innovative approach to employee participation in a Norwegian retail chain
Authors: Brøgger Benedicte
Published: May 2010

The article discusses practical experiences with establishing conditions for employee participation in retailing. Social dialogue and human resource management perspectives frame the discussion. These are two different systems for organizing relations between employers and employees. Companies that do not have either are called ‘bleak houses’. There are many ‘bleak houses’ in retailing, and work conditions leave much to be desired. This increases transaction costs and has adverse effects on work climate and productivity. An innovative approach to employee participation was tried out through a series of R&D projects in a Norwegian retail chain. The research strategy was based on a participatory approach called ‘democratic dialogue’.
Workplace training in a deregulated training system: Experiences from Australia’s automotive industry
Authors: Cooney Richard
Published: May 2010

Vocational education and training (VET) in Australia has been widely deregulated as the country has moved to an employer-led VET system. This deregulated system has seen a growing emphasis on more job-specific and firm-specific forms of training. This article explores these developments by examining the training of frontline team leaders in Australia’s automotive industry. The article finds that the automotive companies in Australia have pulled back on their commitment to broad-based skill development at work and that the training they provide is tending to become more job-specific and firm-specific, as they seek to implement standardized global production systems.
Spontaneous Acute Tumor Lysis Syndrome as a Cause of Early Deaths in Short-Term Carcinogenicity Studies Using p53+/– Mice
Authors: Vogel P. , Pletcher J. M. , Liang Y.
Published: May 2010

Acute tumor lysis syndrome (ATLS) is a potentially lethal condition precipitated by the massive release of intracellular components such as nucleic acids, potassium, and phosphorus, following a rapid and widespread lysis of tumor cells. Herein, the authors describe the high incidence and characteristic histopathologic lesions of acute ATLS in p53-deficient mice used in 2 short-term carcinogenicity studies. ATLS was a frequent cause of early death in p53+/– mice in these studies and was consistently associated with the presence of disseminated lymphoma and leukemia. Although a heavy tumor burden and leukemia were present in all affected mice, the absence of ATLS in other mice with equally severe lymphoma and leukemia indicates that these tumor burdens are necessary but insufficient to cause ATLS in mice. The hallmark histopathologic findings of ATLS in mice are the disseminated microemboli composed of nuclear and cytoplasmic debris derived from lysed tumor cells. The mechanical obstruction of capillary beds by these microemboli appeared to be the proximate cause of the early deaths of mice in these studies. Microemboli may contribute to the pathogenesis of acute renal failure and other clinical signs associated with ATLS in other species. Recognition of ATLS in laboratory animals is critical in studies intended to evaluate the efficacy and/or toxicity of anticancer treatments, where early deaths due to ATLS might otherwise be attributed to test article toxicity. Further studies on the role of microemboli in the pathogenesis of ATLS may elucidate pathogenetic mechanisms and lead to improved approaches to clinical management and treatment of this potentially lethal condition.
Review article: Time-dependent failure criteria for polymer matrix composites: a review
Authors: Guedes Rui Miranda
Published: April 2010

This article reviews several theoretical approaches for lifetime predictions proposed for polymer and polymer-based matrix composites. All these theories can be classified as global and homogenous approaches. Actually, regarding engineering applications, the global and homogeneous analyses are more convenient. Fracture mechanics, damage mechanics, and energy-based failure criteria are presented and illustrated with published experimental data.
How Should the Internal Structure of Personality Inventories Be Evaluated?
Authors: Hopwood Christopher J. , Donnellan M. Brent
Published: May 2010

Personality trait inventories often perform poorly when their structure is evaluated with confirmatory factor analysis (CFA). The authors demonstrate poor CFA fit for several widely used personality measures with documented evidence of criterion-related validity but also show that some measures perform well from an exploratory factor analytic perspective. In light of these results, the authors suggest that the failure of these measures to fit CFA models is because of the inherent complexity of personality, issues related to its measurement, and issues related to the application and interpretation of CFA models. This leads to three recommendations for researchers interested in the structure and assessment of personality traits: (a) utilize and report on a range of factor analytic methods, (b) avoid global evaluations regarding the internal validity of multiscale personality measures based on model fit according to conventional CFA cutoffs, and (c) consider the substantive and practical implications of model modifications designed to improve fit.
Cultural Differences in Expectations of Change and Tolerance for Contradiction: A Decade of Empirical Research
Authors: Spencer-Rodgers Julie , Williams Melissa J. , Kaiping Peng
Published: May 2010

Since the publication of Peng and Nisbett’s seminal paper on dialectical thinking, a substantial amount of empirical research has replicated and expanded on the core finding that people differ in the degree to which they view the world as inherently contradictory and in constant flux. Dialectical thinkers (who are more often members of East Asian than Western cultures) show greater expectation of change in tasks related to explanation and prediction and greater tolerance of contradiction in tasks involving the reconciliation of contradictory information. The authors show how these effects are manifested in the domains of the self, emotional experience, psychological well-being, attitudes and evaluations, social categorization and perception, and judgment and decision making. They note important topics in need of further investigation and offer predictions concerning possible cultural differences in unexplored domains as a function of the presence or absence of naïve dialecticism.
Oxytocin and Human Social Behavior
Authors: Campbell Anne
Published: May 2010

Despite a general consensus that oxytocin (OT) has prosocial effects, there is no clear agreement on how these effects are achieved. Human research on OT is reviewed under three broad research initiatives: attachment and trust, social memory, and fear reduction. As an organizing perspective for scholars’ current knowledge, a tentative model of the causes and effects of alterations in OT level is proposed. The model must remain provisional until conceptual and methodological problems are addressed that arise from a failure to distinguish between traits and states, differing research paradigms used in relation to OT as an independent versus dependent variable, and the possibility that OT effects depend on the initial emotional state of the individual. Social and personality psychologists have important roles to play in developing more rigorous and creative research designs.
Reviving Campbell’s Paradigm for Attitude Research
Authors: Kaiser Florian G. , Byrka Katarzyna , Hartig Terry
Published: May 2010

Because people often say one thing and do another, social psychologists have abandoned the idea of a simple or axiomatic connection between attitude and behavior. Nearly 50 years ago, however, Donald Campbell proposed that the root of the seeming inconsistency between attitude and behavior lies in disregard of behavioral costs. According to Campbell, attitude— behavior gaps are empirical chimeras. Verbal claims and other overt behaviors regarding an attitude object all arise from one “behavioral disposition.” In this article, the authors present the constituents of and evidence for a paradigm for attitude research that describes individual behavior as a function of a person’s attitude level and the costs of the specific behavior involved. In the authors’ version of Campbell’s paradigm, they propose a formal and thus axiomatic rather than causal relationship between an attitude and its corresponding performances. The authors draw implications of their proposal for mainstream attitude theory, empirical research, and applications concerning attitudes.
Who speaks? Discourse, the subject and the study of identity in international politics
Authors: Epstein Charlotte
Published: May 2010

This article aims to show the theoretical added value of focussing on discourse to study identity in international relations (IR). I argue that the discourse approach offers a more theoretically parsimonious and empirically grounded way of studying identity than approaches developed in the wake of both constructivism and the broader ‘psychological turn’. My starting point is a critique of the discipline’s understanding of the ‘self’ uncritically borrowed from psychology. Jacques Lacan’s ‘speaking subject’ offers instead a non-essentialist basis for theorizing about identity that has been largely overlooked. To tailor these insights to concerns specific to the discipline I then flesh out the distinction between subject-positions and subjectivities. This crucial distinction is what enables the discourse approach to travel the different levels of analyses, from the individual to the state, in a way that steers clear of the field’s fallacy of composition, which has been perpetuated by the assumption that what applies to individuals applies to states as well. Discourse thus offers a way of studying state identities without presuming that the state has a self. I illustrate this empirically with regards to the international politics of whaling.
Therapeutic developments in spinal muscular atrophy
Authors: Sproule Douglas M. , Kaufmann Petra
Published: May 2010

Spinal muscular atrophy (SMA), a potentially devastating disease marked by progressive weakness and muscle atrophy resulting from the dysfunction and loss of motor neurons of the spinal cord, has emerged in recent years as an attractive target for therapeutic intervention. Caused by a homozygous mutation to the Survival of Motor Neurons 1 (SMN1) gene on chromosome 5q, the severity of the clinical phenotype in SMA is modulated by the function of a related protein, Survival of Motor Neurons 2 (SMN2). SMN2 predominantly produces an unstable SMN transcript lacking exon 7; only about 10% of the transcription product produces a full-length, functional SMN protein. Several therapeutic strategies have targeted this gene with the goal of producing increased full-length SMN transcript, thereby modifying the underlying mechanism. Drugs that have increased SMN2 function, in vitro, are now explored for potential therapeutic benefit in this disease. Alternative approaches, including neuroprotective, muscle anabolic, gene and cell replacement strategies, also hold promise. The recent advances in preclinical research and the development of a wider range of animal models for SMA continue to provide cautious optimism that effective treatments for SMA will eventually emerge.
Determinants of community-acquired pneumonia in children and young adults in primary care
Authors: Teepe J. , Grigoryan L. , Verheij T. J. M.
Published: May 2010

Most studies on determinants of community-acquired pneumonia (CAP) in primary care have focused primarily on the elderly. Using a case–control study in four Dutch healthcare centres, determinants of CAP among children and young adults were identified.

Cases included 156 young adults (aged 16–40 yrs) and 107 children (aged 0–15 yrs) diagnosed with CAP during 1999–2008. For each case, three controls were selected from the same age group. Separate logistic regression analyses were used to identify determinants in young adults and children.

Lower age, asthma and previous upper respiratory tract infections (URTIs) were independently associated with CAP in children. Increasing age, asthma, three or more children at home, current smoking and three or more previous URTIs were independent determinants of CAP in young adults.

The present study has three remarkable findings: 1) increasing age was an independent determinant of CAP in young adults; 2) having young children increased the risk of the development of CAP in young adults; and 3) the number of previous URTIs was independently associated with CAP in both children and young adults, possibly due to higher infection susceptibility. Further studies are required in order to better understand the aetiology of CAP and permit better diagnosis and treatment of this serious condition.
Fine-tuning structural RNA alignments in the twilight zone
Authors: Bremges Andreas , Schirmer Stefanie , Giegerich Robert
Published: April 2010

Background

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably.

Results

Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices.

Conclusions

Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences
Authors: Lane Jérôme , Duroux Patrice , Lefranc Marie-Paule
Published: April 2010

Background

The antigen receptors, immunoglobulins (IG) and T cell receptors (TR), are specific molecular components of the adaptive immune response of vertebrates. Their genes are organized in the genome in several loci (7 in humans) that comprise different gene types: variable (V), diversity (D), joining (J) and constant (C) genes. Synthesis of the IG and TR proteins requires rearrangements of V and J, or V, D and J genes at the DNA level, followed by the splicing at the RNA level of the rearranged V-J and V-D-J genes to C genes. Owing to the particularities of IG and TR gene structures related to these molecular mechanisms, conventional bioinformatic software and tools are not adapted to the identification and description of IG and TR genes in large genomic sequences. In order to answer that need, IMGT®, the international ImMunoGeneTics information system®, has developed IMGT/LIGMotif, a tool for IG and TR gene annotation. This tool is based on standardized rules defined in IMGT-ONTOLOGY, the first ontology in immunogenetics and immunoinformatics.

Results

IMGT/LIGMotif currently annotates human and mouse IG and TR loci in large genomic sequences. The annotation includes gene identification and orientation on DNA strand, description of the V, D and J genes by assigning IMGT® labels, gene functionality, and finally, gene delimitation and cluster assembly. IMGT/LIGMotif analyses sequences up to 2.5 megabase pairs and can analyse them in batch files.

Conclusions

IMGT/LIGMotif is currently used by the IMGT® biocurators to annotate, in a first step, IG and TR genomic sequences of human and mouse in new haplotypes and those of closely related species, nonhuman primates and rat, respectively. In a next step, and following enrichment of its reference databases, IMGT/LIGMotif will be used to annotate IG and TR of more distantly related vertebrate species. IMGT/LIGMotif is available at http://www.imgt.org/ligmotif/.
A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing
Authors: Shimada Makoto K , Hayakawa Yosuke , Takeda Jun-ichi , Gojobori Takashi , Imanishi Tadashi
Published: April 2010

Background

Alternative splicing (AS) is a key molecular process that endows biological functions with diversity and complexity. Generally, functional redundancy leads to the generation of new functions through relaxation of selective pressure in evolution, as exemplified by duplicated genes. It is also known that alternatively spliced exons (ASEs) are subject to relaxed selective pressure. Within consensus sequences at the splice junctions, the most conserved sites are dinucleotides at both ends of introns (splice dinucleotides). However, a small number of single nucleotide polymorphisms (SNPs) occur at splice dinucleotides. An intriguing question relating to the evolution of AS diversity is whether mutations at splice dinucleotides are maintained as polymorphisms and produce diversity in splice patterns within the human population. We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database.

Results

We found 212 validated SNPs at splice dinucleotides (sdSNPs); these were confirmed to be consistent with the GT-AG rule at either allele. Moreover, 53 of them were observed to neighbor ASEs (AE dinucleotides). No significant differences were observed between sdSNPs at AE dinucleotides and those at constitutive exons (CE dinucleotides) in SNP properties including average heterozygosity, SNP density, ratio of predicted alleles consistent with the GT-AG rule, and scores of splice sites formed with the predicted allele. We also found that the proportion of non-conserved exons was higher for exons with sdSNPs than for other exons.

Conclusions

sdSNPs are found at CE dinucleotides in addition to those at AE dinucleotides, suggesting two possibilities. First, sdSNPs at CE dinucleotides may be robust against sdSNPs because of unknown mechanisms. Second, similar to sdSNPs at AE dinucleotides, those at CE dinucleotides cause differences in AS patterns because of the arbitrariness in the classification of exons into alternative and constitutive type that varies according to the dataset. Taking into account the absence of differences in sdSNP properties between those at AE and CE dinucleotides, the increased proportion of non-conserved exons found in exons flanked by sdSNPs suggests the hypothesis that sdSNPs are maintained at the splice dinucleotides of newly generated exons at which negative selection pressure is relaxed.
Functional bias in molecular evolution rate of Arabidopsis thaliana
Authors: Warren Andrew S , Anandakrishnan Ramu , Zhang Liqing
Published: May 2010

Background

Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the rate of molecular evolution for individual genes to be dependent on their biological function. Whether this expectation holds for genes duplicated by whole genome duplication is not known.

Results

We empirically demonstrate here, using duplicated genes generated from the Arabidopsis thaliana α-duplication event, that the rate of molecular evolution of genes duplicated in this event depend on biological function. Using functional clustering based on gene ontology annotation of gene pairs, we show that some duplicated genes, such as defense response genes, are under weaker purifying selection or under stronger diversifying selection than other duplicated genes, such as protein translation genes, as measured by the ratio of nonsynonymous to synonymous divergence (dN/dS).

Conclusions

These results provide empirical evidence indicating that molecular evolution rate for genes duplicated in whole genome duplication, as measured by dN/dS, may depend on biological function, which we characterize using gene ontology annotation. Furthermore, the general approach used here provides a framework for comparative analysis of molecular evolution rate for genes based on their biological function.
SNP identification, verification, and utility for population genetics in a non-model genus
Authors: Williams Larissa M , Ma Xin , Boyko Adam R , Bustamante Carlos D , Oleksiak Marjorie F
Published: April 2010

Background

By targeting SNPs contained in both coding and non-coding areas of the genome, we are able to identify genetic differences and characterize genome-wide patterns of variation among individuals, populations and species. We investigated the utility of 454 sequencing and MassARRAY genotyping for population genetics in natural populations of the teleost, Fundulus heteroclitus as well as closely related Fundulus species (F. grandis, F. majalis and F. similis).

Results

We used 454 pyrosequencing and MassARRAY genotyping technology to identify and type 458 genome-wide SNPs and determine genetic differentiation within and between populations and species of Fundulus. Specifically, pyrosequencing identified 96 putative SNPs across coding and non-coding regions of the F. heteroclitus genome: 88.8% were verified as true SNPs with MassARRAY. Additionally, putative SNPs identified in F. heteroclitus EST sequences were verified in most (86.5%) F. heteroclitus individuals; fewer were genotyped in F. grandis (74.4%), F. majalis (72.9%), and F. similis (60.7%) individuals. SNPs were polymorphic and showed latitudinal clinal variation separating northern and southern populations and established isolation by distance in F. heteroclitus populations. In F. grandis, SNPs were less polymorphic but still established isolation by distance. Markers differentiated species and populations.

Conclusions

In total, these approaches were used to quickly determine differences within the Fundulus genome and provide markers for population genetic studies.