bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growing cognition from recycled parts
Authors: Leech Robert , Mareschal Denis , Cooper Richard P. 
Published: July 2008

AbstractIn this response, we reiterate the importance of development (both ontogenetic and phylogenetic) in the understanding of a complex cognitive skill – analogical reasoning. Four key questions structure the response: Does relational priming exist, and is it sufficient for analogy? What do we mean by relations as transformations? Could all or any relations be represented as transformations? And what about the challenge of more complex analogies? In addressing these questions we bring together a number of supportive commentaries, strengthening our emergentist case for analogy (in particular with insights from comparative psychology), and review new supportive evidence. We also rebut those commentaries that ignore development at their peril. Along the way, we revisit the main assumptions underlying the analogy as relational priming (ARP) account of analogy, clarifying and elaborating as necessary.
The origin of addictions by means of unnatural decision
Authors: Ahmed Serge H. 
Published: July 2008

AbstractThe unified framework for addiction (UFA) formulated by Redish et al. is a tour de force. It uniquely predicts that there should be multiple addiction syndromes and pathways – a diversity that would reflect the complexity of the mammalian brain decision system. Here I explore some of the evolutionary and developmental ramifications of UFA and derive several new avenues for research.
Human drug addiction is more than faulty decision-making
Authors: Hart Carl L. , Krauss Robert M. 
Published: July 2008

AbstractWe commend Redish et al. for the progress they have made in bringing a measure of theoretical order to the processes that underlie drug addiction. However, incorporating information about situations in which drug users do not exhibit faulty decision-making into the theory would greatly enhance its generality and practical value. This commentary draws attention to the relevant human substance abuse literature.
Role of affective associations in the planning and habit systems of decision-making related to addiction
Authors: Kiviniemi Marc T. , Bevins Rick A. 
Published: July 2008

AbstractThe model proposed by Redish et al. considers vulnerabilities within decision systems based on expectancy-value assumptions. Further understanding of processes leading to addiction can be gained by considering other inputs to decision-making, particularly affective associations with behaviors. This consideration suggests additional decision-making vulnerabilities that might explain addictive behaviors.
Negative affects are parts of the addiction syndrome
Authors: Le Moal Michel 
Published: July 2008

AbstractDecision-making is a complex activity for which emotions and affects are essential. Maladaptive choices depend on negative affects. Vulnerabilities to drug or non-drug objects depend on previous psychopathological comorbidities. Premorbid individual characteristics allow us to understand why some individuals – and not others – enter into the addiction cycle. Moreover, plasticity of reward neurocircuitry is, at least in past, responsible for these vulnerabilities leading to compulsive drug use.
Linking addictions to everyday habits and plans
Authors: Neal David T. , Wood Wendy 
Published: July 2008

AbstractRedish et al. trace vulnerabilities in habit and planning systems almost exclusively to pharmacological effects of addictive substances on underlying brain systems. As we discuss, however, these systems also can be disrupted by purely psychological factors inherent in normal decision-making and everyday behavior. A truly unified model must integrate the contribution of both sets of factors in driving addiction.
Addiction as vulnerabilities in the decision process
Authors: Redish A. David , Jensen Steve , Johnson Adam 
Published: July 2008

AbstractIn our target article, we proposed that addiction could be envisioned as misperformance of a decision-making machinery described by two systems (deliberative and habit systems). Several commentators have argued that Pavlovian learning also produces actions. We agree and note that Pavlovian action-selection will provide several additional vulnerabilities. Several commentators have suggested that addiction arises from sociological parameters. We note in our response how sociological effects can change decision-making variables to provide additional vulnerabilities. Commentators generally have agreed that our theory provides a framework within which to site addiction and treatment, but additional work will be needed to determine whether our taxonomy will help identify and treat subpopulations within the addicted community.
Abstract fluctuation theorem
Authors: WOJTKOWSKI MACIEJ P. 
Published: July 2008

AbstractWe formulate an abstract fluctuation theorem which sheds light on mathematical relations between the fluctuation theorems of Bochkov and Kuzovlev [Contribution to the general theory of thermal fluctuations in nonlinear systems. Sov. Phys.–JETP45 (1977), 125] and Jarzynski [Hamiltonian derivation of a detailed fluctuation theorem. J. Stat. Phys.98 (2001), 77–102] on the one hand, and those of Evans and Searles [Equilibrium microstates which generate second law violating steady states. Phys. Rev. E 50 (1994), 1645–1648] and Gallavotti and Cohen [Dynamical ensembles in stationary states. J. Stat. Phys.80 (1995), 931–970] on the other.
An insertion operator preserving infinite reduction sequences
Authors: CHEMOUIL DAVID 
Published: July 2008

A common way to show the termination of the union of two abstract reduction systems, provided both systems terminate, is to prove that they enjoy a specific property (some sort of ‘commutation’ for instance). This specific property is actually used to show that, for the union not to terminate, one of the systems must itself be non-terminating, which leads to a contradiction. Unfortunately, the property may be impossible to prove because some of the objects that are reduced do not enjoy an adequate form.Hence the purpose of this paper is threefold:–First, it introduces an operator enabling us to insert a reduction step on such an object, and therefore to change its shape, while still preserving the ability to use the property. Of course, some new properties will need to be verified.–Second, as an instance of our technique, the operator is applied to relax a well-known lemma stating the termination of the union of two termination abstract reduction systems.–Finally, this lemma is applied in a peculiar and then in a more general way to show the termination of some lambda calculi with inductive types augmented with specific reductions dealing with:(i)copies of inductive types;(ii)the representation of symmetric groups.
Mathematical modelling of linearly elastic shells
Authors: Ciarlet Philippe G. 
Published: July 2008

The objective of this article is to lay down the proper mathematical foundations
of the two-dimensional theory of linearly elastic shells. To this end,
it provides, without any recourse to any a priori assumptions of a geometrical
or mechanical nature, a mathematical justification of two-dimensional
linear shell theories, by means of asymptotic methods, with the thickness as
the ‘small’ parameter.A major virtue of this approach is that it naturally leads to precise mathematical
definitions of linearly elastic ‘membrane’ and ‘flexural’ shells. Another
noteworthy feature is that it highlights in particular the role played by two
fundamental tensors, each associated with a displacement field of the middle
surface, the linearized change of metric and linearized change of curvature
tensors.More specifically, under fundamentally distinct sets of assumptions bearing
on the geometry of the middle surface, on the boundary conditions, and
on the order of magnitude of the applied forces, it is shown that the three-dimensional
displacements, once properly scaled, converge (in H1, or in L2,
or in ad hoc completions) as the thickness approaches zero towards a ‘two-dimensional’
limit that satisfies either the linear two-dimensional equations
of a ‘membrane’ shell (themselves divided into two subclasses) or the linear
two-dimensional equations of a ‘flexural’ shell. Note that this asymptotic analysis
automatically provides in each case the ‘limit’ two-dimensional equations,
together with the function space over which they are well-posed.The linear two-dimensional shell equations that are most commonly used
in numerical simulations, namely Koiter's equations, Naghdi's equations, and
‘shallow’ shell equations, are then carefully described, mathematically analysed,
and likewise justified by means of asymptotic analyses.The existence and uniqueness of solutions to each one of these linear two-dimensional
shell equations are also established by means of crucial inequalities
of Korn's type on surfaces, which are proved in detail at the beginning
of the article.This article serves as a mathematical basis for the numerically oriented
companion article by Dominique Chapelle, also in this issue of Acta Numerica.
Self-reported dietary energy intake of normal weight, overweight and obese adolescents
Authors: Vance Vivienne A , Woodruff Sarah J , McCargar Linda J , Husted Janice , Hanning Rhona M 
Published: July 2008

AbstractObjectiveThe purpose of the present paper was to assess dietary energy reporting as a function of sex and weight status among Ontario and Alberta adolescents, using the ratio of energy intake (EI) to estimated BMR (BMRest).DesignData were collected using the FBQ, a validated web-based dietary assessment tool (including a 24 h dietary recall, FFQ, and food and physical activity behavioural questions). BMI was calculated from self-reported height and weight and participants were classified as normal weight, overweight or obese. BMR was calculated using the WHO equations (based on weight). Reporting status was identified using the ratio EI:BMRest.SettingData were collected in public, Catholic and private schools in Ontario and Alberta, Canada.SubjectsA total of 1917 (n876 male andn1041 female) students (n934 grade 9 andn984 grade 10) participated.ResultsThe mean EI:BMRestratio across all participants was 1·4 (sd0·6), providing evidence of under-reporting for the total sample. Females under-reported more than males (t= 6·27,P< 0·001), and under-reporting increased with increasing weight status for both males (F= 33·21,P< 0·001) and females (F= 14·28,P< 0·001). After removing those who reported eating less to lose weight, the EI:BMRestwas 1·56 (sd0·6) for males and 1·4 (sd0·6) for females.ConclusionThe present study highlights methodological challenges associated with self-reported dietary data. Systematic differences in under-reporting of dietary intake by gender and weight status were observed using a web-based survey, similar to observations made using paper-based 24 h recalls and dietitian interviews.
Asfaw Receives 2008 New International Award
Authors: Whaler Kathryn A. , Asfaw Laike Mariam 
Published: July 2008

Laike Mariam Asfaw became the director of the Addis Ababa Geophysical Observatory (AAO) at Addis Ababa University, Ethiopia, in 1978. His quiet calm and dedication have ensured a continuous, high‐quality data stream throughout the often politically turbulent period since. He is also deeply involved in the geophysical education of his country's science students, understanding, awareness‐raising, and advising on its seismic and related hazards, and the promotion of its science on the international stage.The AAO was founded in the International Geophysical Year (IGY) as a geomagnetic observatory, still one of the few in Africa. Originally using paper records, hourly mean data have been produced since the observatory's inception; minute mean values have been available since 2000. It is now an International Real‐Time Magnetic Observatory Network (INTERMAGNET) observatory, indicating that it adheres to the highest standards of operation and, through satellite communication, provides data in near real time. Seismometer installation took place in 1959 and was upgraded with digital equipment in 1997. The AAO now also manages the Incorporated Research Institutions for Seismology (IRIS) broadband and other short‐period digital seismic stations in Ethiopia, and is an auxiliary Comprehensive Nuclear‐Test‐Ban Treaty Organization station. A continuously running GPS receiver has recently augmented the instrument base, and AAO is an International Global Navigation Satellite System (GNSS) Service station. The observatory's development and expansion and commitment of overseas funds would not have happened without Laike's leadership. He also ensures that AAO staff and students are actively involved in research based on the observatory's data.
Groundwater Science and Policy: An International Overview
Authors: Robins Nick 
Published: July 2008

While global demand for water increases, the risks from pollution and the uncertainty of climate heighten the threat to available resources. One fifth of the world's freshwater reserves lie underground in the form of groundwater, whereas surface water systems account for a mere two hundredths of the global reserve, and the remainder is locked up—for the moment—in the polar ice caps. However, because groundwater is out of sight, to many this means out of mind. As a result, much of the world's groundwater is poorly managed and exploited for short‐term gain at the expense of longer‐term protection.In response to requirements that had been outlined in the European Commission's Water Framework Directive (2000/60/EC) of 2000, the Commission's European “daughter,” Groundwater Directive (2006/118/EC, adopted in December 2006) clarifies the objectives outlined in the Water Framework Directive for groundwater protection in Europe.
Effects of substitutions in the CXXC active-site motif of the extracytoplasmic thioredoxin ResA
Authors: Lewin Allison , Crow Allister , Hodson Christopher T. C. , Hederstedt Lars , Le Brun Nick E. 
Published: July 2008

The thiol–disulfide oxidoreductase ResA from Bacillus subtilis fulfils a reductive role in cytochrome c maturation. The pKa values for the CEPC (one-letter code) active-site cysteine residues of ResA are unusual for thioredoxin-like proteins in that they are both high (&gt;8) and within 0.5 unit of each other. To determine the contribution of the inter-cysteine dipeptide of ResA to its redox and acid–base properties, three variants (CPPC, CEHC and CPHC) were generated representing a stepwise conversion into the active-site sequence of the high-potential DsbA protein from Escherichia coli. The substitutions resulted in large decreases in the pKa values of both the active-site cysteine residues: in CPHC (DsbA-type) ResA, ΔpKa values of −2.5 were measured for both cysteine residues. Increases in midpoint reduction potentials were also observed, although these were comparatively small: CPHC (DsbA-type) ResA exhibited an increase of +40 mV compared with the wild-type protein. Unfolding studies revealed that, despite the observed differences in the properties of the reduced proteins, changes in stability were largely confined to the oxidized state. High-resolution structures of two of the variants (CEHC and CPHC ResA) in their reduced states were determined and are discussed in terms of the observed changes in properties. Finally, the in vivo functional properties of CEHC ResA are shown to be significantly affected compared with those of the wild-type protein.
Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference
Authors: Morcos Faruck , Lamanna Charles , Sikora Marcin , Izaguirre Jesús 
Published: July 2008

Abstract
Summary: Cytoprophet is a software tool that allows prediction and visualization of protein and domain interaction networks. It is implemented as a plug-in of Cytoscape, an open source software framework for analysis and visualization of molecular networks. Cytoprophet implements three algorithms that predict new potential physical interactions using the domain composition of proteins and experimental assays. The algorithms for protein and domain interaction inference include maximum likelihood estimation (MLE) using expectation maximization (EM); the set cover approach maximum specificity set cover (MSSC) and the sum-product algorithm (SPA). After accepting an input set of proteins with Uniprot ID/Accession numbers and a selected prediction algorithm, Cytoprophet draws a network of potential interactions with probability scores and GO distances as edge attributes. A network of domain interactions between the domains of the initial protein list can also be generated. Cytoprophet was designed to take advantage of the visual capabilities of Cytoscape and be simple to use. An example of inference in a signaling network of myxobacterium Myxococcus xanthus is presented and available at Cytoprophet's website.
Availability: http://cytoprophet.cse.nd.edu
Contact: cytoprophet@cse.nd.edu
Supplementary information: Examples and supplementary data are accessible at http://cytoprophet.cse.nd.edu
Robust and efficient identification of biomarkers by classifying features on graphs
Authors: Hwang TaeHyun , Sicotte Hugues , Tian Ze , Wu Baolin , Kocher Jean-Pierre , Wigle Dennis A. , Kumar Vipin , Kuang Rui 
Published: July 2008

AbstractMotivation: A central problem in biomarker discovery from large-scale gene expression or single nucleotide polymorphism (SNP) data is the computational challenge of taking into account the dependence among all the features. Methods that ignore the dependence usually identify non-reproducible biomarkers across independent datasets. We introduce a new graph-based semi-supervised feature classification algorithm to identify discriminative disease markers by learning on bipartite graphs. Our algorithm directly classifies the feature nodes in a bipartite graph as positive, negative or neutral with network propagation to capture the dependence among both samples and features (clinical and genetic variables) by exploring bi-cluster structures in a graph. Two features of our algorithm are: (1) our algorithm can find a global optimal labeling to capture the dependence among all the features and thus, generates highly reproducible results across independent microarray or other high-thoughput datasets, (2) our algorithm is capable of handling hundreds of thousands of features and thus, is particularly useful for biomarker identification from high-throughput gene expression and SNP data. In addition, although designed for classifying features, our algorithm can also simultaneously classify test samples for disease prognosis/diagnosis.Results: We applied the network propagation algorithm to study three large-scale breast cancer datasets. Our algorithm achieved competitive classification performance compared with SVMs and other baseline methods, and identified several markers with clinical or biological relevance with the disease. More importantly, our algorithm also identified highly reproducible marker genes and enriched functions from the independent datasets.Availability: Supplementary results and source code are available at http://compbio.cs.umn.edu/Feature_Class.Contact: kuang@cs.umn.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Is there an acceleration of the CpG transition rate during the mammalian radiation?
Authors: Peifer M. , Karro J. E. , von Grünberg H. H. 
Published: July 2008

Abstract
Motivation: In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates.
Results: When using this modified method to reproduce the supporting analysis, the evidence of the rate shift vanished. Our analysis suggests that the CpG-specific rate has been constant over the relevant time period and that the asserted acceleration of the CpG rate is likely an artifact of the original model.
Contact: peifer@uni-graz.at
Supplementary information: Supplementary data are available at Bioinformatics online.
Mixture models for protein structure ensembles
Authors: Hirsch Michael , Habeck Michael 
Published: July 2008

AbstractMotivation: Protein structure ensembles provide important insight into the dynamics and function of a protein and contain information that is not captured with a single static structure. However, it is not clear a priori to what extent the variability within an ensemble is caused by internal structural changes. Additional variability results from overall translations and rotations of the molecule. And most experimental data do not provide information to relate the structures to a common reference frame. To report meaningful values of intrinsic dynamics, structural precision, conformational entropy, etc., it is therefore important to disentangle local from global conformational heterogeneity.Results: We consider the task of disentangling local from global heterogeneity as an inference problem. We use probabilistic methods to infer from the protein ensemble missing information on reference frames and stable conformational sub-states. To this end, we model a protein ensemble as a mixture of Gaussian probability distributions of either entire conformations or structural segments. We learn these models from a protein ensemble using the expectation–maximization algorithm. Our first model can be used to find multiple conformers in a structure ensemble. The second model partitions the protein chain into locally stable structural segments or core elements and less structured regions typically found in loops. Both models are simple to implement and contain only a single free parameter: the number of conformers or structural segments. Our models can be used to analyse experimental ensembles, molecular dynamics trajectories and conformational change in proteins.Availability: The Python source code for protein ensemble analysis is available from the authors upon request.Contact: michael.habeck@tuebingen.mpg.de
Contaminants in marine ecosystems: developing an integrated indicator framework using biological-effect techniques
Authors: Thain John E. , Vethaak A. Dick , Hylland Ketil 
Published: July 2008

Abstract
Thain, J. E., Vethaak, A. D., and Hylland, K. 2008. Contaminants in marine ecosystems: developing an integrated indicator framework using biological-effect techniques. – ICES Journal of Marine Science, 65: 1508–1514. Input of contaminants is an important pressure in most urbanized coastal areas, but establishing appropriate indicators of their presence and effects has been challenging. Such indicators would, at the very least, have to integrate chemical and biological data. One difficulty has arisen because the measurements provide information on different levels of biological organization (gene level up to community), although it is not obvious how this information could be conceptually linked. In addition, there are complicating factors, such as the differing ecological relevance of measurements, natural variation, confounding factors, and knowledge of background level or responses for each method. The challenge of how to take these issues forwards is discussed in light of current scientific thinking and of meeting international obligations. First, an integrated approach must be developed to using biological-effect techniques with chemical measurements, and second, assessment tools are required. Proposals for both of these have been initiated by ICES and OSPAR working groups and workshops. Concomitantly, steps have been taken to develop integrated assessment tools on a national basis. These show promise but highlight the difficulties of using biological-effect measures as indicators of ecosystem health.