bluuebunny/crossref_metadata_2025_split huggingface dataset:
A model of mechanical interactions between heart and lungs
Authors: Fontecave Jallon Julie , Abdulhay Enas , Calabrese Pascale , Baconnier Pierre , Gumery Pierre-Yves 
Published: November 2009

To study the mechanical interactions between heart, lungs and thorax, we propose a mathematical model combining a ventilatory neuromuscular model and a model of the cardiovascular system, as described by Smith
et al.
(Smith, Chase, Nokes, Shaw & Wake 2004
Med. Eng. Phys.
26
, 131–139. (
doi:10.1016/j.medengphy.2003.10.001
)). The respiratory model has been adapted from Thibault
et al
. (Thibault, Heyer, Benchetrit & Baconnier 2002
Acta Biotheor
.
50
, 269–279. (
doi:10.1023/A:1022616701863
)); using a Liénard oscillator, it allows the activity of the respiratory centres, the respiratory muscles and rib cage internal mechanics to be simulated. The minimal haemodynamic system model of Smith includes the heart, as well as the pulmonary and systemic circulation systems. These two modules interact mechanically by means of the pleural pressure, calculated in the mechanical respiratory system, and the intrathoracic blood volume, calculated in the cardiovascular model. The simulation by the proposed model provides results, first, close to experimental data, second, in agreement with the literature results and, finally, highlighting the presence of mechanical cardiorespiratory interactions.
An integrated formulation of anisotropic force–calcium relations driving spatio-temporal contractions of cardiac myocytes
Authors: Tracqui Philippe , Ohayon Jacques 
Published: November 2009

Isolated cardiac myocytes exhibit spontaneous patterns of rhythmic contraction, driven by intracellular calcium waves. In order to study the coupling between spatio-temporal calcium dynamics and cell contraction in large deformation regimes, a new strain-energy function, describing the influence of sarcomere length on the calcium-dependent generation of active intracellular stresses, is proposed. This strain-energy function includes anisotropic passive and active contributions that were first validated separately from experimental stress–strain curves and stress–sarcomere length curves, respectively. An extended validation of this formulation was then conducted by considering this strain-energy function as the core of an integrated mechano-chemical three-dimensional model of cardiac myocyte contraction, where autocatalytic intracellular calcium dynamics were described by a representative two-variable model able to generate realistic intracellular calcium waves similar to those observed experimentally. Finite-element simulations of the three-dimensional cell model, conducted for different intracellular locations of triggering calcium sparks, explained very satisfactorily, both qualitatively and quantitatively, the contraction patterns of cardiac myocytes observed by time-lapse videomicroscopy. This integrative approach of the mechano-chemical couplings driving cardiac myocyte contraction provides a comprehensive framework for analysing active stress regulation and associated mechano-transduction processes that contribute to the efficiency of cardiac cell contractility in both physiological and pathological contexts.
A note on semi-discrete modelling in the life sciences
Authors: Mailleret Ludovic , Lemesle Valérie 
Published: November 2009

Semi-discrete models are a particular class of hybrid dynamical systems that undergo continuous dynamics most of the time but repeatedly experience discrete changes at some given moments. In the life sciences, since the first semi-discrete model was derived to describe population dynamics by Beverton & Holt (Beverton & Holt 1957 InFisheries investigations, series 2, vol. 19), a large body of literature has been concerned with such modelling approaches. The aim of the present contribution is twofold. On the one hand, it provides a comprehensive introduction to semi-discrete modelling through two illustrative examples: the classical work by Beverton and Holt is recalled and an original example on immigration in a population model affected by a strong Allee effect is worked out. On the other hand, a short overview of the different applications of semi-discrete models in the life sciences is proposed.
Approximating the distribution of population size in stochastic multiregional matrix models with fast migration
Authors: Alonso Juan Antonio , Sanz Luis 
Published: November 2009

In this work we deal with a multiregional model in discrete time for an age-structured population which lives in an environment that changes randomly with time and is distributed in different spatial patches. In addition, and as is often the case in applications, we assume that migration is fast with respect to demography. Using approximate aggregation techniques we make use of the existence of different time scales in the model and reduce the dimension of the system obtaining a stochastic Leslie model in which the variables are the total population in each age class. Literature shows that, under reasonable conditions, the distribution of population size in matrix models with environmental stochasticity is asymptotically lognormal, and is characterized by two parameters, stochastic growth rate (s.g.r.) and scaled logarithmic variance (s.l.v.), that, in most practical cases, cannot be computed exactly. We show that the s.g.r. and the s.l.v. of the original multiregional model can be approximated by those corresponding to the reduced stochastic Leslie model, therefore simplifying its analysis. Moreover, we illustrate the usefulness of the reduction procedure by presenting some practical cases in which, although the explicit computation of the s.g.r. and the s.l.v. of the original multiregional model is not feasible, we can calculate its analogues for the reduced model.
A multiformalism and multiresolution modelling environment: application to the cardiovascular system and its regulation
Authors: Hernández Alfredo I. , Le Rolle Virginie , Defontaine Antoine , Carrault Guy 
Published: November 2009

The role of modelling and simulation in the systemic analysis of living systems is now clearly established. Emerging disciplines, such as systems biology, and worldwide research actions, such as the Physiome Project or the Virtual Physiological Human, are based on an intensive use of modelling and simulation methodologies and tools. One of the key aspects in this context is to perform an efficient integration of various models representing different biological or physiological functions, at different resolutions, spanning through different scales. This paper presents a multiformalism modelling and simulation environment (M2SL) that has been conceived to ease model integration. A given model is represented as a set of coupled and atomic model components that may be based on different mathematical formalisms with heterogeneous structural and dynamical properties. A co-simulation approach is used to solve these hybrid systems. The pioneering model of the overall regulation of the cardiovascular system proposed by Guyton and co-workers in 1972 has been implemented under M2SL and a pulsatile ventricular model based on a time-varying elastance has been integrated in a multi-resolution approach. Simulations reproducing physiological conditions and using different coupling methods show the benefits of the proposed environment.
Application of interval iterations to the entrainment problem in respiratory physiology
Authors: Demongeot Jacques , Waku Jules 
Published: November 2009

We present here some theoretical and numerical results about interval iterations. We consider first an application of the interval iterations theory to the problem of entrainment in respiratory physiology for which the classical point iterations theory fails. Then, after a brief review of some of the main aspects of point iterations, we explain what is meant by the term ‘interval iterations’. It consists essentially in replacing in the point iterations the function to iterate by a set-valued map. We present both theoretical and numerical aspects of this new type of iterations and we observe the dynamical behaviours encountered, such as fixed intervals and interval limit cycles. The comparison between point and interval iterations is carried out with respect to a parameterε, which determines the thickness of a neighbourhood around the function to iterate. We will finally focus our attention on the Verhulst and Ricker functions largely used in population dynamics, which exhibit various asymptotic behaviours.
Why bodies? Twelve reasons for including bodily expressions in affective neuroscience
Authors: de Gelder Beatrice 
Published: November 2009

Why bodies? It is rather puzzling that given the massive interest in affective neuroscience in the last decade, it still seems to make sense to raise the question ‘Why bodies’ and to try to provide an answer to it, as is the goal of this article. There are now hundreds of articles on human emotion perception ranging from behavioural studies to brain imaging experiments. These experimental studies complement decades of reports on affective disorders in neurological patients and clinical studies of psychiatric populations. The most cursory glance at the literature on emotion in humans, now referred to by the umbrella term of social and affective neuroscience, shows that over 95 per cent of them have used faces as stimuli. Of the remaining 5 per cent, a few have used scenes or auditory information including human voices, music or environmental sounds. But by far the smallest number has looked into whole-body expressions. As a rough estimate, a search on PubMed today, 1 May 2009, yields 3521 hits for emotion × faces, 1003 hits for emotion × music and 339 hits for emotion × bodies. When looking in more detail, the body × emotion category in fact yields a majority of papers on well-being, nursing, sexual violence or organ donation. But the number of cognitive and affective neuroscience studies of emotional body perception as of today is lower than 20.
Why then have whole bodies and bodily expressions not attracted the attention of researchers so far? The goal of this article is to contribute some elements for an answer to this question. I believe that there is something to learn from the historical neglect of bodies and bodily expressions. I will next address some historical misconceptions about whole-body perception, and in the process I intend not only to provide an impetus for this kind of work but also to contribute to a better understanding of the significance of the affective dimension of behaviour, mind and brain as seen from the vantage point of bodily communication. Subsequent sections discuss available evidence for the neurofunctional basis of facial and bodily expressions as well as neuropsychological and clinical studies of bodily expressions.
Computation of emotions in man and machines
Authors: Robinson Peter , el Kaliouby Rana 
Published: November 2009

The importance of emotional expression as part of human communication has been understood since Aristotle, and the subject has been explored scientifically since Charles Darwin and others in the nineteenth century. Advances in computer technology now allow machines to recognize and express emotions, paving the way for improved human–computer and human–human communications.Recent advances in psychology have greatly improved our understanding of the role of affect in communication, perception, decision-making, attention and memory. At the same time, advances in technology mean that it is becoming possible for machines to sense, analyse and express emotions. We can now consider how these advances relate to each other and how they can be brought together to influence future research in perception, attention, learning, memory, communication, decision-making and other applications.The computation of emotions includes both recognition and synthesis, using channels such as facial expressions, non-verbal aspects of speech, posture, gestures, physiology, brain imaging and general behaviour. The combination of new results in psychology with new techniques of computation is leading to new technologies with applications in commerce, education, entertainment, security, therapy and everyday life. However, there are important issues of privacy and personal expression that must also be considered.
Affective loop experiences: designing for interactional embodiment
Authors: Höök Kristina 
Published: November 2009

Involving our corporeal bodies in interaction can create strong affective experiences. Systems that both can be influenced by and influence users corporeally exhibit a use quality we name anaffective loopexperience. In an affective loop experience, (i) emotions are seen as processes, constructed in the interaction, starting from everyday bodily, cognitive or social experiences; (ii) the system responds in ways that pull the user into the interaction, touching upon end users' physical experiences; and (iii) throughout the interaction the user is an active, meaning-making individual choosing how to express themselves—the interpretation responsibility does not lie with the system. We have built several systems that attempt to create affective loop experiences with more or less successful results. For example,eMotolets users send text messages between mobile phones, but in addition to text, the messages also have colourful and animated shapes in the background chosen through emotion-gestures with a sensor-enabled stylus pen.Affective Diaryis a digital diary with which users can scribble their notes, but it also allows forbodily memorabiliato be recorded from body sensors mapping to users' movement and arousal and placed along a timeline. Users can see patterns in their bodily reactions and relate them to various events going on in their lives.The experiences of building and deploying these systems gave us insights into design requirements for addressing affective loop experiences, such as how to design for turn-taking between user and system, how to create for ‘open’ surfaces in the design that can carry users' own meaning-making processes, how to combine modalities to create for a ‘unity’ of expression, and the importance of mirroring user experience in familiar ways that touch upon their everyday social and corporeal experiences.But a more important lesson gained from deploying the systems is how emotion processes are co-constructed and experienced inseparable from all other aspects of everyday life. Emotion processes are part of our social ways of being in the world; they dye our dreams, hopes and bodily experiences of the world. If we aim to design for affective interaction experiences, we need to place them into this larger picture.
The Hawaiian Bobtail Squid (Euprymna scolopes): A Model to Study the Molecular Basis of Eukaryote-Prokaryote Mutualism and the Development and Evolution of Morphological Novelties in Cephalopods
Authors: Lee Patricia N. , McFall-Ngai Margaret J. , Callaerts Patrick , de Couet H. Gert 
Published: November 2009

INTRODUCTIONThe Hawaiian bobtail squid, Euprymna scolopes, is a cephalopod whose small size, short lifespan, rapid growth, and year-round availability make it suitable as a model organism. E. scolopes is studied in three principal contexts: (1) as a model of cephalopod development; (2) as a model of animal-bacterial symbioses; and (3) as a system for studying adaptations of tissues that interact with light. E. scolopes embryos can be obtained continually and can be reared in the laboratory over an entire generation. The embryos and protective chorions are optically clear, facilitating in situ developmental observations, and can be manipulated experimentally. Many molecular protocols have been developed for studying E. scolopes development. This species is best known, however, for its symbiosis with the luminous marine bacterium Vibrio fischeri and has been used to study determinants of symbiont specificity, the influence of symbiosis on development of the squid light organ, and the mechanisms by which a stable association is achieved. Both partners can be grown independently under laboratory conditions, a feature that offers the unusual opportunity to manipulate the symbiosis experimentally. Molecular and genetic tools have been developed for V. fischeri, and a large expressed sequence tag (EST) database is available for the host symbiotic tissues. Additionally, comparisons between light organ form and function to those of the eye can be made. Both types of tissue interact with light, but have divergent embryonic development. As such, they offer an opportunity to study the molecular basis for the evolution of morphological novelties.
True Yams(Dioscorea):A Biological and Evolutionary Link between Eudicots and Grasses
Authors: Mignouna Hodeba D. , Abang Mathew M. , Asiedu Robert , Geeta R. 
Published: November 2009

INTRODUCTIONDioscorea(true yams) is a large genus that contains species important as food (with edible tubers) or as sources of bioactive substances used in a range of applications.Dioscoreais a major staple food in many parts of the world, especially in West Africa and the Pacific islands, and serves as a famine food in many regions. It is a critically important but neglected crop, which is likely to increase in importance as climate change leads to necessary changes in global food systems. It is a herbaceous, climbing, tropical monocot that looks rather like a dicot, and is part of a lineage that is relatively closely related to the phylogenetically derived group containing the grasses. Therefore, it represents an important biological link between the eudicots and grasses--groups that contain all the model flowering plant species--and has the potential to fill gaps in our knowledge of plant biology and evolution. Yams also offer us the possibility to gain new insights into processes such as tuberization and sex determination, which cannot be studied in current model organisms. This combination of rising importance due to its socioeconomic significance and interesting biology and evolutionary position justify its potential as a model organism. This potential remains to be harnessed, and much of the current work on yam is directed toward its role as a food crop. This aspect will remain important, but its potential for answering questions of basic biological interest will be a major motivation for researchers interested in this organism.
The Embryonic Development of the Hawaiian Bobtail Squid (Euprymna scolopes)
Authors: Lee Patricia N. , Callaerts Patrick , de Couet H. Gert 
Published: November 2009

INTRODUCTIONA staging series based on easily distinguishable morphological features is a basic and necessary tool for developmental studies. It provides a consistent reference for comparisons between independent studies, negates the need to know when fertilization occurred, allows correlation of the phase of development with the time of development (to facilitate collection of embryos at specific stages), and allows comparisons between species. Given the growing interest in Hawaiian bobtail squid (Euprymna scolopes) as a contemporary cephalopod developmental system, this article provides a detailed survey of E. scolopes embryogenesis from cleavage through hatching under controlled environmental conditions, including detailed descriptions of externally visible morphological features that are easily distinguished in either live or freshly fixed embryos under a dissecting microscope. Photomicrographs are also provided to aid in the accurate and rapid staging of E. scolopes embryos.
Labeling Pinocytotic Vesicles and Cytoplasm with Fluorescent Dextrans or Ficolls for Imaging
Authors: Chazotte Brad 
Published: November 2009

INTRODUCTIONThe eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships is of great importance. Dextran, a high-molecular-weight poly-D-glucose, and ficoll, a synthetic polymer of epichlorhydrin and sucrose, are electroneutral, hydrophilic polysaccharides whose size can be varied. This variability in size coupled with their membrane impermeability can make them useful for studying fluid-phase pinocytosis, the size of membrane pores (e.g., nuclear membrane pores), or the environmental conditions and size of a cell compartment. This article presents a method for labeling live or fixed cells with substituted forms of dextran or ficoll attached to a fluorescent conjugate. In the event that the desired probe is not available commercially, this article also provides a method for covalently attaching a fluorophore to substituted polysaccharide.
Phenotypic Analysis of Arabidopsis Mutants: Root Elongation under Salt/Hormone-Induced Stress
Authors: Lee Byeong-ha , Zhu Jian-Kang 
Published: November 2009

INTRODUCTIONAbiotic stress, such as high salt or low temperature, adversely affects plant growth and development. Salt stress inhibits seed germination, retards plant growth, and accelerates senescence. Freezing or drought stress can cause cell damage and plant death. The following parameters can be used to evaluate plant tolerance to salt, drought, or freezing stress: root elongation (described here), fresh weight gain, seed germination, electrolyte leakage, or water loss measurement. Several stress mutants have been characterized using these tests, including hos1 and hos2, which show higher expression of some stress-regulated genes when exposed to low-temperature stress; hos5, which shows higher expression of some stress-regulated genes under abscisic acid (ABA) and salt treatments; sfr mutants, which are deficient in freezing tolerance; and eskimo1, which is constitutively freezing-tolerant. To determine whether a mutant shows altered response to osmotic stress or to specific ions, various concentrations of salts can be used. Mannitol can also be used to impose osmotic stress, and ABA can be used to impose hormone stress. Among the salts used in this protocol, Li+ is considered a toxic analog of Na+, whereas Cs+ is a toxic cation related to K+. The levels of stress suggested in this protocol may need to be adjusted, depending on the ecotype and growth conditions used.
Preparation of Soluble GST Fusion Proteins
Authors: Rebay Ilaria , Fehon Richard G. 
Published: November 2009

INTRODUCTIONA wide variety of plasmid vectors are commercially available for the production of fusion proteins in bacterial cells. Most are also designed to incorporate a tag that allows affinity purification of the expressed fusion protein from bacterial cell extracts. The most commonly used are vectors that incorporate a portion of the glutathione-S-transferase (GST) enzyme that is able to bind to immobilized glutathione and vectors that use a polyhistidine tag which binds immobilized nickel ions with high affinity. This protocol describes preparation of a soluble GST fusion protein, isolated using glutathione agarose beads.
Imaging Synaptogenesis by Measuring Accumulation of Synaptic Proteins: Figure 1.
Authors: Dean Camin , Scheiffele Peter 
Published: November 2009

INTRODUCTIONSynapse formation and modification involve the successive recruitment of pre- and post-synaptic signaling molecules. The procedure presented here investigates the function of specific synaptic factors in gain- and loss-­of-function experiments by measuring protein accumulation at synapses using quantitative immunohistochemistry, confocal microscopy, and image analysis. Although the procedure is described for dissociated cultures of hippocampal neurons, it can be extended to various neuronal cell types in culture.