Parametric-equation representation of biconcave erythrocytes

The representation of the shape of a biconcave erythrocyte by a set of three parametric equations was achieved by using the expressions that transform the curvilinear coordinates from the disc-cyclide coordinate system [denoted J2R; Moon and Spencer (1988), Field Theory Handbook, Springer-Verlag, Berlin] to Cartesian coordinates. The equations are products of elliptic functions, so the challenge was to relate the three major ’shape-defining’ measurements of the human erythrocyte in Cartesian coordinates to three parameters in the new curvilinear coordinates, to give a realistic representation of the shape of the membrane-surface. The relationships between the coefficients of the Cartesian degree-4 surface that describes the discocyte and the coordinate transformation equations were derived with the aid of Mathematica; and the membrane-surface of the cell was drawn using the ParametricPlot3D function in this ‘package’. By having the erythrocyte shape expressed in its new form it is readily amenable to further transformations that might be used to model those changes in shape that are seen when the cells are immersed in media of various osmolalities, or when they change metabolic ’states’. On the other hand, the relationship between the coefficients of the Cartesian expression for the disc-cyclide surface is relevant to image analysis of erythrocytes, as determined by physical methods that rely on Cartesian imaging ’slices’. These methods include confocal microscopy and various nuclear magnetic resonance microimaging procedures.     

Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space

A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative ‘regmean structure’ is obtained by simulated annealing in torsion angle space with the program CYANA using as input data the experimental restraints, restraints for the atom positions relative to the average Cartesian coordinates, and restraints for the torsion angles relative to the corresponding principal cluster average values of the ensemble. The method was applied to 11 proteins for which NMR structure ensembles are available, and compared to alternative, commonly used simple approaches for selecting a single representative structure, e.g. the structure from the ensemble that best fulfills the experimental and steric restraints, or the structure from the ensemble that has the lowest RMSD value to the average Cartesian coordinates. In all cases our method found a structure in torsion angle space that is significantly closer to the mean coordinates than the alternatives while maintaining the same quality as individual conformers. The method is thus suitable to generate representative single structure representations of protein structure ensembles in torsion angle space. Since in the case of NMR structure calculations with CYANA the single structure is calculated in the same way as the individual conformers except that weak positional and torsion angle restraints are added, we propose to represent new NMR structures by a ‘regmean bundle’ consisting of the single representative structure as the first conformer and all but one original individual conformers (the original conformer with the highest target function value is discarded in order to keep the number of conformers in the bundle constant). In this way, analyses that require a single structure can be carried out in the most meaningful way using the first model, while at the same time the additional information contained in the ensemble remains available.     

French Roots of French Neo-Lamarckisms, 1879–1985

This essay attempts to describe the neo-Lamarckian atmosphere that was dominant in French biology for more than a century. Firstly, we demonstrate that there were not one but at least two French neo-Lamarckian traditions. This implies, therefore, that it is possible to propose a clear definition of a (neo)Lamarckian conception, and by using it, to distinguish these two traditions. We will see that these two conceptions were not dominant at the same time. The first French neo-Lamarckism (1879–1931) was structured by a very mechanic view of natural processes. The main representatives of this first period were scientists such as Alfred Giard (1846–1908), Gaston Bonnier (1853–1922) and Félix Le Dantec (1869–1917). The second Lamarckism – much more vitalist in its inspiration – started to develop under the supervision of people such as Albert Vandel (1894–1980) and Pierre-Paul Grassé (1895–1985). Secondly, this essay suggests that the philosophical inclinations of these neo-Lamarckisms reactivated a very ancient and strong dichotomy of French thought. One part of this dichotomy is a material, physicalist tradition, which started with René Descartes but developed extensively during the 18th and 19th centuries. The other is a spiritual and vitalist reaction to the first one, which also had a very long history, though it is most closely associated with the work of Henri Bergson. Through Claude Bernard, the first neo-Lamarckians tried to construct a mechanical and determinist form of evolutionary theory which was, in effect, a Cartesian theory. The second wave of neo-Lamarckians wanted to reconsider the autonomy and reactivity of life forms, in contrast to purely physical systems.     

Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes

We present what to our knowledge is a new method of optimized torsion-angle normal-mode analysis, in which the normal modes move along curved paths in Cartesian space. We show that optimized torsion-angle normal modes reproduce protein conformational changes more accurately than Cartesian normal modes. We also show that orthogonalizing the displacement vectors from torsion-angle normal-mode analysis and projecting them as straight lines in Cartesian space does not lead to better performance than Cartesian normal modes. Clearly, protein motion is more naturally described by curved paths in Cartesian space.     

Animism,fetishism, and objectivism as strategies for knowing (or not knowing) the world

Animistic or ‘relational’ ontologies encountered in non-Western (i.e. premodern) settings pose a challenge to Western (i.e. modern) knowledge production, as they violate fundamentalassumptions of Cartesian science. Naturalscientists who have tried seriously to incorporate subject-subject relations into their intellectual practice (e.g. Uexküll, Bateson) have inexorably been relegated to the margins. Surrounded by philosophers and sociologists of science (e.g. Latour) announcing the end of Cartesian objectivism, however,late modern or ‘post-modern’ anthropologists discussing animistic understandings of nature will be excused for taking them more seriously than their predecessors. It is incumbent on them to analytically sort out what epistemological options there are, and to ask why pre-modern, modern, and post-modern people will tend to deal with culture/nature or subject/object hybridity in such different ways. Animism, fetishism, and objectivism can be understood as alternative responses to universal semiotic anxieties about where or how to draw boundaries between persons and things.     

Comparability of Cartesian Diver,Gilson, Warburg and Winkler methods of measuring the respiratory rates of aquatic invertebrates in ecological studies

Summary Comparison of Cartesian Diver-Winkler measurements of respiratory rates in larvae of the damselfly Pyrrhosoma nymphula, and Cartesian Diver-Gilson comparisons in the snail Potamopyrgus jenkinsi are descibed. Measurements of oxygen uptake using these different methods do not differ significantly for the same species of animal at the same temperature. Published data likewise suggest that Warburg and Winkler measurements can give similar results.All these methods, therefore, appear to be equally suitable for ecological work, providing they are used carefully and with a sound knowledge of the biology of the animal under investigation.     

An S-Curve-Based Approach of Identifying Biological Sequences

The main idea of S-curve diagram is to assign different angle values (from 0° to 180°) to different nucleotide acid residues or to different protein amino acids, and then according to cos α _j and sin α _j , the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences—the degree of similarity—is put forward on the basis of the S-curve diagram. To put it in detail, the least square approach is first adopted to obtain a straight line equation according to the S-curve diagram, then according to the distance formula of the point to the straight line, the average ratio of square sum for the distance between the S-curve and the straight line is calculated, and finally, the similarity of the biological sequences is presented by the new standard—the degree of similarity. As is shown by the experimental results, the S-curve diagram can better represent biological sequences (such as protein’s) within Cartesian coordinate system, and the mutation point of biological sequence. Thus, it turns out that the new standard—the degree of similarity is of obviously great advantage.     

Coleridge's “Theory of Life”

Coleridge has been seen by some not so much as a poet spoiled by philosophy, but as a philosopher who was also a poet. It could be argued that his major endeavor was an attempt to save the life sciences form the mechanistic interpretation which he saw as the outcome of Lockean “mechanico-corpuscularian” philosophy. This contribution describes that endeavour. It shows its connection to the social circumstances of the time. It discussess its relationship to the poetic sensibility of the “Lake poets” and to the German thought which Coleridge absorbed during and after his sojourn in Gottingen in 1798--99. It describes the nature of his “Theory of Life” as seen not only from the posthumous publication itself, but also from the numerous hints and struggles recorded in his voluminous notebooks, letters and lecture notes. It is concluded that, although never adequately assembled, it forms the only serious attempt to construct a profound alternative to the ultimately mechanistic biology of Charles Darwin and the physiologists of the second half of the century. As such it strongly influenced the young Richard Owen and, as is well known, was eventually overwhelmed by the Darwin-Huxley synthesis of the 1860s. Nevertheless, insofar as Coleridge's concept of life ultimately derived from his ambition to find a way of healing the Cartesian divide, we may wonder whether the recent upsurge in consciousness studies may cause us to look again at his panentheistic ideas and, discarding the obsolete and fanciful metaphysics, recast them into a more acceptable form. This revised version was published online in July 2006 with corrections to the Cover Date.     

Triple-loop model of path control by head direction and place cells

 Arthropods as well as mammals are able to return straight home after a random search excursion under conditions that are designed to exclude all external cues. After a brief clarification of the terminology, two principal systems of information processing that can achieve this performance are introduced and analysed: Polar versus Cartesian path integration. The different demands and achievements of the two systems are confronted with neurophysiological findings on the functioning of the hippocampus, and with a recent comprehensive model of how the hippocampal place cells perform path integration. To connect the neurophysiological findings with the behavior of the animal, a new model is developed. It achieves three functionally diverse performances: maintenance and control of a compass direction, navigation by path integration, and formation of goals by connecting non-spatial features with their location. This is done by three interconnected feedback loops, set by a common reference variable. Their information-processing structure enables the animal not only to home but also to go straight from any stored goal to any other, without explicit representation of the distance between them, and without a topological arrangement of the store. The model explains behaviors not yet understood and predicts still undiscovered performances. Because it allows the isolation of orienting from storing functions yet also shows how they can be connected, the model may help to reconcile conflicting views on the function of the hippocampus. Received: 17 June 1999 / Accepted in revised form: 20 March 2000     

Automated processing of cephalograms, facial photographs and dental casts

An automated methodology has been developed for analyzing cephalograms, facial photographs, and dental models. A digitizer is used as an input device for converting all three forms of data into Cartesian co-ordinates. The data are stored on computer disks for data processing.     

In what sense is contemporary medicine dualistic?

Medicine's inability to humanely respond to the concerns of its patients has often been attributed to its Cartesian dualism of mind and body. More recently, this inability has been ascribed to medicine's penchant for isolating biological disease as its sole proper concern to the exclusion of experienced illness. This dualism of disease and illness is claimed to be an outgrowth of the Cartesian dualism but the differences and similiarities between these two forms of dualism is not clear. This paper seeks to clarify their relationship through an examination of their historical origins.Disease is currently identified and characterized by a process of clinico-pathological correlation. By this means clinical impressions are corrected in light of autopsy findings. Our current mode of clinico-pathological correlation originated in Paris in the early nineteenth century with the work of Xavier Bichat and others. The theory of knowledge implicit within this clinico-pathological approach to the body is described and compared to that of Descartes. Though medicine does pursue certain Cartesian goals for knowledge, such as knowledge of the patient that does not rely upon his candor, it ultimately espouses neither a Cartesian theory of knowledge nor a Cartesian theory of the body. With pathological inquiry modeled after the autopsy as the final word in the identification and characterization of disease, the patient's capacity for self-knowledge and interpretation — not an entity called mind — is isolated away from his body. This approach to the body means that objective evidence of disease is valued to the exclusion of subjective evidence.If the shortcomings of modern biomedicine are to be effectively addressed, not only must the interdependence of disease and illness be acknowledged. The very canons of medical evidence must be revised. Subjective evidence must be rehabilitated and rejuvenated with better methods of subjective clinical investigation. Host factors relevant to the healing and knowing of sickness must be elucidated so that medicine may rediscover the sentience of its patients. Department of Psychiatry and Behavioral Sciences University of Washington Seattle, WA 98195, U.S.A.     

Ion induced deformation of soft tissue

In this paper the effects of changing the ion concentration in and around a sample of soft tissue are investigated. The triphasic theory developed by Laiet al. (1990,Biomechanics of Diarthrodial Joints, Vol. 1, Berlin, Springer-Verlag) is reduced to two coupled partial differential equations involving fluid ion concentration and tissue solid deformation. These equations are given in general form for Cartesian, cylindrical and spherical geometries. After solving the two equations quantities such as fluid velocity, fluid pressure, chemical potentials and chemical expansion stress may be easily calculated. In the Cartesian geometry comparison is made with the experimental and theoretical work of Myerset al. (1984,ASME J. biomech. Engng,106, 151–158). This dealt with changing the ion concentration of a salt shower on a strip of bovine articular cartilage. Results were obtained in both free swelling and isometric tension states, using an empirical formula to acount for ion induced deformation. The present theory predicts lower ion concentrations inside the tissue than this earlier work. A spherical sample of tissue subjected to a change in salt bath ion concentration is also considered. Numerical results are obtained for both hypertonic and hypotonic bathing solutions. Of particular interest is the finding that tissue may contract internally before reaching a final swollen equilibrium state or swell internally before finally contracting. By considering the relative magnitude, and also variation throughout the time course of terms in the governing equations, an even simpler system is deduced. As well as being linear the concentration equation in the new system is uncoupled. Results obtained from the linear system compare well with those from the spherical section. Thus, biological swelling situations may be modelled by a simple system of equations with the possibility, of approximate analytic solutions in certain cases.     

Contrast sensitivity functions to stimuli defined in Cartesian, polar and hyperbolic coordinates

Recent electrophysiological studies indicate that cells in the LGN, V1, V2, and V4 areas in monkeys are specifically sensitive to Cartesian, polar and hyperbolic stimuli. We have characterized the contrast sensitivity functions (CSF) to stimuli defined in these coordinates with the two-alternatives forced-choice paradigm. CSFs to Cartesian, concentric, and hyperbolic stimuli have had similar shapes, with peak sensitivity at approximately 3 c/deg. However, the Cartesian CSF peak sensitivity has been at least 0.1 log units higher than that to stimuli in any other coordinate system. The concentric-Bessel CSF has a low-pass shape, peaking at 1.5 c/deg or below. The radial CSF has a bell shape with maximum sensitivity at 8 c/360 degrees. Only the concentric-Bessel CSF could be explained in terms of the components of maximum amplitude of the Fourier transform. Neural models, which in previous studies predicted the responses to Cartesian and polar Glass patterns, failed to account for the full CSFs data.     

Identifification of Substrate Channels and Protein Cavities

A grid-based algorithm is presented for identifying and displaying channels and cavities in a given protein structure. A point on a regular Cartesian grid is defined to be located in a cavity or a channel if the point has neighbouring grid points in the direction of at least two Cartesian axes, which are located inside the molecule. The cavities or channels can be displayed as clusters of these grid points or as the part of the surface and the amino acid residues lying next to these grid points. The algorithm was tested successfully using the gramicidin A dimer, different cytochrome P450s, and the proteolytic enzyme trypsin.Electronic Supplementary Material available.     

A correction for axis misalignment in the joint angle curves representing knee movement in gait analysis

This paper derives a simple mathematical model relating changes in the orientations of the two Cartesian coordinate systems involved in recording knee movement and the varus-valgus and the internal-external rotation angles for describing the knee's motion. Rotation matrices are given for changing the orientations of the two Cartesian coordinate systems in such a way that the quadratic variations in the varus-valgus and in the external-internal angles are minimal. These estimated rotation matrices are used to correct for axis misalignment. The correction is calibrated by considering the impact of the new orientation of the thigh Cartesian coordinate system on the hip joint angles. The procedure is applied to kinematic data collected on normal subjects. The uncertainty about the specification of the thigh Cartesian coordinate system is shown to explain some of the between subject variability in the varus-valgus and in the internal-external rotation angles curves.     

Advances in Geometric Morphometrics

Geometric morphometrics is the statistical analysis of form based on Cartesian landmark coordinates. After separating shape from overall size, position, and orientation of the landmark configurations, the resulting Procrustes shape coordinates can be used for statistical analysis. Kendall shape space, the mathematical space induced by the shape coordinates, is a metric space that can be approximated locally by a Euclidean tangent space. Thus, notions of distance (similarity) between shapes or of the length and direction of developmental and evolutionary trajectories can be meaningfully assessed in this space. Results of statistical techniques that preserve these convenient properties—such as principal component analysis, multivariate regression, or partial least squares analysis—can be visualized as actual shapes or shape deformations. The Procrustes distance between a shape and its relabeled reflection is a measure of bilateral asymmetry. Shape space can be extended to form space by augmenting the shape coordinates with the natural logarithm of Centroid Size, a measure of size in geometric morphometrics that is uncorrelated with shape for small isotropic landmark variation. The thin-plate spline interpolation function is the standard tool to compute deformation grids and 3D visualizations. It is also central to the estimation of missing landmarks and to the semilandmark algorithm, which permits to include outlines and surfaces in geometric morphometric analysis. The powerful visualization tools of geometric morphometrics and the typically large amount of shape variables give rise to a specific exploratory style of analysis, allowing the identification and quantification of previously unknown shape features.     

Estrogen receptors,antiestrogens, and non-small cell lung cancer

This review considers data on expression of different types of estrogen receptors (ERα and ERβ) in in vitro cultured cells of non-small cell lung cancer and also in human and animal lung tumors. Estrogens are shown to play an important role in genesis and development of non-small cell lung cancer because the estrogen-stimulated cell proliferation as well as antiestrogen-caused inhibition of proliferation occurred only in the cells expressing different types of estrogen receptors. In general, the situation is similar to that observed in breast cancer, but in the cells of non-small cell lung cancer not ERα are expressed in more than half of cases but ERβ. Just estrogen receptors β play the crucial role in inducing cell proliferation in response to estrogens, and ERβ is a prognostic marker of a favorable course of non-small cell lung cancer. Data on the interactions between ER and EGFR signaling pathways, as well as on the additive antitumor effect of antiestrogens (tamoxifen and fulvestrant) combined with tyrosine kinase inhibitors (gefitinib, erlotinib, and vandetanib) are considered. The review also includes data on the influence of estrogens on genesis and development of lung cancer in humans and animals and the frequency of ERα and ERβ expression in non-small cell lung cancer in tissues from patients of the two sexes. Problems of quantitative determination of α and β estrogen receptors in the tumor cells are also discussed.     

Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator.

We have devised a Cartesian combination operator and coding scheme for improving the performance of genetic algorithms applied to the protein folding problem. The genetic coding consists of the C alpha Cartesian coordinates of the protein chain. The recombination of the genes of the parents is accomplished by: (1) a rigid superposition of one parent chain on the other, to make the relation of Cartesian coordinates meaningful, then, (2) the chains of the children are formed through a linear combination of the coordinates of their parents. The children produced with this Cartesian combination operator scheme have similar topology and retain the long-range contacts of their parents. The new scheme is significantly more efficient than the standard genetic algorithm methods for locating low-energy conformations of proteins. The considerable superiority of genetic algorithms over Monte Carlo optimization methods is also demonstrated. We have also devised a new dynamic programming lattice fitting procedure for use with the Cartesian combination operator method. The procedure finds excellent fits of real-space chains to the lattice while satisfying bond-length, bond-angle, and overlap constraints.     

Sexes,species, and genomes: why males and females are not like humans and chimpanzees

This paper describes, analyzes, and critiques the construction of separate “male” and “female” genomes in current human genome research. Comparative genomic work on human sex differences conceives of the sexes as like different species, with different genomes. I argue that this construct is empirically unsound, distortive to research, and ethically questionable. I propose a conceptual model of biological sex that clarifies the distinction between species and sexes as genetic classes. The dynamic interdependence of the sexes makes them “dyadic kinds” that are not like species, which are “individual kinds.” The concept of sex as a “dyadic kind” may be fruitful as a remedy to the tendency to conceive of the sexes as distinct, binary classes in biological research on sex more generally.     

The holistic person; or, the ideology of egalitarianism

Over the past decade and more, Western practices bearing on social life have been marked by a turn against Cartesian dualism. In particular, sociological analysts, political activists, and many ordinary Westerners have come increasingly to advocate an appreciation of the person in terms of the mind-body construed as inextricably one. To account for this, comparative material from Inuit hunter-gatherers and the Western New Age movement is brought to bear. Using this material, the holistic person is interpreted as a discourse about individual moral frailty, ideologically pertinent in societies where egalitarianism of outcome is the dominant cultural ethos. This analysis is related to Giddens's account of 'late modernity', specifically as this is informed by 'life politics'.