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PubMed2005

A filter-based evolutionary algorithm for constrained optimization.

We introduce a filter-based evolutionary algorithm (FEA) for constrained optimization. The filter used by an FEA explicitly imposes the concept of dominance on a partially ordered solution set. We show that the algorithm is provably robust for both linear and nonlinear problems and constraints. FEAs use a finite pattern of mutation offsets, and our analysis is closely related to recent convergence results for pattern search methods. We discuss how properties of this pattern impact the ability of an FEA to converge to a constrained local optimum.

Algorithms↗
PubMed2006

An extension of Geiringer's theorem for a wide class of evolutionary search algorithms.

The frequency with which various elements of the search space of a given evolutionary algorithm are sampled is affected by the family of recombination (reproduction) operators. The original Geiringer theorem tells us the limiting frequency of occurrence of a given individual under repeated application of crossover alone for the classical genetic algorithm. Recently, Geiringer's theorem has been generalized to include the case of linear GP with homologous crossover (which can also be thought of as a variable length GA). In the current paper we prove a general theorem which tells us that under rather mild conditions on a given evolutionary algorithm, call it A, the stationary distribution of a certain Markov chain of populations in the absence of selection is unique and uniform. This theorem not only implies the already existing versions of Geiringer's theorem, but also provides a recipe of how to obtain similar facts for a rather wide class of evolutionary algorithms. The techniques which are used to prove this theorem involve a classical fact about random walks on a group and may allow us to compute and/or estimate the eigenvalues of the corresponding Markov transition matrix which is directly related to the rate of convergence towards the unique limiting distribution.

Algorithms↗
PubMed2001

The molecular basis of nuclear genetic code change in ciliates.

BACKGROUND: The nuclear genetic code has changed in several lineages of ciliates. These changes, UAR to glutamine and UGA to cysteine, imply that eukaryotic release factor 1 (eRF1), the protein that recognizes stop codons and terminates translation, changes specificity. Here we test whether changes in eRF1 drive genetic code evolution. RESULTS: Database sequence analysis reveals numerous genetic code alterations in ciliates, including UGA --> tryptophan in Blepharisma americanum and the distantly related Colpoda. We sequenced eRF1 from four ciliates: B. americanum, a heterotrich that independently derived the same eRF1 specificity as Euplotes, and three spirotrichs, Stylonychia lemnae, S. mytilus, and Oxytricha trifallax, that independently derived the same genetic code as Tetrahymena (UAR --> glutamine). Distantly related ciliates with similar codes show characteristic changes in eRF1. We used a sliding window analysis to test associations between changes in specific eRF1 residues and changes in the genetic code. The regions of eRF1 that display convergent substitutions are identical to those identified in a recently reported nonsense suppression mutant screen in yeast. CONCLUSIONS: Genetic code change by stop codon reassignment is surprisingly frequent in ciliates, with UGA --> tryptophan occurring twice independently. This is the first description of this code, previously found only in bacteria and mitochondria, in a eukaryotic nuclear genome. eRF1 has evolved strikingly convergently in lineages with variant genetic codes. The strong concordance with biochemical data indicates that our methodology may be generally useful for detecting molecular determinants of biochemical changes in evolution.

Amino Acid Sequence↗
PubMedDate not supplied

[The point of view of the radiotherapist].

During the last decade, stereotactic radiotherapy has widely improved in France. Thus one should study the present situation and its future trend. QUANTITATIVE NEED: Considering single dose radiotherapy, there are about 900 to 1,000 cases treated per year. However, the trend towards more fractionated treatment will disturb this temporary equilibrium; thus more machine time will be necessary. QUALITATIVE NEED: Stereotactic radiotherapy is practiced by multi-disciplinary teams including physicians, physicists and scientific specialists. Radiotherapists and physicist are responsible for treatment planning and evaluation as well as for clinical and methodological research. Accordingly, they should possess computers, treatment planning systems, etc. Such teams are necessary to carry out complex irradiations. GENERAL EVOLUTION: Fractionation of irradiation nowadays seems mandatory for most intracranial tumors except metastases and small regular arteriovenous malformations. Heterogeneity of lesion dose is related to the geometry and the physics of convergent fixed or mobile beams. It can be improved and the healthy tissue irradiation can be diminished using the multi-isocentric planning for complex lesion or with micro multi leaf collimators. MODALITIES OF STEREOTACTIC RADIOTHERAPY ACCORDING TO LESION TYPE: For neurinomas of the acoustic nerve, fractionated stereotactic radiotherapy yields few of the complications published after single dose stereotactic radiotherapy. The same can be said for meningiomas although some series reported very few complications after single dose stereotactic radiotherapy. Solitary metastases without systemic evolution, not situated on the mid-line, are favorable candidates for palliative single dose stereotactic radiotherapy. The conjunction with total brain irradiation seems to be useful. Small arteriovenous malformations will be treated with single dose stereotactic radiotherapy, whereas voluminous and/or geometrically complex nidus could benefit from protons or photon beams modulated by micro multi leaf collimators and a few fractions. EXTRA-CRANIAL STEREOTACTIC RADIOTHERAPY: Single dose stereotactic radiotherapy and fractionated stereotactic radiotherapy will be used as boost in various situations such as massif facial and in all sorts of tumors in the body specially when lesions are close to critical organs.

Brain Neoplasms↗
PubMed1981

Diet and teeth. Dietary hypotheses and human evolution.

Hypotheses concerning the diet of early hominids have played an important role in discussions on human evolution. Three investigations have helped define the extent to which dietary hypotheses may be taken and still be testable. Comparative anatomy is a fairly coarse approach, which despite convergences allows only the most specialized diets to be ruled out. A biomechanical analysis makes it clear that the changes in jaw and tooth form are subtle and outside the resolution given by present understanding of cranial function. Analysis of the microscopic tooth wear of extant species has been carried out. Major dietary types can be distinguished by their microwear. The microwear on fossil hominids appears to rule out certain diets that have been proposed for them.

Animals↗
PubMed2001

Modularity, evolution, and the binding problem: a view from stability theory.

Any biological object, and specifically the brain, is the result of evolution. Evolution proceeds by accumulation and combination of stable intermediate states-as is well known, survival of the fittest really means survival of the stable. Simple examples abound: for instance, human emotional response involves both a fast archaic loop bypassing the cortex, and a slower cortical loop; motion control architecture in vertebrates is believed to involve combinations of simple motor primitives. However, in themselves, accumulations and combinations of stable elements have no reason to be stable. Hence the hypothesis that evolution will favor a particular form of stability, which automatically guarantees stability in combination. Such a form of stability, which we refer to as 'contraction,' can be characterized mathematically. Thus, contraction theory may help guide functional modeling of the central nervous system, and conversely it provides a systematic method to build arbitrarily complex robots out of simpler elements. Furthermore, contraction theory may shed light on the problem of perceptual unity (binding problem) by providing simple models and conditions for the overall convergence of a large number of specialized processing elements connected through networks of feedback loops.

Biological Evolution↗
PubMed1997

The evolution of eyes.

Eyes are the preeminent source of sensory information for the brain in most species, and many features of eyes reflect evolutionary solutions to particular selective pressures, both from the nonbiological environment and from other animals. As a result, the evolution of eyes, among all the sense organs, has attracted considerable attention from scientists. Paired eyes in the three major phyla, vertebrates, arthropods and mollusks, have long been considered to be classic examples of evolutionary convergence. At the macroscopic level, this must be true since they arise from different tissues and have evolved radically different solutions to the common problem of collecting and focusing light. However, opsin, the light-absorbing receptor protein, has a significant amount of shared DNA sequence homology across the phyla, and recently it has been discovered that some part of ocular development in different phyla is coordinated by a homologous, gene, Pax-6. So, although eyes from diverse phyla are clearly not homologous, neither can they be viewed as resulting solely from convergence. Instead, this shows that homology at the molecular level of organization does not predict homology at the organ or organismic level. The presence of homologous constituent molecules in nonhomologous structures reminds us that molecules are not eyes.

Animals↗
PubMed1990

Body composition and the evolution of the Macropodidae (Potorous, Dendrolagus, and Macropus).

The segmental distribution of body weight and the proportions of skin, muscle, and bone are compared for three genera of the Macropodidae (Potorous, Dendrolagus, and Macropus) and one genus of the Petauridae (Pseudocheirus). Potorous and Macropus possess high proportions of muscle mass to total body weight, high concentrations of musculature in the lumbar extensors, thigh, and tail, and disproportionate ratios of forelimb: hindlimb bone and forelimb: hindlimb muscle which correspond to disproportions of intermembral length. These species converge with high-speed terrestrial runners in some traits and remain distinctive in others. Macropus, larger, more muscular, and faster than Potorous, appears to store and return energy to the hopping cycle more efficiently. Dendrolagus has less than three-fourths the musculature of the other macropod genera, low proportions of the back extensor muscles compared to the other macropods, and relatively more equal ratios of forelimb:hindlimb bone and forelimb:hindlimb muscle. This species converges with slow-moving arboreal climbers such as Pseudocheirus. These data on body mass and tissue proportions translate directly into center of gravity, strength-to-weight ratio, and muscular (kinetic) chains, key elements of macropod evolution. The geometric similarity of muscle between smaller potoroids and larger macropodids, and assumption critical to allometric comparison, is not confirmed.

Adaptation, Biological↗
PubMed2001

Pancreas development in zebrafish: early dispersed appearance of endocrine hormone expressing cells and their convergence to form the definitive islet.

To begin to understand pancreas development and the control of endocrine lineage formation in zebrafish, we have examined the expression pattern of several genes shown to act in vertebrate pancreatic development: pdx-1, insulin (W. M. Milewski et al., 1998, Endocrinology 139, 1440-1449), glucagon, somatostatin (F. Argenton et al., 1999, Mech. Dev. 87, 217-221), islet-1 (Korzh et al., 1993, Development 118, 417-425), nkx2.2 (Barth and Wilson, 1995, Development 121, 1755-1768), and pax6.2 (Nornes et al., 1998, Mech. Dev. 77, 185-196). To determine the spatial relationship between the exocrine and the endocrine compartments, we have cloned the zebrafish trypsin gene, a digestive enzyme expressed in differentiated pancreatic exocrine cells. We found expression of all these genes in the developing pancreas throughout organogenesis. Endocrine cells first appear in a scattered fashion in two bilateral rows close to the midline during mid-somitogenesis and converge during late-somitogenesis to form a single islet dorsal to the nascent duodenum. We have examined development of the endocrine lineage in a number of previously described zebrafish mutations. Deletion of chordamesoderm in floating head (Xnot homolog) mutants reduces islet formation to small remnants, but does not delete the pancreas, indicating that notochord is involved in proper pancreas development, but not required for differentiation of pancreatic cell fates. In the absence of knypek gene function, which is involved in convergence movements, the bilateral endocrine primordia do not merge. Presence of trunk paraxial mesoderm also appears to be instrumental for convergence since the bilateral endocrine primordia do not merge in spadetail mutants. We discuss our findings on zebrafish pancreatogenesis in the light of evolution of the pancreas in chordates.

Amino Acid Sequence↗
PubMed2006

On the application of magic echo cycles for quadrupolar echo spectroscopy of spin-1 nuclei.

Magic echo cycles are introduced for performing quadrupolar echo spectroscopy of spin-1 nuclei. An analysis is performed via average Hamiltonian theory showing that the evolution under chemical shift or static field inhomogeneity can be refocused simultaneously with the quadrupolar interaction using these cycles. Due to the higher convergence in the Magnus expansion, with sufficient RF power, magic echo based quadrupolar echo spectroscopy outperforms the conventional two pulse quadrupolar echo in signal to noise. Experiments highlighting a signal to noise enhancement over the entire bandwidth of the quadrupolar pattern of a powdered sample of deuterated polyethelene are shown.

Algorithms↗
PubMed1985

Levels of association theory.

Three levels of association theory are distinguished: (a) empirical laws relating operationally definable units; (b) theoretical concepts of association, supported by converging lines of evidence; and (c) theories assimilating concepts of association into more elaborate structures. These levels correspond roughly to stages in the evolution of association theory from the mid-19th century to the present. Ebbinghaus's major contribution as a theorist was to accomplish the transition from the first level to the second. The analysis of serial learning in terms of his conception of multiple types of associations may prove to have greater generality than has yet been realized. However, to account for many phenomena of practical and theoretical interest, this model requires augmentation by a control concept that provides a basis for organization beyond serial linkages of units.

Association↗
PubMed2001

Clinical characteristics of double pylorus.

BACKGROUND: Double pylorus can occur as either a congenital abnormality or an acquired complication of peptic ulcer disease. There has been no report of long-term follow-up of a large series of patients treated for double pylorus. The objective of this study was to determine the course of double pylorus in 20 patients by serial endoscopic examination. METHODS: Among 102,958 endoscopic examinations conducted from 1987 to 1999, a diagnosis of double pylorus was made in 20 patients, 18 of whom were followed from 2 months to 10 years. The demographics, clinical presentations, and outcome, as well as endoscopic patterns of double pylorus, were retrospectively reviewed. The rates of ulcer recurrence and symptoms were estimated and compared. RESULTS: Most fistulous rings were located on the lesser curve of the gastric antrum (75%). Evolution from an original ulcer to fistula was observed in 9 patients. The fistula disappeared in 1 patient, remained open in 12, and converged with the normal pyloric ring in 5 patients. One or more associated systemic diseases and extensive treatment with various drugs were noted in 12 patients. Eradication of Helicobacter pylori in infected patients resulted in a lower percentage of patients with symptoms (36% vs. 100%) and ulcer recurrence (55% vs. 100%) compared with uninfected patients, but the differences were not statistically significant. CONCLUSION: In this study, fistula closure did not occur in the majority of patients. Associated systemic diseases and extensive use of medications might be important factors in persistence of double pylorus. Eradication of Helicobacter pylori was not beneficial in terms of relief of symptoms, prevention of ulcer recurrence, and fistula closure. Surgical intervention should be considered for patients with refractory symptoms, recurrent ulcers, and other complications.

Duodenal Diseases↗
PubMed2000

Manipulation of the phenolic chemistry of willows by gall-inducing sawflies.

The ability to induce galls on plants has evolved independently in many insect orders, but the adaptive significance and evolutionary consequences of gall induction are still largely unknown. We studied these questions by analyzing the concentrations of various plant defense compounds in willow leaves and sawfly galls. We found that the galls are probably nutritionally beneficial for the sawfly larvae, because the concentrations of most defensive phenolics are substantially lower in gall interiors than in leaves. More importantly, changes in chemistry occur in a similar coordinated pattern in all studied willow species, which suggests that the insects control the phenolic biosynthesis in their hosts. The resulting convergence of the chemical properties of the galls both within and between host species indicates that the role of plant chemistry in the evolution of host shifts may be fundamentally less significant in gallers than in other phytophagous insects.

Animals↗
PubMed1984

The impact of object relations theory on psychodynamic group therapy.

Object relations theory is seen as a conceptual framework that adds to the classical Freudian structural theory. The synchrony between the two theories is manifest in psychodynamic group psychotherapy. This paper explores the convergence of these theories, emphasizing concepts from object relations theory and focusing on three major aspects as they appear in therapy groups: the evolution of the transference neurosis, group membership as a transitional phenomenon, and group therapy for the resolution of ego-syntonic character pathology. Examples of patients emerging from schizoid to paranoid and then to depressive positions of ego organization illustrate the concepts.

Adult↗
PubMed2004

DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution.

Biological in vitro selection techniques, such as RNA aptamer methods and mRNA display, have proven to be powerful approaches for engineering molecules with novel functions. These techniques are based on iterative amplification of biopolymer libraries, interposed by selection for a desired functional property. Rare, promising compounds are enriched over multiple generations of a constantly replicating molecular population, and subsequently identified. The restriction of such methods to DNA, RNA, and polypeptides precludes their use for small-molecule discovery. To overcome this limitation, we have directed the synthesis of combinatorial chemistry libraries with DNA "genes," making possible iterative amplification of a nonbiological molecular species. By differential hybridization during the course of a traditional split-and-pool combinatorial synthesis, the DNA sequence of each gene is read out and translated into a unique small-molecule structure. This "chemical translation" provides practical access to synthetic compound populations 1 million-fold more complex than state-of-the-art combinatorial libraries. We carried out an in vitro selection experiment (iterated chemical translation, selection, and amplification) on a library of 10(6) nonnatural peptides. The library converged over three generations to a high-affinity protein ligand. The ability to genetically encode diverse classes of synthetic transformations enables the in vitro selection and potential evolution of an essentially limitless collection of compound families, opening new avenues to drug discovery, catalyst design, and the development of a materials science "biology."

Catalysis↗
PubMed1999

Putting More Genetics into Genetic Algorithms.

The majority of current genetic algorithms (GAs), while inspired by natural evolutionary systems, are seldom viewed as biologically plausible models. This is not a criticism of GAs, but rather a reflection of choices made regarding the level of abstraction at which biological mechanisms are modeled, and a reflection of the more engineering-oriented goals of the evolutionary computation community. Understanding better and reducing this gap between GAs and genetics has been a central issue in an interdisciplinary project whose goal is to build GA-based computational models of viral evolution. The result is a system called Virtual Virus (VIV). The VIV incorporates a number of more biologically plausible mechanisms, including a more flexible genotype-to-phenotype mapping. In VIV the genes are independent of position, and genomes can vary in length and may contain noncoding regions, as well as duplicative or competing genes. Initial computational studies with VIV have already revealed several emergent phenomena of both biological and computational interest. In the absence of any penalty based on genome length, VIV develops individuals with long genomes and also performs more poorly (from a problem-solving viewpoint) than when a length penalty is used. With a fixed linear length penalty, genome length tends to increase dramatically in the early phases of evolution and then decrease to a level based on the mutation rate. The plateau genome length (i.e., the average length of individuals in the final population) generally increases in response to an increase in the base mutation rate. When VIV converges, there tend to be many copies of good alternative genes within the individuals. We observed many instances of switching between active and inactive genes during the entire evolutionary process. These observations support the conclusion that noncoding regions serve a positive step in understanding how GAs might exploit more of the power and flexibility of biological evolution while simultaneously providing better tools for understanding evolving biological systems.

Journal Article↗
PubMed1999

Encephalization, adaptation and evolution of chiroptera: A statistical analysis with further evidence for bat monophyly.

As part of a large-scale study on brain morphometrics and adaptations in mammals, we addressed the problem of chiropteran evolution. A specific statistical framework was designed to test which of two competing hypotheses (bat monophyly vs. diphyly) is more strongly supported by quantitative brain data. Our analyses, based on 120 species, revealed that megabats and microbats were more closely related to each other than to primates, and illustrated the convergent adaptations of the brain of bats to similar trophic (i.e. feeding related) niches. Ecologically-corrected characters were then used to derive a new phylogeny which also supports the chiropteran clade. The monophyletic origin of bats is the preferred hypothesis to explain brain quantitative evolution in chiropterans and primates.

Adaptation, Physiological↗
PubMed2002

Lipocalin-type and hematopoietic prostaglandin D synthases as a novel example of functional convergence.

Prostaglandin (PG) D2 is a major PG produced in the central nervous system and is involved in the regulation of sleep and pain responses through DP receptors. It is also actively produced by mast cells, basophils, and Th2 cells, acting as an allergic mediator through DP and CRTH2 receptors. PGD2 is further dehydrated to produce PGJ2, delta12-PGJ2, and 15-deoxy-delta(12,14)-PGJ2, the last being a ligand for the nuclear receptor PPARgamma. PGD synthase (PGDS) catalyzes the isomerization of PGH2 to PGD2 in the presence of sulfhydryl compounds. Two distinct types of PGDS have been identified: one is the lipocalin-type PGDS (L-PGDS); and the other, the hematopoietic PGDS (H-PGDS). We isolated the human and mouse cDNAs and genes for L-PGDS and H-PGDS, determined their X-ray crystallographic structures, examined their tissue distribution profiles and cellular localization, and generated gene-knockout mice and human enzyme-overexpressing transgenic mice. L-PGDS and H-PGDS are quite different from each other, in terms of their amino acid sequence, tertiary structure, evolutional origin, chromosomal and cellular localization, tissue distribution, and also functional relevance. Therefore, L-PGDS and H-PGDS are considered to be a novel example of functional convergence.

Animals↗