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PubMed2005

The slow-scale stochastic simulation algorithm.

Reactions in real chemical systems often take place on vastly different time scales, with "fast" reaction channels firing very much more frequently than "slow" ones. These firings will be interdependent if, as is usually the case, the fast and slow reactions involve some of the same species. An exact stochastic simulation of such a system will necessarily spend most of its time simulating the more numerous fast reaction events. This is a frustratingly inefficient allocation of computational effort when dynamical stiffness is present, since in that case a fast reaction event will be of much less importance to the system's evolution than will a slow reaction event. For such situations, this paper develops a systematic approximate theory that allows one to stochastically advance the system in time by simulating the firings of only the slow reaction events. Developing an effective strategy to implement this theory poses some challenges, but as is illustrated here for two simple systems, when those challenges can be overcome, very substantial increases in simulation speed can be realized.

Journal Article↗

PubMed1994

Cytomegalovirus colitis in HIV-1-infected patients: a prospective research in 55 patients.

OBJECTIVE: To determine criteria for the diagnosis of cytomegalovirus (CMV) colitis and to analyse stages of the course and prognosis of CMV colonic involvement in HIV-1-infected patients. DESIGN: Prospective search for CMV colonic involvement with systematic biopsies to search for CMV intranuclear inclusion bodies and for CMV culture. The evolution of CMV colonic involvement was estimated using further coloscopies and autopsy. SETTING: Infectious diseases department in a tertiary referral teaching hospital in Paris, France. PARTICIPANTS: Fifty-five consecutive patients with HIV-1 infection, who had not previously received anti-CMV drugs, and who had at least one coloscopy performed. RESULTS: According to initial coloscopy, colitis, either ulcerative or inflammatory, was found in nine (16%) out of the 55 patients, CMV intranuclear inclusions were present in the colon of four (7%) patients, and colonic cultures were positive for CMV in 15 (27%) patients. The results of the initial coloscopy showed a positive correlation between endoscopic colitis (either ulcerative or inflammatory), CMV inclusions and positive CMV culture from colonic biopsies. The absence of endoscopic ulcerative lesions had a 98% (49 out of 50) negative predictive value for recording CMV inclusions in the colon (95% confidence interval, 89-100). CMV inclusions were recorded in three out of five ulcerative colitis. Male homosexuality, HIV-1 infection stages IVB, C1, D or E, according to the Centers for Disease Control and Prevention classification, CD4 lymphocyte count < 200 x 10(6)/l and CMV viraemia also correlated positively with CMV colonic involvement. During the observation period (mean, 7.3 months), the estimated incidence of CMV colitis according to coloscopic studies was 13%. Deterioration in condition was the most frequent spontaneous evolution of CMV colonic infection, whereas anti-CMV treatment resulted in an improvement. Ulcerative lesions occurred earlier in patients with colonic CMV inclusions or positive colonic CMV culture than in patients without CMV colonic involvement at the initial coloscopy. CMV colitis occurred late in the course of HIV-1 infection, on average 4 months before death. The presence of CMV inclusions was an indicator of poor prognosis with earlier occurrence of CMV viraemia and retinitis and no survival after 9 months. CONCLUSIONS: These results confirm that the colon is a target organ for CMV in HIV-1-infected patients. Coloscopy should be used to diagnose CMV colitis, because of the close correlation between endoscopic and histological data (i.e., intranuclear inclusions). This combination allows us to propose an evolutive staging of CMV colonic involvement and provide stratification criteria to assess the efficacy of anti-CMV drugs.

AIDS-Related Opportunistic Infections↗

PubMed2005

Influence of chain length on the alpha-beta bifurcation in oligomeric glass formers.

A series of oligo(propylene glycol) dimethyl ethers has been investigated using dielectric spectroscopy in order to relate features of the glass transition dynamics to the number of monomer units N in the chain. The results show that (i) when scaled with the glass transition temperature, the beta relaxations systematically become faster for larger N whereas the alpha relaxations display nearly identical temperature evolutions, i.e., the alpha-beta bifurcation shifts towards shorter times for larger N, (ii) the bifurcation scenario displays a crossover in behavior at N approximately 10 monomer units, signaling the transition from oligomeric to polymeric behavior, and (iii) the beta relaxation has a cooperative nature.

Journal Article↗

PubMed2006

Clonal and non-clonal chromosome aberrations and genome variation and aberration.

The theoretical view that genome aberrations rather than gene mutations cause a majority of cancers has gained increasing support from recent experimental data. Genetic aberration at the chromosome level is a key aspect of genome aberration and the systematic definition of chromosomal aberrations with their impact on genome variation and cancer genome evolution is of great importance. However, traditionally, efforts have focused on recurrent clonal chromosome aberrations (CCAs). The significance of stochastic non-clonal chromosome aberrations (NCCAs) is discussed in this paper with emphasis on the simple types of NCCAs that have until recently been considered "non-significant background". Comparison of various subtypes of transitional and late-stage CCAs with simple and complex types of NCCAs has uncovered a dynamic relationship among NCCAs, CCAs, overall genomic instability, and karyotypic evolution, as well as the stochastic nature of cancer evolution. Here, we review concepts and methodologies to measure NCCAs and discuss the possible causative mechanism and consequences of NCCAs. This study raises challenging questions regarding the concept of cancer evolution driven by stochastic chromosomal aberration mediated genome irregularities that could have repercussions reaching far beyond cancer and organismal genomes.

Chromosome Aberrations↗

PubMed1976

Chromosome banding pattern relationships of hares, rabbits, and pikas (order Lagomorpha). A phyletic interpretation.

The chromosome banding patterns of the domestic rabbit, Oryctolagus cuniculus, the brush rabbit, Sylvilagus bachmani, and the snowshoe hare, Lepus americanus, are nearly identical except for minor differences in the amount of constitutive heterochromatin present. The major mechanisms of chromosome evolution in leporid lagomorphs are centric fusion and addition of heterochromatin. The G- and C-banding patterns of the pika, Ochotona princeps, revealed little easily recognized structural homology with the leporid species. Several tentative banding pattern matches were found for segments of some chromosomes of Ochotona, indicating that tandem fusions may have been responsible for structural modification of the early lagomorph genome. Chromosome evolution in the lagomorphs and the use of chromosomal data in studies of mammalian systematics are discussed.

Animals↗

PubMed1996

Ultra-rapid and ultradian cycling in bipolar affective illness.

BACKGROUND: Rapid-cycling bipolar disorder is defined as four or more affective episodes yearly. The conventionally recognised limit in episode duration is usually considered 24 hours (i.e. a cycle duration of 48 hours). We report a small series of intensively observed bipolar patients who showed much faster patterns of mood oscillation. METHODS: Detailed, systematic, longitudinal assessment of five bipolar patients during extended in-patient psychiatric evaluation were conducted, including retrospective life charting and prospective evaluation of daily mood by self and blinded observer ratings, and motor activity recording. RESULTS: Our data demonstrate a spectrum of cycling frequencies in rapid-cyclers, including distinct, clinically robust mood shifts that occur at frequencies faster than once per 24 hours. Affective oscillations spanned a range of cycling frequencies from four episodes per year (rapid cycling) to those occurring within the course of weeks to several days (ultra-rapid cycling), to distinct, abrupt mood shifts of less than 24 hours duration (ultra-ultra rapid or ultradian cycling). The time of onset and duration of these ultradian affective fluctuations are highly variable and they are observed in bipolar patients without evidence of personality disorder. CONCLUSIONS: The potential clinical and theoretical implications of these first systematic observations of ultra-rapid and ultradian cycling in the context of the evolution of otherwise classical bipolar affective illness are discussed.

Adult↗

PubMedDate not supplied

[Patterns of intraspecific variability in carp fishes of the dace subfamily: ecological factors and pathways of phenotypic transformation].

The inverstigation of geographical and ecological variations of wide-spread species of daces allows to reveal regular patterns of phenotypic transformations with limited number of their possible ways. The set of characters involved and the directions of their changes are specific for both examined taxa and putative factors of subspeciation. Two basic groups of evolutionary and ecological situations leading to the intensive intraspecific divergence are considered: living or spawning in brackish water and heavy anthropogeneous pollution. Striking morphological similarity was found between populations from zones of hydrochemical anomalies and some remote populations inhabiting non-polluted fresh water bodies. The author discusses possible nature of these isomorphisms and cases of regular phenotype transformation and their implications for microevolutionary and systematic studies in fish. The data obtained suggest key role of water mineralization in evolution of the subfamily of dace fish.

Animals↗

PubMed1996

[The problem of systemic mutation].

The problems of the rearrangement of genome architecture during speciation are considered. The history of the problem of the role of systemic mutations in evolution is analyzed. The author's own phenomenological data on the spatial rearrangement of the chromosomal apparatus of germline tissue (that is regarded as systemic mutations) during the phylogeny of a number of dipterous insects are systematized. A concept on the essence of systemic mutations and their crucial role in saltatory transformation of genomes in the course of species evolution is advanced.

Animals↗

PubMed1982

[Historic and functional biology: the inadequacy of a system theory of evolution].

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and the important historical questions of evolutionary biology in its scientific context is recommended.

Animals↗

PubMed2002

Shallow genomics, phylogenetics, and evolution in the family Drosophilidae.

The effects of the genomic revolution are beginning to be felt in all disciplines of the biological sciences. Evolutionary biology in general, and phylogenetic systematics in particular, are being revolutionized by these advances. The advent of rapid nucleotide sequencing techniques have provided phylogenetic biologists with the tools required to quickly and efficiently generate large amounts of character information. We use family Drosophilidae as a model system to study phylogenetics and genome evolution by combining high throughput sequencing methods from the field genomics and standard phylogenetic methodology. This paper presents preliminary results from this work. Separate data partitions, based on either gene function or linkage group, are compared to a combined analysis of all the data to assess support on phylogenetic trees.

Animals↗

PubMed1996

[Magnetic resonance tomography of vasogenic brain edema in animal experiments].

PURPOSE: To systematically evaluate modern magnetic resonance imaging (MRI) techniques of studying brain oedema, an animal model of vasogenic oedema is needed. MATERIAL AND METHODS: We developed such a model by stereotactically cannulating the caudate nucleus in 11 Wistar-rats and infusing a solution of albumin. The way the oedema developed was imaged by MRI and then correlated histologically (three animals) and macroscopically after infusion of Evans' blue (two animals). RESULTS: The extension of the infusion oedema was the same in both MRI and histology as well as at direct inspection of the specimen after infusion of Evans blue. With continuous acquisition of T1-weighted images after infusion of a 1% solution of Gd-DTPA we were able to demonstrate the dynamics of oedema evolution and bulk flow. CONCLUSION: We believe that this infusion oedema is a suitable model for systematically investigating both signal behaviour and pathogenesis of vasogenic brain oedema by MRI.

Animals↗

PubMed1999

Variable and invariable DNA repeat characters revealed by taxonprint approach are useful for molecular systematics.

A specially optimized restriction analysis of highly repetitive DNA elements, called DNA taxonprint, was applied for phylogenetic study of primates and lizards. It was shown that electrophoretic bands of DNA repeats revealed by the taxonprint technique have valuable properties for molecular systematics. Approximately half of taxonprint bands (TB) are invariable and do not disappear from the genomes during evolution or change spontaneously. Presumably these invariable bands are restriction fragments of dispersed DNA repeats. Another group represents variable taxonprint bands that differ even between closely related species. These variable bands are probably represented by tandem DNA repeats and could be used as species-specific markers. It was shown that taxonprint bands are independent characters since the appearance of a new taxonprint band does not change the previous band pattern. Phylogenetic reconstruction carried out on taxonprint data demonstrated that this approach could be of general utility for molecular systematics and species identification.

Animals↗

PubMed2006

Paleobiology and comparative morphology of a late Neandertal sample from El Sidron, Asturias, Spain.

Fossil evidence from the Iberian Peninsula is essential for understanding Neandertal evolution and history. Since 2000, a new sample approximately 43,000 years old has been systematically recovered at the El Sidrón cave site (Asturias, Spain). Human remains almost exclusively compose the bone assemblage. All of the skeletal parts are preserved, and there is a moderate occurrence of Middle Paleolithic stone tools. A minimum number of eight individuals are represented, and ancient mtDNA has been extracted from dental and osteological remains. Paleobiology of the El Sidrón archaic humans fits the pattern found in other Neandertal samples: a high incidence of dental hypoplasia and interproximal grooves, yet no traumatic lesions are present. Moreover, unambiguous evidence of human-induced modifications has been found on the human remains. Morphologically, the El Sidrón humans show a large number of Neandertal lineage-derived features even though certain traits place the sample at the limits of Neandertal variation. Integrating the El Sidrón human mandibles into the larger Neandertal sample reveals a north-south geographic patterning, with southern Neandertals showing broader faces with increased lower facial heights. The large El Sidrón sample therefore augments the European evolutionary lineage fossil record and supports ecogeographical variability across Neandertal populations.

Anatomy, Comparative↗

PubMed2002