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PubMed1997

The emergence of the non-cellular phase of life on the fine-grained clayish particles of the early Earth's regolith.

A scenario of the origin of the very first ribonucleoproteinoid virus-like complexes, which is based on their synthesis in the interlaminar spaces of clayish grain regolith of the primitive Earth, about 4 billion years ago when water in the form of liquid drops first appeared. The proposed model explains the origin of chirality of modern biopolymers as a result of preferential adsorption of biomonomers on such grains.

Adsorption↗
PubMed2006

Equivalence of trans paths in ion channels.

We explore stochastic models for the study of ion transport in biological cells. Analysis of these models explains and explores an interesting feature of ion transport observed by biophysicists. Namely, the average time it takes ions to cross certain ion channels is the same in either direction, even if there is an electric potential difference across the channels. It is shown for simple single ion models that the distribution of a path (i.e., the history of location versus time) of an ion crossing the channel in one direction has the same distribution as the time-reversed path of an ion crossing the channel in the reverse direction. Therefore, not only is the mean duration of these paths equal, but other measures, such as the variance of passage time or the mean time a path spends within a specified section of the channel, are also the same for both directions of traversal. The feature is also explored for channels with interacting ions. If a system of interacting ions is in reversible equilibrium (net flux is zero), then the equivalence of the left-to-right trans paths with the time-reversed right-to-left trans paths still holds. However, if the system is in equilibrium, but not reversible equilibrium, then such equivalence need not hold.

Journal Article↗
PubMed2001

Spatial structure and habitat variation in a grasshopper hybrid zone.

A hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae) in northern Spain has been analyzed for variation in morphology and ecology. These species are readily distinguished by the number of stridulatory pegs on the hind femur. Both sexes are fully winged and inhabit disturbed habitats throughout the study area. We develop a maximum-likelihood approach to fitting a two-dimensional cline to geographical variation in quantitative traits and for estimating associations of population mean with local habitat. This method reveals a cline in peg number approximately 30 km south of the Picos de Europa Mountains that shows substantial deviations in population mean compared with the expectations of simple tension zone models. The inclusion of variation in local vegetation in the model explains a significant proportion of the residual variation in peg number, indicating that habitat-genotype associations contribute to the observed spatial pattern. However, this association is weak, and a number of populations continue to show strong deviations in mean even after habitat is included in the final model. These outliers may be the result of long-distance colonization of sites distant from the cline center or may be due to a patchy pattern of initial contact during postglacial expansion. As well as contrasting with the smooth hybrid zones described for Chorthippus parallelus, this situation also contrasts with the mosaic hybrid zones observed in Gryllus crickets and in parts of the hybrid zone between Bombina toad species, where habitat-genotype associations account for substantial amounts of among-site variation.

Animals↗
PubMed2003

Gates and oscillators: a network model of the brain clock.

The suprachiasmatic nuclei (SCN) control circadian oscillations of physiology and behavior. Measurements of electrical activity and of gene expression indicate that these heterogeneous structures are composed of both rhythmic and nonrhythmic cells. A fundamental question with regard to the organization of the circadian system is how the SCN achieve a coherent output while their constituent independent cellular oscillators express a wide range of periods. Previously, the consensus output of individual oscillators had been attributed to coupling among cells. The authors propose a model that incorporates nonrhythmic "gate" cells and rhythmic oscillator cells with a wide range of periods, that neither requires nor excludes a role for interoscillator coupling. The gate provides daily input to oscillator cells and is in turn regulated (directly or indirectly) by the oscillator cells. In the authors' model, individual oscillators with initial random phases are able to self-assemble so as to maintain cohesive rhythmic output. In this view, SCN circuits are important for self-sustained oscillation, and their network properties distinguish these nuclei from other tissues that rhythmically express clock genes. The model explains how individual SCN cells oscillate independently and yet work together to produce a coherent rhythm.

Animals↗
PubMed2001

Correctional officers' intention of accepting or refusing to make HIV preventive tools accessible to inmates.

The aim of this study was to identify the factors which explain correctional officers' intention of accepting or refusing to make HIV preventive tools (condoms, bleach, tattooing equipment, and syringes) accessible to inmates. A total of 957 officers completed a questionnaire that took into account determinants from several social-cognitive behavior theories. The results indicated that only 21.4% of officers were favorable toward making accessible all of the preventive tools. The theoretical model explained 87% of the intention variance, p < .0001. Self-efficacy (beta = .35), personal normative belief (beta = .29), social determinants (beta = .21) and the affective dimension of attitude (beta = .19) were significant determinants. Moreover, officers with a high level of intention differed from those with a low level of intention on several points of the theoretical model. In conclusion, the results clearly indicated that several difficulties must be overcome before HIV preventive tools as a whole can be made accessible to inmates.

Adult↗
PubMed1998

Defective regulation of leukemic hematopoiesis in chronic myeloid leukemia.

Over the last two decades considerable knowledge has been acquired about the distribution of cell types within the dominant leukemic (Ph+/BCR-ABL+) clone that results in human chronic myeloid leukemia (CML). Evidence is now growing to indicate that three key biological changes affecting the development of such clones are: (1) an increased probability of differentiation at the level of the most primitive leukemic stem cells; (2) an increased turnover rate of the leukemic progenitors at all stages of differentiation: and (3) their increased ability to survive under conditions of factor-deprivation. Such a model explains the long latent period for the development of CML as well as why normal stem cells may persist in large numbers but still fail to compete in contributing to the daily output of mature blood cells in patients with disease. The recent development of new genetic and transplant models of human CML may now allow the molecular basis of these biological disturbances to be delineated and more effective therapeutic strategies developed.

Cell Count↗
PubMed2007

A fast biologically inspired algorithm for recurrent motion estimation.

We have previously developed a neurodynamical model of motion segregation in cortical visual area V1 and MT of the dorsal stream. The model explains how motion ambiguities caused by the motion aperture problem can be solved for coherently moving objects of arbitrary size by means of cortical mechanisms. The major bottleneck in the development of a reliable biologically inspired technical system with real-time motion analysis capabilities based on this neural model is the amount of memory necessary for the representation of neural activation in velocity space. We propose a sparse coding framework for neural motion activity patterns and suggest a means by which initial activities are detected efficiently. We realize neural mechanisms such as shunting inhibition and feedback modulation in the sparse framework to implement an efficient algorithmic version of our neural model of cortical motion segregation. We demonstrate that the algorithm behaves similarly to the original neural model and is able to extract image motion from real world image sequences. Our investigation transfers a neuroscience model of cortical motion computation to achieve technologically demanding constraints such as real-time performance and hardware implementation. In addition, the proposed biologically inspired algorithm provides a tool for modeling investigations to achieve acceptable simulation time.

Algorithms↗
PubMed2001

Determinants of physical performance in ambulatory patients on hemodialysis.

BACKGROUND: Physical performance measures, particularly gait speed, have been useful as predictors of loss of independence, institutionalization, and mortality in older nonuremic individuals. Gait speed has not been evaluated as a predictor of these important outcomes in patients on hemodialysis, nor have the determinants of gait speed in the dialysis population been studied. METHODS: We performed a cross-sectional analysis to determine whether demographic, clinical, or nutritional status variables were related to physical performance in a group of 46 hemodialysis patients treated at three University of California San Francisco-affiliated dialysis units. Three physical performance measures were examined, including gait speed, time to climb stairs, and time to rise from a chair five times in succession. Forward stepwise linear-regression analysis was performed with each physical performance measure as the dependent variable and the following candidate predictor variables: age, gender, body mass index, dialysis vintage, Kt/V, albumin, blood urea nitrogen, creatinine, hematocrit, lean body mass, phase angle, ferritin, and the following comorbidities: hypertension, diabetes mellitus, coronary artery disease, peripheral vascular disease, and cerebrovascular disease. RESULTS: Subjects included 31 men and 15 women aged 22 to 87 years (mean +/- SD, 52 +/- 17). The mean gait speed for the group was 113.1 +/- 34.5 cm/s (low compared with norms established for persons of similar age). Results of multivariable regression showed that age, albumin, and Kt/V were important determinants of gait speed in this population. Overall, the model explained 52% of the variability in gait speed (r = 0.72, P < 0.0001). Qualitatively similar results were obtained using stair-climbing time or chair-rising time as the dependent variables, except that comorbidity was more important than age for stair climbing. The addition of physical activity level to the models did not eliminate the associations of albumin or Kt/V with physical performance. CONCLUSIONS: Physical performance is significantly impaired in ambulatory hemodialysis patients and is related to age, serum albumin, and dialysis dose. Prospective studies are needed to determine whether modification of dialysis dose or nutritional interventions can improve physical performance in patients on hemodialysis.

Adult↗
PubMed2003

Modification point depth and genome growth in genetic programming.

The evolutionary computation community has shown increasing interest in arbitrary-length representations, particularly in the field of genetic programming. A serious stumbling block to the scalability of such representations has been bloat: uncontrolled genome growth during an evolutionary run. Bloat appears across the evolutionary computation spectrum, but genetic programming has given it by far the most attention. Most genetic programming models explain this phenomenon as a result of the growth of introns, areas in an individual which serve no functional purpose. This paper presents evidence which directly contradicts intron theories as applied to tree-based genetic programming. The paper then uses data drawn from this evidence to propose a new model of genome growth. In this model, bloat in genetic programming is a function of the mean depth of the modification (crossover or mutation) point. Points far from the root are correspondingly less likely to hurt the child's survivability in the next generation. The modification point is in turn strongly correlated to average parent tree size and to removed subtree size, both of which are directly linked to the size of the resulting child.

Algorithms↗
PubMed1978

The role of uptake of noradrenaline of its positive inotropic effect in relation to muscle geometry. Statistical evaluation.

1. The influence of saturable drug uptake on the drug concentration near the receptor sites was shown theoretically to depend on the geometry of the preparation; increases in the volume/surface ratio (V/S) of the preparation decrease the sensitivity of the preparation to an agonist inactivated in the tissue. 2. The positive inotropic effect of (-)-noradrenaline was found to depend on the ratio V/S of the preparation; papillary muscles with larger V/S were less sensitive to the drug and showed steeper noradrenaline concentration-effect curves. 3. An algorithm for the statistical estimation of the parameters of the saturable uptake process was derived. It was applied to the positive inotropic noradrenaline effect in relation to muscle geometry. As an analysis of variance showed, the model explained a significant proportion of the shift of (-)-noradrenaline concentration-effect curves associated with variation in size of the preparation.

Animals↗
PubMed1982

Arrays of particles in the sarcolemma of the distal accessory flexor muscle of the lobster.

Freeze-fracture of the distal accessory flexor muscle reveals the presence of randomly distributed arrays of P- and E-face particles. The particles are arranged in regularly spaced rows which parallel one another and, in general, the long axis of the muscle fiber. P- and E-face arrays differ in their structure and are apparently complementary. A model explaining the apparent interrelationship of the P- and E-face arrays is presented. The functional significance of the arrays is not known.

Animals↗
PubMed2006

Explaining school children's fruit and vegetable consumption: the contributions of availability, accessibility, exposure, parental consumption and habit in addition to psychosocial factors.

We studied the contributions of parental fruit and vegetable (F&V) consumption, availability and accessibility of F&V in the home, exposure to F&V, and habit, in addition to psychosocial factors, in explaining F&V consumption in 4-12-year-old children. Furthermore, we looked for effect modification by ethnicity and gender. Children's parents (n = 1739) completed a questionnaire assessing psychosocial and additional factors regarding their children's F&V consumption. Consumption was assessed by a food-frequency questionnaire. The model explained the children's F&V consumption better when the additional factors were included (R2 = .49 and R2 = .50 for fruit consumption, and R2 = .33 and R2 = .33 for vegetable consumption). Stepwise multi-level regression analyses revealed that habit was the most influential correlate of F&V consumption. It is concluded that nutrition education interventions aimed at stimulating F&V consumption among children should take into account that the consumption of fruit and that of vegetables are clearly different behaviors, with different influencing factors for boys and girls and children of native or non-native background. Furthermore, interventions to increase F&V consumption should include strategies aimed at making these behaviors habitual.

Adult↗
PubMed2006

Derivation of ozone flux-yield relationships for lettuce: a key horticultural crop.

Ozone flux-response relationships were derived for lettuce, employing a multiplicative approach to model the manner in which stomatal conductance is influenced by key environmental variables, using a dataset collected during field experimentation in Crete and yield-response relationships derived from parallel open-top chamber experiments. Regional agronomic practices were adopted throughout. Computed versus measured data revealed that the derived model explained 51% (P<0.001) of the observed variation in stomatal conductance. Concentration-based indices were compared with flux-based indices. Analyses revealed a significant relationship between accumulated stomatal ozone flux and yield employing flux threshold cut-offs up to 4 nmol m(-2) s(-1). Regressions employing very low or zero flux thresholds resulted in the strongest yield-flux relationships (explaining approximately 80% (P<0.05) of the variation in the dataset).

Crops, Agricultural↗
PubMed1986

Viroid processing: a model involving the central conserved region and hairpin I.

A model is proposed for the processing of oligomeric viroid replication intermediates into monomeric, circular progeny viroids. The model identifies a thermodynamically extremely stable base-paired configuration that partially or completely dimeric, as well as higher, viroid oligomers can assume and postulates that this structure, which involves structural features common to all viroids (the central conserved region and secondary hairpin I), is essential for precise cleavage and ligation. The model explains why recombinant plasmids containing tandem repeats of two or more viroid sequence equivalents are highly infectious when inoculated into viroid-susceptible plants, why certain plasmids containing partially duplicated viroid-specific inserts are less infectious, and why plasmids containing monomeric inserts are noninfectious or at best marginally infectious. The model also accounts for the fact that vector-derived sequences on either or both sides of the viroid sequence(s) of a restriction fragment are precisely excised and are lacking in progeny viroids.

Base Sequence↗
PubMed2005

DNase II is a member of the phospholipase D superfamily.

MOTIVATION: DNase II is an endodeoxyribonuclease involved in apoptosis and essential for the mammalian development. Despite the understanding of biochemical properties of this enzyme, its structure and relationships to other protein families remain unknown. RESULTS: Using protein fold-recognition we found that DNase II exhibits a catalytic domain common to the phospholipase D superfamily. Our model explains the available experimental data and provides the first structural platform for sequence-function analyses of this important nuclease.

Amino Acid Sequence↗
PubMed2000

The polymerase subunit of a dsRNA virus plays a central role in the regulation of viral RNA metabolism.

Bacteriophage &phi;6 has a three-segmented double-stranded (ds) RNA genome, which resides inside a polymerase complex particle throughout the entire life cycle of the virus. The polymerase subunit P2, a minor constituent of the polymerase complex, has previously been reported to replicate both &phi;6-specific and heterologous single-stranded (ss) RNAs, giving rise to dsRNA products. In this study, we show that the enzyme is also able to use dsRNA templates to perform semi-conservative RNA transcription in vitro without the assistance of other proteins. The polymerase synthesizes predominantly plus-sense copies of &phi;6 dsRNA, medium and small segments being more efficient templates than the large one. This distribution of the test-tube reaction products faithfully mimics viral transcription in vivo. Experiments with chimeric ssRNAs and dsRNAs show that short terminal nucleotide sequences can account for the difference in efficiency of RNA synthesis. Taken together, these results suggest a model explaining important aspects of viral RNA metabolism regulation in terms of enzymatic properties of the polymerase subunit.

Bacteriophage phi 6↗
PubMed1985

Impact of environment on state university hospital performance. An explanatory model.

This article, by means of a path model, shows the impact of environment on state university hospital performance. The state environment is shown to affect systematically the intensity of local competition, the reputation of the medical school, the financial independence of the parent university, the allocation of indigent care dollars, the nature of governance and management, and the performance of the hospital. Results show that while certain environments are predictably more supportive of universities and university hospitals, these environments tend also to attract health care competition. Competition is shown to pressure hospitals into greater efficiency, but competition is shown also to hurt viability. But a hospital management that pays attention to the hospital environment is shown to help both efficiency and viability. The model explains respectively 37% and 46% of the variance in hospital efficiency and viability.

Data Collection↗