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At least 1,513 records · Page 84Linked to original sources
PubMed2000

A new three-dimensional dose distribution reduction scheme for tubular organs.

In tubular structures, spatial aspects of the dose distribution may be important in determining the normal tissue response. Conventional dose-volume-histograms (DVHs) and dose-surface-histograms (DSHs) lack spatial information and may not be adequate to represent the three-dimensional (3D) dose data. A new 3D dose distribution data reduction scheme which preserves its longitudinal and circumferential character is presented. Dose distributions were generated at each axial level for esophagus or rectum in 123 patients with lung cancer or prostate cancer. Dose distribution histograms at each axial level were independently analyzed along the esophageal or rectal circumference to generate dose-circumference-histogram (DCH) sheets. Two types of plots were then generated from the DCH sheet. The first considered the percentage of the circumference at each axial level receiving various doses. The second considered the minimum dose delivered to any percentage of the circumference at each axial level. The DCH as a treatment planning tool can be easily implemented in a 3D planing system and is potentially useful for the study of the relationship between the complication risk and the longitudinal and circumferential dose distributions.

Dose-Response Relationship, Radiation↗
PubMed2002

Necessary conditions for a maximum likelihood estimate to become asymptotically unbiased and attain the Cramer-Rao lower bound. II. Range and depth localization of a sound source in an ocean waveguide.

Analytic expressions for the first order bias and second order covariance of a maximum-likelihood estimate (MLE) are applied to the problem of localizing an acoustic source in range and depth in a shallow water waveguide with a vertical hydrophone array. These expressions are then used to determine necessary conditions on sample size, or equivalently signal-to-noise ratio (SNR), for the localization MLE to become asymptotically unbiased and attain minimum variance as expressed by the Cramer-Rao lower bound (CRLB). These analytic expressions can be applied in a similar fashion to any ocean-acoustic inverse problem involving random data. Both deterministic and completely randomized signals embedded in independent and additive waveguide noise are investigated. As the energy ratio of received signal to additive noise (SANR) descends to the lower operational range of a typical passive localization system, source range and depth estimates exhibit significant biases and have variances that can exceed the CRLB by orders of magnitude. The spatial structure of the bias suggests that acoustic range and depth estimates tend to converge around particular range and depth cells for moderate SANR values.

Environment↗
PubMed2001

Cooperation and competition in the evolution of ATP-producing pathways.

Heterotrophic organisms generally face a trade-off between rate and yield of adenosine triphosphate (ATP) production. This trade-off may result in an evolutionary dilemma, because cells with a higher rate but lower yield of ATP production may gain a selective advantage when competing for shared energy resources. Using an analysis of model simulations and biochemical observations, we show that ATP production with a low rate and high yield can be viewed as a form of cooperative resource use and may evolve in spatially structured environments. Furthermore, we argue that the high ATP yield of respiration may have facilitated the evolutionary transition from unicellular to undifferentiated multicellular organisms.

Adenosine Triphosphate↗
PubMed2001

Tropical origins for recent North Atlantic climate change.

Evidence is presented that North Atlantic climate change since 1950 is linked to a progressive warming of tropical sea surface temperatures, especially over the Indian and Pacific Oceans. The ocean changes alter the pattern and magnitude of tropical rainfall and atmospheric heating, the atmospheric response to which includes the spatial structure of the North Atlantic Oscillation (NAO). The slow, tropical ocean warming has thus forced a commensurate trend toward one extreme phase of the NAO during the past half-century.

Journal Article↗
PubMed2004

Synfire chains and cortical songs: temporal modules of cortical activity.

How can neural activity propagate through cortical networks built with weak, stochastic synapses? We find precise repetitions of spontaneous patterns of synaptic inputs in neocortical neurons in vivo and in vitro. These patterns repeat after minutes, maintaining millisecond accuracy. Calcium imaging of slices reveals reactivation of sequences of cells during the occurrence of repeated intracellular synaptic patterns. The spontaneous activity drifts with time, engaging different cells. Sequences of active neurons have distinct spatial structures and are repeated in the same order over tens of seconds, revealing modular temporal dynamics. Higher order sequences are replayed with compressed timing.

2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-ben↗
PubMed2006

Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens" and "Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans".

Mekel-Bobrov et al. and Evans et al. (Reports, 9 Sept. 2005, p. 1720 and p. 1717, respectively) examined sequence data from modern humans within two gene regions associated with brain development, ASPM and microcephalin, and concluded that selection of these genes must be ongoing. We show that models of human history that include both population growth and spatial structure can generate the observed patterns without selection.

Adaptation, Biological↗
PubMed1991

Animal choice behavior and the evolution of cognitive architecture.

Animals process sensory information according to specific computational rules and, subsequently, form representations of their environments that form the basis for decisions and choices. The specific computational rules used by organisms will often be evolutionarily adaptive by generating higher probabilities of survival, reproduction, and resource acquisition. Experiments with enclosed colonies of bumblebees constrained to foraging on artificial flowers suggest that the bumblebee's cognitive architecture is designed to efficiently exploit floral resources from spatially structured environments given limits on memory and the neuronal processing of information. A non-linear relationship between the biomechanics of nectar extraction and rates of net energetic gain by individual bees may account for sensitivities to both the arithmetic mean and variance in reward distributions in flowers. Heuristic rules that lead to efficient resource exploitation may also lead to subjective misperception of likelihoods. Subjective probability formation may then be viewed as a problem in pattern recognition subject to specific sampling schemes and memory constraints.

Animals↗
PubMed1997

Spatial Variability of Turbulent Mixing in the Abyssal Ocean

Ocean microstructure data show that turbulent mixing in the deep Brazil Basin of the South Atlantic Ocean is weak at all depths above smooth abyssal plains and the South American Continental Rise. The diapycnal diffusivity there was estimated to be less than or approximately equal to 0.1 x 10(-4) meters squared per second. In contrast, mixing rates are large throughout the water column above the rough Mid-Atlantic Ridge, and the diffusivity deduced for the bottom-most 150 meters exceeds 5 x 10(-4) meters squared per second. Such patterns in vertical mixing imply that abyssal circulations have complex spatial structures that are linked to the underlying bathymetry.

Journal Article↗
PubMed1997

Imaging of intermittency in ripple-wave turbulence

The dynamics of a fluid surface filled with high-amplitude ripples were studied with a technique (diffusing light photography) that resolves the height at all locations instantaneously. Even when nonlinearities are strong enough to generate a (Kolmogorov) cascade from long wavelength (where energy is input) to shorter wavelength, the resulting turbulent state contains large coherent spatial structures. The appearance of these structures in a thermal equilibrium state (with the same average energy) would be highly improbable.

Journal Article↗
PubMed1998

Propagating activity patterns in large-scale inhibitory neuronal networks.

The propagation of activity is studied in a spatially structured network model of gamma-aminobutyric acid-containing (GABAergic) neurons exhibiting postinhibitory rebound. In contrast to excitatory-coupled networks, recruitment spreads very slowly because cells fire only after the postsynaptic conductance decays, and with two possible propagation modes. If the connection strength decreases monotonically with distance (on-center), then propagation occurs in a discontinuous manner. If the self- and nearby connections are absent (off-center), propagation can proceed smoothly. Modest changes in the synaptic reversal potential can result in depolarization-mediated waves that are 25 times faster. Functional and developmental roles for these behaviors and implications for thalamic circuitry are suggested.

Feedback↗
PubMed1999

Regular and irregular patterns in semiarid vegetation

Vegetation in many semiarid regions is strikingly patterned, forming regular stripes on hillsides and irregular mosaics on flat ground. A simple model of plant and water dynamics based on ecologically realistic assumptions and with reasonable parameter values captures both of these types of patterns. The regular patterns result from a Turing-like instability; the irregular patterns arise when the ecological dynamics amplify slight small-scale topographic variability. Because of the close agreement between observations and these theoretical results, this system provides a clear example of how nonlinear mechanisms can be important in determining the spatial structure of plant communities.

Journal Article↗
PubMed2000

Reinterpreting space, time lags, and functional responses in ecological models.

Natural enemy-victim interactions are of major applied importance and of fundamental interest to ecologists. A key question is what stabilizes these interactions, allowing the long-term coexistence of the two species. Three main theoretical explanations have been proposed: behavioral responses, time-dependent factors such as delayed density dependence, and spatial heterogeneity. Here, using the powerful moment-closure technique, we show a fundamental equivalence between these three elements. Limited movement by organisms is a ubiquitous feature of ecological systems, allowing spatial structure to develop; we show that the effects of this can be naturally described in terms of time lags or within-generation functional responses.

Animals↗
PubMed2006

Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahía del Tóbari, Mexico.

Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase alpha-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.

Ammonia↗
PubMed2005

Effects of growth in the presence of subinhibitory concentrations of dicloxacillin on Staphylococcus epidermidis and Staphylococcus haemolyticus biofilms.

Low concentrations of antibiotics can inhibit microbial adherence to medical device surfaces. However, little is known about the changes that occur in the physiology of bacteria within biofilms formed in the presence of subinhibitory (sub-MIC) concentrations of antibiotics. In this study, the densities and matrix compositions of biofilms formed by two coagulase-negative Staphylococcus species in the absence and in the presence of sub-MIC concentrations of dicloxacillin were evaluated. Biofilms formed in the presence of sub-MIC concentrations of dicloxacillin contained less biomass, and there were notable changes in the composition of the biofilm matrix. Changes in the spatial structure were also verified by confocal scanning laser microscopy, indicating that biofilms grown in the presence of sub-MIC concentrations of dicloxicilln had a lower cell density. Physiological alterations in the bacteria within biofilms grown in the presence of subinhibitory concentrations of the antibiotic were also evaluated. The results showed that there were differences in bacterial surface characteristics when cultures were grown in the presence of sub-MIC concentrations of dicloxacillin, including decreased hydrophobicity and decreased expression of the exopolysaccharide poly-N-acetylglucosamine. The elemental composition of the cell surface was also analyzed, and whereas in Staphylococcus epidermidis there were decreases in the oxygen and nitrogen contents, in Staphylococcus haemolyticus there were increases in these two parameters. Additionally, increases in resistance to several antibiotics were observed for the cells within biofilms formed in the presence of dicloxacillin.

Biofilms↗
PubMed2006

RNA-protein interactions at the initial and terminal stages of protein biosynthesis as investigated by Lev Kisselev (on the occasion of his 70th anniversary).

This review highlights studies by Lev L. Kisselev and his colleagues on the initial and terminal stages of protein biosynthesis, which cover the period of the last 45 years (1961-2006). They investigated spatial structure of tRNAs, structure and functions of aminoacyl-tRNA-synthetases of higher organisms, and the final step of protein synthesis, termination of translation. L. Kisselev and his team have made three major contributions to these fields of molecular biology; (i) they proposed the hypothesis on the role of anticodon triplet of tRNA in recognition by cognate aminoacyl-tRNA synthetase, which has been experimentally confirmed and is now included in textbooks; (ii) identified primary structures and functions of two eukaryotic protein factors (eRF1 and eRF3) playing a pivotal role in translation termination; (iii) characterized a structural basis for stop codon recognition by eRF1 within the ribosome and discovered the negative structural elements of eRF1, limiting its recognition of one or two stop-codons.

Amino Acyl-tRNA Synthetases↗
PubMedDate not supplied

[Noncoding sequences of the eukaryotic genome as an additional protection of genes from chemical mutagens].

A quantitative model was developed that detects a new function of noncoding sequences in the eukaryotic genome, namely, the protection of coding sequences from chemical (mainly endogenous) mutagens. It was shown that, under common ecological conditions, the number of nucleotides damaged by mutagens in coding sequences of the genome is inversely proportional to the size of their noncoding counterparts. Noncoding sequences can differently protect single genetic loci from chemical mutagens by the formation of specific spatial structures of the protected loci in the interphase nuclei. The significant differences in genome sizes between species (paradox C) can be explained by different contributions of noncoding sequences to the total effect of genome protection from endogenous chemical mutagens.

Animals↗
PubMed2002

Stripe patterns in the magnetic reorientation of a glass-forming nematic liquid crystal.

We study spontaneous pattern formation in a glass-forming nematic liquid crystal during the magnetically induced dynamic Fréedericksz transition. Pattern growth rates and wavelengths as functions of the magnetic field are extracted from optical transmission textures of thin planar cells. The characteristics of the observed stripe pattern can be related to viscoelastic parameters of the nematic by means of a linear stability analysis of director fluctuation modes. The viscous properties of the material allow to vary the time scales of the experiment with temperature by orders of magnitude, leaving the spatial structure of the pattern essentially unchanged. We find that the ratios of shear and rotational viscosity coefficients relevant for the pattern wavelength selection remain constant in the temperature range investigated, whereas their absolute values change by almost two orders.

Journal Article↗
PubMed1995

Transcription factors and pattern formation in the developing lung.

During development of the respiratory tract embryonic cells are instructed to organize themselves along an axis and differentiate, such that proximal structures (trachea) greatly differ from those in distal alveoli. Pattern formation relates to this process of organization, and it is believed to be transcriptionally regulated in many developmental systems. Although the lung is the site of expression of many transcription factors, such as Hox, retinoid receptors, hepatocyte nuclear factors, and myc, among others, little information is available on how they influence lung pattern. Functional studies so far have directly implicated the product of the protooncogene N-myc and the retinoic acid receptors as transcriptional regulators of lung patterning, and it is likely that tissue-specific homeobox genes, such as the thyroid transcription factor-1, play an important role in distal lung formation. This review describes several aspects of transcription factors possibly involved in lung patterning, including structure, spatial distribution, and their putative functions.

Aging↗