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1.
Signal processing in the cerebral cortex is thought to involve a common multi-purpose algorithm embodied in a canonical cortical
micro-circuit that is replicated many times over both within and across cortical regions. Operation of this algorithm produces
widely distributed but coherent and relevant patterns of activity. The theory of Coherent Infomax provides a formal specification
of the objectives of such an algorithm. It also formally derives specifications for both the short-term processing dynamics
and for the learning rules whereby the connection strengths between units in the network can be adapted to the environment
in which the system finds itself. A central assumption of the theory is that the local processors can combine reliable signal
coding with flexible use of those codes because they have two classes of synaptic connection: driving connections which specify
the information content of the neural signals, and contextual connections which modulate that signal processing. Here, we
make the biological relevance of this theory more explicit by putting more emphasis upon the contextual guidance of ongoing
processing, by showing that Coherent Infomax is consistent with a particular Bayesian interpretation for the contextual guidance
of learning and processing, by explicitly specifying rules for on-line learning, and by suggesting approximations by which
the learning rules can be made computationally feasible within systems composed of very many local processors. 相似文献
2.
An important question in cell biology is whether cells are able to measure size, either whole cell size or organelle size. Perhaps cells have an internal chemical representation of size that can be used to precisely regulate growth, or perhaps size is just an accident that emerges due to constraint of nutrients. The eukaryotic flagellum is an ideal model for studying size sensing and control because its linear geometry makes it essentially one-dimensional, greatly simplifying mathematical modeling. The assembly of flagella is regulated by intraflagellar transport (IFT), in which kinesin motors carry cargo adaptors for flagellar proteins along the flagellum and then deposit them at the tip, lengthening the flagellum. The rate at which IFT motors are recruited to begin transport into the flagellum is anticorrelated with the flagellar length, implying some kind of communication between the base and the tip and possibly indicating that cells contain some mechanism for measuring flagellar length. Although it is possible to imagine many complex scenarios in which additional signaling molecules sense length and carry feedback signals to the cell body to control IFT, might the already-known components of the IFT system be sufficient to allow length dependence of IFT? Here we investigate a model in which the anterograde kinesin motors unbind after cargo delivery, diffuse back to the base, and are subsequently reused to power entry of new IFT trains into the flagellum. By mathematically modeling and simulating such a system, we are able to show that the diffusion time of the motors can in principle be sufficient to serve as a proxy for length measurement. We found that the diffusion model can not only achieve a stable steady-state length without the addition of any other signaling molecules or pathways, but also is able to produce the anticorrelation between length and IFT recruitment rate that has been observed in quantitative imaging studies. 相似文献
3.
Bassidy Dembele Avner Friedman Abdul-Aziz Yakubu 《Bulletin of mathematical biology》2010,72(4):914-930
In this paper, we introduce a deterministic malaria model for determining the drug administration protocol that leads to the
smallest first malaria episodes during the wet season. To explore the effects of administering the malaria drug on different
days during the wet season while minimizing the potential harmful effects of drug overdose, we define 40 drug administration
protocols. Our results fit well with the clinical studies of Coulibaly et al. at a site in Mali. In addition, we provide protocols
that lead to smaller number of first malaria episodes during the wet season than the protocol of Coulibaly et al. 相似文献
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We consider the estimation of a nonparametric smooth function of some event time in a semiparametric mixed effects model from
repeatedly measured data when the event time is subject to right censoring. The within-subject correlation is captured by
both cross-sectional and time-dependent random effects, where the latter is modeled by a nonhomogeneous Ornstein–Uhlenbeck
stochastic process. When the censoring probability depends on other variables in the model, which often happens in practice,
the event time data are not missing completely at random. Hence, the complete case analysis by eliminating all the censored
observations may yield biased estimates of the regression parameters including the smooth function of the event time, and
is less efficient. To remedy, we derive the likelihood function for the observed data by modeling the event time distribution
given other covariates. We propose a two-stage pseudo-likelihood approach for the estimation of model parameters by first
plugging an estimator of the conditional event time distribution into the likelihood and then maximizing the resulting pseudo-likelihood
function. Empirical evaluation shows that the proposed method yields negligible biases while significantly reduces the estimation
variability. This research is motivated by the project of hormone profile estimation around age at the final menstrual period
for the cohort of women in the Michigan Bone Health and Metabolism Study. 相似文献
6.
《Biotechnic & histochemistry》2013,88(2):148-153
Formalin has long been the standard fixative for clinical routines worldwide. After the Formaldehyde Standard became law in the US in 1987, as a result of increasing concerns about the potential carcinogenicity of formaldehyde, attempts have been made to find safer alternatives. Alcoholic formalin is a useful fixative, because in addition to fixation, dehydration also is begun. For centuries, honey has been known to be an antibacterial agent with the potential to preserve compounds without harmful effects on its users. We compared the effects of honey fixation with other routine fixatives using conventional histochemical and immunohistochemical staining methods. Our results demonstrated that tissues fixed in either honey or alcoholic formalin and 10% neutral buffered formalin (NBF) have similar histomorphology. Honey fixation showed minor histomorphological differences among the various tissues; however, it did not influence affect correct diagnostic conclusions. Our results suggested that honey can be used as a safe alternative to formalin in histopathology. 相似文献
7.
Kankshita Swaminathan Magdy S Alabady Kranthi Varala Emanuele De Paoli Isaac Ho Dan S Rokhsar Aru K Arumuganathan Ray Ming Pamela J Green Blake C Meyers Stephen P Moose Matthew E Hudson 《Genome biology》2010,11(2):1-18
Background
Miscanthus × giganteus (Mxg) is a perennial grass that produces superior biomass yields in temperate environments. The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid.Results
A survey of the complex Mxg genome was conducted using 454 pyrosequencing of genomic DNA and Illumina sequencing-by-synthesis of small RNA. We found that the coding fraction of the Mxg genome has a high level of sequence identity to that of other grasses. Highly repetitive sequences representing the great majority of the Mxg genome were predicted using non-cognate assembly for de novo repeat detection. Twelve abundant families of repeat were observed, with those related to either transposons or centromeric repeats likely to comprise over 95% of the genome. Comparisons of abundant repeat sequences to a small RNA survey of three Mxg organs (leaf, rhizome, inflorescence) revealed that the majority of observed 24-nucleotide small RNAs are derived from these repetitive sequences. We show that high-copy-number repeats match more of the small RNA, even when the amount of the repeat sequence in the genome is accounted for.Conclusions
We show that major repeats are present within the triploid Mxg genome and are actively producing small RNAs. We also confirm the hypothesized origins of Mxg, and suggest that while the repeat content of Mxg differs from sorghum, the sorghum genome is likely to be of utility in the assembly of a gene-space sequence of Mxg. 相似文献8.
This paper studies a class of dynamical systems that model multi-species ecosystems. These systems are ‘resource bounded’
in the sense that species compete to utilize an underlying limiting resource or substrate. This boundedness means that the
relevant state space can be reduced to a simplex, with coordinates representing the proportions of substrate utilized by the
various species. If the vector field is inward pointing on the boundary of the simplex, the state space is forward invariant
under the system flow, a requirement that can be interpreted as the presence of non-zero exogenous recruitment. We consider
conditions under which these model systems have a unique interior equilibrium that is globally asymptotically stable. The
systems we consider generalize classical multi-species Lotka–Volterra systems, the behaviour of which is characterized by
properties of the community (or interaction) matrix. However, the more general systems considered here are not characterized
by a single matrix, but rather a family of matrices. We develop a set of ‘explicit conditions’ on the basis of a notion of
‘uniform diagonal dominance’ for such a family of matrices, that allows us to extract a set of sufficient conditions for global
asymptotic stability based on properties of a single, derived matrix. Examples of these explicit conditions are discussed. 相似文献
9.
Proton magnetic resonance and chemical reactivity studies have demonstrated the presence of a tyrosine charge relay system in angiotensin which is analogous to the serine charge relay system present at the active site of serine proteases. Receptor activation by angiotensin can be explained by electronic effects deriving from an interaction of the charge relay system with stacking of the histidine and phenylalanine rings. Experiments with serine protease inhibitors suggest the possibility that mechanistic features of the interaction of angiotensin with its receptors may apply to other phenoxyl hormones including certain peptides, steroids and catecholamines. 相似文献
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Known high nitrogen utilization efficiency (NUE1, biomass per unit plant N) China lines of sorghum, China 17 and San Chi San, were compared with relatively low NUE1 U.S. lines, CK60 and Tx623, for both their physiological and biochemical adaptations to tolerate an imposed N stress in the greenhouse. Assimilation efficiency indices (ACi) were significantly greater for the China lines than the U.S. lines at both low and high soil nitrogen levels by about two-fold. Chlorophyll levels in leaves of high NUE1 lines were lower at both soil N treatments. Immunoblots of leaf extracts of sorghum subjected to N stress indicated reduced levels of both phosphoenolpyruvate carboxylase (PEPcase) and ribulose 1,5-bisphosphate carboxylase (Rubisco) while NADP-malic enzyme levels, in general, appear not to be affected. However, NUE1 China line, China 17, retained a significantly greater PEPcase activity than the less-NUE1 U.S. lines, and also the NUE1 China line San Chi San, when grown under N stress conditions. This suggests that PEPcase and enzymes associated with phosphoenolpyruvate synthesis, perhaps, are significant factors in maintaining relatively high photosynthesis under N stress. Carbon isotope ratios of leaves from sorghum genotypes, as indicated by 13C values, became less negative when sorghum plants were grown under N stress, but a genotypic variation either at a low or high N was not observed. 相似文献
13.
The findings on the navigational mechanisms of homing pigeons and the available data on those of wild birds, in particular migrants, are compared. There are important parallels in the use of the magnetic field and the sun for directional orientation. Also the findings on the navigational ‘map’, its preferred use by experienced birds and the strategy of using route information to acquire the necessary knowledge to establish the ‘map’, obtained in pigeons studies, can probably be generalized to wild birds and migrants in their home region. It seems that birds share a common navigational system. Special development of migratory birds, however, is the innate migration program that enables young first‐time migrants to reach their still unknown wintering area. 相似文献
14.
Martin Bock Amit Kumar Tyagi Jan-Ulrich Kreft Wolfgang Alt 《Bulletin of mathematical biology》2010,72(7):1696-1731
Voronoi tessellations have been used to model the geometric arrangement of cells in morphogenetic or cancerous tissues, however,
so far only with flat hyper-surfaces as cell-cell contact borders. In order to reproduce the experimentally observed piecewise
spherical boundary shapes, we develop a consistent theoretical framework of multiplicatively weighted distance functions,
defining generalized finite Voronoi neighborhoods around cell bodies of varying radius, which serve as heterogeneous generators
of the resulting model tissue. The interactions between cells are represented by adhesive and repelling force densities on
the cell contact borders. In addition, protrusive locomotion forces are implemented along the cell boundaries at the tissue
margin, and stochastic perturbations allow for non-deterministic motility effects. Simulations of the emerging system of stochastic
differential equations for position and velocity of cell centers show the feasibility of this Voronoi method generating realistic
cell shapes. In the limiting case of a single cell pair in brief contact, the dynamical nonlinear Ornstein–Uhlenbeck process
is analytically investigated. In general, topologically distinct tissue conformations are observed, exhibiting stability on
different time scales, and tissue coherence is quantified by suitable characteristics. Finally, an argument is derived pointing
to a tradeoff in natural tissues between cell size heterogeneity and the extension of cellular lamellae. 相似文献
15.
Wang Q Montmain G Ruano E Upadhyaya M Dudley S Liskay RM Thibodeau SN Puisieux A 《Human genetics》2003,112(2):117-123
DNA mismatch repair (MMR) is the process by which incorrectly paired DNA nucleotides are recognized and repaired. A germline mutation in one of the genes involved in the process may be responsible for a dominantly inherited cancer syndrome, hereditary nonpolyposis colon cancer. Cancer progression in predisposed individuals results from the somatic inactivation of the normal copy of the MMR gene, leading to a mutator phenotype affecting preferentially repeat sequences (microsatellite instability, MSI). Recently, we identified children with a constitutional deficiency of MMR activity attributable to a mutation in the h MLH1 gene. These children exhibited a constitutional genetic instability associated with clinical features of de novo neurofibromatosis type 1 (NF1) and early onset of extracolonic cancer. Based on these observations, we hypothesized that somatic NF1 gene mutation was a frequent and possibly early event in MMR-deficient cells. To test this hypothesis, we screened for NF1 mutations in cancer cells. Genetic alterations were identified in five out of ten tumor cell lines with MSI, whereas five MMR-proficient tumor cell lines expressed a wild-type NF1 gene. Somatic NF1 mutations were also detected in two primary tumors exhibiting an MSI phenotype. Finally, a 35-bp deletion in the murine Nf1 coding region was identified in mlh1-/- mouse embryonic fibroblasts. These observations demonstrate that the NF1 gene is a mutational target of MMR deficiency and suggest that its inactivation is an important step of the malignant progression of MMR-deficient cells. 相似文献
16.
Metfies K Borsutzki P Gescher C Medlin LK Frickenhaus S 《Molecular ecology resources》2008,8(1):99-102
The recent introduction of phylochips that contain molecular probes facilitates environmental microbial identification in a single experiment without previous cultivation. A set of probes recognizing species at different taxonomic levels is denoted as a hierarchical set. Application of hierarchical probe sets on a DNA microarray allows the assessment of biodiversity with different resolutions. It significantly increases the robustness of the results retrieved from phylochip experiments because of the possible consistency checks of hybridization across different taxonomic levels. Here, we present a computer program, phylo-chipanalyser, for the hierarchy editing and the evaluation of phylochip data generated from hierarchical probe sets. 相似文献
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1. Crude gammadelta-dioxovalerate was synthesized from laevulinate by two different methods and was purified by Sephadex chromatography. Some analytical reactions of the compound are described. 2. gammadelta-Dioxovalerate is a substrate for glyoxalase I and the GSH derivative formed by this enzyme is hydrolysed by glyoxalase II to form d-alpha-hydroxyglutarate. The K(m) of glyoxalase I for gammadelta-dioxovalerate is 1.0x10(-3)m at pH5.8.3. The u.v.-absorption spectrum of thiol ester, synthesized enzymically from gammadelta-dioxovalerate and GSH by glyoxalase I, is almost identical with that for S-lactoylglutathione. Some optical properties of this thiol ester were measured. 4. Attempts to show reversibility of the glyoxalase system reactions with d-alpha-hydroxyglutarate as substrate were unsuccessful. 5. The possible metabolic role of the gammadelta-dioxovalerate reaction is discussed. It is suggested that one of the metabolic functions of the glyoxalase system may be to provide a mechanism for the entry of this compound into the tricarboxylic acid cycle. 相似文献
19.
Dominic G. Hildebrand Simon Lehle Andreas Borst Sebastian Haferkamp Frank Essmann Klaus Schulze-Osthoff 《Cell cycle (Georgetown, Tex.)》2013,12(12):1922-1927
Due to its role in aging and antitumor defense, cellular senescence has recently attracted increasing interest. However, there is currently no single specific marker that can unequivocally detect senescent cells. Here, we identified α-L-fucosidase (α-Fuc) as a novel sensitive biomarker for cellular senescence. Regardless of the stress stimulus and cell type, α-Fuc activity was induced in all canonical types of cellular senescence, including replicative, DNA damage- and oncogene-induced senescence. Strikingly, in most models the degree of α-Fuc upregulation was higher than the induction of senescence-associated β-galactosidase (SA-β-Gal), the current gold standard for senescence detection. As α-Fuc is convenient and easy to measure, we suggest its utility as a valuable marker, in particular in cells with low SA-β-Gal activity. 相似文献
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