pinecone/core-2020-05-10-deduplication huggingface dataset:
Stochastic effects in intercellular calcium spiking in hepatocytes

Texto completo borrador de autor.We carry out a Monte Carlo simulation of stochastic effects for two models of intercellular calcium wave propagation in rat hepatocytes. Both models involve gap junction diffusion by a second messenger. We find that, in general, the stochastic effects improve agreement with experiment, for a reasonable choice of model parameters. Both stochastic models exhibit baseline fluctuations and variations in the peak heights of Ca2+. In addition, we find for one model that there is a distribution of latency times, rather than a single latency time, with a distribution width which is comparable to the experimental observation of spike widths. We also find for the other model with low gap junction diffusion that it is possible for cell multiplets to oscillate independently initially, but to subsequently become synchronized.This work was supported in part by NSF Grant\ud
number DMR9813409 and the DGES (Spain) projects\ud
PB97-0141-C02-01 and BFM2000-1108.Peer reviewe
Analysis of a circular code model

A circular code has been identified in the protein (coding) genes of both eukaryotes and prokaryotes by using a statistical method called Trinucleotide Frequency method (TF method) [Arquès & Michel, (1996) J.Theor. Biol. 182, 45-58]. Recently, a probabilistic model based on the nucleotide frequencies with a hypothesis of absence of correlation between successive bases on a DNA strand, has been proposed by Koch & Lehmann [(1997) J.Theor. Biol. 189, 171-174] for constructing some particular circular codes. Their interesting method which we call here Nucleotide Frequency method (NF method), reveals several limits for constructing the circular code observed with protein genes
Heterochronic detection through a function for the ontogenetic variation of bone shape

Heterochrony, evolutionary modifications in the rates and/or the timing of development, is widely recognized as an important agent of evolutionary change. In this paper, we are concerned with the detection of this evolutionary mechanism through the analysis of long bone growth. For this, we provide a function sigma (t) for the ontogenetic variation of bone shape by taking the ratio of two Gompertz curves explaining, respectively, the relative contribution to long bone growth of (a) endochondral ossification and (b) periosteal ossification. The significance of the fitting of this function to empirical data was tested in Anas platyrhynchos (Anseriformes). In this function sigma(t), the time t(m) at which periosteal growth rate first equalizes endochondral growth rate was taken as the timing parameter to be compared between taxa. On the other hand, the maximum rate of ontogenetic change in bone shape (maximum slope, beta) from hatching to t(m) was taken as the rate parameter to be compared. Comparisons of these parameters between the plesiomorphic condition and the derived character state would provide evidence for hypornorphosis (earlier occurrence of t(m)), hypermorphosis (delayed occurrence of t(m)), deceleration (smaller beta) or acceleration (higher beta).\ud
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Regarding the phylogenetic context, the ancestral condition for the character of interest should be estimated to polarize the direction of the heterochronic change. We have quantified the influence of the phylogenetic history on the variation of adult bone shape in a sample of 13 species of Anseriformes and 17 species from other neornithine orders of birds by using permutational phylogenetic regressions. Phylogenetic effects are significant, and this fact allows the optimization of bone shape onto a phylogenetic tree of Anseriformes to estimate the ancestral condition for Anas platyrhynchos
A mathematical model for germinal centre kinetics and affinity maturation

We present a mathematical model which reproduces experimental data on the germinal centre (GC) kinetics of the primed primary immune response and on affinity maturation observed during the reaction. We show that antigen masking by antibodies which are produced by emerging plasma cells can drive affinity maturation and provide a feedback mechanism by which the reaction is stable against variations in the initial antigen amount over several orders of magnitude. This provides a possible answer to the long-standing question of the role of antigen reduction in driving affinity maturation. By comparing model predictions with experimental results, we propose that the selection probability of centrocytes and the recycling probability of selected centrocytes are not constant but vary during the GC reaction with respect to time. It is shown that the efficiency of affinity maturation is highest if clones with an affinity for the antigen well above the average affinity in the GC leave the GC for either the memory or plasma cell pool. It is further shown that termination of somatic hypermutation several days before the end of the germinal centre reaction is beneficial for affinity maturation. The impact on affinity maturation of simultaneous initiation of memory cell formation and somatic hypermutation vs. delayed initiation of memory cell formation is discussed
Zipf's Law in Importance of Genes for Cancer Classification Using
  Microarray Data

Microarray data consists of mRNA expression levels of thousands of genes
under certain conditions. A difference in the expression level of a gene at two
different conditions/phenotypes, such as cancerous versus non-cancerous, one
subtype of cancer versus another, before versus after a drug treatment, is
indicative of the relevance of that gene to the difference of the high-level
phenotype. Each gene can be ranked by its ability to distinguish the two
conditions. We study how the single-gene classification ability decreases with
its rank (a Zipf's plot). Power-law function in the Zipf's plot is observed for
the four microarray datasets obtained from various cancer studies. This
power-law behavior in the Zipf's plot is reminiscent of similar power-law
curves in other natural and social phenomena (Zipf's law). However, due to our
choice of the measure of importance in classification ability, i.e., the
maximized likelihood in a logistic regression, the exponent of the power-law
function is a function of the sample size, instead of a fixed value close to 1
for a typical example of Zipf's law. The presence of this power-law behavior is
important for deciding the number of genes to be used for a discriminant
microarray data analysis.Comment: 11 pages, 5 figures. submitte
Congruence as a predictor of occupational stress

[Abstract]: This study examined the relation among nine measures of Holland's concept of
congruence and the relation of these measures and occupational stress. Holland's
Self-Directed Search (Holland, 1985b) and the Occupational Stress Inventory
(Osipow & Spokane, 1987) were administered to 154 fully-employed adults. Two
correlated factors accounted for the pattern of correlations among the congruence
measures. The first factor was defined by measures which made use of the hexagonal
arrangement of types and the second was based simply on discrepancies between the
letters representing the person's type and the job environment. A number of markers
for the second factor were related to stress and strain. Iachan's M index (Iachan,
1984;1990) was the best predictor, accounting for seven percent of variance on total
stress scores and nine percent of variance on total strain scores. It is suggested that the
relation between congruence and stress, like the relation between congruence and job
satisfaction (Spokane, 1985), is significant but rather small and dependent on the
measure of congruence used
Predicting occupational strain and job satisfaction: the role of stress, coping, personality, and affectivity variables

Four studies employed path analysis to examine how measures of occupational stressors, coping resources, and negative affectivity (NA) and positive affectivity (PA) interact to predict occupational strain. The Occupational Stress Inventory (Osipow & Spokane, 1987) was used to measure stress, strain, and coping. The Positive and Negative Affectivity Schedule (Watson, Clark, & Tellegen, 1988) was\ud
used for the affectivity variables. The hypothesised model showed NA and PA as background dispositional variables that influenced relations among stress, strain, and coping while still allowing stress and coping to have a direct influence on strain. Goodness of fit indices were acceptable with the model predicting 15 per cent of the variance in stress, 24 per cent of coping, and 70 per cent of strain. Study 2 replicated these findings. Study 3 added a positive outcome variable, job satisfaction (JSI: Brayfield & Rothe, 1951) to the model. The expanded model again fit the data well. A fourth study added a global measure of personality (NEO-FFI: Costa & McCrae, 1991) to the model tested in Study 3. Results indicated that personality measures did not add\ud
anything to the prediction of job satisfaction and strain in a model that already included measures of stressors, coping resources, NA and PA. The series of four studies yielded a reliable structural model that highlights the influence of organizational and dispositional variables on occupational strain and job satisfaction
Time discounting in relation to career preferences

[Abstract]: The present study used a longitudinal design to test aspects of Kirby and Herrnstein's (1995)
theory of time discounting. Specifically, the prediction that preferences reverse due to changes in delay was tested in a longitudinal study of career-path selections made by
employees in a Hong Kong real estate consultancy. Over a three-year period, 16 of 23 subjects reversed their career preference from a future senior managerial position to a lesser management role available earlier. Organizational and cultural factors which may have influenced these preference changes are discussed and areas of future research suggested.
The study provides supporting evidence from the career selection perspective that preferences are not necessarily invariant across time
Matching Structures by Computing Minimal Paths on a Manifold

International audienceThe general problem of matching structures is very pervasive in computer vision and image processing. The research presented here tackles the problem of object matching in a very general perspective. It is formulated for the matching of surfaces. It applies to objects having small or large deformation and arbitrary topological changes. The process described hinges on a geodesic distance equation for a family of curves or surfaces embedded in the graph of a cost function. This geometrical approach to object matching has the advantage that the similarity criterion can be used to define the shape of the cost function. Matching paths are computed on the cost manifolds using distance maps. These distance maps are generated by solving a general partial differential equation which is a generalization of the geodesic dis- tance evolution scheme introduced by R. Kimmel, A. Amir, and A. F. Bruckstein (1995, IEEE Trans. Pattern Anal. Mach. Intell. 17, 635-640). An Eulerian level-set formulation is also introduced, leading to a numerical scheme used for solving par- tial differential equations originating from hyperbolic conservation laws, which has proven to be very robust and stable
Spider diagrams: a diagrammatic reasoning system

Spider diagrams combine and extend Venn diagrams and Euler circles to express constraints on sets and their relationships with other sets. These diagrams can be used in conjunction with object-oriented modelling notations such as the Unified Modelling Language. This paper summarises the main syntax and semantics of spider diagrams. It also introduces inference rules for reasoning with spider diagrams and a rule for combining spider diagrams. This system is shown to be sound but not complete. Disjunctive diagrams are considered as one way of enriching the system to allow combination of diagrams so that no semantic information is lost. The relationship of this system of spider diagrams to other similar systems, which are known to be sound and complete, is explored briefly
The effect of a discrete signal on context conditioning: Assessment by preference and freezing tests

Contains fulltext :
                  27742.pdf (publisher's version ) (Open Access)Four experiments with rats assessed conditioning to contextual cues after the delivery of footshocks that were either signaled by a discrete stimulus or unsignaled. Two different tests were used. The first was a context preference test in which subjects were allowed to move freely in a brightly lit, unconditionally aversive context and the former shock context. The second test consisted of scoring freezing behavior while the animals were confined to the former conditioning context. During context preference tests, signaled-shock animals spent more time in the conditioning context and/or entered that context more frequently than did unsignaled-shock subjects. However, freezing tests largely failed to detect a difference between groups. These results were discussed in terms of possible interactions between the formation of context-shock, signal-shock, and context-signal associations and their effect on performance in each of the two types of tests
Evaluative Conditioning: Arti-fact or -fiction?—A Reply to Baeyens, De Houwer, Vansteenwegen, and Eelen (1998)

Baeyens et al.(1998) claim that Field and Davey's (1997) controversial study of conceptual conditioning offers little threat to current conceptions of evaluative conditioning. This article addresses some of the questions posed by Baeyenset al.First, some criticisms of the conceptual conditioning study appear to be based on a misunderstanding of the procedure. Second, we address the issues surrounding the so-called Type-X procedure. Specifically, we begin by reviewing the status of studies that have used a procedure different from the Type-X procedure. It is then argued that, although the Type-X procedure has been used in only a portion of EC research, it has been used primarily in those studies whose outcome has been used to argue that evaluative conditioning (EC) is functionally distinct from autonomic conditioning. We then review the evidence from non-Type-X procedures that EC is a distinct form of learning. Finally, an attempt is made to explain why between-subject controls should be used as a matter of course in this field of research
Carbon flux distribution in antibiotic-producing chemostat cultures of Streptomyces lividans.

The carbon metabolism of derivatives of Streptomyces lividans growing under phosphate limitation in chemostat cultures and producing the antibiotics actinorhodin and undecylprodigiosin was investigated. By applying metabolic flux analysis to a stoichiometric model, the relationship between antibiotic production, biomass accumulation, and carbon flux through the major carbon metabolic pathways (the Embden Meyerhoff Parnas and pentose-phosphate pathways) was analyzed. Distribution of carbon flux through the catabolic pathways was shown to be dependent on growth rate, as well as on the carbon and energy source (glucose or gluconate) used. Increasing growth rates promoted an increase in the flux of carbon through glycolysis and the pentose-phosphate pathway. The synthesis of both actinorhodin and undecylprodigiosin was found to be inversely related to flux through the pentose-phosphate pathway
Pituitary adenylate cyclase-activating polypeptide induces astrocyte differentiation of precursor cells from developing cerebral cortex

El pdf del artículo es la versión post-print.Ciliary neurotrophic factor and bone morphogenetic proteins induce astrocytogenesis in the developing rat brain by stimulating STAT- and Smad-dependent signaling, respectively. We previously found that stimulation of the cAMP-dependent signaling pathway also triggers differentiation of cerebral cortical precursor cells into astrocytes, providing an additional mechanism to promote astrocyte differentiation. In this study, we show that pituitary adenylate cyclase-activating polypeptide (PACAP), but not the related vasoactive intestinal peptide, induces astrocyte differentiation of cortical precursor cells, even after a transient exposure. Cortical precursors were found to express predominantly the short isoform of the PACAP-specific PAC1 receptor, which couples to adenylate cyclase. Consistent with this notion, we determined that exposure of cortical precursors to PACAP resulted in a dose-dependent increase in cAMP production. Pretreatment of cells with the cAMP antagonist Rp-cAMPS prevented astrocyte differentiation. Thus, PACAP acts as an extracellular signal to trigger cortical precursor cell differentiation into astrocytes via stimulation of intracellular cAMP production.This work was partially supported by grants from the U.S. Public Health Service (DK-49670) and the Community of Madrid (08.5/0028/2001.1). I.V. was partially supported by a fellowship from the University of Cádiz (Spain).Peer Reviewe
Development of a species-specific polymerase chain reaction assay for Gardnerella vaginalis

The nucleotide sequence of the region between the 16S and 23S rRNA genes of the facultative anaerobic bacteriumGardnerella vaginalishas been determined, together with the 5′ proximal 500 nucleotides of the 23S rRNA gene. Regions suited for the development of specific, probe-confirmable polymerase chain reaction (PCR) assays were selected. PCR assays were evaluated with respect to sensitivity and specificity, the latter in comparison with a number ofG. vaginalisreference strains and closely related species likeBifidobacteriumspp. In an initial diagnostic study it appeared that the PCR test detectedG. vaginalisin 40% of women irrespective of their clinical status. Ten out of 11 patients suffering from bacterial vaginosis as defined on the basis of clinical parameters were carryingG. vaginalis
Detection of anomalous structural behaviour using wavelet analysis

Author's manuscript version. The version of record is available from the publisher via: doi:10.1006/mssp.2001.1449
Copyright © 2002 Elsevier Science Ltd. All rights reserved.Structural health monitoring (SHM) can be defined as the continuous monitoring of
a bridge’s state properties, such as static and dynamic response, in order to diagnose
the onset of anomalous structural behaviour. This involves measuring and
evaluating the state properties and relating these to defined performance parameters.
The process of measuring state properties, either continuously or periodically,
produces large quantities of data and by careful analysis of these data, sudden and
gradual changes in the bridge’s behaviour can be identified and characterised. The
ability of wavelet transforms to detect abrupt changes, gradual change beginnings
and ends of events make them well suited for the analysis of bridge health
monitoring data. This paper presents the application of wavelet analysis to identify
events and changes in structural state in a bridge during and after its construction
Ultrasound increases plasmid-mediated gene transfer to dystrophic muscles without collateral damage

Studies have shown that ultrasound, used either alone or in combination with microbubble contrast agents, can increase cell membrane permeability to plasmid DNA. Because ultrasound is a non-painful and well-established tool in clinical medicine, its potential to enhance DNA uptake into the muscles of patients with muscular dystrophy is conceptually attractive. Therefore, we evaluated the ability of ultrasound pulses (1 MHz; 1.5 W/cm2) to increase exogenous (LacZ) gene expression in normal wild-type and dystrophic Dmd(mdx/mdx) mice after plasmid DNA injection into muscle. We also ascertained whether co-injection of lipid-encapsulated perfluoropropane microbubbles (Definity) or pretreatment with hyaluronidase could further increase the level of gene transfer to ultrasound-treated muscles. The use of ultrasound did not increase transfection efficiency in normal mice. In contrast, dystrophic mice demonstrated an increase in the number of transfected fibers (threefold) as well as the amount of LacZ protein (22-fold) after ultrasound exposure, provided that Definity was also co-injected with the DNA. Pretreatment of muscles with hyaluronidase before ultrasound exposure was not effective in augmenting the level of gene transfer. Under the optimal conditions for dystrophic muscle transfection (ultrasound + Definity), there was no associated increase in muscle damage. Hence ultrasound may provide a safe and effective method for enhancing gene transfer to dystrophic muscles, thereby increasing the prospects for therapeutic application of naked DNA in muscular dystrophy patients.Peer reviewed: YesNRC publication: N
Characterization of the BOLD signal in functional MRI

In the last two decades, functional magnetic resonance imaging (fMRI) has become an important and widely used imaging technique for functional brain mapping. However, blood oxygen level dependent (BOLD) technique is quite insensitive and task invoked BOLD signal change at 3T is typically in the order of a few percent. Furthermore, the coupling between BOLD signal changes and neuronal activities is quite complicated, involving a cascade of events remaining poorly understood even today. In this thesis, some of the basic characteristics of the BOLD signal are investigated. Better understanding of the BOLD signal characteristics can be beneficial for the design of BOLD fMRI experiment aimed to improve the time efficiency. It can also provide guidelines for developing fMRI data processing strategies.



In study I and II, a single-shot dual-echo spiral acquisition technique was used for characterizing the T2* changes associated with motor activation task. In study I, the optimal strategy for head motion correction was investigated. Based on the improvement in the detection of brain activation, the best strategy is to perform the head motion correction using the imaging data from the second echo and then apply the derived motion correction parameters to the first echo, instead of conducting motion correction of the individual echoes independently. In study II, several aspects of brain mapping methods based on T2*-weighted imaging and T2* (R2*=1/T2*) mapping were quantitatively compared, including the detected activation volume, functional contrast, signal-to-noise ratio, and contrast-to-noise ratio. fMRI studies based T2* mapping have the following potential advantages: maximum functional contrast, independence of echo time; and reduced inflow effects. The sensitivity for brain activation detection is significantly correlated with the contrast-to-noise ratio, which is determined by both the signal-to-noise ratio and functional contrast.



In study III, the hemodynamic responses to functional activation were characterized using T2*-weighted BOLD imaging, arterial spin labeling, and bolus tracking of MRI contrast agent. In addition to the BOLD signal change, the relative cerebral blood flow and cerebral blood volume associated with brain activation were independently determined.



In study IV, the characteristics of the global signal in resting-state fMRI were investigated. It was found that the global signal time courses and regional contributions differ individually. However, after removing the contribution from the cerebral spinal fluid, a consistent brain network responsible for the remaining global signal changes was identified. The involved brain regions include: posterior cingulate cortex, precuneus, superior temporal gyrus, medial frontal gyrus and the cerebellar vermis, which is likely to be related to the perception and cognitive processes of the brain occurred in the specific environments during resting-state fMRI