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At least 811 records · Page 45Linked to original sources
PubMed1999

Using partial directed coherence to describe neuronal ensemble interactions.

This paper illustrates the use of the recently introduced method of partial directed coherence in approaching how interactions among neural structures change over short time spans that characterize well defined behavioral states. Central to the method is its use of multivariate time series modelling in conjunction with the concept of Granger causality. Simulated neural network models were used to illustrate the technique's power and limitations when dealing with neural spiking data. This was followed by the analysis of multi-unit activity data illustrating dynamical change in the interaction of thalamo-cortical structures in a behaving rat.

Action Potentials↗
PubMed2002

Cortical neuronal ensembles driven by dorsal horn spinal neurones with spontaneous activity in the cat.

Simultaneous recordings of cortical activity, recorded as the cortical local field potential (CLFP) in the contralateral posterior sigmoid gyrus, and the spinal activity, recorded as the cord dorsum potential (CDP) of the L6 lumbar segment, were made in the anaesthetized cat. The electrodes were positioned in somatosensory regions where the largest spontaneous negative CLFPs and CDPs were recorded. We found that spontaneous negative CLFPs were preceded by spontaneous negative CDPs with a mean latency of 14.4+/-3.5 ms. Amplitude of these spontaneous negative CLFPs was abolished after section of the dorsal columns and ipsilateral dorsolateral funiculus. It is concluded that the neurones of the primary somatosensory cortex can be driven by dorsal horn spinal neurones producing the spontaneous negative CDPs. This suggests very strongly that spontaneous neuronal activity in somatosensory regions of the brain is generated not only by ongoing activity of neurones located at supraspinal sites, but also by ongoing activity of spinal neurones.

Action Potentials↗
PubMed1998

Step cycle-related oscillatory properties of inferior olivary neurons recorded in ensembles.

This study was conducted to characterize patterns of discharge from the dorsal accessory olive during different behavioural states. To accomplish this goal, adult rats were chronically implanted with arrays of microwires (25-50 microns) to record from as many as 23 neurons from the dorsal accessory olive bilaterally during locomotor paradigms or at rest. Olivary neurons discharged sporadically at low firing frequencies (1-5 Hz) when the rat was at rest. However, during locomotor paradigms involving constant speed treadmill locomotion, olivary neurons discharged rhythmically at frequencies which closely matched step cycle frequencies. The rhythmic nature of olivary discharge was maintained even during brief periods of inconsistent gait. During treadmill locomotion utilizing variable acceleration/deceleration paradigms olivary neurons discharged at 3 Hz frequencies. Electrical stimulation of peripheral afferents resulted in rhythmic discharge of olivary neurons at frequencies harmonic with the rate of stimulation. These data suggest that oscillatory patterns of discharge exhibited by the inferior olivary nucleus are only seen during rhythmic behavioral tasks or stimulation paradigms. Further, the dissociation between the rhythmic nature of the task and the continued oscillation suggests that oscillatory activity of the inferior olive may be due both to an intrinsic rhythm as well as related to ongoing sensorimotor input.

Animals↗
PubMed2001

Activated brain regions in musicians during an ensemble: a PET study.

As in visual processing, we speculated that, in music processing, different brain regions would activate according to the mode of music listening. Using motets by a famous composer, we studied changes in regional cerebral blood flow (rCBF) with positron emission tomography associated with concentrating on the alto-part within the harmony (alto-part-listening condition) compared to listening to the harmony as a whole (harmony-listening condition). The alto-part-listening condition was associated with bilateral increases of rCBF in superior parietal lobules, precunei, premotor areas and orbital frontal cortices. Superior parietal lobules are likely to be responsible for auditory selective attention to the alto part within the harmony and the analysis of tone pitch on a mental score. The precuneus possibly participated in writing tones of the alto part on a mental score. Based on our findings, we propose that both auditory selective attention and analytic processing play an important role in concentrating on a certain vocal part within a harmony. During the harmony-listening condition, temporal poles, the anterior portion of the cingulate gyrus, occipital cortex and the medial surface of the cerebellum were bilaterally activated. Further studies are necessary to clarify the difference in music processing between musicians and nonmusicians.

Adult↗
PubMed2000

Stability problems with artificial neural networks and the ensemble solution.

Artificial neural networks (ANNs) are very popular as classification or regression mechanisms in medical decision support systems despite the fact that they are unstable predictors. This instability means that small changes in the training data used to build the model (i.e. train the ANN) may result in very different models. A central implication of this is that different sets of training data may produce models with very different generalisation accuracies. In this paper, we show in detail how this can happen in a prediction system for use in in-vitro fertilisation. We argue that claims for the generalisation performance of ANNs used in such a scenario should only be based on k-fold cross-validation tests. We also show how the accuracy of such a predictor can be improved by aggregating the output of several predictors.

Algorithms↗
PubMed2000

Memory trace reactivation in hippocampal and neocortical neuronal ensembles.

During active behavior, patterns of hippocampal and neocortical neuronal activity reflect ongoing inputs and their contexts. Recent neurophysiological investigations have shown that during 'off-line' periods, traces of these experiences are spontaneously reactivated in both structures. Although the functional importance of this phenomenon remains to be demonstrated, it does provide clues about the nature and mechanisms of memory retrieval and consolidation.

Animals↗
PubMed2001

Detection of multiple protein conformational ensembles in solution via deconvolution of charge-state distributions in ESI MS.

Monitoring the changes in charge-state distributions of protein ions in electrospray ionization (ESI) mass spectra has become one of the commonly accepted tools to detect large-scale conformational changes of proteins in solution. However, these experiments produce only qualitative, low-resolution information. Our goal is to develop a procedure that would produce quantitative data on protein conformational isomers coexisting in solution at equilibrium. To that end, we have examined the evolution of positive ion charge-state distributions in the

Animals↗
PubMed2000

Multistate equilibrium unfolding of Escherichia coli dihydrofolate reductase: thermodynamic and spectroscopic description of the native, intermediate, and unfolded ensembles.

The thermodynamic and spectroscopic properties of a cysteine-free variant of Escherichia coli dihydrofolate reductase (AS-DHFR) were investigated using the combined effects of urea and temperature as denaturing agents. Circular dichroism (CD), absorption, and fluorescence spectra were recorded during temperature-induced unfolding at different urea concentrations and during urea-induced unfolding at different temperatures. The first three vectors obtained by singular-value decomposition of each set of unfolding spectra were incorporated into a global analysis of a unique thermodynamic model. Although individual unfolding profiles can be described as a two-state process, a simultaneous fit of 99 vectors requires a three-state model as the minimal scheme to describe the unfolding reaction along both perturbation axes. The model, which involves native (N), intermediate (I), and unfolded (U) states, predicts a maximum apparent stability, DeltaG degrees (NU), of 6 kcal mol(-)(1) at 15 degrees C, an apparent m(NU) value of 2 kcal mol(-)(1) M(-)(1), and an apparent heat capacity change, DeltaC(p)()(-NU), of 2.5 kcal mol(-)(1) K(-)(1). The intermediate species has a maximum stability of approximately 2 kcal mol(-)(1) and a compactness closer to that of the native than to that of the unfolded state. The population of the intermediate is maximal ( approximately 70%) around 50 degrees C and falls below the limits of detection of > or =2 M urea or at temperatures of <35 or >65 degrees C. The fluorescence properties of the equilibrium intermediate resemble those of a transient intermediate detected during refolding from the urea-denatured state, suggesting that a tryptophan-containing hydrophobic cluster in the adenosine-binding domain plays a key role in both the equilibrium and kinetic reactions. The CD spectroscopic properties of the native state reveal the presence of two principal isoforms that differ in ligand binding affinities and in the packing of the adenosine-binding domain. The relative populations of these species change slightly with temperature and do not depend on the urea concentration, implying that the two native isoforms are well-structured and compact. Global analysis of data from multiple spectroscopic probes and several methods of unfolding is a powerful tool for revealing structural and thermodynamic properties of partially and fully folded forms of DHFR.

Circular Dichroism↗
PubMed2005

Araneoid egg case silk: a fibroin with novel ensemble repeat units from the black widow spider, Latrodectus hesperus.

Araneoid spiders use specialized abdominal glands to manufacture up to seven different protein-based silks/glues that have diverse physical properties. The fibroin sequences that encode egg case fibers (cover silk for the egg case sac) and the secondary structure of these threads have not been previously determined. In this study, MALDI tandem TOF mass spectrometry (MS/MS) and reverse genetics were used to isolate the first egg case fibroin, named tubuliform spidroin 1 (TuSp1), from the black widow spider, Latrodectus hesperus. Real-time quantitative PCR analysis demonstrates TuSp1 is selectively expressed in the tubuliform gland. Analysis of the amino acid composition of raw egg case silk closely aligns with the predicted amino acid composition from the primary sequence of TuSp1, which supports the assertion that TuSp1 represents a major component of egg case fibers. TuSp1 is composed of highly homogeneous repeats that are 184 amino acids in length. The long stretches of polyalanine and glycine-alanine subrepeats, which account for the crystalline regions of minor ampullate and major ampullate fibers, are very poorly represented in TuSp1. However, polyserine blocks and short polyalanine stretches were highly iterated within the primary sequence, and (13)C NMR spectroscopy demonstrated that the majority of alanine was found in a beta-sheet structure in post-spun egg case silk. The TuSp1 repeat unit does not display substantial sequence similarity to any previously described fibroin genes or proteins, suggesting that TuSp1 is a highly divergent member of the spider silk gene family.

Amino Acid Sequence↗
PubMed2006

The gamma-secretase complex: membrane-embedded proteolytic ensemble.

Gamma-secretase is responsible for the proteolytic processing of a variety of membrane-associated fragments derived from type I integral membrane proteins, including the amyloid beta-protein precursor and the Notch receptor. This enzyme is composed of four different integral membrane proteins: presenilin, nicastrin, Aph-1, and Pen-2. During assembly and maturation of the protease complex, presenilin is endoproteolyzed into two subunits, each of which contributes one aspartate to the active site of an aspartyl protease. Substrate apparently interacts with an initial docking site before passing in whole or in part between the two presenilin subunits to the internal water-containing active site. The ectodomain of nicastrin also interacts with the N-terminus of the substrate as an essential step in substrate recognition and processing. Sites for allosteric regulation on the protease complex allow selective inhibition or modulation of APP processing without interfering with Notch signaling, and such selective agents may represent promising leads for the development of Alzheimer's disease therapeutics. Elucidation of detailed structural features of gamma-secretase and other membrane-embedded proteases is the next frontier in understanding how these enzymes carry out hydrolysis within the lipid bilayer.

Amyloid Precursor Protein Secretases↗
PubMed1998

Protein denaturation: a small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c.

Solution X-ray scattering was used to study the equilibrium unfolding of cytochrome c as a function of guanidine hydrochloride concentration at neutral pH. The radius of gyration (Rg) shows a cooperative transition with increasing denaturant with a similar Cm to that observed with circular dichroism. However, the lack of an isoscattering point in the X-ray scattering patterns suggests the equilibrium unfolding is not simply a two-state process. Singular value decomposition (SVD) analysis was applied to the scattering patterns to determine the number of distinct scattering species. SVD analysis reveals the existence of three components, suggesting that at least three equilibrium states of the protein exist. A model was employed to determine the thermodynamic parameters and the scattering profiles of the three equilibrium states. These scattering profiles show that one state is native (N). The other two states (U1, U2) are unfolded, with U2 being fully unfolded and U1 having some residual structure. Using the thermodynamic parameters to calculate fractional populations, U1 is maximally populated at intermediate denaturant concentrations while U2 is maximally populated at high denaturant concentrations. It is likely that there is a multiplicity of denatured states with U1 and U2 representing an average of the denatured states populated at intermediate and high denaturant concentrations, respectively.

Animals↗
PubMed2000

A lattice study of multimolecular ensembles of protein models. Effect of sequence on the final state: globules, aggregates, dimers, fibrillae.

Three sequences of simple protein models on the two-dimensional square lattice have been chosen for a study of the behavior of different classes of proteins as a function of temperature and concentration using multimolecular systems under periodic boundary conditions. The results of the dynamic simulations have shown the profound influence that the intermolecular contacts can have on the accessibility of the states the various sequences can reach; this makes possible the formation of different kinds of structures under the control not only of sequence and temperature but also of concentration that can become the main driving force for the formation of ordered lamellar structures for sequences properly designed.

Algorithms↗
PubMedDate not supplied

Development of linear, ensemble, and nonlinear models for the prediction and interpretation of the biological activity of a set of PDGFR inhibitors.

A QSAR modeling study has been done with a set of 79 piperazyinylquinazoline analogues which exhibit PDGFR inhibition. Linear regression and nonlinear computational neural network models were developed. The regression model was developed with a focus on interpretative ability using a PLS technique. However, it also exhibits a good predictive ability after outlier removal. The nonlinear CNN model had superior predictive ability compared to the linear model with a training set error of 0.22 log(IC50) units (R2 = 0.93) and a prediction set error of 0.32 log(IC50) units (R2 = 0.61). A random forest model was also developed to provide an alternate measure of descriptor importance. This approach ranks descriptors, and its results confirm the importance of specific descriptors as characterized by the PLS technique. In addition the neural network model contains the two most important descriptors indicated by the random forest model.

Linear Models↗
PubMed2005

Self-assembly of neutral platinum-based supramolecular ensembles incorporating oxocarbon dianions and oxalate.

Five neutral platinum-based macrocycles incorporating cyclic oxocarbondianions, squarate and croconate and their acyclic analogue, oxalate, have been synthesized in 90-95% yield via self-assembly. The combination of the diplatinum molecular clip with all three dianions afforded molecular rectangles, whereas a platinum-based 60 degrees acceptor unit produced a supramolecular rhomboid with croconate ion but a triangle with squarate ion. In all cases, multinuclear NMR spectra were consistent with the formation of single highly symmetrical species. The three rectanglular and the rhomboid assemblies were characterized by single-crystal X-ray crystallography. The triangular species was characterized by FAB mass spectrometry.

Anions↗