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At least 721 records · Page 40Linked to original sources

PubMed2004

An ensemble method for gene discovery based on DNA microarray data.

The advent of DNA microarray technology has offered the promise of casting new insights onto deciphering secrets of life by monitoring activities of thousands of genes simultaneously. Current analyses of microarray data focus on precise classification of biological types, for example, tumor versus normal tissues. A further scientific challenging task is to extract disease-relevant genes from the bewildering amounts of raw data, which is one of the most critical themes in the post-genomic era, but it is generally ignored due to lack of an efficient approach. In this paper, we present a novel ensemble method for gene extraction that can be tailored to fulfill multiple biological tasks including (i) precise classification of biological types; (ii) disease gene mining; and (iii) target-driven gene networking. We also give a numerical application for (i) and (ii) using a public microarrary data set and set aside a separate paper to address (iii).

Algorithms↗

PubMed2002

Can simple particle shapes be used to model scalar optical properties of an ensemble of wavelength-sized particles with complex shapes?

We compute the scalar optical properties of size-shape distributions of wavelength-sized randomly oriented homogeneous particles with different nonaxially symmetric geometries and investigate how well they can be modeled with a simple spherical, spheroidal, or cylindrical particle model. We find that a spherical particle model can be used to determine the extinction and scattering cross sections, the single-scattering albedo, and the asymmetry parameter with an error of less than 2%, whereas the extinction-to-backscatter ratio Reb is reproduced only with an error of 9%. The cylindrical and spheroidal particle models yield slightly improved results for Reb that deviate from those obtained for the complex particle ensemble by 7% and 5%, respectively. Large discrepancies between results of the different models are observed for the linear depolarization ratio, thus indicating limitations of models based on simple particle shapes.

Models, Theoretical↗

PubMed2003

Sex-steroid modulation of growth hormone (GH) secretory control: three-peptide ensemble regulation under dual feedback restraint by GH and IGF-I.

Technical, genetic, and clinical developments have unveiled a burgeoning array of novel effectors of GH secretion. The present appraisal of central neuroregulatory components of the somatotropic axis highlights a simplifying concept of ensemble control by the final common peptides, GH-releasing hormone (GHRH), GH-releasing peptide(s) (GHRP, ghrelin), and somatostatin. These potent signals act individually, antagonistically, and synergistically to direct pulsatile GH secretion. GHRH, GHRP/ghrelin, and somatostatin further adapt to autonegative feedback by GH and IGF-I. Estradiol modulates the impact of each of the primary peptidyl inputs; viz.: (i) enhances submaximally effective feedforward by discrete pulses of (injected) recombinant human GHRH-1,44-amide (as defined by increased agonistic potency and pituitary sensitivity); (ii) potentiates the submaximally stimulatory effects of GHRP-2, a hexapeptidyl mimetic of ghrelin; (iii) blunts dose-dependent inhibition of fasting GH secretion by somatostatin- 14; and (iv) relieves rhGH-enforced negative feedback on GHRP-2 (but not on basal, exercise, or GHRH)-stimulated GH secretion. The foregoing estrogenic activities collectively augment GH secretory burst mass by amplifying feedforward (via both GHRH and GHRP) and attenuating feedback (imposed by somatostatin and GH). Whether testosterone fully mimics the foregoing mechanistic actions of estradiol is not known. In conclusion, the present conceptual platform of tri-peptide-directed feedforward and GH/IGF-I-mediated feedback should aid in unraveling some of the complex regulatory dynamics targeted by sex-steroid hormones.

Animals↗

PubMed2004

[Experimental investigation on the reproducibility of ensemble-averaged electromyographic gait analysis data in the area of experimental and clinical orthopaedics].

With suitable application and signal processing methods, surface electromyography is a comparatively simple instrument for investigating the temporal pattern of the muscular activity of a walking subject. The influence of changes both in the external experimental conditions (e.g. orthopedic shoe design) and in the human locomotor system (due to disease or therapy) on the individual muscular gait characteristics can be documented in this way. The usefulness of this kind of investigation is basically limited by the reproducibility of the gait analytical findings of the subject, who is examined at different times with unchanged bodily state and under identical experimental conditions unchanged. In our experiments we observed that the reproducibility of electromyographic activity curves obtained by ensemble averaging over a sufficiently high number of full strides differs for different muscles and in different subjects. Within the same experimental session it is very high and considerably better than in experiments done on different days. In examinations done on different days the basic characteristics of the activity curves are reproduced better than the absolute height of the amplitudes. In view of these findings the differences observed in the gait analysis of patients in the course of operative or conservative therapy have to be interpreted very carefully as to their true origin.

Algorithms↗

PubMed2003

Ensemble averaging and multiple statistical testing of EMG activities of cyclically repeated body motions. A tool for muscle function analysis in experimental and clinical orthopaedics.

Coupled with suitable computerized signal recording and processing methods surface electromyography can be a powerful tool for the analysis of muscle activity in specific body movements. It can be used for this purpose in experimental and in clinical diagnostic orthopaedics as well as in physiotherapy. We describe in this paper a motion analysis system comprising this feature. It has been employed for the diagnosis of the basic angular kinematics and muscle function in human gait and other cyclically repeatable movements of the human locomotive system. Changes in the temporal characteristics of the movements and the muscle activity due to changed physical or experimental conditions can be systematically investigated this way. Such changes can be the result of surgical and/or conservative orthopaedic therapy, a long term physiotherapeutic program, or modified walking conditions as in experimental orthopaedics. They are displayed and validated by signal ensemble averaging and subsequent multiple statistical testing (e.g. by a suitably adapted Bonferroni criterion). The efficiency of the system is demonstrated by an exemplary gait analysis of selected kinematic and muscular effects caused by an experimental simulation of a leg length inequality.

Algorithms↗

PubMedDate not supplied

Discrimination of communication calls in the squirrel monkey: "call detectors" or "cell ensembles"?

Single cells in the primary auditory cortex of the awake squirrel monkey were tested for their responses to intraspecific communication calls presented to the monkey normally ("calls") and backwards ("llacs"). These two groups of signals were similarly effective in eliciting responses, and response patterns were of the same nature and equally diverse. In about 2% of the cells the time structure of a response to at least one "llac" was virtually a "mirror image" of the response to the corresponding "call". In about 34% of the cells, for at least one vocalization, at one intensity or other, the time distribution of response peaks closely approximated in time with the envelope of a particular spectral component of the call, corresponding with the cell's best frequency. These results suggest that complex sounds may be represented in the auditory cortex by the synchronized activity of functional cell ensembles in which differently tuned individual members are distributed throughout the cochleotopic space according to their best frequencies.

Animals↗

PubMed2005

Cortical ensemble adaptation to represent velocity of an artificial actuator controlled by a brain-machine interface.

Monkeys can learn to directly control the movements of an artificial actuator by using a brain-machine interface (BMI) driven by the activity of a sample of cortical neurons. Eventually, they can do so without moving their limbs. Neuronal adaptations underlying the transition from control of the limb to control of the actuator are poorly understood. Here, we show that rapid modifications in neuronal representation of velocity of the hand and actuator occur in multiple cortical areas during the operation of a BMI. Initially, monkeys controlled the actuator by moving a hand-held pole. During this period, the BMI was trained to predict the actuator velocity. As the monkeys started using their cortical activity to control the actuator, the activity of individual neurons and neuronal populations became less representative of the animal's hand movements while representing the movements of the actuator. As a result of this adaptation, the animals could eventually stop moving their hands yet continue to control the actuator. These results show that, during BMI control, cortical ensembles represent behaviorally significant motor parameters, even if these are not associated with movements of the animal's own limb.

Adaptation, Physiological↗

PubMed2006

Kinetic definition of protein folding transition state ensembles and reaction coordinates.

Using distributed molecular dynamics simulations we located four distinct folding transitions for a 39-residue betabetaalphabeta protein fold. To characterize the nature of each room temperature transition, we calculated the probability of transmission for 500 points along each free energy barrier. We introduced a method for determining transition states by employing the transmission probability, Ptrans, and determined which conformations were transition state ensemble members (Ptrans approximately 0.5). The transmission probability may be used to characterize the barrier in several ways. For example, we ran simulations at 82 degrees C, determined the change in Ptrans with temperature for all 2,000 conformations, and quantified Hammond behavior directly using Ptrans correlation. Additionally, we propose that diffusion along Ptrans may provide the configurational diffusion rate at the top of the barrier. Specifically, given a transition state conformation x0 with estimated Ptrans=0.5, we selected a large set of subsequent conformations from independent trajectories, each exactly a small time deltat after x0 (250 ps). Calculating Ptrans for the new trial conformations, we generated the P(Ptrans|deltat=250 ps) distribution that reflected diffusion. This approach provides a novel perspective on the diffusive nature of a protein folding transition and provides a framework for a quantitative study of activated relaxation kinetics.

Computer Simulation↗

PubMed2001

Dentate gyrus and ca1 ensemble activity during spatial reference frame shifts in the presence and absence of visual input.

In rats shuttling between a variably placed landmark of origin and a fixed goal, place fields of hippocampal CA1 cells encode location in two spatial reference frames. On the initial part of the outbound journey, place fields encode location with respect to the origin while on the final segment, place fields are aligned with the goal (Gothard et al., 1996b). An abrupt switch of reference frame can be induced experimentally by shortening the distance between the origin and the goal. Two linked hypotheses concerning this effect were addressed: (1) that the persistent, landmark-referenced firing results from some internal dynamic process (e.g., path integration or "momentum") and is not a result of maintained sensory input from the landmark of origin; and (2) that this hypothetical process is generated by connections either within CA3 or between CA3 and CA1, in which case the effect might be absent from the dentate gyrus. Neuronal ensemble recordings were made simultaneously from CA1 and the dentate gyrus as rats shuttled on a linear track between a variably located box and a goal, under light or dark conditions. The box-referenced firing persisted significantly longer in the dark in both hippocampal subfields, suggesting a competitive interaction between an internal dynamic process and external sensory cues. The similarity between reference frame transitions in the dentate gyrus and the CA1 region suggests that this process probably occurs before CA3, possibly in the entorhinal cortex or subiculum.

Action Potentials↗

PubMed2001

Postural sway of subjects wearing the U.S. Army chemical protective ensemble after functional activity.

BACKGROUND: This study assessed the effects of wearing the chemical protective clothing ensemble (CPE) vs. the battle dress uniform (BDU) on postural sway after 18 min of simulated field activity. Postural sway is a measure of static balance where a person maintains his/her center of gravity over his/her base of support by swaying fore to aft usually around the ankle joint axis. HYPOTHESES: Subjects' postural sway would increase more post-exercise while wearing the CPE vs. the BDU. The increase in postural sway while wearing the CPE would be due to decreased visual and somatosensory inputs. METHODS: Static balance was measured on 25 subjects pre- and post-exercise on the NeuroCom SMART Balance Master using the Sensory Organization Test protocol. Following a test-retest, repeated measures design, each subject completed the protocol twice, once while wearing only the BDU and once while wearing the CPE. RESULTS: A 2 x 2 repeated measures, multivariate analysis of variance revealed no significant difference between the static balance of subjects wearing the CPE vs. wearing the BDU pre- or post-exercise. CONCLUSIONS: The authors suggest that the wearing of the CPE does not affect static balance, even after completing 18 min of functional tasks. Future research should objectively quantify the amount of fatigue postexercise and employ a protocol that has been previously shown to increase postural sway.

Adult↗

PubMed2001

Reactivation of hippocampal ensemble activity patterns in the aging rat.

In young rats, the pattern of neuronal ensemble activity correlations expressed among hippocampal pyramidal cells during behavior persists during subsequent quiet wakefulness and slow-wave sleep, a process that may facilitate the consolidation of episodic memories. The present study explored the hypothesis that age-related changes in this process might contribute to memory impairments observed during normal aging. Neuronal activity was recorded from CA1 pyramidal cells, and in both young and old rats, there was a strong similarity between the resting epoch activity patterns and those from the preceding behavior epoch. This similarity was strongest during sharp-wave events. There were no detectable differences in the reactivation process or the decay rate between the young and old age groups. Thus, age differences in spatial memory do not appear to be explainable by differences in the spontaneous reactivation of familiar patterns within the hippocampus during the immediate postbehavior period.

Aging↗

PubMed2002

Taste-specific neuronal ensembles in the gustatory cortex of awake rats.

In gustatory cortex, single-neuron activity reflects the multimodal processing of taste stimuli. Little is known, however, about the interactions between gustatory cortical (GC) neurons during tastant processing. Here, these interactions were characterized. It was found that 36% (85 of 237) of neuron pairs, including many (61%) in which one or both single units were not taste specific, produced significant cross-correlations (CCs) to a subset of tastants across a hundreds of milliseconds timescale. Significant CCs arose from the coupling between the firing rates of neurons as those rates changed through time. Such coupling significantly increased the amount of tastant-specific information contained in ensembles. These data suggest that taste-specific GC assemblies may transiently form and coevolve on a behaviorally appropriate timescale, contributing to rats' ability to discriminate tastants.

Action Potentials↗

PubMed2002

Rapid generation of a representative ensemble of N-glycan conformations.

Glycosylated proteins are ubiquitous components of extracellular matrices and cellular surfaces where their oligosaccharide moieties are implicated in a wide range of cell-cell and cell-matrix recognition events. Glycans constitute highly flexible molecules. Only a small number of glycan X-ray structures is available for which sufficient electron density for an entire oligosaccharide chain has been observed. An unambiguous structure determination based on NMR-derived geometric constraints alone is often not possible. Time consuming computational approaches such as Monte Carlo calculations and molecular dynamics simulations have been widely used to explore the conformational space accessible to complex carbohydrates. The generation of a comprehensive data base for N-glycan fragments based on long time molecular dynamics simulations is presented. The fragments are chosen in such a way that the effects of branched N-glycan structures are taken into account. The prediction database constitutes the basis of a procedure to generate a complete set of all possible conformations for a given N-glycan. The constructed conformations are ranked according to their energy content. The resulting conformations are in reasonable agreement with experimental data. A web interface has been established (http://www.dkfz.de/spec/glydict/), which enables to input any N-glycan of interest and to receive an ensemble of generated conformations within a few minutes.

Carbohydrate Conformation↗

PubMed2004

Nociceptive responses of anterior cingulate cortical ensembles in behaving rats.

OBJECTIVE: To confirm the role of anterior cingulated cortices (ACC) in the coding of pain affect by exploring the neural ensemble coding pattern within the anterior cingulate cortex in behaving rats with a multichannel recording technique. METHODS: In five adult male Sprague-Dawley rats, two arrays of eight stainless steel microwires were bilaterally implanted into ACC. Noxious radiant heat stimulation was applied to the tail, bilateral fore-paws and hind-paws of freely moving rats. Neuroelectric signals were obtained from the microwires and sent to a multichannel recording device via cables and connectors. The time stamps of neuronal activities were stored on a personal computer for off-line analysis. RESULTS: Noxious heat stimuli evoked predominantly excitatory and sustained neural activity within ACC, reflecting the processing of pain unpleasantness; pain-related anticipatory responses could be seen near the stimulation start, indicating the behavioral preparation for escape; ACC neurons had broad receptive fields by showing quite similar pain-related responses to stimuli on either side of the hind-paw, suggesting that they are not eligible for the localization of a stimulus. CONCLUSION: ACC has played a major role in processing the affective-motivational aspect of pain.

Animals↗

PubMed2004

Application of the ensemble nonequilibrium response spectroscopy to shaker potassium channel gating.

Standard electrophysiology techniques study relaxation transients in voltage-gated ion channels generated by discrete voltage steps. The nonequilibrium response spectroscopy involves analyzing responses to fluctuating potentials. We apply the ensemble NRS method to gating kinetics of Shaker potassium ion channels. We evaluate various proposed Markov models of channel gating from the nonequilibrium response viewpoint. These new NRS protocols can be used to test otherwise indistinguishable models or improve estimates for parameters of channel kinetics models.

Animals↗

PubMed2003

Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources.

Amino Acid Sequence↗

PubMed1992

Contact lens wear with the USAF Protective Integrated Hood/Mask chemical defense ensemble.

The Protective Integrated Hood/Mask (PIHM) chemical defense aircrew ensemble blows air from the mask's plenum across the visor at a rate of approximately 15 L/min in order to prevent fogging of the visor and to cool the aircrew member's face. This study was designed to determine the effect of the PIHM airflow on soft contact lens (SCL) dehydration, contact lens comfort, and corneal integrity. There were 26 subjects who participated in this study: 15 SCL wearers, 6 rigid gas-permeable (RGP) wearers, and 5 nonspectacle wearing controls. Contrast acuity with the 3 Regan charts, subjective comfort, and relative humidity (RH) and temperature readings under the PIHM mask were monitored every 0.5 h during 6-h laboratory rides. Slit-lamp examinations and SCL water content measurements with a hand-held Abbe refractometer were made before and after the rides. High RH under the mask may have accounted for the moderate SCL dehydration (8.3%), no decrease in contrast acuity for any group, and lack of corneal stress. Although all groups experienced some inferior, epithelial, punctate keratopathy, RGP wearers had the most significant. SCLs performed relatively well in the PIHM mask environment. Testing with other parameter designs is necessary before recommending RGPs with the PIHM system.

Aerospace Medicine↗

PubMed2006

Physical fitness, menstrual cycle disorders and smoking habit in Croatian National Ballet and National Folk Dance Ensembles.

The study investigated differences in morphological, motor and functional abilities between folk and ballet dancers. The sample comprised 51 female subjects: Croatian National Ballet (N=30) and Croatian National Folk Ensemble "LADO" (N=21). The data regarding menstrual cycle, menarche, number of births and smoking habit were collected and the morphological, motor and functional abilities measured. Significant correlations between the amount of fat tissue and number of births were found in both groups. Folk dancers were as tall as ballet dancers but weighted more and had a larger body frame (p<0.001). Ballet dancers were more flexible but there were no differences in absolute maximal oxygen uptake (2.65 vs. 2.35 L/min, p=0.101). Still, as the ballet dancers weighted less, their relative maximal oxygen uptake was significantly higher (37.62 vs. 50.22 mL/kg/min, p<0.001). Also, a high number of 45% of smokers among professional ballet and professional folk dancers was found.

Adult↗