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At least 1,243 records · Page 69Linked to original sources
PubMed1992

Siebrandus Sixtius: evidence of rheumatoid arthritis of the robust reaction type in a seventeenth century Dutch priest.

Rheumatoid arthritis of the robust reaction type has been diagnosed in a seventeenth century Dutch priest, Siebrandus Sixtius, based on pictorial evidence of typical hand deformities and historical evidence affirming that he had chronic nodular rheumatism for many years. This case report, in conjunction with other pictorial depictions of probable rheumatoid arthritis, questions the view that rheumatoid arthritis is a modern disease which prevailed in the New World and was found in the Old World only after the discovery of America.

Arthritis, Rheumatoid↗
PubMed2003

A molecular marker map in 'Kanota' x 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework.

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota x Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using chi2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.

Avena↗
PubMed1985

A fast-twitch oxidative-glycolytic muscle with a robust inward calcium current.

This report describes the histochemical and physiological properties of a rat skeletal muscle with a robust activity-dependent slow inward Ca2+ current. The muscle, the flexor digitorum brevis (FDB), is a small plantar flexor from the hindfoot. It is a homogeneous muscle consisting of approximately 90% fast-twitch oxidative-glycolytic (type IIA) fibers. Stimulation of the FDB with repetitive stimulus trains (30 or 50 Hz for 330 ms, 1 train/s for 2-5 min) produced a slow increase in the base-line or resting tension of the muscle between trains. This progressive increase in resting tension appears to be due to the activation of voltage-dependent slow Ca2+ channels, since it could be eliminated (i) by stimulating the muscle in a medium containing 2 mM EGTA and without Ca2+, and (ii) by the addition of either Co2+ or verapamil. The presence of a slow current may be associated with an increase in K+ efflux as stimulation continues, and with a prolongation of relaxation time. We also propose that the slow Ca2+ current may contribute to the allosteric activation of phosphorylase kinase during muscle activity. The FDB provides an excellent preparation to investigate the regulation of muscle metabolism by intra- and extra-cellular Ca2+ during exercise.

Action Potentials↗
PubMed2002

Robust relational parsing over biomedical literature: extracting inhibit relations.

We describe the design of a robust parser for identifying and extracting biomolecular relations from the biomedical literature. Separate automata over distinct syntactic domains were developed for extraction of nominal-based relational information versus verbal-based relations. This allowed us to optimize the grammars separately for each module, regardless of any specific relation resulting in significantly better performance. A unique feature of this system is the use of text-based anaphora resolution to enhance the results of argument binding in relational extraction. We demonstrate the performance of our system on inhibition-relations, and present our initial results measured against an annotated text used as a gold standard for evaluation purposes. The results represent a significant improvement over previously published results on extracting such relations from Medline: Precision was 90%, Recall 57%, and Partial Recall 22%. These results demonstrate the effectiveness of a corpus-based linguistic approach to information extraction over Medline.

Abstracting and Indexing↗
PubMed2003

A robust subspace algorithm for principal component analysis.

We present a noise robust PCA algorithm which is an extension of the Oja subspace algorithm and allows tuning the noise sensitivity. We derive a loss function which is minimized by this algorithm and interpret it in a noisy PCA setting. Results on the local stability analysis of this algorithm are given and it is shown that the locally stable equilibria are those which minimize the loss function.

Algorithms↗
PubMed1996

A unified neural bigradient algorithm for robust PCA and MCA.

A new instantaneous-gradient search algorithm for computing a principal component or minor component type solution is proposed. The algorithm can use normalized Hebbian or anti-Hebbian learning in a unified formula. Starting from one-unit rule, a multi-unit algorithm is developed which can simultaneously extract several robust counterparts of the principal or minor eigenvectors of the data covariance matrix. Standard principal or minor components emerge as special cases from the general non-quadratic criterion. The learning rule is analyzed mathematically, and the theoretical results are verified by simulations. The proposed bigradient approach can be applied to blind separation of independent source signals from their linear mixtures.

Algorithms↗
PubMed2004

Robustness of metabolic map reconstruction.

With the ever increasing amount of genomic data available, the interest for generating biochemical pathways has grown tremendously. So far, mainly complete genomes have been used to reconstruct the biochemical pathways and their associated interactions. However, a large number of low coverage genomes, as well as other sources of partial genomic data, are currently available for many organisms. In order to be able to use incomplete data for metabolic reconstruction, the inherent properties of this procedure need to be investigated. In this short note, we describe the robustness and predictive power of metabolic reconstructions using partial information from Schizosaccharomyces pombe. We also discuss the implications of the results on reference genome projects as well as other large-scale sequencing data.

Chromosome Mapping↗
PubMed2005

Noise-robust soft clustering of gene expression time-course data.

Clustering is an important tool in microarray data analysis. This unsupervised learning technique is commonly used to reveal structures hidden in large gene expression data sets. The vast majority of clustering algorithms applied so far produce hard partitions of the data, i.e. each gene is assigned exactly to one cluster. Hard clustering is favourable if clusters are well separated. However, this is generally not the case for microarray time-course data, where gene clusters frequently overlap. Additionally, hard clustering algorithms are often highly sensitive to noise. To overcome the limitations of hard clustering, we applied soft clustering which offers several advantages for researchers. First, it generates accessible internal cluster structures, i.e. it indicates how well corresponding clusters represent genes. This can be used for the more targeted search for regulatory elements. Second, the overall relation between clusters, and thus a global clustering structure, can be defined. Additionally, soft clustering is more noise robust and a priori pre-filtering of genes can be avoided. This prevents the exclusion of biologically relevant genes from the data analysis. Soft clustering was implemented here using the fuzzy c-means algorithm. Procedures to find optimal clustering parameters were developed. A software package for soft clustering has been developed based on the open-source statistical language R. The package called Mfuzz is freely available.

Algorithms↗
PubMed2006

PRIMA: peptide robust identification from MS/MS spectra.

In proteomics, tandem mass spectrometry is the key technology for peptide sequencing. However, partially due to the deficiency of peptide identification software, a large portion of the tandem mass spectra are discarded in almost all proteomics centers because they are not interpretable. The problem is more acute with the lower quality data from low end but more popular devices such as the ion trap instruments. In order to deal with the noisy and low quality data, this paper develops a systematic machine learning approach to construct a robust linear scoring function, whose coefficients are determined by a linear programming. A prototype, PRIMA, was implemented. When tested with large benchmarks of varying qualities, PRIMA consistently has higher accuracy than commonly used software MASCOT, SEQUEST and X! Tandem.

Amino Acid Sequence↗
PubMed2006

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

Computational studies of large macromolecular assemblages have come a long way during the past 10 years. With the explosion of computer power and parallel computing, timescales of molecular dynamics simulations have been extended far beyond the hundreds of picoseconds timescale. However, limitations remain for studies of large-scale conformational changes occurring on timescales beyond nanoseconds, especially for large macromolecules. In this review, we describe recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information. Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin.

Algorithms↗
PubMed2003

Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres.

Telomere molecular biology is far more complex than originally thought. Understanding biological systems is aided by study of evolutionary variants, and Drosophila telomeres are remarkable variants. Drosophila lack telomerase and the arrays of simple repeats generated by telomerase in almost all other organisms; instead, Drosophila telomeres are long tandem arrays of two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements found to have a bona fide role in cell structure, revealing an unexpected link between telomeres and what is generally considered to be parasitic DNA. In addition to providing insight into the cellular functions performed by telomeres, analysis of HeT-A and TART is providing insight into the evolution of chromosomes, retrotransposons, and retroviruses. Recent studies show that retrotransposon telomeres constitute a robust system for maintaining chromosome ends. These telomeres are now known to predate the separation of extant Drosophila species, allowing ample time for elements and hosts to coevolve interesting mechanisms.

Animals↗
PubMed2005

Robustness of computerized lesion detection and classification scheme across different breast US platforms.

PURPOSE: To evaluate the performance of a computerized detection and diagnosis method with breast ultrasonographic (US) images obtained with US equipment from two different manufacturers. MATERIALS AND METHODS: Two independent clinical breast US databases were used in this performance study. Data collection and database use were HIPAA-compliant and followed institutional review board-approved protocols, with waiver of informed consent. One database consisted of 1740 images obtained in 458 women with Philips US equipment. The other database consisted of 151 images obtained in 151 women with Siemens US equipment. The testing protocols included independent testing and round-robin analysis. The computerized scheme detects potential lesions, calculates imaging features for all candidate lesions, and subsequently classifies candidate lesions into different categories. Two separate classification tasks were evaluated: distinction between all actual lesions and false-positive detections and distinction between actual cancers and all other detected lesion candidates. Statistical analysis was performed by using both receiver operating characteristic (ROC) and free-response ROC methods. RESULTS: For the distinction between all actual lesions and false-positive detections, area under the ROC curve (A(z)) values ranged between 0.87 and 0.95 for different testing protocols. In two instances, the difference in performance between databases was significant (P < .01), but it was shown that this was due to the difference in size of the databases. In the distinction of cancer from all other detections, the A(z) values ranged between 0.80 and 0.86. No statistically significant difference was found among the different testing protocols in this instance. CONCLUSION: These results indicate that the performance of this fully automated computerized lesion detection and classification method, which demonstrated robustness over the different US equipment used, is promising.

Adolescent↗
PubMed1998

Effect of the shift of the sleep-wake cycle on three robust endocrine markers of the circadian clock.

To determine the effect of a phase shift in sleep on the circadian clock, thyroid-stimulating hormone (TSH), cortisol, and melatonin, three robust markers of the circadian clock, were analyzed using a 10-min blood sampling procedure. In an initial experiment eight subjects were studied during two experimental sessions: once under baseline conditions with normal nighttime sleep from 2300 to 0700 (baseline) and once after a night of sleep deprivation followed by daytime sleep from 0700 to 1500 (day 1). In a second experiment, carried out on seven subjects, the 24-h hormone profiles of the first day (day 1) were compared with those of the second day (day 2) of the sleep shift. During the night of sleep deprivation (day 1) the TSH surge was higher than during baseline conditions, whereas melatonin and cortisol rhythms remained unaffected. On day 2 the amplitude of the nocturnal TSH surge was reduced in comparison to day 1, whereas the amplitudes of melatonin and cortisol rhythms were unchanged. There was a clear phase shift in the three endocrine rhythms. Triiodothyronine levels were slightly higher in the morning after the first night of sleep deprivation. These results demonstrate that 2 consecutive days of sleep shift are sufficient to affect the timing of the commonly accepted circadian markers, suggesting the existence of a rapid resetting effect on the circadian clock. TSH reacts in a distinctive manner to the sleep-wake cycle manipulation by modulating the amplitude of the nocturnal surge. This amplitude modulation is probably an integral part of the phase-shifting mechanisms controlled by the circadian clock.

Adult↗
PubMed2003

Norepinephrine release in brown adipose tissue remains robust in cold-exposed senescent Fischer 344 rats.

Near the end of life, old F344 rats undergo a transition, marked by spontaneous and rapidly declining function. Food intake and body weight decrease, and these rats, which we call senescent, develop severe hypothermia in the cold due in part to blunted brown fat [brown adipose tissue (BAT)] thermogenesis. We tested the hypothesis that this attenuation may involve diminished sympathetic signaling by measuring cold-induced BAT norepinephrine release in freely moving rats using linear microdialysis probes surgically implanted into interscapular BAT 24 and 48 h previously. In response to 2 h at 15 degrees C, senescent rats increased BAT norepinephrine release 6- to 10-fold but did not maintain homeothermy. This increase was comparable to that of old presenescent (weight stable) rats that did maintain homeothermy during even greater cold exposure (2 h at 15 degrees C followed by 1.5 h at 8 degrees C). Tail temperatures, an index of vasoconstrictor responsiveness to cold, exhibited similar cooling curves in presenescent and senescent rats. Thus cold-induced sympathetic signaling to BAT and tail vasoconstrictor responsiveness remain robust in senescent rats and cannot explain their cold-induced hypothermia.

Adipose Tissue, Brown↗
PubMed2005

Development of a robust central auditory synapse in congenital deafness.

Within the medial nucleus of the trapezoid body (MNTB) in the auditory brain stem, there is a large central synapse known as the calyx of Held, which mediates high-fidelity glutamatergic transmission. We investigated the effects of congenital deafness on the development of pre- and postsynaptic parameters of synaptic strength at the calyx of Held. Whole cell recordings of evoked excitatory postsynaptic currents (EPSCs) and immunohistochemistry of GluR1-4 subunits were performed using brain stem slices from congenitally deaf or hearing mice at postnatal days P5 and P12. In both hearing and deaf mice there was a similar developmental decrease in the NMDA component of the evoked EPSC. There was a concurrent increase in release probability and number of release sites, contributing to a fivefold increase in evoked AMPA-mediated EPSC amplitude. The increase in release probability is opposite to that found in previous studies at the calyx of Held in the rat. There was also a seven- to eightfold increase in the size of the readily releasable pool of vesicles and a decrease in tetanic depression. The postsynaptic glutamate receptor subunits were similarly developmentally regulated and unaffected by deafness. GluR1 and 4 dominated at both ages. There was a decrease in expression of GluR1-3 from P5 to P12 and a shift from GluR2 to GluR3, indicating that AMPA receptor complexes at P12 are predominantly calcium-permeable. These results demonstrate that early development at this robust synapse proceeds normally with congenital deafness, suggesting that auditory nerve activity does not affect the development of synaptic strength at the calyx of Held.

Animals↗
PubMed2006

Symmetric interactions within a homogeneous starburst cell network can lead to robust asymmetries in dendrites of starburst amacrine cells.

Starburst amacrine cells in the mammalian retina respond asymmetrically to movement along their dendrites; centrifugal movement elicits stronger responses in each dendrite than centripetal movement. It has been suggested that the asymmetrical response can be attributed to intrinsic properties of the processes themselves. But starburst cells are known to release and have receptors for both GABA and acetylcholine. We tested whether interactions within the starburst cell network can contribute to their directional response properties. In a computational model of interacting starburst amacrine cells, we simulated the response of individual dendrites to moving light stimuli. By setting the model parameters for "synaptic connection strength" (cs) to positive or negative values, overlapping starburst dendrites could either excite or inhibit each other. For some values of cs, we observed a very robust inward/outward asymmetry of the starburst dendrites consistent with the reported physiological findings. This is the case, for example, if a starburst cell receives inhibition from other starburst cells located in its surround. For other values of cs, individual dendrites can respond best either to inward movement or respond symmetrically. A properly wired network of starburst cells can therefore account for the experimentally observed asymmetry of their response to movement, independent of any internal biophysical or biochemical properties of starburst cell dendrites.

Acetylcholine↗
PubMed2006

Intrinsic bursters increase the robustness of rhythm generation in an excitatory network.

The pre-Botzinger complex (pBC) is a vital subcircuit of the respiratory central pattern generator. Although the existence of neurons with pacemaker-like bursting properties in this network is not questioned, their role in network rhythmogenesis is unresolved. Modeling is ideally suited to address this debate because of the ease with which biophysical parameters of individual cells and network architecture can be manipulated. We modeled the parameter variability of experimental data from pBC bursting pacemaker and nonpacemaker neurons using a modified version of our previously developed pBC neuron and network models. To investigate the role of pacemakers in networkwide rhythmogenesis, we simulated networks of these neurons and varied the fraction of the population made up of pacemakers. For each number of pacemaker neurons, we varied the amount of tonic drive to the network and measured the frequency of synchronous networkwide bursting produced. Both excitatory networks with all-to-all coupling and sparsely connected networks were explored for several levels of synaptic coupling strength. Networks containing only nonpacemakers were able to produce networkwide bursting, but with a low probability of bursting and low input and output ranges. Our results indicate that inclusion of pacemakers in an excitatory network increases robustness of the network by more than tripling the input and output ranges compared with networks containing no pacemakers. The largest increase in dynamic range occurs when the number of pacemakers in the network is greater than 20% of the population. Experimental tests of our model predictions are proposed.

Afferent Pathways↗
PubMed1999

Multisecond oscillations in firing rate in the basal ganglia: robust modulation by dopamine receptor activation and anesthesia.

Multisecond oscillations in firing rate in the basal ganglia: robust modulation by dopamine receptor activation and anesthesia. Studies of CNS electrophysiology have suggested an important role for oscillatory neuronal activity in sensory perception, sensorimotor integration, and movement timing. In extracellular single-unit recording studies in awake, immobilized rats, we have found that many tonically active neurons in the entopeduncular nucleus (n = 15), globus pallidus (n = 31), and substantia nigra pars reticulata (n = 31) have slow oscillations in firing rate in the seconds-to-minutes range. Basal oscillation amplitude ranged up to +/-50% of the mean firing rate. Spectral analysis was performed on spike trains to determine whether these multisecond oscillations were significantly periodic. Significant activity in power spectra (in the 2- to 60-s range of periods) from basal spike trains was found for 56% of neurons in these three nuclei. Spectral peaks corresponded to oscillations with mean periods of approximately 30 s in each nucleus. Multisecond baseline oscillations were also found in 21% of substantia nigra dopaminergic neurons. The dopamine agonist apomorphine (0.32 mg/kg iv, n = 10-15) profoundly affected multisecond oscillations, increasing oscillatory frequency (means of spectral peak periods were reduced to approximately 15 s) and increasing the regularity of the oscillations. Apomorphine effects on oscillations in firing rate were more consistent from unit to unit than were its effects on mean firing rates in the entopeduncular nucleus and substantia nigra. Apomorphine modulation of multisecond periodic oscillations was reversed by either D1 or D2 antagonists and was mimicked by the combination of selective D1 (SKF 81297) and D2 (quinpirole) agonists. Seventeen percent of neurons had additional baseline periodic activity in a faster range (0.4-2.0 s) related to ventilation. Multisecond periodicities were rarely found in neurons in anesthetized rats (n = 29), suggesting that this phenomenon is sensitive to overall reductions in central activity. The data demonstrate significant structure in basal ganglia neuron spiking activity at unexpectedly long time scales, as well as a novel effect of dopamine on firing pattern in this slow temporal domain. The modulation of multisecond periodicities in firing rate by dopaminergic agonists suggests the involvement of these patterns in behaviors and cognitive processes that are affected by dopamine. Periodic firing rate oscillations in basal ganglia output nuclei should strongly affect the firing patterns of target neurons and are likely involved in coordinating neural activity responsible for motor sequences. Modulation of slow, periodic oscillations in firing rate may be an important mechanism by which dopamine influences motor and cognitive processes in normal and dysfunctional states.

Anesthesia, General↗