Biomedical subjects

Robert E Kearney

Publications and source records attributed to Robert E Kearney.

12 recordsLinked to original sources

PubMed2007

Methods for peptide identification by spectral comparison.

BACKGROUND: Tandem mass spectrometry followed by database search is currently the predominant technology for peptide sequencing in shotgun proteomics experiments. Most methods compare experimentally observed spectra to the theoretical spectra predicted from the sequences in protein databases. There is a growing interest, however, in comparing unknown experimental spectra to a library of previously identified spectra. This approach has the advantage of taking into account instrument-dependent factors and peptide-specific differences in fragmentation probabilities. It is also computationally more efficient for high-throughput proteomics studies. RESULTS: This paper investigates computational issues related to this spectral comparison approach. Different methods have been empirically evaluated over several large sets of spectra. First, we illustrate that the peak intensities follow a Poisson distribution. This implies that applying a square root transform will optimally stabilize the peak intensity variance. Our results show that the square root did indeed outperform other transforms, resulting in improved accuracy of spectral matching. Second, different measures of spectral similarity were compared, and the results illustrated that the correlation coefficient was most robust. Finally, we examine how to assemble multiple spectra associated with the same peptide to generate a synthetic reference spectrum. Ensemble averaging is shown to provide the best combination of accuracy and efficiency. CONCLUSION: Our results demonstrate that when combined, these methods can boost the sensitivity and specificity of spectral comparison. Therefore they are capable of enhancing and complementing existing tools for consistent and accurate peptide identification.

Journal Article↗

PubMed2006

Quantitative proteomics analysis of the secretory pathway.

We report more than 1400 proteins of the secretory-pathway proteome and provide spatial information on the relative presence of each protein in the rough and smooth ER Golgi cisternae and Golgi-derived COPI vesicles. The data support a role for COPI vesicles in recycling and cisternal maturation, showing that Golgi-resident proteins are present at a higher concentration than secretory cargo. Of the 1400 proteins, 345 were identified as previously uncharacterized. Of these, 230 had their subcellular location deduced by proteomics. This study provides a comprehensive catalog of the ER and Golgi proteomes with insight into their identity and function.

Animals↗

PubMed2005

Multicomponent internal recalibration of an LC-FTICR-MS analysis employing a partially characterized complex peptide mixture: systematic and random errors.

In high-throughput proteomics, a promising current approach is the use of liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) of tryptic peptides from complex mixtures of proteins. To apply this method, it is necessary to account for any systematic measurement error, and it is useful to have an estimate of the random error expected in the measured masses. Here, we analyze by LC-FTICR-MS a complex mixture of peptides derived from a sample previously characterized by LC-QTOF-MS. Application of a Bayesian probability model of the data and partial knowledge of the composition of the sample suffice to estimate both the systematic and random errors in measured masses.

Amino Acid Sequence↗

PubMed2005

Increasing peptide identification in tandem mass spectrometry through automatic function switching optimization.

Comprehensive proteomic studies that employ MS directed peptide sequencing are limited by optimal peptide separation and MS and tandem MS data acquisition routines. To identify the optimal parameters for data acquisition, we developed a system that models the automatic function switching behavior of a mass spectrometer using an MS-only dataset. Simulations were conducted to characterize the number and the quality of simulated fragmentation as a function of the data acquisition routines and used to construct operating curves defining tandem mass spectra quality and the number of peptides fragmented. Results demonstrated that one could optimize for quality or quantity, with the number of peptides fragmented decreasing as quality increased. The predicted optimal operating curve indicated that significant improvements can be realized by selecting the appropriate data acquisition parameters. The simulation results were confirmed experimentally by testing 10 LC MS/MS data acquisition parameter sets on an LC-Q-TOF-MS. Database matching of the experimental fragmentation returned peptide scores consistent with the predictions of the model. The results of the simulations of mass spectrometer data acquisition routines reveal an inverse relationship between the quality and the quantity of peptide identifications and predict an optimal operating curve that can be used to select an optimal data acquisition parameter for a given (or any) sample.

Algorithms↗

PubMed2005

A least-squares parameter estimation algorithm for switched hammerstein systems with applications to the VOR.

A "Multimode" or "switched" system is one that switches between various modes of operation. When a switch occurs from one mode to another, a discontinuity may result followed by a smooth evolution under the new regime. Characterizing the switching behavior of these systems is not well understood and, therefore, identification of multimode systems typically requires a preprocessing step to classify the observed data according to a mode of operation. A further consequence of the switched nature of these systems is that data available for parameter estimation of any subsystem may be inadequate. As such, identification and parameter estimation of multimode systems remains an unresolved problem. In this paper, we 1) show that the NARMAX model structure can be used to describe the impulsive-smooth behavior of switched systems, 2) propose a modified extended least squares (MELS) algorithm to estimate the coefficients of such models, and 3) demonstrate its applicability to simulated and real data from the Vestibulo-Ocular Reflex (VOR). The approach will also allow the identification of other nonlinear bio-systems, suspected of containing "hard" nonlinearities.

Algorithms↗

PubMed2005

Automated estimation of the phase between thoracic and abdominal movement signals.

This paper presents a new procedure for the automated estimation of the phase relation between thoracic and abdominal breathing signals measured by inductance plethysmography (RIP). This estimation is achieved using linear filters, binary converters and an exclusive-or gate. The filters are designed offline from prior knowledge of the spectrum of subjects' respiration, reducing computational complexity and providing on-line processing capabilities. Some numerical results based on simulated time series and infant respiration data are provided, showing that the new method is less biased than the Pearson correlation method, commonly used for assessment of thoracoabdominal asynchrony. Our method offers further advantages: 1) it works with uncalibrated measurements; 2) it provides quantitative phase estimates with no need to estimate the underlying frequency of the breathing signals; 3) it does not require nonconvex optimization search algorithms; and 4) it is easy to implement and to automate.

Abdomen↗

PubMed2004

Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling.

Tandem MS has identified 209 proteins of clathrin-coated vesicles (CCVs) isolated from rat brain. An overwhelming abundance of peptides were assigned to the clathrin coat with a 1:1 stoichiometry observed for clathrin heavy and light chains and a 2:1 stoichiometry of clathrin heavy chain with clathrin adaptor protein heterotetramers. Thirty-two proteins representing many of the known components of synaptic vesicles (SVs) were identified, supporting that a main function for brain CCVs is to recapture SVs after exocytosis. A ratio of vesicle-N-ethylmaleimide-sensitive factor attachment protein receptors to target-N-ethylmaleimide-sensitive factor attachment protein receptors, similar to that previously detected on SVs, supports a single-step model for SV sorting during CCV-mediated recycling of SVs. The uncovering of eight previously undescribed proteins, four of which have to date been linked to clathrin-mediated trafficking, further attests to the value of the current organelle-based proteomics strategy.

Animals↗

PubMed2003

Automated detection of focal cortical dysplasia lesions using computational models of their MRI characteristics and texture analysis.

Focal cortical dysplasia (FCD), a malformation of cortical development, is a frequent cause of pharmacologically intractable epilepsy. FCD is characterized on Tl-weighted MRI by cortical thickening, blurring of the gray-matter/white-matter interface, and gray-level hyperintensity. We have previously used computational models of these characteristics to enhance visual lesion detection. In the present study we seek to improve our methods by combining these models with features derived from texture analysis of MRI, which allows measurement of image properties not readily accessible by visual analysis. These computational models and texture features were used to develop a two-stage Bayesian classifier to perform automated FCD lesion detection. Eighteen patients with histologically confirmed FCD and 14 normal controls were studied. On the MRI volumes of the 18 patients, 20 FCD lesions were manually labeled by an expert observer. Three-dimensional maps of the computational models and texture features were constructed for all subjects. A Bayesian classifier was trained on the computational models to classify voxels as cerebrospinal fluid, gray-matter, white-matter, transitional, or lesional. Voxels classified as lesional were subsequently reclassified based on the texture features. This process produced a 3D lesion map, which was compared to the manual lesion labels. The automated classifier identified 17/20 manually labeled lesions. No lesions were identified in controls. Thus, combining models of the T1-weighted MRI characteristics of FCD with texture analysis enabled successful construction of a classifier. This computer-based, automated method may be useful in the presurgical evaluation of patients with severe epilepsy related to FCD.

Adult↗

PubMed2003

NARMAX representation and identification of ankle dynamics.

Representation and identification of a parallel pathway description of ankle dynamics as a model of the nonlinear autoregressive, moving average exogenous (NARMAX) class is considered. A nonlinear difference equation describing this ankle model is derived theoretically and shown to be of the NARMAX form. Identification methods for NARMAX models are applied to ankle dynamics and its properties investigated via continuous-time simulations of experimental conditions. Simulation results show that 1) the outputs of the NARMAX model match closely those generated using continuous-time methods and 2) NARMAX identification methods applied to ankle dynamics provide accurate discrete-time parameter estimates. Application of NARMAX identification to experimental human ankle data models with high cross-validation variance accounted for.

Ankle↗

PubMed2002

Computational models of MRI characteristics of focal cortical dysplasia improve lesion detection.

In many patients, focal cortical dysplasia (FCD) is characterized by minor structural changes that may go unrecognized by standard radiological analysis. We previously demonstrated that visual analysis of a composite map based on three simple models of MRI features of FCD increased the sensitivity of FCD lesion detection, compared to visual analysis of conventional MRI. Here we report on the use of improved methods for characterizing FCD which improve contrast in the composite maps: a Laplacian-based metric for measuring cortical thickness, a convolutional kernel to model blurring of the GM-WM interface, and an operator to measure hyperintense T1 signal. To validate these methods, we processed the MRIs of 14 FCD patients with our original set of image processing operators and an improved set of image processing operators. Comparison of the composite maps associated with the two sets of operators revealed that contrast between lesional tissue and nonlesional cortex was significantly increased in the composite maps associated with the set of improved operators. Increasing this contrast is an important step toward the goal of automated FCD lesion detection.

Brain Mapping↗

PubMed2002

The effect of locomotor training combined with functional electrical stimulation in chronic spinal cord injured subjects: walking and reflex studies.

With the new developments in traumatology medicine, the majority of spinal cord injuries sustained are clinically incomplete and the proportion is likely to continue to rise. Thus, it is necessary to continue to develop new treatment and rehabilitation strategies and understand the factors that can enhance recovery of walking following spinal cord injury (SCI). One new development is the use of functional electrical stimulation (FES) device to assist locomotion. The objective of this review is to present findings from some recent studies on the effect of long-term locomotor training with FES in subjects with SCI. Promising results are shown in all outcome measures of walking, such as functional mobility, speed, spatio-temporal parameters, and the physiological cost of walking. Furthermore, the change in the walking behavior could be associated with plasticity in the CNS organization, as seen by the modification of the stretch reflex and changes in the corticospinal projection to muscles of the lower leg. In conclusion, recovery of walking is an increasing possibility for a large number of people with SCI. New modalities of treatment have become available for this population but most still need to be evaluated for their efficacy. This review has focused on FES assisted walking as a therapeutic modality in subjects with chronic SCI, but it is envisaged that the care and recovery of SCI in the early phase of recovery could also be improved.

Animals↗

PubMed2002

The effects of long-term FES-assisted walking on intrinsic and reflex dynamic stiffness in spastic spinal-cord-injured subjects.

The effects of long-term functional electrical stimulation (FES)-assisted walking on ankle dynamic stiffness were examined in spinal cord-injured (SCI) subjects with incomplete motor function loss. A parallel-cascade system identification method was used to identify intrinsic and reflex contributions to dynamic ankle stiffness at different ankle positions while subjects remained relaxed. Intrinsic stiffness dynamics were well modeled by a linear second-order model relating intrinsic torque to joint position. Reflex stiffness dynamics were accurately described by a linear third-order model relating halfwave rectified velocity to reflex torque. We examined four SCI subjects before and after long-term FES-assisted walking (> 16 mo). Another SCI subject, who used FES for only five months was examined 12 mo latter to serve as a non-FES, SCI control. Reflex stiffness decreased in FES subjects by an average of 53% following FES-assisted walking, intrinsic stiffness also dropped by 45%. In contrast, both reflex and intrinsic stiffness increased in the non-FES, SCI control. These findings suggest that FES-assisted walking may have therapeutic effects, helping to reduce abnormal joint stiffness.

Adult↗