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Automated interictal spike detection and source localization in magnetoencephalography using independent components analysis and spatio-temporal clustering.

OBJECTIVE: Magnetoencephalography (MEG) dipole localization of epileptic spikes is useful in epilepsy surgery for mapping the extent of abnormal cortex and to focus intracranial electrodes. Visually analyzing large amounts of data produces fatigue and error. Most automated techniques are based on matching of interictal spike templates or predictive filtering of the data and do not explicitly include source localization as part of the analysis. This leads to poor sensitivity versus specificity characteristics. We describe a fully automated method that combines time-series analysis with source localization to detect clusters of focal neuronal current generators within the brain that produce interictal spike activity. METHODS: We first use an ICA (independent components analysis) method to decompose the multichannel MEG data and identify those components that exhibit spike-like characteristics. From these detected spikes we then find those whose spatial topographies across the array are consistent with focal neural sources, and determine the foci of equivalent current dipoles and their associated time courses. We then perform a clustering of the localized dipoles based on distance metrics that takes into consideration both their locations and time courses. The final step of refinement consists of retaining only those clusters that are statistically significant. The average locations and time series from significant clusters comprise the final output of our method. RESULTS AND SIGNIFICANCE: Data were processed from 4 patients with partial focal epilepsy. In all three subjects for whom surgical resection was performed, clusters were found in the vicinity of the resectioned area. CONCLUSIONS: The presented procedure is promising and likely to be useful to the physician as a more sensitive, automated and objective method to help in the localization of the interictal spike zone of intractable partial seizures. The final output can be visually verified by neurologists in terms of both the location and distribution of the dipole clusters and their associated time series. Due to the clinical relevance and demonstrated promise of this method, further investigation of this approach is warranted.

Action Potentials↗

Automated protocol for evaluation of electromagnetic component separation (APECS): Application of a framework for evaluating statistical methods of blink extraction from multichannel EEG.

OBJECTIVE: We present APECS (Automated Protocol for Evaluation of Electromagnetic Component Separation), a framework for evaluating the accuracy of blind source separation algorithms in removing artifacts from EEG data. APECS applies multiple, automated procedures to quantify the extent to which blinks are removed, and the degree to which nonocular activity is left intact. METHODS: APECS was used to evaluate blink removal using three BSS algorithms: Second-Order Blind Inference (SOBI) and two Independent Component Analysis (ICA) implementations, FastICA and Infomax. The algorithms were applied to a series of blink-free EEG datasets, which were contaminated with real or simulated blinks. Extracted components were assumed to contain blink activity if correlation of their spatial projectors to a predefined blink template exceeded some threshold, and if polarity inverted above and below the eyes. Blink-related components were then subtracted to produce filtered data. The success of each data decomposition is evaluated through the use of multiple, automated metrics, to determine which decomposition best approximates the ideal solution (complete separation of blink from nonblink activity). RESULTS: The outcomes for the evaluation measures were generally congruent, but also provided different and complementary information about the quality of each data decomposition. Under our testing framework, Infomax outperformed both FastICA and SOBI. Best results were achieved when blink activity loaded onto a single component. CONCLUSIONS: Multiple metrics, both quantitative and qualitative, are important in evaluating algorithms for artifact extraction. SIGNIFICANCE: Failure to achieve complete separation of blink from nonblink activity can affect experimental outcomes, as illustrated here, using an ERP study of word-nonword discrimination. This illustrates the importance of methods for evaluation of artifact extraction results.

Algorithms↗

Automated detection and volume measurement of plexiform neurofibromas in neurofibromatosis 1 using magnetic resonance imaging.

An automated technique for segmentation and volumetric measurement of plexiform neurofibromas (PN) in neurofibromatosis 1 using short T1-inversion recovery magnetic resonance images is presented. The algorithm described implements heuristics derived from human-based recognition of lesions. This technique combines region-based with boundary-based segmentation. Two observers, who performed semi-automated volume calculations and manual tracings to estimate tumor volume, validated this method on 9 PNs of different size and location. This automated method was reproducible (coefficient of variation 0.6-5.6%), yielded similar results to manual tumor tracings (R = 0.999) and will likely improve the ability to measure PNs in ongoing clinical trials.

Algorithms↗

Automated mitral annular tracking: a novel method for evaluating mitral annular motion using two-dimensional echocardiography.

We developed an automated mitral annular tracking method based on a digital processing of high frame rate cineloop images of 2-dimensional echocardiography. In this study, its feasibility and accuracy was validated in 11 healthy volunteers and 16 patients with left ventricular (LV) dysfunction. The mitral annular excursion measured by automated mitral annular tracking agreed well with that measured by 3-dimensional echocardiography and correlated with LV ejection fraction. The longitudinal mitral annular excursion was reduced whereas the radial one was preserved for patients with LV dysfunction compared with control subjects. The novel automated mitral annular tracking method is clinically feasible and has potential capability to quantify the comprehensive mitral annular motion for evaluating LV function in a clinical setting.

Adult↗

Automated quantitation of peripheral blood neutrophil activation in patients with myocardial ischaemia.

BACKGROUND: Coronary ischaemic syndromes are associated with neutrophil activation. The Bayer automated haematology analysers can detect increased light scatter of neutrophil populations, which correlates with neutrophil activation. We aimed to assess the role of an automated analyser in detecting systemic neutrophil activation in peripheral blood samples of patients with coronary ischaemia. METHODS: A prospective cross-sectional study was undertaken in 18 patients with chronic stable angina, 9 with unstable angina and 26 normal control subjects. Whole blood samples were taken to assess neutrophil count and light scatter, and serum samples were taken from some patients for assessment of Troponin T, C-reactive protein (CRP) and myeloperoxidase (MPO). In addition, whole blood was stimulated in vitro with interleukin (IL)-8 and N-formyl-methionyl-leucyl-phenylalanine (fMLP) to assess changes in neutrophil light scatter detected by the analyser. RESULTS: Neutrophil light scatter was increased in patients with chronic stable and unstable angina compared to normal control subjects (normal subjects 74.1 (73.3, 75.0) (mean arbitrary units (95% confidence intervals, (CI)) vs. 78.6 (76.9, 80.3) in the chronic stable angina group P<0.001 and 77.1 (75.3, 79.0) in the unstable angina group P<0.007). In vitro stimulation of whole blood produced comparable increases in neutrophil light scatter when morphological changes in neutrophils were demonstrable under electron microscopy. CONCLUSIONS: Automated measurement of neutrophil activation by light scatter is possible using the Advia 120 analyser and is superior to a neutrophil count in discriminating groups with angina. This technique may be useful in monitoring disease activity and progression in coronary artery disease and in guiding the use of anti-inflammatory therapies.

Adult↗

An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics.

We describe a fully automated high performance liquid chromatography 9.4 tesla Fourier transform ion resonance cyclotron (FTICR) mass spectrometer system designed for proteomics research. A synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial Bruker Daltonics FTICR instrument. The developments incorporated included a dual-ESI-emitter ion source; a dual-channel electrodynamic ion funnel; tandem quadrupoles for collisional cooling and focusing, ion selection, and ion accumulation, and served to significantly improve the sensitivity, dynamic range, and mass measurement accuracy of the mass spectrometer. In addition, a novel technique for accumulating ions in the ICR cell was developed that improved both resolution and mass measurement accuracy. A new calibration methodology is also described where calibrant ions are introduced and controlled via a separate channel of the dual-channel ion funnel, allowing calibrant species to be introduced to sample spectra on a real-time basis, if needed. We also report on overall instrument automation developments that facilitate high-throughput and unattended operation. These included an automated version of the previously reported very high resolution, high pressure reversed phase gradient capillary liquid chromatography (LC) system as the separations component. A commercial autosampler was integrated to facilitate 24 h/day operation. Unattended operation of the instrument revealed exceptional overall performance: Reproducibility (1-5% deviation in uncorrected elution times), repeatability (<20% deviation in detected abundances for more abundant peptides from the same aliquot analyzed a few weeks apart), and robustness (high-throughput operation for 5 months without significant downtime). When combined with modulated-ion-energy gated trapping, the dynamic calibration of FTICR mass spectra provided decreased mass measurement errors for peptide identifications in conjunction with high resolution capillary LC separations over a dynamic range of peptide peak intensities for each spectrum of 10(3), and >10(5) for peptide abundances in the overall separation.

Amino Acid Sequence↗

Analysis of human urine for fifteen phthalate metabolites using automated solid-phase extraction.

We improved our previous analytical method to measure phthalate metabolites in urine as biomarkers for phthalate exposure by automating the solid-phase extraction (SPE) procedure and expanding the analytical capability to quantify four additional metabolites: phthalic acid, mono-3-carboxypropyl phthalate, mono-isobutyl phthalate (miBP), and monomethyl isophthalate. The method, which involves automated SPE followed by isotope dilution-high performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS), allows for the quantitative measurement of 15 phthalate metabolites in urine with detection limits in the low ng/ml range. SPE automation allowed for the unattended sequential extraction of up to 100 samples at a time, and resulted in an increased sample throughput, lower solvent use, and better reproducibility than the manual SPE. Furthermore, the modified method permitted for the first time, the separation and quantification of mono-n-butyl phthalate (mBP) and its structural isomer miBP. The method was validated on spiked pooled urine samples and on pooled urine samples from persons with no known exposure to phthalates.

Automation↗

A comparison of anesthesiology resident and faculty electronic evaluations before and after implementation of automated electronic reminders.

STUDY OBJECTIVE: To develop an automated e-mail reminder system to contact residents and faculty regarding incomplete evaluations. DESIGN, SETTING, INTERVENTION, AND MEASUREMENTS: In the retrospective study, two 9-month periods were evaluated representing pre- and post-introduction of the automated e-mail reminder system. Data collected contained the number of evaluations completed and the rating of residents and faculty at the University of Michigan Health System in 5 different categories on a 5-point scale. MAIN RESULTS: The use of electronic reminders resulted in a nearly 4-fold increase in the number of resident evaluations by faculty from 1050 to 3761. Faculty completing evaluations increased from 40 (61%) to 66 (100%). The mean evaluation scores showed statistically significant but clinically negligible change for resident judgement, interpersonal skills, and intraoperative management. Resident preoperative evaluation and knowledge did not show statistically significant changes. Residents completing evaluations of faculty increased from 244 to 1798, and the number of residents completing evaluations rose from 40 (56%) to 87 (100%). There were no statistically significant changes in the evaluation of faculty except in the category of feedback. CONCLUSION: An automated e-mail reminder system implemented to contact residents and faculty regarding incomplete evaluations for residents and faculty dramatically enhanced participation in the evaluation process.

Anesthesiology↗

Comparison of manual and automated methods to determine horizontal corneal diameter.

PURPOSE: To compare 2 manual methods and 2 automated devices for measuring the horizontal corneal diameter (white-to-white [WTW] distance). SETTING: Department of Ophthalmology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany. METHODS: In 100 eyes of 61 patients, the WTW distance was measured independently by 2 examiners using the following techniques: the Holladay-Godwin gauge, a measuring caliper, Zeiss IOLMaster, and Orbscan II topography system (Bausch & Lomb). The results were compared with measurements on magnified slitlamp photographs of the anterior eye segment. Statistical evaluation was performed using the Bland-Altman method for comparison of measurement techniques. RESULTS: The mean horizontal corneal diameter was 11.91 mm +/- 0.71 (SD) with the measuring caliper, 11.8 +/- 0.60 mm with the Holladay-Godwin gauge, 11.78 +/- 0.43 mm with the Orbscan II, and 12.02 +/- 0.38 mm with the IOLMaster. The coefficient of inter-rater repeatability was 1.30 for the caliper, 0.92 for the Holladay-Godwin gauge, 0.76 for the Orbscan II, 0.50 for the IOLMaster, and 1.16 for the manual measurement in anterior segment images. The results obtained with the caliper were statistically significantly different between the 2 examiners (P<.001). The measurements of examiner 2 using the caliper were significantly different from the measurements of the same examiner using the Holladay-Godwin gauge. This was not the case with the 2 automated devices. CONCLUSIONS: Automated measurement of the WTW distance provides more precise results than measurements using manual methods. The Zeiss IOLMaster had the highest reliability in measuring corneal diameter.

Adult↗

Manual versus automated methods for cleaning reusable accessory devices used for minimally invasive surgical procedures.

We undertook a simulated-use study using quantitative methods to evaluate the cleaning efficacy of ported and non-ported accessory devices used in minimally invasive surgery. We chose laparoscopic scissors and forceps to represent worst-case devices which were inoculated with artificial test soil containing 10(6) cfu/mL Enterococcus faecalis and Geobacillus stearothermophilus and allowed to dry for 1 h. Cleaning was performed manually, as well as by the automated SI-Auto Narrow lumen cleaner. Manual cleaning left two- to 50-fold more soil residuals (protein, haemoglobin and carbohydrate) inside the lumen of non-ported versus ported laparoscopic accessory devices. The SI-Auto Narrow lumen cleaner was more efficient than manual cleaning and achieved >99% reduction in soil parameters in both non-ported (using retro-flushing) and ported laparoscopic devices. Only the automated cleaning of ported devices achieved 10(3)-10(4)-fold reduction in bacterial numbers. Sonication alone (no flushing of inner channel) did not effectively remove soil or organisms from the inner channel. Our findings indicate that non-ported accessory devices cannot be as reliably cleaned as ported devices regardless of the cleaning method used. If non-ported accessory devices are reprocessed, they should be cleaned using retro-flushing in an automated narrow lumen cleaner.

Automation↗

A vertical flow chamber for Xenopus oocyte electrophysiology and automated drug screening.

Xenopus laevis oocytes are used extensively in the study of ion channel coupled receptors. Efficient use of oocytes for ion channel characterization requires a system that is inherently stable, reproducible, minimizes drug volumes, and maximizes oocyte longevity. We have constructed a vertical flow oocyte recording chamber to address the aforesaid issues, where the oocyte is placed in a funnel-shaped chamber and perfused from the bottom of the funnel. The vertical rather than horizontal flow of perfusate results in an unusually stable environment for oocyte recording. Two-electrode voltage clamp recordings from a single oocyte are acquired easily and routinely over several hours while maintaining stable baseline currents and reproducible response profiles. Chamber characteristics were tested using a serotonin ligand-gated ion channel receptor (5-HT3R). Data obtained from this system corresponds well with published data. To further test the stability and reliability of this perfusion chamber, we constructed an automated oocyte perfusion system utilizing a commonly available HPLC autosampler. We were able to obtain dose-response curves for various 5-HT3AR ligands using the automated perfusion system with minimal user intervention. Such a system can easily satisfy need for automated oocyte electrophysiology in academic settings, especially small to medium sized laboratories.

Animals↗

Reliability assessment of an automated forced swim test device using two mouse strains.

The Porsolt forced swim test (FST) is one of the most widely used behavioral tests in the evaluation of the antidepressant effects of drugs. It is based on the fact that these drugs reduce the depression-related behaviors of learned helplessness. The model has been modified for use in mice. In contrast to rats, mice are exposed to forced swimming only once and their immobility behavior is measured and considered a "depression-like" phenotype. Like many other behavioral tests, FST can be affected by observer-related artifacts. In recent years, automated testing systems have been developed to decrease artifacts that may greatly influence the interpretation of results. In this work, we used two strains of mice, i.e., C3H/HeJ and C57BL/6J, which differ in their FST immobility times. We employed a new commercially available automated FST device and a blinded observer-based FST, and we examined their ability to measure behavioral differences between these two mouse strains. Our results suggest that the tested automated FST system generates reliable data comparable to results obtained by trained observers.

Algorithms↗

Automated 96-well liquid-liquid back extraction liquid chromatography-tandem mass spectrometry method for the determination of ABT-202 in human plasma.

A high-throughput bioanalytical method using automated sample transferring, automated liquid-liquid back extraction and liquid chromatography-tandem mass spectrometry was developed in a GLP regulated environment for the determination of ABT-202 in human plasma. Samples of 0.30 ml were transferred into 96-well plate using an automatic liquid handler. Automated liquid-liquid extraction (LLE) was carried out on a 96-channel programmable liquid handling workstation using methyl tert-butyl ether as the extraction solvent. A dual-HPLC with single mass spectrometer configuration was utilized to provide a reliable and routine means to increase sample throughput. The standard curve range was 0.38-95.02 ng/ml. There was no interference from endogenous components in the blank plasma tested. The accuracy (% bias) at the lower limit of quantitation (LLOQ) was 7.7% and the precision (% CV) for samples at the LLOQ was 4.7%. The inter-day % CV and % bias of the quality control samples were < or = 6.8 and < or = 7.6%, respectively. Coefficients of determination, a measure of linearity, ranged from 0.994 to 0.997. The method was accurate and reproducible and was successfully applied to generate plasma concentration-time profiles for human subjects after low oral doses of the compound.

Administration, Oral↗

Performance of the automated Abbott RealTime HIV-1 assay on a genetically diverse panel of specimens from Brazil.

The combination of automated sample preparation and real-time RT-PCR for measurement of HIV-1 viral load has the potential to significantly enhance throughput, reduce operator-associated error, and increase assay sensitivity and dynamic range. In this study, RNA was extracted from the plasma of 91 HIV-1 seropositive Brazilian blood donors using the Abbott m2000sp automated sample preparation system. Viral loads measured using the RealTime HIV-1 (RealTime HIV-1) assay and the Abbott m2000rt instrument were compared to values obtained in the LCx HIV RNA quantitative assay. Subtype was determined for 89 of 91 specimens by sequence/phylogenetic analysis of three genomic regions: gag p24, pol integrase, and env gp41. The panel included 69 subtype B, 1 C, 2 F, and 17 recombinant strains. Eighty-seven specimens were quantified by both assays. Two specimens were quantified only in RealTime HIV-1. Two additional specimens below the detection limit of both assays were also negative on PCR amplification. Viral load results were highly correlated, and good agreement was observed between assays with 90% of values within 0.5 log(10)copies/ml. The RealTime HIV-1 assay and m2000 system offer the advantages of automation while providing reliable quantification of diverse HIV strains.

Automation↗

Performance of the automated Abbott RealTime HIV-1 assay on a genetically diverse panel of specimens from London: comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx HIV RNA Quantitative assays.

Automated RNA extraction and quantitation of HIV-1 by real-time PCR offer potential advantages of efficient sample processing, improved sensitivity, expanded dynamic range and reduced contamination risk. In this study, plasma was collected from 100 HIV-1 infected patients visiting The Courtyard Clinic of St. George's Hospital in London, United Kingdom (UK). Viral loads measured using the automated Abbott RealTime HIV-1 assay (m2000sp sample preparation and m2000rt amplification and detection instruments) were compared to results obtained with Versant HIV-1 RNA 3.0 (bDNA), AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) and LCx HIV RNA Quantitative (LCx HIV) assays. Based on gag p24, pol integrase, and env gp41 sequences, the panel included 26 subtype A, 20 B, 27 C, 10 D, 1 CRF01_AE, 3 CRF02_AG and 13 recombinant viruses. RealTime HIV-1, bDNA, Monitor v1.5 and LCx HIV quantitated 82, 74, 82, and 83% of samples, respectively, with 82, 71, 69 and 80 of the 100 samples measured within the dynamic ranges. Viral loads were highly correlated with 99% of values within 1 log(10) copies/ml between tests. The automated m2000 system and RealTime HIV-1 assay can increase laboratory throughput, enhance overall efficiency and reduce operator-associated errors while providing reliable quantitation of genetically diverse strains of HIV-1.

Automation↗

Quantification of vesicles in differentiating human SH-SY5Y neuroblastoma cells by automated image analysis.

A new automated image analysis method for quantification of fluorescent dots is presented. This method facilitates counting the number of fluorescent puncta in specific locations of individual cells and also enables estimation of the number of cells by detecting the labeled nuclei. The method is here used for counting the AM1-43 labeled fluorescent puncta in human SH-SY5Y neuroblastoma cells induced to differentiate with all-trans retinoic acid (RA), and further stimulated with high potassium (K+) containing solution. The automated quantification results correlate well with the results obtained manually through visual inspection. The manual method has the disadvantage of being slow, labor-intensive, and subjective, and the results may not be reproducible even in the intra-observer case. The automated method, however, has the advantage of allowing fast quantification with explicitly defined methods, with no user intervention. This ensures objectivity of the quantification. In addition to the number of fluorescent dots, further development of the method allows its use for quantification of several other parameters, such as intensity, size, and shape of the puncta, that are difficult to quantify manually.

Algorithms↗

Development and evaluation of an automated atlas-based image analysis method for microPET studies of the rat brain.

An automated method for placement of 3D rat brain atlas-derived volumes of interest (VOIs) onto PET studies has been designed and evaluated. VOIs representing major structures of the rat brain were defined on a set of digitized cryosectioned images of the rat brain. For VOI placement, each PET study was registered with a synthetic PET target constructed from the VOI template. Registration was accomplished with an automated algorithm that maximized the mutual information content of the image volumes. The accuracy and precision of this method for VOI placement was determined using datasets from PET studies of the striatal dopamine and hippocampal serotonin systems. Each evaluated PET study could be registered to at least one synthetic PET target without obvious failure. Registration was critically dependent upon the initial position of the PET study relative to the synthetic PET target, but not dependent on the amount of synthetic PET target smoothing. An evaluation algorithm showed that resultant radioactivity concentration measurements of selected brain structures had errors=2% due to misalignment with the corresponding VOI. Further, radioligand binding values calculated from these measurements were found to be more precise than those calculated from measurements obtained with manually drawn regions of interest (ROIs). Overall, evaluation results demonstrated that this atlas-derived VOI method can be used to obtain unbiased measurements of radioactivity concentration from PET studies. Its automated features, and applicability to different radioligands and brain regions, will facilitate quantitative rat brain PET assessment procedures.

Animals↗

Intelligent software for laboratory automation.

The automation of laboratory techniques has greatly increased the number of experiments that can be carried out in the chemical and biological sciences. Until recently, this automation has focused primarily on improving hardware. Here we argue that future advances will concentrate on intelligent software to integrate physical experimentation and results analysis with hypothesis formulation and experiment planning. To illustrate our thesis, we describe the 'Robot Scientist' - the first physically implemented example of such a closed loop system. In the Robot Scientist, experimentation is performed by a laboratory robot, hypotheses concerning the results are generated by machine learning and experiments are allocated and selected by a combination of techniques derived from artificial intelligence research. The performance of the Robot Scientist has been evaluated by a rediscovery task based on yeast functional genomics. The Robot Scientist is proof that the integration of programmable laboratory hardware and intelligent software can be used to develop increasingly automated laboratories.

Algorithms↗