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PubMed2001

Automated tracking of facial features in patients with facial neuromuscular dysfunction.

Facial neuromuscular dysfunction severely impacts adaptive and expressive behavior and emotional health. Appropriate treatment is aided by quantitative and efficient assessment of facial motion impairment. We validated a newly developed method of quantifying facial motion, automated face analysis (AFA), by comparing it with an established manual marking method, the Maximal Static Response Assay (MSRA). In the AFA, motion of facial features is tracked automatically by computer vision without the need for placement of physical markers or restrictions of rigid head motion. Nine patients (seven women and two men) with a mean age of 39.3 years and various facial nerve disorders (five with Bell's palsy, three with trauma, and one with tumor resection) participated. The patients were videotaped while performing voluntary facial action tasks (brow raise, eye closure, and smile). For comparison with MSRA, physical markers were placed on facial landmarks. Image sequences were digitized into 640 x 480 x 24-bit pixel arrays at 30 frames per second (1 pixel congruent with0.3 mm). As defined for the MSRA, the coordinates of the center of each marker were manually recorded in the initial and final digitized frames, which correspond to repose and maximal response. For the AFA, these points were tracked automatically in the image sequence. Pearson correlation coefficients were used to evaluate consistency of measurement between manual (the MSRA) and automated (the AFA) tracking methods, and paired t tests were used to assess the mean difference between methods for feature tracking. Feature measures were highly consistent between methods, Pearson's r = 0.96 or higher, p < 0.001 for each of the action tasks. The mean differences between the methods were small; the mean error between methods was comparable to the error within the manual method (less than 1 pixel). The AFA demonstrated strong concurrent validity with the MSRA for pixel-wise displacement. Tracking was fully automated and provided motion vectors, which may be useful in guiding surgical and rehabilitative approaches to restoring facial function in patients with facial neuromuscular disorders.

Adult↗

PubMed2002

Identifying sources of variability in scoliosis classification using a rule-based automated algorithm.

STUDY DESIGN: Use of a rule-based automated algorithm to determine sources of variability in radiographic classification. OBJECTIVES: To determine whether unambiguous rules encoded in a computer program would ensure reliable classification. SUMMARY OF BACKGROUND DATA: Reliability problems have been identified in classifications used in surgical planning for patients with thoracic idiopathic scoliosis, but the sources of unreliability are not understood. METHODS: Objective classification methodology was tested on the King et al (1983) scheme. There were two novel components: 1) positions of the corners of vertebrae in radiographs were digitized relative to a defined axis system and used in automated evaluation of spinal shape parameters required for classification; and 2) the assignment of a classification was done with a rule-based algorithm. The algorithm was implemented after some ambiguities and absence of precise definitions in the King et al classification scheme had been resolved. The algorithm was tested with radiographs of patients having adolescent idiopathic scoliosis. RESULTS: The automated procedure could encounter reliability problems in cases in which a lumbar curve was very close to crossing the midline, thoracic and lumbar curves were of approximately equal value, when the apex level in the thoracolumbar region was ambiguous, when a Cobb angle was close to 10 degrees, or when the flexibility index was close to unity. CONCLUSION: Objective measurements and rule-based algorithms can eliminate some sources of interobserver and intraobserver errors in classification of spinal deformity. When classification parameters fall close to the boundaries for classification, reliability problems will persist.

Algorithms↗

PubMed1984

Automated extraction and high-performance liquid chromatographic determination of serum clonazepam.

We have developed a rapid extraction process using the DuPont Prep I automated extractor/concentrator to prepare serum samples for the high-performance liquid chromatographic (HPLC) determination of clonazepam. The drug, at an alkaline pH, is applied to a styrene divinylbenzene preparatory extraction column. The Prep I is a reversible centrifuge that allows the sample to pass through the preparatory column, followed by a wash solution of deionized water. The rotor then reverses direction and dispenses 20 ml of ethyl acetate, which elutes the adsorbed drug into an aluminum cup that is automatically dried at 68 degrees C. The extract is reconstituted with 100 microliters of mobile-phase, 50-mM sodium acetate (pH 5.4):acetonitrile:methanol (450:235:265, vol/vol). The chromatography is performed on a C-18 radial compression cartridge and detection is by absorbance at 313 nm. A plot of peak height ratio against concentration is linear to at least 160 ng/ml. The recovery of clonazepam with this automated extraction is 97.5%, compared with 90.0% for a manual extraction method. The coefficient of variation is 2.9% with the automated extraction. Only propranolol was found to interfere with clonazepam, whereas clorazepate interferes with the elution of the internal standard, nordiazepam.

Autoanalysis↗

PubMed2002

Investigation of capacitor failures in an automated external defibrillator.

Over the past 2 years, the Canadian Medical Devices Bureau has received a number of reports of capacitor failures on the high voltage board of an automated external defibrillator. Twenty-five cases of broken capacitor leads were found during routine preventive maintenance by the biomedical engineering staff of the institutions reporting the incidents. The Bureau has carried out a laboratory investigation to determine the effect of missing capacitors on the energy delivered by the defibrillator and to assess whether these capacitor failures represent a significant risk to patients. Our findings indicate that the automated external defibrillator will not perform acceptably with two broken capacitors. They further suggest that, during preventive maintenance, operators should use a defibrillator analyser to measure the delivered energy output rather than using the internal energy measurement circuit within the automated external defibrillator.

Canada↗

PubMed2004

Attenuated adult biphasic shocks for prolonged pediatric ventricular fibrillation: support for pediatric automated defibrillators.

OBJECTIVE: To evaluate published data regarding the treatment of prolonged pediatric defibrillation, with special emphasis on the use of attenuated adult biphasic shocks for pediatric defibrillation. DESIGN: Review relevant human and animal literature. RESULTS: Rhythm analysis algorithms from two manufacturers of automated external defibrillators can accurately distinguish shockable from nonshockable rhythms in children. Theoretical considerations and transthoracic impedance data from animals and children suggest that pediatric defibrillation doses should not necessarily vary in a simple weight-based manner. Two piglet studies have established that an attenuated adult biphasic dosage can be successfully used for 3.5- to 24-kg animals in ventricular fibrillation. One study established that the attenuated adult biphasic dosage was at least as safe and effective as the standard monophasic weight-based dosing. CONCLUSION: This review supports the American Heart Association's new guidelines for pediatric automated external defibrillator usage: "Automated external defibrillators may be used for children 1 to 8 yrs of age who have no signs of circulation. Ideally the device should deliver a pediatric dose. The arrhythmia detection system used in the device should demonstrate high specificity for pediatric shockable rhythms, i.e., it will not recommend delivery of a shock for nonshockable rhythms."

Adult↗

PubMed2004

Recurrent ventricular fibrillation in out-of-hospital cardiac arrest after defibrillation by police and firefighters: implications for automated external defibrillator users.

OBJECTIVE: To determine the prevalence and frequency of recurrent ventricular fibrillation (VF) in patients defibrillated by police and firefighters only and to determine its relation to survival. DESIGN: Retrospective observational study. SETTING: Out of hospital. PATIENTS: Individuals with witnessed VF arrest in the Rochester, MN, ambulance public service area who had defibrillatory shocks delivered by police and firefighters and return of spontaneous circulation with shocks only. MEASUREMENTS AND MAIN RESULTS: Electrocardiograms were recovered from data cards in automated external defibrillators used by police (n = 49) or firefighters (n = 18) to deliver shocks from December 1996 through December 2003 in the Rochester, MN, ambulance public service area. Patients with witnessed VF arrest were identified for recurrent VF after initial shock success (first one to three shocks). Both police and firefighters deployed automated external defibrillators delivering nonescalating 150-J biphasic truncated exponential waveform shocks (ForeRunner Automated External Defibrillator, Phillips/Heartstream Operation, Seattle, WA). Among 67 patients, 30 (45%) survived to neurologically intact discharge (overall performance category score of 1 in 29 patients and score of 2 in one patient). Twenty-nine patients (43%) regained spontaneous circulation with shocks only and 25 of 29 (86%) survived. VF recurred in 35 of the 67 patients (52%) while being cared for by police or firefighters. Of these 35 patients, no relation was found between the prevalence or frequency of VF recurrence and survival. CONCLUSIONS: VF recurrence is frequent, variable in time of onset, and unrelated to the performance of bystander CPR. The prevalence and frequency of VF recurrence were unpredictable and do not adversely affect survival. Thus, vigilance for recurrent VF is essential to ensure the survival of patients who are in the care of first responders, even after initial restoration of pulses with shocks.

Cardiopulmonary Resuscitation↗

PubMed2004

Lamellar keratectomy using an automated microkeratome.

PURPOSE: To evaluate the effectiveness of treating anterior corneal pathology by performing a superficial lamellar keratectomy with an automated microkeratome. METHODS: Retrospective chart review of 10 eyes (8 patients) seen in a subspecialty referral practice for anterior segment disease. With the use of an automated microkeratome, a lamellar flap was created, which was then surgically excised. RESULTS: Ten eyes of eight patients were followed for a mean of 5.4 months (range, 4 to 10 months). Subjective visual acuity and/or sensation of ocular irritation improved in 10 of 10 eyes. Mean improvement in Snellen best-corrected visual acuity was 1.8 lines (range, -1 to +3 lines). One patient lost 1 line of Snellen acuity due to progression of a posterior subcapsular cataract. Mean change in spherical equivalent was +0.5 diopters (range, -1.60 to +4.25 diopters), and mean improvement in corneal clarity (1 to 4 scale) was 1.8. Mean preoperative pachymetry was 589.0 microm (range, 507 to 741 microm). Mean postoperative pachymetry was 461.3 microm (range, 370 to 564 microm). Recurrence of pathology (band keratopathy and Salzmann's nodular degeneration) occurred in two patients. In one patient, immunohistochemical staining of corneal tissue from the lamellar dissection confirmed the diagnosis of herpes simplex virus type 1 stromal keratitis, improving the course of postoperative care. CONCLUSION: Lamellar keratectomy with the use of an automated microkeratome is a safe and effective method for removing superficial anterior corneal opacities. For selected cases, it offers specific advantages over other surgical modalities. In particular, this procedure may induce far less hyperopic shift than would the equivalent amount of tissue removal by performing excimer laser phototherapeutic keratectomy.

Corneal Opacity↗

PubMed2003

Comparison of pathologist-detected and automated computer-assisted image analysis detected sentinel lymph node micrometastases in breast cancer.

Sentinel lymph node biopsy has stimulated interest in identification of micrometastatic disease in lymph nodes, but identifying small clusters of tumor cells or single tumor cells in lymph nodes can be tedious and inaccurate. The optimal method of detecting micrometastases in sentinel nodes has not been established. Detection is dependent on node sectioning strategy and the ability to locate and confirm tumor cells on histologic sections. Immunohistochemical techniques have greatly enhanced detection in histologic sections; however, comparison of detection methodology has not been undertaken. Automated computer-assisted detection of candidate tumor cells may have the potential to significantly assist the pathologist. This study compares computer-assisted micrometastasis detection with routine detection by a pathologist. Cytokeratin-stained sentinel lymph node sections from 100 patients at the University of Vermont were evaluated by automated computer-assisted cell detection. Based on original routine light microscopy screening, 20 cases that were positive and 80 cases that were negative for micrometastases were selected. One-level (43 cases) or two-level (54 cases) cytokeratin-stained sections were examined per lymph node block. All 100 patients had previously been classified as node negative by using routine hematoxylin and eosin stained sections. Technical staining problems precluded computer-assisted cell detection scanning in three cases. Computer-assisted cell detection detected 19 of 20 (95.0%; 95% confidence interval, 75-100%) cases positive by routine light microscopy. Micrometastases missed by computer-assisted cell detection were caused by cells outside the instrument's scanning region. Computer-assisted cell detection detected additional micrometastases, undetected by light microscopy, in 8 of 77 (10.4%; 95% confidence interval, 5-20%) cases. The computer-assisted cell detection-positive, light microscopy-missed detection rate was similar for cases with one (3 of 30; 10.0%) or two (5 of 47; 10.6%) cytokeratin sections. Metastases detected by routine light microscopy tended to be larger (0.01-0.50 mm) than did metastases detected only by computer-assisted cell detection (0.01-0.03 mm). In a selected series of patients, automated computer-assisted cell detection identified more micrometastases than were identified by routine light microscopy screening of cytokeratin-stained sections. Computer-assisted detection of events that are limited in number or size may be more reliable than detection by a pathologist using routine light microscopy. Factors such as human fatigue, incomplete section screening, and variable staining contribute to missing metastases by routine light microscopy screening. Metastases identified exclusively by computer-assisted cell detection tend to be extremely small, and the clinical significance of their identification is currently unknown.

Breast Neoplasms↗

PubMed2004

Evaluation of an automated subjective refractor.

PURPOSE: To test the validity and repeatability of an automated subjective refractor compared with subjective refraction performed by clinicians. Corrected visual acuity was used to compare the validity of each technique. METHODS: On each of two visits separated by at least 1 week, the following were measured in 60 naive subjects (mean age, 33 +/- 11 years): automated objective refraction (AOR) and automated subjective refraction (ASR) with the Topcon BV-1000, subjective refraction by one of two doctors (DR), and monocular visual acuity with the ASR and DR findings. Repeatability of refraction was calculated as the 95% limits of agreement (LoA) between same-mode measurements from the two visits. The validity of the ASR compared with DR was determined two ways: as the 95% LoA between the two measures and as the mean visual acuity measured with each prescription. RESULTS: The DR and AOR had similar repeatability: 95% LoA = -0.49 to +0.46 D and -0.51 to +0.45 D, respectively. The ASR had poorer repeatability with 95% LoA of -0.70 to + 0.71 D. Because of a calibration (offset) error in the right eye path of the BV-1000, the ASR of the right eye yielded refractions +0.26 +/- 0.41 D higher than the DR. For the right eye, visual acuity was 3.42 +/- 6.09 letters better with the DR than with the ASR, consistent with this calibration error. For the left eye, visual acuity was 1.20 +/- 5.20 letters better for the DR. CONCLUSIONS: Doctor-performed refractions are more valid and repeatable than the ASR performed with the BV-1000, although the differences are small. When calibrated, the BV-1000 gives similar visual acuity values to the DR, although the visual acuity for the DR is more repeatable.

Adolescent↗

PubMedDate not supplied

Computed tomography colonography: automated diameter and volume measurement of colonic polyps compared with a manual technique--in vitro study.

OBJECTIVE: To investigate inter- and intraobserver agreement of automated measurement of polyp diameter in vitro. METHODS: Two phantoms ("QRM" and "Whiting") containing simulated polyps of known diameter and volume were scanned using 16-detector row computed tomography. Two observers estimated polyp diameter using 3 methods: software calipers ("manual"), freehand boundary identification ("semiautomatic"), and automated software segmentation ("fully automatic"). RESULTS: Intraobserver 95% limits of agreement for diameter were narrowest for the fully automatic method (QRM span: 0.39 mm, 0.48 mm; Whiting span: 0.24 mm, 0 mm). Manual estimates were approximately 10 times wider (QRM span: 3.57 mm, 3.21 mm; Whiting span: 3.2 mm, 2.02 mm). Volume estimates were narrowest for the fully automatic method (span: 24.2 mm, 24.1 mm vs. 97.9 mm, 102.9 mm for semiautomatic measurement). Interobserver agreement for diameter was narrowest for the fully automatic method (QRM span: 0.12 mm, Whiting span: 0.16 mm), with the manual method approximately 18 times wider (QRM span: 2.87 mm, Whiting span: 2.18 mm). CONCLUSION: Fully automated measurement of polyp diameter and volume is technically feasible and results in superior inter- and intraobserver agreement.

Colonic Polyps↗

PubMed2003

Factors affecting left ventricular ejection fraction using automated quantitative gated SPECT.

BACKGROUND: Factors affecting the accuracy of left ventricular ejection fraction (LVEF) quantification using automated quantitative gated SPECT have not been adequately investigated in patients in the clinical setting. Therefore, the authors studied the effect of defect size and Tc-99m tetrofosmin dose on the accuracy of LVEF calculation using the automated QGS program. MATERIALS AND METHODS: Thirty-two consecutive patients underwent gated rest and stress myocardial perfusion SPECT after administration of 8 and 27 mCi Tc-99m tetrofosmin, respectively. The LVEF was obtained for both the rest and stress studies using the QGS program and compared with the LVEF obtained using quantitative echocardiography performed within 2 weeks. Myocardial perfusion defects were recorded as scarring, ischemia, or mixed scarring and ischemia in 12 left ventricular segments. The defect size was evaluated by adding the number of affected segments. RESULTS: The mean LVEF calculated using high-dose stress QGS, low-dose rest QGS, and echocardiography was 49.2% +/- 15%, 46.2% +/- 17% and 48.7% +/- 16.9% respectively, with no statistically significant differences. The LVEF obtained using high-dose stress QGS correlated better with echocardiography than did that obtained using low-dose rest QGS (r = 0.86 versus 0.76). In addition, when the high-dose stress LVEF in the 14 patients with normal myocardial perfusion was compared with that in 11 patients who had one- or two-segment perfusion defects, and 7 patients who had perfusion defects in > or = three segments, there was good correlation with echocardiography in the three patient groups (r = 0.85, 0.88, and 0.91, respectively). CONCLUSIONS: Myocardial perfusion defects do not affect the accuracy of LVEF calculation using automated QGS. High-dose gated myocardial SPECT demonstrated better correlation with quantitative echocardiography LVEF results.

Adult↗

PubMed2025

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and limit scalability, thereby restricting the inclusion of appropriate replicates and controls. Although the introduction of liquid handling platforms has improved reproducibility, most existing efforts have automated only a subset of the workflow, and extending automation to efficiently map non-histone proteins, such as chromatin regulators, remains challenging. Here, we present a fully automated implementation of our previously developed single-pot ChIP-seq protocol (Texari et al. 2021), named spa-ChIP-seq, which enables scalable processing of 8 to 96 ChIP-seq samples from crosslinked cells to sequencing-ready library in approximately three days with an estimated cost of $70 per sample. Benchmarking spa-ChIP-seq against manual ChIP-seq performed in parallel demonstrates comparable signal-to-noise ratio between the two workflows. Using spa-ChIP-seq, we systematically evaluate multiple parameters including shearing and crosslinking conditions, buffer compositions, and the ratio of antibody to cell-number. We find, for the first time to our knowledge, that weaker genomic localization signals are sensitive to changing the antibody to cell-number ratio, whereas the stronger signals remain unaffected. This finding underscores the importance of maintaining consistent antibody-to-cell-number ratio for comparative studies, such as treatment responses or chromatin-QTL mapping. The spa-ChIP-seq protocol is publicly available, including deck setups, operational parameters, and scripts. We envision that this robust, cost-efficient protocol will facilitate high-throughput, reproducible ChIP-seq analyses, supporting large-scale studies of antibody validation, compound screening, population genomics, and diagnostic frameworks.

Journal Article↗

PubMed2000

Automation for genomics, part one: preparation for sequencing.

In the past four years, automation for genomics has enabled a 43-fold increase in the total finished human genomic sequence in the world. This two-part noncomprehensive review will provide an overview of different types of automation equipment used in genome sequencing. Part One focuses on equipment involved in DNA preparation, DNA sequencing reactions, and other automated procedures for preparing DNA for running on sequencers or subsequent analysis; it also includes information on the development of these machines at various genome centers. Part Two, to be published in the next issue, will cover sequencing machinery and array technology, and conclude with a look at the future technologies that will revolutionize molecular biology. "Alternate" sequencing technologies (including mass spectrometry, biochips, and single-molecule analysis) will also be examined.

Animals↗

PubMed2000

Automation for genomics, part two: sequencers, microarrays, and future trends.

Automation for genomics has enabled a 43-fold increase in the total finished human genomic sequence in the world in the past four years. This is the second half of a two-part, noncomprehensive review that presents an overview of different types of automation equipment used in genome sequencing. The first part of the review, published in the previous issue, focused on automated procedures used to prepare DNA for sequencing or analysis. This second part of the review presents a look at available DNA sequencers and array technology and concludes with a look at future technologies. Alternate sequencing technologies including mass spectrometry, biochips, and single molecule analysis are included in this review.

Animals↗

PubMed2003

Software for automated analysis of DNA fingerprinting gels.

Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.

Animals↗

PubMed2003

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Manual curation has long been held to be the "gold standard" for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an "uninformative filter" that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Animals↗

PubMed2006

Automated classification of protein crystallization images using support vector machines with scale-invariant texture and Gabor features.

Protein crystallography laboratories are performing an increasing number of experiments to obtain crystals of good diffraction quality. Better automation has enabled researchers to prepare and run more experiments in a shorter time. However, the problem of identifying which experiments are successful remains difficult. In fact, most of this work is still performed manually by humans. Automating this task is therefore an important goal. As part of a project to develop a new and automated high-throughput capillary-based protein crystallography instrument, a new image-classification subsystem has been developed to greatly reduce the number of images that require human viewing. This system must have low rates of false negatives (missed crystals), possibly at the cost of raising the number of false positives. The image-classification system employs a support vector machine (SVM) learning algorithm to classify the blocks making up each image. A new algorithm to find the area within the image that contains the drop is employed. The SVM uses numerical features, based on texture and the Gabor wavelet decomposition, that are calculated for each block. If a block within an image is classified as containing a crystal, then the entire image is classified as containing a crystal. In a study of 375 images, 87 of which contained crystals, a false-negative rate of less than 4% with a false-positive rate of about 40% was consistently achieved.

Algorithms↗

PubMed1999

Automated MAD and MIR structure solution.

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

Algorithms↗