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PubMed2004

APART: automated preprocessing for NMR assignments with reduced tedium.

MOTIVATION: High-throughput NMR structure determination is a goal that will require progress on many fronts, one of which is rapid resonance assignment. An important rate-limiting step in the resonance assignment process is accurate identification of resonance peaks in the NMR spectra. Peak-picking schemes range from incomplete (which lose essential assignment connectivities) to noisy (which obscure true connectivities with many false ones). We introduce an automated preassignment process that removes false peaks from noisy peak lists by requiring consensus between multiple NMR experiments and exploiting a priori information about NMR spectra. This process is designed to accept multiple input formats and generate multiple output formats, in an effort to be compatible with a variety of user preferences. RESULTS: Automated preprocessing with APART rapidly identifies and removes false peaks from initial peak lists, reduces the burden of manual data entry, and documents and standardizes the peak filtering process. Successful preprocessing is demonstrated by the increased number of correct assignments obtained when data are submitted to an automated assignment program. AVAILABILITY: APART is available from http://sir.lanl.gov/NMR/APART.htm CONTACT: npawley@lanl.gov; rmichalczyk@lanl.gov SUPPLEMENTARY INFORMATION: Manual pages with installation instructions, procedures and screen shots can also be found at http://sir.lanl.gov/NMR/APART_Manual1.pdf.

Algorithms↗

PubMed1996

Assessment of an automated cephalometric analysis system.

A system is described which automatically identifies cephalometric landmarks on digital cephalometric radiographs. The accuracy of the automated system in identifying nineteen cephalometric landmarks is assessed. The accuracy obtained with the automated system is less than that of manual tracing. The automated system has particular difficulty in identifying landmarks which lie on poorly defined structures where there is a poor signal to noise ratio.

Artifacts↗

PubMed2002

RiceGAAS: an automated annotation system and database for rice genome sequence.

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.

Automation↗

PubMed2003

Automated blood cell count: a sensitive and reliable method to study corticosterone-related stress in broilers.

In chickens the heterophil/lymphocyte ratio (H/L) has proved to be a valuable tool in stress related research. In general, H/L is determined with the microscopic differential count on a blood film. We evaluated automated analysis for measuring blood cell parameters in relation to corticosterone in a recently introduced corticosterone model. Discrepancies between microscopic and automated counts were found for the percentage of monocytes and basophils. The relative H/L ratio appeared to be sensitive for increased plasma corticosterone levels. However, the increase in heterophil frequencies measured with the hematology analyzer proved to be the most sensitive method for the measurement of changes in plasma corticosterone concentrations. We therefore propose automated hematological analysis as a simple and sensitive tool to study the effects of physiological corticosterone concentrations on blood cell parameters in relation to stress in broiler chickens.

Animals↗

PubMed1993

Automation of medical examiner offices.

General information and principles regarding the automation of medical examiner and coroner offices are presented. Topics discussed include the importance of using available resource groups, questions that should be answered to determine the need for automation, the importance of specifically defining office needs and goals prior to automation, the value of capturing data in multiple ways, the importance of maintaining some hardcopy files, the value of ensuring capability to modify and enlarge the computer system, the need to tailor systems to the needs of specific offices, possibilities for generating money or acquiring equipment at little or no cost, the use of personal computers and commercially available software, the value of having all operations inhouse, transition to new operating systems and environments, and the foreseeable use of emerging technologies.

Coroners and Medical Examiners↗

PubMed2000

A comparative scanning electron microscopic investigation of the efficacy of manual and automated instrumentation of root canals.

The cleaning effectiveness of automated and manual root canal instrumentation was investigated with the aid of a scanning electron microscope. Hand instrumentation was performed with K-Flexofiles used in a reaming working motion and according to the step-back technique and with Hedstrom files used in a filing motion. Automated preparation was performed with the KaVo-Endo Flash device featuring torque-limited rotation using K-Flexofiles, as well as with the mechanical ProFile system using rotary nickel-titanium instruments. Twelve teeth each with either straight or curved root canals were instrumented to size 40. After cracking the roots longitudinally (n = 120), the amount of debris and smear layer were quantified on the basis of a numerical evaluation scale (1 through 5). Comparison of manual instrumentation with the automated KaVo-Endo Flash resulted in an equivalent degree of canal cleaning. Complete cleanliness was not achieved by any of the techniques and devices investigated. Best instrumentation results, especially in curved canals, were obtained with rotary ProFile instruments.

Automation↗

PubMed2002

Improving recognition of drug interactions: benefits and barriers to using automated drug alerts.

BACKGROUND: Clinicians' perceptions about decision support systems may impact the effectiveness of these technologies. OBJECTIVE: To explore clinicians' baseline knowledge of common drug interactions and experiences with automated drug alerts within a provider order entry system as a means to better understand the potential benefits and barriers to using this technology. RESEARCH DESIGN: Cross-sectional survey. SUBJECTS: The study population comprised 263 clinicians practicing within a Southern California Veterans Affairs health care system that used VA's Computerized Patient Record System (CPRS). Response rate was 64%. MEASURES: A 67-item survey (19 questions) was developed to elicit information including: (1) computer use for patient-related activities; (2) recognition of drug interactions; and (3) benefits and barriers to using automated drug alerts. RESULTS: Clinicians correctly categorized 44% (range 11-64%) of all drug-drug pairs, 53% of interacting combinations, and 54% of contraindicated pairs. Providers also correctly categorized 55% (range 24-87%) of 11 drug-disease pairs and 62% of interacting combinations, and 53% of contraindicated pairs. Nearly 90% of clinicians thought drug alerts would be helpful to identify interactions yet 55% of clinicians perceived that the most significant barrier to utilizing existing alerts was poor signal to noise ratio, meaning too many nonrelevant warnings. CONCLUSIONS: Automated drug interaction alerts have the potential to dramatically increase clinicians' recognition of selected drug interactions. However, perceived poor specificity of drug alerts may be an important obstacle to efficient utilization of information and may impede the ability of such alerts to improve patient safety.

Attitude of Health Personnel↗

PubMed1984

Closing the loop: how near is automated anesthesia?

Technologic advances now make automated anesthesia delivery systems theoretically possible; clinical implementation, however, awaits development and refinement in three areas: (1) adjunctive monitoring, which needs to be extremely sophisticated; (2) automated data collection, which will obviate manual record keeping; (3) automated therapeutic intervention, which will control drug, fluid, and gas administration. Reduced health care costs and increased safety are the primary goals; there is also the possibility, however, of increased costs and new hazards.

Anesthesia↗

PubMedDate not supplied

Experience with the JMS fully automated dialysis machine.

A fully automated dialysis machine has been developed and evaluated clinically. It uses highly pure dialysate (produced by a new dialysate cleaning system) instead of the conventional physiologic saline for the processes of priming, guiding blood to the dialysis machine, replenishing fluid, and returning the blood to the body. The piping for the dialysate is in the shape of a loop, and the dialyzer coupler has no mechanical parts that might become contaminated. As a result of these and certain other improvements in machine design, it is now possible to obtain reasonably clean dialysate. For the priming process, the machine uses a volume of up to 4 L of the dialysate after reverse filtration from the dialyzer. Most foreign matter or eluates can be removed from the dialyzer and the blood channels. Before blood is guided out of the body into the dialysis system, the needles inserted in the artery and vein are simultaneously connected to the blood channel, and the dialysate remaining in the channel is removed from the dialyzer. If the patient's blood pressure falls during dialysis, the dialysate can be replenished at any desired flow rate for reverse filtration. Blood return can be started automatically when the planned dialysis time has elapsed and the target water volume has been removed. The cleaned dialysate is infused from the dialyzer into the blood channel by reverse filtration to allow the blood to be returned to the body via both the artery and the vein at the same time. A total of 216 units of this fully automated dialysis machine have been placed in service at two of our facilities. During the 6 month period beginning in July 2001, they were used for 40,000 hemodialysis sessions in 516 patients. During the dialysate preparation process, the endotoxin levels in the reverse osmosis (RO) water, prefilter dialysate, and reverse filtered dialysate were all less than 1 EU/L. The time required to guide blood into the dialyzer (n = 39) decreased from the 4.6 +/- 1.4 minutes with the conventional machines to 3.2 +/- 0.6 minutes with the new machine (p < 0.01). The time required to return blood to the body also decreased from 8.6 +/- 2.2 minutes with the conventional machines to 6.8 +/- 0.7 minutes with the new machine (n = 34). No mechanical trouble was encountered with the fully automated dialysis machine units during the 40,000 hemodialysis sessions, and the workload of the dialysis unit staff in terms of the time needed to guide out and return blood to the body was significantly reduced. Because the machine simplifies the maneuvers required during hemodialysis, it is expected to contribute greatly to preventing medical accidents and in hospital infections associated with hemodialysis.

Aged↗

PubMed2005

Automated non-invasive blood pressure devices: are they suitable for use?

OBJECTIVES: Measurement of blood pressure by a trained observer using a mercury sphygmomanometer is accepted as the gold standard, but there has been an increase in the use of automated devices employing the oscillometric technique. Not all such devices have been clinically validated, and some do not carry an appropriate CE mark. This survey aimed to assess the state of the European Union market for automated non-invasive blood pressure devices in terms of information provided by companies relating to compliance, validation and intended use. METHODS: A total of 116 companies were identified as being potentially active (i.e. manufacturer, supplier, agent or distributor). Of these, 110 that could be contacted were asked to provide details of their company and their non-invasive blood pressure products via a questionnaire. RESULTS: Eighty-six companies were found to be actively involved in the supply of 158 different models of automated non-invasive blood pressure device. These included 54 devices for use on the arm and 62 for use on the wrist (total 116 in our main categories), and 42 others (ambulatory monitors, patient monitors, defibrillators or finger devices). We received responses for 61% (71/116) of the main category arm and wrist devices and 80% (57/71) of these provided claims for CE marking. Of the CE marked devices for which we received a response, 41% (12/29) of arm devices and 39% (11/28) of wrist devices claimed some form of clinical validation, or evidence was found subsequent to the survey. Of these claims, 65% (15/23) related to an earlier, or similar, product and 48% (11/23) were based on published studies. Inconsistencies were found between claims for diagnostic suitability and claims for clinical validation. CONCLUSIONS: A majority of models available on the European Union market were not validated by clinical trial to one of the recognized protocols.

Automation↗

PubMed2006

Exposure to automated drug alerts over time: effects on clinicians' knowledge and perceptions.

OBJECTIVE: We tested whether interval exposure to an automated drug alert system that included approximately 2000 drug-drug interaction alerts increased recognition of selected interacting drug pairs. We also examined other perceptions about computerized order entry. RESEARCH DESIGN: We administered cross-sectional surveys in 2000 and 2002 that included more than 260 eligible clinicians in each time period. SUBJECTS: We studied clinicians practicing in ambulatory settings within a Southern California Veterans Affairs Healthcare System and who responded to both surveys (97 respondents). MEASURES: We sought to measure (1) recognition of selected drug-drug and drug-condition interactions and (2) other benefits and barriers to using automated drug alerts. RESULTS: Clinicians correctly categorized similar percentages of the 7 interacting drug-drug pairs at baseline and follow-up (53% vs. 54%, P = 0.51) but improved their overall recognition of the 3 contraindicated drug-drug pairs (51% vs. 60%, P = 0.01). No significant changes from baseline to follow-up were found for the 8 interacting drug-condition pairs (60% vs. 62%, P = 0.43) or the 4 contraindicated drug-condition pairs (52% vs. 56%, P = 0.24). More providers preferred using order entry at follow-up than baseline (63% vs. 45%, P < 0.001). Signal-to-noise ratio remained the biggest reported problem at follow-up and baseline (54 vs. 57%, P = 0.75). In 2002, clinicians reported seeing a median of 5 drug alerts per week (representing approximately 12.5% of prescriptions entered), with a median 5% reportedly leading to an action. CONCLUSIONS: Interval exposure to automated drug alerts had little to no effect on recognition of selected drug-drug interactions. The primary perceived barrier to effective utilization of drug alerts remained the same over time.

Adult↗

PubMed1997

A simple method for automated allele binning in microsatellite markers.

High-throughput fluorescent genotyping requires a considerable amount of automation for accurate and efficient processing of genetic markers. Automated DNA sequencers and corresponding software products are commercially available that contribute substantially to increased throughput rates for large-scale genotyping projects. However, some conceptually simple tasks still require time-consuming manual intervention that imposes bottlenecks on throughput capacity. One of these tasks is the conversion of imprecise DNA fragment sizes determined by commercial software programs to the underlying discrete alleles that the sizes represent. Here we describe a simple method for assigning allele sizes into their appropriate allele "bins" using least-squares minimization procedures. The method requires no special treatment of family data on plates, internal/external size standards, or electropherogram data manipulation. Tests of the method using the ABI 373A automated DNA sequencer and accompanying Genescan/Genotyper software resulted in accurate automatic classification of all alleles in >80% of 208 markers analyzed, with the remaining 20% being appropriately identified as requiring additional attention to laboratory conditions. Specific characteristics of different markers, including differences in PCR product size and inexact repeat lengths (e.g., 1. 9 bp for a dinucleotide repeat), are accommodated by the method and their properties discussed.

Alleles↗

PubMed2002

FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments.

FIP is a French Collaborating Research Group (CRG) beamline at the European Synchrotron Radiation Facility (ESRF) dedicated exclusively to crystallography of biological macromolecules, with a special emphasis on multiwavelength anomalous diffraction data collection in the 0.7-1.81 A wavelength range. The optics, consisting of long cylindrical grazing-angle mirrors associated with a cryocooled double-crystal monochromator, delivers an optimal beam in the corresponding energy range. The high level of automation, which includes automated crystal centring, automated data-collection management and data processing, makes the use of this beamline very easy. This is illustrated by the large number of challenging structures that have been solved since 1999.

Automation↗

PubMed2002

Automated side-chain model building and sequence assignment by template matching.

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

Algorithms↗

PubMed2001

ERS transform for the automated detection of bronchial abnormalities on CT of the lungs.

The identification of bronchi on Computed Tomography (CT) images of the lungs provides valuable clinical information in patients with suspected airways diseases including bronchiectasis, emphysema, or constrictive obliterative bronchiolitis. The automated recognition of the airways is, therefore, an important part of a diagnosis aid system for resolving potential ambiguities associated with intensity-based feature extractors. On CT images, near-perpendicular cross sections of bronchi normally appear as elliptical rings and this paper presents a novel technique for their recognition. The proposed method, the edge-radius-symmetry (ERS) transform, is based on the analysis of the distribution of edges in local polar coordinates. Pixels are ranked according to local edge (E) strength, radial (R), uniformity and local symmetry (S). A discrete implementation of the technique is provided which reduces the computational cost of the ERS transform by using a geometric approximation of the intensity patterns. The identification of the adjacent pulmonary vessels with template matching then allows for the automated measurement of bronchial dilatation and bronchial wall thickening. Computationally, the method compares favorably with other methods such as the Hough transform. Noise-sensitivity of the technique was evaluated on a set of synthetic images and nine patients under investigation for suspected airways disease. Agreement for the automated scoring of the presence and severity of bronchial abnormalities was demonstrated to be comparable to that of an experienced radiologist (kappa statistics kappa > 0.5 ).

Bronchial Diseases↗

PubMed2005

Data acceptance for automated leukocyte tracking through segmentation of spatiotemporal images.

A crucial task in inflammation research and inflammatory drug validation is leukocyte velocity data collection from microscopic video imagery. Since manual methods are bias-prone and extremely time consuming, automated tracking methods are required to compute cell velocities. However, an automated tracking method is of little practical use unless it is accompanied by a mechanism to validate the tracker output. In this paper, we propose a validation technique that accepts or rejects the output of automated tracking methods. The proposed method first generates a spatiotemporal image from the cell locations given by a tracking method; then, it segments the spatiotemporal image to detect the presence or absence of a leukocyte. For segmenting the spatiotemporal images, we employ an edge-direction sensitive nonlinear filter followed by an active contour based technique. The proposed nonlinear filter, the maximum absolute average directional derivative (MAADD), first computes the magnitude of the mean directional derivative over an oriented line segment and then chooses the maximum of all such values within a range of orientations of the line segment. The proposed active contour segmentation is obtained via growing contours controlled by a two-dimensional force field, which is constructed by imposing a Dirichlet boundary condition on the gradient vector flow (GVF) field equations. The performance of the proposed validation method is reported here for the outputs of three different tracking techniques: the method was successful in 97% of the trials using manual tracking, in 94% using correlation tracking and in 93% using active contour tracking.

Algorithms↗

PubMed2006

Automated diagnostic systems with diverse and composite features for Doppler ultrasound signals.

In this paper, we present the automated diagnostic systems for Doppler ultrasound signals classification with diverse and composite features and determine their accuracies. We compared the classification accuracies of six different classifiers, namely multilayer perceptron neural network (MLP), combined neural network (CNN), mixture of experts (ME), modified mixture of experts (MME), probabilistic neural network (PNN), and support vector machine (SVM), which were trained on diverse or composite features. The present study was conducted with the purpose of answering the question of whether the automated diagnostic systems improve the capability of classification of ophthalmic arterial (OA) and internal carotid arterial (ICA) Doppler signals. Our research demonstrated that the SVM trained on composite feature and the MME trained on diverse features achieved accuracy rates which were higher than that of the other automated diagnostic systems.

Algorithms↗

PubMed2006

Automated semantic analysis of changes in image sequences of neurons in culture.

Quantitative studies of dynamic behaviors of live neurons are currently limited by the slowness, subjectivity, and tedium of manual analysis of changes in time-lapse image sequences. Challenges to automation include the complexity of the changes of interest, the presence of obfuscating and uninteresting changes due to illumination variations and other imaging artifacts, and the sheer volume of recorded data. This paper describes a highly automated approach that not only detects the interesting changes selectively, but also generates quantitative analyses at multiple levels of detail. Detailed quantitative neuronal morphometry is generated for each frame. Frame-to-frame neuronal changes are measured and labeled as growth, shrinkage, merging, or splitting, as would be done by a human expert. Finally, events unfolding over longer durations, such as apoptosis and axonal specification, are automatically inferred from the short-term changes. The proposed method is based on a Bayesian model selection criterion that leverages a set of short-term neurite change models and takes into account additional evidence provided by an illumination-insensitive change mask. An automated neuron tracing algorithm is used to identify the objects of interest in each frame. A novel curve distance measure and weighted bipartite graph matching are used to compare and associate neurites in successive frames. A separate set of multi-image change models drives the identification of longer term events. The method achieved frame-to-frame change labeling accuracies ranging from 85% to 100% when tested on 8 representative recordings performed under varied imaging and culturing conditions, and successfully detected all higher order events of interest. Two sequences were used for training the models and tuning their parameters; the learned parameter settings can be applied to hundreds of similar image sequences, provided imaging and culturing conditions are similar to the training set. The proposed approach is a substantial innovation over manual annotation and change analysis, accomplishing in minutes what it would take an expert hours to complete.

Algorithms↗