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PubMed2007

Automated interpretation of PET/CT images in patients with lung cancer.

PURPOSE: To develop a completely automated method based on image processing techniques and artificial neural networks for the interpretation of combined [(18)F]fluorodeoxyglucose (FDG) positron emission tomography (PET) and computed tomography (CT) images for the diagnosis and staging of lung cancer. METHODS: A total of 87 patients who underwent PET/CT examinations due to suspected lung cancer comprised the training group. The test group consisted of PET/CT images from 49 patients suspected with lung cancer. The consensus interpretations by two experienced physicians were used as the 'gold standard' image interpretation. The training group was used in the development of the automated method. The image processing techniques included algorithms for segmentation of the lungs based on the CT images and detection of lesions in the PET images. Lung boundaries from the CT images were used for localization of lesions in the PET images in the feature extraction process. Eight features from each examination were used as inputs to artificial neural networks trained to classify the images. Thereafter, the performance of the network was evaluated in the test set. RESULTS: The performance of the automated method measured as the area under the receiver operating characteristic curve, was 0.97 in the test group, with an accuracy of 92%. The sensitivity was 86% at a specificity of 100%. CONCLUSIONS: A completely automated method using artificial neural networks can be used to detect lung cancer with such a high accuracy that the application as a clinical decision support tool appears to have significant potential.

Adult↗
PubMed1966

Periodic health examinations using an automated multitest laboratory.

Automated multitest laboratories with automated, electronic, and computer equipment are used as an integral part of a routine periodic health examination for 4,000 patients a month. The automated multitest laboratory provides electrocardiography, anthropometry, chest and breast x-rays, visual acuity tests, tonometry, retinal photography, audiometry, vital capacity determinations, a health questionnaire on prepunched cards, and laboratory tests including eight blood chemistries done simultaneously with direct punched-card output. Before the patient leaves the multitest laboratory, additional indicated procedures are arranged in accordance with programmed computer "advice" rules. When all test reports are received, the computer prints out a summary report for the physician. The advent of automation and computers may introduce a new era of preventive medicine.

Automation↗
PubMed1996

Comparison of automated and manual analysis of interphase in situ hybridization signals in tissue sections and nuclear suspensions.

In this study we compared visual and automated analyses of interphase in situ hybridization (ISH) signals in five prostatic tumor specimens and one normal prostate sample, both in tissue sections and nuclear suspensions. The advantage of tissue sections is preservation of tissue morphology allowing precise analysis of tumor cells only. The advantage of nuclear suspensions is easier access to automated analysis, due to their disaggregated and dispersed cellular appearance. The samples were hybridized with probes for the (peri)centromeric regions of chromosome 1 and Y. The number of ISH signals per nucleus was counted both manually and automatically by means of a commercially available image analysis system. After image analysis the results were interactively corrected using a gallery display. The automatic and manual counts, before and after interactive correction, were then statistically evaluated. We found no significant differences in overall distributions between the automated and the manual counts, before as well as after correction. This was observed for both tissue sections and cellular suspensions. It is therefore concluded that automated analysis of ISH signals is feasible in both nuclear suspensions and in tissue sections, despite a low percentage of nuclei that could be measured on the latter.

Adenocarcinoma↗
PubMed1993

Porcine islet isolation: prospective comparison of automated and manual methods of pancreatic collagenase digestion.

A prospective study was undertaken to compare an automated method of porcine pancreatic digestion with a simpler manual procedure. These techniques have not previously been compared directly. After intraductal distension with collagenase, seven porcine pancreata were divided longitudinally; half of each was digested by the automated method and half by the manual technique. Islet yield and purity were measured. Compared with the manual technique, the automated method isolated a significantly greater total volume of islet tissue (median (range) 3.56 (1.39-5.30) versus 1.07 (0.46-1.92) mm3/g, P = 0.022), increased the median (range) number of 105-microns islet equivalents isolated (5875 (2294-8746) versus 1766 (759-3168) per g, P = 0.022) and improved the islet cleavage index (median (range) 92 (89-99) versus 82 (78-92) per cent, P = 0.035). It is concluded that, although the automated method is more complicated to set up, it greatly improves the yield of intact islets from the porcine pancreas.

Animals↗
PubMed1990

The Athena semi-automated karyotyping system.

In this article we describe Athena, a system that provides for semi-automated karyotyping of metaphase spreads. The system is based upon the Macintosh II computer. It uses software that is written entirely in C and consists of approximately 200 Kbytes of executable code. Athena provides automated segmentation of metaphase images into individual chromosomes, automated measurements on each banded chromosome, and automated classification into the standard Paris-convention karyotype. Furthermore, the system provides the ability to construct one or more chromosome data bases to represent the types of metaphase spreads and staining techniques that may be used in a given laboratory. Because we believe that it is impossible to construct a system that can achieve perfect segmentation, perfect separation of touching and overlapping chromosomes, perfect localization of the centromeres, and perfect classification, the system offers the possibility for interaction at each of the above stages using the well-accepted Macintosh user interface.

Centromere↗
PubMed1990

Mutational analysis of human NRAS genes in malignant melanoma: rapid methods for oligonucleotide hybridization and manual and automated direct sequencing of products generated by the polymerase chain reaction.

Three methods to detect single base mutations in codon 61 of the human NRAS gene from human melanoma DNA are described and compared: oligonucleotide hybridization analysis and direct manual and automated sequence analysis. Point mutations are detected by oligonucleotide hybridization and direct manual and direct automated sequence analysis of in vitro amplified genomic DNA. Heterozygosity for mutant alleles is reliably detected by oligonucleotide hybridization and by direct manual, but not by direct automated, sequence analysis. Generating single-stranded DNA via "asymmetric polymerase chain reaction (PCR)" and utilizing alpha 35S-dATP as radiolabel for manual sequencing and fluorescent-dye labeled primers for automated sequencing (Applied Biosystems, Inc.), we can obtain sequence information from either strand. The use of several of these methodologies to detect single base changes in the human NRAS gene is illustrated. In addition, the use of these and other related techniques to define the involvement of RAS oncogenes in human melanomas more precisely is reviewed.

Automation↗
PubMed2005

A randomised public-health trial on automation-assisted screening for cervical cancer in Finland: performance with 470,000 invitations.

Our objective was to evaluate automation-assisted screening, in comparison to the conventional method, in a routine population-based cervical cancer-screening programme. Our study is based on an individually randomised design involving approximately 160,000 invitees and 110,000 attendees every year. From 1999 to 2001, 471,297 women were invited to attend and 330,445 smears were screened (attendance rate 70.1%), of which 220,254 were tested conventionally and 110,191 were tested using the automation-assisted method. Cytologic Papanicolaou group II findings were reported slightly more often (RR = 1.04) in the automation-assisted method than in the conventional screening arm. There were 1,291 cases of histologically confirmed dysplasia or carcinoma (0.4% of the screened), one-third of which were severe dysplasia or a more severe finding (CIN3+). The detection rates of histologically verified findings were similar between the 2 screening arms. In Finland, the screening programme has been effective. As the detection rates, particularly of CIN3+, were similar between the screening arms, we will continue the automation-assisted method in the routine screening programme. Further follow-up for interval cancer incidence is required, however, to measure if the effect of screening is the same between the arms. A similar evaluation design is feasible to any other major or competing modification of the screening test or other element in the programme.

Adult↗
PubMed2003

Development, principles, and applications of automated ice fabric analyzers.

We review the recent development of automated techniques to determine the fabric and texture of polycrystalline ice. The motivation for the study of ice fabric is first outlined. After a brief introduction to the relevant optical concepts, the classic manual technique for fabric measurement is described, along with early attempts at partial automation. Then, the general principles behind fully automated techniques are discussed. We describe in some detail the similarities and differences of the three modern instruments recently developed for ice fabric studies. Next, we discuss briefly X-ray, radar, and acoustic techniques for ice fabric characterization. We also discuss the principles behind automated optical techniques to measure fabric in quartz rock samples. Finally, examples of new applications that have been facilitated by the development of the ice fabric instruments are presented.

Automation↗
PubMed2005

CHASE, a charge-assisted sequencing algorithm for automated homology-based protein identifications with matrix-assisted laser desorption/ionization time-of-flight post-source decay fragmentation data.

We describe CHASE, a novel algorithm for automated de novo sequencing based on the mass spectrometric (MS) fragmentation analysis of tryptic peptides. This algorithm is used for protein identification from sequence similarity criteria and consists of four steps: (1) derivatization of tryptic peptides at the N-terminus with a negatively charged reagent; (2) post-source decay (PSD) fragmentation analysis of peptides; (3) interpretation of the mass peaks with the CHASE algorithm and reconstruction of the amino acid sequence; (4) transfer of these data to software for protein identifications based on sequence homology (Basic Local Alignment Search Tool, BLAST). This procedure deduced the correct amino acid sequence of tryptic peptide samples and also was able to deduce the correct sequence from difficult mass patterns and identify the amino acid sequence. This allows complete automation of the process starting from MS fragmentation of complex peptide mixtures at low concentration (e.g. from silver-stained gel bands) to identification of the protein. We also show that if PSD data are collected in a single spectrum (instead of the segmented mode offered by conventional matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation), the complete workflow from MS-PSD data acquisition to similarity-based identification can be completely automated. This strategy may be applied to proteomic studies for protein identification based on automated de novo sequencing instead of MS or tandem MS patterns. We describe the Charge Assisted Sequencing Engine (CHASE) algorithm, the working protocol, the performance of the algorithm on spectra from MALDI-TOFMS and the data comparison between a TOF and a TOF-TOF instrument.

Algorithms↗
PubMed2006

Automation, parallelism, and robotics for proteomics.

The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomics-based information with other related research areas.

Animals↗
PubMed2003

Quantitation of midazolam in human plasma by automated chip-based infusion nanoelectrospray tandem mass spectrometry.

An automated chip-based infusion nanoelectrospray ionization (nanoESI) platform was used to demonstrate reproducible quantitation of drug molecules from biological matrices. Three sample preparation strategies were explored including protein precipitation of plasma with acetonitrile, de-salting of the plasma, and a combination of protein precipitation with subsequent de-salting of the dried and reconstituted extract. The best results were obtained when fortified human plasma samples containing midazolam were precipitated with acetonitrile containing alprazolam as the internal standard (IS). The supernatant was concentrated to dryness, reconstituted in aqueous acid, and de-salted by automated reversed-phase solid-phase extraction (SPE) prior to infusion nanoESI-MS/MS. Analyses employed a triple quadrupole mass spectrometer operated in selected reaction monitoring (SRM) mode. Each sample was infused for approximately 10 s and the resulting ion current profiles were integrated. Area ratios were used for regression analysis of standard samples (1.5-500 ng/mL). Quality control samples (3, 250, and 400 ng/mL) in five replicates from three different analysis days demonstrated intra-assay precision (< or =16%), inter-assay precision (< or =5%), and overall accuracy (+/-9% deviation). Infusion reproducibility of the assay was established by analyzing extracts after storage for 24 h at ambient temperature. Control plasma samples from six different sources probed the potential utility of this technique for the analysis of clinical samples. At the lower limit of quantitation (LLQ), variability and mean overall accuracy were < or =13% CV and +/-3% deviation, respectively, while at the upper limit of quantitation (ULQ) variability and mean overall accuracy were < or =9% CV and +/-9% deviation, respectively. Inter-chip variability was established by determining standard sample extracts across five different chips (< or =12% CV). Throughput for the assay was 55 s per sample, although this time may be shortened to 40 s per sample with recent improvements in the automated nanoESI system. No contamination or carryover was observed using this promising automated nanoESI-MS/MS platform.

Automation↗
PubMed2005

Automated accurate mass data processing using a gas chromatograph/time-of-flight mass spectrometer in drug discovery.

A gas chromatograph/time-of-flight (GCT) mass spectrometer, with high mass measurement accuracy to within 5 ppm, has been used for the automated accurate mass analysis of multicomponent mixtures and drug discovery compounds. A multicomponent mixture was analyzed several times over the course of a week to assess the reproducibility and ruggedness of the automated method while operating the GCT in electron ionization mode. For example, the data for 31 radical cations generated via electron ionization was processed using automated software (i.e. OpenLynx) to provide for mass accuracies less than 5 ppm for nearly 100% of the ions from multiple injection data. Mass accuracies of the radical anions of polyaromatic hydrocarbons generated via negative chemical ionization, and protonated pyridines and quinolines generated via methane chemical ionization, were mainly less than 5 ppm from multiple injection data. In addition, the automated method has been used for the accurate mass analysis of drug discovery compounds.

Automation↗
PubMed2003

Tool command language automation of the modular ion cyclotron data acquisition system (MIDAS) for data-dependent tandem Fourier transform ion cyclotron resonance mass spectrometry.

This manuscript describes the addition of data-dependent automation to the modular ion cyclotron resonance data acquisition system (MIDAS). The automation is made possible by developments and incorporation of a tool command language (Tcl) interpreter for automated acquisition. To accomplish the automation, real-time generation of excitation waveforms and scriptable data post-processing has been implemented into the MIDAS source code. In addition a new excitation event has also been added to allow for run-time generation of a single notch stored waveform inverse Fourier transform (SWIFT) excitation event. Examples of these new features and discussion of their enhancement to the existing data station are presented.

Adrenocorticotropic Hormone↗
PubMed2007

Synthesis modules and automation in F-18 labeling.

Fast implementation of PET into clinical studies and research has resulted in high demands in the automated modules for the preparation of PET radiopharmaceuticals in a safe and reproducible manner. 18F-labeled radiotracers are of considerable interest due to longer half-life of fluorine-18 allowing remote site application, as demonstrated by [18F]FDG. In this chapter, the state of the art of commercially available modules for [18F]FDG is reviewed with the emphasis on multibatch production of this important radiotracer. Examples are given on the syntheses of other clinically relevant 18F-labeled radiotracers by using existing [18F]FDG synthesizers or with the help of general-purpose [18F]nucleophilic fluorination modules. On-going research and progress in the automation of complex radio labeling procedures followed by development of flexible multipurpose automated apparatus are discussed. The contribution of radiochemists in facilitating automation via introduction of new 18F-labeling techniques and labeling synthons, on-line reactions and purifications etc. is outlined.

Alkylation↗
PubMed2006

Repeatability of nerve conduction measurements using automation.

OBJECTIVE: To quantify nerve conduction study (NCS) reproducibility utilizing an automated NCS system (NC-stat, NeuroMetrix, Inc.). METHOD: Healthy volunteers without neuropathic symptoms participated in the study. Their median, ulnar, peroneal, and tibial nerves were tested twice (7 days apart) by the same technician with an NC-stat instrument. Pre-fabricated electrode arrays specific to each nerve were used. Both motor responses (compound motor action potential [CMAP] and F-waves - all nerves) and sensory responses (sensory nerve action potentials [SNAP] - median and ulnar nerves only) were recorded following supramaximal stimuli. Automated algorithms determined all NCS parameters: distal motor latency (DML), mean F-wave latency (FWL), distal sensory latency (DSL), CMAP amplitude, and SNAP amplitude. Latency was adjusted for skin temperature deviation from reference. Pearson correlation coefficient (CC), intraclass correlation coefficient (ICC), coefficient of variance (CoV), and relative intertrial variation (RIV) were calculated. RESULTS: Fifteen subjects participated in either upper or lower extremity studies with nine participating in both. With the exception of CMAP amplitude, all parameters had CoV less than 0.06. Upper extremity amplitude parameters had CCs greater than 0.85. CCs for latencies were greater than 0.80 except for the median nerve FWL (CC = 0.69). For lower extremity nerves, ICCs were highest for mean FWL (>0.90), followed by DML (>0.82) and then CMAP (peroneal 0.33, tibial 0.73). The 10th to 90th RIV percentiles were bounded by +/-7% for F-wave latencies; +/- 9% for all DSLs; and +/- 11% for DML (except peroneal at 15%). CONCLUSIONS: The reproducibility of NCS parameters obtained with an automated NCS instrument compared favorably with traditional electromyography laboratories. F-wave latencies had the highest repeatability, followed by DML, DSL, SNAP and CMAP amplitude. Given their high reproducibility, automated NCS instrument may encourage wider utilization of NCS in clinical and research applications.

Action Potentials↗
PubMed1996

Sample preparation with an automated robotic workstation for organic acid analysis by gas chromatography-mass spectrometry.

We attempted to automate sample preparation for analysis of organic acids by gas chromatography-mass spectrometry using a computer-controlled, automated robotic workstation that is integrated and connected to the gas chromatography-mass spectrometry (HP-5890/5971) system. Of the two methods developed, one employed solvent extraction, while the other utilized a silica, solid-phase extraction cartridge. Both automated methods were compared to a manual, solvent extraction procedure used routinely in our laboratory. Normal, spiked urine, and urine from patients with a variety of metabolic abnormalities were analyzed. The robotic workstation did not meet all our requirements for a rapid, reliable, laboratory device. Recoveries with the automated procedures were less than with the manual method, and some organic acids important in the diagnosis of inborn errors of metabolism were not detected. Additionally, the robotic device had mechanical and design problems that made it slower and less reliable than the manual procedure.

Automation↗
PubMed1990

Development of an automated procedure for fluorescent DNA sequencing.

We describe here the development of a procedure for complete automation of the dideoxynucleotide DNA sequencing chemistry using fluorescent dye-labeled oligonucleotide primers. This procedure combines rapid preparation of template DNA using a modification of the polymerase chain reaction, automation of the DNA sequencing reactions using a robotic laboratory workstation, and subsequent analysis of the fluorescent-labeled reaction products on a commercial automated fluorescent sequencer. Using this procedure, we were able to produce sufficient quantities of template DNA directly from bacterial colonies or bacteriophage plaques, perform the DNA sequencing reactions on these templates, and load the reaction products on the fluorescent DNA sequencer in a single work day. This scheme for automation of the fluorescent DNA sequencing method allows the fluorescent sequencer to be run at its full capacity every day and eliminates much of the labor required to obtain a high level of data output. Currently, we are able to perform and analyze 16 fluorescent-labeled reactions every day, with an average output of over 7000 bp per sequencer run.

Automation↗
PubMed2005

Proposal of automation of candidate reference method for the accurate serum cholesterol assay in clinical laboratories.

BACKGROUND: In 2001, Japan Society of Clinical Chemistry (JSCC) recommended the cholesterol dehydrogenase (CD)-UV method as a comparative method for serum cholesterol measurement in Japan. Although the CD-UV method is intended to standardize routine laboratory tests, it requires complex manipulations, and has been difficult to use for the evaluation of clinical laboratories. We therefore attempted to automate this method using reagents specified by JSCC and developed a simple automated method. METHODS: We evaluated the simple automated method using 2 general instruments (JCA-BM12 and H-7170S). The linearity was confirmed for the range over 15.52 mmol/l. The coefficients of variation for 20 measurements of serum containing 2.5 and 6.1 mmol/l of cholesterol were < 1.0%, respectively. No interference by bilirubin, ditauro bilirubin, hemoglobin and chylomicrons was observed in this method. When measurement data with JCA-BM12 were compared with those using the comparative method, the correlation coefficient was 0.999 (n=23), the regression formula was y=0.992x - 0.0036 (mmol/l), and the bias was 0.8%. A similar data was obtained with H-7170S. Thus, in both comparisons, the bias was within the target (+/- 3.0%). CONCLUSIONS: This automated method provides a valid means of implementing the serum cholesterol measuring method recommended by JSCC.

Automation↗