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PubMed2005

Automated projection spectroscopy (APSY).

This work presents the automated projection spectroscopy (APSY) method for the recording of discrete sets of j projections from N-dimensional (N > or = 3) NMR experiments at operator-selected projection angles and automatic identification of the correlation cross peaks. The result from APSY is the fully automated generation of the complete or nearly complete peak list for the N-dimensional NMR spectrum from a geometric analysis of the j experimentally recorded, low-dimensional projections. In the present implementation of APSY, two-dimensional projections of the N-dimensional spectrum are recorded by using techniques developed for projection-reconstruction spectroscopy [Kupce,E.& Freeman, R. (2004) J. Am. Chem. Soc. 126, 6429-6440]. All projections are peak-picked with the available automated routine atnos. The previously undescribed algorithm GAPRO (geometric analysis of projections) uses vector algebra to identify subgroups of peaks in different projections that arise from the same resonance in the N-dimensional spectrum, and from these subgroups it calculates the peak positions in the N-dimensional frequency space. Unambiguous identification thus can be achieved for all cross peaks that are not overlapped with other peaks in at least one of the N dimensions. Because of the correlation between the positions of corresponding peaks in multiple projections, uncorrelated noise is efficiently suppressed, so that APSY should be quite widely applicable for correlation spectra of biological macromolecules, which have intrinsically low peak density in the N-dimensional spectral space.

Journal Article↗

PubMed1990

Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay.

DNA diagnostics, the detection of specific DNA sequences, will play an increasingly important role in medicine as the molecular basis of human disease is defined. Here, we demonstrate an automated, nonisotopic strategy for DNA diagnostics using amplification of target DNA segments by the polymerase chain reaction (PCR) and the discrimination of allelic sequence variants by a colorimetric oligonucleotide ligation assay (OLA). We have applied the automated PCR/OLA procedure to diagnosis of common genetic diseases, such as sickle cell anemia and cystic fibrosis (delta F508 mutation), and to genetic linkage mapping of gene segments in the human T-cell receptor beta-chain locus. The automated PCR/OLA strategy provides a rapid system for diagnosis of genetic, malignant, and infectious diseases as well as a powerful approach to genetic linkage mapping of chromosomes and forensic DNA typing.

Base Sequence↗

PubMedDate not supplied

Clinical validation of automated spirometry used in surveys of large occupational groups: comparison with conventional water spirometry.

An accurate, rugged automated spirometer which provides immediate data is useful both clinically and for screening large groups with various environmental exposures. Because the need for such surveys has been increasing, we compared a computerized mass flow-meter with a conventional water spirometer. The same forced expiration was measured by both instruments in the laboratory and during an occupational survey. Mean values for forced vital capacity (FVC) were 96 cc greater by the automated technique in the laboratory (this equals 2.2% of the value by the conventional method, with a correlation, r, of 0.998) and 97 cc greater in the field (2.3% of the conventional method; r = 0.995). Differences between the two methods in the laboratory and field for forced expiratory volume in one second (FEV 1.0) were +24 cc (0.68%; r = 0.996) and +47 cc (1.6%; r = 0.996) and for forced expiratory flow (FEF)25-75--179cc/sec (4.18%; r = 0.968) and -63 cc/sec (2.1%; r = 0.992), respectively. For FVC and FEV1.0, the differences between paired values were less than or equal to 10% of the value by water spirometry in all instances and less than or equal to 5% in 95.5% and 96% of comparisons, respectively. For FEF 25-75 the differences between paired values were less than or equal to 20% in 97.2% and less than or equal to 10% in 84.7% of comparisons. These findings confirm the validity of the measurements provided by the automated spirometer.

Autoanalysis↗

PubMed2006

An automated algorithm for determining respiratory rate by photoplethysmogram in children.

BACKGROUND: We have developed an automated algorithm to allow the measurement of respiratory rate directly from the photoplethysmogram (pulse oximeter waveform). AIM: To test the algorithm's ability to determine respiratory rate in children. METHODS: A convenience sample of patients attending a paediatric Accident and Emergency Department was monitored using a purpose-built pulse oximeter and the photoplethysmogram (PPG) recorded. Respiration was also recorded by an observer activating a push-button switch in synchronization with the child's breathing. The switch marker signals were processed to derive a manual respiratory rate that was compared with the wavelet-based oximeter respiratory rate derived from the PPG signal. RESULTS: Photoplethysmograms were obtained from 18 children aged 18 mo to 12 y, breathing spontaneously at rates of 17 to 27 breaths per minute. There was close correspondence between the wavelet-based oximeter respiration rate and the manual respiratory rate, with the difference between them being less than one breath per minute in all children. CONCLUSION: Our automated algorithm allows the accurate determination of respiratory rate from photoplethysmograms of a heterogeneous group of children. We believe that our automated wavelet-based signal-processing techniques could soon be easily incorporated into current pulse oximetry technology.

Algorithms↗

PubMed2002

Semi-automation of the polymerase chain reaction for laboratory confirmation of meningococcal disease.

Demand for accurate high-throughput detection and characterisation of medically important bacteria has increased dramatically within research and clinical laboratories. Liquid-handling robots have been developed to achieve high levels of accuracy and reproducibility. Assay automation can play a key role in the modern diagnostic laboratory and the data presented here shows that automated PCR is comparable with manual methods. Importantly, automation is preferred when high-quality results cannot be guaranteed using manual methods. This is particularly important when results are required quickly for public health management.

Bacteriological Techniques↗

PubMedDate not supplied

Willingness of high school students to perform cardiopulmonary resuscitation and automated external defibrillation.

OBJECTIVE: To evaluate the willingness of high school students to perform cardiopulmonary resuscitation (CPR) and automated external defibrillation (AED). METHODS: A convenience sample of high school students was surveyed regarding how they would respond if they witnessed a cardiac arrest. Participants were first shown a video segment on the operation of an automated external defibrillator. They were then shown a series of video clips depicting six different cardiac arrest scenarios: motor vehicle collision (MVC) with facial bleeding, pediatric drowning, intravenous (IV) drug user, choking family member, victim of differing race, and victim with facial vomitus. Following each video, the subjects were asked how they would respond had they actually witnessed a similar event. RESULTS: With parental permission and institutional review board approval, 683 students participated, representing 6.8% of the total student body. Of these, 585 (86%) were trained in CPR and 142 (21%) in AED. One hundred six participants (16%) had witnessed a cardiac arrest prior to the survey. Of these, 24 (23%) had intervened in some way. Twenty (19%) had performed mouth-to-mouth resuscitation (MMR), 15 (14%) had performed chest compressions (CC), and one (0.9%) had performed AED. Across all six mock scenarios and all 683 respondents collectively (4,098 simulated cardiac arrest events), the respondents indicated they would be willing to perform AED 1,308 times (32%). In comparison, the respondents indicated they would be willing to perform MMR 1,768 times (43%) and CC 2,249 times (55%). More respondents were willing to intervene on behalf of a child or family member, while fewer were willing to act in the setting of blood, vomitus, or an IV drug user (p < 0.05). There was no association between willingness to intervene and prior experience with any of the interventions. Fear of infection, legal consequences, and fear of harming the patient were the most frequently cited reasons for not intervening. CONCLUSIONS: Among high school students, few are willing to perform automated external defibrillation. Willingness to perform MMR and CC appears to depend on the circumstances.

Adolescent↗

PubMed2001

Pseudo-outbreak of Mycobacterium chelonae and Methylobacterium mesophilicum caused by contamination of an automated endoscopy washer.

OBJECTIVE: To evaluate an unusual number of rapidly growing acid-fast bacilli, later identified as Mycobacterium chelonae, and pink bacteria, later identified as Methylobacterium mesophilicum, from fungal cultures obtained by bronchoscopy. DESIGN: Outbreak investigation. SETTING: An academic medical center performing approximately 500 bronchoscopies and 4,000 gastrointestinal endoscopies in 1998. PATIENTS: Patients undergoing bronchoscopy July 21 to October 2, 1998. METHODS: The infection control department reviewed patient charts and bronchoscopy logs; obtained cultures of source water, faucets, washers, unopened glutaraldehyde, glutaraldehyde from the washers, and endoscopes; observed endoscope and bronchoscope cleaning and disinfecting procedures; reviewed glutaraldehyde monitoring records; and sent M. chelonae isolates for DNA fingerprinting. RESULTS: M. chelonae, M. mesophilicum, gram-negative bacteria, and various molds grew from endoscopes, automated washers, and glutaraldehyde from the washers but not from unopened glutaraldehyde. The endoscopy unit regularly monitored the pH of glutaraldehyde, and the logs contained no deficiencies. The above sources remained positive for the same organisms after a glutaraldehyde cleaning cycle of the automated washers. DNA finger-printing of the M. chelonae revealed that they were clonally related. CONCLUSIONS: The automated washers were contaminated with a biofilm that rendered them resistant to decontamination. The washers then contaminated the endoscopes and bronchoscopes they were used to disinfect. Our institution purchased new endoscopes and a new paracetic acid sterilization system.

Academic Medical Centers↗

PubMed2003

Transurethral ureterorenolithotripsy using new automated irrigation/suction system controlling pressure and flow compared with standard irrigation: a randomized pilot study.

PURPOSE: To compare in a random fashion an automated irrigation/suction pump system with the standard pressurized technique during transurethral ureterorenolithotripsy. PATIENTS AND METHODS: Between July 2001 and December 2001, 47 patients were prospectively included. Prior to randomization, rigid instruments were allocated to 25 patients (group R) and flexible instruments to 22 patients (group F) according to stone location. The groups R and F were then randomized separately, and the pressurized technique was employed in groups R1 and F1, while the automated system was employed in groups R2 and F2. Operative time, amount of liquid consumed, and stone-free rate at the end of the procedure were analyzed. RESULTS: For the entire series, ureteroscopy time using the automated system (mean 42 +/- 17[SD] minutes; range 15-90 minutes) was 35% less than with the pressurized technique (mean 65 +/- 25 minutes; range 20-135 minutes) (P = 0.04 Wilcoxon score). The stone-free rate was significantly higher in groups R2 + F2 (92%) than in groups R1 + F1 (69%) (P = 0.048). CONCLUSION: With the ENDO FMS UROLOGY system, there was a significant reduction in the mean ureteroscopy time: 32% less with the rigid instrument and 53% less with the flexible instrument. This seems to be attributable to a wider working space and highly improved visibility. The integrated suction at constant flow allows efficient evacuation of stone fragments while limiting cavity pressure. These results, obtained on 47 patients, should be confirmed by larger randomized studies.

Humans↗

PubMed2003

Determinants of satisfaction with an automated alcohol evaluation program.

High rates of untreated mental illness cause serious health problems in the United States and worldwide. The use of computer-administered therapy has the potential to increase access to mental health care for certain patient populations. An online version of an alcohol check-up was developed that guided subjects through a series of standardized questionnaires, and provided them with feedback designed to enhance their appreciation of the negative aspects of their alcohol use. Ratings of the helpfulness of the questionnaires were evaluated in order to determine the characteristics of individuals who would potentially benefit from an automated substance abuse intervention, and to learn which aspects of an automated program would be most useful. Over a period of 25 months, 1,455 individuals participated in the study, 83% of whom had an Alcohol Use Disorders Identification Test (AUDIT) score indicative of problem drinking. Subjects with alcohol problems found the on-line program more useful than other subjects. The questionnaire which compared subjects' alcohol use to national norms, provided the most helpful and also the most unexpected information. Alcohol abusers with high levels of ambivalence about their drinking and other measures of motivation for change found the program more helpful than those with lower motivation. Automated therapy made available to the general public via the Internet can be accessed by large numbers of individuals. The interaction can be useful to patients with significant levels of substance abuse.

Adult↗

PubMed2003

Automated electrophysiology: high throughput of art.

Electrophysiological measurements, in particular, patch clamping, have long been regarded as the "gold standard" for assaying ion channels. Despite its high information content, the technique suffers from laborious, manual processing by highly skilled workers and extremely low throughput. Recently, a number of researchers have started to automate patch clamping by either automating conventional micropipette-based patch clamping or developing planar microelectrode arrays. This article reviews the brief history of these emerging technologies and discusses the technical details, advantages, and disadvantages of each approach and technique. As will be evident from the discussion, two types of automated patch-clamping technologies are emerging. The first places emphasis on data quality, comparable to conventional patch clamping, and the second has much higher throughput. Future developments will include sophisticated patch-clamping devices with both high-quality data and high throughput capabilities and further integration of patch clamping with other cell-based assays.

Animals↗

PubMed2005

A randomized, controlled trial of an automated wireless messaging system for diabetes.

BACKGROUND: Aggressive management of blood glucose reduces future diabetes-related complications, but this is difficult to achieve. METHODS: This randomized, controlled study tested the effect of using a wireless two-way pager-based automated messaging system to improve diabetes control through facilitated self-management. The system sent health-related messages to patients, with automatic forwarding of urgent patient responses to the health care team. RESULTS: Participants in both the experimental (pager) and the control groups experienced an average hemoglobin A1c decrease of 0.1-0.3%. More patients in the pager group were normotensive, and more felt that their health care was better by the end of the study. A total of 79% of participants enjoyed using the pager, and 68% wanted to continue using the system. CONCLUSIONS: Utilizing a wireless, automated messaging system in clinical practice is a feasible, low-cost, interactive way to facilitate diabetes self-management, which is acceptable to patients. While providing a convenient way for patients and providers to communicate, this system can support automated recording and ready retrieval of these real-time interactions.

Blood Pressure↗

PubMed2006

A comparison of Listeria monocytogenes serovar 4b isolates of clinical and food origin in Austria by automated ribotyping and pulsed-field gel electrophoresis.

In this study, two typing methods, automated ribotyping and pulsed-field gel electrophoresis (PFGE), were evaluated for the subtyping of Listeria monocytogenes serotype 4b. The strains originated from patients and food samples collected in Austria during 2001-2005 and from Europe and North America in the World Health Organization collaborative study on the subtyping of this species. The largest group of Austrian clinical isolates was of the same PFGE subtype as those isolated from foodborne outbreaks in Switzerland and in the United States. Another subtype of clinical isolates from Austria was indistinguishable to that obtained from isolates responsible for a foodborne outbreak in the United States in 1985. Although the discriminatory power of PFGE was higher than that of automated ribotyping, some PFGE types were differentiated by ribotyping. Thus, combining data obtained by both automated ribotyping and PFGE increases the strain discrimination. Still, many of the Austrian strains remain indistinguishable from strains of foodborne outbreaks in other countries although there is no known epidemiological relation. This complies to previous studies which show the highly clonal nature of L. monocytogenes 4b strains which are responsible for both large outbreaks and sporadic cases.

Animals↗

PubMedDate not supplied

Bioreactor design for successive culture of anchorage-dependent cells operated in an automated manner.

A novel bioreactor system was designed to perform a series of batchwise cultures of anchorage-dependent cells by means of automated operations of medium change and passage for cell transfer. The experimental data on contamination frequency ensured the biological cleanliness in the bioreactor system, which facilitated the operations in a closed environment, as compared with that in flask culture system with manual handlings. In addition, the tools for growth prediction (based on growth kinetics) and real-time growth monitoring by measurement of medium components (based on small-volume analyzing machinery) were installed into the bioreactor system to schedule the operations of medium change and passage and to confirm that culture proceeds as scheduled, respectively. The successive culture of anchorage-dependent cells was conducted with the bioreactor running in an automated way. The automated bioreactor gave a successful culture performance with fair accordance to preset scheduling based on the information in the latest subculture, realizing 79- fold cell expansion for 169 h. In addition, the correlation factor between experimental data and scheduled values through the bioreactor performance was 0.998. It was concluded that the proposed bioreactor with the integration of the prediction and monitoring tools could offer a feasible system for the manufacturing process of cultured tissue products.

Algorithms↗

PubMed1997

CD31/PECAM automated and quantitative immunocytochemical assays in breast carcinomas: correlation with patient follow-up.

The purpose of this study was to determine the prognostic significance of quantitative CD31 immunohistochemical assays. CD31 assays were performed on a series of 167 breast carcinoma specimens under optimal technical conditions that involved frozen sections, an automated immunoperoxidase technique, and computer-assisted analysis of digitized colored microscopic images. Results of automated quantitative immunohistochemical assays were correlated with patient follow-up (9.6 years). Patients were divided into two subgroups: those who had axillary lymph node-positive (N+) disease and those who had lymph node-negative (N-) disease. The marked immunocytochemical expression of CD31 in tumors (cutoff point, 20%) was significantly (P = .033) associated with a poor overall survival rate (Kaplan-Meier, log rank test); however, a significant association was not observed in the N+ and N- subgroups. CD31-immunostained tumor cell surfaces larger than 20% correlated with the metastasis-free survival rate (P = .004) in all patients and in the N+ subgroup (P = .005) but not in the N- subgroup. In addition, marked immunocytochemical expression of CD31 correlated with the short-term disease-free survival rate (P = .04) in the N+ subgroup but not in the N- subgroup. In multivariate analysis (proportional hazards regression, Cox model) the prognostic significance of CD31 was independent of tumor size and histologic type but not of grade. The results suggest that, under optimal technical conditions (automated and quantitative immunohistochemical assays on frozen sections), immunohistochemical expression of CD31 is a significant prognostic indicator of overall and metastasis-free survival rates. CD31 has limited prognostic value, however, and is not a completely independent prognostic indicator because it is related to nodal status.

Adult↗

PubMed1998

GeneNet: a gene network database and its automated visualization.

MOTIVATION: Gene networks that provide the regulation of physiological processes are the basic feature of organisms. Information regarding the regulation of gene expression and signal transduction pathways is increasing rapidly. However, the information is hard to formalize and systematize. Ways and means for automated visualization of the gene networks based on their formalized description are needed. RESULTS: The object-oriented database GeneNet and the software for its automated visualization have been developed. The main principles of a formalized description of the gene network have been worked out. Antiviral response and erythropoiesis are provided as examples to show how this is achieved. The GeneNet graphical user interface written in Java provides automated generation of the gene network diagrams and allows visualization and exploration of the GeneNet database through the Internet. A system of filters allows the selection of particular components of the network for visualization. AVAILABILITY: The GeneNet database and its graphical user interface are available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneN et/ CONTACT: fedor@bionet.nsc.ru

Computational Biology↗

PubMed1999

An automated comparative analysis of 17 complete microbial genomes.

MOTIVATION: As sequenced genomes become larger and sequencing becomes faster, there is a need to develop accurate automated genome comparison techniques and databases to facilitate derivation of genome functionality; identification of enzymes, putative operons and metabolic pathways; and to derive phylogenetic classification of microbes. RESULTS: This paper extends an automated pair-wise genome comparison technique (Bansal et al., Math. Model. Sci. Comput., 9, 1-23, 1998, Bansal and Bork, in First International Workshop of Declarative Languages, Springer, pp. 275-289, 1999) used to identify orthologs and gene groups to derive orthologous genes in a group of genomes and to identify genes with conserved functionality. Seventeen microbial genomes archived at ftp://ncbi.nlm.nih.gov/genbank/genomes have been compared using the automated technique. Data related to orthologs, gene groups, gene duplication, gene fusion, orthologs with conserved functionality, and genes specifically orthologous to Escherichia coli and pathogens has been presented and analyzed. AVAILABILITY: A prototype database is available at ftp://www.mcs.kent.edu/arvind/intellibio / orthos.html. The software is free for academic research under an academic license. The detailed database for every microbial genome in NCBI is commercially available through intellibio software and consultancy corporation (Web site: http://www.mcs.kent.edu/årvind/intellibio . html). CONTACT: arvind@mcs.kent.edu.

Algorithms↗

PubMed2000

MaxSub: an automated measure for the assessment of protein structure prediction quality.

MOTIVATION: Evaluating the accuracy of predicted models is critical for assessing structure prediction methods. Because this problem is not trivial, a large number of different assessment measures have been proposed by various authors, and it has already become an active subfield of research (Moult et al. (1997,1999) and CAFASP (Fischer et al. 1999) prediction experiments have demonstrated that it has been difficult to choose one single, 'best' method to be used in the evaluation. Consequently, the CASP3 evaluation was carried out using an extensive set of especially developed numerical measures, coupled with human-expert intervention. As part of our efforts towards a higher level of automation in the structure prediction field, here we investigate the suitability of a fully automated, simple, objective, quantitative and reproducible method that can be used in the automatic assessment of models in the upcoming CAFASP2 experiment. Such a method should (a) produce one single number that measures the quality of a predicted model and (b) perform similarly to human-expert evaluations. RESULTS: MaxSub is a new and independently developed method that further builds and extends some of the evaluation methods introduced at CASP3. MaxSub aims at identifying the largest subset of C(alpha) atoms of a model that superimpose 'well' over the experimental structure, and produces a single normalized score that represents the quality of the model. Because there exists no evaluation method for assessment measures of predicted models, it is not easy to evaluate how good our new measure is. Even though an exact comparison of MaxSub and the CASP3 assessment is not straightforward, here we use a test-bed extracted from the CASP3 fold-recognition models. A rough qualitative comparison of the performance of MaxSub vis-a-vis the human-expert assessment carried out at CASP3 shows that there is a good agreement for the more accurate models and for the better predicting groups. As expected, some differences were observed among the medium to poor models and groups. Overall, the top six predicting groups ranked using the fully automated MaxSub are also the top six groups ranked at CASP3. We conclude that MaxSub is a suitable method for the automatic evaluation of models.

Algorithms↗

PubMed2002

Adaptive algorithm of automated annotation.

MOTIVATION: It is common knowledge that the avalanche of data arriving from the sequencing projects cannot be annotated either experimentally or manually by experts. The need for a reliable and convenient tool for automated sequence annotation is broadly recognized. RESULTS: Here, we describe the Adaptive Algorithm of Automated Annotation (A(4)) based on a statistical approach to this problem. The mathematical model relates a set of homologous sequences and descriptions of their functional properties, and calculates the probabilities of transferring a sequence description onto its homologue. The proposed model is adaptive, its parameters (distribution characteristics, transference probabilities, thresholds, etc.) are dynamic, i.e. are generated individually for the sequences and various functional properties (words of the description). The proposed technique significantly outperforms the widely used test for frequency threshold, which is a special case of our model realized for the simplest set of parameters. The prediction technique has been realized as a computer program and tested on a random sequence sampling from SWISS-PROT. AVAILABILITY: The automated annotation program based on the proposed algorithm is available through the Web browser at http://www.genebee.msu.su/services/annot/basic.html.

Algorithms↗