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PubMed2006

Proteome informatics I: bioinformatics tools for processing experimental data.

Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions to sophisticated software for large-scale protein structure determination. This review considers the available and ready to use tools that can help end-users to interpret, validate and generate biological information from their experimental data. It concentrates on bioinformatics tools for 2-DE analysis, for LC followed by MS analysis, for protein identification by PMF, by peptide fragment fingerprinting and by de novo sequencing and for data quantitation with MS data. It also discloses initiatives that propose to automate the processes of MS analysis and enhance the quality of the obtained results.

Algorithms↗

PubMed1993

Assessment of central, peripheral, and autonomic nervous system functions in vibrating tool operators: neuroelectrophysiological studies.

To evaluate the effects of vibrating tool operation (i.e., combined stressors of local vibration, noise, cold climate, and heavy work) on the central, peripheral, and autonomic nervous systems, the short-latency somatosensory and brain stem auditory evoked potentials (SSEP and BAEP), the distribution of sensory median nerve conduction velocities (DCV), conventional median nerve conduction velocities (NCV), and the electrocardiographic R-R interval variability (CVRR) were measured in three groups of male vibrating tool operators and age-matched male healthy adults. Two components of the CVRR reflecting parasympathetic activity (C-CVRSA) and sympathetic activity (C-CVMWSA) were also examined. In the first group of vibrating tool operators (15 chain saw operators), all parameters of DCV (V10-V90 velocities) and sensory and motor nerve conduction velocities of NCV were significantly slowed. All peak latencies of SSEP were significantly prolonged, while no significant differences were found in the interpeak latencies of SSEP. The N9 peak latency of SSEP was significantly related to total working days. In the second group of the operators (12 chain saw and 8 brush saw operators), the I-V interpeak and V peak latencies of BAEP were significantly prolonged in the 12 chain saw operators; the I-V interpeak latency of BAEP was significantly correlated with the working years in the 8 brush saw operators. In the third group of vibrating tool operators, i.e., 13 operators with a history of vibration-induced white finger (VWF group) and 11 operators without VWF (non-VWF group), both the CVRR and C-CVRSA were significantly reduced in the VWF group; only the CVRR was significantly reduced in the non-VWF group. Similarly, the faster velocities of DCV (V70, V80, and V90 velocities) were significantly slowed in both the VWF and non-VWF groups. In conclusion, it is suggested that vibrating tool operation affects the faster sensory and motor nerve fibers, the parasympathetic activity, and the auditory pathway from the acoustic nerve to the brain stem.

Adult↗

PubMed2001

Use of an interactive tool to assess patients' willingness-to-pay.

Assessment of willingness to pay (WTP) has become an important issue in health care technology assessment and in providing insight into the risks and benefits of treatment options. We have accordingly explored the use of an interactive method for assessment of WTP. To illustrate our methodology, we describe the development and testing of an interactive tool to administer a WTP survey in a dental setting. The tool was developed to measure patient preference and strength of preference for three dental anesthetic options in a research setting. It delivered written and verbal formats simultaneously, including information about the risks and benefits of treatment options, insurance, and user-based WTP scenarios and questions on previous dental experience. Clinical information was presented using a modified decision aid. Subjects could request additional clinical information and review this information throughout the survey. Information and question algorithms were individualized, depending on the subject's reported clinical status and previous responses. Initial pretesting resulted in substantial modifications to the initial tool: shortening the clinical information (by making more of it optional reading) and personalizing the text to more fully engage the user. In terms of results 196 general population subjects were recruited using random-digit dialing in southwestern Ontario, Canada. Comprehension was tested to ensure the instrument clearly conveyed the clinical information; the average score was 97%. Subjects rated the instrument as easy/very easy to use (99%), interesting/very interesting (91%), and neither long nor short (72.4%). Most subjects were comfortable/very comfortable with a computer (84%). Indirect evaluation revealed most subjects completed the survey in the expected time (30 min). Additional information was requested by 50% of subjects, an average of 2.9 times each. Most subjects wanted this type of information available in the provider's office for use in clinical decision making (92%). Despite extensive pretesting, three "bugs" remained undiscovered until live use. We have demonstrated that the detailed information, complex algorithms, and cognitively challenging questions involved in a WTP survey can be successfully administered using a tailor-made, patient-based, interactive computer tool. Key lessons regarding the use of such tools include allowing the user to set the pace of information flow and tailor the content, engaging the user by personalizing the textual information, inclusion of tests of comprehension and offering opportunities for correction, and pretesting by fully mimicking the live environment.

Adult↗

PubMed2001

Woodworking activities by early humans: a plant residue analysis on Acheulian stone tools from Peninj (Tanzania).

The emergence of the Acheulian stone tool industry, between 1.7 and 1.5 m.y.a., constitutes one of the earliest evidences of complex behavior in the process of human evolution. The major technological breakthrough with the Acheulian industry was the beginning of the manufacture of bifacially shaped heavy-duty tools. Handaxes made with a predetermined form and a high degree of symmetry are the main characteristic of the Acheulian tradition. The tools are shaped through a long knapping sequence with a remarkable increase in the technical skills of the makers, compared with the older Oldowan tradition, implying a high degree of planning and foresight. Until recently, the function of these early bifacial tools remained unknown. A large number of these artefacts were found at Peninj in Tanzania, and phytolith analyses on handaxes have yielded for the first time unambiguous evidence of their function as woodworking tools.

Animals↗

PubMed2001

Preliminary results of an outcome tool used for evaluation of surgical treatment for fecal incontinence.

PURPOSE: The lack of an outcome tool to evaluate the outcome of surgical and medical treatment for fecal incontinence makes interpretation of success difficult. The purpose of this study was to evaluate a preliminary outcome tool for fecal incontinence. METHOD: Since 1994 an extensive database has prospectively been collected on all females undergoing an overlapping sphincter repair for fecal incontinence by a single surgeon. A simple incontinence form designed to examine outcome, developed by colon and rectal surgeons, was filled out preoperatively and postoperatively. RESULTS: Of 206 females evaluated for surgical treatment of their fecal incontinence, 65 underwent surgical treatment from January 1994 until July 1999. The mean age was 49 (range, 23-80) years, and the mean follow-up was 10 (range, 1-50) months. When comparing each variable (problems holding gas, staining of undergarments, accidental bowel movements, and need to wear pads) and lifestyle issue (physical, social, and sexual activities) preoperatively and postoperatively, there was significant improvement in all areas. Three parameters were chosen (change in accidental bowel movements, improvement in two of three lifestyle areas, and improvement in one of three lifestyle areas) to examine individual items from the database and to determine if they affected outcome. No single variable has a significant effect on the outcome. A scoring system was devised from the questionnaire. From preoperatively to postoperatively, there was a median 14-point improvement that was statistically significant. CONCLUSIONS: This preliminary tool to examine outcome for fecal incontinence measures parameters that are significantly improved by overlapping sphincteroplasty. More work is needed to refine and validate this tool because a standard outcome tool is needed for reporting the results of surgical treatment of fecal incontinence.

Adult↗

PubMed1995

Coding medical concepts: a controlled experiment with a computerised coding tool.

In clinical routine there is a growing need to encode medical concepts with available standard coding systems. The coding process can be time consuming and may significantly add to daily paperwork, particularly regarding patients with multiple diagnoses and in busy clinical environments with a high turnover of patients. We have developed a generic computerised encoding tool--the PADS encoder--to ensure rapid, correct and complete coding of diagnoses in daily routine. The tool is integrated into an electronic patient record system (PADS, Patient Archiving & Documentation System) and takes full advantage of the user friendly Macintosh interface. The tool was tested in a controlled experiment by 18 clinicians who encoded a total of 666 medical concepts in each protocol (study protocol vs. control). The following positive findings were significantly associated with the use of the computerised coding tool: the number of correctly encoded medical concepts was higher (99.55% vs. 86.1%), coding errors were lower (0% vs. 10.81%), more modifier codes were encoded correctly (increase by up to 43%), less coding errors were made (decrease by up to 43%), the overall rate of correctly encoded and complete main and modifier codes was increased by 31.27% (97.29% vs. 66.02%), coding time was reduced by 50%. This paper presents data to suggest that a computerised coding tool can produce more complete data of higher quality and can save time compared with the traditional approach to encode medical concepts.

Computer Communication Networks↗

PubMed2004

[Cardiovascular risk assessment for informed decision making. Validity of prediction tools].

BACKGROUND AND PURPOSE: Patient involvement in health care decisions is increasingly requested. The authors investigated whether currently available assessment tools for prediction of cardiovascular risk can be used for individual risk prediction as a basis of informed decision making. METHODS: The authors searched for risk assessment tools and respective validation studies in Medline (until August 16, 2004) and the Cochrane Library (issue 2/2004). The following criteria were used for evaluation of prognostic studies: (1) discrimination between risk groups; (2) predictive values; (3) prognostic agreement; (4) transferability across populations. RESULTS: A total of twelve assessment tools were identified. The Framingham function, Sheffield Tables, Canadian Tables, Framingham Categorial, New Zealand, Joint British, and European Charts (1994 and 1998) are based on the Framingham Study; PROCAM Risk Score, UKPDS Risk Engine, and SCORE Risk Charts use different source data. Framingham-based instruments overestimate cardiovascular risk of Central-European populations by at least 30%, with substantial regional variation even within a country (between 30% and 100%, British Regional Heart Study). Therefore, prior to application the assessment tools would need recalibration using regional data of cardiovascular mortality and adjustment for social class differences. Published sensitivity, specificity, and C-statistics for external validation (area under the curve [AUC] approximately 0.6) are clearly inferior to internal validation (AUC approximately 0.8). Agreement between instruments beyond chance is moderate (kappa approximately 0.5). No studies on external validation could be identified for the new European SCORE Risk Charts and UKPDS Risk Engine. CONCLUSION: Validation of currently available assessment tools for cardiovascular risk prediction is inadequate. Uncritical use may lead to substantial under- or overestimation of individual cardiovascular risk and inappropriate treatment decisions.

Adult↗

PubMed2004

Performance of four clinical screening tools to select peri- and early postmenopausal women for dual X-ray absorptiometry.

Several methods to select postmenopausal women for dual X-ray absorptiometry (DXA) have been proposed. We decided to compare the performance of three clinical decision rules (SCORE, ORAI, OST) with the usual case-finding strategy based on the presence of a major risk factor for future fracture (CFMRF). The study subjects were 2009 healthy, white, peri- or early postmenopausal women participating in the Danish Osteoporosis Prevention Study (DOPS). DXA results expressed as T-scores and scores on SCORE, ORAI, OST and CFMRF were extracted from the DOPS database. First, we evaluated the screening tools as originally described by the developers. The resulting sensitivities and specificities ranged from 18% to 92% and from 66% to 85%, respectively. Only OST achieved a high sensitivity (92%) with respect to femoral neck T-score < or = -2.5; however, the sensitivity with respect to lumbar spine T-score < or = -2.5 was only 51%. Next, the performance of the screening tools was evaluated against T-score < or = -2.0 (and T-score < or = -2.5) in at least one of the regions: femoral neck, total hip or lumbar spine. Using ROC curve analysis, we determined cut-offs yielding sensitivities as close as possible to 90%. The CFMRF and the ORAI tool were too coarse to yield 90% sensitivity. The performances of OST and SCORE were equal from a clinical perspective in that the sensitivities and the specificities varied from 89% to 94% and from 23% to 28%, respectively. The performance of CFMRF was no better than could be expected by chance, yielding a sensitivity of 19% and a specificity of 85%. Applying SCORE or OST 75% of the women would have to be referred for densitometry to identify 90% of the women with T-score < or = -2.0 (or T-score < or = -2.5) in at least one region. In conclusion, our results question the utility of all the evaluated tools for screening peri- and early postmenopausal women for low BMD. However, if a decision on referral has to be made, it may be based on the simple OST rule, which performed as well as or better than any of the other tools.

Absorptiometry, Photon↗

PubMed2003

The potential of mechanism-based bioanalytical tools in ecotoxicological exposure and effect assessment.

The current challenge to ecotoxicology is to develop tools that allow rapid and cost-efficient detection of those environmental chemicals or their combinations that are responsible for sublethal, chronic toxic effects in exposed organisms. Bioanalytical tools may meet these challenges, particularly if they are mechanism-based. Technically, bioanalytical tools allow rapid and cost-efficient analysis of environmental matrices. Mechanism-based, bioanalytical tools, however, do not only indicate that certain chemicals are there, but-and this is the major advantage of mechanism-based bioanalytical tools (MBBTs)-they indicate that chemicals with a specific mode of toxic action or a specific toxic potential are there. In this way MBBTs bridge exposure and effect assessment and help in a faster identification of the causative agent(s). Several principles of MBBTs, including immunoassays, enzyme inhibition assays, receptor assays and gene induction assays are briefly discussed and their application in processes such as bioassay-directed fractionation is illustrated. The focus of this manuscript is the analytical power of MBBTs in exposure and effect assessment. MBBTs have, however, a much broader potential and can support research on other challenges in ecotoxicology such as mixture effects or multiple effects caused by single pollutants or by various stresses simultaneously.

Biological Assay↗

PubMed2003

Effect-directed analysis: a promising tool for the identification of organic toxicants in complex mixtures?

Wastewater effluents, groundwater, surface water, sediments, soils and air particulate matter are often contaminated by a multitude of chemicals. Since often no a priori knowledge of relevant toxicants exists, chemical analysis alone is not an appropriate tool for hazard assessment. Instead, a linkage of effect data and hazardous compounds is required. For that purpose, effect-directed analysis (EDA) was developed, which is based on a combination of biotesting, fractionation procedures and chemical analytical methods. Since a controversial discussion about the prospects of success in relation to the expense exists, the current methodological state of EDA for organic toxicants in complex mixtures and important results are reviewed in this paper with the aim of establishing criteria for the successful use of this promising tool. While EDA is a powerful tool to identify specifically acting individual toxicants close to the source of emission, it is inappropriate for screening purposes and often may fail in remote areas where the concentrations of specific toxicants are too low relative to the nonspecific toxicity of the whole mixture of natural and anthropogenic compounds. The biological tools have to be carefully selected with respect to their ability to detect specific effects and their significance in hazard assessment. Sophisticated chemical tools are required to identify individual toxicants in mixtures of thousands of compounds, which are typical for contaminated environments.

Air Pollutants↗

PubMed2005

Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications.

Prediction of which peptides can bind major histocompatibility complex (MHC) molecules is commonly used to assist in the identification of T cell epitopes. However, because of the large numbers of different MHC molecules of interest, each associated with different predictive tools, tool generation and evaluation can be a very resource intensive task. A methodology commonly used to predict MHC binding affinity is the matrix or linear coefficients method. Herein, we described Average Relative Binding (ARB) matrix methods that directly predict IC(50) values allowing combination of searches involving different peptide sizes and alleles into a single global prediction. A computer program was developed to automate the generation and evaluation of ARB predictive tools. Using an in-house MHC binding database, we generated a total of 85 and 13 MHC class I and class II matrices, respectively. Results from the automated evaluation of tool efficiency are presented. We anticipate that this automation framework will be generally applicable to the generation and evaluation of large numbers of MHC predictive methods and tools, and will be of value to centralize and rationalize the process of evaluation of MHC predictions. MHC binding predictions based on ARB matrices were made available at http://epitope.liai.org:8080/matrix web server.

Animals↗

PubMed2006

TUGAI: An integrated simulation tool for ecological assessment of alternative water management strategies in a degraded river delta.

The development of ecologically sound water allocation strategies that account for the needs of riverine ecosystems is a pressing issue, especially in semiarid river basins. In the Aral Sea Basin, a search for strategies to mitigate ecological and socioeconomic deterioration has been in process since the early 1990s. The Geographic Information System-based simulation tool TUGAI has been developed to support the policy determination process by providing a simple, problem-oriented method to assess ecological effects of alternative water management strategies for the Amudarya River. It combines a multiobjective water allocation model with simple, spatially explicit statistical and rule-based models of landscape dynamics. Changes in environmental conditions are evaluated by a fuzzy habitat suitability index for Populus euphratica, which is the dominant species of the characteristic riverine Tugai forests. Water management scenarios can be developed by altering spatiotemporal water distribution in the delta area or the amount of water inflow into the delta. Outcomes of scenario analysis are qualitative comparisons of the ecological effects of different options for a time period of up to 28 years. The given approach utilizes different types of knowledge, from quantitative hydrological data to qualitative local expert knowledge. The main purpose of the tool is to integrate the knowledge in a comprehensive way to make it available for discussions on alternative policies in moderated workshops with stakeholders. In this article, the modules of the tool, their integration, and three hypothetical scenarios are presented. Based on the experience gained when developing the TUGAI tool, we propose that the general framework can be transferred to other areas where tradeoffs in water allocation between the environment and other water users are of major concern. The potential for a simulation tool to structure and inform a complex resource management situation by involving local experts and stakeholders in the development of possible future scenarios will become increasingly valuable for transparent and participatory resource management.

Conservation of Natural Resources↗

PubMed2003

Tufted capuchins (Cebus apella) attribute value to foods and tools during voluntary exchanges with humans.

This research examined exchange and value attribution in tufted capuchin monkeys ( Cebus apella). We presented subjects with opportunities to obtain various foods and a tool from an experimenter in exchange for the foods or tool in the subjects' possession. The times elapsed before the first chow biscuits were expelled and/or an exchange took place were recorded as the dependent measures. Laboratory chow biscuits, grapes, apples, and a metal bolt (a tool used to probe for syrup) were used as experimental stimuli. The subjects demonstrated the ability to recognize that exchanges could occur when an experimenter was present with a desirable food. Results indicate that subjects exhibited significant variation in their willingness to barter based upon the types of foods that were both in their possession and presented by the experimenter. Subjects more readily traded chow biscuits for fruit, and more readily traded apples for grapes than grapes for apples. During the exchange of tools and food, the subjects preferred the following in descending order when the probing apparatus was baited with sweet syrup: grapes, metal bolts, and chow biscuits. However when the apparatus was not baited, the values changed to the following in descending order: grapes, chow, and metal bolts. These results indicate that tufted capuchins recognize opportunities to exchange and engage in a simple barter system whereby low-valued foods are readily traded for more highly valued food. Furthermore, these capuchins demonstrate that their value for a tool changes depending upon its utility.

Animals↗

PubMedDate not supplied

Validation tools for variable subset regression.

Variable selection is applied frequently in QSAR research. Since the selection process influences the characteristics of the finally chosen model, thorough validation of the selection technique is very important. Here, a validation protocol is presented briefly and two of the tools which are part of this protocol are introduced in more detail. The first tool, which is based on permutation testing, allows to assess the inflation of internal figures of merit (such as the cross-validated prediction error). The other tool, based on noise addition, can be used to determine the complexity and with it the stability of models generated by variable selection. The obtained statistical information is important in deciding whether or not to trust the predictive abilities of a specific model. The graphical output of the validation tools is easily accessible and provides a reliable impression of model performance. Among others, the tools were employed to study the influence of leave-one-out and leave-multiple-out cross-validation on model characteristics. Here, it was confirmed that leave-multiple-out cross-validation yields more stable models. To study the performance of the entire validation protocol, it was applied to eight different QSAR data sets with default settings. In all cases internal and external model performance was good, indicating that the protocol serves its purpose quite well.

Quantitative Structure-Activity Relationship↗

PubMed2006

ADAAPT: Amgen's data access, analysis, and prediction tools.

The Amgen's Data Access Analysis Prediction Tools (ADAAPT) system is a desktop decision support tool developed to provide flexible access and analysis of chemical and biological data. The system is platform independent, adaptable, easily deployed, and scalable. It consists of four main modules: access, analysis, prediction, and tools. The access module contains numerous user interfaces designed to retrieve data easily. The analysis module provides standard computational tools to perform property calculation, QSAR/QSPR, and statistical analyses. The prediction module contains in-house models to calculate a drug-likeness score and absorption index. Finally, the tools module provides a wide array of features that are of general interest to our scientists.

Computer Systems↗

PubMed2006

Validation of the asthma impact survey, a brief asthma-specific quality of life tool.

BACKGROUND: The Asthma Impact Survey (AIS-6) is a new six question asthma outcome tool for which information on validity has not been published. OBJECTIVE: To provide validation for the AIS-6 as a brief asthma-specific quality of life tool. METHODS: Surveys were sent to a random sample of members of a large managed care organization who were at least 35 years of age and in the two-year period preceding the survey had either (1) at least one documented asthma-related medical encounter, or (2) at least a 6 months supply of asthma medication dispensed. In addition to the AIS-6, the survey included a validated quality of life tool [the mini-Asthma Quality of Life Questionnaire (AQLQ)]; a validated asthma control questionnaire [the Asthma Therapy Assessment Questionnaire (ATAQ)]; a validated symptom severity scale (AOMS); and information regarding demographics, co-morbidities, asthma severity, and asthma management. The results of the AIS-6 were compared to the results of the other tools by means of correlation and factor analysis. Independent predictors of AIS-6 and AQLQ scores were determined by multiple stepwise linear regression analyses. RESULTS: AIS-6 scores were significantly related to female sex, educational level, income, smoking, body mass index (BMI), COPD, steroid use, and hospitalization history in bivariate analyses. The AIS-6 score significantly correlated (r = - 0.84, p < 0.0001) with the AQLQ total score and loaded on the three factors (activity, symptoms, and concern/bother) reflected by the survey information and on which the AQLQ also loaded. Significant but somewhat smaller correlations were found between the AIS-6 and the ATAQ (r = 0.70, p < 0.0001) and the AOMS (r = 0.55, p < 0.0001). Independent predictors were the same for the AIS-6 and AQLQ and included oral steroid use, COPD history, BMI, female sex, educational level, and hospitalization in the past year. CONCLUSION: These data support the validity of the short six-question AIS-6 as an asthma-specific quality of life tool.

Adult↗

PubMed1983

A test rig for the measurement of vibration in hand-held power tools.

The purpose of the present project was to study the possibility of using a test rig for the measurement of vibration and noise from hand-held power tools. A test rig was designed to give the same effect on tool handle vibration as the human hand/arm system. Work was simulated by feeding the material to be processed against the tool, clamped into the rig, with the aid of a co-ordinate table. It was designed for use in studies of impact drills, chain saws, grinders and similar power tools. The report describes a proposal for testing the vibration properties of impact drills. Drilling with the test rig was compared with manual drilling. The difference in the acceleration level between the two methods was about 1 dB for ISO-weighted values in the critical direction. Both methods showed good reproducibility. The possibility of conducting noise level tests of a power tool in the rig was studied and the results are reported separately.

Journal Article↗

PubMed1993

An approach to ergonomics evaluation of hand tools.

Based on current knowledge of cumulative trauma disorders in the hand and forearm, related to the use of hand tools, an analysis was undertaken of variables to be considered in ergonomics evaluation of hand tools. Measurement methods were developed and an evaluation station was implemented. Measurement methods are physical, physiological or psychophysical. They focus on the tool, and on the effect of typical use of the tool on the operator. The evaluation station serves as a resource in the development, selection, and testing of tools for a given purpose.

Journal Article↗