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PubMed1999

Capillary electrophoresis and capillary electrochromatography of organic pollutants.

Capillary electrophoresis (CE) has a unique capability for separation of analytes of environmental concern, particularly those that are more polar and ionic, based on the complementary separation principle of electrophoresis. In the past few years, CE has been selectively used to analyze various classes of compounds having current or potential environmental relevance. This review outlines the current status of CE for the determination of environmental pollutants, based predominantly on research results published from the beginning of 1997 to early 1999. Covered are environmental pollutants of all types except pesticides and inorganics. Certain naturally produced toxins are also covered because of their significant impacts upon human health and the environment. CE methods, as with all methods, must be judged on their ability to provide approaches that are reliable, sensitive, selective, and rapid, while meeting "green chemistry" initiatives for pollution prevention. We also compare CE methods to benchmark environmental techniques involving gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and high performance liquid chromatography (HPLC).

Animals↗

PubMed2006

Report on a multicenter fMRI quality assurance protocol.

Temporal stability during an fMRI acquisition is very important because the blood oxygen level-dependent (BOLD) effects of interest are only a few percent in magnitude. Also, studies involving the collection of groups of subjects over time require stable scanner performance over days, weeks, months, and even years. We describe a protocol designed by one of the authors that has been tested for several years within the context of a large, multicenter collaborative fMRI research project (FIRST-BIRN). A full description of the phantom, the quality assurance (QA) protocol, and the several calculations used to measure performance is provided. The results obtained with this protocol at multiple sites over time are presented. These data can be used as benchmarks for other centers involved in fMRI research. Some issues with the various protocol measures are highlighted and discussed, and possible protocol improvements are also suggested. Overall, we expect that other fMRI centers will find this approach to QA useful and this report may facilitate developing a similar QA protocol locally. Based on the findings reported herein, the authors are convinced that monitoring QA in this way will improve the quality of fMRI data.

Brain Mapping↗

PubMed1999

Three-dimensional kinematics and trunk muscle myoelectric activity in the elderly spine - a database compared to young people.

OBJECTIVE: To establish a database of lumbar spine kinematics and muscle activation profiles for a healthy elderly population. DESIGN: Spine motion parameters and muscle activation profiles of the elderly were identified and quantified in part by comparison with an existing database of younger people. BACKGROUND: Databases are often used as a benchmark to establish what is "normal", or for developing appropriate exercise programs or diagnostic methodologies. METHODS: Twelve people (average age 69 yr) performed full range of motion movements about the flexion, lateral bending and axial twist axes of the lumbar spine. Fourteen torso muscles (7 per side) were monitored with electromyographic electrodes and the signals normalized to maximum voluntary efforts. RESULTS: The elderly were slower moving, and had a reduced range of motion in full flexion and lateral bend but not in axial twist. Furthermore there was more coupled motion evident in the twisting efforts of the elderly. Abdominal muscles appeared to become more active, earlier in the lateral bending movement. CONCLUSIONS: Loss of motion is normal with age together with subtle changes in the way the spine moves and groups of muscles are recruited around the torso. RELEVANCE: Quantification of "normal" changes associated with aging will enable clinicians and scientists to distinguish normal changes from pathology.

Aged↗

PubMed1997

Application of autonomous neural network systems to medical pattern classification tasks.

This paper presents a study of the application of autonomously learning multiple neural network systems to medical pattern classification tasks. In our earlier work, a hybrid neural network architecture has been developed for on-line learning and probability estimation tasks. The network has been shown to be capable of asymptotically achieving the Bayes optimal classification rates, on-line, in a number of benchmark classification experiments. In the context of pattern classification, however, the concept of multiple classifier systems has been proposed to improve the performance of a single classifier. Thus, three decision combination algorithms have been implemented to produce a multiple neural network classifier system. Here the applicability of the system is assessed using patient records in two medical domains. The first task is the prognosis of patients admitted to coronary care units; whereas the second is the prediction of survival in trauma patients. The results are compared with those from logistic regression models, and implications of the system as a useful clinical diagnostic tool are discussed.

Artificial Intelligence↗

PubMed1995

Clinical utility of the polymerase chain reaction to diagnose Mycoplasma pneumoniae infection.

The diagnosis of Mycoplasma pneumoniae infection currently relies on serological methods which may be slow to produce diagnostic results and may be inconvenient for both the clinician and the patient. This study was designed to assess whether or not the polymerase chain reaction (PCR) is a useful additional diagnostic method. Comparison was therefore made with serology as it is routinely practiced. PCR was used to examine for the presence of M. pneumoniae DNA in throat swab specimens obtained from 99 hospitalized patients investigated for a range of respiratory pathogens including M. pneumoniae. PCR detected M. pneumoniae DNA in 24 adults and 25 children, which is significantly more than the 32 patients found to be antibody positive by the particle agglutination test (p = 0.001). M. pneumoniae DNA was not detected in any of the throat swabs from 32 apparently healthy volunteers. PCR inhibitors were not detected in any of the samples tested. Significantly more children (88%) than adults (38%) were found to be anti-mycoplasma antibody-positive (p < 0.0001). Routine clinical practice was reflected in the fact that 56 patients (57%) had indeterminate serological results because only single sera were obtained. The sensitivity and specificity of PCR were assessed to be 92% and 98% respectively, using a combination of serological and clinical data as the benchmark. PCR appears to have advantages over serological testing, both with respect to accuracy and convenience of single specimen testing. The poor performance of serological tests in adults makes PCR especially useful in this age group.

Adult↗

PubMed2000

SAWTED: structure assignment with text description--enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons.

MOTIVATION: Sequence database search methods often identify putative sub-threshold hits of known function or structure for a given query sequence. It is widespread practice to filter these hits by hand using knowledge of function and other factors; to the expert, some hits may appear more sensible than others. SAWTED (Structure Assignment With Text Description) is an automated solution to this post-filtering problem which will be applicable to large scale genome assignments. RESULTS: A standard document comparison algorithm is applied to text descriptions extracted from SWISS-PROT annotations. The added value of SAWTED in combination with PSI-BLAST has been shown with a benchmark of difficult remote homologues taken from the SCOP structure database. AVAILABILITY: A WAWTED PSI-BLAST Web server is available to perform sensitive searches against the protein structure database (http://www.bmm.icnet.uk/servers/sawted). CONTACT: R.MacCallum@icrf.icnet.uk

Algorithms↗

PubMed2026

Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.

MOTIVATION: Exome sequencing is widely used for genetic studies; however, accurate detection of copy number variants (CNV) in paralogous genes is challenging due to short-read mapping ambiguity and extensive copy-number variation. The human genome contains several hundred paralogous genes, many of which are known to harbor disease-associated CNVs. Existing exome CNV callers are primarily designed for rare CNV detection in uniquely mappable regions and are not well-suited for paralogous genes. METHODS: We describe a computational method (EdgeCopy) for copy number profiling of paralogous genes using whole-exome sequence data. EdgeCopy aggregates reads mapped to all copies of paralogous genes and relates observed read depth to copy number for multiple exome samples using an approximate composite likelihood function. The likelihood function is optimized using numerical optimization to obtain gene-level fractional copy number estimates that are discretized and refined using a Hidden Markov Model to obtain exon-level copy number estimates. RESULTS: Benchmarking of Edgecopy using experimental copy number data showed high concordance (mean = 0.973) for six disease-associated paralogous genes. We evaluated performance using whole-exome data from approximately 2400 samples across five continental populations from the 1000 Genomes Project. EdgeCopy shows robust concordance with whole-genome sequencing based estimates (0.974-0.982) across populations and 130 paralogous genes spanning a wide range of copy-number variation. In comparison, copy number analysis using a state-of-the-art exome CNV caller failed to estimate copy number for paralogous genes with very high mapping ambiguity and showed much lower concordance (0.565) for CNV events compared to EdgeCopy (0.908). AVAILABILITY: EdgeCopy is freely available at https://github.com/vibansal-lab/edgecopy.

Humans↗

PubMed1998

The development of a quality information system: a case study of Mexico.

One of the primary obstacles in the implementation of continuous quality improvement (CQI) programmes in developing countries is the lack of timely and appropriate information for decentralized decision-making. The integrated quality information system (QIS) described herein demonstrates Mexico's unique effort to package four separate, yet mutually reinforcing, tools for the generation and use of quality-related information at all levels of the Mexican national health care system. The QIS is one element of the continuous quality improvement programme administered by the Secretariat of Health in Mexico. Mexico's QIS was designed to be flexible and capable of adapting to local needs, while at the same time allowing for the standardization of health care quality assurance indicators, and subsequent ability to measure and compare the quality performance of health facilities nationwide. The flexibility of the system extends to permit the optimal use of available data by health care managers at all levels of the health care system, as well as the generation of new information in important areas often neglected in more traditional information systems. Mexico's QIS consists of four integrated components: 1) a set of client and provider surveys, to assess specific issues in the quality of health services delivered; 2) client and provider national satisfaction surveys; 3) a sentinel health events strategy; and 4) a national Comparative Performance Evaluation System, for use by the Secretariate of Health for the quality assessment of state and provincial health care services (internal benchmarking). The QIS represents another step in Mexico's ongoing effort to use data for effective decision-making in the planning, monitoring and evaluation of services delivered by the national health care system. The design and application of Mexico's QIS provides a model for decentralized decision-making that could prove useful for developing countries, where the effective use of quality indicators is often limited. Further, the system could serve as a mechanism for motivating positive change in the way information is collected and used in the process of ensuring high quality health care service delivery.

Benchmarking↗

PubMedDate not supplied

Feasibility of a multi-state outcomes program for cardiopulmonary rehabilitation.

BACKGROUND: Outcomes validate program performance and patient benefits received from cardiac and pulmonary rehabilitation. However, outcomes have little meaning without test standardization and the ability to benchmark data with other programs. The purpose of this article is to demonstrate the feasibility for measuring standardized outcomes in a large number of rehabilitation programs. METHODS: The subjects included 928 cardiac patients and 222 pulmonary patients from 35 cardiac and 31 pulmonary rehabilitation programs. The SF-36 Health Survey, patient knowledge test, and 6-minute distance walk were administered before and after completion of the rehabilitation program. The patients completed rehabilitation according to the program guidelines at their respective site. RESULTS: Significant (P < 0.05) improvements were demonstrated for cardiac and pulmonary rehabilitation in each of the eight health concepts within the SF-36. In addition, patient knowledge and distance walked significantly (P < 0.05) improved for both cardiac and pulmonary rehabilitation. CONCLUSIONS: Although this study does not document the effectiveness of rehabilitation for patients, it does demonstrate that the collection and analysis of standardized outcomes among many cardiac and pulmonary rehabilitation sites is feasible.

Benchmarking↗

PubMed2003

Methods and rationale for derivation of a reference dose for methylmercury by the U.S. EPA.

In 2001, the U.S. Environmental Protection Agency derived a reference dose (RfD) for methylmercury, which is a daily intake that is likely to be without appreciable risk of deleterious effects during a lifetime. This derivation used a series of benchmark dose (BMD) analyses provided by a National Research Council (NRC) panel convened to assess the health effects of methylmercury. Analyses were performed for a number of endpoints from three large longitudinal cohort studies of the neuropsychological consequences of in utero exposure to methylmercury: the Faroe Islands, Seychelles Islands, and New Zealand studies. Adverse effects were identified in the Faroe Islands and New Zealand studies, but not in the Seychelles Islands. The NRC also performed an integrative analysis of all three studies. The EPA applied a total uncertainty factor (UF) of 10 for intrahuman toxicokinetic and toxicodynamic variability and uncertainty. Dose conversion from cord blood mercury concentrations to maternal methylmercury intake was performed using a one-compartment model. Derivation of potential RfDs from a number of endpoints from the Faroe Islands study converged on 0.1 microg/kg/day, as did the integrative analysis of all three studies. EPA identified several areas for which further information or analyses is needed. Perhaps the most immediately relevant is the ratio of cord:maternal blood mercury concentration, as well as the variability around this ratio. EPA assumed in its dose conversion that the ratio was 1.0; however, available data suggest it is perhaps 1.5-2.0. Verification of a deviation from unity presumably would be translated directly into comparable reduction in the RfD. Other areas that EPA identified as significant areas requiring further attention are cardiovascular consequences of methylmercury exposure and delayed neurotoxicity during aging as a result of previous developmental or adult exposure.

Cohort Studies↗

PubMed2005

Using mass distribution information to model the human thigh for body segment parameter estimation.

Accurate estimations of body segment inertial parameters (BSPs) are required to calculate the kinetics of motion. The purpose of this study was to develop a geometric model of the human thigh segment based on mass distribution properties determined from dual energy x ray absorptiometry (DEXA). One hundred subjects from four populations underwent a DEXA scan and anthropometric measurements were taken. The mass distribution properties of the thigh segment were determined for 20 subjects, a geometric model was developed, and the model was applied to the remaining 80 subjects. The model was validated by comparing to benchmark DEXA measurements. Four other popular models in the literature were also evaluated in the same manner No one set of predictors performed best for a particular group or BSP, however modeling the mass distribution properties of the segment allows the assumption of constant density while still accurately representing the inertial properties of the segment and provides promise for future development of BSP models.

Absorptiometry, Photon↗

PubMed2006

Making working memory work: a computational model of learning in the prefrontal cortex and basal ganglia.

The prefrontal cortex has long been thought to subserve both working memory (the holding of information online for processing) and executive functions (deciding how to manipulate working memory and perform processing). Although many computational models of working memory have been developed, the mechanistic basis of executive function remains elusive, often amounting to a homunculus. This article presents an attempt to deconstruct this homunculus through powerful learning mechanisms that allow a computational model of the prefrontal cortex to control both itself and other brain areas in a strategic, task-appropriate manner. These learning mechanisms are based on subcortical structures in the midbrain, basal ganglia, and amygdala, which together form an actor-critic architecture. The critic system learns which prefrontal representations are task relevant and trains the actor, which in turn provides a dynamic gating mechanism for controlling working memory updating. Computationally, the learning mechanism is designed to simultaneously solve the temporal and structural credit assignment problems. The model's performance compares favorably with standard backpropagation-based temporal learning mechanisms on the challenging 1-2-AX working memory task and other benchmark working memory tasks.

Algorithms↗

PubMedDate not supplied

An adaptive ant colony system algorithm for continuous-space optimization problems.

Ant colony algorithms comprise a novel category of evolutionary computation methods for optimization problems, especially for sequencing-type combinatorial optimization problems. An adaptive ant colony algorithm is proposed in this paper to tackle continuous-space optimization problems, using a new objective-function-based heuristic pheromone assignment approach for pheromone update to filtrate solution candidates. Global optimal solutions can be reached more rapidly by self-adjusting the path searching behaviors of the ants according to objective values. The performance of the proposed algorithm is compared with a basic ant colony algorithm and a Square Quadratic Programming approach in solving two benchmark problems with multiple extremes. The results indicated that the efficiency and reliability of the proposed algorithm were greatly improved.

Algorithms↗

PubMed2004

Benchmarking home care services in The Netherlands.

A benchmark study of home care institutions in the Netherlands evaluated them principally in terms of efficiency and client and staff surveys. Efficiency was measured on the basis of production and expenditure data. Those chosen as "best-practice" agencies tend to focus on their core duties and perform fewer ancillary services, have smaller care teams and operate with fewer hierarchical levels.

Attitude of Health Personnel↗

PubMed2026

A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.

The rapid growth of genomic sequencing demands fast, accurate, and scalable analysis methods. In viral genomic classification, expanding labeled reference collections can make supervised models costly to update and dependent on fixed label sets, motivating retrieval-based genomic classification as a simpler, more flexible alternative. We present a unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification across three viral classification tasks: hepatitis C virus (HCV) genotyping, COVID-19 discrimination, and human papillomavirus (HPV) genotyping. We compare standard sequence encodings (one-hot, k-mers, FCGR) with dense embeddings (dna2vec, DNABERT). For each representation, we evaluate supervised classifiers (Random Forest, Decision Tree, XGBoost) and retrieval-based classification, where sequence vectors are indexed with FAISS and labels are assigned via similarity-weighted k-NN. Furthermore, we benchmark multiple FAISS index types (Flat, IVF, HNSW, IVFPQ, OPQ) to characterize accuracy-speed-memory trade-offs at scale. The results show that XGBoost and retrieval using Flat or IVF indexes achieve strong classification performance under different computational profiles. Compressed indexes such as IVFPQ and OPQ substantially reduce memory usage, although their accuracy loss depends on the dataset and representation. Overall, supervised XGBoost provides a favorable accuracy-size trade-off, while retrieval-based classification remains competitive and allows labeled reference sequences to be incorporated without retraining a global classifier. This benchmark provides practical guidance for selecting sequence representations, classifiers, and vector-search indexes under different accuracy, memory, and update requirements.

Genome, Viral↗

PubMed2006

Relationship between Medicare's hospital compare performance measures and mortality rates.

CONTEXT: In response to concerns about the quality of care in US hospitals, the Centers for Medicare & Medicaid Services began measuring hospital performance and reporting this performance on their Web site, Hospital Compare. It is unknown whether these process performance measures are related to hospital-level outcomes. OBJECTIVE: To determine whether quality measured with the process measures used in Hospital Compare are correlated with and predictive of hospitals' risk-adjusted mortality rates. DESIGN, SETTING, AND PARTICIPANTS: Cross-sectional study of hospital care between January 1 and December 31, 2004, for acute myocardial infarction, heart failure, and pneumonia at acute care hospitals in the United States included on the Hospital Compare Web site. Ten process performance measures included in Hospital Compare were compared with hospital risk-adjusted mortality rates, which were measured using Medicare Part A claims data. MAIN OUTCOME MEASURES: Condition-specific inpatient, 30-day, and 1-year risk-adjusted mortality rates. RESULTS: A total of 3657 acute care hospitals were included in the study based on their performance as reported in Hospital Compare. Across all acute myocardial infarction performance measures, the absolute reduction in risk-adjusted mortality rates between hospitals performing in the 25th percentile vs those performing in the 75th percentile was 0.005 for inpatient mortality, 0.006 for 30-day mortality, and 0.012 for 1-year mortality (P<.001 for each comparison). For the heart failure performance measures, the absolute mortality reduction was smaller, ranging from 0.001 for inpatient mortality (P = .03) to 0.002 for 1-year mortality (P = .08). For the pneumonia performance measures, the absolute reduction in mortality ranged from 0.001 for 30-day mortality (P = .05) to 0.005 for inpatient mortality (P<.001). Differences in mortality rates for hospitals performing in the 75th percentile on all measures within a condition vs those performing lower than the 25th percentile on all reported measures for acute myocardial infarction ranged between 0.008 (P = .06) and 0.018 (P = .008). For pneumonia, the effects ranged between 0.003 (P = .09) and 0.014 (P<.001); for heart failure, the effects ranged between -0.013 (P = .06) and -0.038 (P = .45). CONCLUSIONS: Hospital performance measures predict small differences in hospital risk-adjusted mortality rates. Efforts should be made to develop performance measures that are tightly linked to patient outcomes.

Benchmarking↗

PubMed2006

Approaches to the evaluation of outbreak detection methods.

BACKGROUND: An increasing number of methods are being developed for the early detection of infectious disease outbreaks which could be naturally occurring or as a result of bioterrorism; however, no standardised framework for examining the usefulness of various outbreak detection methods exists. To promote comparability between studies, it is essential that standardised methods are developed for the evaluation of outbreak detection methods. METHODS: This analysis aims to review approaches used to evaluate outbreak detection methods and provide a conceptual framework upon which recommendations for standardised evaluation methods can be based. We reviewed the recently published literature for reports which evaluated methods for the detection of infectious disease outbreaks in public health surveillance data. Evaluation methods identified in the recent literature were categorised according to the presence of common features to provide a conceptual basis within which to understand current approaches to evaluation. RESULTS: There was considerable variation in the approaches used for the evaluation of methods for the detection of outbreaks in public health surveillance data, and appeared to be no single approach of choice. Four main approaches were used to evaluate performance, and these were labelled the Descriptive, Derived, Epidemiological and Simulation approaches. Based on the approaches identified, we propose a basic framework for evaluation and recommend the use of multiple approaches to evaluation to enable a comprehensive and contextualised description of outbreak detection performance. CONCLUSION: The varied nature of performance evaluation demonstrated in this review supports the need for further development of evaluation methods to improve comparability between studies. Our findings indicate that no single approach can fulfil all evaluation requirements. We propose that the cornerstone approaches to evaluation identified provide key contributions to support internal and external validity and comparability of study findings, and suggest these be incorporated into future recommendations for performance assessment.

Benchmarking↗

PubMedDate not supplied

Demystifying "QI".

In the continuing pursuit of performance excellence, many quality improvement models such as CQI, TQM, ISO, Six Sigma, and the Malcolm Baldrige criteria for performance excellence have been introduced and implemented with varying degrees of success.

Aged↗