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Results for “Performance benchmarking”

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PubMed1996

Comparison of four human studies of perinatal exposure to methylmercury for use in risk assessment.

Newer data from human epidemiologic studies of methylmercury (MeHg) poisoning in which perinatal exposure occurred are available from four distinct populations. The results of an Iraqi grain-consuming population are compared to results from studies performed in fish-consuming groups in the Faroe Islands, the Seychelles Islands and in Peruvian fishing villages. A comparison of the results indicate that the Iraqi population does not represent a sensitive subpopulation within a perinatal group, but rather the relative lower threshold identified from this study was the results of confounders. Use of this benchmark dose for regulatory purposes may place a severe limitation upon fish consumption in the United States that is not fully supported by the scientific data.

Denmark↗

PubMed2026

RUMINA: high-throughput deduplication of unique molecular identifiers for amplicon and whole-genome sequencing with enhanced error correction.

MOTIVATION: Unique molecular identifiers (UMIs) are widely used in next-generation sequencing to enable accurate molecular counting and error correction. However, challenges remain in accurately collapsing UMI clusters, especially when read counts are low or sparse read clusters arise from barcode sequencing errors. RESULTS: We present RUMINA, a Rust-based pipeline for UMI-aware deduplication and error correction, optimized for both amplicon and shotgun sequencing. RUMINA supports multiple UMI cluster strategies, alongside majority-rule read selection independent of mapping quality, as well as discrete handling of 1-2 read clusters, paired-end merging, and read-length stratification. Benchmarking using simulated HIV population sequencing data and real-world iCLIP and TCR datasets showed that RUMINA improves ultra-low frequency SNV detection (0.01%-1%), reduces false positives, enhances reproducibility, and processes sequencing data up to 10-fold faster than existing tools. By integrating UMI- and sequence-level correction in a high-performance framework, RUMINA offers a fast, scalable, and robust solution for UMI-enabled sequencing workflows. AVAILABILITY AND IMPLEMENTATION: RUMINA is implemented in Rust and distributed as open-source code and precompiled binaries. Source code and installation instructions are available at https://github.com/greninger-lab/rumina. Documentation associated with this manuscript is available at https://github.com/greninger-lab/rumina_paper.

High-Throughput Nucleotide Sequencing↗

PubMed2002

X-ray emission of a xenon gas jet plasma diagnosed with Thomson scattering.

We present the results of a benchmark experiment aimed at validating recent calculation techniques for the emission properties of medium and high-Z multicharged ions in hot plasmas. We use space- and time-resolved M-shell x-ray spectroscopy of a laser-produced gas jet xenon plasma as a primary diagnostic of the ionization balance dynamics. We perform measurements of the electron temperature, electron density, and average charge state by recording simultaneous spectra of ion acoustic and electron plasma wave Thomson scattering. A comparison of the experimental x-ray spectra with calculations performed ab initio with a non-local-thermodynamic-equilibrium collisional-radiative model based on the superconfiguration formalism, using the measured plasma parameters, is presented and discussed.

Journal Article↗

PubMedDate not supplied

Using continuous quality improvement strategies to reduce repeated admissions for inpatient psychiatric treatment.

A multidisciplinary performance improvement team was chartered to examine the problem of repeated admissions to psychiatric hospitals. It was also asked to devise an intervention strategy to reduce the number of readmissions, including the number of patients with three or more admissions in a 12-month period and the number of days patients spend in hospital beds. Multivoting, benchmarking, and a review of medical records for 88 psychiatric patients who had been hospitalized three or more times in 1 year were the methods used to gather data on client characteristics. An analysis of the data suggested that these high-end users had similar patterns of service utilization prior to their hospitalizations. The team identified 11 of these patterns as triggers that appear to signal early stages of decompensation that can lead to hospitalization. The team implemented an early intervention and prevention system by using the triggers as criteria for initiating a change in treatment plans. A study of the effectiveness of the Triggers Intervention and Prevention System (TIPS) was undertaken over the next 2 years. An automated program for deriving the triggers from the emergency services database was developed. Initial results that TIPS is an effective means of reducing recidivism and that the triggers can identify high-end users. Some of the triggers were deemed to be more effective than others in the early identification of individuals who may need to be hospitalized. A comparison of hospitalization rates for the pre- and postimplementation periods of TIPS showed a significant reduction in the number of patients who had three or more hospitalizations, fewer total admissions, and a shorter average length of stay. During 1995, the triggers were successful in the early identification of all patients who had more than one admission. The teams used the Design, Measure, Assess, Improve method recommended by the Joint Commission on Accreditation of Healthcare Organizations.

Efficiency, Organizational↗

PubMed2006

EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences.

BACKGROUND: Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms. RESULTS: We proposed a novel clustering-based ensemble algorithm named EMD for de novo motif discovery by combining multiple predictions from multiple runs of one or more base component algorithms. The ensemble approach is applied to the motif discovery problem for the first time. The algorithm is tested on a benchmark dataset generated from E. coli RegulonDB. The EMD algorithm has achieved 22.4% improvement in terms of the nucleotide level prediction accuracy over the best stand-alone component algorithm. The advantage of the EMD algorithm is more significant for shorter input sequences, but most importantly, it always outperforms or at least stays at the same performance level of the stand-alone component algorithms even for longer sequences. CONCLUSION: We proposed an ensemble approach for the motif discovery problem by taking advantage of the availability of a large number of motif discovery programs. We have shown that the ensemble approach is an effective strategy for improving both sensitivity and specificity, thus the accuracy of the prediction. The advantage of the EMD algorithm is its flexibility in the sense that a new powerful algorithm can be easily added to the system.

Algorithms↗

PubMedDate not supplied

National quality efforts: what continuing and staff development educators need to know.

In 1994, the American Nurses Association initiated a series of activities currently referred to as Nursing's Quality Initiative. This first step toward public accountability was based on the premise that all nurses must become more knowledgeable about the measurement, improvement, and benchmarking of clinical costs, quality, and outcomes specific to nursing. The American Nurses Association has not been working alone to advance quality health care. Rather, it has taken an active role in several collaborative activities, including those of the National Quality Forum. The National Quality Forum has focused on a variety of issues, including nursing care performance measurement, an activity in which the American Nurses Association has been involved. It is up to professional nursing, the National Quality Forum, and all who have interest in the provision (or receipt) of quality health care to advance quality in a collaborative, coordinated way.

American Nurses' Association↗

PubMedDate not supplied

The Glasgow Coma Scale and other neurological observations.

The primary tool used by nurses to assess a patient's neurological status is the neurological observation chart incorporating the Glasgow Coma Scale. This article explains the correct use of the chart and how to interpret the findings.

Arousal↗

PubMed2025

Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.

Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, host identification for these viruses remains challenging due to the limitations in scaling cultivation-based approaches and the uncertain reliability and relative low resolution of in silico predictions - particularly for understudied viral taxa. Towards this, Hi-C proximity ligation uses sequenced, cross-linked virus and host genomic fragments to infer virus-host linkages and has now been applied in at least 10 studies. However, its accuracy remains unknown. Here we assess Hi-C performance in recovering virus-host interactions using synthetic communities (SynComs) composed of four marine bacterial strains and nine phages with known interactions and then apply optimized bioinformatic protocols to natural soil samples. In SynComs, standard Hi-C sample preparations and analyses showed poor normalized contact score performance (26% specificity, 100% sensitivity, incorrect matches up to class level) that could be dramatically improved by Z-score filtering (Z ≥ 0.5, 99% specificity), though at reduced sensitivity (62% down from 100%). Detection limits were established as reproducibility was poor below minimal phage abundances of 105 PFU/mL. Applying optimized bioinformatic protocols to natural soil samples, we compared virus-host linkages inferred from proximity-ligated Hi-C sequencing with predictions generated by in silico homology-based and machine learning-based bioinformatic approaches. Prior to Z-score thresholding, agreement was relatively high at the phylum to family levels (72%), but not at the genus (43%) or species (15%) levels. Z-score thresholding reduced sensitivity (only 34% of predictions were retained), with only modest improvements in congruence with bioinformatic methods (48% or 18% at genus or species levels, respectively). Regardless, this led to 79 genus-level-congruent virus-host linkages and 293 new ones revealed by Hi-C alone, i.e., providing many new virus-host interactions to explore in already well-studied climate-critical soils. Overall, these findings provide empirical benchmarks and methodological guidelines to improve the accuracy and reliability of Hi-C for virus-host linkage studies in complex microbial communities.

Benchmarking↗

PubMed1998

Psychophysics of reading. XVII. Low-vision performance with four types of electronically magnified text.

Most people with low vision need magnification to read. Page navigation is the process of moving a magnifier during reading. Modern electronic technology can provide many alternatives for navigating through text. This study compared reading speeds for four methods of displaying text. The four methods varied in their page-navigation demands. The closed-circuit television (CCTV) and MOUSE methods involved manual navigation. The DRIFT method (horizontally drifting text) involved no manual navigation, but did involve both smooth-pursuit and saccadic eye movements. The rapid serial visual presentation (RSVP) method involved no manual navigation, and relatively few eye movements. There were 7 normal subjects and 12 low-vision subjects (7 with central-field loss, CFL group, and 5 with central fields intact, CFI group). The subjects read 70-word passages at speeds that yielded good comprehension. Taking the CCTV reading speed as a benchmark, neither the normal nor low-vision subjects had significantly different speeds with the MOUSE method. As expected from the reduced navigational demands, normal subjects read faster with the DRIFT method (85% faster) and the RSVP method (169%). The CFI group read significantly faster with DRIFT (43%) and RSVP (38%). The CFL group showed no significant differences in reading speed for the four methods.

Adolescent↗

PubMed2002

Improving cardiac rehabilitation: a view from the United Kingdom.

Cardiac rehabilitation has assumed more prominence over the past decade, due largely to an increase in user demand, an improvement in the evidence base and an enhancement of its status. This paper presents a view from the United Kingdom and suggests some ways in which cardiac rehabilitation can be improved by focusing on a number of key issues: service organisation and delivery, process and outcome measurement, performance management, and education, training and continuing professional development. The paper concludes that there is a need to make cardiac rehabilitation more widely available using creative and flexible approaches to enhance access, participation and adherence.

Benchmarking↗

PubMed2005

[Quality measurement between illusion and reality--is the quality of medical care measurable?].

The current implementation of external quality assurance focuses on identical, albeit simple univariate procedures. This approach proves to be inefficient, exhibiting low specificity. Definitions of performance indicators were classified by the local steering committee and applied to Bavarian obstetric data augmented with multivariate and confidence interval analyses as well as statistical simulations. A highly selected group of units with multivariate extreme values was audited. Blind application of federal regimes without further in-depth analysis of concomitant data is inefficient and may lead to wrong conclusions. Exclusive univariate analyses of performance indicators are not enough. Multivariate analyses have a higher specificity. Classification reveals an imbalance in the indicator set with respect to varying degrees of coverage as well as a bias towards outcome. Deficiencies in the organisational processes crucial for quality of care are often only revealed by dedicated cause and effect analyses within the hospital, thus constituting an essential prerequisite for desired changes in health care policies. It is unlikely that mere publication of performance indicators in the impending quality report will generate lucidity in spite of abundant structure. The installation of standardised programmes with identical computation rules may appear convincing as long as no doubt is cast upon the efficacy of the performance indicators in respect to their intended usage as well as upon the expected feedback effects. The experience so far however teaches us that these elements may be essential yet although not sufficient.

Benchmarking↗

PubMed2005

Improving sequence-based fold recognition by using 3D model quality assessment.

MOTIVATION: The ability of a simple method (MODCHECK) to determine the sequence-structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-like models. RESULTS: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile-profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information. CONTACT: d.jones@cs.ucl.ac.uk

Algorithms↗

PubMed2004

Class decomposition for GA-based classifier agents--a Pitt approach.

This paper proposes a class decomposition approach to improve the performance of GA-based classifier agents. This approach partitions a classification problem into several class modules in the output domain, and each module is responsible for solving a fraction of the original problem. These modules are trained in parallel and independently, and results obtained from them are integrated to form the final solution by resolving conflicts. Benchmark classification data sets are used to evaluate the proposed approaches. The experiment results show that class decomposition can help achieve higher classification rate with training time reduced.

Journal Article↗

PubMed2003

RAPTOR: optimal protein threading by linear programming.

This paper presents a novel linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph of the protein 3D structure template, the protein threading problem is formulated as a large scale integer programming (IP) problem. The IP formulation is then relaxed to a linear programming (LP) problem, and then solved by the canonical branch-and-bound method. The final solution is globally optimal with respect to energy functions. In particular, our energy function includes pairwise interaction preferences and allowing variable gaps which are two key factors in making the protein threading problem NP-hard. A surprising result is that, most of the time, the relaxed linear programs generate integral solutions directly. Our algorithm has been implemented as a software package RAPTOR-RApid Protein Threading by Operation Research technique. Large scale benchmark test for fold recognition shows that RAPTOR significantly outperforms other programs at the fold similarity level. The CAFASP3 evaluation, a blind and public test by the protein structure prediction community, ranks RAPTOR as top 1, among individual prediction servers, in terms of the recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR also performs very well in recognizing the hard Homology Modeling (HM) targets. RAPTOR was implemented at the University of Waterloo and it can be accessed at http://www.cs.uwaterloo.ca/~j3xu/RAPTOR_form.htm.

Algorithms↗

PubMedDate not supplied

Performance of the '100 top hospitals': what does the report card report?

We examine whether Medicare patients with acute myocardial infarction (AMI) admitted to one of HCIA-Mercer's "100 top hospitals" received better care or had better outcomes than patients treated in other hospitals. Among four hospital peer groups, the top 100 hospitals had similar thirty-day mortality and use of aspirin, beta-blockers, and reperfusion compared with their peers, but lower lengths-of-stay and in-hospital costs, with similar or lower readmission rates. Our findings suggest that the 100 Top Hospitals study may be better suited for identifying hospitals with higher performance on financial and operating measures than superior clinical performance in treating elderly AMI patients. However, there was no evidence that quality was sacrificed for increased financial efficiency among the top 100 hospitals.

Aged↗

PubMedDate not supplied

The dark side of P4P.

Examine the pitfalls of pay for performance and learn why some physicians and others are deeply concerned about the idea of incentive pay and fear it will have a negative impact on patient care.

American Medical Association↗

PubMed2003

New benchmarks from tokamak experiments for theoretical calculations of the dielectronic satellite spectra of heliumlike ions.

Dielectronic satellite spectra of heliumlike argon, recorded with a high-resolution x-ray crystal spectrometer at the National Spherical Torus Experiment, were found to be inconsistent with existing predictions resulting in unacceptable values for the power balance and suggesting the unlikely existence of non-Maxwellian electron energy distributions. These problems were resolved with calculations from a new atomic code. It is now possible to perform reliable electron-temperature measurements and to eliminate the uncertainties associated with determinations of non-Maxwellian distributions.

Journal Article↗

PubMed2003

Using medium-fill simulation to establish a benchmark microbiological contamination rate for low-risk-level compounding.

A benchmark contamination rate for prefilled syringe compounding was determined by using a medium-fill-simulation method. One thousand thirty-five 1-mL tuberculin syringes were aseptically filled with 0.9 mL of sterile soybean-casein digest medium and capped. These syringes were placed into clear nonsterile plastic bags and incubated at 35 degrees C for seven days, then inspected for cloudiness or colony formation indicative of bacterial growth. The operation was performed by two certified pharmacy technicians in an ISO Class 5 vertical-airflow biological safety cabinet in a typical inpatient pharmacy compounding area over two days. The technicians wore protective garments and gloves and followed standard procedures of preparing sterile injections. The adequacy of the methodology was verified by using four syringes that contained deliberately contaminated medium and incubating them along with 15 aseptically prepared syringes at 35 degrees C for seven days. Colony formation in the four syringes containing contaminated medium was directly observed and differentiated from the control syringes, which confirms the validity of the method. No bacterial growth was detected in any of the 1035 medium-filled syringes studied. Therefore, the contamination rate for aseptic compounding operation was less than 0.1%. Medium-fill-simulation testing of 1035 prefilled tuberculin syringes yielded no contamination. A contamination rate of less than 0.1% should be achievable and expected for this type of low-risk pharmacy preparation after pharmacies validate their own compounding operation.

Bacteria↗

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