PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Performance benchmarking”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81Linked to original sources
PubMed2025

CountASAP: a lightweight, easy to use python package for processing ASAPseq data.

BACKGROUND: Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. RESULTS: To address this lack of a dedicated tool for ASAPseq data processing, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences. We directly compare the performance and user-friendliness of CountASAP to existing tools using similarly-structured data from a more common sequencing experiment: cellular indexing of transcriptomes and epitopes by sequencing (CITEseq). Further benchmarking against existing tools helps to identify proper defaults for CountASAP and assess the agreement of outputs from all tested software. A final test using a novel ASAPseq dataset provides evidence that CountASAP can generate biologically meaningful results that correlate well with paired chromatin accessibility data. CONCLUSIONS: CountASAP shows good agreement with existing, well-tested data processing tools in the analysis of similarly-structured benchmarking data. CountASAP runs efficiently on a standard laptop, has user-friendly documentation, a one-step installation, and represents the first and only tool designed specifically for the processing of ASAPseq data.

Software↗
PubMed1999

Low-cost ISDN videoconferencing equipment for orthopaedic second opinions.

We validated the application of low-cost ISDN videoconferencing equipment for telemedicine. A telemedicine benchmark was designed and four different office videoconferencing systems were evaluated, all using basic-rate ISDN connections (128 kbit/s). All the low-cost systems showed generally good or acceptable performance for clinical use. We also investigated the feasibility of videoconferencing for an orthopaedic second-opinion service. Eight point-to-point conferences were conducted to discuss real clinical cases by use of interactive sharing of medical images. The average duration of each session was 35 min. Encouraging results were obtained.

Costs and Cost Analysis↗
PubMed2004

Data feedback efforts in quality improvement: lessons learned from US hospitals.

BACKGROUND: Data feedback is a fundamental component of quality improvement efforts, but previous studies provide mixed results on its effectiveness. This study illustrates the diversity of hospital based efforts at data feedback and highlights successful strategies and common pitfalls in designing and implementing data feedback to support performance improvement. METHODS: Open ended interviews with 45 clinical and administrative staff in eight US hospitals in 2000 concerning their perceptions about the effectiveness of data feedback in supporting performance improvement efforts were analysed. The hospitals were chosen to represent a range of sizes, geographical regions, and beta blocker improvement rates over a 3 year period. Data were organized and analyzed in NUD-IST 4 using the constant comparative method of qualitative data analysis. RESULTS: Although the data feedback efforts at the hospitals were diverse, the interviews suggested that seven key themes may be important: (1) data must be perceived by physicians as valid to motivate change; (2) it takes time to develop the credibility of data within a hospital; (3) the source and timeliness of data are critical to perceived validity; (4) benchmarking improves the meaningfulness of data feedback; (5) physician leaders can enhance the effectiveness of data feedback; (6) data feedback that profiles an individual physician's practices can be effective but may be perceived as punitive; (7) data feedback must persist to sustain improved performance. Embedded in several themes was the view that the effectiveness of data feedback depends not only on the quality and timeliness of the data, but also on the organizational context in which such efforts are implemented. CONCLUSIONS: Data feedback is a complex and textured concept. Data feedback strategies that might be most effective are suggested, as well as potential pitfalls in using data to promote performance improvement.

Adrenergic beta-Antagonists↗
PubMedDate not supplied

Efficient information theoretic strategies for classifier combination, feature extraction and performance evaluation in improving false positives and false negatives for spam e-mail filtering.

Spam emails are considered as a serious privacy-related violation, besides being a costly, unsolicited communication. Various spam filtering techniques have been so far proposed, mainly based on Naïve Bayesian algorithms. Other Machine Learning algorithms like Boosting trees, or Support Vector Machines (SVM) have already been used with success. However, the number of False Positives (FP) and False Negatives (FN) resulting through applying various spam e-mail filters still remains too high and the problem of spam e-mail categorization cannot be solved completely from a practical viewpoint. In this paper, we propose a novel approach for spam e-mail filtering based on efficient information theoretic techniques for integrating classifiers, for extracting improved features and for properly evaluating categorization accuracy in terms of FP and FN. The goal of the presented methodology is to empirically but explicitly minimize these FP and FN numbers by combining high-performance FP filters with high-performance FN filters emerging from a previous work of the authors [Zorkadis, V., Panayotou, M., & Karras, D. A. (2005). Improved spam e-mail filtering based on committee machines and information theoretic feature extraction. Proceedings of the International Joint Conference on Neural Networks, July 31-August 4, 2005, Montreal, Canada]. To this end, Random Committee-based filters along with ADTree-based ones are efficiently combined through information theory, respectively. The experiments conducted are of the most extensive ones so far in the literature, exploiting widely accepted benchmarking e-mail data sets and comparing the proposed methodology with the Naive Bayes spam filter as well as with the Boosting tree methodology, the classification via regression and other machine learning models. It is illustrated by means of novel information theoretic measures of FP & FN filtering performance that the proposed approach is very favorably compared to the other rival methods. Finally, it is found that the proposed information theoretic Boolean features present a remarkably high spam categorization performance.

Algorithms↗
PubMedDate not supplied

Left ventricular ejection fraction test rates for Medicare beneficiaries with heart failure.

The left ventricular ejection fraction (LVEF) test rate is increasingly used as a quality of care indicator for patients with heart failure. Our study produced benchmark LVEF test rates in a Medicare fee-for-service population for consideration by a clinical panel assembled by the Health Care Financing Administration. Our sample consisted of 46,583 beneficiaries admitted to the hospital for heart failure and with a complete set of Medicare fee-for-service bills dated 1996 or 1997. The national 2-year LVEF test rate was 79% for Medicare fee-for-service beneficiaries hospitalized for heart failure. Except for 1 state, the test rate ranged from 61% to 89% across states. Our analysis demonstrates the feasibility of using billing data to compute LVEF test rates. Using a 2-year time window and measuring tests performed in outpatient as well as inpatient settings, we find a higher LVEF test rate than has been reported by most previous studies.

Aged↗
PubMed2026

Prostate morcellation devices: a systematic review and meta-analysis of clinical outcomes and efficiency.

OBJECTIVE: To systematically evaluate the efficiency and safety of different prostate morcellators used during prostate enucleation for benign prostatic hyperplasia (BPH). METHODS: A systematic review was performed according to the Preferred Reporting Items for Systematic Review and Meta-analyses guidelines. PubMed/Medline, Scopus, and Web of Science were searched for studies published between October 2012 and May 2025. Studies reporting clinical outcomes of morcellators used during prostate enucleation were included. Primary outcome was morcellation efficiency (g/min). Secondary outcomes included intraoperative complications, device malfunction, and cost when available. Risk of bias (RoB) was assessed using the Risk Of Bias In Non-randomised Studies of Interventions (ROBINS-I), RoB 2 tool, and European Association of Urology case-series criteria. Random-effects meta-analyses and multilevel meta-regression adjusted for prostate volume were conducted. RESULTS: A total of 22 studies comprising 5980 patients were included, most undergoing holmium laser enucleation of the prostate. The most frequently evaluated devices were the Piranha™ (Richard Wolf GmbH, Knittlingen, Germany) and Lumenis VersaCut™ (Lumenis Ltd., Yokneam, Israel; 12 and 13 studies, respectively), followed by DrillCut™ (Karl Storz SE & Co. KG, Tuttlingen, Germany), MultiCut™ (Asclepion Laser Technologies GmbH, Jena, Germany), and Cyber Blade™ (Quanta System SpA, Milan, Italy) systems. Unadjusted weighted mean morcellation efficiency was 7.80 g/min (95% confidence interval [CI] 6.26-9.34 g/min) for Piranha, 4.70 g/min (95% CI 3.61-5.79 g/min) for VersaCut, 5.90 g/min (95% CI 3.16-8.64 g/min) for DrillCut, and 9.59 g/min (95% CI 4.78-14.39 g/min) for MultiCut. In volume-adjusted meta-regression using Piranha as reference, VersaCut remained significantly less efficient (-2.75 g/min; 95% CI -4.58 to -0.92 g/min; P = 0.003), with an even greater difference in prostates >70 mL (-4.34 g/min). Bladder mucosal injury was the most frequently reported complication; however, relatively rare across all devices. Meta-analysis demonstrated a significantly higher risk with VersaCut compared to Piranha (risk ratio 3.22, 95% CI 1.81-5.71), with low heterogeneity. CONCLUSION: This systematic review provides a contemporary clinical benchmark of the efficiency and safety of currently available prostate morcellators. Oscillating blade systems, particularly the Piranha morcellator, demonstrated higher morcellation efficiency and a more favourable safety profile than reciprocating blade devices, with the largest performance differences observed in patients with larger prostates.

Humans↗
PubMed2002

Finding motifs in the twilight zone.

MOTIVATION: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs. RESULTS: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits. AVAILABILITY: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Algorithms↗
PubMed2003

Physician performance assessment: nonequivalence of primary care measures.

BACKGROUND: Assessment of the performance of primary care physicians requires multiple, reliable measures. This article explores the appropriateness of selected Health Plan Employer Data and Information Set (HEDIS) measures, developed to assess health plans, to assess individual physician performance. OBJECTIVES: To determine the consistency and reliability of 4 measures of primary care physician performance measures: cancer screening, diabetic management, patient satisfaction, and ambulatory costs. METHODS: The study population consisted of all 194 family practitioners and general internists providing ambulatory services in 1998 to a defined patient panel of 320,000 adult health maintenance organization members. Administrative data on physician practice and performance were assessed with multiple regression and analysis of variance. RESULTS: Each performance measure was significantly related to 1 or 2 of the other measures: high cancer screening rates with good diabetic management and high patient satisfaction, good diabetic management with high cancer screening rates, high patient satisfaction with high cancer screening rates and high ambulatory costs, or high ambulatory costs with higher patient satisfaction. Although 76% of the physicians ranked in the highest third for at least 1 measure, 81% of these high performers ranked in the lower third for at least 1 other measure. Three percent of physicians ranked exclusively in the top or bottom third on all measures. CONCLUSIONS: Care should be taken in assessing physicians based on narrow performance measures. Assessments of individual physicians with current performance measures might identify areas in which improvement is needed and to provide feedback to improve performance quality and efficiency. However, assumptions should not be made from one measure of performance to another.

Adult↗
PubMed2004

A new tool for measurement of process-based performance of multispecialty tertiary care hospitals.

There is an increasing need of a model for the process-based performance measurement of multispecialty tertiary care hospitals for quality improvement. Analytic hierarchy process (AHP) is utilized in this study to evolve such a model. Each step in the model was derived by group-discussions and brainstorming sessions among experienced clinicians and managers. This tool was applied to two tertiary care teaching hospitals in Barbados and India. The model enabled identification of specific areas where neither hospital performed very well, and helped to suggest recommendations to improve those areas. AHP is recommended as a valuable tool to measure the process-based performance of multispecialty tertiary care hospitals.

Barbados↗
PubMedDate not supplied

Benchmark matrix and guide: Part III.

The final article in the "Benchmark Matrix and Guide" series developed by Headquarters Air Force Logistics Command completes the discussion of the last three categories that are essential ingredients of a successful total quality management (TQM) program. Detailed behavioral objectives are listed in the areas of recognition, process improvement, and customer focus. These vertical categories are meant to be applied to the levels of the matrix that define the progressive stages of the TQM: business as usual, initiation, implementation, expansion, and integration. By charting the horizontal progress level and the vertical TQM category, the quality management professional can evaluate the current state of TQM in any given organization. As each category is completed, new goals can be defined in order to advance to a higher level. The benchmarking process is integral to quality improvement efforts because it focuses on the highest possible standards to evaluate quality programs.

Employee Performance Appraisal↗
PubMed2002

Wastewater treatment benchmark: what can be achieved with simple control?

In this paper a simple control strategy is applied to and assessed on the wastewater treatment benchmark. The controllers used in the presented control strategy are PI controllers, feedforward control and a step-feed procedure. The controlled variables are not directly the effluent concentrations but other process variables which have an effect on the effluent. The setting of set-points is also analyzed to select the values with the best performance. Set-point analysis has shown that with an optimal setting of set-points under stormy influent conditions, the achieved plant performance is also retained for rainy and dry influent conditions. The evaluation of plant performance indicates that with the proposed control strategy, a lower number of effluent violations has been achieved, as well as lower energy consumption and lower sludge production, when compared to results published up to now. Only the effluent quality criterion deteriorated.

Algorithms↗
PubMed2002

Public reporting of hospital patient satisfaction: the Rhode Island experience.

This article describes a collaborative process for legislatively mandated public reporting of health care performance in Rhode Island that began with hospital patient satisfaction. The goals of the report were both quality improvement and public accountability. Key features addressed include: the legislative context for public reporting; widespread participation of stakeholders; the structure for decision making; and the use of formative testing with cognitive interviews to get responses of consumers and others about the report readability and comprehensibility. This experience and the lessons learned can guide other States considering public reporting on health care performance.

Adolescent↗
PubMed2005

Pay for performance and the hospital quality initiative.

This paper describes the history of the Hospital Quality Initiative (HQI) and describes plans that the Centers for Medicare and Medicaid Services (CMS) have for this data set. There are suggestions on how to improve physician acceptance of these benchmarks and how an institution can improve compliance rates with the data elements. There is also a discussion with respect to weaknesses and strengths of HQI. The advantages occuring to both the patient and physician when the physician participates in the HQI initiative are emphasized.

Benchmarking↗
PubMedDate not supplied

Performance standards improve American Board of Surgery In-Training Examination scores.

PURPOSE: Although several studies have evaluated factors affecting American Board of Surgery In-Training Examination (ABSITE) performance, none has examined the impact of setting a minimally acceptable standard. It was hypothesized that establishing such a criterion would improve ABSITE scores. METHODS: An expectation for residents to score at the 35th percentile or higher was established in 1996. The proportion of test scores above or below the 35th and 50th percentiles for the time periods before and after institution of the standard were compared using Fisher's exact test. The subsequent performance of residents scoring below the 35th percentile was analyzed for the 2 time periods. RESULTS: After the institution of the standard, the proportion of scores below the 35th percentile decreased from 46.7% to 21.9% (p = 0.0005). Similarly, the proportion of scores at or above the national average increased from 42.1% to 65.6% (p = 0.0005). After establishing the standard, fewer residents continued to have scores below the criterion in subsequent years. CONCLUSIONS: Establishing a performance criterion improved ABSITE scores. The decision to institute a standard must be individualized for each program. The rationale for the standard and a plan to assist residents failing to achieve the benchmark must be communicated.

Journal Article↗
PubMed2005

Scalar relativistic all-electron density functional calculations on periodic systems.

Scalar relativistic effects are included in periodic boundary conditions calculations with Gaussian orbitals. This approach is based on the third-order Douglas-Kroll-Hess approximation, allowing the treatment of all electrons on an equal footing. With this methodology, we are able to perform relativistic all-electron density functional calculations using the traditional local spin-density and generalized gradient approximations (GGA), as well as meta-GGA and hybrid density functionals. We present benchmark results for the bulk metals Pd, Ag, Pt, and Au, and the large band gap semiconductors AgF and AgCl.

Journal Article↗
PubMed2026

Ori-Finder-Arch: An Updated Web Server for the Annotation and Visualization of Archaeal Replication Origins.

Archaea are promising chassis organisms in biotechnology, and the accurate annotation of their chromosomal replication origins (oriCs) is the key to unlocking their full potential. However, the existing Ori-Finder 2 web server suffers from low accuracy, slow speed, and limited scalability. In this study, we present Ori-Finder-Arch, an updated web server for high-performance oriC prediction in archaea. This pipeline integrates HMMER-based replication initiation protein (RIP) annotation, refined consensus motif recognition, and GC profile-based DNA unwinding element (DUE) detection. On a benchmark set of experimentally validated oriCs, Ori-Finder-Arch achieved a recall of 95.6% and a precision of 86.0%, substantially outperforming Ori-Finder 2 (62.2% and 63.6%, respectively), while running 4.75 times faster and supporting diverse assembly levels. When applied to the available archaeal assemblies, it successfully annotated 17,472 oriCs. Meanwhile, the web server provides interactive visualizations at different levels. In conclusion, Ori-Finder-Arch offers an efficient, accurate, and user-friendly platform for advanced studies of archaeal DNA replication initiation and synthetic biology applications, and is freely available at https://tubic.org/Ori-Finder-Arch/ and https://tubic.tju.edu.cn/Ori-Finder-Arch/.

Archaea↗
PubMed2005

Sparse multinomial logistic regression: fast algorithms and generalization bounds.

Recently developed methods for learning sparse classifiers are among the state-of-the-art in supervised learning. These methods learn classifiers that incorporate weighted sums of basis functions with sparsity-promoting priors encouraging the weight estimates to be either significantly large or exactly zero. From a learning-theoretic perspective, these methods control the capacity of the learned classifier by minimizing the number of basis functions used, resulting in better generalization. This paper presents three contributions related to learning sparse classifiers. First, we introduce a true multiclass formulation based on multinomial logistic regression. Second, by combining a bound optimization approach with a component-wise update procedure, we derive fast exact algorithms for learning sparse multiclass classifiers that scale favorably in both the number of training samples and the feature dimensionality, making them applicable even to large data sets in high-dimensional feature spaces. To the best of our knowledge, these are the first algorithms to perform exact multinomial logistic regression with a sparsity-promoting prior. Third, we show how nontrivial generalization bounds can be derived for our classifier in the binary case. Experimental results on standard benchmark data sets attest to the accuracy, sparsity, and efficiency of the proposed methods.

Algorithms↗