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PubMed2005

The development and implementation of a regional network of physiotherapists for exercise therapy in patients with peripheral arterial disease, a preliminary report.

BACKGROUND: Exercise therapy (ET) is the main conservative and proven effective treatment of patients with intermittent claudication. Currently, the most frequent exercise prescription is a single 'go home and walk' advise, without supervision or follow-up. There is no evidence to support the efficacy of this advise and compliance is known to be low. Therefore, a systematic approach was used to guarantee quality and standardisation of treatment, optimal guideline adherence and improved of inter-professional communication between vascular surgeons and physiotherapists. In this preliminary report we would like to outline the steps taken for the development and implementation of the Network Exercise Therapy Parkstad. METHODS: In October 2003 all 59 regional physiotherapy practices were invited to attend a symposium regarding ET in a physiotherapeutic setting. Attending physiotherapists interested in providing ET and willing to follow a certified course on ET, were asked to register. Three tastk groups were formed to accomplish the set targets: Exercise therapy education, Exercise therapy implementation and continuity, and Inter-professional communication in the Parkstad region. RESULTS: In total 27 physiotherapists, from 22 different practices followed the educational program and are now trained and accredited to provide ET according to the guideline of the Royal Dutch Society for Physiotherapy. A web-based database was designed to contain information on disease specific items provided by the vascular surgery department, and aspects with respect to ET registered by the physiotherapist. The information is regularly updated and available online. Access to the database is restricted to vascular surgeons and physiotherapists in the network. The secondary purpose of the database is to register essential benchmark data for future analysis of ET in a physiotherapeutic setting in the Netherlands and to enable physiotherapists continuous feedback on patient performance. A triage system was developed to detect patients with a compromised cardiac history. This group receives ET at the in-hospital department of revalidation with the possibility of immediate consultation of a cardiologist in case of cardiac complications or even CPR. CONCLUSION: The Network Exercise Therapy Parkstad of supervised ET is the first initiative in the Netherlands to provide ET close to the patient's home environment. With the implementation of supervised ET in an outpatient physiotherapeutic setting for all eligible patients with symptomatic PAD, the access to care has been improved. A web-based communication system provides physiotherapists and vascular surgeons with all the necessary and continues updated patient information. Future research, currently in progress, will investigate the therapeutic benefits and cost-effectiveness of exercise therapy in a physiotherapeutic setting.

Ambulatory Care↗
PubMed2002

Benchmarks of support in internal medicine residency training programs.

PURPOSE: To identify benchmarks of financial and staff support in internal medicine residency training programs and their correlation with indicators of quality. METHOD: A survey instrument to determine characteristics of support of residency training programs was mailed to each member program of the Association of Program Directors of Internal Medicine. Results were correlated with the three-year running average of the pass rates on the American Board of Internal Medicine certifying examination using bivariate and multivariate analyses. RESULTS: Of 394 surveys, 287 (73%) were completed: 74% of respondents were program directors and 20% were both chair and program director. The mean duration as program director was 7.5 years (median = 5), but it was significantly lower for women than for men (4.9 versus 8.1; p =.001). Respondents spent 62% of their time in educational and administrative duties, 30% in clinical activities, 5% in research, and 2% in other activities. Most chief residents were PGY4s, with 72% receiving compensation additional to base salary. On average, there was one associate program director for every 33 residents, one chief resident for every 27 residents, and one staff person for every 21 residents. Most programs provided trainees with incremental educational stipends, meals while oncall, travel and meeting expenses, and parking. Support from pharmaceutical companies was used for meals, books, and meeting expenses. Almost all programs provided meals for applicants, with 15% providing travel allowances and 37% providing lodging. The programs' board pass rates significantly correlated with the numbers of faculty fulltime equivalents (FTEs), the numbers of resident FTEs per office staff FTEs, and the numbers of categorical and preliminary applications received and ranked by the programs in 1998 and 1999. Regression analyses demonstrated three independent predictors of the programs' board pass rates: number of faculty (a positive predictor), percentage of clinical work performed by the program director (a negative predictor), and financial support from pharmaceutical companies (also a negative predictor). CONCLUSIONS: These results identify benchmarks of financial and staff support provided to internal medicine residency programs. Some of these benchmarks are correlated with board pass rate, an accepted indicator of quality in residency training. Program directors and chairs can use this information to identify areas that may benefit from enhanced financial and administrative support.

Benchmarking↗
PubMed2004

Benchmark data and power calculations for evaluating disease outbreak detection methods.

INTRODUCTION: Early detection of disease outbreaks enables public health officials to implement immediate disease control and prevention measures. Computer-based syndromic surveillance systems are being implemented to complement reporting by physicians and other health-care professionals to improve the timeliness of disease-outbreak detection. Space-time disease-surveillance methods have been proposed as a supplement to purely temporal statistical methods for outbreak detection to detect localized outbreaks before they spread to larger regions. OBJECTIVE: The aims of this study were twofold: 1) to design and make available benchmark data sets for evaluating the statistical power of space-time early detection methods and 2) to evaluate the power of the prospective purely temporal and space-time scan statistics by applying them to the benchmark data sets at different parameter settings. METHODS: Simulated data sets based on the geography and population of New York City were created, including effects of outbreaks of varying size and location. Data sets with no outbreak effects were also created. Scan statistics were then run on these data sets, and the resulting power performances were analyzed and compared. RESULTS: The prospective space-time scan statistic performs well for a spectrum of outbreak models. By comparison, the prospective purely temporal scan statistic has higher power for detecting citywide outbreaks but lower power for detecting geographically localized outbreaks. CONCLUSIONS: The benchmark data sets created for this study can be used successfully for formal statistical power evaluations and comparisons. If an anomaly caused by an outbreak is local, purely temporal surveillance methods might be unable to detect it, in which case space-time methods would be necessary for early detection.

Benchmarking↗
PubMed1999

Lessons from Europe on quality improvement: report on the Velen Castle WHO meeting.

BACKGROUND: In conjunction with the German Ministry of Health, the European Regional Office of the World Health Organization (WHO/EURO) held a workshop, "Experiences with Quality Management in an International Context," at Velen Castle, Velen (Nordrhein-Westfalen), Germany, January 15-17, 1998. The approximately 50 participants were selected in part on the basis of recommendations of their respective countries' health ministries. IMPLEMENTATION AND EVALUATION OF QUALITY MANAGEMENT: Possible ways to introduce quality management ranged from introduction of specific process control projects to total quality management (TQM) and reengineering. STRATEGIES FOR IMPLEMENTING QUALITY MANAGEMENT: Working group sessions identified specific strategies for high-level managers, health care providers, and various kinds of consumers to facilitate quality management. For example, managers need to transmit a vision, create a quality management infrastructure, develop reporting structures, establish a system of incentives, and manage the hospital according to the principles of continuous improvement. QUALITY MANAGEMENT MODELS AND TOOLS: Hospitals and other health care providers in Sweden are testing various methods and systems to assess and improve their organizations' ability to meet patients' demands. Benchmarking is being used as a tool for quality management of diabetes care (DiabCare-France). The benchmarking data are processed centrally and made available to the health care providers in a user-friendly format for application to their own quality improvement processes. Clinical databases-registries containing process and outcome data for a well-defined patient population-can be used for quality and technology assessment, to answer questions of treatment effectiveness, and as an information tool. PRINCIPLES AND STRATEGIES FOR QUALITY MANAGEMENT AND DEVELOPMENT: Successful implementation of quality improvement benefits from local, professional, and national policies and objectives. A balance of incentives can reward efficiency or specific activities. Laws, rules, and regulations can be useful, especially if used sparingly. More education is needed at all levels of the health care system about how to understand and use information and information systems. Research is needed on what processes result in favorable outcomes. Despite optimism about the cost-saving potential of quality improvement efforts, many interventions are likely to be cost-effective without actually saving costs. Public release of performance data requires careful consideration, with participation of the professions.

Benchmarking↗
PubMed2005

Early experience with pay-for-performance: from concept to practice.

CONTEXT: The adoption of pay-for-performance mechanisms for quality improvement is growing rapidly. Although there is intense interest in and optimism about pay-for-performance programs, there is little published research on pay-for-performance in health care. OBJECTIVE: To evaluate the impact of a prototypical physician pay-for-performance program on quality of care. DESIGN, SETTING, AND PARTICIPANTS: We evaluated a natural experiment with pay-for-performance using administrative reports of physician group quality from a large health plan for an intervention group (California physician groups) and a contemporaneous comparison group (Pacific Northwest physician groups). Quality improvement reports were included from October 2001 through April 2004 issued to approximately 300 large physician organizations. MAIN OUTCOME MEASURES: Three process measures of clinical quality: cervical cancer screening, mammography, and hemoglobin A1c testing. RESULTS: Improvements in clinical quality scores were as follows: for cervical cancer screening, 5.3% for California vs 1.7% for Pacific Northwest; for mammography, 1.9% vs 0.2%; and for hemoglobin A1c, 2.1% vs 2.1%. Compared with physician groups in the Pacific Northwest, the California network demonstrated greater quality improvement after the pay-for-performance intervention only in cervical cancer screening (a 3.6% difference in improvement [P = .02]). In total, the plan awarded 3.4 million dollars (27% of the amount set aside) in bonus payments between July 2003 and April 2004, the first year of the program. For all 3 measures, physician groups with baseline performance at or above the performance threshold for receipt of a bonus improved the least but garnered the largest share of the bonus payments. CONCLUSION: Paying clinicians to reach a common, fixed performance target may produce little gain in quality for the money spent and will largely reward those with higher performance at baseline.

Benchmarking↗
PubMed2006

Early perioperative outcomes and pancreaticoduodenectomy in a general surgery residency training program.

Current trends in national health care are triggering a reassessment of training in general surgery. Currently, 75% of general surgery residents seek postgraduate fellowship training, and significant debate has occurred regarding the best manner for surgeons to acquire competency in performing complex operations. Pancreaticoduodenectomy (PD) is a complex procedure performed infrequently by most surgical graduates. From 1990 through 1997, the average number of PD operations performed per general surgery graduate ranged from 1.5 to 2.5. We examine the surgical outcomes following PD performed by surgical resident staff in a university-based general surgery training program. Between January 2001 and October 2004, 164 patients underwent PD for periampullary disease. Data were prospectively entered into a computerized database, including resident participation. We analyzed 30-day mortality and morbidity rates. Perioperative outcomes were 30-day mortality (2.2%), pancreatic fistula (6.1%), reoperation (2.2%), average length of hospital stay (13.5 days), mean operating time (489 minutes), and median estimated blood loss (1274 ml per case). PD can be performed with an acceptable morbidity and mortality within the teaching structure of a general surgery training program. These outcomes are likely related to the performance of PD at a high-volume, tertiary center by a single surgeon and compare favorably to best-practice benchmark outcomes.

Adenocarcinoma↗
PubMed2005

Misdiagnosis of appendicitis and the use of diagnostic imaging.

BACKGROUND: CT and ultrasound (US) are increasingly recommended to establish the diagnosis of appendicitis, but population-based rates of misdiagnosis (negative appendectomy [NA]) have not improved over time. The objective of this study was to determine the relationship between CT/US and NA in common practice. STUDY DESIGN: Using data from the Group Health Cooperative on all patients undergoing appendectomy between 1980 and 1999, a longitudinal study was conducted to determine the frequency of NA over time and a case-control, medical record-based study of a subset of patients from the 1990s was conducted to determine the accuracy of CT/US. RESULTS: Of 4,058 patients undergoing appendectomy (mean age 31 +/- 18.6 [SD] years, 49.6% women), 631 (15.5%) had an NA. The overall incidence of NA remained stable over time at 1.5/10,000 patient-years, as did the age and gender adjusted rate (incident rate ratio 0.95, 95% CI 0.97, 1.01). In 1999, nearly 40% of patients had either CT or US. The aggregate sensitivity of these tests was only 74.2% (95% CI 65.7, 83.7), with a positive predictive value of 95.1% (95% CI 91.5, 96.8). CT scans were 88.3% sensitive, with 97.2% positive predictive value (95% CI 92.9, 100). Ultrasounds were 69.5% sensitive, with a positive predictive value of 94.1% (95% CI 89.6, 96.4). More than one in five tests obtained in patients with NA were positive for appendicitis (21.7% for CT and 20.8% for US). CONCLUSIONS: The rate of NA was unchanged over time despite the introduction and use of CT/US, and this appeared to be related to the inconsistent performance characteristics of the tests. This study cautions against overreliance on CT/US in diagnosing appendicitis and emphasizes the need for test benchmarking in routine practice before establishing protocols for presumed appendicitis.

Appendectomy↗
PubMed2026

Investigating cross-organism prediction of prokaryotic essential proteins using unsupervised language model and ensemble strategy.

Cross-organism prediction of essential proteins is a critical task for drug discovery and microbial engineering, yet the generalizability of existing machine learning models across diverse species remains a significant challenge. In this study, we propose DeepPEP, a large language model-based framework designed to reliably transfer essential protein annotations between distantly related organisms. Utilizing 66 curated prokaryotic datasets, we systematically evaluated DeepPEP's cross-organism performance under various conditions. Initial pairwise predictions revealed a correlation between performance and evolutionary distance; however, further investigation demonstrated that integrating training data from multiple organisms yields superior predictive power. In a benchmark scenario designed to simulate real-world applications, DeepPEP outperformed the state-of-the-art tool Geptop 2.0, showcasing a robust ability to identify species-specific essential proteins. Finally, a case study on novel genomes confirmed the model's practical effectiveness. Our results suggest that DeepPEP is a powerful strategy for prokaryotic essential protein prediction, and the rigorous evaluation framework established in this study provides a new benchmark for the field.

Large Language Models↗
PubMed2000

Patient satisfaction after carotid endarterectomy using a selective policy of local anesthesia.

BACKGROUND: Patient satisfaction after carotid endarterectomy has not been specifically studied or reported. Results of carotid endarterectomy using either local or general anesthesia have been widely reported, and outcomes are not significantly different for either technique. Patient satisfaction data were obtained in order to determine whether patients preferred one method of anesthesia over another. Data regarding outcome may be added to the surgical literature as benchmark data when comparing operative carotid endarterectomy to newer techniques. METHODS: During a 30-month period, 186 consecutive carotid endarterectomies were performed on 169 patients by a single surgeon with assistance from senior surgical residents. All patients were offered local anesthesia using a cervical block technique with intraoperative supplementation. Patients for whom local anesthesia was inappropriate or who declined were operated on using general endotracheal anesthesia. Results of operation were tabulated including indication for operation, method of anesthesia, intraoperative and postoperative complications, and mortality, and completion of a patient satisfaction survey form either on postoperative visit or by telephone questionnaire. RESULTS: Of 169 patients who underwent carotid endarterectomy, 151 (89%) completed the satisfaction survey form. One hundred fourteen (62%) had local anesthesia and 71 patients (38%) had general anesthesia. There was 1 stroke (0.5%) and 1 death (0.5%) in the series. Perioperative complications including temporary cranial nerve injury, neck hematoma, myocardial infarction, and restenosis were noted and not significantly different in either the general anesthesia or local anesthesia group. Patient satisfaction data including intraoperative discomfort, postoperative pain, attentiveness of the operating room staff, and length of stay were all tabulated. There was no statistically significant difference in satisfaction between the general anesthesia group and the local anesthesia group (chi-square and Fisher's exact test). Additionally, satisfaction with the procedure was extremely high. CONCLUSIONS: Patient outcome and perception of pain and recovery were not statistically significantly different in patients undergoing carotid endarterectomy using local anesthesia compared with general anesthesia. Overall patient satisfaction was extremely high. Patients should be offered carotid endarterectomy using an anesthesia technique with which the surgeon and patients are both comfortable, having confidence that the outcome is not related to anesthesia technique and that patients will be highly satisfied.

Aged↗
PubMed2006

A practical Monte Carlo MU verification tool for IMRT quality assurance.

Quality assurance (QA) for intensity-modulated radiation therapy (IMRT) treatment planning and beam delivery, using ionization chamber measurements and film dosimetry in a phantom, is time consuming. The Monte Carlo method is the most accurate method for radiotherapy dose calculation. However, a major drawback of Monte Carlo dose calculation as currently implemented is its slow speed. The goal of this work is to bring the efficiency of Monte Carlo into a practical range by developing a fast Monte Carlo monitor unit (MU) verification tool for IMRT. A special estimator for dose at a point called the point detector has been used in this research. The point detector uses the next event estimation (NEE) method to calculate the photon energy fluence at a point of interest and then converts it to collision kerma by the mass energy absorption coefficient assuming the presence of transient charged particle equilibrium. The MU verification tool has been validated by comparing the calculation results with measurements. It can be used for both patient dose verification and phantom QA calculation. The dynamic leaf-sequence log file is used to rebuild the actual MLC leaf sequence in order to predict the dose actually received by the patient. Dose calculations for 20 patient plans have been performed using the point detector method. Results were compared with direct Monte Carlo simulations using EGS4/MCSIM, which is a well-benchmarked Monte Carlo code. The results between the point detector and MCSIM agreed to within 2%. A factor of 20 speedup can be achieved with the point detector method compared with direct Monte Carlo simulations.

Body Burden↗
PubMed2006

Classification of movement intention by spatially filtered electromagnetic inverse solutions.

We couple standardized low-resolution electromagnetic tomography, an inverse solution for electroencephalography (EEG) and the common spatial pattern, which is here conceived as a data-driven beamformer, to classify the benchmark BCI (brain-computer interface) competition 2003, data set IV. The data set is from an experiment where a subject performed a self-paced left and right finger tapping task. Available for analysis are 314 training trials whereas 100 unlabelled test trials have to be classified. The EEG data from 28 electrodes comprise the recording of the 500 ms before the actual finger movements, hence represent uniquely the left and right finger movement intention. Despite our use of an untrained classifier, and our extraction of only one attribute per class, our method yields accuracy similar to the winners of the competition for this data set. The distinct advantages of the approach presented here are the use of an untrained classifier and the processing speed, which make the method suitable for actual BCI applications. The proposed method is favourable over existing classification methods based on an EEG inverse solution, which rely either on iterative algorithms for single-trial independent component analysis or on trained classifiers.

Algorithms↗
PubMed2025

LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.

MOTIVATION: Differential expression analysis plays a vital role in omics research enabling precise identification of features that associate with different phenotypes. This process is critical for uncovering biological differences between conditions, such as disease versus healthy states. In proteomics, several statistical methods have been used, ranging from simple t-tests to more advanced methods like DEqMS, limma and ROTS. However, a flexible method for reproducibility-optimized statistics tailored for clinical omics data has been lacking. RESULTS: In this study, we developed LimROTS, a hybrid method that integrates a linear regression model and the empirical Bayes approach with reproducibility optimized statistics, to create a novel moderated ranking statistic, for robust and flexible analysis of proteomics data. We validated its performance using twenty-one proteomics gold standard spike-in datasets with different protein mixtures, MS instruments, and techniques for benchmarking. This hybrid approach improves accuracy and reproducibility of complex proteomics data, making LimROTS a powerful tool for high-dimensional omics data analysis. AVAILABILITY AND IMPLEMENTATION: LimROTS has been implemented as an R/Bioconductor package, available at https://doi.org/doi:10.18129/B9.bioc.LimROTS. Additionally, the code used in this study is available in GitHub repository https://github.com/AliYoussef96/LimROTSmanuscript.

Bayes Theorem↗
PubMed2003

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.

MOTIVATION: The biological literature is a major repository of knowledge. Many biological databases draw much of their content from a careful curation of this literature. However, as the volume of literature increases, the burden of curation increases. Text mining may provide useful tools to assist in the curation process. To date, the lack of standards has made it impossible to determine whether text mining techniques are sufficiently mature to be useful. RESULTS: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup. We provided a training corpus of 862 articles consisting of journal articles curated in FlyBase, along with the associated lists of genes and gene products, as well as the relevant data fields from FlyBase. For the test, we provided a corpus of 213 new ('blind') articles; the 18 participating groups provided systems that flagged articles for curation, based on whether the article contained experimental evidence for gene expression products. We report on the evaluation results and describe the techniques used by the top performing groups.

Abstracting and Indexing↗
PubMed2005

Detection performance theory for ultrasound imaging systems.

A rigorous statistical theory for characterizing the performance of medical ultrasound systems for lesion detection tasks is developed. A design strategy for optimizing ultrasound systems should be to adjust parameters for maximum information content, which is obtained by maximizing the ideal observer performance. Then, given the radio-frequency data, image and signal processing algorithms are designed to extract as much diagnostically relevant information as possible. In this paper, closed-form and low-contrast approximations of ideal observer performance are derived for signal known statistically detection tasks. The accuracy of the approximations are tested by comparing with Monte Carlo techniques. A metric borrowed and modified from photon imaging, Generalized Noise Equivalent Quanta, is shown to be a useful and measurable target-independent figure of merit when adapted for ultrasound systems. This theory provides the potential to optimize design tradeoffs for detection tasks. For example it may help us understand how to push the limits of specific features, such as spatial resolution, without significantly compromising overall detection performance.

Algorithms↗
PubMed2005

The cost-effectiveness of the English smoking treatment services: evidence from practice.

AIMS: To investigate the cost-effectiveness of English specialist smoking cessation services. DESIGN: Combination of observational cost and outcome data from English smoking cessation services to calculate cost-effectiveness ratios. Multivariate analysis of factors influencing variation in services' cost-effectiveness. SETTING: Fifty-eight of the 92 specialist smoking cessation services in England in 2000/01. METHODS: Services' costs were estimated using survey data which described services' configurations, staffing, interventions delivered and development. Information on services' throughput and outcomes (as biochemically validated 4-week smoking cessation rates) were obtained from routine sources. With reference to relevant literature and assumptions about relapse and background cessation rates, 4-week cessation rates were converted first to 1-year rates. One-year cessation rates were adjusted to reflect the likely permanent smoking cessation rate attributable to service intervention and finally attributable life-years gained were calculated. A wide variety of sensitivity analyses was performed to test the robustness of the average cost-effectiveness ratio, calculated by combining the cost and life-year gained estimates, for all services. With additional data on deprivation levels in services' areas, ordinary least-squares regression techniques were used to investigate variations in individual services' costs per client and cost-effectiveness ratios. FINDINGS: Using an up-to-date estimate for health gain accrued by stopping smoking, the average cost per life gained was pound 684 (95% CI 557811), falling to pound 438 when savings in future health-care costs were counted. With the worst case assumptions, the estimate of cost-effectiveness rose to pound 2693 per life-year saved (pound 2293 including future health-care costs) and fell to pound 227 (pound 102) under the most favourable assumptions. Findings are comparable to previous published studies. The regression results suggest that different factors influence cost per client and the net cost per life-year saved, indicating that decision makers should be careful in setting performance targets for these services. CONCLUSIONS: In 2000/01, English smoking cessation services provided cost-effective services operating well below the benchmark of pound 20,000 per quality-adjusted life-year saved (QALY) that is used by the National Institute for Clinical Excellence in the United Kingdom.

Cost-Benefit Analysis↗
PubMed1997

A sequential learning scheme for function approximation using minimal radial basis function neural networks.

This article presents a sequential learning algorithm for function approximation and time-series prediction using a minimal radial basis function neural network (RBFNN). The algorithm combines the growth criterion of the resource-allocating network (RAN) of Platt (1991) with a pruning strategy based on the relative contribution of each hidden unit to the overall network output. The resulting network leads toward a minimal topology for the RBFNN. The performance of the algorithm is compared with RAN and the enhanced RAN algorithm of Kadirkamanathan and Niranjan (1993) for the following benchmark problems: (1) hearta from the benchmark problems database PROBEN1, (2) Hermite polynomial, and (3) Mackey-Glass chaotic time series. For these problems, the proposed algorithm is shown to realize RBFNNs with far fewer hidden neurons with better or same accuracy.

Algorithms↗