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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↗

Benchmarking methods for measuring biosynthetic gene cluster similarity and determination of gene cluster families.

MOTIVATION: Natural products are often produced by a set of biosynthetic enzymes that are encoded by genes clustered together in the producer's genome, referred to as a biosynthetic gene cluster (BGC). The ability to compare and cluster BGCs is essential for several applications, including predicting which bacteria will make a known product and assessing the potential diversity of natural products produced by a set of bacteria. There are multiple methods for comparing and clustering BGCs based on their similarity, but there has been a lack of investigation into how strongly BGC similarity relates to product structural similarity and how these methods perform relative to each other. RESULTS: Using publicly available databases, we developed a benchmark dataset to assess how well different BGC similarity metrics correlate with the structural similarity of their products and how well these methods cluster BGCs. We found that all methods showed moderate correlation between BGC and structural similarity, with correlations improving for more similar BGCs and varying significantly by BGC biosynthetic class. Analysis of outliers revealed some outliers were due to mistakes or omissions in public datasets, while others represented deviation between BGC similarity and product structural similarity. All methods generally performed better on clustering metrics, with BiG-SCAPE performing the best after errors in the public datasets had been corrected. AVAILABILITY AND IMPLEMENTATION: Scripts and data required to reproduce the results are available at https://github.com/aswalker-lab/BGC-clustering-benchmark and processed similarity, clusters, and scaffolds are also available at https://huggingface.co/datasets/allie-walker/BGC-clustering-benchmark. Code is also available at Zenodo: 10.5281/zenodo.17373546.

Multigene Family↗

A benchmark for Affymetrix GeneChip expression measures.

MOTIVATION: The defining feature of oligonucleotide expression arrays is the use of several probes to assay each targeted transcript. This is a bonanza for the statistical geneticist, who can create probeset summaries with specific characteristics. There are now several methods available for summarizing probe level data from the popular Affymetrix GeneChips, but it is difficult to identify the best method for a given inquiry. RESULTS: We have developed a graphical tool to evaluate summaries of Affymetrix probe level data. Plots and summary statistics offer a picture of how an expression measure performs in several important areas. This picture facilitates the comparison of competing expression measures and the selection of methods suitable for a specific investigation. The key is a benchmark data set consisting of a dilution study and a spike-in study. Because the truth is known for these data, we can identify statistical features of the data for which the expected outcome is known in advance. Those features highlighted in our suite of graphs are justified by questions of biological interest and motivated by the presence of appropriate data.

Algorithms↗

SABmark--a benchmark for sequence alignment that covers the entire known fold space.

The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem.

Algorithms↗

Benchmark studies of induced radioactivity produced in LHC materials, Part II: Remanent dose rates.

A new method to estimate remanent dose rates, to be used with the Monte Carlo code FLUKA, was benchmarked against measurements from an experiment that was performed at the CERN-EU high-energy reference field facility. An extensive collection of samples of different materials were placed downstream of, and laterally to, a copper target, intercepting a positively charged mixed hadron beam with a momentum of 120 GeV c(-1). Emphasis was put on the reduction of uncertainties by taking measures such as careful monitoring of the irradiation parameters, using different instruments to measure dose rates, adopting detailed elemental analyses of the irradiated materials and making detailed simulations of the irradiation experiment. The measured and calculated dose rates are in good agreement.

Benchmarking↗

Benchmarking of MCNP for calculating dose rates at an interim storage facility for nuclear waste.

During the operation of research facilities at Research Centre Jülich, Germany, nuclear waste is stored in drums and other vessels in an interim storage building on-site, which has a concrete shielding at the side walls. Owing to the lack of a well-defined source, measured gamma spectra were unfolded to determine the photon flux on the surface of the containers. The dose rate simulation, including the effects of skyshine, using the Monte Carlo transport code MCNP is compared with the measured dosimetric data at some locations in the vicinity of the interim storage building. The MCNP data for direct radiation confirm the data calculated using a point-kernel method. However, a comparison of the modelled dose rates for direct radiation and skyshine with the measured data demonstrate the need for a more precise definition of the source. Both the measured and the modelled dose rates verified the fact that the legal limits (<1 mSv a(-1)) are met in the area outside the perimeter fence of the storage building to which members of the public have access. Using container surface data (gamma spectra) to define the source may be a useful tool for practical calculations and additionally for benchmarking of computer codes if the discussed critical aspects with respect to the source can be addressed adequately.

Benchmarking↗

The skyshine benchmark experiment revisited.

With the coming renaissance of nuclear power, heralded by new nuclear power plant construction in Finland, the issue of qualifying modern tools for calculation becomes prominent. Among the calculations required may be the determination of radiation levels outside the plant owing to skyshine. For example, knowledge of the degree of accuracy in the calculation of gamma skyshine through the turbine hall roof of a BWR plant is important. Modern survey programs which can calculate skyshine dose rates tend to be qualified only by verification with the results of Monte Carlo calculations. However, in the past, exacting experimental work has been performed in the field for gamma skyshine, notably the benchmark work in 1981 by Shultis and co-workers, which considered not just the open source case but also the effects of placing a concrete roof above the source enclosure. The latter case is a better reflection of reality as safety considerations nearly always require the source to be shielded in some way, usually by substantial walls but by a thinner roof. One of the tools developed since that time, which can both calculate skyshine radiation and accurately model the geometrical set-up of an experiment, is the code RANKERN, which is used by Framatome ANP and other organisations for general shielding design work. The following description concerns the use of this code to re-address the experimental results from 1981. This then provides a realistic gauge to validate, but also to set limits on, the program for future gamma skyshine applications within the applicable licensing procedures for all users of the code.

Air↗

Bacterial lipopolysaccharide exposure alters aflatoxin B(1) hepatotoxicity: benchmark dose analysis for markers of liver injury.

Aflatoxin B(1) (AFB(1)) is a fungal toxin that causes both acute hepatotoxicity and hepatocellular carcinoma in humans and experimental animals. Previous studies demonstrated that a small, noninjurious dose of bacterial lipopolysaccharide (LPS) augments the hepatotoxicity of AFB(1) through activation of inflammatory cells and production of soluble inflammatory mediators (Barton et al., 2000b, 2001). This study was conducted to examine the effect of LPS on the dose-response relationship for AFB(1)-induced liver injury. Male Sprague-Dawley rats (250-350g) were treated with AFB(1) (0.1 mg/kg-6.3 mg/kg, ip) and 4 h later with a noninjurious dose of E. coli LPS (7.4 x 10(6) EU/kg, iv). Twenty-four h after AFB(1) administration, hepatic parenchymal cell injury was estimated from elevations in serum alanine aminotransferase and aspartate aminotransferase activities. Injury to intrahepatic bile ducts was evaluated from increased serum gamma-glutamyl transferase and alkaline phosphatase activities. Based on benchmark dose (BMD) analysis, the AFB(1) BMD for parenchymal cell injury was decreased 10-fold by LPS cotreatment, whereas AFB(1) BMDs for bile duct injury were decreased nearly 20-fold. The data suggest that concurrent inflammation renders the liver considerably more sensitive to the hepatotoxic effects of AFB(1).

Aflatoxin B1↗

Identification of a critical dose level for risk assessment: developments in benchmark dose analysis of continuous endpoints.

The benchmark dose (BMD) method has been recommended to replace the no-observed-adverse-effect-level (NOAEL) approach in health risk assessment of chemical substances. In the present article, developments in BMD analysis from continuous experimental data are proposed. The suggested approach defines the BMD as the dose at which the slope of the S-shaped dose-response relationship changes the most in the low-dose region. This dose resides in a region where the sensitivity to chemical exposure may start to change noticeably. It is shown that the response (defined as a percent change relative to the magnitude, or size, of response) corresponding to the dose where the slope changes the most depends on the geometrical shape of the dose-response curve; the response becomes lower as the curve becomes more asymmetrical and threshold-like in the low-dose region. Given a symmetrical case, described by the Hill function, the response associated with the critical dose level becomes 21% (defined as a percent change relative to the magnitude, or size, of response). According to a limiting case of asymmetry and threshold-like characteristics, reflected by a Gompertz curve, the response corresponding to the dose of interest becomes as low as 7.3% (defined as a percent change relative to the magnitude, or size, of response). Use of a response in the range of 5-10% when estimating the BMD conservatively accounts for uncertainties associated with the proposed strategy, and may be appropriate in a risk assessment point of view. The present investigation also indicated that a BMD defined according to the suggested procedure may be estimated more precisely relative to BMDs defined under other approaches for continuous data.

Animals↗

Strategies for defining financial benchmarks for the research mission in academic health centers.

Valid financial benchmarks are needed for the research mission in academic health centers (AHCs). Databases listing institutional success in obtaining sponsored research funding are publicly available. However, these databases are generally not adjusted for AHC size, confounding useful comparisons between institutions. The authors suggest simple strategies, which depend on a form of ratio analysis, to circumvent this limitation. Annual rates of growth (rates of return, R(f)) are determined for total National Institutes of Health research grant dollars, number of research grants, and average dollars per research grant for 15 U.S. AHCs. Selected institutions are compared to one another and to the total pool of medical school funding. Performance is evaluated over a ten-year period (1992-2001) to illustrate the advantages, limitations, and applications of the ratio analysis approach. Alternative strategies are suggested for individual AHCs to evaluate their departmental and organizational performance, again without regard to institution size, and also dependent on ratios. Application of these strategies, especially when individualized to the particular AHC, permits more accurate assessment of past performance and more accurate and effective planning for future growth.

Academic Medical Centers↗

A benchmark project to improve cost and quality outcomes for CABG patients.

Today's health care environment is forcing health care providers to find ways to provide more effective and efficient care. This article describes a collaborative benchmark project that examined acute care for coronary artery bypass graft surgery patients and reduced costs and improved patient outcomes.

Benchmarking↗

Better Medicare Cost Report data are needed to help hospitals benchmark costs and performance.

To evaluate costs and achieve cost control in the face of new technology and demands for efficiency from both managed care and governmental payers, hospitals need to benchmark their costs against those of other comparable hospitals. Since they typically use Medicare Cost Report (MCR) data for this purpose, a variety of cost accounting problems with the MCR may hamper hospitals' understanding of their relative costs and performance. Managers and researchers alike need to investigate the validity, accuracy, and timeliness of the MCR's cost accounting data.

Accounting↗

Benchmarking for the competitive marketplace.

One would get little argument these days regarding the importance of performance measurement in the health care industry. The traditional approach has been the straightforward use of measurable units such as financial comparisons and clinical indicators (e.g., length of stay). Also we in the health care industry have traditionally benchmarked our performance and strategies against those most like ourselves. Today's competitive market demands a more customer-focused set of performance measures that go beyond traditional approaches such as customer service. The most important task in today's environment is to study the customers' emerging priorities and adjust our business to meet those priorities.

Ambulatory Care↗

Using benchmarking practices for the learning resource center.

Structured ongoing and systematic evaluation is required to ensure up-to-date resources and continuous quality improvement plans to meet the learning needs of the diverse student population and the complex needs of patients. Using benchmarking to achieve evaluation goals in the learning resource center has great merit as schools of nursing respond to consumer demand for improvement, rapid changes resulting from changing patient needs, and the technology explosion.

Benchmarking↗

Total joint replacement: baseline benchmark data for interdisciplinary outcomes management.

PURPOSE: The purpose of this review was to define and describe 2 years of adverse outcome variances for elective primary or revision of major total joint replacement in terms of baseline benchmark data. DESIGN: Descriptive variance. METHODS: Retrospective review of patients with greater than 4 days in acute care after total joint replacement, patients with unexpected comorbidities that required medical subspecialist management, patients who were transferred to a higher level of care, and patients who did not survive postoperatively. FINDINGS: This review indicates that patients treated on a higher volume dedicated orthopaedic unit experience fewer adverse outcomes and shorter length of stay than patients treated on a general surgical unit. CONCLUSIONS: Patients who are treated on a dedicated orthopaedic unit experience significantly fewer adverse outcomes or outcome variations. Costs can be effectively managed, and optimal clinical patient outcomes can be achieved with few complications. Treatment strategies can be used as a template for enhanced care processes for this population.

Aged↗

Benchmarking the communication of continuous improvement activities.

Communication of a continuous improvement program in a large medical center was assessed using a formal benchmarking process with four non-health care organizations. Results indicated that continuous improvement must be integrated with the corporate strategic plan, must focus on customer satisfaction, and have active leadership support. A common framework should link different continuous improvement methodologies. Ongoing, open, multimedia two-way communication is required. Continuous improvement activities need to be integrated into all employees' daily work.

Benchmarking↗

Implementing achievable benchmarks in preventive health: a controlled trial in residency education.

PURPOSE: To evaluate the Preventive Health Achievable Benchmarks Curriculum, a multifaceted improvement intervention that included an objective, practice-based performance evaluation of internal medicine and pediatric residents' delivery of preventive services. METHOD: The authors conducted a nonrandomized experiment of intervention versus control group residents with baseline and follow-up of performance audited for 2001-2004. All 130 internal medicine and 78 pediatric residents at two continuity clinics at the University of Alabama School of Medicine, Birmingham, participated. Performance of preventive care was assessed by structured chart review. The multifaceted feedback curriculum included individualized performance feedback, academic detailing by faculty, and collective didactic sessions. The main outcome was difference in receipt of preventive care for patients seen by intervention and control residents, comparing baseline and follow-up. RESULTS: Charts were reviewed for 3,958 patients. Receipt of preventive care increased for patients of intervention residents, but not for patients of control residents. For the intervention group, significant increases occurred for five of six indicators in internal medicine: smoking screening, quit smoking advice, colon cancer screening, pneumonia vaccine, and lipid screening; and four of six in pediatrics: parental quit smoking advice, car seats, car restraints, and eye alignment (p < .05 for all). For control residents, no consistent improvements were seen. There was greater improvement for intervention than for control residents for four of six indicators in internal medicine, and two of six in pediatrics. CONCLUSIONS: Using a multifaceted feedback curriculum, the authors taught residents about the care they provide and improved documented patient care.

Adult↗

Intensive care unit length of stay: Benchmarking based on Acute Physiology and Chronic Health Evaluation (APACHE) IV.

OBJECTIVE: To revise and update the Acute Physiology and Chronic Health Evaluation (APACHE) model for predicting intensive care unit (ICU) length of stay. DESIGN: Observational cohort study. SETTING: One hundred and four ICUs in 45 U.S. hospitals. PATIENTS: Patients included 131,618 consecutive ICU admissions during 2002 and 2003, of which 116,209 met inclusion criteria. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The APACHE IV model for predicting ICU length of stay was developed using ICU day 1 patient data and a multivariate linear regression procedure to estimate the precise ICU stay for randomly selected patients who comprised 60% of the database. New variables were added to the previous APACHE III model, and advanced statistical modeling techniques were used. Accuracy was assessed by comparing mean observed and mean predicted ICU stay for the excluded 40% of patients. Aggregate mean observed ICU stay was 3.86 days and mean predicted 3.78 days (p < .001), a difference of 1.9 hrs. For 108 (93%) of 116 diagnoses, there was no significant difference between mean observed and mean predicted ICU stay. The model accounted for 21.5% of the variation in ICU stay across individual patients and 62% across ICUs. Correspondence between mean observed and mean predicted length of stay was reduced for patients with a short (< or =1.7 days) or long (> or =9.4 days) ICU stay and a low (<20%) or high (>80%) risk of death on ICU day 1. CONCLUSIONS: The APACHE IV model provides clinically useful ICU length of stay predictions for critically ill patient groups, but its accuracy and utility are limited for individual patients. APACHE IV benchmarks for ICU stay are useful for assessing the efficiency of unit throughput and support examination of structural, managerial, and patient factors that affect ICU stay.

APACHE↗