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PubMed2005

Quantum and quasiclassical studies of the O(3P)+HCl-->OH+Cl(2P) reaction using benchmark potential surfaces.

We have performed quantum mechanical (QM) dynamics calculations within the independent-state approximation with new benchmark triplet A" and A' surfaces [B. Ramachandran et al., J. Chem. Phys. 119, 9590 (2003)] for the rovibronic state-to-state measurements of the reaction O(3P)+HCl(v=2,j=1,6,9)-->OH(v'j')+Cl(2P) [Zhang et al., J. Chem. Phys. 94, 2704 (1991)]. The QM and experimental rotational distributions peak at similar OH(j') levels, but the QM distributions are significantly narrower than the measurements and previous quasiclassical dynamics studies. The OH(low j) populations observed in the measurements are nearly absent in the QM results. We have also performed quasiclassical trajectory with histogram binning (QCT-HB) calculations on these same benchmark surfaces. The QCT-HB rotational distributions, which are qualitatively consistent with measurements and classical dynamics studies using other surfaces, are much broader than the QM results. Application of a Gaussian binning correction (QCT-GB) dramatically narrows and shifts the QCT-HB rotational distributions to be in very good agreement with the QM results. The large QCT-GB correction stems from the special shape of the joint distribution of the classical rotational/vibrational action of OH products. We have also performed QM and QCT calculations for the transition, O+HCl(v=0,T=300 K)-->OH(v'j')+Cl from threshold to approximately 130 kcal mol(-1) collision energy as a guide for possible future hyperthermal O-atom measurements. We find in general a mixed energy release into translation and rotation consistent with a late barrier to reaction. Angular distributions at high collision energy are forward peaked, consistent with a stripping mechanism. Direct collisional excitation channel cross sections, O+HCl(v=0,T=300 K)-->O+HCl(v'=1), in the same energy range are large, comparable in magnitude to the reactive channel cross sections. Although the (3)A" state dominates most collision processes, above approximately 48 kcal mol(-1), the (3)A' state plays the major role in collisional excitation.

Journal Article↗

PubMed2005

Ab initio study on the spectroscopy of CuCl2. II. Benchmark calculations on the X2Pi g-C2Deltag and X2Pi g-D2Deltag transitions.

The X (2)Pi(g)-C (2)Delta(g) and X (2)Pi(g)-D (2)Delta(g) transitions on CuCl(2) have been studied using the most sophisticated nondynamic and dynamic electronic correlation treatments. We report here ab initio benchmark calculations using especially developed basis sets to study, at the complete active space self-consistent field plus second-order Møller-Plesset algorithm (CASSCF+CASPT2) and CASSCF+ACPF levels, the transition energies as well as the corresponding equilibrium geometries (ACPF-averaged coupled pair functional). The spin-orbit (SO) effects of both atoms were included in a second step through the effective Hamiltonian formalism, using the calibrated SO effective potentials developed by the Stuttgart group. Without SO at the CASSCF+ACPF level, the vertical excitation energy for the (2)Delta(g) state is 6711 cm(-1) and the symmetric stretching equilibrium Cu-Cl distance is 4.04 a.u. The inclusion of the SO effects leads to a pure (2)Delta(g) Omega=5/2C state and a Omega=3/2 (0.7% (2)Pi(g),99.3% (2)Delta(g))D state. The calculated transition energies for the C and D states are 6340 and 8020 cm(-1), in good agreement with the spin-orbit splitting recent values from gas-phase and rare-gas matrix isolation laser induced fluorescence experiments. The present benchmark results show, as was recently done for the X (2)Pi(g)-(2)Sigma(g) transition, the rather poor performance of all the density functional theory-based descriptions for the (2)Delta(g) state, which largely overestimate its T(e), systematically placing it around 19 000 cm(-1). The CASSCF+CASPT2 method also overestimates, by around 50%, the X (2)Pi(g)-(2)Delta(g) transition energy, showing that only large variational calculations can produce reliable spectroscopic results for this kind of complex systems where delicate electronic correlation effects have to be carefully dealt with.

Journal Article↗

PubMed1996

Benchmarking and supplier networking--best practice approaches.

This article examines the approach adopted by a health service to benchmark outside the health industry and to network with its own suppliers in its quest for best practice. The Maryborough District Health Service was selected for funding under the Commonwealth Government's Best Practice in the Health Sector Program. This rural health service is setting a fine example of how generic benchmarking can be used to increase efficiency and improve outcomes in an environment of change, increasing demands, and contracting resources. The organisation has networked with its suppliers with a view to ensuring that, as a customer, it has access to the best quality goods and services. The objective is to improve the services and quality of patient care provided by the health service and to minimise its cost structures.

Australia↗

PubMed1996

A comparison of speeds of personal computers using an x-ray scattering Monte Carlo benchmark.

In recent years personal computers, PCs, have become more popular and competitive with other computers, in terms of price and memory, to run Monte Carlo (MC) programmes. A few years ago some work was performed to test computer speed, mainly other than PCs, using the MC code EGS4. In the present work a Monte Carlo neutron and photon code, MCNP version 4.2 and 4A, was used to test the speed of various PCs. A benchmark was written, with previously checked results, to test the PCs' speed. PCs used in the test were based on the Intel 486 (33, 66 and 100 MHz) and pentium 90. The benchmark was also used on an upgraded SunSparcstation 4/360. The pentium speed was found ot be about 3.5, 2 and 1.5 times faster than that of the 33, 66 and 100 MHz, respectively. The 33 MHz speed was comparable to that of the SunSparcstation. It is concluded that the application of MC code, the cost of the PC and the required speed of results may influence the choice of the PC.

Equipment Design↗

PubMed2006

Estimation of the benchmark dose by structural equation models.

While epidemiological data typically contain a multivariate response and often also multiple exposure parameters, current methods for safe dose calculations, including the widely used benchmark approach, rely on standard regression techniques. In practice, dose-response modeling and calculation of the exposure limit are often based on the seemingly most sensitive outcome. However, this procedure ignores other available data, is inefficient, and fails to account for multiple testing. Instead, risk assessment could be based on structural equation models, which can accommodate both a multivariate exposure and a multivariate response function. Furthermore, such models will allow for measurement error in the observed variables, which is a requirement for unbiased estimation of the benchmark dose. This methodology is illustrated with the data on neurobehavioral effects in children prenatally exposed to methylmercury, where results based on standard regression models cause an underestimation of the true risk.

Biometry↗

PubMed2005

Benchmarks for work performance of pediatric psychologists.

OBJECTIVE: To establish benchmarks for work performance of pediatric psychologists. METHODS: All full members of the Society of Pediatric Psychology, Division 54 of the American Psychological Association (N = 1043), were recruited for participation in a mail survey. Four hundred and seventy surveys were returned (45%); 356 usable surveys (34%) were included in the analyses. Surveys assessed work-settings, academic appointments, salary, performance expectations and evaluations, and satisfaction. RESULTS: Most of the survey respondents, 63%, worked in a hospital setting. On average, survey respondents were directly accountable for generating half, 52%, of their salary. Salary covered by institutions was most frequently provided for nonrevenue generating activities such as administration and teaching. Most of the sample (78%) indicated clear performance expectations and criteria. CONCLUSIONS: Findings update and expand previously established benchmarks for work performance and have implications for the practice of pediatric psychology in an ever-changing health care environment.

Academic Medical Centers↗

PubMed2001

A new tool for benchmarking cardiovascular fluoroscopes.

This paper reports the status of a new cardiovascular fluoroscopy benchmarking phantom. A joint working group of the Society for Cardiac Angiography and Interventions (SCAI) and the National Electrical Manufacturers Association (NEMA) developed the phantom. The device has been adopted as NEMA standard XR 21-2000, 'Characteristics of and Test Procedures for a Phantom to Benchmark Cardiac Fluoroscopic and Photographic Performance' in August 2000. The test ensemble includes imaging-field geometry, spatial resolution, low-contrast iodine detectability, working thickness range, motion unsharpness, and phantom entrance dose. The phantom tests systems under conditions simulating normal clinical use for fluoroscopically guided invasive and interventional procedures. Test procedures rely on trained human observers.

Cardiovascular Diseases↗

PubMed2026

Benchmarking Assembly-Free K-mer Methods for Species Identification in Complex Plant Groups: A Case Study in Populus.

Species identification in taxonomically complex plant groups is frequently limited by the inadequacy of organellar markers, whose phylogenetic signal is disrupted by cytonuclear discordance and chloroplast capture. Using the taxonomically complex genus Populus as a model, we evaluated an assembly-free k-mer workflow against a curated SNP reference benchmark. Whole-genome resequencing data from 235 Populus individuals were curated to a 202-individual, 34-species reference dataset in which all retained species are strictly monophyletic in a genome-wide SNP analysis. Independent maximum likelihood analyses further confirmed that the 31 non-hybrid backbone species each maintained high-support monophyly, while taxa of documented reticulate origin showed placement patterns consistent with their reticulate histories. ABBA-BABA D-statistics detected widespread residual allele sharing within the backbone, though the strongest signals did not correspond to the species pairs responsible for the few k-mer identification failures. Against this benchmark, complete plastomes showed limited resolution, recovering only 3.0% species monophyly and 71.1% nearest-neighbor assignment. The optimized k-mer workflow, operating directly on raw reads without assembly or alignment, recovered 91.2% species monophyly, 99.0% nearest-neighbor assignment, and 98.0% group-average assignment. K-mer length was the primary accuracy-controlling parameter, with k = 31 falling within a stable accuracy plateau. Distance-based metrics reached near-saturation at 0.2× sequencing depth, indicating that low-coverage genome skimming can support scalable nuclear genome-based identification with standard computational resources. K-mer distance heatmaps also flagged unusual genomic affinities in hybrid-origin and outlier samples, providing a rapid screen for subsequent population genomic analyses. These results support assembly-free k-mer distances as an efficient tool for reference-based species identification and sample screening in complex plant groups, with residual limitations concentrated near recently diverged species boundaries. Model-based phylogenomic, coalescent, and network analyses remain necessary for resolving deeper species relationships and detailed introgression histories.

Populus↗

PubMed2025

Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater.

Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmarked four targeted enrichment methods suited for whole-genome sequencing including custom and off-the-shelf amplicon and probe-based methods. Our custom HA tiled-amplicon panel was sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes. However, its reliance on conserved and intact primer-binding sites limited primer design to fewer subtypes. A previously published universal amplicon method targeted all IAV subtypes, but it performed poorly in wastewater due to its reliance on intact genome segments. Probe-capture methods were resilient to RNA degradation and mismatches, potentially enabling broader surveillance and detection of emerging strains. However, probes were costly, labor-intensive, and less sensitive than tiled-amplicon. When testing compatibility of sequencing methods with upstream virus concentration and extraction methods, ultrafiltration-based virus concentration outperformed large-volume direct extraction with all four sequencing methods. This set of benchmarking comparisons and custom panels provides needed information for the translation of IAV genomic sequencing into a routine component of wastewater surveillance.

Journal Article↗

PubMed2003

Benchmark dose risk assessment for formaldehyde using airflow modeling and a single-compartment, DNA-protein cross-link dosimetry model to estimate human equivalent doses.

Formaldehyde induced squamous-cell carcinomas in the nasal passages of F344 rats in two inhalation bioassays at exposure levels of 6 ppm and above. Increases in rates of cell proliferation were measured by T. M. Monticello and colleagues at exposure levels of 0.7 ppm and above in the same tissues from which tumors arose. A risk assessment for formaldehyde was conducted at the CIIT Centers for Health Research, in collaboration with investigators from Toxicological Excellence in Risk Assessment (TERA) and the U.S. Environmental Protection Agency (U.S. EPA) in 1999. Two methods for dose-response assessment were used: a full biologically based modeling approach and a statistically oriented analysis by benchmark dose (BMD) method. This article presents the later approach, the purpose of which is to combine BMD and pharmacokinetic modeling to estimate human cancer risks from formaldehyde exposure. BMD analysis was used to identify points of departure (exposure levels) for low-dose extrapolation in rats for both tumor and the cell proliferation endpoints. The benchmark concentrations for induced cell proliferation were lower than for tumors. These concentrations were extrapolated to humans using two mechanistic models. One model used computational fluid dynamics (CFD) alone to determine rates of delivery of inhaled formaldehyde to the nasal lining. The second model combined the CFD method with a pharmacokinetic model to predict tissue dose with formaldehyde-induced DNA-protein cross-links (DPX) as a dose metric. Both extrapolation methods gave similar results, and the predicted cancer risk in humans at low exposure levels was found to be similar to that from a risk assessment conducted by the U.S. EPA in 1991. Use of the mechanistically based extrapolation models lends greater certainty to these risk estimates than previous approaches and also identifies the uncertainty in the measured dose-response relationship for cell proliferation at low exposure levels, the dose-response relationship for DPX in monkeys, and the choice between linear and nonlinear methods of extrapolation as key remaining sources of uncertainty.

Administration, Inhalation↗

PubMed2003

Determination of an occupational exposure guideline for manganese using the benchmark method.

An occupational risk assessment for manganese (Mn) was performed based on benchmark dose analysis of data from two epidemiological studies providing dose-response information regarding the potential neurological effects of exposure to airborne Mn below the current Occupational Safety and Health Administration (OSHA) Permissible Exposure Level (PEL) of 5 mg Mn/m3. Based on a review of the scientific evidence regarding the toxicity of Mn, it was determined that the most appropriate measure of exposure to airborne Mn for the subclinical effects measured in these studies is recent (rather than historical or cumulative) concentration of Mn in respirable (rather than total) particulate. For each of the studies analyzed, the individual exposure and response data from the original study had been made available by the investigators. From these two studies benchmark concentrations calculated for eight endpoints ranged from 0.09 to 0.27 mg Mn/m3. From our evaluation of these results, and considering the fact that the subtle, subclinical effects represented by the neurological endpoints tested in these studies do not represent material impairment, we believe an appropriate occupational exposure guideline for manganese would be in the range of 0.1 to 0.3 mg Mn/m3, based on the respirable particulate fraction only, and expressed as an 8-hour time-weighted average.

Air Pollutants, Occupational↗

PubMed1998

The Quality of Surgical Care Project: benchmark standards of open resection for abdominal aortic aneurysm in Western Australia.

BACKGROUND: The Quality of Surgical Care Project (QSCP) was established in May 1996, to evaluate surgical outcomes and where indicated, recommend changes to improve the quality of surgical care in Western Australia (WA). The purpose of this study is to establish benchmark standards in WA for operative mortality, 5-year survival and length of stay in all patients who were surgically treated for aneurysm of the abdominal aorta (AAA) in WA. METHODS: The WA Linked Database was used to link the morbidity and mortality records of all patients admitted and surgically treated for AAA in WA from 1985 to 1994. The linked chains of de-identified hospital morbidity and death records were selected using diagnostic and procedure codes pertaining to AAA. Three groups were separated for analysis: those admitted for rupture, those admitted for elective repair, and those who were admitted to hospital as an emergency without mention of rupture but who underwent repair for AAA. Independent analysis for gender and patients 80 years or more were included in the study. Patients were excluded from the study if they were less than 55 years of age. RESULTS: A total of 1475 cases (1257 males, 218 females) were identified. The mean age in elective cases was 70.4 years in males and 72.4 years in females, and for rupture the mean ages were 71.9 and 74.8 years, respectively. Median length of stay for males was 12 days for elective cases. Admission type or age did not significantly influence length of stay. Thirty-day mortality in males was 4.4% for elective repair and 36.7% for ruptured AAA and 5-year survival was 71.7 and 47.7%, respectively. The overall case fatality rate for ruptured AAA was 79.3% which included those cases who died from rupture without being admitted to hospital. CONCLUSIONS: These community-wide data provide a realistic measure of surgical performance for open repair of AAA. The outcomes for elective and rupture repair for AAA compare favourably with standards reported by international centres of excellence. They also support the use of this procedure in patients over 80 years of age with rupture. This information can be used for ongoing audit purposes and as a benchmark for the introduction of new treatment modalities.

Aged↗

PubMed1997

Multimedia benchmarking analysis for three risk assessment models: RESRAD, MMSOILS, and MEPAS.

This paper is one in a series that describes results of a benchmarking analysis initiated by the Department of Energy (DOE) and the United States Environmental Protection Agency (EPA). An overview of the study is provided in a companion paper by Laniak et al. presented in this journal issue. The three models used in the study--RESRAD (DOE), MMSOILS (EPA), and MEPAS (DOE)--represent analytically-based tools that are used by the respective agencies for performing human exposure and health risk assessments. Both single media and multimedia benchmarking scenarios were developed and executed. In this paper, the multimedia scenario is examined. That scenario consists of a hypothetical landfill that initially contained uranium-238 and methylene chloride. The multimedia models predict the fate of these contaminants, plus the progeny of uranium-238, through the unsaturated zone, saturated zone, surface water, and atmosphere. Carcinogenic risks are calculated from exposure to the contaminants via multiple pathways. Results of the tests show that differences in model endpoint estimates arise from both differences in the models' mathematical formulations and assumptions related to the implementation of the scenarios.

Air Pollutants, Radioactive↗

PubMed2006

Relation between benchmark dose and no-observed-adverse-effect level in clinical research: effects of daily alcohol intake on blood pressure in Japanese salesmen.

The benchmark dose (BMD) is defined as the dose that corresponds to a specific change in an adverse response compared to the response in unexposed subjects, and the lower 95% confidence limit is termed the benchmark dose level (BMDL). In this study, the threshold of daily ethanol intake affecting blood pressure was calculated by both the BMD approach and multiple logistic regression analysis to clarify the relation between the BMDL and no-observed-adverse-effect level (NOAEL). Systolic and diastolic blood pressures (SBP and DBP) and daily ethanol intake were explored in 1,100 Japanese salesmen. The SBP and DBP were positively related to daily ethanol intake (p < 0.001) when adjusting for possible confounders such as age, body mass index, and smoking status. The adjusted risk for hypertension (SBP >or= 140 mmHg or DBP >or= 90 mmHg) increased significantly when daily ethanol intake exceeded 60 g/day, and the categorical dose of interest was 60.1-90 g/day. The BMDL and BMD of ethanol intake for increased SBP and DBP were estimated to be approximately 60 and 75 g/day, respectively. These findings suggest that the BMDL and BMD correspond to the NOAEL and lowest-observed-adverse-effect level, respectively, if the sample number of clinical data is large enough to confirm the dose-response association.

Adolescent↗

PubMed2006

Comparing experimental designs for benchmark dose calculations for continuous endpoints.

The BMD (benchmark dose) method that is used in risk assessment of chemical compounds was introduced by Crump (1984) and is based on dose-response modeling. To take uncertainty in the data and model fitting into account, the lower confidence bound of the BMD estimate (BMDL) is suggested to be used as a point of departure in health risk assessments. In this article, we study how to design optimum experiments for applying the BMD method for continuous data. We exemplify our approach by considering the class of Hill models. The main aim is to study whether an increased number of dose groups and at the same time a decreased number of animals in each dose group improves conditions for estimating the benchmark dose. Since Hill models are nonlinear, the optimum design depends on the values of the unknown parameters. That is why we consider Bayesian designs and assume that the parameter vector has a prior distribution. A natural design criterion is to minimize the expected variance of the BMD estimator. We present an example where we calculate the value of the design criterion for several designs and try to find out how the number of dose groups, the number of animals in the dose groups, and the choice of doses affects this value for different Hill curves. It follows from our calculations that to avoid the risk of unfavorable dose placements, it is good to use designs with more than four dose groups. We can also conclude that any additional information about the expected dose-response curve, e.g., information obtained from studies made in the past, should be taken into account when planning a study because it can improve the design.

Animals↗

PubMedDate not supplied

A standard timing benchmark for EGS4 Monte Carlo calculations.

A Fortran 77 Monte Carlo source code built from the EGS4 Monte Carlo code system has been used for timing benchmark purposes on 29 different computers. This code simulates the deposition of energy from an incident electron beam in a 3-D rectilinear geometry such as one would employ to model electron and photon transport through a series of CT slices. The benchmark forms a standalone system and does not require that the EGS4 system be installed. The Fortran source code may be ported to different architectures by modifying a few lines and only a moderate amount of CPU time is required ranging from about 5 h on PC/386/387 to a few seconds on a massively parallel supercomputer (a BBN TC2000 with 512 processors).

Electrons↗

PubMed1990

Initial test of the benchmark chemical approach for predicting microbial transformation rates in aquatic environments.

Using 2,4-dichlorophenoxyacetic acid methyl ester (2,4-DME) as a benchmark chemical, we determined relative pseudo-first-order rate coefficients for the butoxyethyl ester of 2,4-dichlorophenoxyacetic acid (2,4-DBE), methyl parathion, and methyl-3-chlorobenzoate in a diversity of microbial samples, including water, sediment, biofilm, and floating microbial mats collected from a laboratory mesocosm as well as from streams, lakes, and wetlands in Georgia and Florida. The decreasing order of reactivity for relative microbial transformation rates was 2,4-DBE > 2,4-DME > methyl-3-chlorobenzoate > methyl parathion. Half-lives of the chemicals varied about 60-fold depending on the chemical and microbial sample. Relative rate coefficients, however, typically varied only about threefold for field-collected samples. Relative rate coefficients determined with samples from a laboratory mesocosm were consistently low compared with the field sample data. Overall, the data indicated that microbial transformation rates of a chemical can be satisfactorily inferred for a wide variety of microbial habitats-such as water, biofilm, or a sediment-on the basis of its transformation rate relative to that of an appropriate benchmark chemical by using a single type of microbial sample.

Journal Article↗

PubMed2004

Percentile benchmarks in patients with rheumatoid arthritis: Health Assessment Questionnaire as a quality indicator (QI).

Physicians are in need of a simple objective, standardized tool to compare their patients with rheumatoid arthritis, as a group and individually, with national standards. The Disability Index of the Health Assessment Questionnaire (HAQ-DI) is a simple, robust tool that can fulfill these needs. However, use of this tool as a quality indicator (QI) is hampered by the unavailability of national reference values or benchmarks based on large, multicentric, heterogenous longitudinal patient cohorts. We utilized the 20-year longitudinal prospective data from 11 data banks of Arthritis Rheumatism and Aging Medical Information to calculate reference values for HAQ-DI. Overall, 6436 patients with rheumatoid arthritis were longitudinally followed for 32,324 person-years over the 20 years from 1981 to 2000. There were 64,647 HAQ-DI measurements, with an average of 19 measurements per person. Overall, 75% of patients were women and 89% were Caucasian; the median baseline age was 58.4 years and the median baseline HAQ-DI was 1.13. Few patients were treated with biologics. The HAQ-DI values had a Gaussian distribution except for the approximately 10% of observations showing no disability. Percentile benchmarks allow disability outcomes to be compared and contrasted between different patient populations. Reference values for the HAQ-DI, presented here numerically and graphically, can be used in clinical practice as a QI measure to track functional disability outcomes and to measure response to therapy, and by arthritis patients in self-management programs.

Antirheumatic Agents↗