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PubMed2006

A probabilistic framework for non-cancer risk assessment.

Risk assessment involves an analysis of the relationship between exposure and health related outcomes to derive an allowable exposure level or to estimate a low-dose risk. Acceptable levels of human exposure for non-cancer effects generally are derived by dividing an experimental no-observed-adverse-effect-level or a lower confidence limit benchmark dose by a product of several uncertainty factors. This paper presents a hierarchical modeling framework for a probabilistic approach to non-cancer risk assessment. The hierarchical model integrates the distributions of uncertainty factors and the distribution of the actual exposure level to construct the dose-response model for the proportion of population at risk and the dose-response model for the expected proportion of population at risk for a given exposure distribution. The proposed approach is based on the use of the BMDL (lower confidence limit on the benchmark dose) as a POD (point of departure) for risk assessment of non-cancer effects.

Animals↗
PubMed1996

Predicting the severity of motor vehicle accident injuries using models of ordered multiple choice.

This paper presents statistical evidence showing how variations in the attributes of road users can lead to variations in the probabilities of sustaining different levels of injury in motor vehicle accidents. Data from New South Wales, Australia, is used to estimate two models of multiple choice which are reasonably commonplace in the econometrics literature: the ordered logit model and the ordered probit model. Our estimated parameters are significantly different from zero at small levels of significance and have signs which are consistent with our prior beliefs. As a benchmark for comparison, we consider the risks faced by a 33-year-old male driver of a 10-year-old motor vehicle who is involved in a head-on collision while travelling at 42 kilometres per hour. We estimate that this benchmark victim will remain uninjured with a probability of almost zero, will require treatment from a medical officer with a probability of approximately 0.7, will be admitted to hospital with a probability of approximately 0.3, and will be killed with a probability of almost zero. We find that increases in the age of the victim and vehicle speed lead to slight increases in the probabilities of serious injury and death. Other factors which have a similar or greater effect on the probabilities of different types of injury include seating position, blood alcohol level, vehicle type, vehicle make and type of collision.

Acceleration↗
PubMed2003

Fungal phyA gene expressed in potato leaves produces active and stable phytase.

Fungal phyA gene from Aspergillus ficuum (niger) was cloned and expressed in potato leaves. The recombinant enzyme was stable and catalytically active. The expressed protein in the leaves of the dicotyledonous plant retained most physical and catalytic properties of the benchmark A. ficuum phytase. The expressed enzyme was, however, 15% less glycosylated than the native phytase. The usual bi-hump pH optima profile, which is characteristic of the fungal phytase, was altered; however, the pH optimum at 5.0 was unchanged for phytate and at 4.0 for synthetic substrate p-nitrophenyl phosphate. The temperature was, however, unchanged. The expressed phytase was found to be as sensitive as the native enzyme to the inhibitory action of pseudo substrate, myo-inositol hexasulfate, while losing about 90% of the activity at 20 microM inhibitor concentration. Similar to the benchmark phytase, the expressed phytase in leaves was completely inactivated by Arg modifier phenylglyoxal at 60 nM. In addition, the expressed phytase in the leaves was inhibited by antibody raised against a 20-mer internal peptide, which is present on the surface of the molecule as shown by the X-ray deduced 3D structure of fungal phytase. Taken together, the biochemical evidences indicate that fungal phytase when cloned and expressed in potato leaves produces a stable and active biocatalyst. 'Biofarming,' therefore, is an alternative way to produce functional hydrolytic enzymes as exemplified by the expression of A. ficuum (niger) phyA gene in potato leaf.

6-Phytase↗
PubMed2003

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals.

The nature of the control of water/proton selectivity in biological channels is a problem of a fundamental importance. Most studies of this issue have proposed that an interference with the orientational requirements of the so-called proton wire is the source of selectivity. The elucidation of the structures of aquaporins, which have evolved to prevent proton transfer (PT), provided a clear benchmark for exploring the selectivity problem. Previous simulations of this system have not examined, however, the actual issue of PT, but only considered the much simpler task of the transfer of water molecules. Here we take aquaporin as a benchmark and quantify the origin of the water/proton selectivity in this and related systems. This is done by evaluating in a consistent way the free energy profile for transferring a proton along the channel and relating this profile to the relevant PT rate constants. It is found that the water/proton selectivity is controlled by the change in solvation free energy upon moving the charged proton from water to the channel. The reason for the focus on the elegant concept of the proton wire and the related Grotthuss-type mechanism is also considered. It is concluded that these mechanisms are clearly important in cases with flat free energy surfaces (e.g., in bulk water, in gas phase water chains, and in infinitely long channels). However, in cases of biological channels, the actual PT mechanism is much less important than the energetics of transferring the proton charge from water to different regions in the channels.

Amino Acid Motifs↗
PubMed2006

Direct descent curvature optimal control with a modification algorithm and its application to nonlinear process.

This paper presents a direct descent second order or direct descent curvature algorithm with some modifications for the optimal control computations. This algorithm is compared with Hamiltonian methods in the literature. The proposed algorithm has generated numerically robust solutions with respect to conjugate points. The weighting matrix updating scheme was developed to improve the second-order optimal control algorithm, tested the performance of the algorithm, and shown on the benchmark and industrial process. The time-varying optimal feedback (TVOFB) gains are also generated along the trajectory as byproducts. If the trajectory deviates from the optimal trajectory for any reason (i.e., changing of system parameters, step disturbance into the plant, changing of initial conditions), it is held on the optimal trajectory by means of the optimal feedback. Simulations have been given for controlling the Van der Pol and bioreactor system, which are nonlinear benchmark systems.

Journal Article↗
PubMed2003

New local potential useful for genome annotation and 3D modeling.

A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance-dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar to (but not identical with) the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10% more structures identified correctly as the most likely structural match in a fold library, and 20% more structures correctly narrowed down to a set of five possible candidates. JThread also improves the average sequence alignment accuracy significantly, from 53% to 62% of residues aligned correctly. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.

Animals↗
PubMed2002

US EPA's acute reference exposure methodology for acute inhalation exposures.

The US Environmental Protection Agency (EPA) National Center for Environmental Assessment is engaged in the development of a methodology for Agency use to perform risk assessments for non-cancer effects due to acute inhalation exposures. The methodology will provide general guidance for deriving chemical-specific acute exposure benchmarks called acute reference exposures (AREs). Chemical-specific AREs are analogous to reference concentra tions (RfCs) for chronic non-cancer effects and will be incorporated in chemical-specific files in the US EPA's Integrated Risk Information System (IRIS) as they are developed and reviewed. AREs will have wide applicability in assessing the potential health risks of accidental and routine acute releases of chemicals to the environment. The proposed methodology for ARE development provides a framework for choosing an optimal derivation approach, depending on the type of data available, from the no-observed-adverse-effect level (NOAEL), benchmark concentration (BMC), or categorical regression approaches. Uncertainty factors are applied to the point of departure, determined by one of the recommended approaches, to derive the ARE. Due to the capability to use more exposure-response information than the NOAEL approach allows, exposure-response analyses such as BMC and categorical regression are favored as methods to develop the point of departure when the available database will support such analyses. The NOAEL approach is suitable when the data are insufficient to support exposure-response modeling. Applications of the proposed ARE methodology are illustrated by the derivation of example AREs for hydrogen sulfide and hexachlorocyclopentadiene, which showcase the categorical regression and NOAEL approaches, respectively. In addition, a recent review of the proposed ARE methodology by the US EPA Risk Assessment Forum is discussed.

Air Pollutants↗
PubMedDate not supplied

Transfer rates from freestanding birth centers. A comparison with the National Birth Center Study.

This article reviews retrospective data derived from Sharp The BirthPlace. San Diego for 1993-94 and from the University of California. Irvine, Birthing Center for 1994 and compares these findings to data obtained from the National Birth Center Study (NBCS). The focus of this article is on intrapartum transfer rates from the two freestanding birth centers as a critical clinical indicator. Cause-specific transfer rates were calculated for eight clinical conditions. Data suggest that cause-specific intrapartum transfer rates are influenced by factors such as risk profile of the client population, distance to the referral center and mechanisms of transfer, definitions and diagnostic criteria used, and clinical practice guidelines. Reports from the literature, such as NBCS data, might serve as points of reference, but are likely not appropriate baseline indicators (benchmarks of "best practice") for clinical events, against which individual performance can be measured; rather, these benchmarks should be individually defined, based on characteristics unique to each birth center.

Birthing Centers↗
PubMed2002

Local weighting schemes for protein multiple sequence alignment.

This paper describes three weighting schemes for improving the accuracy of progressive multiple sequence alignment methods: (1) global profile pre-processing, to capture for each sequence information about other sequences in a profile before the actual multiple alignment takes place; (2) local pre-processing; which incorporates a new protocol to only use non-overlapping local sequence regions to construct the pre-processed profiles; and (3) local-global alignment, a weighting scheme based on the double dynamic programming (DDP) technique to softly bias global alignment to local sequence motifs. The first two schemes allow the compilation of residue-specific multiple alignment reliability indices, which can be used in an iterative fashion. The schemes have been implemented with associated iterative modes in the PRALINE multiple sequence alignment method, and have been evaluated using the BAliBASE benchmark alignment database. These tests indicate that PRALINE is a toolbox able to build alignments with very high quality. We found that local profile pre-processing raises the alignment quality by 5.5% compared to PRALINE alignments generated under default conditions. Iteration enhances the quality by a further percentage point. The implications of multiple alignment scoring functions and iteration in relation to alignment quality and benchmarking are discussed.

Amino Acid Motifs↗
PubMed1998

A survey of infection control professional staffing patterns at University HealthSystem Consortium institutions.

BACKGROUND: Proper staffing of infection control departments has long been a topic of interest. The most complete report on the subject, the Study on the Efficacy of Nosocomial Infection Control, was published in 1985. To provide current benchmarking comparison data for expected staff reductions at the University of Michigan Health System, a survey of University HealthSystem Consortium members was performed. METHODS: A survey tool was developed to obtain general demographic, staffing, and case-mix information. An infection control professional at each institution was contacted to obtain most of the information. Additional information was obtained from standard references. RESULTS: Responses were obtained from 45 University HealthSystem Consortium members (67%). Full-time equivalent ratios were based on the following parameters and compared for the institutions: number of occupied beds (according to occupancy rate, median 137 occupied beds/full-time equivalent), number of intensive care unit beds (median 28 beds/full-time equivalent), number of admissions or discharges (median 6686 admissions/full-time equivalent), number of ambulatory care visits (median 104,426 visits/full-time equivalent), and case-mix index (median 1.75). CONCLUSIONS: Many institutions are using benchmarking comparison data to make decisions regarding staff reductions. This survey provides preliminary data for determining the "best practice" in staffing for infection control departments. More information may be needed to evaluate other factors that affect infection control professionals' workload.

Academic Medical Centers↗
PubMed1998

Infection surveillance in home care: device-related incidence rates.

BACKGROUND: Four home health agencies of different sizes, including a rural agency with many branch offices, participated in a surveillance study. METHODS: These agencies used the same definitions for symptomatic urinary tract infections in patients with urinary catheters and for bloodstream infections in patients receiving intravenous therapy. Identical data and methods were used for calculating infection rates, with device-days consistently used as the denominator. Each agency's primary goal was to develop baseline information about its own infection rates and to use these statistics to detect problems and trends. Chart audits were performed if trends or problems were identified. A secondary goal was to compare or benchmark infection rates, because there is almost no published information in this area of home care. RESULTS: We found that our mean infection rates for symptomatic urinary tract infection among patients with urinary catheters and for bloodstream infection among patients receiving intravenous therapy were similar among the four agencies. The mean rates for all four agencies were 4.5 symptomatic urinary tract infections/1000 device-days and 1.1 bloodstream infections/1000 device-days. CONCLUSION: The methods used here can be implemented in other home care agencies. Using the same definitions, collecting data for the same type of infections, and using the same rate calculations make infection control benchmarking possible between home health agencies.

Home Care Services↗
PubMed2001

Comparison of dose-responses of contact allergens using the guinea pig maximization test and the local lymph node assay.

The guinea pig maximization test (GPMT) has been used as a method for the prediction of skin sensitizing potential for over 30 years. Besides hazard identification, risk assessment of sensitizing chemicals requires the assessment of potency. For the determination of potency based on lowest effective dose levels, dose-response studies are required. In the standard GPMT a single concentration is used for intracutaneous and topical induction and the assay provides a qualitative assessment of allergenicity. This paper presents data derived from quantitative evaluation of the sensitizing potency of chemicals in the GPMT, based on multiple concentrations. We performed the GPMT in accordance with the original procedure of Magnusson and Kligman; and included in this procedure a range of intradermal and topical concentrations for induction. Three allergens with different sensitizing potencies, diethylamine (DEA), tetramethyl thiuram disulfide (TMTD) and zinc dimethyl dithiocarbamate (ZDMC) were tested. The data obtained with this test procedure were compared to data we previously obtained using the local lymph node assay (LLNA). Both the GPMT and the LLNA showed dose response relationships for the three chemicals tested. For the chemicals tested, both tests differed in the relative potencies based on benchmark concentrations. While both tests ranked DEA as the least potent allergen, the GPMT ranked ZDMC more potent than TMTD, the reverse being found in the LLNA. The nature of the data provided in the LLNA makes it likely that benchmarks as defined with this test are more reliable than that defined in the GPMT. However, further validation with human data is necessary.

Allergens↗
PubMed1998

Study of lung density corrections in a clinical trial (RTOG 88-08). Radiation Therapy Oncology Group.

PURPOSE: To investigate the effect of lung density corrections on the dose delivered to lung cancer radiotherapy patients in a multi-institutional clinical trial, and to determine whether commonly available density-correction algorithms are sufficient to improve the accuracy and precision of dose calculation in the clinical trials setting. METHODS AND MATERIALS: A benchmark problem was designed (and a corresponding phantom fabricated) to test density-correction algorithms under standard conditions for photon beams ranging from 60Co to 24 MV. Point doses and isodose distributions submitted for a Phase III trial in regionally advanced, unresectable non-small-cell lung cancer (Radiation Therapy Oncology Group 88-08) were calculated with and without density correction. Tumor doses were analyzed for 322 patients and 1236 separate fields. RESULTS: For the benchmark problem studied here, the overall correction factor for a four-field treatment varied significantly with energy, ranging from 1.14 (60Co) to 1.05 (24 MV) for measured doses, or 1.17 (60Co) to 1.05 (24 MV) for doses calculated by conventional density-correction algorithms. For the patient data, overall correction factors (calculated) ranged from 0.95 to 1.28, with a mean of 1.05 and distributional standard deviation of 0.05. The largest corrections were for lateral fields, with a mean correction factor of 1.11 and standard deviation of 0.08. CONCLUSIONS: Lung inhomogeneities can lead to significant variations in delivered dose between patients treated in a clinical trial. Existing density-correction algorithms are accurate enough to significantly reduce these variations.

Algorithms↗
PubMed2001

Prediction of operative mortality after valve replacement surgery.

OBJECTIVES: We sought to develop national benchmarks for valve replacement surgery by developing statistical risk models of operative mortality. BACKGROUND: National risk models for coronary artery bypass graft surgery (CABG) have gained widespread acceptance, but there are no similar models for valve replacement surgery. METHODS: The Society of Thoracic Surgeons National Cardiac Surgery Database was used to identify risk factors associated with valve surgery from 1994 through 1997. The population was drawn from 49,073 patients undergoing isolated aortic valve replacement (AVR) or mitral valve replacement (MVR) and from 43,463 patients undergoing CABG combined with AVR or MVR. Two multivariable risk models were developed: one for isolated AVR or MVR and one for CABG plus AVR or CABG plus MVR. RESULTS: Operative mortality rates for AVR, MVR, combined CABG/AVR and combined CABG/ MVR were 4.00%, 6.04%, 6.80% and 13.29%, respectively. The strongest independent risk factors were emergency/salvage procedures, recent infarction, reoperations and renal failure. The c-indexes were 0.77 and 0.74 for the isolated valve replacement and combined CABG/valve replacement models, respectively. These models retained their predictive accuracy when applied to a prospective patient population undergoing operation from 1998 to 1999. The Hosmer-Lemeshow goodness-of-fit statistic was 10.6 (p = 0.225) for the isolated valve replacement model and 12.2 (p = 0.141) for the CABG/valve replacement model. CONCLUSIONS: Statistical models have been developed to accurately predict operative mortality after valve replacement surgery. These models can be used to enhance quality by providing a national benchmark for valve replacement surgery.

Aged↗
PubMed2006

Universal access -- but when? Treating the right patient at the right time: access to electrophysiology services in Canada.

The Canadian Cardiovascular Society Access to Care Working Group has published a series of commentaries on access to cardiovascular care in Canada. The present article reviews the evidence for timely access to electrophysiology services. Using the best available evidence along with expert consensus by the Canadian Heart Rhythm Society, the panel proposed a series of benchmarks for access to the full scope of electrophysiology services, from initial consultation through to operative procedures. The proposed benchmarks are presented herein.

Canada↗
PubMed2006

Treating the right patient at the right time: access to cardiovascular nuclear imaging.

Cardiovascular nuclear medicine uses agents labelled with radioisotopes that can be imaged with cameras (single-photon emission tomography [SPECT] or positron emission tomography [PET]) capable of detecting gamma photons to show physiological parameters such as myocardial perfusion, myocardial viability or ventricular function. There is a growing body of literature providing guidelines for the appropriate use of these techniques, but there are little data regarding the appropriate timeframe during which the procedures should be accessed. An expert working group composed of cardiologists and nuclear medicine specialists conducted an Internet search to identify current wait times and recommendations for wait times for a number of cardiac diagnostic tools and procedures, including cardiac catheterization and angioplasty, bypass grafting and vascular surgery. These data were used to estimate appropriate wait times for cardiovascular nuclear medicine procedures. The estimated times were compared with current wait times in each province. Wait time benchmarks were developed for the following: myocardial perfusion with either exercise or pharmacological stress and SPECT or PET imaging; myocardial viability assessment with either fluorodeoxyglucose SPECT or PET imaging, or thallium-201 SPECT imaging; and radionuclide angiography. Emergent, urgent and nonurgent indications were defined for each clinical examination. In each case, appropriate wait time benchmarks were defined as within 24 h for emergent indications, within three days for urgent indications and within 14 days for nonurgent indications. Substantial variability was noted from province to province with respect to access for these procedures. For myocardial perfusion imaging, mean emergent/urgent wait times varied from four to 24 days, and mean nonurgent wait times varied from 15 to 158 days. Only Ontario provided limited access to viability assessment, with fluorodeoxyglucose available in one centre. Mean emergent/urgent wait times for access to viability assessment with thallium-201 SPECT imaging varied from three to eight days, with the exception of Newfoundland, where an emergent/urgent assessment was not available; mean nonurgent wait times varied from seven to 85 days. Finally, for radionuclide angiography, mean emergent/urgent wait times varied from two to 20 days, and nonurgent wait times varied from eight to 36 days. Again, Newfoundland centres were unable to provide emergent/urgent access. The publication of these data and proposed wait times as national targets is a step toward the validation of these recommendations through consultation with clinicians caring for cardiac patients across Canada.

Canada↗
PubMed2006

Treating the right patient at the right time: Access to cardiac catheterization, percutaneous coronary intervention and cardiac surgery.

The Canadian Cardiovascular Society Access to Care Working Group was formed with a mandate to use the best science and information available to establish reasonable triage categories and safe wait times for common cardiovascular services and procedures through a series of commentaries. The present commentary discusses the rationale for access benchmarks for cardiac catheterization and revascularization procedures for patients with stable angina, and access benchmarks for cardiac catheterization and surgery for patients with valvular heart disease. Literature on standards of care, wait times and wait list management was reviewed. A survey of cardiac centres in Canada was performed to develop an inventory of current practices in identifying and triaging patients. The Working Group recommends the following medically acceptable wait times for access to cardiac catheterization: 14 days for symptomatic aortic stenosis and six weeks for patients with stable angina and other valvular disease. For percutaneous coronary intervention in stable patients with high-risk anatomy, immediate revascularization or a wait time of 14 days is recommended; six weeks is recommended for all other patients. The target for bypass surgery in those with high-risk anatomy or valve surgery in patients with symptomatic aortic stenosis is 14 days; for all others, the target is six weeks. All stakeholders must affirm the appropriateness of these standards and work continuously to achieve them. There is an ongoing need to continually reassess current risk stratification methods to limit adverse events in patients on waiting lists and assist clinicians in triaging patients for invasive therapies.

Angioplasty, Balloon, Coronary↗
PubMedDate not supplied

Developmental toxicity of butyl benzyl phthalate in the rat using a multiple dose study design.

The developmental toxicity of butyl benzyl phthalate (BBP) was investigated in the rat using ten dose groups between 270 and 2100 mg/kg/day. Exposure was by daily gavage from gestation day 5 through 16 or gestation day 5 through 20. Dose-response data were analyzed using the benchmark approach by fitting dose-response models to the various endpoints. BBP induced increased liver and kidney weights in dams, accompanied by liver enzyme increases in maternal serum. Extramedullary hematopoiesis, which was already substantial in control pregnant animals, was increased after BBP treatment. Fetotoxicity included increased resorptions, reduced fetal weights, increased incidence of skeletal anomalies, and reduced fetal testis weights in the presence of an increased incidence of retarded testicular descent. As embryotoxicity was found at lower dosages compared to observed maternal toxicity, BBP appeared to be a specifically embryotoxic compound. The extended exposure protocol (gestation day 5 through 20) appeared more sensitive for measuring fetotoxic effects. We recommend the use of more doses in toxicity tests, together with the benchmark approach as an appropriate and more accurate method for analyzing dose-response data compared to the NOAEL approach.

Abnormalities, Drug-Induced↗