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PubMed2000

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

The biological role, biochemical function, and structure of uncharacterized protein sequences is often inferred from their similarity to known proteins. A constant goal is to increase the reliability, sensitivity, and accuracy of alignment techniques to enable the detection of increasingly distant relationships. Development, tuning, and testing of these methods benefit from appropriate benchmarks for the assessment of alignment accuracy.Here, we describe a benchmark protocol to estimate sequence-to-sequence and sequence-to-structure alignment accuracy. The protocol consists of structurally related pairs of proteins and procedures to evaluate alignment accuracy over the whole set. The set of protein pairs covers all the currently known fold types. The benchmark is challenging in the sense that it consists of proteins lacking clear sequence similarity. Correct target alignments are derived from the three-dimensional structures of these pairs by rigid body superposition. An evaluation engine computes the accuracy of alignments obtained from a particular algorithm in terms of alignment shifts with respect to the structure derived alignments. Using this benchmark we estimate that the best results can be obtained from a combination of amino acid residue substitution matrices and knowledge-based potentials.

Algorithms↗

PubMed2002

Effects of zinc contamination on a natural nematode community in outdoor soil mesocosms.

The effect of zinc on the indigenous nematode fauna of a sandy soil was determined in an experimentally contaminated outdoor field plot. The aims of the study were to describe and quantify the changes in density of separate nematode taxa and total nematodes, and the changes in the number of taxa, species diversity, community maturation, and species composition in response to zinc exposure with time, and to compare the observed responses with benchmark concentrations for soil as derived from the species sensitivity distribution (SSD) for zinc toxicity. Speciation of zinc in pore water was considered and CaCl2-exchangeable zinc concentrations were used as a measure of the bioavailable zinc fraction. After contamination, a reduction of total zinc and an increase of labile sorbed zinc over time occurred, concurrent with various changes in soil and biological characteristics. Data analyses on the nematode species revealed different sensitivity levels for several population and community endpoints to zinc exposure. Based on no observed effect concentration (NOEC) values, the most sensitive community-level response was obtained with principal response curve (PRC) analysis, which incorporates all density data in a single analysis. The PRC-based community NOECs were 56, 100, and 100 mg total Zn/kg dry soil after 3, 10, and 22 months of exposure, respectively. Based on 0.01 M CaCl2-exchangeable zinc, the community response appeared to increase, as NOECs were 4.9, 4.4, and 0.67 mg exchangeable Zn/kg dry weight. Total density was least sensitive, followed by diversity of taxa and the Shannon-Wiener index. NOECs for separate species covered a broad range from sensitive to tolerant species. This range of sensitivities was similar to the one found for other species groups tested in the field plot soil. A comparison was made between benchmark concentrations HC5 and HC50 derived from the general SSD of soil organisms for zinc and the nematode response data. These comparisons roughly confirm the predictions of the SSD model, that is, the community NOEC is in agreement with the benchmark that should protect the soil ecosystem's integrity, and large adverse effects were found at the benchmark derived for setting remediation urgency.

Animals↗

PubMed1990

A review of the Buehler guinea pig skin sensitization test and its use in a risk assessment process for human skin sensitization.

The Buehler test is a valuable procedure for screening the sensitization potential of chemicals prior to human exposure. Our experience of over 20 years has shown it to be effective in detecting strong, moderate, and most weak sensitizers. The topical exposure inherent in the Buehler test allows it to be utilized to investigate dose responses, cross reactivity between structurally related chemicals, and the sensitization potential of contaminants in raw material mixtures. For safety assessment purposes, Buehler test results provide an initial indication of the sensitization potential of the material in question under relevant, but exaggerated, exposure conditions. These results can be compared to results on benchmark chemicals to assess sensitization risk for subsequent human exposure. Optimizing the sensitivity of the Buehler test requires adherence to the published methodology and proper interpretation of the challenge and rechallenge data obtained. Adjuvant-type test methods are generally considered to be more sensitive than topical methods. However, when done properly, topical test procedures such as the Buehler test or the open epicutaneous test can accurately detect most chemicals with any realistic potential for sensitizing humans by the topical route. Moreover, from a risk assessment perspective, these topical tests avoid the problems of overestimating the weak sensitization potential of many topically applied materials or underestimating the sensitization potential of very strong sensitizers; both are potential concerns with invasive adjuvant-type test methods. The Buehler test or other topical test methods are particularly valuable for comparative sensitization risk assessment since human sensitization data on benchmark materials are all derived from topical exposure. The risk assessment is developed by comparing the guinea pig data on the new material versus relevant benchmark chemicals or formulations and also by evaluating the existing human sensitization data on the benchmark material. These data are then utilized to predict human sensitization risk from topical exposure to the new material. Confirmation of human safety can be derived from human repeat insult patch testing (HRIPT) and other clinical tests such as the product use test and the diagnostic patch test. Utilized in this manner, the Buehler test is an integral component of an overall skin sensitization safety assessment program for a new chemical or product formulation.

Animals↗

PubMed2004

Using a visual plate waste study to monitor menu performance.

Two visual plate waste studies were conducted in 1-week phases over a 1-year period in an acute care hospital. A total of 383 trays were evaluated in the first phase and 467 in the second. Food items were ranked for consumption from a low (1) to high (6) score, with a score of 4.0 set as the benchmark denoting a minimum level of acceptable consumption. In the first phase two entrees, four starches, all of the vegetables, sliced white bread, and skim milk scored below the benchmark. As a result six menu items were replaced and one was modified. In the second phase all entrees scored at or above 4.0, as did seven vegetables, and a dinner roll that replaced sliced white bread. Skim milk continued to score below the benchmark. A visual plate waste study assists in benchmarking performance, planning menu changes, and assessing effectiveness.

Food Preferences↗

PubMed2005

Cytochrome b and Bayesian inference of whale phylogeny.

In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.

Animals↗

PubMed2002

Thresholds for human detection of patient setup errors in digitally reconstructed portal images of prostate fields.

PURPOSE: Computer-assisted methods to analyze electronic portal images for the presence of treatment setup errors should be studied in controlled experiments before use in the clinical setting. Validation experiments using images that contain known errors usually report the smallest errors that can be detected by the image analysis algorithm. This paper offers human error-detection thresholds as one benchmark for evaluating the smallest errors detected by algorithms. Unfortunately, reliable data are lacking describing human performance. The most rigorous benchmarks for human performance are obtained under conditions that favor error detection. To establish such benchmarks, controlled observer studies were carried out to determine the thresholds of detectability for in-plane and out-of-plane translation and rotation setup errors introduced into digitally reconstructed portal radiographs (DRPRs) of prostate fields. METHODS AND MATERIALS: Seventeen observers comprising radiation oncologists, radiation oncology residents, physicists, and therapy students participated in a two-alternative forced choice experiment involving 378 DRPRs computed using the National Library of Medicine Visible Human data sets. An observer viewed three images at a time displayed on adjacent computer monitors. Each image triplet included a reference digitally reconstructed radiograph displayed on the central monitor and two DRPRs displayed on the flanking monitors. One DRPR was error free. The other DRPR contained a known in-plane or out-of-plane error in the placement of the treatment field over a target region in the pelvis. The range for each type of error was determined from pilot observer studies based on a Probit model for error detection. The smallest errors approached the limit of human visual capability. The observer was told what kind of error was introduced, and was asked to choose the DRPR that contained the error. Observer decisions were recorded and analyzed using repeated-measures analysis of variance. RESULTS: The thresholds of detectability averaged over all observers were approximately 2.5 mm for in-plane translations, 1.6 degrees for in-plane rotations, 1 degrees for out-of-plane rotations, and 8% change in magnification for out-of-plane translations along the central axis. When one inexperienced observer is excluded, the average threshold for change in magnification is 5%. Experienced observers tended to perform better, but differences between groups were not statistically significant. Thresholds were computed as averages over all observers. Because of the broad range of observer capabilities, some detection tasks were too difficult for some observers, leading to missing threshold values in our data analysis. The missing values were excluded from computation of the average thresholds reported above. The effect of the missing values is to bias the average values toward the best human performance. CONCLUSIONS: Under favorable conditions, humans can detect small errors in setup geometry. The thresholds for error detection reported in this study are believed to represent rigorous but reasonable benchmarks that can be incorporated into studies evaluating algorithms for computer-assisted detection of setup errors in electronic portal images.

Diagnostic Errors↗

PubMed2001

Measuring and improving patients' and families' perceptions of care in a system of pediatric hospitals.

BACKGROUND: Shriners Hospitals for Children (SHC) is a network of 22 pediatric specialty hospitals that provide medical care free of charge to children up to 18 years of age and that serve as referral centers for children with complex orthopedic and burn problems. In 1998 the SHC system began using The Picker Institute's Patient and Family Perception of Care inpatient survey throughout its hospitals. SYSTEMWIDE IMPLEMENTATION: A broad-based implementation plan was developed to promote acceptance of the perception of care topic and provide education on performance improvement. In 1999 a work group was formed to prioritize areas for improvement, survey benchmark hospitals, and identify best practices in benchmark hospitals. This work group first focused on the dimensions of Partnership Between Families and Clinicians and Information and Education to the Child. In May 1999 the work group began the task of identifying best practices in these two priority dimensions from the SHC benchmark hospitals. Surveys were submitted to those hospitals, asking what they perceived as being the reasons they scored well in those areas. The results of these surveys were used to identify key practices in these benchmark hospitals that are of significant importance in patient and family perceptions of quality care. NEXT STEPS: The challenge is to facilitate cross-facility interactions to understand and adopt best practices. Focus groups will be conducted to further delineate the dimensions with higher problem scores. The SHC system plans to expand the patient surveys to outpatients, to allow for the evaluation of the full complement of hospital patients.

Burn Units↗

PubMed2005

Adsorption characteristics of tripodal thiol-functionalized porphyrins on gold.

X-ray photoelectron and Fourier transform infrared spectroscopy studies are reported for self-assembled monolayers (SAMs) of two tripodal thiol-functionalized metalloporphyrins (Zn and Cu) and three benchmark tripods on gold substrates. The tripodal unit common to all five molecules is 1-(phenyl)-1,1,1-tris(4-mercaptomethylphenyl)methane (Tpd). Both porphyrins contain S-acetyl-protected thiols and are linked to the 4-position of the phenyl ring of Tpd via a phenylethyne group. The benchmark molecules include (1) two tripods containing a bromine atom at the 4-position of the apical phenyl ring, one a free thiol and the other its S-acetyl-protected analogue, and (2) a S-acetyl-protected tripod containing a phenylethyne unit at the 4-position of the apical phenyl group. Together, the spectroscopic studies reveal that none of the five tripodal molecules bond to the gold surface via all three sulfur atoms. Instead, the average number of bound thiols ranges from 1.5 to 2, with the porphyrinic molecules generally falling at the middle to upper end of the range and the smallest benchmark tripods falling at the lower end. Similar surface binding is found for the S-acetyl-protected and free benchmark tripods, indicating that the presence of the protecting group does not influence binding. Furthermore, the surface binding characteristics of the SAMs are not sensitive to deposition conditions such as solvent type, deposition time, or temperature of the solution.

Adsorption↗

PubMed2006

Can delivery room management impact the length of hospital stay in premature infants?

OBJECTIVES: To evaluate the impact of initiating early nasal continuous positive airway pressure (ENCPAP) on the length of hospital stay (LOS) for the very low birth weight (VLBW) infants. STUDY DESIGN: LOS at the George Washington University Hospital (GW) after the institution of ENCPAP policy was compared to benchmark values using two-tail t-tests. The incidence of neonatal morbidity was calculated using Bonferroni corrected 95% confidence interval as compared to benchmark rates (alpha=0.001). Comparisons were repeated after stratification of the population into four birth weight subcategories: group A (GrpA) (501 to 750 g), GrpB (751 to 1000 g), GrpC (1001 to 1250 g) and GrpD (1251 to 1500 g). RESULTS: We studied 228 consecutive VLBW infants (birth weight: 995+/-294 g and gestational age: 27.7+/-2.7 weeks). Compared to benchmark values, the GW experience was associated with a significant reduction of 5.1 days in LOS (55.9+/-25.2 vs 61+/-32 days; P=0.04). The decrease in LOS was consistent in all subgroups, but was most noticeable in infants of the smallest weight subcategory (LOS in GrpA=86+/-21 vs 104+/-32, P=0.004; in GrpB=69.9+/-16.7 vs 79+/-27, P=0.018; in GrpC=48.2+/-13 vs 56+/-22, P<0.001 and in GrpD=31.7+/-12.5 vs 40+/-19, P=0.003). In the overall population, a lower incidence of chronic lung disease (CLD) (17.8 vs 29%, P<0.001) was also noted. There were no differences in mortality rates (9 vs 14%), or the incidence of necrotizing enterocolitis (NEC) (8 vs 6%) or intraventricular hemorrhage (6.2 vs 9%) between GW and the established benchmark rates. CONCLUSION: ENCPAP may reduce LOS in VLBW infants in our study population. This relatively shorter LOS was associated with a lower incidence of CLD, which may be a contributing factor.

Continuous Positive Airway Pressure↗

PubMed2005

ORANGE: a Monte Carlo dose engine for radiotherapy.

This study presents data for the verification of ORANGE, a fast MCNP-based dose engine for radiotherapy treatment planning. In order to verify the new algorithm, it has been benchmarked against DOSXYZ and against measurements. For the benchmarking, first calculations have been done using the ICCR-XIII benchmark. Next, calculations have been done with DOSXYZ and ORANGE in five different phantoms (one homogeneous, two with bone equivalent inserts and two with lung equivalent inserts). The calculations have been done with two mono-energetic photon beams (2 MeV and 6 MeV) and two mono-energetic electron beams (10 MeV and 20 MeV). Comparison of the calculated data (from DOSXYZ and ORANGE) against measurements was possible for a realistic 10 MV photon beam and a realistic 15 MeV electron beam in a homogeneous phantom only. For the comparison of the calculated dose distributions and dose distributions against measurements, the concept of the confidence limit (CL) has been used. This concept reduces the difference between two data sets to a single number, which gives the deviation for 90% of the dose distributions. Using this concept, it was found that ORANGE was always within the statistical bandwidth with DOSXYZ and the measurements. The ICCR-XIII benchmark showed that ORANGE is seven times faster than DOSXYZ, a result comparable with other accelerated Monte Carlo dose systems when no variance reduction is used. As shown for XVMC, using variance reduction techniques has the potential for further acceleration. Using modern computer hardware, this brings the total calculation time for a dose distribution with 1.5% (statistical) accuracy within the clinical range (less then 10 min). This means that ORANGE can be a candidate for a dose engine in radiotherapy treatment planning.

Algorithms↗

PubMed2022

Improving risk indexes for Alzheimer's disease and related dementias for use in midlife.

Knowledge of a person's risk for Alzheimer's disease and related dementias (ADRDs) is required to triage candidates for preventive interventions, surveillance, and treatment trials. ADRD risk indexes exist for this purpose, but each includes only a subset of known risk factors. Information missing from published indexes could improve risk prediction. In the Dunedin Study of a population-representative New Zealand-based birth cohort followed to midlife (N = 938, 49.5% female), we compared associations of four leading risk indexes with midlife antecedents of ADRD against a novel benchmark index comprised of nearly all known ADRD risk factors, the Dunedin ADRD Risk Benchmark (DunedinARB). Existing indexes included the Cardiovascular Risk Factors, Aging, and Dementia index (CAIDE), LIfestyle for BRAin health index (LIBRA), Australian National University Alzheimer's Disease Risk Index (ANU-ADRI), and risks selected by the Lancet Commission on Dementia. The Dunedin benchmark was comprised of 48 separate indicators of risk organized into 10 conceptually distinct risk domains. Midlife antecedents of ADRD treated as outcome measures included age-45 measures of brain structural integrity [magnetic resonance imaging-assessed: (i) machine-learning-algorithm-estimated brain age, (ii) log-transformed volume of white matter hyperintensities, and (iii) mean grey matter volume of the hippocampus] and measures of brain functional integrity [(i) objective cognitive function assessed via the Wechsler Adult Intelligence Scale-IV, (ii) subjective problems in everyday cognitive function, and (iii) objective cognitive decline measured as residualized change in cognitive scores from childhood to midlife on matched Weschler Intelligence scales]. All indexes were quantitatively distributed and proved informative about midlife antecedents of ADRD, including algorithm-estimated brain age (β's from 0.16 to 0.22), white matter hyperintensities volume (β's from 0.16 to 0.19), hippocampal volume (β's from -0.08 to -0.11), tested cognitive deficits (β's from -0.36 to -0.49), everyday cognitive problems (β's from 0.14 to 0.38), and longitudinal cognitive decline (β's from -0.18 to -0.26). Existing indexes compared favourably to the comprehensive benchmark in their association with the brain structural integrity measures but were outperformed in their association with the functional integrity measures, particularly subjective cognitive problems and tested cognitive decline. Results indicated that existing indexes could be improved with targeted additions, particularly of measures assessing socioeconomic status, physical and sensory function, epigenetic aging, and subjective overall health. Existing premorbid ADRD risk indexes perform well in identifying linear gradients of risk among members of the general population at midlife, even when they include only a small subset of potential risk factors. They could be improved, however, with targeted additions to more holistically capture the different facets of risk for this multiply determined, age-related disease.

Alzheimer’s disease↗

PubMed2002

Potentiation of noise-induced hearing loss by low concentrations of hydrogen cyanide in rats.

Noise-induced hearing loss is the most prevalent occupational injury in the United States despite the adoption of clear permissible exposure limits and protocols for hearing conservation. This study identifies low-level chemical asphyxiant exposure as a risk factor capable of potentiating noise-induced hearing loss. Rats were exposed to 10, 30, and 50 ppm hydrogen cyanide (HCN) alone for 3.5 h (n = 28) or in combination with 2 h octave band noise exposure (100 dB(lin); n = 28). Additional groups received noise exposure alone (n = 16) and no treatment other than placement in an inhalation chamber with clean air and quiet (n = 16). Pure tone compound action potential (CAP) thresholds were determined 4 weeks following the exposure in order to assess pure tone auditory sensitivity and permanent threshold impairment. Cochleae from an additional 13 subjects were processed for light microscopy to permit assessment of hair cell loss. The results demonstrate that the noise exposure alone impaired CAP threshold by about 10 dB, averaged between 12-40 kHz, and produced a 5% loss of outer hair cells at the base of the cochlea, but no inner hair cell loss. The combined exposure to noise and HCN caused a cyanide dose-dependent CAP threshold impairment that exceeds the noise exposure alone. This effect reached statistical significance at a HCN level of 30 ppm. Combined exposure also produced more outer hair cell loss than noise alone. HCN alone did not cause significant hearing loss or hair cell loss. A risk assessment analysis was conducted for the auditory threshold data using benchmark dose software published by the U. S. EPA (BMDS version 1.3). A continuous model showed that the data could be described by a linear function. For a benchmark response corresponding to a 5 dB increase in auditory threshold above the effect of noise alone, the lower bound on the 95% confidence interval for the benchmark dose was 9 ppm. The benchmark dose that impaired auditory threshold 10% above the effect of noise alone had a lower bound of 2 ppm. The lower bound to the HCN dose that produced a 1 SD elevation in noise-induced hearing loss was 16 ppm. These exposure levels provide a range of concentrations below to slightly above the short-term exposure limit for HCN. However, if these levels are adjusted for an 8 h time-weighted average (TWA), the resulting levels are below the permissible exposure level (PEL) for HCN.

Animals↗

PubMed2001

Care management of work injuries: results of a 1-year pilot outcome assurance program.

A 1-year pilot study was conducted, linking the efforts of a workers' compensation managed care organization with those of an occupational health clinic and emergency department of manage work-related injuries and associated work disability. Sustained (> 90 day), injury-specific return-to-work outcomes, modified by job title, were compared with loosely managed and well-managed benchmarks. The mean return-to-work outcome, measured as lost workdays (LWDs), was 5.11 +/- 21.0 LWDs for 418 workers. These results exceeded benchmarks for both loosely managed care, 14.0 +/- 17.2 LWDs, P < 0.001 (8.9 fewer LWDs/case), and optimally case-managed care, 6.99 +/- 7.64 LWDs, P = 0.044 (1.9 fewer LWDs/case). An estimate of the value of these saved LWDs to the employers-at $200 per workday was $740,400 for the loosely managed benchmarks and $157,000 for the well-managed benchmarks. The Outcome Assurance Program virtually eliminated typical delays in the diagnosis and medical management of these injured workers.

Accidents, Occupational↗

PubMed2003

How reassuring are risk comparisons to pollution standards and emission limits?

Pollutant emissions or ambient levels are often justified by reference to a higher benchmark, such as a public health standard or permit limit. However, does this risk comparison persuade the public audiences to whom it is frequently directed that such pollution levels are "acceptable"? A substantial proportion of people living within one mile of New Jersey's industrial facilities, perhaps as much as half, is indeed reassured by a comparison to such benchmarks. Positive attitudes toward discharge limits were linked to speaking English at home; positive attitudes toward drinking water standards were associated with seeing local benefits of industry as outweighing its risks, not speaking English, and relative youth (49 years old or less). Three scenarios involving drinking water contamination varied pre- and post-treatment levels of the pollutant, though all post-treatment levels were below the standard. In all cases great concern was expressed, with no significant differences across scenarios; net benefits, being white, and non-English speaking were linked to lower concern. Relative trust seems a better explanation of different attitudes toward benchmark comparisons than varying levels of knowledge, but both hypotheses have drawbacks that merit further testing. These results imply that people with negative views of industry or government, the ones officials might most wish to reassure, will tend to doubt that regulatory benchmarks offer a valid risk comparison.

Adult↗

PubMed2005

The effect of a new toothpaste containing potassium nitrate and triclosan on gingival health, plaque formation and dentine hypersensitivity.

OBJECTIVES: The purpose of this study was to investigate the effect of a new toothpaste containing an antiplaque and antiinflammatory agent (0.3% triclosan), a desensitizing agent (5% potassium nitrate) and an anticaries agent (0.76% sodium monofluorophosphate (SMFP)) on gingival health, plaque formation and dentine hypersensitivity in a 12-week home study. The efficacy of the test toothpaste was compared with that of a control toothpaste containing 5% potassium nitrate and 0.76% SMFP and a benchmark product containing only 0.76% SMFP. MATERIAL AND METHODS: One hundred and two healthy volunteers, who had a minimum of 20 natural permanent teeth with no probing depth >4 mm and at least one sensitive tooth, participated in this study. Following enrollment, the subjects received a dental prophylaxis and instruction in brushing technique. After a 4-week pre-experimental phase, baseline gingival bleeding index (GBI), plaque index (PI) and visual analogue scales (VASs) indicating dentine hypersensitivity levels responding to tactile and air stimuli were assessed. The subjects were then randomly given one of the three toothpastes; test, control, or benchmark toothpaste, and a soft-filamented toothbrush for home use. The GBI, PI and VASs were re-examined at weeks 4 and 12. RESULTS: Overall, the GBI scores were significantly reduced compared with baseline in all groups (p<0.01). However, there was no significant difference in GBI score among the three comparison groups. The PI score decreased in the test group and benchmark group from baseline to the end of study, whereas there was no significant change in the control group. Post hoc comparison indicated that the PI score was not statistically different between the three groups. There was a significant difference between the three treatment groups for sensitivity. For both the tactile and air stimuli, the reductions in VAS sensitivity scores for the test group and the control group were significantly greater compared with the benchmark group. Although the sensitivity score for air stimulus decreased more rapidly from baseline to week 4 in the test group, there was no overall difference between the test group and the control group. CONCLUSIONS: This study demonstrated that the new toothpaste was effective in reducing dentine hypersensitivity. More studies are needed to further determine the potential interaction between triclosan and potassium nitrate in dentifrices.

Adult↗

PubMed2004

External validation of compliance to perfusion quality indicators.

PURPOSE: There exists a significant gap between the expected and delivered level of quality received in America's hospitals. As a result, clinical outcomes of critical services such as coronary artery bypass graft (CABG) surgery have received unparalleled scrutiny. Medical information technology companies like Solucient and insurance carriers such as Blue Cross of California have identified and published a list of hospitals that demonstrate superior quality and patient outcomes for CABG procedures. These 'benchmark' programs serve as a reminder that closing the quality gap is possible. Unfortunately, none of these rankings (report cards) provide programs that fail to achieve benchmark status with detailed information on the processes or methods necessary to improve performance. METHOD: After identifying hospitals within the Fresenius Medical Care Extracorporeal Alliance (FMCEA) system that were judged as top performers (benchmark programs) by either Solucient ('100 Top Cardiovascular Hospitals', Evanston, IL 60201) or Blue Cross of California ('Centers of Expertise', Newbury Park, CA 91320), 12 months of continuous collection of CPB-related quality indicator data were analyzed for compliance to the FMCEA evidence-based Quality Indicator Program (QIP). A comparison of compliance to the FMCEA CPB indicators was made between the benchmark FMCEA hospitals and the FMCEA peer group hospitals. RESULTS: Seven CPB process indicators were compared: 1) lowest sustained mean arterial pressure, 2) lowest sustained cardiac index, 3) lowest sustained mixed venous oxygen saturation, 4) lowest sustained hematocrit, 5) lowest activated clotting time, 6) highest sustained arterial blood temperature and 7) average sodium bicarbonate administered. Analysis of hospitals in the FMCEA system designated by Blue Cross of California as 'Centers of Expertise' revealed statistically significantly greater compliance (p < 0.05) in all but one CPB indicator. Hospitals in the FMCEA system designated by Solucient's '100 Top Cardiovascular Hospitals' listing revealed statistically significantly greater compliance to all but three CPB quality indicators. CONCLUSIONS: Successful compliance with the majority of FMCEA CPB process indicators correlates with external recognition from two report card systems demonstrating superior hospital performance. Analysis of compliance to process indicators may provide useful guidelines to improve the standard of care in CABG surgery in many hospitals.

Coronary Artery Bypass↗

PubMed1999

Hidden Markov models that use predicted secondary structures for fold recognition.

There are many proteins that share the same fold but have no clear sequence similarity. To predict the structure of these proteins, so called "protein fold recognition methods" have been developed. During the last few years, improvements of protein fold recognition methods have been achieved through the use of predicted secondary structures (Rice and Eisenberg, J Mol Biol 1997;267:1026-1038), as well as by using multiple sequence alignments in the form of hidden Markov models (HMM) (Karplus et al., Proteins Suppl 1997;1:134-139). To test the performance of different fold recognition methods, we have developed a rigorous benchmark where representatives for all proteins of known structure are matched against each other. Using this benchmark, we have compared the performance of automatically-created hidden Markov models with standard-sequence-search methods. Further, we combine the use of predicted secondary structures and multiple sequence alignments into a combined method that performs better than methods that do not use this combination of information. Using only single sequences, the correct fold of a protein was detected for 10% of the test cases in our benchmark. Including multiple sequence information increased this number to 16%, and when predicted secondary structure information was included as well, the fold was correctly identified in 20% of the cases. Moreover, if the correct secondary structure was used, 27% of the proteins could be correctly matched to a fold. For comparison, blast2, fasta, and ssearch identifies the fold correctly in 13-17% of the cases. Thus, standard pairwise sequence search methods perform almost as well as hidden Markov models in our benchmark. This is probably because the automatically-created multiple sequence alignments used in this study do not contain enough diversity and because the current generation of hidden Markov models do not perform very well when built from a few sequences.

Amino Acid Sequence↗

PubMed2003

Developing meaningful metrics of clinical productivity for military treatment facility anesthesiology departments and operative services.

Comparing clinical productivity is important for strategic planning and the evaluation of resource allocation in any large organization. This process of benchmarking performance allows for the comparison of groups with similar characteristics. However, this process is often difficult when comparing the operative service productivity of large and small military treatment facilities because of the significant heterogeneity in mission focus and case complexity. However, in this article, we describe the application of a new method of benchmarking operative service productivity based on normalizing data for operating room sites, cases, and total American Society of Anesthesiologists units produced per hour. We demonstrate how these benchmarks allow for valid comparisons of operative service productivity among these military treatment facilities and how the data could be used in expanding or contracting operating locations. In addition, these benchmarks are compared with those derived from the use of this system in the civilian sector.

Analysis of Variance↗