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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↗
PubMed1996

Matching using estimated propensity scores: relating theory to practice.

Matched sampling is a standard technique in the evaluation of treatments in observational studies. Matching on estimated propensity scores comprises an important class of procedures when there are numerous matching variables. Recent theoretical work (Rubin, D. B. and Thomas, N., 1992, The Annals of Statistics 20, 1079-1093) on affinely invariant matching methods with ellipsoidal distributions provides a general framework for evaluating the operating characteristics of such methods. Moreover, Rubin and Thomas (1992, Biometrika 79, 797-809) uses this framework to derive several analytic approximations under normality for the distribution of the first two moments of the matching variables in samples obtained by matching on estimated linear propensity scores. Here we provide a bridge between these theoretical approximations and actual practice. First, we complete and refine the nomal-based analytic approximations, thereby making it possible to apply these results to practice. Second, we perform Monte Carlo evaluations of the analytic results under normal and nonnormal ellipsoidal distributions, which confirm the accuracy of the analytic approximations, and demonstrate the predictable ways in which the approximations deviate from simulation results when normal assumptions are violated within the ellipsoidal family. Third, we apply the analytic approximations to real data with clearly nonellipsoidal distributions, and show that the theoretical expressions, although derived under artificial distributional conditions, produce useful guidance for practice. Our results delineate the wide range of settings in which matching on estimated linear propensity scores performs well, thereby providing useful information for the design of matching studies. When matching with a particular data set, our theoretical approximations provide benchmarks for expected performance under favorable conditions, thereby identifying matching variables requiring special treatment. After matching is complete and data analysis is at hand, our results provide the variances required to compute valid standard errors for common estimators.

Analysis of Variance↗
PubMedDate not supplied

[Equity and fairness in the Mexican health system reform].

OBJECTIVE: To assess the equity and fairness of the Mexican health system reform that occurred in the late 1990's. MATERIAL AND METHODS: The Mexican reform process was evaluated using the benchmark-system designed by Daniels et al. This benchmark system was adapted to the Mexican setting by adding specific indicators. A documentary review of the Mexican reform process was conducted to score its performance for each benchmark. RESULTS: Except for housing and nutrition components, the reform included few actions related to health determinants. For health care, the main reform initiatives were those related to extending the coverage of essential health services and decentralizing health care provision to the states. Reform initiatives included few activities related to fair financing, tiering, emphasis on second and third level care, accountability, and transparency. CONCLUSIONS: The late nineties reform of the Mexican health system had some positive effect on access of the poor to health care and administrative efficiency, but little impact on fair financing, quality of care, and democratic governance. The English version of this paper is available at: http://www.insp.mx/salud/index.html.

Adolescent↗
PubMed2003

Containing revenue-cycle costs.

Healthcare organizations can achieve revenue-cycle improvement while maintaining optimum staffing levels by taking a three-step approach-developing a plan, measuring costs, and using benchmarks to measure performance. Planned cost reductions can be achieved without a negative impact on the organization. Cost-reduction strategies should look at purchased services, staffing, and the cost-to-collect ratio. Healthcare organizations should reach target performance levels before implementing a cost-reduction strategy.

Accounts Payable and Receivable↗
PubMedDate not supplied

Quality of care for hypertension and diabetes in federal- versus commercial-managed care organizations.

Initiatives to improve quality in primary care include use of performance measures to benchmark health care organizations. We looked for an objective way to compare primary care quality in the Veterans Affairs (VA) with that of private sector. We analyzed performance measures of the Health Plan and Employer Data Information Set (HEDIS) used in ambulatory care for hypertension and diabetes and compared a sample data from a network of VA hospitals with those from National Committee for Quality Assurance's The State of Health Care Quality 2002 Report. The VA data were comparable to the national data. Performance on the hypertension control measure was slightly below the HEDIS national average but better than the regional commercial average. VA's performance on all diabetes measures was higher. Although the VA network had a large influx in patient base recently, the quality of outpatient care in hypertension and diabetes as measured by standardized performance indicators in the network compared favorably with commercial Health Maintenance Organizations in the private sector.

Diabetes Mellitus↗
PubMed2001

Comparison of RTP dose distributions in heterogeneous phantoms with the BEAM Monte Carlo simulation system.

Therapeutic treatment plan evaluation is often based on examining the radiotherapy treatment planning (RTP) system dose distributions in the target and surrounding normal structures. To study the effects of tissue inhomogeneities on photon dose distributions, we compared FOCUS RTP system dose distributions from the measurement-based Clarkson and model-based MultiGrid Superposition (MGS) algorithms with those from the BEAM Monte Carlo code system in a set of heterogeneous phantoms. The phantom inhomogeneities mimic relevant clinical treatment sites, which include lung slab, lung-bone slab, bone-lung slab, mediastinum, and tumor geometries. The benchmark comparisons were performed in lung densities of 0.20 and 0.31 g/cm3, and a bone density of 2.40 g/cm3 for 5x5 cm2 and 10x10 cm2, 6- and 15-MV photon beams. Benchmark comparison results show that the MGS model and BEAM doses match better than 3% or 3 mm, and the MGS model is more accurate than the Clarkson model in all phantoms. The MGS model, unlike the Clarkson model, predicts the build-down and build-up of dose near tissue interfaces and penumbra broadening in lung associated with high energy beams. The Clarkson model overestimates the dose in lung by a maximum of 10% compared to BEAM. Dose comparisons suggest turning-off the effective path length inhomogeneity correction in the Clarkson model for lung treatments.

Algorithms↗
PubMed2005

Errors in laboratory medicine: practical lessons to improve patient safety.

CONTEXT: Patient safety is influenced by the frequency and seriousness of errors that occur in the health care system. Error rates in laboratory practices are collected routinely for a variety of performance measures in all clinical pathology laboratories in the United States, but a list of critical performance measures has not yet been recommended. The most extensive databases describing error rates in pathology were developed and are maintained by the College of American Pathologists (CAP). These databases include the CAP's Q-Probes and Q-Tracks programs, which provide information on error rates from more than 130 interlaboratory studies. OBJECTIVES: To define critical performance measures in laboratory medicine, describe error rates of these measures, and provide suggestions to decrease these errors, thereby ultimately improving patient safety. SETTING: A review of experiences from Q-Probes and Q-Tracks studies supplemented with other studies cited in the literature. DESIGN: Q-Probes studies are carried out as time-limited studies lasting 1 to 4 months and have been conducted since 1989. In contrast, Q-Tracks investigations are ongoing studies performed on a yearly basis and have been conducted only since 1998. Participants from institutions throughout the world simultaneously conducted these studies according to specified scientific designs. The CAP has collected and summarized data for participants about these performance measures, including the significance of errors, the magnitude of error rates, tactics for error reduction, and willingness to implement each of these performance measures. MAIN OUTCOME MEASURES: A list of recommended performance measures, the frequency of errors when these performance measures were studied, and suggestions to improve patient safety by reducing these errors. RESULTS: Error rates for preanalytic and postanalytic performance measures were higher than for analytic measures. Eight performance measures were identified, including customer satisfaction, test turnaround times, patient identification, specimen acceptability, proficiency testing, critical value reporting, blood product wastage, and blood culture contamination. Error rate benchmarks for these performance measures were cited and recommendations for improving patient safety presented. CONCLUSIONS: Not only has each of the 8 performance measures proven practical, useful, and important for patient care, taken together, they also fulfill regulatory requirements. All laboratories should consider implementing these performance measures and standardizing their own scientific designs, data analysis, and error reduction strategies according to findings from these published studies.

Clinical Laboratory Techniques↗
PubMed2006

Quality improvement in healthcare in New Zealand. Part 1: what would a high-quality healthcare system look like?

This Special Series attempts to define what a high-quality healthcare system would look like for New Zealand. The Series focuses on the dimensions of a quality service - safety, access, equity, effectiveness, efficiency, and patient centeredness - not only elucidating in plain language what these dimensions are, but how they might be measured and improved. The central premise is that clinicians need to become involved in measuring and improving the quality of healthcare provided. To assist clinicians, the Series will cover ways to measure the effectiveness of care they provide with articles on clinical audit and clinical indicators, and also to examine the pros and cons of the measures of efficiency used by the funders - organisational performance indicators, and benchmarking. The Series will wrap up with a vision of how we might continue to improve quality through embedding clinical governance into District Health Boards, so that their performance is measured in both quality and fiscal terms.

Health Knowledge, Attitudes, Practice↗
PubMed2000

Interlibrary loan in primary access libraries: challenging the traditional view.

INTRODUCTION: Primary access libraries serve as the foundation of the National Network of Libraries of Medicine (NN/LM) interlibrary loan (ILL) hierarchy, yet few published reports directly address the important role these libraries play in the ILL system. This may reflect the traditional view that small, primary access libraries are largely users of ILL, rather than important contributors to the effectiveness and efficiency of the national ILL system. OBJECTIVE: This study was undertaken to test several commonly held beliefs regarding ILL system use by primary access libraries. HYPOTHESES: Three hypotheses were developed. HI: Colorado and Wyoming primary access libraries comply with the recommended ILL guideline of adhering to a hierarchical structure, emphasizing local borrowing. H2: The closures of two Colorado Council of Medical Librarians (CCML) primary access libraries in 1996 resulted in twenty-three Colorado primary access libraries' borrowing more from their state resource library in 1997. H3: The number of subscriptions held by Colorado and Wyoming primary access libraries is positively correlated with the number of items they loan and negatively correlated with the number of items they borrow. METHODS: The hypotheses were tested using the 1992 and 1997 DOCLINE and OCLC data of fifty-four health sciences libraries, including fifty primary access libraries, two state resource libraries, and two general academic libraries in Colorado and Wyoming. The ILL data were obtained electronically and analyzed using Microsoft Word 98, Microsoft Excel 98, and JMP 3.2.2. RESULTS: CCML primary access libraries comply with the recommended guideline to emphasize local borrowing by supplying each other with the majority of their ILLs, instead of overburdening libraries located at higher levels in the ILL hierarchy (H1). The closures of two CCML primary access libraries appear to have affected the entire ILL system, resulting in a greater volume of ILL activity for the state resource library and other DOCLINE libraries higher up in the ILL hierarchy and highlighting the contribution made by CCML primary access libraries (H2). CCML primary access libraries borrow and lend in amounts that are proportional to their collection size, rather than overtaxing libraries at higher levels in the ILL hierarchy with large numbers of requests (H3). LIMITATIONS: The main limitations of this study were the small sample size and the use of data collected for another purpose, the CCML ILL survey. CONCLUSIONS: The findings suggest that there is little evidence to support several commonly held beliefs regarding ILL system use by primary access libraries. In addition to validating the important contributions made by primary access libraries to the national ILL system, baseline data that can be used to benchmark current practice performance are provided.

Benchmarking↗
PubMed2003

Benchmarking for best practice environmental management.

Benchmarking of environmental performance to demonstrate the achievement of best practice environmental management is a component of a new form of licensing of industrial discharges in Western Australia. The paper describes the approaches to benchmarking for the critical environmental issues for an alumina refinery and wastewater treatment plant. It also describes the lessons learnt from the benchmarking process on appropriate methods, the benefits and difficulties in the benchmarking process, and changes that would assist benchmarking for best practice environmental management.

Aluminum Oxide↗
PubMed2004

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.

MOTIVATION: Prediction of which peptides will bind a specific major histocompatibility complex (MHC) constitutes an important step in identifying potential T-cell epitopes suitable as vaccine candidates. MHC class II binding peptides have a broad length distribution complicating such predictions. Thus, identifying the correct alignment is a crucial part of identifying the core of an MHC class II binding motif. In this context, we wish to describe a novel Gibbs motif sampler method ideally suited for recognizing such weak sequence motifs. The method is based on the Gibbs sampling method, and it incorporates novel features optimized for the task of recognizing the binding motif of MHC classes I and II. The method locates the binding motif in a set of sequences and characterizes the motif in terms of a weight-matrix. Subsequently, the weight-matrix can be applied to identifying effectively potential MHC binding peptides and to guiding the process of rational vaccine design. RESULTS: We apply the motif sampler method to the complex problem of MHC class II binding. The input to the method is amino acid peptide sequences extracted from the public databases of SYFPEITHI and MHCPEP and known to bind to the MHC class II complex HLA-DR4(B1*0401). Prior identification of information-rich (anchor) positions in the binding motif is shown to improve the predictive performance of the Gibbs sampler. Similarly, a consensus solution obtained from an ensemble average over suboptimal solutions is shown to outperform the use of a single optimal solution. In a large-scale benchmark calculation, the performance is quantified using relative operating characteristics curve (ROC) plots and we make a detailed comparison of the performance with that of both the TEPITOPE method and a weight-matrix derived using the conventional alignment algorithm of ClustalW. The calculation demonstrates that the predictive performance of the Gibbs sampler is higher than that of ClustalW and in most cases also higher than that of the TEPITOPE method.

Algorithms↗
PubMed2000

Determining the artifact sensitivity of recent pulse oximeters during laboratory benchmarking.

This study aimed to investigate and compare the performance of the algorithms contained in the newest generation of pulse oximeters (Masimo SET in IVY2000, Nellcor Oxismart N-3000, Agilent M3 rev. B) against a traditional pulse oximeter (Agilent CMS rel. A.0). The benchmark was performed in an efficient and reproducible way in the laboratory environment using patient signal recordings complemented by a two-hand volunteer motion test. A novel method of creating artifact/reference signal pairs from a clinical database, the noise-mix-composition (NMC), was developed. The new method enabled the simulation of critical clinical situations in a more realistic way than the usual two hand volunteer studies. An advantage of the laboratory tests over live clinical studies was that a continuous saturation reference was available, allowing accurate on-going determination of the SpO2 error. A new quantitative performance measure, the non-performance index (NPI), was developed and applied to the benchmark results. It covers the 3 performance aspects of a pulse oximeter: (1) SpO2 accuracy, (2) pulse rate accuracy and (3) drop out times. These factors were weighted according to clinical importance determined by a survey. During the restricted conditions of steady state and forced motion test on healthy volunteers Masimo/Ivy's pulse oximeter performed best with a 2.6 fold improvement over the conventional technology. Clear improvements were also found for Agilent's M3 (1.6 fold) and Nellcor's N-3000 (1.6 fold). In contrast, the clinically oriented NMC study yielded the best performance improvement--as measured in NPI numbers--for Agilent's M3 rev. B (1.6 fold) and due to more frequent SpO2 errors only 1.5 for Masimo and 1.3 for N-3000. A large difference was found for the dropout rate: the lowest was achieved by Masimo (3.0% of total time), the largest by Nellcor N-3000 (24.1% of total time), a factor which was rated high by clinicians. Very pronounced improvements (between 2.3 and 3.4 fold) on all of the newer devices were found for the pulse rate. The NMC turned out to be a very useful tool for generating a standard signal set for algorithm development and benchmarking purposes that eliminates repetitive clinical testing in early stages. The applicability of its results needs confirmation by clinical live studies.

Artifacts↗
PubMedDate not supplied

Key performance indicators to assess laboratory operations. Action-packed benchmarking with HBSI (HBS International Inc.).

The first article of this series highlighted the five most widely used performance measurement systems for comparing laboratory and clinical department operations. This column has since taken an in-depth tour of two of the systems, the MECON PEERx and the Laboratory Management Index Program. We also have taken a slight detour to discuss the ORYX initiative, which has been mandated for certain types of health-care organizations accredited by the Joint Commission. In this issue we return to a more detailed analysis of one of the five most commonly used benchmarking systems for clinical services, HBS International, Inc.

Benchmarking↗
PubMed2026

Fairness-aware supervised hierarchical contrastive semantic learning for sexual dimorphism analysis.

MOTIVATION: Sexual dimorphism is a fundamental biological determinant driving systematic differences in disease susceptibility, progression, and clinical outcomes. However, current sex-combined AI-based genomic models often exhibit algorithmic bias and fail to capture these sex-specific mechanisms, creating a critical barrier to unbiased precision medicine. Ensuring fairness in the context of sexual dimorphism requires understanding and addressing the distinct biological mechanisms functioning in each sex, rather than focusing solely on equalizing predictive performance. RESULTS: We propose a fairness-aware supervised hierarchical contrastive learning approach, called FairHICON, to discover unbiased sex-common and sex-specific predictive features. Evaluations on cancer and asthma transcriptomic datasets demonstrate that FairHICON significantly outperforms state-of-the-art benchmarks, improving predictive performance by up to 9% while effectively reducing the performance gap between male and female sexes. Furthermore, prognostic validation confirms that the identified sex-specific pathways stratify patient survival significantly better within their corresponding sex groups. This validates FairHICON to elucidate the molecular heterogeneity of sexual dimorphism, advancing inclusive precision medicine. AVAILABILITY AND IMPLEMENTATION: The source code and data is available at https://github.com/datax-lab/FairHICON.

Sex Characteristics↗
PubMed1997

Asthma: benchmarking for quality improvement.

BACKGROUND: Linked medical and pharmacy claims can be used to identify patients with asthma and benchmark current practice standards. METHOD: This was a 3-year study of five independent practice association style health maintenance organizations with an annual enrollment of 870,000. More than 28,000 members were identified with claims for asthma. OBJECTIVE: The intent of this study was to benchmark current asthma practice. Before quality improvement projects can be implemented baseline data are required. RESULTS: The prevalence of asthma varied by geographic regions. Specialty care was associated with greater use of anti-inflammatory medications and more refills of these drugs. Refill rates for inhaled corticosteroids for all patients was low. Specialty care of asthmatic members was associated with a lower rate of emergency service events and hospitalizations. CONCLUSIONS: Linked medical and pharmacy claims' databases can be used to benchmark current practice performance and serve as a reference for quality improvement programs. Appropriate use of specialty care may improve asthma outcomes.

Adolescent↗
PubMed2006

Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides.

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.

Cobalt↗
PubMed2005

Assessing the limits of genomic data integration for predicting protein networks.

Genomic data integration--the process of statistically combining diverse sources of information from functional genomics experiments to make large-scale predictions--is becoming increasingly prevalent. One might expect that this process should become progressively more powerful with the integration of more evidence. Here, we explore the limits of genomic data integration, assessing the degree to which predictive power increases with the addition of more features. We focus on a predictive context that has been extensively investigated and benchmarked in the past-the prediction of protein-protein interactions in yeast. We start by using a simple Naive Bayes classifier for integrating diverse sources of genomic evidence, ranging from coexpression relationships to similar phylogenetic profiles. We expand the number of features considered for prediction to 16, significantly more than previous studies. Overall, we observe a small, but measurable improvement in prediction performance over previous benchmarks, based on four strong features. This allows us to identify new yeast interactions with high confidence. It also allows us to quantitatively assess the inter-relations amongst different genomic features. It is known that subtle correlations and dependencies between features can confound the strength of interaction predictions. We investigate this issue in detail through calculating mutual information. To our surprise, we find no appreciable statistical dependence between the many possible pairs of features. We further explore feature dependencies by comparing the performance of our simple Naive Bayes classifier with a boosted version of the same classifier, which is fairly resistant to feature dependence. We find that boosting does not improve performance, indicating that, at least for prediction purposes, our genomic features are essentially independent. In summary, by integrating a few (i.e., four) good features, we approach the maximal predictive power of current genomic data integration; moreover, this limitation does not reflect (potentially removable) inter-relationships between the features.

Algorithms↗