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At least 1,711 records · Page 95Linked to original sources
PubMed2004

EuCliD--a medical registry.

OBJECTIVES: The European Clinical Database EuCliD small star, filled has been developed as a tool for supervising selected quality indicators of about 200 European dialysis centers. Major efforts had to be made to comply with local and European laws regarding data security. METHOD: EuCliD is a Lotus Notes based flat-file database currently containing medical data of more than 14,000 dialysis patients from 10 European countries. Another 15,000 patients from 150 centers in 4 South-American countries will be added soon. Data are entered either manually or by means of interfaces to existing local data managing systems. This information is transferred to a central Lotus Notes Server. Data evaluation was performed with statistical tools like SPSS. RESULTS: EuCliD is used as a part of the CQI (Continuous Quality Improvement) management system of Fresenius Medical Care (FMC) dialysis units. Each participating dialysis center receives (currently every half year) benchmarking reports at a regular interval. The benchmark for all quality parameters is the weighted mean of the corresponding data of all centers. CONCLUSIONS: An obvious impact of data sampling and data evaluation on the quality of the treatments could be observed within the first one and a half years of working with EuCliD. This also concerns important outcome predictors like Kt/V and hemoglobin concentration as the outcome itself expressed in hospitalization days and survival rates. With the help of EuCliD the user is able to sample clinical data, identify problems, search for solutions with the aim of improving the dialysis treatment quality and guarantee a high-class treatment quality for all patients.

Benchmarking↗
PubMed2004

Correction of error in respiratory resistance measurements made with the flow-interruption technique during mechanical ventilation: evaluation of the puritan bennett 7200 and 840 ventilators.

BACKGROUND: Calculation of total inspiratory resistance (Rtot) for patients on ventilatory support is typically based on measurement of airflow velocity and airway opening pressure during end-inspiratory occlusion by the inspiratory valve in the ventilator. Systematic error is introduced into Rtot measurements because the inspiratory valve closes over a period of time (not instantaneously, so gas continues to flow into the circuit while the valve is shutting) and because the circuit tubing is a distensible compartment between the occluding valve and the respiratory system. The Rtot-measurement error can be minimized with a rapidly-shutting occlusion valve positioned at the airway opening, or, alternatively, by mathematical correction that accounts for the valve-closure period and circuit tubing characteristics. METHODS: In a bench study we measured Rtot with the Puritan Bennett 7200 and 840 ventilators (using the inspiratory valves that are built into those ventilators) and compared those measurements to measurements made with a rapidly-shutting valve at the airway opening. We deemed the rapid-occlusion-valve measurements the best available (benchmark) values. We also studied the closure characteristics of the ventilators' inspiratory occlusion valves and created equations for mathematical correction of Rtot values measured with those valves. RESULTS: Compared to the benchmark measurements, the measurements from the Puritan Bennett 7200 averaged 23.2% relative error and 2.6 cm H2O/L/s absolute error. Measurements from the Puritan Bennett 840 averaged 7.3% relative error and 1.0 cm H2O/L/s absolute error. Mathematical correction for the circuit tubing and valve-closure time reduced the average relative and absolute error to 3.0% and 0.4 cm H2O/L/s, respectively, for the Puritan Bennett 7200, and to 4.5% and 0.3 cm H2O/L/s, respectively, for the Puritan Bennett 840. CONCLUSIONS: The Puritan Bennett 840 measures Rtot more accurately than the Puritan Bennett 7200. Our equations to mathematically correct Rtot measurements made with the PB7200 and PB840 are useful in settings where very accurate Rtot measurements are necessary.

Airway Resistance↗
PubMed2004

Customer service and today's hospital security professional.

Customer service, benchmarking, and budget control have supplanted enforcement as the essential parts of hospital security operations, according to the author. In the article he emphasizes and illustrates the need for security satisfaction surveys and benchmarking to enable the budget process to go smoothly.

Benchmarking↗
PubMed2004

ED sees 50% reduction in time from triage to ED bed.

You can see dramatic real-world improvements with benchmarking. Some facilities benchmark by modeling a single facility with a successful program. Lehigh Valley Hospital in Allentown, PA, reduced its time from triage to ED bed from 37.8 minutes monthly average to 16.8 minutes monthly average. Saint Rita's Medical Center in Lima, OH, slashed overall length of stay from 190 minutes to 150 minutes.

Benchmarking↗
PubMed2005

A cross-sectional study of reproductive indices and fawn mortality in farmed white-tailed deer.

Data were obtained from a questionnaire administered to a random sample of Canadian and United States white-tailed deer (WTD) farmers. Reproductive indices and survival of fawns from birth until 1 y of age were examined. Major factors in limiting herd increase were a low reproductive rate (88 fawns per 100 does exposed to bucks) and a 30% mortality of fawns from birth until 1 y of age. The latter figure differs from reported mortality rates in fallow deer and red deer/wapiti. The unacceptably high neonatal mortality on WTD farms was determined to be as important to herd productivity as failure to produce a live fawn. Industry wide, "benchmark" estimates of reproductive performance, mortality rates, and productivity are provided, allowing farmers to compare their herds against these "benchmarks" to identify areas needing improvement.

Animal Husbandry↗
PubMed2005

Culture change is critical part in improved outcomes.

Fully integrating benchmarking helps make clinicians fully engaged. Guiding principles put safety and quality ahead of cost savings and revenue increases. Benchmarking data help earn trust and business support of high-volume payer.

Benchmarking↗
PubMed1998

Using scientific evidence to improve hospital library services: Southern Chapter/Medical Library Association journal usage study.

BACKGROUND: Journal usage studies, which are useful for budget management and for evaluating collection performance relative to library use, have generally described a single library or subject discipline. The Southern Chapter/Medical Library Association (SC/MLA) study has examined journal usage at the aggregate data level with the long-term goal of developing hospital library benchmarks for journal use. METHODS: Thirty-six SC/MLA hospital libraries, categorized for the study by size as small, medium, or large, reported current journal title use centrally for a one-year period following standardized data collection procedures. Institutional and aggregate data were analyzed for the average annual frequency of use, average costs per use and non-use, and average percent of non-used titles. Permutation F-type tests were used to measure difference among the three hospital groups. RESULTS: Averages were reported for each data set analysis. Statistical tests indicated no significant differences between the hospital groups, suggesting that benchmarks can be derived applying to all types of hospital libraries. The unanticipated lack of commonality among heavily used titles pointed to a need for uniquely tailored collections. CONCLUSION: Although the small sample size precluded definitive results, the study's findings constituted a baseline of data that can be compared against future studies.

Benchmarking↗
PubMed1996

Cost-effectiveness of clozapine monitoring after the first 6 months.

BACKGROUND: Clozapine is effective in treating patients with schizophrenia who do not respond to conventional neuroleptic drugs. The drug is unique in that it is available only with a US Food and Drug Administration-mandated system for weekly monitoring of patients' white blood cell counts. No study has been conducted to evaluate the cost-effectiveness of this mandatory monitoring system. METHODS: A benchmark case was established by utilizing cumulative incidence rates of agranulocytosis from a recent study with a large sample of clozapine-treated patients. We assumed a 20% mortality among patients with agranulocytosis, $30.61 in monitoring costs each week, and 14.4 years of remaining life expectancy after detection of agranulocytosis. Based on these bench-mark assumptions, cost-effectiveness ratios in dollars per quality-adjusted life-year were calculated for the first, second, and third 6-month periods during which a patient was receiving clozapine. Sensitivity analyses were performed with more conservative assumptions in 5 alternative scenarios. RESULTS: In the benchmark case, costs per quality-adjusted life-year gained were $61,694, $925,418, and $420,644 for the first, second, and third 6-month periods of clozapine treatment, respectively. In the alternative scenarios, these costs ranged from $7923 to $46,056 for the first 6-month period and from $54,025 to $690,850 for the second and third 6-month periods. CONCLUSIONS: While the costs of monitoring patients with schizophrenia in the first 6-month period of clozapine treatment seem to be justifiable, monitoring thereafter may not be cost-effective because of the very low incidence of agranulocytosis in the later periods.

Adult↗
PubMed2006

Computational design of proteins stereochemically optimized in size, stability, and folding speed.

Artificial proteins potentially barrier-free in the folding kinetics are approached computationally under the guidance of protein-folding theories. The smallest and fastest folding globular protein triple-helix-bundle (THB) is so modified as to minimize or eliminate its presumed barriers in folding speed. As the barriers may reside in the ordering of either secondary or tertiary structure, the elements of both secondary and tertiary structure in the protein are targeted for prenucleation with suitable stereochemically constrained amino acid residues. The required elements of topology and sequence for the THB are optimized independently; first the topology is optimized with simulated annealing in polypeptides of highly simplified alphabet; next, the sequence in side chains is optimized using the standard inverse design methods. The resultant three best-adapted THBs, variable in topology and distinctive in sequences, are assessed by comparing them with a few benchmark proteins. The results of mainly molecular dynamics (MD) comparisons, undertaken in explicit water at different temperatures, show that the designed sequences are favorably placed against the chosen benchmarks as THB proteins potentially thermostable in the native folds. Folding simulation experiments with MD establish that the designed sequences are rapid in the folding of individual helices, but not in the evolution of tertiary structure; energetic cum topological frustrations remain but could be the artifacts of the starting conformations that were chosen in the THBs in the folding simulations. Overall, a practical high-throughput approach for de novo protein design has been developed that may have fruitful application for any type of tertiary structure.

Amino Acid Sequence↗
PubMed2004

Estimation of an optimal radiotherapy utilization rate for melanoma: a review of the evidence.

BACKGROUND: Radiotherapy is not used commonly in the treatment of patients with malignant melanoma. The benchmark optimal radiotherapy utilization rates for melanoma are largely unknown, despite the fact that melanoma is a very common cancer. METHODS: To develop an evidence-based benchmark for the optimal proportion of patients with melanoma who should receive radiotherapy, the authors reviewed major treatment guidelines for melanoma. A radiotherapy decision tree was constructed showing the clinical features of melanoma patients for whom radiotherapy was indicated based on evidence. The proportions of melanoma patients with indications for radiotherapy were obtained from epidemiologic data and were used to calculate the optimal proportion of melanoma patients who should receive radiotherapy. RESULTS: The proportion of patients with melanoma for whom radiotherapy is indicated at some point in their illness, according to the best available evidence, was calculated at 23% of all melanoma patients. The utilization rates of radiotherapy for melanoma recorded in actual practice were 13% in New South Wales, 6% in data from the American College of Surgeons, and 1% according to Surveillance, Epidemiology, and End Results data. CONCLUSIONS: Strategies for implementing the evidence-based guidelines are recommended to overcome the shortfall in the use of radiotherapy in the treatment of patients with melanoma.

Australia↗
PubMed2007

Large-scale plant protein subcellular location prediction.

Current plant genome sequencing projects have called for development of novel and powerful high throughput tools for timely annotating the subcellular location of uncharacterized plant proteins. In view of this, an ensemble classifier, Plant-PLoc, formed by fusing many basic individual classifiers, has been developed for large-scale subcellular location prediction for plant proteins. Each of the basic classifiers was engineered by the K-Nearest Neighbor (KNN) rule. Plant-PLoc discriminates plant proteins among the following 11 subcellular locations: (1) cell wall, (2) chloroplast, (3) cytoplasm, (4) endoplasmic reticulum, (5) extracell, (6) mitochondrion, (7) nucleus, (8) peroxisome, (9) plasma membrane, (10) plastid, and (11) vacuole. As a demonstration, predictions were performed on a stringent benchmark dataset in which none of the proteins included has > or =25% sequence identity to any other in a same subcellular location to avoid the homology bias. The overall success rate thus obtained was 32-51% higher than the rates obtained by the previous methods on the same benchmark dataset. The essence of Plant-PLoc in enhancing the prediction quality and its significance in biological applications are discussed. Plant-PLoc is accessible to public as a free web-server at: (http://202.120.37.186/bioinf/plant). Furthermore, for public convenience, results predicted by Plant-PLoc have been provided in a downloadable file at the same website for all plant protein entries in the Swiss-Prot database that do not have subcellular location annotations, or are annotated as being uncertain. The large-scale results will be updated twice a year to include new entries of plant proteins and reflect the continuous development of Plant-PLoc.

Plant Proteins↗
PubMed2003

Optimized Slater-type basis sets for the elements 1-118.

Seven different types of Slater type basis sets for the elements H (Z = 1) up to E118 (Z = 118), ranging from a double zeta valence quality up to a quadruple zeta valence quality, are tested in their performance in neutral atomic and diatomic oxide calculations. The exponents of the Slater type functions are optimized for the use in (scalar relativistic) zeroth-order regular approximated (ZORA) equations. Atomic tests reveal that, on average, the absolute basis set error of 0.03 kcal/mol in the density functional calculation of the valence spinor energies of the neutral atoms with the largest all electron basis set of quadruple zeta quality is lower than the average absolute difference of 0.16 kcal/mol in these valence spinor energies if one compares the results of ZORA equation with those of the fully relativistic Dirac equation. This average absolute basis set error increases to about 1 kcal/mol for the all electron basis sets of triple zeta valence quality, and to approximately 4 kcal/mol for the all electron basis sets of double zeta quality. The molecular tests reveal that, on average, the calculated atomization energies of 118 neutral diatomic oxides MO, where the nuclear charge Z of M ranges from Z = 1-118, with the all electron basis sets of triple zeta quality with two polarization functions added are within 1-2 kcal/mol of the benchmark results with the much larger all electron basis sets, which are of quadruple zeta valence quality with four polarization functions added. The accuracy is reduced to about 4-5 kcal/mol if only one polarization function is used in the triple zeta basis sets, and further reduced to approximately 20 kcal/mol if the all electron basis sets of double zeta quality are used. The inclusion of g-type STOs to the large benchmark basis sets had an effect of less than 1 kcal/mol in the calculation of the atomization energies of the group 2 and group 14 diatomic oxides. The basis sets that are optimized for calculations using the frozen core approximation (frozen core basis sets) have a restricted basis set in the core region compared to the all electron basis sets. On average, the use of these frozen core basis sets give atomic basis set errors that are approximately twice as large as the corresponding all electron basis set errors and molecular atomization energies that are close to the corresponding all electron results. Only if spin-orbit coupling is included in the frozen core calculations larger errors are found, especially for the heavier elements, due to the additional approximation that is made that the basis functions are orthogonalized on scalar relativistic core orbitals.

Journal Article↗
PubMed2004

Improvement of parallelization performance of GAMESS: global sum and (semi-)direct integral calculation in multireference perturbation calculation.

Performance benchmark tests of the multireference perturbation theory (MRPT2) calculation in the GAMESS suite of programs have been performed on a 128-node PC cluster system. The benchmark results point to two kinds of problems with GAMESS: network delay and slow access to disk files. To overcome these bottlenecks, we employ (semi-)direct atomic orbital integral calculations and a new algorithm for the "global sum" operation. These modifications produce remarkable performance improvements, especially in the 128-node PC cluster system, which was almost twice as fast in our version as in the original version. The modification of "global sum" also improved the performance of other types of molecular orbital calculations in GAMESS, such as density functional theory.

Journal Article↗
PubMed2005

Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer.

Important questions exist regarding the quality of force fields used in molecular dynamics (MD) simulations and their interoperable use with other available MD implementations. NAMD is one of the most efficient and scalable parallel molecular dynamics codes for large-scale biomolecular simulations in the open source domain. It is the aim of this article to analyze and compare the dynamics of a benchmark DNA dodecamer d(CTTTTGCAAAAG)2 system, including its binding to a specific drug molecule arising from the use of various simulation protocols in NAMD using Amber98, with the dynamics arising from simulations of the same dodecamer using Amber98 in the AMBER package, one of the most well-established simulation codes for nucleic acids. Based upon a set of validation benchmarks, the details of which are discussed, we find that nucleic acid simulations using NAMD give meaningful results and that the essential features of the resulting dynamics are similar to those arising from the AMBER package. This sets the stage for reliable large-scale simulations of nucleic acids using NAMD.

Computer Simulation↗
PubMed2002

NIST physical standards for DNA-based medical testing.

As DNA and RNA become major targets for clinical laboratory analysis, benchmark reagents will play an increasingly important role in standardization. Reliable national and international nucleic acid standards promote automation and third-party reimbursement for clinical testing. Furthermore, nucleic acid standards provide materials for quality assurance and quality control (QA/QC), and proficiency testing. Standard methods and training initially evolved from consensus guidelines endorsed by professional societies and governmental agencies. The National Institute of Standards and Technology (NIST), a nonregulatory agency of the U.S. Department of Commerce, develops and certifies physical and chemical standards in support of national commerce, manufacturing, and science. In its role supporting U.S. science and industry, the NIST responds to specific standards needs, most recently for medically and biologically important analytes. Broad-based consensus developed through interdisciplinary NIST workshops initiated development of NIST-certified DNA standards. Such materials serve the diagnostic community and help manufacturers benchmark a variety of DNA diagnostic testing platforms. Here we summarize the NIST experience and programs for development of national standards for DNA-based medical diagnostic testing.

Clinical Laboratory Techniques↗
PubMed2002

Validating the performance of the mammary sentinel lymph node team.

BACKGROUND AND OBJECTIVES: The mammary sentinel lymph node (SLN) procedure has the potential to improve the accuracy and lower the morbidity of axillary staging in breast cancer patients, but results are closely linked to experience and can vary widely between institutions. Standardized performance measures need to be established in order to optimize the transition to SLN biopsy only. METHODS: Performance data were prospectively collected for the first 156 mammary SLN procedures performed by three surgeons in our institution. RESULTS: Seventy-five cases were required to achieve an SLN visualization rate of > 80% on preoperative lymphoscintigraphy. The SLN visualization rate was 90% for the last 52 cases. Two surgeons required 25 cases before consistently achieving a > or = 90% SLN identification rate in the operating room and one required 15 cases. The metastasis detection rate increased from 22% for the first 52 cases to 31% for the last 52 cases. The false negative rate for the procedure was 5%. CONCLUSIONS: The following performance criteria and benchmarks are suggested for validating the performance of the SLN team: (1) SLN visualization rate on preoperative lymphoscintigraphy > or = 80%, (2) SLN identification rate in the operating room > or = 90%, (3) False negative rate for the procedure 5%. Thirty procedures per surgeon were sufficient to achieve these benchmarks in our group.

Axilla↗
PubMed1996

Protein fold recognition using sequence-derived predictions.

In protein fold recognition, one assigns a probe amino acid sequence of unknown structure to one of a library of target 3D structures. Correct assignment depends on effective scoring of the probe sequence for its compatibility with each of the target structures. Here we show that, in addition to the amino acid sequence of the probe, sequence-derived properties of the probe sequence (such as the predicted secondary structure) are useful in fold assignment. The additional measure of compatibility between probe and target is the level of agreement between the predicted secondary structure of the probe and the known secondary structure of the target fold. That is, we recommend a sequence-structure compatibility function that combines previously developed compatibility functions (such as the 3D-1D scores of Bowie et al. [1991] or sequence-sequence replacement tables) with the predicted secondary structure of the probe sequence. The effect on fold assignment of adding predicted secondary structure is evaluated here by using a benchmark set of proteins (Fischer et al., 1996a). The 3D structures of the probe sequences of the benchmark are actually known, but are ignored by our method. The results show that the inclusion of the predicted secondary structure improves fold assignment by about 25%. The results also show that, if the true secondary structure of the probe were known, correct fold assignment would increase by an additional 8-32%. We conclude that incorporating sequence-derived predictions significantly improves assignment of sequences to known 3D folds. Finally, we apply the new method to assign folds to sequences in the SWISSPROT database; six fold assignments are given that are not detectable by standard sequence-sequence comparison methods; for two of these, the fold is known from X-ray crystallography and the fold assignment is correct.

Amino Acid Sequence↗
PubMed2002

A study on protein sequence alignment quality.

One of the most central methods in bioinformatics is the alignment of two protein or DNA sequences. However, so far large-scale benchmarks examining the quality of these alignments are scarce. On the other hand, recently several large-scale studies of the capacity of different methods to identify related sequences has led to new insights about the performance of fold recognition methods. To increase our understanding about fold recognition methods, we present a large-scale benchmark of alignment quality. We compare alignments from several different alignment methods, including sequence alignments, hidden Markov models, PSI-BLAST, CLUSTALW, and threading methods. For most methods, the alignment quality increases significantly at about 20% sequence identity. The difference in alignment quality between different methods is quite small, and the main difference can be seen at the exact positioning of the sharp rise in alignment quality, that is, around 15-20% sequence identity. The alignments are improved by using structural information. In general, the best alignments are obtained by methods that use predicted secondary structure information and sequence profiles obtained from PSI-BLAST. One interesting observation is that for different pairs many different methods create the best alignments. This finding implies that if a method that could select the best alignment method for each pair existed, a significant improvement of the alignment quality could be gained.

Computational Biology↗