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PubMed2002

[Quality of medical database to valorize the DRG model by ISA cost indicators].

BACKGROUND: The use of the French version of the DRG model is focused on cost allocation, based on the case-mix system and the use a weight called ISA (Synthetic Index of Activity) for each DRG. However, this administrative database is becoming more and more used by both researchers and health policy makers for health planning and benchmarking. In France, data abstraction and coding of medical records is done by physicians. The objective of this study was to determine the accuracy of a database of the discharge summaries used for DRGs and to compare consequences of inappropriate coding on budget estimation and risk adjustment. METHODS: Samples of discharge summaries from six cardiology units were recoded by trained physicians in data abstracting and coding. Comparison between initial and recoded diagnoses (errors on main diagnosis or on comorbidities) used by the DRG system algorithm, and the original and final case-mix were performed. The before and after abstracted data were stratified and compared by principal diagnosis (myocardial infarction or congestive heart failure) and discharge status (dead or alive). MAIN RESULTS: Comorbidities were underreported by physicians of cardiology units compared to reabstracted data (mean number of secondary diagnoses per summary: 2.1 vs. 3.6, p<0.001), especially those which had a minimal impact on the DRG classification. In spite of a 15% rate of wrong DRGs, there was no significant difference in the total amount of ISA after data reviewing. Underreporting of comorbidities is more important for medical records of dead patients at discharge but, without significant effect on rate of change in DRG and amount of ISA. CONCLUSION: Discharge summaries used in the French DRGs system consistently underestimate the presence of comorbid conditions, which has direct implications for policy-makers comparing performance between hospital units. Both clinical practitioners and policy makers should be aware of this bias when assessing patient's quality of care or performing health planning through discharge summaries.

Age Factors↗
PubMed1992

A new transducer for facet force measurement in the lumbar spine: benchmark and in vitro test results.

A new transducer capable of direct measurement of time-dependent loads in human lumbar facet joints was developed and tested. The transducer was comprised of a force-sensitive resistor (FSR) in series with a pressure-sensitive film. A wide range of experiments revealed the performance attributes and limitations of the FSR. The output signal of the FSR is actually sensitive to both force and area of contact independently. Therefore, a pressure-sensitive film was used to quantify the contact area. At least two transformation equations were calculated for each FSR corresponding to known contact areas. Each equation was a linearization of the log of the FSR output vs the log of the applied ramp loads. Coefficients of determination (CD) were calculated for small (21 mm2) and large (32 mm2) contact areas, and were found to exceed 0.900 for all data. The average of nine cycles was nearly linear for some FSRs (CD of 0.999). FSR output signal and contact area were recorded in cadaveric lumbar facets under ramp load. The appropriate transformation equation was determined by a linear interpolation between benchmark equations based on the contact area measured in vitro. Facet force measurements compared well with those of other researchers. The transducer was found to be quite easy to use.

Calibration↗
PubMed2003

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

BACKGROUND: The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. RESULTS: The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs) of 89.9% over a set of 672 alignments. The T-COFFEE method on a data set of families with <8 sequences gave 91.4% accuracy, significantly better than CLUSTALW (88.9%) and all other methods considered here. The complete suite is available from http://www.compbio.dundee.ac.uk. CONCLUSIONS: The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94.5% with 52.5% accuracy for alignments in the 0-10 percentage identity range. This suggests that further improvements in accuracy will be possible in the future.

Amino Acid Sequence↗
PubMed1998

Radiation therapy for rectosigmoid and rectal cancer: results of the 1992-1994 Patterns of Care process survey.

PURPOSE: To determine the US national practice standards for patients with adenocarcinoma of the rectum treated in radiation oncology facilities. MATERIALS AND METHODS: A national survey of 57 institutions identified 507 eligible patients who received radiation therapy as a component of their treatment for rectal cancer. A stratified two-stage cluster sampling with simple random sampling at each stage for each stratum was used and on-site surveys were performed. RESULTS: Of the 507 patients, 378 (75%) received postoperative therapy, 110 (22%) received preoperative therapy, 17 (2%) received both preoperative and postoperative therapy, and less than 0.5% received intraoperative radiation alone. To more accurately assess the utilization of modern radiation techniques as well as recommendations of the National Cancer Institute (NCI)-sponsored, randomized, postoperative, adjuvant combined modality therapy rectal cancer trials into current practice, the analysis was limited to the 243 (48%) patients with tumor, node, and metastasis staging system classification T3 and/or N1-2M0 disease who underwent conventional surgery with negative margins. Although only 7% were treated on a clinical trial, 90% received chemotherapy for a median of 21 weeks. Most were treated with modern radiation treatment techniques. In contrast, techniques to identify and help exclude the small bowel from the radiation field were not routinely used. CONCLUSION: Despite the fact that only 7% of patients with T3 and/or N1-2M0 disease were treated on a clinical trial, such trials appear to have resulted in a positive influence on the standard of practice within the oncology community. Although there are still some deficiencies, the majority of these patients received combined modality therapy and were treated with modern radiation therapy techniques.

Adenocarcinoma↗
PubMed2005

Descriptor-based protein remote homology identification.

Here, we report a novel protein sequence descriptor-based remote homology identification method, able to infer fold relationships without the explicit knowledge of structure. In a first phase, we have individually benchmarked 13 different descriptor types in fold identification experiments in a highly diverse set of protein sequences. The relevant descriptors were related to the fold class membership by using simple similarity measures in the descriptor spaces, such as the cosine angle. Our results revealed that the three best-performing sets of descriptors were the sequence-alignment-based descriptor using PSI-BLAST e-values, the descriptors based on the alignment of secondary structural elements (SSEA), and the descriptors based on the occurrence of PROSITE functional motifs. In a second phase, the three top-performing descriptors were combined to obtain a final method with improved performance, which we named DescFold. Class membership was predicted by Support Vector Machine (SVM) learning. In comparison with the individual PSI-BLAST-based descriptor, the rate of remote homology identification increased from 33.7% to 46.3%. We found out that the composite set of descriptors was able to identify the true remote homolog for nearly every sixth sequence at the 95% confidence level, or some 10% more than a single PSI-BLAST search. We have benchmarked the DescFold method against several other state-of-the-art fold recognition algorithms for the 172 LiveBench-8 targets, and we concluded that it was able to add value to the existing techniques by providing a confident hit for at least 10% of the sequences not identifiable by the previously known methods.

Algorithms↗
PubMed2003

A clinical practice guideline for treatment of septic arthritis in children: efficacy in improving process of care and effect on outcome of septic arthritis of the hip.

BACKGROUND: The development of clinical practice guidelines is a central precept of the evidence-based-medicine movement. The purposes of this study were to develop a guideline for the treatment of septic arthritis in children and to evaluate its efficacy with regard to improving the process of care and its effect on the outcome of septic arthritis of the hip in children. METHODS: A clinical practice guideline was developed by an interdisciplinary expert committee using evidence-based techniques. Efficacy was evaluated by comparing a historical control group of thirty consecutive children with septic arthritis of the hip managed before the utilization of the guideline with a prospective cohort group of thirty consecutive children treated with use of the guideline. Benchmark parameters of process and outcome were compared between groups. RESULTS: The patients treated with use of the guideline, compared with those treated without use of the guideline, had a significantly higher rate of performance of initial and follow-up C-reactive protein tests (93% compared with 13% and 70% compared with 7%), lower rate of initial bone-scanning (13% compared with 40%), lower rate of presumptive drainage (13% compared with 47%), greater compliance with recommended antibiotic therapy (93% compared with 7%), faster change to oral antibiotics (3.9 compared with 6.9 days), and shorter hospital stay (4.8 compared with 8.3 days). There were no significant differences between the groups with regard to other process variables, and there were no significant differences with regard to outcome variables, including readmission to the hospital, recurrent infection, recurrent drainage, development of osteomyelitis, septic osteonecrosis, or limitation of motion. CONCLUSIONS: Patients treated according to the septic arthritis clinical practice guideline had less variation in the process of care and improved efficiency of care without a significant difference in outcome.

Anti-Bacterial Agents↗
PubMed2025

insilicoSV: a flexible grammar-based framework for structural variant simulation and placement.

SUMMARY: Structural variants (SVs) are key drivers of genetic variation and disease in the genome. Their discovery remains challenging, however, in large part due to the scarcity of validated SV callsets and comprehensive benchmarks, which are essential for method development and evaluation. The growing number of data-driven learning-based approaches for SV discovery, in particular, requires large, diverse, and well-balanced training datasets to achieve reliable performance. To address this need, SV simulation has served as a key tool for assessing method performance and training SV models. However, existing SV simulators only support a fixed and limited set of SV classes and do not provide fine-grained control over the placement of SVs within specific contexts of the genome. Here we present insilicoSV, a versatile framework for SV simulation, which models SVs using a simple and flexible grammar, allowing users to easily define standard and custom arbitrary genome rearrangements, as well as encode genome placement constraints. This design allows insilicoSV to naturally support new and bespoke SV types, such as the complex rearrangements of cancer genomes. In addition to grammar-based modeling, insilicoSV provides built-in support for 26 predefined SV types, placement of user-provided SVs, small variant simulation, streamlined workflows for the simulation of genome evolution and genome mixtures, read simulation, alignment, and visualization. These features enable the creation of comprehensive genomic datasets for a variety of downstream applications, such as in-depth benchmarking of alignment and variant calling methods, as well as training of data-driven learning-based approaches for SV detection. AVAILABILITY AND IMPLEMENTATION: insilicoSV is available under the MIT license at https://github.com/PopicLab/insilicoSV and https://doi.org/10.5281/zenodo.17402009.

Software↗
PubMed1998

Nonoperative treatment of biliary tract disease.

The rise of minimally invasive surgical techniques during the past 20 years has been one of the more dramatic developments in modern medicine. Minimally invasive procedures are now widely accepted for treatment of diseases involving many different organ systems. Minimally invasive procedures may be more common and more accepted in the treatment of diseases of the biliary tract than in any other area. The development of laparoscopic cholecystectomy serves as a benchmark for minimally invasive procedures, and it is now the standard of care for the treatment of cholelithiasis. Today, not only is laparoscopic cholecystectomy one of the most common operations performed in the United States, but many new techniques have been developed that allow minimally invasive treatment of a variety of biliary tract diseases. The development of nonoperative techniques for treatment of biliary tract disease has accompanied the rapid developments in minimally invasive surgical techniques. This article describes the nonoperative treatment of biliary tract disease.

Algorithms↗
PubMed2006

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.

Journal Article↗
PubMed2005

Application of analytic hierarchy process for measuring and comparing the global performance of intensive care units.

PURPOSE: To develop a model for the global performance measurement of intensive care units (ICUs) and to apply that model to compare the services for quality improvement. MATERIALS AND METHODS: Analytic hierarchy process, a multiple-attribute decision-making technique, is used in this study to evolve such a model. The steps consisted of identifying the critical success factors for the best performance of an ICU, identifying subfactors that influence the critical factors, comparing them pairwise, deriving their relative importance and ratings, and calculating the cumulative performance according to the attributes of a given ICU. Every step in the model was derived by group discussions, brainstorming, and consensus among intensivists. RESULTS: The model was applied to 3 ICUs, 1 each in Barbados, Trinidad, and India in tertiary care teaching hospitals of similar setting. The cumulative performance rating of the Barbados ICU was 1.17 when compared with that of Trinidad and Indian ICU, which were 0.82 and 0.75, respectively, showing that the Trinidad and Indian ICUs performed 70% and 64% with respect to Barbados ICU. The model also enabled identifying specific areas where the ICUs did not perform well, which helped to improvise those areas. CONCLUSIONS: Analytic hierarchy process is a very useful model to measure the global performance of an ICU.

Barbados↗
PubMed1997

Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 2. Applications.

Validation of a method that uses a genetic neural network with electrostatic and steric similarity matrices (SM/GNN) to obtain quantitative structure-activity relationships (QSARs) is performed with eight data sets. Biological and physicochemical properties from a broad range of chemical classes are correlated and predicted using this technique. Quantitatively the results compare favorably with the benchmarks obtained by a number of well-established QSAR methods; qualitatively the models are consistent with the published descriptions on the relative contribution of steric and electrostatic factors. The results demonstrate the general utility of this method in deriving QSARs. The implication of the importance of molecular alignment and possible methodological improvements are discussed.

Cholinesterase Inhibitors↗
PubMed2002

The Blood Stocks Management Scheme, a partnership venture between the National Blood Service of England and North Wales and participating hospitals for maximizing blood supply chain management.

BACKGROUND AND OBJECTIVES: The Blood Stocks Management Scheme (BSMS) has been established as a joint venture between the National Blood Service (NBS) in England and North Wales and participating hospitals to monitor the blood supply chain. MATERIALS AND METHODS: Stock and wastage data are submitted to a web-based data-management system, facilitating continuous and complete red cell data collection and 'real time' data extraction. RESULTS: The data-management system enables peer review of performance in respect of stock holding levels and red cell wastage. CONCLUSIONS: The BSMS has developed an innovative web-based data-management system that enables data collection and benchmarking of practice, which should drive changes in stock management practice, therefore optimizing the use of donated blood.

Blood Banks↗
PubMed2004

Calculation of excited-state properties using general coupled-cluster and configuration-interaction models.

Using string-based algorithms excitation energies and analytic first derivatives for excited states have been implemented for general coupled-cluster (CC) models within CC linear-response (LR) theory which is equivalent to the equation-of-motion (EOM) CC approach for these quantities. Transition moments between the ground and excited states are also considered in the framework of linear-response theory. The presented procedures are applicable to both single-reference-type and multireference-type CC wave functions independently of the excitation manifold constituting the cluster operator and the space in which the effective Hamiltonian is diagonalized. The performance of different LR-CC/EOM-CC and configuration-interaction approaches for excited states is compared. The effect of higher excitations on excited-state properties is demonstrated in benchmark calculations for NH(2) and NH(3). As a first application, the stationary points of the S(1) surface of acetylene are characterized by high-accuracy calculations.

Journal Article↗
PubMed1997

Using video-oriented instructions to speed up sequence comparison.

MOTIVATION: This document presents an implementation of the well-known Smith-Waterman algorithm for comparison of proteic and nucleic sequences, using specialized video instructions. These instructions, SIMD-like in their design, make possible parallelization of the algorithm at the instruction level. RESULTS: Benchmarks on an ULTRA SPARC running at 167 MHz show a speed-up factor of two compared to the same algorithm implemented with integer instructions on the same machine. Performance reaches over 18 million matrix cells per second on a single processor, giving to our knowledge the fastest implementation of the Smith-Waterman algorithm on a workstation. The accelerated procedure was introduced in LASSAP--a LArge Scale Sequence compArison Package software developed at INRIA--which handles parallelism at higher level. On a SUN Enterprise 6000 server with 12 processors, a speed of nearly 200 million matrix cells per second has been obtained. A sequence of length 300 amino acids is scanned against SWISSPROT R33 (1,8531,385 residues) in 29 s. This procedure is not restricted to databank scanning. It applies to all cases handled by LASSAP (intra- and inter-bank comparisons, Z-score computation, etc.

Algorithms↗
PubMed2025

Approximating edit distances between complex tandem repeats efficiently.

MOTIVATION: Extended tandem repeats (TRs) have been associated with 60 or more diseases over the past 30&#x2009;years. Although most TRs have single repeat units (or motifs), complex TRs with different units have recently been correlated with some brain disorders. Of note, a population-scale analysis shows that complex TRs at one locus can be divergent, and different units are often expanded between individuals. To understand the evolution of high TR diversity, it is informative to visualize a phylogenetic tree. To do this, we need to measure the edit distance between pairs of complex TRs by considering duplication and contraction of units created by replication slippage. However, traditional rigorous algorithms for this purpose are computationally expensive. RESULTS: We here propose an efficient heuristic algorithm to estimate the edit distance with duplication and contraction of units (EDDC, for short). We select a set of frequent units that occur in given complex TRs, encode each unit as a single symbol, compress a TR into an optimal series of unit symbols that partially matches the original TR with the minimum Levenshtein distance, and estimate the EDDC between a pair of complex TRs from their compressed forms. Using substantial synthetic benchmark datasets, we demonstrate that the estimated EDDC is highly correlated with the accurate EDDC, with a Pearson correlation coefficient of >0.983, while the heuristic algorithm achieves orders of magnitude performance speedup. AVAILABILITY AND IMPLEMENTATION: The software program hEDDC that implements the proposed algorithm is available at https://github.com/Ricky-pon/hEDDC (DOI: 10.5281/zenodo.14732958).

Algorithms↗
PubMed2005

Classification of microarray data with factor mixture models.

MOTIVATION: The classification of few tissue samples on a very large number of genes represents a non-standard problem in statistics but a usual one in microarray expression data analysis. In fact, the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. We consider high-density oligonucleotide microarray data, where the expression level is associated to an 'absolute call', which represents a qualitative indication of whether or not a transcript is detected within a sample. The 'absolute call' is generally not taken in consideration in analyses. RESULTS: In contrast to frequently used cluster analysis methods to analyze gene expression data, we consider a problem of classification of tissues and of the variables selection. We adopted methodologies formulated by Ghahramani and Hinton and Rocci and Vichi for simultaneous dimensional reduction of genes and classification of tissues; trying to identify genes (denominated 'markers') that are able to distinguish between two known different classes of tissue samples. In this respect, we propose a generalization of the approach proposed by McLachlan et al. by advising to estimate the distribution of log LR statistic for testing one versus two component hypothesis in the mixture model for each gene considered individually, using a parametric bootstrap approach. We compare conditional (on 'absolute call') and unconditional analyses performed on dataset described in Golub et al. We show that the proposed techniques improve the results of classification of tissue samples with respect to known results on the same benchmark dataset. AVAILABILITY: The software of Ghahramani and Hinton is written in Matlab and available in 'Mixture of Factor Analyzers' on http://www.gatsby.ucl.ac.uk/~zoubin/software.html while the software of Rocci and Vichi is available upon request from the authors.

Algorithms↗
PubMed1997

Synthesis and characterization of supramolecular protein aggregates: self-assembled, molecularly-ordered, tubes from electrostatic complementation of glutamine synthetase dodecamers.

Dodecameric Escherichia coli glutamine synthetase (GS) is formed from identical subunits arranged in face-to-face hexameric rings. In the presence of Zn2+ and other transition metal ions the individual dodecamers 'stack' to form protein tubes. Previous results have suggested that six binuclear intermolecular metal binding sites are generated at each dodecamer-dodecamer interface by juxtaposition of the N-terminal helices of each subunit adjacent to an analogous helix from a docked dodecamer. In principle, replacement of one of the metal binding sites within each pair of helices with charged amino acids could generate electrostatic interactions that would provide the basis for heterospecific protein-protein interactions. In turn, this would allow for ordered assembly of protein tubes with alternating, chemically distinguishable, components. This hypothesis was tested by replacement of one of the metalligating histidines (His12) with aspartic acid, arginine or cysteine. The H12C mutant was further elaborated by selective thiol modification, with either of the charged reagents 2-iodo-acetic acid or 2-chloro-acetamidine, which yield glutamate (H12C-IA) or arginine (H12C-CA) mimics at position 12. Light scattering and electron microscopy were used to monitor the 'stacking ability' of these variants in the presence of Zn2+. No, or few, GS 'tubes' were observed in solutions containing only H12D, H12R, H12C-CA or H12C-IA, in the presence or absence of Zn2+. In contrast, in mixtures containing H12C-CA and either H12D or H12C-IA, the complementary GS variants stack in the presence of 100 microM Zn2+, with apparent second order rate constants that are comparable to the wild type dodecamers. Fluorescence energy transfer experiments with fluorescein-labeled H12C-IA (donor) and rhodamine-labeled H12C-CA (acceptor) were performed and compared with the energy transfer efficiency with mixtures containing variable ratios of acceptor-labeled and donor-labeled wild type GS; the wild type mixtures provide a benchmark for the extent of energy transfer expected in random linear arrangements of donor and acceptor. The efficiency of metal-dependent energy transfer in mixtures containing the acceptor-labeled H12C-CA and the donor-labeled H12C-IA was 3.2-fold greater than expected for a random distribution of charged variants. Together, the results indicate that the charged variants provide a mechanism for heterospecific interaction between chemically distinguishable dodecamers that align in an ordered one-dimensional array.

Binding Sites↗