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PubMed2006

[Hemodialysis prospective multicentric quality study].

In medicine a considerable amount of resources are used in research, but very little attention is paid to ensuring that the findings of research are implemented in routine clinical practice. This prospective study has the aim to evaluate the efficiency of some clinical management strategies (feedback, benchmarking and improving plans) on haemodialysis treatment results in 4 different dialysis centres. We collected consensus data related to haemodialysis results every 6-8 months and informed each centre about its own results (feedback) and how these related to the others(benchmarking). We designed improving plans for any bad result detected. By the end of two years of follow up, 294 patients had been included in the study. The results obtained at the end of the study had improved in comparison with those obtained at the beginning (statistically significant) for the following indicators: % of patients with Hb< 11 g/dl, % patients with Kt/v < 1.2, mean Kt/v, mean albumin, % patients with albumin< 3.5 g/dl y % patients with C reactive protein (CRP) > 5 mg/dl. No statistical changes were found in: mean erythropoietin (EPO) doses, blood pressure (BP), phosphorus plasmatic,calcium-phosphorus product, parathormone (PTHi) and vascular access distribution. We explained the absence of any improvement because of adequate start indicators in some areas (BP and vascular access), therapy with limited efficiency (calcitriol, calcium carbonate and others), lack of support resources (dietetic unit) or inadequate design/implementation of improving plans.In conclusion, our intervention illustrates that combined clinical management strategies(feedback, benchmarking and improving plans) are efficiency in improving some areas of haemodialysis treatment (anaemia, dialysis dose, nutrition and inflammation), although it does not improve calcium phosphate metabolism related indicators.

Aged↗
PubMed1996

Comparative effects of haloacetic acids in whole embryo culture.

A major class of disinfection by-products in drinking water are the haloacetic acids. Both dichloro- and trichloroacetic acids are teratogenic when administered to rats throughout organogenesis. However, there is little information regarding the developmental toxicity of other haloacetic acids. Therefore, 3-6 somite staged CD-1 mouse embryos were exposed to acetic acid (AA) or mono- (M), di- (D), and tri- (T) substituted fluoro- (F), chloro- (C), or bromo- (B) acetic acids in whole embryo culture in order to evaluate the effects of these agents on development. A 24 hour exposure to the haloacetic acids produced dysmorphogenesis. Effects on neural tube development ranged from prosencephalic hypoplasia to non-closure defects throughout the cranial region. Exposure to the haloacetic acids affected optic development, produced malpositioned and/or hypoplastic pharyngeal arches, and resulted in perturbation of heart development. In order to determine the relative toxicities of these agents, benchmark concentrations were calculated as the lower 95% confidence interval of the concentration that produced a 5% increase in neural tube defects. The benchmark concentrations occurred over a wide range with DFA (5912.6 microM) and MBA (2.7 microM) at the extremes. Using the benchmark concentrations to compare the chemicals gives a ranking of the agents in order of increasing potency as: DFA < TFA < DCA < AA < TBA < or = TCA < DBA < MCA < MBA. TCA and DCA have demonstrated ability to disrupt development in vivo but were among the least potent haloacetic acids in vitro. Because of the potential for widespread exposure to haloacetic acids in drinking water and the incomplete toxicity profile of these chemicals, further work on their developmental effects is warranted.

Abnormalities, Drug-Induced↗
PubMed2002

FROST: a filter-based fold recognition method.

To assess the reliability of fold assignments to protein sequences, we developed a fold recognition method called FROST (Fold Recognition-Oriented Search Tool) based on a series of filters and a database specifically designed as a benchmark for this new method under realistic conditions. This benchmark database consists of proteins for which there exists, at least, another protein with an extensively similar 3D structure in a database of representative 3D structures (i.e., more than 65% of the residues in both proteins can be structurally aligned). Because the testing of our method must be carried out under conditions similar to those of real fold recognition experiments, no protein pair with sequence similarity detectable using standard sequence comparison methods such as FASTA is included in the benchmark database. While using FROST, we achieved a coverage of 60% for a rate of error of 1%. To obtain a baseline for our method, we used PSI-BLAST and 3D-PSSM. Under the same conditions, for a 1% error rate, coverages for PSI-BLAST and 3D-PSSM were 33 and 56%, respectively.

Algorithms↗
PubMed2003

A novel shape complementarity scoring function for protein-protein docking.

Shape complementarity is the most basic ingredient of the scoring functions for protein-protein docking. Most grid-based docking algorithms use the total number of grid points at the binding interface to quantify shape complementarity. We have developed a novel Pairwise Shape Complementarity (PSC) function that is conceptually simple and rapid to compute. The favorable component of PSC is the total number of atom pairs between the receptor and the ligand within a distance cutoff. When applied to a benchmark of 49 test cases, PSC consistently ranks near-native structures higher and produces more near-native structures than the traditional grid-based function, and the improvement was seen across all prediction levels and in all categories of the benchmark. Without any post-processing or biological information about the binding site except the complementarity-determining region of antibodies, PSC predicts the complex structure correctly for 6 test cases, and ranks at least one near-native structure in the top 20 predictions for 18 test cases. Our docking program ZDOCK has been parallelized and the average computing time is 4 minutes using sixteen IBM SP3 processors. Both ZDOCK and the benchmark are freely available to academic users (http://zlab.bu.edu/~ rong/dock).

Binding Sites↗
PubMed2003

RDOCK: refinement of rigid-body protein docking predictions.

We present a simple and effective algorithm RDOCK for refining unbound predictions generated by a rigid-body docking algorithm ZDOCK, which has been developed earlier by our group. The main component of RDOCK is a three-stage energy minimization scheme, followed by the evaluation of electrostatic and desolvation energies. Ionic side chains are kept neutral in the first two stages of minimization, and reverted to their full charge states in the last stage of brief minimization. Without side chain conformational search or filtering/clustering of resulting structures, RDOCK represents the simplest approach toward refining unbound docking predictions. Despite its simplicity, RDOCK makes substantial improvement upon the top predictions by ZDOCK with all three scoring functions and the improvement is observed across all three categories of test cases in a large benchmark of 49 non-redundant unbound test cases. RDOCK makes the most powerful combination with ZDOCK2.1, which uses pairwise shape complementarity as the scoring function. Collectively, they rank a near-native structure as the number-one prediction for 18 test cases (37% of the benchmark), and within the top 4 predictions for 24 test cases (49% of the benchmark). To various degrees, funnel-like energy landscapes are observed for these 24 test cases. To the best of our knowledge, this is the first report of binding funnels starting from global searches for a broad range of test cases. These results are particularly exciting, given that we have not used any biological information that is specific to individual test cases and the whole process is entirely automated. Among three categories of test cases, the best results are seen for enzyme/inhibitor, with a near-native structure ranked as the number-one prediction for 48% test cases, and within the top 10 predictions for 78% test cases. RDOCK is freely available to academic users at http://zlab.bu.edu/ approximately rong/dock.

Algorithms↗
PubMed2005

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.

Recognizing structural similarity without significant sequence identity has proved to be a challenging task. Sequence-based and structure-based methods as well as their combinations have been developed. Here, we propose a fold-recognition method that incorporates structural information without the need of sequence-to-structure threading. This is accomplished by generating sequence profiles from protein structural fragments. The structure-derived sequence profiles allow a simple integration with evolution-derived sequence profiles and secondary-structural information for an optimized alignment by efficient dynamic programming. The resulting method (called SP(3)) is found to make a statistically significant improvement in both sensitivity of fold recognition and accuracy of alignment over the method based on evolution-derived sequence profiles alone (SP) and the method based on evolution-derived sequence profile and secondary structure profile (SP(2)). SP(3) was tested in SALIGN benchmark for alignment accuracy and Lindahl, PROSPECTOR 3.0, and LiveBench 8.0 benchmarks for remote-homology detection and model accuracy. SP(3) is found to be the most sensitive and accurate single-method server in all benchmarks tested where other methods are available for comparison (although its results are statistically indistinguishable from the next best in some cases and the comparison is subjected to the limitation of time-dependent sequence and/or structural library used by different methods.). In LiveBench 8.0, its accuracy rivals some of the consensus methods such as ShotGun-INBGU, Pmodeller3, Pcons4, and ROBETTA. SP(3) fold-recognition server is available on http://theory.med.buffalo.edu.

Algorithms↗
PubMed2006

SimFold energy function for de novo protein structure prediction: consensus with Rosetta.

Predicting protein tertiary structures by in silico folding is still very difficult for proteins that have new folds. Here, we developed a coarse-grained energy function, SimFold, for de novo structure prediction, performed a benchmark test of prediction with fragment assembly simulations for 38 test proteins, and proposed consensus prediction with Rosetta. The SimFold energy consists of many terms that take into account solvent-induced effects on the basis of physicochemical consideration. In the benchmark test, SimFold succeeded in predicting native structures within 6.5 A for 12 of 38 proteins; this success rate was the same as that by the publicly available version of Rosetta (ab initio version 1.2) run with default parameters. We investigated which energy terms in SimFold contribute to structure prediction performance, finding that the hydrophobic interaction is the most crucial for the prediction, whereas other sequence-specific terms have weak but positive roles. In the benchmark, well-predicted proteins by SimFold and by Rosetta were not the same for 5 of 12 proteins, which led us to introduce consensus prediction. With combined decoys, we succeeded in prediction for 16 proteins, four more than SimFold or Rosetta separately. For each of 38 proteins, structural ensembles generated by SimFold and by Rosetta were qualitatively compared by mapping sampled structural space onto two dimensions. For proteins of which one of the two methods succeeded and the other failed in prediction, the former had a less scattered ensemble located around the native. For proteins of which both methods succeeded in prediction, often two ensembles were mixed up.

Alanine↗
PubMed2006

Prediction of protein subcellular localization.

Because the protein's function is usually related to its subcellular localization, the ability to predict subcellular localization directly from protein sequences will be useful for inferring protein functions. Recent years have seen a surging interest in the development of novel computational tools to predict subcellular localization. At present, these approaches, based on a wide range of algorithms, have achieved varying degrees of success for specific organisms and for certain localization categories. A number of authors have noticed that sequence similarity is useful in predicting subcellular localization. For example, Nair and Rost (Protein Sci 2002;11:2836-2847) have carried out extensive analysis of the relation between sequence similarity and identity in subcellular localization, and have found a close relationship between them above a certain similarity threshold. However, many existing benchmark data sets used for the prediction accuracy assessment contain highly homologous sequences-some data sets comprising sequences up to 80-90% sequence identity. Using these benchmark test data will surely lead to overestimation of the performance of the methods considered. Here, we develop an approach based on a two-level support vector machine (SVM) system: the first level comprises a number of SVM classifiers, each based on a specific type of feature vectors derived from sequences; the second level SVM classifier functions as the jury machine to generate the probability distribution of decisions for possible localizations. We compare our approach with a global sequence alignment approach and other existing approaches for two benchmark data sets-one comprising prokaryotic sequences and the other eukaryotic sequences. Furthermore, we carried out all-against-all sequence alignment for several data sets to investigate the relationship between sequence homology and subcellular localization. Our results, which are consistent with previous studies, indicate that the homology search approach performs well down to 30% sequence identity, although its performance deteriorates considerably for sequences sharing lower sequence identity. A data set of high homology levels will undoubtedly lead to biased assessment of the performances of the predictive approaches-especially those relying on homology search or sequence annotations. Our two-level classification system based on SVM does not rely on homology search; therefore, its performance remains relatively unaffected by sequence homology. When compared with other approaches, our approach performed significantly better. Furthermore, we also develop a practical hybrid method, which combines the two-level SVM classifier and the homology search method, as a general tool for the sequence annotation of subcellular localization.

Algorithms↗
PubMed2002

Effects of membrane partitioning and other physical chemical properties on the apparent potency of "membrane active" compounds evaluated using red blood cell lysis assays.

The membrane-destabilizing properties of Amphotericin B and Zwittergent were used as benchmark compounds for examining in detail their membrane-altering effects in a series of human red blood cell lysis assays. The procedures included examining dose responses and the effects of different cell concentrations on potency in rbc lysis assays. In order to enhance detection of subtle membrane effects, we also used a range of NaCl concentrations to osmotically stress the rbc's. Using the benchmark compounds, a set of conditions was developed for examination of subtle membrane effects that may be applied to series of compounds with suspected membrane-perturbation activity. A group of experiments was defined that allow detection of the most important membrane-modifying behaviors among a diverse group of compounds. From an initial screen of bacterial growth inhibition over 150 compounds were examined for membrane-altering properties using the limited experimental protocols developed from the benchmark compounds. Several dose-response patterns were observed as useful for classifying compounds based on their tendency to alter membrane integrity and to partition into the lipids of membranes, as well as their propensity to form aggregates or precipitates. The methods may prove generally useful for distinguishing compounds whose primary activity is membrane destabilization from more interesting and useful pharmacological mechanisms of action.

Amphotericin B↗
PubMed2000

Biochemical characterization of cloned Aspergillus fumigatus phytase (phyA).

The gene for Aspergillus fumigatus phytase (phyA) was cloned and expressed in Pichia pastoris. The enzyme expressed was purified to near homogeneity using sequential ion-exchange chromatography and was characterized biochemically. Although A. fumigatus phytase shows 66.2% sequence homology with A. ficuum phytase, the most widely studied enzyme, the cloned phytase showed identical molecular weight and temperature optima profile to the benchmark phytase. The pH profile of activity and kinetic parameters, however, differed from A. ficuum phytase. The cloned enzyme contains the septapeptide RHGARYP motif, which is also identical to the active site motif of A. ficuum phytase. Chemical probing of the active site Arg residues using both cyclohexanedione and phenylglyoxal resulted in the inactivation of phytase. The cloned A. fumigatus phytase, however, was more resistant to phenylglyoxal-induced inactivation. Both cloned A. fumigatus and A. ficuum phytases were identically affected by cyclohexanedione. Both the thermal characterization data and kinetic parameters of cloned and expressed A. fumigatus phytase indicate that this biocatalyst is not superior to the benchmark enzyme. The sequence difference between A. fumigatus and A. ficuum phytase may explain why the former enzyme catalyzes poorly compared to the benchmark enzyme. In addition, differential sensitivity toward the Arg modifier, phenylglyoxal, indicates a different chemical environment at the active site for each of the phytases.

6-Phytase↗
PubMed1998

Non-cancer risk assessment for nickel compounds: issues associated with dose-response modeling of inhalation and oral exposures.

This report presents the results of noncancer dose-response modeling for inhalation and oral exposures to nickel compounds using the NOAEL/LOAEL and benchmark dose (BMD) approaches. Several key issues associated with the implementation of the BMD approach were examined. Primary among them are difficulties associated with use of data for which the dose-response shape is poorly defined: nonuniqueness of maximum likelihood estimates and lower bounds equal to zero. In addition, several generalizable properties of the "hybrid approach" for modeling continuous endpoints were identified. A hybrid modeling approach allows one to consider "biological significance" on an individual (rather than group) basis; differences between individual- and group-based biological significance in the definition of benchmark response (BMR) levels are elucidated. In particular, it is shown that BMDs defined using group-based BMRs may be more like LOAELs than NOAELs. Application of cross-chemical and cross-endpoint comparisons suggest that, for chronic inhalation exposure, nickel sulfate appears to be as toxic or more toxic than nickel subsulfide and nickel oxide, although the high response rates for the latter two compounds at the lowest chronically administered concentration make such conclusions problematic. A nickel reference concentration could be derived based on the most sensitive benchmark concentration for chronic inhalation exposure to nickel sulfate, 1.7 x 10(-3) mg Ni/m3 for lung fibrosis in male rats. Analyses of oral studies of nickel sulfate and nickel chloride suggest that an appropriate basis for the nickel oral reference dose would be a BMD of 4-5 mg Ni/kg/day, based on increased prenatal mortality. (Uncertainty factors were not determined and neither an RfD nor an RfC was derived in this paper.) The BMD approach provides appropriate quantitative support for toxicological judgment; this paper addresses specific issues associated with the role of the BMD approach in noncancer risk assessment. Resolution of these and other issues may require the accumulation of a number of case studies such as the one presented here.

Administration, Oral↗
PubMed2004

Semi-active control of a cable-stayed bridge under multiple-support excitations.

This paper presents a semi-active strategy for seismic protection of a benchmark cable-stayed bridge with consideration of multiple-support excitations. In this control strategy, Magnetorheological (MR) dampers are proposed as control devices, a LQG-clipped-optimal control algorithm is employed. An active control strategy, shown in previous researches to perform well at controlling the benchmark bridge when uniform earthquake motion was assumed, is also used in this study to control this benchmark bridge with consideration of multiple-support excitations. The performance of active control system is compared to that of the presented semi-active control strategy. Because the MR fluid damper is a controllable energy- dissipation device that cannot add mechanical energy to the structural system, the proposed control strategy is fail-safe in that bounded-input, bounded-output stability of the controlled structure is guaranteed. The numerical results demonstrated that the performance of the presented control design is nearly the same as that of the active control system; and that the MR dampers can effectively be used to control seismically excited cable-stayed bridges with multiple-support excitations.

Computer Simulation↗
PubMed2002

Assessment of injury to fish and wildlife resources in the Grand Calumet River and Indiana Harbor Area of Concern, USA.

This article is the second in a series of three that describes the results of a Natural Resource Damage Assessment (NRDA) conducted in the Grand Calumet River and Indiana Harbor Area of Concern (IHAOC). The assessment area is located in northwest Indiana and was divided into nine reaches to facilitate the assessment. This component of the NRDA was undertaken to determine if fish and wildlife resources have been injured due to exposure to contaminants that are associated with discharges of oil or releases of other hazardous substances. To support this assessment, information was compiled on the chemical composition of sediment and tissues; on the toxicity of whole sediments, pore water, and elutriates to fish; on the status of fish communities; and on fish health. The data on each of these indicators were compared to regionally relevant benchmarks to assess the presence and extent of injury to fish and wildlife resources. The results of this assessment indicate that injury to fish and wildlife resources has occurred throughout the assessment area, with up to five distinct lines of evidence demonstrating injury within the various reaches. Based on the frequency of exceedance of the benchmarks for assessing sediment and tissue chemistry data, total polychlorinated biphenyls is the primary bioaccumulative contaminant of concern in the assessment area. It is important to note, however, that this assessment was restricted by the availability of published bioaccumulation-based sediment quality guidelines, tissue residue guidelines, and other benchmarks of sediment quality conditions. The availability of chemistry data for tissues also restricted this assessment in certain reaches of the assessment area. Furthermore, insufficient information was located to facilitate identification of the substances that are causing or substantially contributing to effects on fish (i.e., sediment toxicity, impaired fish health, or impaired fish community structure). Therefore, substances not included on the list of COCs cannot necessarily be considered to be of low priority with respect to sediment injury (e.g., metals, polycyclic aromatic hydrocarbons, alkanes, alkenes, organochlorine pesticides, phthalates, dioxins, and furans, etc.).

Animals↗
PubMed2006

Age-dependent percentile for waist circumference for Japanese children based on the 1992-1994 cross-sectional national survey data.

The aim of this study was to set forth an age-dependent percentile for waist circumference of Japanese children and to compare the reference with data from other countries. We utilized the 1992-1994 cross-sectional national survey data on waist circumference as measured at two benchmark sites in 10,614 Japanese children (5,851 boys, 4,763 girls) aged 6.0-18.0 years for constructing the reference by the LMS method. Japanese children had smaller waist circumference percentile values as compared to those of Dutch and US children, but had comparable or larger percentile values as compared to those of UK children. We suspect that the observed ethnic differences may be in part due to the differences in benchmark in waist circumference measurements in each country. We present for the first time an age-dependent percentile for waist circumference for Japanese children. It is mandatory to standardize a benchmark site for waist circumference for more meaningful international comparison.

Adolescent↗
PubMed2026

Precision targeting of teacher burnout using network-informed ecological momentary interventions.

Teacher well-being affects classroom functioning and workforce stability, yet generic digital programs rarely use person-specific affect dynamics to select support. This cluster-randomised trial evaluated whether micro-interventions selected from high expected influence (EI) nodes in teachers' contemporaneous affect networks produced larger changes in burnout-related EI and everyday happiness than content-matched random allocation. The objectives were to estimate allocation effects on changes in estimated network summaries and happiness, evaluate network change as a statistical mediator, examine personality moderation, and benchmark simpler allocation rules. A two-arm cluster randomised platform trial was conducted in 84 public schools across four urban districts in H Province. After a 14&#xa0;day baseline of ecological momentary assessment (EMA), person specific partial correlation networks were estimated for happiness, exhaustion, detachment, efficacy and rumination. An optimisation engine prioritised three brief micro-intervention types per teacher according to baseline EI, while the active control received the same library without network information. EMA continued for 8&#xa0;weeks; Bayesian multilevel models, permutation-based mediation, and benchmarking analyses were applied. EI-based targeting produced larger reductions in the composite EI-change index than active control (mean difference 0.11, 95% credible interval 0.08 to 0.14) and higher week 7 EMA happiness (4.4 points on a 0 to 100 scale, 95% credible interval 2.7 to 6.0), with a positive arm by week slope difference of 0.62 points per week (95% credible interval 0.39 to 0.85). Model-based mediation estimates were consistent with approximately one half of the happiness difference being statistically associated with change in the composite EI-change index (average conditional mediation estimate 3.5 points, 95% credible interval 2.0 to 5.2). Benchmarking showed smaller gains under severity, threshold, or group-level centrality rules. Effects were stronger among teachers higher in conscientiousness. The findings indicate that integrating EMA, network modelling, and EI-driven optimisation yields measurable gains beyond content-matched exposure, providing a proof of concept for district-scale precision mental health that requires prospective implementation testing. Replication in additional regions, expanded node sets, and longer follow up are warranted to assess durability and generalisability.

Female↗
PubMed2004

Effect of age on the use of evidence-based therapies for acute myocardial infarction.

BACKGROUND: Previous studies have documented an underuse of evidence-based therapies in patients with acute myocardial infarction (AMI). However, many of these studies failed to consider contraindications to therapy, the effect of age (ie, elderly vs non-elderly patients) on use, or both. The objective of this study was to determine whether elderly patients are less likely than non-elderly patients to receive evidence-based AMI treatments, both before and after the consideration of contraindications to therapy. METHODS: A retrospective chart review of a random sample of 5131 patients with AMI who were admitted to 1 of 44 hospitals in Ontario was conducted for the fiscal years 1994 to 1996. Using the Canadian Cardiovascular Research Team (CCORT)/Canadian Cardiovascular Society (CCS) Quality Indicators for AMI Care, we classified patients as being eligible or ideal (ie, no contraindications to treatment) candidates to receive aspirin, beta-blockers, thrombolysis, angiotensin-converting enzyme inhibitors (ACEIs), or statins or to undergo lipid profiling. The proportions of eligible and ideal patients who received treatment were calculated, and the latter were compared with benchmarks. RESULTS: The median age of the cohort was 69 years; 63% were of the patients were aged > or =65 years. There was underperformance of prescribing treatments in ideal candidates relative to benchmarks (eg, aspirin at discharge: 78.6% vs 90% benchmark). The odds of ideal (ie, no contraindications) elderly candidates receiving various evidence-based AMI treatments were consistently less than that of non-elderly patients with AMI, with the exception of ACEIs at discharge (odds ratio, 1.46; 95% CI, 1.22-1.74). CONCLUSIONS: Despite adjustments for contraindications to therapy, the underuse of AMI treatments, particularly in elderly patients, was found.

Adrenergic beta-Antagonists↗
PubMed2006

Annual bed statistics give a misleading picture of hospital surge capacity.

STUDY OBJECTIVE: I describe how annual hospital surge capacity is affected by within-year variation in patient volume and bed supply. METHODS: Surge capacity was measured as the percentage and total number of hospital beds that are not occupied by patients. Administrative data were used to calculate these bed statistics for 78 hospitals in New Jersey--statewide and by emergency planning regions--in 2003. Annual bed statistics were compared to more refined calculations for each day of the year. Calculated numbers of empty beds were compared to federal disaster planning benchmarks. RESULTS: Annual bed statistics showed no major limitations on surge capacity. Statewide occupancy rates were well below 80% (ie, more than 20% of beds were empty), and the number of empty beds that were set up and staffed (ie, maintained) was well above federal disaster planning benchmarks. In contrast, daily bed statistics reveal long periods in 2003 when regional and statewide surge capacity was severely strained. Strained capacity was most likely to occur on Tuesdays through Fridays and least likely to occur on weekends. On 212 days, statewide occupancy of maintained beds met or exceeded 85%. This occupancy rate met or exceeded 90% and 95% on 88 and 4 days, respectively. On 288 days, the statewide number of empty maintained beds fell below the federal planning benchmark. CONCLUSION: Annual bed statistics give a misleading picture of hospital surge capacity. Analysis of surge capacity should account for daily variation in patient volume and within-year variation in bed supply.

Bed Occupancy↗
PubMed2005

An optimized experimental protocol based on neuro-evolutionary algorithms application to the classification of dyspeptic patients and to the prediction of the effectiveness of their treatment.

OBJECTIVE: This paper aims to present a specific optimized experimental protocol (EP) for classification and/or prediction problems. The neuro-evolutionary algorithms on which it is based and its application with two selected real cases are described in detail. The first application addresses the problem of classifying the functional (FD) or organic (OD) forms of dyspepsia; the second relates to the problem of predicting the 6-month follow-up outcome of dyspeptic patients treated by helicobacter pylori (HP) eradication therapy. METHODS AND MATERIAL: The database built by the multicentre observational study, performed in Italy by the NUD-look Study Group, provided the material studied: a collection of data from 861 patients with previously uninvestigated dyspepsia, being referred for upper gastrointestinal endoscopy to 42 Italian Endoscopic Services. The proposed EP makes use of techniques based on advanced neuro-evolutionary systems (NESs) and is structured in phases and steps. The use of specific input selection (IS) and training and testing (T and T) techniques together with genetic doping (GenD) algorithm is described in detail, as well as the steps taken in the two benchmark and optimization protocol phases. RESULTS: In terms of accuracy results, a value of 79.64% was achieved during optimization, with mean benchmark values of 64.90% for the linear discriminant analysis (LDA) and 68.15% for the multi layer perceptron (MLP), for the classification task. A value of 88.61% was achieved during optimization for the prediction task, with mean benchmark values of 49.32% for the LDA and 70.05% for the MLP. CONCLUSIONS: The proposed EP has led to the construction of inductors that are viable and usable on medical data which is representative but highly not linear. In particular, for the classification problem, these new inductors may be effectively used on the basal examination data to support doctors in deciding whether to avoid endoscopic examinations; whereas, in the prediction problem, they may support doctors' decisions about the advisability of eradication therapy. In both cases the variables selected indicate the possibility of reducing the data collection effort and also of providing information that can be used for general investigations on symptom relevance.

Algorithms↗