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PubMed2002

Pretreatment prognostic factors for survival in patients with advanced urothelial tumors treated in a phase I/II trial with paclitaxel, cisplatin, and gemcitabine.

BACKGROUND: New chemotherapeutic agents, including paclitaxel and gemcitabine, are active in advanced bladder carcinoma, and combination regimens with these agents have shown promising results. Unlike conventional chemotherapy regimens, such as methotrexate, vinblastine, doxorubicin, and cisplatin, there are no data available on key predictive factors for response and survival with these novel agents. Since this information is needed for selection of patients for these new combinations and for stratification purposes in ongoing randomized trials, the authors aimed to study the predictive factors for response and survival to the current regimen containing cisplatin, paclitaxel, and gemcitabine. METHODS: The authors studied 56 patients with advanced urothelial tumors treated on a Phase I/II trial of paclitaxel, cisplatin, and gemcitabine (TCG) to identify pretreatment characteristics that were prognostic for survival using this novel combination. The pretreatment characteristics analyzed were age, gender, Eastern Cooperative Oncology Group performance status, histopathology (pure transitional versus other), visceral (liver, lung, or bone) metastasis, number of sites of disease, lactate dehydrogenase, and hemoglobin. RESULTS: The factors that were associated with a worse survival in univariate analysis were performance status > 0, presence of visceral metastasis, and more than one site of malignant disease. In a multivariate model, performance status (P = 0.044) and visceral disease (P = 0.008) showed independent statistical significance for decreased survival. Patients were then grouped based on these two independent prognostic factors. Median survival times in the groups of patients with zero, one, or two of these risk factors were 32.8 months, 17 months, and 9.6 months, respectively (P = 0.0005). CONCLUSIONS: A pretreatment performance status > 0 and the presence of visceral metastasis have a profound impact on survival when using the TCG regimen. These two variables will be used to stratify patients in the upcoming Phase III randomized trial comparing this TGC regimen with a gemcitabine/cisplatin regimen in advanced urothelial tumors.

Adult↗

PubMed2004

Assessing the cognitive abilities that differentiate patients with Alzheimer's disease from normals: single and multiple factor models.

BACKGROUND: Understanding the structure of cognitive abilities in Alzheimer's disease (AD) has considerable practical and theoretical importance. Some investigators have argued that a single cognitive process underlies the deficits seen in AD, while others have argued for multiple cognitive processes. As deficits in cognitive abilities may reflect the pathological process or processes occurring in AD, determination of the structure of abilities in AD is important. OBJECTIVES: The purpose of this study was to assess the utility of single and multiple ability factor models in differentiating patients with AD from normals. RESULTS: Findings show that although a single factor model accounts for a large part of the variability of a battery of measures used to differentiate patients and normals, a multiple factor model performed substantially better based on multiple fit criteria. CONCLUSIONS: At least in this sample, a multiple ability factor model of cognitive abilities fit data better than a single factor model in differentiating patients with AD from normals.

Activities of Daily Living↗

PubMed2002

Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches.

The Drosophila segment polarity genes constitute the last tier in the segmentation cascade; their job is to maintain the boundaries between parasegments and provide positional "read-outs" within each parasegment for the entire developmental history of the animal. These genes constitute a relatively well-defined network with a relatively well-understood patterning task. In a previous publication (von Dassow et al. 2000. Nature 406:188-192) we showed that a computer model predicts the segment polarity network to be a robust boundary-making device. Here we elaborate those findings. First, we explore the constraints among parameters that govern the network model. Second, we test architectural variants of the core network, and show that the network tolerates a wide variety of adjustments in design. Third, we evaluate several topologically identical models that incorporate more or less molecular detail, finding that more-complex models perform noticeably better than simplified ones. Fourth, we discuss two instances in which the failure of the network model to behave in a life-like fashion highlights mechanistic details that need further experimental investigation. We conclude with an explanation of how the segment polarity network can be understood as an interwoven conspiracy of simple dynamical elements, several bistable switches and a homeostat. The robustness with which the network as a whole maintains a spatial regime of stable cell state emerges from generic dynamical properties of these simple elements.

Animals↗

PubMed1984

An econometric model of internal migration and development: extensions and tests.

The author extends a previous work on migration in Italy "from 1958-1976 to 1958-1981, tests for the stability of the model and its coefficients, and uses the model for policy simulations and forecasting. The model performs as well over the extended sample period as over the original period and, even more important..., the model is found to be quite stable. This is remarkable in view of the economic turmoil that characterized the years by which the original sample period was extended."

Demography↗

PubMed2006

QSAR study of anticoccidial activity for diverse chemical compounds: prediction and experimental assay of trans-2-(2-nitrovinyl)furan.

In this work we report a QSAR model that discriminates between chemically heterogeneous classes of anticoccidial and non-anticoccidial compounds. For this purpose we used the Markovian Chemicals in silico Design (MARCH-INSIDE) approach J. Mol. Mod.2002, 8, 237-245; J. Mol. Mod.2003, 9, 395-407]. Linear discriminant analysis allowed us to fit the discriminant function. This function correctly classifies 86.67% of anticoccidial compounds and 96.23% of inactive compounds in the training series. Overall classification is 94.12%. We validated the model by means of an external predicting series, with 86.96% of global predictability. Remarkably, the present model is based on topological as well as configuration-dependent molecular descriptors. Therefore, the model performs timely calculations and allows discrimination between Z/E and chiral isomers. Finally, to exemplify the use of the model in practice we report the prediction and experimental assay of trans-2-(2-nitrovinyl)furan. It is notable that lesion control was 72.86% at mg/kg of body weight with respect to 60% at 125 mg/kg for amprolium (control drug). The back-projection map for this compound predicts a high level of importance for the double bond and for the nitro group in the trans position. We conclude that the MARCH-INSIDE approach enables the accurate fast track identification of anticoccidial hits. Moreover, trans-2-(2-nitrovinyl)furan seems to be a promising drug for the treatment of coccidiosis.

Animals↗

PubMed2025

Predicting natural variation in the yeast phenotypic landscape with machine learning.

Most organismal traits result from the complex interplay of many genetic and environmental factors, making their prediction difficult. Here, we used machine learning (ML) models to explore phenotype predictions for 223 traits measured across 1011 genome-sequenced Saccharomyces cerevisiae strains isolated worldwide. We benchmarked a ML pipeline with multiple linear and non-linear models to predict phenotypes from genotypes and gene expression, and determined gradient boosting machines as the best-performing model. Gene function disruption scores and gene presence/absence emerged as best predictors, suggesting a considerable contribution of the accessory genome in controlling phenotypes. The prediction accuracy broadly varied among phenotypes, with stress resistance being easier to predict compared to growth across nutrients. ML identified relevant genomic features linked to phenotypes, including high-impact variants with established relationships to phenotypes, despite these being rare in the population. Near-perfect accuracies were achieved when other phenomics data mostly in similar conditions were used, suggesting that useful information can be conveyed across phenotypes. Overall, our study underscores the power of ML to interpret the functional outcome of genetic variants.

Genetic Variation↗

PubMed2002

Impact of different measures of comorbid disease on predicted mortality of intensive care unit patients.

BACKGROUND: Valid comparison of patient survival across ICUs requires adjustment for burden of chronic illness. The optimal measure of comorbidity in this setting remains uncertain. OBJECTIVES: To examine the impact of different measures of comorbid disease on predicted mortality for ICU patients. DESIGN: Retrospective cohort study. SUBJECTS: Seventeen thousand eight hundred ninety-three veterans from 17 geographically diverse VA Medical Centers and 43 ICUs were studied, admitted between February 1, 1996 and July 31, 1997. MEASURES: ICD-9-CM codes reflecting comorbid disease from hospital stays before and including the index hospitalization from local VA computer databases were extracted, and three measures of comorbid disease were then compared: (1) an APACHE-weighted comorbidity score using comorbid diseases used in APACHE, (2) a count of conditions described by Elixhauser, and (3) Elixhauser comorbid diseases weighted independently. Univariate analyses and multivariate logistic regression models were used to determine the contribution of each measure to in-hospital mortality predictions. RESULTS: Models using independently weighted Elixhauser comorbidities discriminated better than models using an APACHE-weighted score or a count of Elixhauser comorbidities. Twenty-three and 14 of the Elixhauser conditions were significant univariate and multivariable predictors of in-hospital mortality, respectively. In a multivariable model including all available predictors, comorbidity accounted for less (8.4%) of the model's uniquely attributable chi statistic than laboratory values (67.7%) and diagnosis (17.7%), but more than age (4.0%) and admission source (2.1%). Excluding codes from prior hospitalizations did not adversely affect model performance. CONCLUSIONS: Independently weighted comorbid conditions identified through computerized discharge abstracts can contribute significantly to ICU risk adjustment models.

APACHE↗

PubMed2006

Population pharmacokinetics of darbepoetin alfa in healthy subjects.

AIM: To develop and evaluate a population pharmacokinetic (PK) model of the long-acting erythropoiesis-stimulating protein, darbepoetin alfa in healthy subjects. METHODS: PK profiles were obtained from 140 healthy subjects receiving single intravenous and/or single or multiple subcutaneous doses of darbepoetin alfa (0.75-8.0 microg kg(-1), or either 80 or 500 microg). Data were analysed by a nonlinear mixed-effects modelling approach using NONMEM software. Influential covariates were identified by covariate analysis emphasizing parameter estimates and their confidence intervals, rather than stepwise hypothesis testing. The model was evaluated by comparing simulated profiles (obtained using the covariate model) to the observed profiles in a test dataset. RESULTS: The population PK model, including first-order absorption, two-compartment disposition and first-order elimination, provided a good description of data. Modelling indicated that for a 70-kg human, the observed nearly twofold disproportionate dose-exposure relationship at the 8.0 microg kg(-1)-dose relative to the 0.75 microg kg(-1)-dose may reflect changing relative bioavailability, which increased from approximately 48% at 0.75 microg kg(-1) to 78% at 8.0 microg kg(-1). The covariate analysis showed that increasing body weight may be related to increasing clearance and central compartment volume, and that the absorption rate constant decreased with increasing age. The full covariate model performed adequately in a fixed-effects prediction test against an external dataset. CONCLUSION: The developed population PK model describes the inter- and intraindividual variability in darbepoetin alfa PK. The model is a suitable tool for predicting the PK response of darbepoetin alfa using clinically untested dosing regimens.

Darbepoetin alfa↗

PubMed2006

Validation of two prognostic models predicting outcome at two years after diagnosis in a new cohort of children with epilepsy: the Dutch Study of Epilepsy in Childhood.

PURPOSE: To validate two prognostic models for childhood-onset epilepsy designed to predict a terminal remission of <6 months at 2 years after diagnosis in children referred to the hospital. METHODS: A hospital-based cohort of children with newly diagnosed epilepsy was recruited and followed up for 2 years to validate previously developed models. One model was based on variables collected at intake, and the other was based on intake variables plus variables collected during the first 6 months of follow-up. The accuracy of both models was estimated by measuring the area under the receiver-operant-characteristic curves (ROC area). RESULTS: The ROC area of the model developed with intake variables was 0.69 [95% confidence interval (CI), 0.64-0.74] for the original cohort and 0.62 (95% CI, 0.55-0.69) for the validation cohort. The best combination of sensitivity and specificity for the original cohort was 61.6% and 69.1%, whereas it was 60.0% and 61.4% for the validation cohort. For the model with intake and 6-month variables combined, the ROC area was 0.78 (95% CI, 0.73-0.82) for the original cohort and 0.71 (95% CI, 0.64-0.78) for the validation cohort. The sensitivity and specificity were 72.6% and 73.1%, respectively, for the original cohort and 67.4% and 60.2%, respectively, for the validation cohort. CONCLUSIONS: Although both models predict outcome better than chance, they are insufficiently accurate to be of practical value. Both models performed marginally less well with the validation cohort than with the original cohort, but in both instances, the model based on intake and 6-month variables was more accurate.

Adolescent↗

PubMed1993

Quality of laboratory performance in testing for human immunodeficiency virus type 1 antibody. Identification of variables associated with laboratory performance.

To identify factors that may affect the quality of laboratory performance of human immunodeficiency virus type 1 (HIV-1) antibody testing, the Centers for Disease Control and Prevention Model Performance Evaluation Program surveyed laboratories in 1989 that performed enzyme immunoassay (EIA) and Western blot tests for HIV-1 antibody. Panels of 10 HIV-1-antibody-positive and antibody-negative plasma samples, some of which were duplicates, were mailed to program-participating laboratories. Laboratories were also mailed survey questionnaires to ascertain their laboratory characteristics and testing practices. Using 1988 data, researchers previously found that the overall analytic performance of laboratories performing HIV-1 antibody testing was independently associated with the following: (1) requiring a minimum degree of testing personnel; (2) having written criteria for identifying unsatisfactory specimens; (3) requiring in-house training for testing personnel; (4) having tested more than 10,000 specimens; (5) being identified as an "other" laboratory type; (6) having more than 24 months of testing experience; (7) laboratory uses specific (Abbott) materials for EIA; and (8) testing specimens collected by family-planning clinics. To verify these findings, we performed multivariate analysis on 1989 performance data. For the 1989 EIA analytic sensitivity, significant positive (P < or = .05) associations were detected with having written criteria for identifying unsatisfactory specimens and with having tested more than 10,000 specimens. For the 1989 overall EIA analytic performance, a significant negative (P < or = .05) association was found with using specific (Abbott) EIA materials, and a significant positive (P < or = .05) association was found with having tested more than 10,000 specimens. For Western blot results, the only significant (P < or = .05) associations were for both analytic sensitivity and overall analytic performance and having tested more than 10,000 specimens.

Blotting, Western↗

PubMed2005

Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method.

A recently developed force-matching method for obtaining effective force fields for condensed matter systems from ab initio molecular dynamics (MD) simulations has been applied to fit a simple nonpolarizable two-site pairwise force field for liquid hydrogen fluoride. The ab initio MD in this case was a Car-Parrinello (CP) MD simulation of 64 HF molecules at nearly ambient conditions within the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure included a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The performance of the force-match potential was examined for the gas-phase dimer and for the liquid phase at various temperatures. The model was able to reproduce correctly the bent structure and energetics of the gas-phase dimer, while the results for the structural properties, self-diffusion, vibrational spectra, density, and thermodynamic properties of liquid HF were compared to both experiment and the CP MD simulation. The force-matching model performs well in reproducing nearly all of the liquid properties as well as the aggregation behavior at different temperatures. The model is computationally cheap and compares favorably to many more computationally expensive potential energy functions for liquid HF.

Chemistry, Physical↗

PubMed2026

Genetic Susceptibility to Incisional Hernia Evaluation of Hernia Polygenic Risk Scores.

OBJECTIVES: Incisional hernia (IH) affects 13-30% of people after abdominal surgery, resulting in substantial morbidity and costs. While clinical risk factors have been studied extensively, genomic risk for IH is incompletely understood. We aimed to evaluate the impact of polygenic risk scores (PRS) on IH risk prediction. METHODS: We created and evaluated three PRS for abdominal hernia, ventral hernia and latent hernia susceptibility for prediction of IH in an institutional biobank. The primary outcome was defined as the diagnosis or repair of an IH based on ICD-9/10-CM/PCS and CPT codes. Clinical covariates included age, sex, body mass index (BMI), smoking status, index procedure type, and perioperative surgical site infection. A phenome-wide association study (PheWAS) was performed to assess clinical associations with increased PRS. We then tested the ability of the PRS to improve prediction for IH by modeling clinical covariates with and without PRS in patients who underwent abdominal surgery. Model performance was assessed using 10 iterations of 5-fold cross-validation to estimate Brier scores and area under the receiver operating characteristic curve (AUROC), which were compared using cross-model Bayesian analysis of variance. RESULTS: In 55,809 subjects, assessed PRS was significantly associated with incisional, umbilical, and ventral hernia on PheWAS, with 1.19 greater odds of developing IH per 1-SD increase in PRS (95% CI: 1.13-1.25, P < 0.001). Of 9,909 subjects who underwent qualifying abdominal surgery, 706 developed IH. In this cohort, the latent hernia susceptibility PRS was associated with a 16% increased hazard of developing IH per 1-SD increase (HR 1.16; 95% CI: 1.07-1.26; P < 0.001). Compared to a predictive model using clinical covariates (Brier score = 0.047, 95% CI: 0.046-0.048; AUROC = 0.660, 95% CI: 0.653-0.666), addition of the PRS showed similar Brier score and AUROC estimates (Brier score = 0.047, 95% CI: 0.046-0.048; AUROC: 0.667, 95% CI: 0.661-0.673) at five years. Cross-model Bayesian analysis demonstrated >99% probability of practical equivalence when trying to detect a difference of ≥ 0.02. CONCLUSION: All three PRS for hernia were independently associated with IH, suggesting that genomic factors contribute significantly to IH development. However, none of the three PRS meaningfully improved clinical IH risk prediction in patients who underwent abdominal surgery. This suggests that clinical comorbidities and surgical techniques may be equally as important as genomic architecture.

Bayesian analysis↗

PubMed1991

Adequacy of a systems structure in the modeling of training effects on performance.

A systems model of training effects on performance was applied to eight initially untrained subjects who were volunteers for an endurance training program for the purpose of verifying the statistical adequacy of the systems structure. In the model initially proposed by T. W. Calvert, E. W. Banister, M. V. Savage, and T. Bach (IEEE Trans. Syst. Man Cybern. 6: 94-102, 1976), the performance changes were related to the successive training loads by three first-order transfer functions. In the present study, the number of first-order components was statistically tested. A model including only one component, which had a positive effect on the performance, provided a significant fit with the performances in every subject. A second component significantly improved the fit in only two subjects. This further component, which had a negative effect on performance, was identified as fatigue. Nevertheless, a two-antagonistic component model is proposed to provide a good representation of the training responses. However, the low level of exercise demands and the inaccuracy of the fit could have impaired the evidencing of a fatiguing effect during the presently studied training protocol.

Adult↗

PubMed2006

Prediction of dry matter intake throughout lactation in a dynamic model of dairy cow performance.

In the dynamic modeling of dairy cow performance over a full lactation, the difference between net energy intake and net energy used for maintenance, growth, and output in milk accumulates in body reserves. A simple dynamic model of net energy balance was constructed to select, out of some common dry matter intake (DMI) prediction equations, the one that resulted in a minimum cumulative bias in body energy deposition. Dry matter intake was predicted using the Cornell Net Carbohydrate and Protein System, Agricultural Research Council, or National Research Council (NRC) DMI equations from body weight (BW) and predicted fat-corrected milk yield. The instantaneous BW of cows at progressive weeks of lactation was simulated as the numerical integral of the BW change obtained from the predicted net energy balance. Predicted DMI and BW from each DMI equation, using either of 2 equations to describe maintenance energy expenditures, were compared statistically against observed data from 21 herd average published full lactation data sets. All DMI equations underpredicted BW and DMI, but the NRC DMI equation resulted in the minimum cumulative error in predicted BW and DMI. As a general solution to prevent predicted BW from deviating substantially over time from the observed BW, a lipostatic feedback mechanism was integrated into the NRC DMI equation as a 2-parameter linear function of the relative size of simulated body reserves and week of lactation. Residual sum of squares was reduced on average by 52% for BW predictions and by 41% for DMI predictions by inclusion of the negative feedback with parameters taken from the average of all 21 least squares fits. Similarly, root mean square prediction error (%) was reduced by 30% on average for BW predictions and by 23% for DMI predictions. Inclusion of a feedback of energy reserves onto predicted DMI, simulating lipostatic regulation of BW, solved the problem of final BW deviation within a dynamic model and improved its DMI prediction to a satisfactory level.

Adipose Tissue↗

PubMed2003

Performance, treatment pathways, and effects of alternative policy options for screening for developmental dysplasia of the hip in the United Kingdom.

AIMS: To compare, using a decision model, performance, treatment pathways and effects of different newborn screening strategies for developmental hip dysplasia with no screening. METHODS: Detection rate, radiological absence of subluxation at skeletal maturity and avascular necrosis of the femoral head, as favourable and unfavourable treatment outcomes respectively, were compared for the following strategies: clinical screening alone using the Ortolani and Barlow tests; the addition of static and dynamic ultrasound examination of the hips of all infants (universal ultrasound) or restricted to infants with defined risk factors (selective ultrasound); "no screening" (that is, clinical diagnosis only). RESULTS: Universal or selective ultrasound detects more more affected children (76% and 60% respectively) than clinical screening alone (35%), results in a higher proportion of affected children with favourable treatment outcomes (92% and 88% respectively) than clinical screening alone (78%) or no screening (75%), and the highest proportion of these achieved without recourse to surgery (64% and 79% respectively) compared with clinical screening alone (18%). However, ultrasound based strategies are also associated with the highest number of unfavourable treatment outcomes arising in unaffected children treated following a false positive screening result. The detection rate of clinical screening alone becomes similar to that reported for universal ultrasound when based on studies using experienced examiners (80%) rather than junior medical staff (35%). CONCLUSION: From the largely observational data available, ultrasound based screening strategies appear to be most sensitive and effective but are associated with the greatest risk of potential adverse iatrogenic effects arising in unaffected children.

Child↗

PubMed2002

Finding downbeats with a relaxation oscillator.

A relaxation oscillator model of neural spiking dynamics is applied to the task of finding downbeats in rhythmical patterns. The importance of downbeat discovery or 'beat induction' is discussed, and the relaxation oscillator model is compared to other oscillator models. In a set of computer simulations the model is tested on 35 rhythmical patterns. The model performs well, making good predictions in 34 of 35 cases. In an analysis we identify some shortcomings of the model and relate model behavior to dynamical properties of relaxation oscillators.

Attention↗

PubMed2006

Assessment of the human epidermis model SkinEthic RHE for in vitro skin corrosion testing of chemicals according to new OECD TG 431.

Based on two successfully completed ECVAM validation studies for in vitro skin corrosion testing of chemicals, the National Co-ordinators of OECD Test Guideline Programme endorsed in 2002 two new test guidelines: TG 430 'Transcutaneous Electrical Resistance assay' and TG 431 'Human Skin Model Test'. To allow all suitable in vitro human reconstructed (dermal or epidermal) models to be used for skin corrosion testing, the OECD TG 431 defines general and functional conditions that the model must meet before it will be routinely used for skin corrosion testing. In addition, the guideline requires correct prediction of 12 reference chemicals and assessment of intra- and inter-laboratory variability. To show that the OECD TG 431 concept works, in 2003 ZEBET tested several chemicals from the ECVAM validation trials on the SkinEthic reconstituted human epidermal (RHE) model. Based on knowledge that reconstructed human skin models perform similarly in toxicological studies, it was decided to adopt the validated EpiDerm skin corrosion test protocol and prediction model to the SkinEthic model. After minor technical changes, classifications were obtained in concordance with those reported for the validated human skin models EPISKIN and EpiDerm. To allow adequate determination of inter-laboratory reproducibility, a blind trial was conducted in three laboratories -- ZEBET (D), Safepharm (UK) and BASF (D), in which the 12 endorsed reference chemicals were tested. Results obtained with the SkinEthic epidermal model were reproducible, both within and between laboratories, and over time. Concordance between the in vitro predictions of skin corrosivity potential obtained with the SkinEthic model and the predictions obtained with the accepted tests of OECD TG 430 and TG 431 was very good. The new test was able to distinguish between corrosive and non-corrosive reference chemicals with an accuracy of 93%.

Caustics↗

PubMed1996

Change processes in a creation of meaning event.

Creation of meaning events are in-therapy change episodes that occur when a patient seeks to understand the meaning of an emotional experience. A performance model of this task was developed in an earlier study. The present study was conducted to determine which client performance components distinguish successful from unsuccessful creation of meaning episodes. Measures of referential activity were also applied to the events and uncovered important features of the therapist intervention that accompanied successful meaning making. The implications of these results for psychotherapy are discussed.

Adult↗