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At least 217 records · Page 12Linked to original sources
PubMed1989

Future imperfect: the limitations of clinical prediction models and the limits of clinical prediction.

Stepwise regression procedures are often used to identify a small set of variables that serve as important predictors of clinical outcome and to construct prediction models based on those variables. Several theoretical and practical limitations of this process are discussed and highlighted with a variety of examples from published reports. Wider appreciation of these limitations should encourage the development of more relevant models, and thereby improve the quality of clinical prediction.

Models, Statistical↗
PubMed2005

Three-dimensional structure prediction of bovine AP lyase, BAP1: prediction of interaction with DNA and alterations as a result of Arg176-->Ala, Asp282-->Ala, and His308-->Asn mutations.

BAP1 is an apurinic/apyrimidinic lyase (AP lyase) that plays an important role in the repair of DNA damage. The present study deals with the prediction of the 3D structure of bovine AP lyase based on its sequence homology with human AP lyase. The predicted 3D model of bovine AP1 shows remarkable similarity with human endonuclease in the overall 3D fold. However, significant differences in the model and the X-ray structure were located at some of the important sites. We have analyzed the active center of the enzyme and other sites that are involved in DNA repair. A number of amino acids bind the bases located in the major/minor grooves of DNA. An insertion of Arg176 in the major groove and Met270 in the minor groove caps the DNA bound enzyme's active site, stabilizing the extra helical AP site conformation and effectively locking the protein onto the AP-DNA. Three BAP1 mutants were also modeled and analyzed as regards the changes in the structure. Substitution of Arg176-->Ala leads to the loss of DNA binding whereas mutation of Asp282-->Ala and His308-->Asn leads to a decrease in the enzymatic activity.

Amino Acid Substitution↗
PubMed2026

Protocol to predict gene expression from transcriptomic data using PREDICT.

Linking DNA sequence variation to context-specific transcriptional programs is a critical challenge in regulatory genomics, especially for non-model organisms. Here, we present PREDICT, a modular Python package for discovering cis-regulatory elements and transcription factor binding motifs. We describe steps to identify enriched k-mers from differentially expressed genes, map them to known motifs, quantify their impact on gene expression, and visualize motif co-occurrences. PREDICT provides a robust, k-mer-based approach to uncover regulatory logic in diverse genomic systems. For complete details on the use and execution of this protocol, please refer to Yen et al. and Liu et al.1,2.

Gene Expression Profiling↗
PubMed2002

Predicting anxious response to a social challenge: the predictive utility of the social interaction anxiety scale and the social phobia scale in a college population.

Trait anxiety is believed to be a hierarchical construct composed of several lower-order factors (Adv. Behav. Res. Therapy, 15 (1993) 147; J. Anxiety Disorders, 9 (1995) 163). Assessment devices such as the Social Interaction Anxiety Scale, the Social Phobia Scale (SIAS and SPS; Behav. Res. Therapy, 36 (4) (1998) 455), and the Anxiety Sensitivity Index (ASI; Behav. Res. Therapy, 24 (1986) 1) are good measures of the presumably separate lower-order factors. This study compared the effectiveness of the SIAS, SPS, ASI-physical scale and STAI-T (State-Trait Anxiety Inventory. Palo Alto, CA: Consulting Psychologists Press (1970)) as predictors of anxious response to a social challenge (asking an aloof confederate out on a date). Consistent with the hierarchical model of anxiety, the measures of trait anxiety were moderately correlated with each other and each was a significant predictor of anxious response. The specific measures of trait social anxiety were slightly better predictors of anxious response to the social challenge than was either the ASI-physical scale or the STAI-T. The results provide evidence of the predictive validity of these social trait measures and some support for their specificity in the prediction of anxious response to a social challenge.

Adult↗
PubMedDate not supplied

Is it possible to predict limb viability in complex Gustilo IIIB and IIIC tibial fractures? A comparison of two predictive indices.

The patient with severe lower limb trauma presents a management dilemma; whether to amputate primarily or to attempt limb salvage. In recent years, many predictive indices have been published which purport to identify limbs which are non-viable. We retrospectively applied two recently described indices, the Mangled Extremity Severity Score (MESS) and the Limb Salvage Index (LSI), to 54 limbs in 50 patients with either Gustilo IIIB or IIIC complex tibial fractures. There were 22 amputations (40.7 per cent) in the series. The mean MESS score in the limb salvage group was 3.8 (range 2-10), and the mean MESS score in the amputation group was 7.7 (range 4-13) (P < 0.0001). The mean LSI score in the limb salvage group was 3.6 (range 3-8), and the mean LSI score in the amputation group was 6.9 (P < 0.01). However, in the group with MESS scores > 7 (which recommends amputation), there were three limbs which were salvaged with acceptable functional outcome. Similarly, in those with LSI scores > 6 (which recommends amputation), there were seven limbs successfully salvaged. A MESS > 7 offered a greater relative risk of amputation (9.2) than a LSI score > 6 (5.3). We found both indices of use in predicting limb salvage and functional outcome. However, neither is sufficiently accurate to be considered absolutely reliable in clinical practice.

Adolescent↗
PubMed2002

Combining fuzzy querying of imprecise data and predictive microbiology using category-based reasoning for prediction of the possible microbial spoilage in foods: application to Listeria monocytogenes.

Various predictive models of microbial behavior have been created and extensive data collection has been done by numerous private or public laboratories. However, significant differences between predicted and observed values in foods have been observed and need to be stressed, understood and explained as much as possible. In this paper, we present a software tool (currently at the level of a prototype) able: (i) to store in a database all relevant information expressed on one hand as qualitative or quantitative data and on the other hand as precise or imprecise data; (ii) to retrieve the more relevant information from the database using queries where criteria may be expressed as fuzzy values in order to enhance the flexibility of the search: (iii) to compute, in addition to the nearest data, an estimation of searched values using statistical models. The architecture of this software tool is structured as a category-based reasoning system. Example queries about Listeria monocytogenes (L. monocytogenes) illustrate the functionalities of this tool.

Computer Simulation↗
PubMed1987

Radial keratotomy: analysis of efficacy and predictability in 1,058 consecutive cases. Part II: Predictability.

Effectiveness and predictability of anterior radial keratotomy to correct myopia and/or astigmatism were evaluated in 1,058 consecutive surgeries. The surgical technique, results, and comparison to other series are detailed in Part I. In this paper, a retrospective study for predicting the change in refraction of eyes having radial keratotomy with and without astigmatism incisions, statistically derived predictors accounted for 72.9% of the variations in outcome.

Adult↗
PubMed2005

Predicting the impact of new health technologies on average length of stay: development of a prediction framework.

OBJECTIVES: The aim of this study was to develop a framework to predict the impact of new health technologies on average length of hospital stay. METHODS: A literature search of EMBASE, MEDLINE, Web of Science, and the Health Management Information Consortium databases was conducted to identify papers that discuss the impact of new technology on length of stay or report the impact with a proposed mechanism of impact of specific technologies on length of stay. The mechanisms of impact were categorized into those relating to patients, the technology, or the organization of health care and clinical practice. RESULTS: New health technologies have a variable impact on length of stay. Technologies that lead to an increase in the proportion of sicker patients or increase the average age of patients remaining in the hospital lead to an increase in individual and average length of stay. Technologies that do not affect or improve the inpatient case mix, or reduce adverse effects and complications, or speed up the diagnostic or treatment process should lead to a reduction in individual length of stay and, if applied to all patients with the condition, will reduce average length of stay. CONCLUSIONS: The prediction framework we have developed will ensure that the characteristics of a new technology that may influence length of stay can be consistently taken into consideration by assessment agencies. It is recognized that the influence of technology on length of stay will change as a technology diffuses and that length of stay is highly sensitive to changes in admission policies and organization of care.

Biomedical Technology↗
PubMed2003

Predicting drug metabolism: a site of metabolism prediction tool applied to the cytochrome P450 2C9.

The aim of the present study is to develop a method for predicting the site at which molecules will be metabolized by CYP 2C9 (cytochrome P450 2C9) using a previously reported protein homology model of the enzyme. Such a method would be of great help in designing new compounds with a better pharmacokinetic profile, or in designing prodrugs where the compound needs to be metabolized in order to become active. The methodology is based on a comparison between alignment-independent descriptors derived from GRID Molecular Interaction Fields for the CYP 2C9 active site, and a distance-based representation of the substrate. The predicted site of metabolism is reported as a ranking list of all the hydrogen atoms of each substrate molecule. Eighty-seven CYP 2C9-catalyzed oxidative reactions reported in the literature have been analyzed. In more than 90% of these cases, the hydrogen atom ranked at the first, second, or third position was the experimentally reported site of oxidation.

Animals↗
PubMed1999

Predicting patients' responses to psychotherapy: are some more predictable than others?

Patient profiling predicts improvement across psychotherapy sessions on the basis of intake clinical characteristics. Patients completed questionnaires before their 1st session and at other points during treatment. After using hierarchical linear modeling to calculate expected courses of improvement, 1/2 of the sample was divided into 1 of 2 groups: those whose treatment responses across sessions matched or exceeded their expected courses (75% of the sample) and those whose responses failed to match expectations. A discriminant function analysis indicated that the groups could be differentiated on the basis of intake characteristics; that is, patients with higher discriminant scores were more likely than those with low discriminant scores to have responded to psychotherapy as predicted. Successful cross-validation of the predictor weights was performed with the other 1/2 of the sample.

Adult↗
PubMed2006

Stress versus discrete negative emotions in the prediction of physical complaints: does predictive utility vary across ethnic groups?

Reports of stress and negative emotion are important predictors of health. However, whether discrete emotions or stress measures are more useful, whether they contribute independently to outcome, and whether they relate to health equally across ethnic groups remain unclear. In the current study, 207 US-born European American, US-born African American, Black English-speaking Caribbean, and Dominican men aged 40 years and older completed measures of somatic symptoms, trait emotions, and stress. Sadness and stress independently predicted symptom reports, even when examined concurrently, and with demographics controlled; trait anger did not predict symptoms. Moreover, the relations between trait emotions and symptoms varied across groups. Levels of sadness were associated with greater symptoms among US-born European American and Dominican men, but negatively associated among Black English-speaking Caribbean men, and the relations for anger also differed marginally across groups. The results underscore the importance of differentiating among discrete emotions and stress and considering ethnic interactions when examining reports of somatic symptomology. We suggest that the impact of psychological characteristics on health must be considered within cultural and ethnic contexts to be fully understood.

Adult↗
PubMed2001

Computer-aided 3-D simulation and prediction of craniofacial surgery: a new approach.

Background: In plastic and reconstructive craniofacial surgery, careful preoperative planning is essential. In complex cases of craniofacial synostosis, rapid prototyping models are used to simulate the surgery and reduce operating time. Recently, 3-D CT model surgery has been introduced for presurgical planning and prediction of the postoperative result. Objective: For simulation of craniofacial surgery a computer-based system was developed that allows visualization and manipulation of CT-data using computer graphics techniques. Surgical procedures in all areas of the bony skull can be performed interactively. Results: The case of a child with scaphocephalus is presented. Surgery is planned using the craniofacial surgery simulator described above. Conclusion: The computer-based interactive surgery simulation systems presented here allow precise visualization of craniofacial surgery. The accurate computer-aided 3-D simulation of bone displacements is also the prerequisite for transfer of the simulated surgery using a navigation system for surgery. Thus the preoperatively planned procedure could be transferred directly to the operating table. Copyright 2001 European Association for Cranio-Maxillofacial Surgery.

Journal Article↗
PubMed1974

Prediction of secondary structure of proteins. A comparison of the phi, psi angles previously predicted for cytochrome c with recent x-ray crystallographic findings.

Newer data from the x-ray crystallographic studies of tuna heart ferrocytochrome c have increased the number of residues in alpha-helical segments. This provided an objective test of our method of predicting varphi,Psi values for cytochrome c using the sequences of 18 cytochromes c and twenty 20 x 20 tables for the varphi,Psi values of tripeptides in 10 other proteins whose three-dimensional structures were known from x-ray crystallographic studies. Of the 32 residues now considered from x-ray data to be in alpha-helices, 27 had been predicted to be in the alpha-helical domain.

Animals↗
PubMed2004

Predicting effective caloric value of nonnutritive factors: I. Pellet quality and II. Prediction of consequential formulation dead zones.

Two experiments were conducted with male broilers to 1) establish a methodology for predicting effective caloric value (ECV), defined as dietary caloric density (CD) necessary for broilers to achieve specific BW and feed conversion ratio (FCR) combinations under standardized conditions and 2) quantify the ECV attributable to pellet quality (PQ), defined as the pellet to pellet fines ratio in the feeder. In experiment 1, chicks were reared to 56 d on diets varying in CD. Dietary caloric densities examined ranged from 2,650 to 3,250 kcal of MEn/kg. Pen BW, feed intake, and FCR were measured at 21, 42, and 56 d. On 42 and 56 d, carcass traits were measured. Increasing CD significantly enhanced BW, energy consumption, and FCR. Feed intake remained similar across the upper 3 CD treatments to 42 d. By d 56, feed consumption tended to decline as CD increased. Increasing CD beyond 3,066 kcal of MEn/kg diet did not increase lean tissue accretion, while fat deposition rose disproportionately. Experiment 1 results enabled development of equations whereby CD, hence ECV, might be predicted using BW and FCR. In experiment 2, 38-d-old broilers were used to evaluate PQ effects on growth, feed intake, FCR, and behavior in a 7-d FCR assay. The BW gain and FCR were significantly enhanced by pelleting and were positively correlated with PQ. Feed intake was not affected by PQ. The experiment 1 model was validated for experiment 2, as it closely estimated the CD for diets of similar PQ used in experiment 1. Results suggest pelleting contributes 187 kcal/kg of diet at 100% PQ and that the ECV declines curvilinearly as PQ falls. Birds were observed eating less and resting more as PQ increased, suggesting that ECV of pelleting is mediated by energy expenditure for activity. These studies provide a method for estimating ECV of nonnutritive factors that impact BW, FCR, or both. Further, the application reveals potential for creation of formulation "dead zones" whereby dietary changes to enhance CD may be offset due to reduced ECV.

Animal Nutritional Physiological Phenomena↗
PubMed1991

Mortality prediction models in intensive care: acute physiology and chronic health evaluation II and mortality prediction model compared.

OBJECTIVE: To compare the Acute Physiology and Chronic Health Evaluation (APACHE II) score with the Mortality Prediction Model (MPM). DESIGN: A prospective study. SETTING: A nine-bed ICU in a 300-bed, nonteaching secondary hospital. PATIENTS: Three hundred thirty-two consecutive, unselected adults. MEASUREMENTS AND MAIN RESULTS: We found a good correlation between APACHE II and MPM; their performance expressed as area under the receiver operating characteristics curve was nearly the same. Goodness-of-fit between observed and expected occurrences was better for APACHE II than for admission MPM, which overestimated deaths. Because we evaluate patients early, often in the Emergency Department, we felt that a "lead-time bias" could explain this discrepancy. Reevaluation after initial stabilization improved the performance of the MPM model to the level of APACHE II. CONCLUSIONS: Our investigation indicates that both APACHE II and MPM are good predictors of hospital outcome in our population, but the level of intensive care services received before conventional ICU admission modifies accuracy of predictive models. In any study of outcome using comparative studies of classification systems, confounding biases should be measured.

Adult↗
PubMed2002

Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy.

The task of predicting the cysteine-bonding state in proteins starting from the residue chain is addressed by implementing a new hybrid system that combines a neural network and a hidden Markov model (hidden neural network). Training is performed using 4136 cysteine-containing segments extracted from 969 nonhomologous proteins of well-resolved three-dimensional structure. After a 20-fold cross-validation procedure, the efficiency of the prediction scores as high as 88% and 84%, when measured on cysteine and protein basis, respectively. These results outperform previously described methods for the same task.

Cysteine↗
PubMed1979

Secondary structure prediction of anterior pituitary hormones. Lack of correlation between predicted values and circular dichroism data.

The secondary structures of human somatotropin, human choriomammotropin, ovine and porcine prolactin, human, ovine and porcine beta-lipotropin, human and ovine lutropin, human thyrotropin, human corticotropin, alpha-melanotropin and human beta-melanotropin have been predicted by the method of Chou & Fasman. Predicted contents of alpha-helix and beta-sheet do not correspond well with values estimated from circular dichroism spectra.

Adrenocorticotropic Hormone↗